Journal Article
. 2007 Jan; 23(6):657-63.
doi: 10.1093/bioinformatics/btl646.

A faster circular binary segmentation algorithm for the analysis of array CGH data

E S Venkatraman 1 Adam B Olshen  
Affiliations
  • PMID: 17234643
  •     438 citations

Abstract

Motivation: Array CGH technologies enable the simultaneous measurement of DNA copy number for thousands of sites on a genome. We developed the circular binary segmentation (CBS) algorithm to divide the genome into regions of equal copy number. The algorithm tests for change-points using a maximal t-statistic with a permutation reference distribution to obtain the corresponding P-value. The number of computations required for the maximal test statistic is O(N2), where N is the number of markers. This makes the full permutation approach computationally prohibitive for the newer arrays that contain tens of thousands markers and highlights the need for a faster algorithm.

Results: We present a hybrid approach to obtain the P-value of the test statistic in linear time. We also introduce a rule for stopping early when there is strong evidence for the presence of a change. We show through simulations that the hybrid approach provides a substantial gain in speed with only a negligible loss in accuracy and that the stopping rule further increases speed. We also present the analyses of array CGH data from breast cancer cell lines to show the impact of the new approaches on the analysis of real data.

Availability: An R version of the CBS algorithm has been implemented in the "DNAcopy" package of the Bioconductor project. The proposed hybrid method for the P-value is available in version 1.2.1 or higher and the stopping rule for declaring a change early is available in version 1.5.1 or higher.

Gene-resolution analysis of DNA copy number variation using oligonucleotide expression microarrays.
Herbert Auer, David L Newsom, +7 authors, Karl Kornacker.
BMC Genomics, 2007 May 02; 8. PMID: 17470268    Free PMC article.
Sparse representation and Bayesian detection of genome copy number alterations from microarray data.
Roger Pique-Regi, Jordi Monso-Varona, +3 authors, Shahab Asgharzadeh.
Bioinformatics, 2008 Jan 22; 24(3). PMID: 18203770    Free PMC article.
Feedback circuit among INK4 tumor suppressors constrains human glioblastoma development.
Ruprecht Wiedemeyer, Cameron Brennan, +15 authors, Lynda Chin.
Cancer Cell, 2008 Apr 09; 13(4). PMID: 18394558    Free PMC article.
Widespread duplications in the genomes of laboratory stocks of Dictyostelium discoideum.
Gareth Bloomfield, Yoshimasa Tanaka, +2 authors, Robert R Kay.
Genome Biol, 2008 Apr 24; 9(4). PMID: 18430225    Free PMC article.
Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing.
Peter J Campbell, Philip J Stephens, +21 authors, P Andrew Futreal.
Nat Genet, 2008 Apr 29; 40(6). PMID: 18438408    Free PMC article.
Highly Cited.
MD-SeeGH: a platform for integrative analysis of multi-dimensional genomic data.
Bryan Chi, Ronald J deLeeuw, +3 authors, Wan L Lam.
BMC Bioinformatics, 2008 May 22; 9. PMID: 18492270    Free PMC article.
A probe-density-based analysis method for array CGH data: simulation, normalization and centralization.
Hung-I Harry Chen, Fang-Han Hsu, +5 authors, Yidong Chen.
Bioinformatics, 2008 Jul 08; 24(16). PMID: 18603568    Free PMC article.
On the frequency of copy number variants.
Iuliana Ionita-Laza, Nan M Laird, +2 authors, Christoph Lange.
Bioinformatics, 2008 Aug 12; 24(20). PMID: 18689430    Free PMC article.
Segmentation-based detection of allelic imbalance and loss-of-heterozygosity in cancer cells using whole genome SNP arrays.
Johan Staaf, David Lindgren, +7 authors, Markus Ringnér.
Genome Biol, 2008 Sep 18; 9(9). PMID: 18796136    Free PMC article.
Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios.
Johan Staaf, Johan Vallon-Christersson, +5 authors, Markus Ringnér.
BMC Bioinformatics, 2008 Oct 04; 9. PMID: 18831757    Free PMC article.
SIGMA2: a system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes.
Raj Chari, Bradley P Coe, +6 authors, Wan L Lam.
BMC Bioinformatics, 2008 Oct 09; 9. PMID: 18840289    Free PMC article.
Global reorganization of replication domains during embryonic stem cell differentiation.
Ichiro Hiratani, Tyrone Ryba, +7 authors, David M Gilbert.
PLoS Biol, 2008 Oct 10; 6(10). PMID: 18842067    Free PMC article.
Highly Cited.
MSB: a mean-shift-based approach for the analysis of structural variation in the genome.
Lu-Yong Wang, Alexej Abyzov, +2 authors, Mark Gerstein.
Genome Res, 2008 Nov 28; 19(1). PMID: 19037015    Free PMC article.
High-resolution mapping of copy-number alterations with massively parallel sequencing.
Derek Y Chiang, Gad Getz, +7 authors, Eric S Lander.
Nat Methods, 2008 Dec 02; 6(1). PMID: 19043412    Free PMC article.
Highly Cited.
A der(8)t(8;11) chromosome in the Karpas-620 myeloma cell line expresses only cyclin D1: yet both cyclin D1 and MYC are repositioned in close proximity to the 3'IGH enhancer.
Amel Dib, Oleg K Glebov, +2 authors, W Michael Kuehl.
DNA Repair (Amst), 2008 Dec 10; 8(3). PMID: 19064000    Free PMC article.
Exploratory analysis of the copy number alterations in glioblastoma multiforme.
Pablo Freire, Marco Vilela, +10 authors, Jonas S Almeida.
PLoS One, 2008 Dec 31; 3(12). PMID: 19115005    Free PMC article.
Neurobeachin (NBEA) is a target of recurrent interstitial deletions at 13q13 in patients with MGUS and multiple myeloma.
Julie O'Neal, Feng Gao, +7 authors, Michael H Tomasson.
Exp Hematol, 2009 Jan 13; 37(2). PMID: 19135901    Free PMC article.
Genomic copy number determination in cancer cells from single nucleotide polymorphism microarrays based on quantitative genotyping corrected for aneuploidy.
Edward F Attiyeh, Sharon J Diskin, +8 authors, John M Maris.
Genome Res, 2009 Jan 15; 19(2). PMID: 19141597    Free PMC article.
A flexible rank-based framework for detecting copy number aberrations from array data.
Thomas LaFramboise, Wendy Winckler, Roman K Thomas.
Bioinformatics, 2009 Jan 30; 25(6). PMID: 19176555    Free PMC article.
A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods.
Henrik Bengtsson, Amrita Ray, Paul Spellman, Terence P Speed.
Bioinformatics, 2009 Feb 06; 25(7). PMID: 19193730    Free PMC article.
Cancer gene discovery in mouse and man.
Jenny Mattison, Louise van der Weyden, Tim Hubbard, David J Adams.
Biochim Biophys Acta, 2009 Mar 17; 1796(2). PMID: 19285540    Free PMC article.
Review.
Combining chromosomal arm status and significantly aberrant genomic locations reveals new cancer subtypes.
Tal Shay, Wanyu L Lambiv, +2 authors, Eytan Domany.
Cancer Inform, 2009 Apr 09; 7. PMID: 19352461    Free PMC article.
Analysis of DNA copy number alterations in ovarian serous tumors identifies new molecular genetic changes in low-grade and high-grade carcinomas.
Kuan-Ting Kuo, Bin Guan, +7 authors, Tian-Li Wang.
Cancer Res, 2009 Apr 23; 69(9). PMID: 19383911    Free PMC article.
RJaCGH: Bayesian analysis of aCGH arrays for detecting copy number changes and recurrent regions.
Oscar M Rueda, Ramon Diaz-Uriarte.
Bioinformatics, 2009 May 08; 25(15). PMID: 19420051    Free PMC article.
Characterization of a naturally occurring breast cancer subset enriched in epithelial-to-mesenchymal transition and stem cell characteristics.
Bryan T Hennessy, Ana-Maria Gonzalez-Angulo, +24 authors, Gordon B Mills.
Cancer Res, 2009 May 14; 69(10). PMID: 19435916    Free PMC article.
Highly Cited.
Genome-wide massively parallel sequencing of formaldehyde fixed-paraffin embedded (FFPE) tumor tissues for copy-number- and mutation-analysis.
Michal R Schweiger, Martin Kerick, +5 authors, Hans Lehrach.
PLoS One, 2009 May 15; 4(5). PMID: 19440246    Free PMC article.
High-throughput multiplex sequencing to discover copy number variants in Drosophila.
Bryce Daines, Hui Wang, +3 authors, Rui Chen.
Genetics, 2009 Jun 17; 182(4). PMID: 19528327    Free PMC article.
A computational procedure to identify significant overlap of differentially expressed and genomic imbalanced regions in cancer datasets.
Silvio Bicciato, Roberta Spinelli, +7 authors, Cristina Battaglia.
Nucleic Acids Res, 2009 Jun 23; 37(15). PMID: 19542187    Free PMC article.
Rare structural variants found in attention-deficit hyperactivity disorder are preferentially associated with neurodevelopmental genes.
J Elia, X Gai, +18 authors, P S White.
Mol Psychiatry, 2009 Jun 24; 15(6). PMID: 19546859    Free PMC article.
Highly Cited.
Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances.
Thomas LaFramboise.
Nucleic Acids Res, 2009 Jul 03; 37(13). PMID: 19570852    Free PMC article.
Highly Cited.
Hidden Markov models for the assessment of chromosomal alterations using high-throughput SNP arrays.
Robert B Scharpf, Giovanni Parmigiani, Jonathan Pevsner, Ingo Ruczinski.
Ann Appl Stat, 2009 Jul 18; 2(2). PMID: 19609370    Free PMC article.
Analysis of array-CGH data using the R and Bioconductor software suite.
Winfried A Hofmann, Anja Weigmann, +6 authors, Doris Steinemann.
Comp Funct Genomics, 2009 Aug 22;. PMID: 19696946    Free PMC article.
CGHnormaliter: an iterative strategy to enhance normalization of array CGH data with imbalanced aberrations.
Bart P P van Houte, Thomas W Binsl, +2 authors, Jaap Heringa.
BMC Genomics, 2009 Aug 28; 10. PMID: 19709427    Free PMC article.
Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis.
Ronglai Shen, Adam B Olshen, Marc Ladanyi.
Bioinformatics, 2009 Sep 18; 25(22). PMID: 19759197    Free PMC article.
Highly Cited.
Segmentation and estimation for SNP microarrays: a Bayesian multiple change-point approach.
Yu Chuan Tai, Mark N Kvale, John S Witte.
Biometrics, 2009 Sep 22; 66(3). PMID: 19764955    Free PMC article.
Statistical issues in the analysis of DNA Copy Number Variations.
Nathan E Wineinger, Richard E Kennedy, +3 authors, Hemant K Tiwari.
Int J Comput Biol Drug Des, 2008 Jan 01; 1(4). PMID: 19774103    Free PMC article.
Review.
A new chromosome x exon-specific microarray platform for screening of patients with X-linked disorders.
Stavros Bashiardes, Ludmila Kousoulidou, +7 authors, Philippos C Patsalis.
J Mol Diagn, 2009 Sep 26; 11(6). PMID: 19779134    Free PMC article.
Rearrangement of CRLF2 in B-progenitor- and Down syndrome-associated acute lymphoblastic leukemia.
Charles G Mullighan, J Racquel Collins-Underwood, +21 authors, Karen R Rabin.
Nat Genet, 2009 Oct 20; 41(11). PMID: 19838194    Free PMC article.
Highly Cited.
An optimization framework for unsupervised identification of rare copy number variation from SNP array data.
Gökhan Yavas, Mehmet Koyutürk, +2 authors, Thomas LaFramboise.
Genome Biol, 2009 Oct 24; 10(10). PMID: 19849861    Free PMC article.
A statistical change point model approach for the detection of DNA copy number variations in array CGH data.
Jie Chen, Yu-Ping Wang.
IEEE/ACM Trans Comput Biol Bioinform, 2009 Oct 31; 6(4). PMID: 19875853    Free PMC article.
The transcription unit architecture of the Escherichia coli genome.
Byung-Kwan Cho, Karsten Zengler, +5 authors, Bernhard Ø Palsson.
Nat Biotechnol, 2009 Nov 03; 27(11). PMID: 19881496    Free PMC article.
Highly Cited.
High resolution discovery and confirmation of copy number variants in 90 Yoruba Nigerians.
Hajime Matsuzaki, Pei-Hua Wang, +2 authors, Glenn K Fu.
Genome Biol, 2009 Nov 11; 10(11). PMID: 19900272    Free PMC article.
Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays.
Tatiana Popova, Elodie Manié, +3 authors, Marc Henri Stern.
Genome Biol, 2009 Nov 12; 10(11). PMID: 19903341    Free PMC article.
Inferring tumor progression from genomic heterogeneity.
Nicholas Navin, Alexander Krasnitz, +13 authors, Michael Wigler.
Genome Res, 2009 Nov 12; 20(1). PMID: 19903760    Free PMC article.
Highly Cited.
Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content.
Nathan M Springer, Kai Ying, +12 authors, Patrick S Schnable.
PLoS Genet, 2009 Dec 04; 5(11). PMID: 19956538    Free PMC article.
Highly Cited.
A genome-wide analysis of array-based comparative genomic hybridization (CGH) data to detect intra-species variations and evolutionary relationships.
Apratim Mitra, George Liu, Jiuzhou Song.
PLoS One, 2009 Dec 04; 4(11). PMID: 19956659    Free PMC article.
Comprehensive characterization of the DNA amplification at 13q34 in human breast cancer reveals TFDP1 and CUL4A as likely candidate target genes.
Lorenzo Melchor, Laura Paula Saucedo-Cuevas, +7 authors, Javier Benítez.
Breast Cancer Res, 2009 Dec 10; 11(6). PMID: 19995430    Free PMC article.
A small-cell lung cancer genome with complex signatures of tobacco exposure.
Erin D Pleasance, Philip J Stephens, +37 authors, Peter J Campbell.
Nature, 2009 Dec 18; 463(7278). PMID: 20016488    Free PMC article.
Highly Cited.
Complex landscapes of somatic rearrangement in human breast cancer genomes.
Philip J Stephens, David J McBride, +30 authors, Michael R Stratton.
Nature, 2009 Dec 25; 462(7276). PMID: 20033038    Free PMC article.
Highly Cited.
Identification of two critically deleted regions within chromosome segment 7q35-q36 in EVI1 deregulated myeloid leukemia cell lines.
An De Weer, Bruce Poppe, +9 authors, Frank Speleman.
PLoS One, 2010 Jan 20; 5(1). PMID: 20084277    Free PMC article.
Integrating the multiple dimensions of genomic and epigenomic landscapes of cancer.
Raj Chari, Kelsie L Thu, +10 authors, Wan L Lam.
Cancer Metastasis Rev, 2010 Jan 29; 29(1). PMID: 20108112    Free PMC article.
Review.
Whole-genome sequencing of a laboratory-evolved yeast strain.
Carlos L Araya, Celia Payen, Maitreya J Dunham, Stanley Fields.
BMC Genomics, 2010 Feb 05; 11. PMID: 20128923    Free PMC article.
A new highly penetrant form of obesity due to deletions on chromosome 16p11.2.
R G Walters, S Jacquemont, +92 authors, J S Beckmann.
Nature, 2010 Feb 05; 463(7281). PMID: 20130649    Free PMC article.
Highly Cited.
CNV Workshop: an integrated platform for high-throughput copy number variation discovery and clinical diagnostics.
Xiaowu Gai, Juan C Perin, +7 authors, Peter S White.
BMC Bioinformatics, 2010 Feb 06; 11. PMID: 20132550    Free PMC article.
Selective regain of egfr gene copies in CD44+/CD24-/low breast cancer cellular model MDA-MB-468.
Konstantin Agelopoulos, Burkhard Greve, +8 authors, Burkhard Brandt.
BMC Cancer, 2010 Mar 05; 10. PMID: 20199686    Free PMC article.
A method for detecting significant genomic regions associated with oral squamous cell carcinoma using aCGH.
Ki-Yeol Kim, Jin Kim, +2 authors, In-Ho Cha.
Med Biol Eng Comput, 2010 Mar 23; 48(5). PMID: 20306232
Conditional random pattern model for copy number aberration detection.
Fuhai Li, Xiaobo Zhou, +2 authors, Stephen T C Wong.
BMC Bioinformatics, 2010 Apr 24; 11. PMID: 20412592    Free PMC article.
The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance.
Santosh S Atanur, Inanç Birol, +23 authors, Timothy J Aitman.
Genome Res, 2010 May 01; 20(6). PMID: 20430781    Free PMC article.
Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types.
Tyrone Ryba, Ichiro Hiratani, +7 authors, David M Gilbert.
Genome Res, 2010 May 01; 20(6). PMID: 20430782    Free PMC article.
Highly Cited.
High-resolution genomic and expression analyses of copy number alterations in HER2-amplified breast cancer.
Johan Staaf, Göran Jönsson, +10 authors, Ake Borg.
Breast Cancer Res, 2010 May 13; 12(3). PMID: 20459607    Free PMC article.
TumorBoost: normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays.
Henrik Bengtsson, Pierre Neuvial, Terence P Speed.
BMC Bioinformatics, 2010 May 14; 11. PMID: 20462408    Free PMC article.
CNstream: a method for the identification and genotyping of copy number polymorphisms using Illumina microarrays.
Arnald Alonso, Antonio Julià, +6 authors, Sara Marsal.
BMC Bioinformatics, 2010 May 21; 11. PMID: 20482829    Free PMC article.
Tumor cells disseminate early, but immunosurveillance limits metastatic outgrowth, in a mouse model of melanoma.
Jo Eyles, Anne-Laure Puaux, +12 authors, Jean-Pierre Abastado.
J Clin Invest, 2010 May 27; 120(6). PMID: 20501944    Free PMC article.
Highly Cited.
The correlation pattern of acquired copy number changes in 164 ETV6/RUNX1-positive childhood acute lymphoblastic leukemias.
Henrik Lilljebjörn, Charlotte Soneson, +9 authors, Thoas Fioretos.
Hum Mol Genet, 2010 Jun 02; 19(16). PMID: 20513752    Free PMC article.
A classification model for distinguishing copy number variants from cancer-related alterations.
Irina Ostrovnaya, Gouri Nanjangud, Adam B Olshen.
BMC Bioinformatics, 2010 Jun 08; 11. PMID: 20525196    Free PMC article.
SEURAT: visual analytics for the integrated analysis of microarray data.
Alexander Gribov, Martin Sill, +5 authors, Antony Unwin.
BMC Med Genomics, 2010 Jun 08; 3. PMID: 20525257    Free PMC article.
Using next-generation sequencing for high resolution multiplex analysis of copy number variation from nanogram quantities of DNA from formalin-fixed paraffin-embedded specimens.
Henry M Wood, Ornella Belvedere, +16 authors, Pamela Rabbitts.
Nucleic Acids Res, 2010 Jun 08; 38(14). PMID: 20525786    Free PMC article.
FACADE: a fast and sensitive algorithm for the segmentation and calling of high resolution array CGH data.
Bradley P Coe, Raj Chari, Calum MacAulay, Wan L Lam.
Nucleic Acids Res, 2010 Jun 17; 38(15). PMID: 20551132    Free PMC article.
CGHpower: exploring sample size calculations for chromosomal copy number experiments.
Ilari Scheinin, José A Ferreira, +3 authors, Bauke Ylstra.
BMC Bioinformatics, 2010 Jun 23; 11. PMID: 20565750    Free PMC article.
Genomic and biological characterization of exon 4 KRAS mutations in human cancer.
Manickam Janakiraman, Efsevia Vakiani, +18 authors, David B Solit.
Cancer Res, 2010 Jun 24; 70(14). PMID: 20570890    Free PMC article.
Highly Cited.
Genomic subtypes of breast cancer identified by array-comparative genomic hybridization display distinct molecular and clinical characteristics.
Göran Jönsson, Johan Staaf, +20 authors, Ake Borg.
Breast Cancer Res, 2010 Jun 26; 12(3). PMID: 20576095    Free PMC article.
Structural and operational complexity of the Geobacter sulfurreducens genome.
Yu Qiu, Byung-Kwan Cho, +3 authors, Karsten Zengler.
Genome Res, 2010 Jul 02; 20(9). PMID: 20592237    Free PMC article.
Integrative analysis reveals selective 9p24.1 amplification, increased PD-1 ligand expression, and further induction via JAK2 in nodular sclerosing Hodgkin lymphoma and primary mediastinal large B-cell lymphoma.
Michael R Green, Stefano Monti, +9 authors, Margaret A Shipp.
Blood, 2010 Jul 16; 116(17). PMID: 20628145    Free PMC article.
Highly Cited.
Computational analysis of whole-genome differential allelic expression data in human.
James R Wagner, Bing Ge, +3 authors, Mathieu Blanchette.
PLoS Comput Biol, 2010 Jul 16; 6(7). PMID: 20628616    Free PMC article.
Array comparative genomic hybridization analysis of Trichoderma reesei strains with enhanced cellulase production properties.
Marika Vitikainen, Mikko Arvas, +3 authors, Markku Saloheimo.
BMC Genomics, 2010 Jul 21; 11. PMID: 20642838    Free PMC article.
Analysis of the copy number profiles of several tumor samples from the same patient reveals the successive steps in tumorigenesis.
Eric Letouzé, Yves Allory, +2 authors, Frédéric Guyon.
Genome Biol, 2010 Jul 24; 11(7). PMID: 20649963    Free PMC article.
Copy number and gene expression differences between African American and Caucasian American prostate cancer.
Amy E Rose, Jaya M Satagopan, +10 authors, Iman Osman.
J Transl Med, 2010 Jul 24; 8. PMID: 20649978    Free PMC article.
Determining frequent patterns of copy number alterations in cancer.
Franck Rapaport, Christina Leslie.
PLoS One, 2010 Aug 17; 5(8). PMID: 20711339    Free PMC article.
On the genome-wide analysis of copy number variants in family-based designs: methods for combining family-based and population-based information for testing dichotomous or quantitative traits, or completely ascertained samples.
Amy Murphy, Sungho Won, +3 authors, Christoph Lange.
Genet Epidemiol, 2010 Aug 19; 34(6). PMID: 20718041    Free PMC article.
Highly aneuploid zebrafish malignant peripheral nerve sheath tumors have genetic alterations similar to human cancers.
Guangjun Zhang, Sebastian Hoersch, +3 authors, Nancy Hopkins.
Proc Natl Acad Sci U S A, 2010 Sep 15; 107(39). PMID: 20837522    Free PMC article.
Copy number analysis identifies novel interactions between genomic loci in ovarian cancer.
Kylie L Gorringe, Joshy George, +13 authors, Australian Ovarian Cancer Study.
PLoS One, 2010 Sep 17; 5(9). PMID: 20844748    Free PMC article.
A survey of analysis software for array-comparative genomic hybridisation studies to detect copy number variation.
Anis Karimpour-Fard, Laura Dumas, +2 authors, Lawrence E Hunter.
Hum Genomics, 2010 Sep 18; 4(6). PMID: 20846932    Free PMC article.
Review.
Advances in understanding cancer genomes through second-generation sequencing.
Matthew Meyerson, Stacey Gabriel, Gad Getz.
Nat Rev Genet, 2010 Sep 18; 11(10). PMID: 20847746
Highly Cited. Review.
Somatic structural rearrangements in genetically engineered mouse mammary tumors.
Ignacio Varela, Christiaan Klijn, +12 authors, David J Adams.
Genome Biol, 2010 Oct 15; 11(10). PMID: 20942901    Free PMC article.
A bayesian analysis for identifying DNA copy number variations using a compound poisson process.
Jie Chen, Ayten Yiğiter, Yu-Ping Wang, Hong-Wen Deng.
EURASIP J Bioinform Syst Biol, 2010 Oct 27; 2010. PMID: 20976296    Free PMC article.
Mapping of genetic abnormalities of primary tumours from metastatic CRC by high-resolution SNP arrays.
José María Sayagués, Celia Fontanillo, +10 authors, Alberto Orfao.
PLoS One, 2010 Nov 10; 5(10). PMID: 21060790    Free PMC article.
KC-SMARTR: An R package for detection of statistically significant aberrations in multi-experiment aCGH data.
Jorma J de Ronde, Christiaan Klijn, +4 authors, Lodewyk Fa Wessels.
BMC Res Notes, 2010 Nov 13; 3. PMID: 21070656    Free PMC article.
Estimating Shared Copy Number Aberrations for Array CGH Data: The Linear-Median Method.
Y-X Lin, V Baladandayuthapani, V Bonato, K-A Do.
Cancer Inform, 2010 Nov 18; 9. PMID: 21082039    Free PMC article.
Highly parallel SNP genotyping reveals high-resolution landscape of mono-allelic Ube3a expression associated with locus-wide antisense transcription.
Koji Numata, Chihiro Kohama, Kuniya Abe, Hidenori Kiyosawa.
Nucleic Acids Res, 2010 Dec 07; 39(7). PMID: 21131283    Free PMC article.
A pilot genome-wide association study shows genomic variants enriched in the non-tumor cells of patients with well-differentiated neuroendocrine tumors of the ileum.
Kyle M Walsh, Murim Choi, +14 authors, Josephine Hoh.
Endocr Relat Cancer, 2010 Dec 09; 18(1). PMID: 21139019    Free PMC article.
Genomic safe harbors permit high β-globin transgene expression in thalassemia induced pluripotent stem cells.
Eirini P Papapetrou, Gabsang Lee, +11 authors, Michel Sadelain.
Nat Biotechnol, 2010 Dec 15; 29(1). PMID: 21151124    Free PMC article.
Highly Cited.
Microarray-based maps of copy-number variant regions in European and sub-Saharan populations.
Christian Vogler, Leo Gschwind, +11 authors, Andreas Papassotiropoulos.
PLoS One, 2010 Dec 24; 5(12). PMID: 21179565    Free PMC article.
DiNAMIC: a method to identify recurrent DNA copy number aberrations in tumors.
Vonn Walter, Andrew B Nobel, Fred A Wright.
Bioinformatics, 2010 Dec 25; 27(5). PMID: 21183584    Free PMC article.
Somatic mutation profiles of MSI and MSS colorectal cancer identified by whole exome next generation sequencing and bioinformatics analysis.
Bernd Timmermann, Martin Kerick, +17 authors, Michal R Schweiger.
PLoS One, 2011 Jan 05; 5(12). PMID: 21203531    Free PMC article.
Highly Cited.
Amplification of the ch19p13.2 NACC1 locus in ovarian high-grade serous carcinoma.
Ie-Ming Shih, Kentaro Nakayama, +3 authors, Tian-Li Wang.
Mod Pathol, 2011 Jan 18; 24(5). PMID: 21240255    Free PMC article.
A novel SNP analysis method to detect copy number alterations with an unbiased reference signal directly from tumor samples.
Alex Lisovich, Uma R Chandran, +5 authors, Robert W Sobol.
BMC Med Genomics, 2011 Jan 29; 4. PMID: 21269491    Free PMC article.
Estimation of parent specific DNA copy number in tumors using high-density genotyping arrays.
Hao Chen, Haipeng Xing, Nancy R Zhang.
PLoS Comput Biol, 2011 Feb 08; 7(1). PMID: 21298078    Free PMC article.
ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads.
Christopher A Miller, Oliver Hampton, Cristian Coarfa, Aleksandar Milosavljevic.
PLoS One, 2011 Feb 10; 6(1). PMID: 21305028    Free PMC article.
Highly Cited.
Acute sensitivity of the oral mucosa to oncogenic K-ras.
Louise van der Weyden, Maria P Alcolea, +3 authors, David J Adams.
J Pathol, 2011 Mar 08; 224(1). PMID: 21381032    Free PMC article.
Comparative analysis of copy number variation detection methods and database construction.
Asako Koike, Nao Nishida, Daiki Yamashita, Katsushi Tokunaga.
BMC Genet, 2011 Mar 10; 12. PMID: 21385384    Free PMC article.
Genomic profiling of advanced-stage oral cancers reveals chromosome 11q alterations as markers of poor clinical outcome.
Srikant Ambatipudi, Moritz Gerstung, +5 authors, Manoj B Mahimkar.
PLoS One, 2011 Mar 10; 6(2). PMID: 21386901    Free PMC article.
Making sense of cancer genomic data.
Lynda Chin, William C Hahn, Gad Getz, Matthew Meyerson.
Genes Dev, 2011 Mar 17; 25(6). PMID: 21406553    Free PMC article.
Highly Cited. Review.
Topographic enhancement mapping of the cancer-associated breast stroma using breast MRI.
Nima Nabavizadeh, Catherine Klifa, +10 authors, Catherine C Park.
Integr Biol (Camb), 2011 Mar 19; 3(4). PMID: 21416100    Free PMC article.
Array comparative genomic hybridization identifies novel potential therapeutic targets in cholangiocarcinoma.
Siobhan C McKay, Kristian Unger, +4 authors, Duncan R C Spalding.
HPB (Oxford), 2011 Apr 16; 13(5). PMID: 21492330    Free PMC article.
Network-guided analysis of genes with altered somatic copy number and gene expression reveals pathways commonly perturbed in metastatic melanoma.
Armand Valsesia, Donata Rimoldi, +15 authors, Brian J Stevenson.
PLoS One, 2011 Apr 16; 6(4). PMID: 21494657    Free PMC article.
GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers.
Craig H Mermel, Steven E Schumacher, +3 authors, Gad Getz.
Genome Biol, 2011 Apr 30; 12(4). PMID: 21527027    Free PMC article.
Highly Cited.
Breast tumors from CHEK2 1100delC-mutation carriers: genomic landscape and clinical implications.
Taru A Muranen, Dario Greco, +7 authors, Heli Nevanlinna.
Breast Cancer Res, 2011 May 06; 13(5). PMID: 21542898    Free PMC article.
Clonality: an R package for testing clonal relatedness of two tumors from the same patient based on their genomic profiles.
Irina Ostrovnaya, Venkatraman E Seshan, Adam B Olshen, Colin B Begg.
Bioinformatics, 2011 May 07; 27(12). PMID: 21546399    Free PMC article.
An all-statistics, high-speed algorithm for the analysis of copy number variation in genomes.
Chih-Hao Chen, Hsing-Chung Lee, +6 authors, H C Lee.
Nucleic Acids Res, 2011 May 18; 39(13). PMID: 21576227    Free PMC article.
A fast and accurate method to detect allelic genomic imbalances underlying mosaic rearrangements using SNP array data.
Juan R González, Benjamín Rodríguez-Santiago, +5 authors, Luis A Pérez-Jurado.
BMC Bioinformatics, 2011 May 19; 12. PMID: 21586113    Free PMC article.
On the adaptive partition approach to the detection of multiple change-points.
Yinglei Lai.
PLoS One, 2011 Jun 02; 6(5). PMID: 21629694    Free PMC article.
Genome-scale analysis of replication timing: from bench to bioinformatics.
Tyrone Ryba, Dana Battaglia, +2 authors, David M Gilbert.
Nat Protoc, 2011 Jun 04; 6(6). PMID: 21637205    Free PMC article.
A fused lasso latent feature model for analyzing multi-sample aCGH data.
Gen Nowak, Trevor Hastie, Jonathan R Pollack, Robert Tibshirani.
Biostatistics, 2011 Jun 07; 12(4). PMID: 21642389    Free PMC article.
The nuclear deubiquitinase BAP1 is commonly inactivated by somatic mutations and 3p21.1 losses in malignant pleural mesothelioma.
Matthew Bott, Marie Brevet, +15 authors, Marc Ladanyi.
Nat Genet, 2011 Jun 07; 43(7). PMID: 21642991    Free PMC article.
Highly Cited.
Parent-specific copy number in paired tumor-normal studies using circular binary segmentation.
Adam B Olshen, Henrik Bengtsson, +3 authors, Venkatraman E Seshan.
Bioinformatics, 2011 Jun 15; 27(15). PMID: 21666266    Free PMC article.
SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data.
Xutao Deng.
BMC Bioinformatics, 2011 Jul 01; 12. PMID: 21714929    Free PMC article.
Concurrent loss of the PTEN and RB1 tumor suppressors attenuates RAF dependence in melanomas harboring (V600E)BRAF.
F Xing, Y Persaud, +16 authors, D B Solit.
Oncogene, 2011 Jul 05; 31(4). PMID: 21725359    Free PMC article.
Highly Cited.
Integrated genomics of ovarian xenograft tumor progression and chemotherapy response.
Ashley Stuckey, Andrew Fischer, +7 authors, Alexander S Brodsky.
BMC Cancer, 2011 Jul 26; 11. PMID: 21781307    Free PMC article.
Analysis of the coding genome of diffuse large B-cell lymphoma.
Laura Pasqualucci, Vladimir Trifonov, +14 authors, Riccardo Dalla-Favera.
Nat Genet, 2011 Aug 02; 43(9). PMID: 21804550    Free PMC article.
Highly Cited.
Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV.
Jarupon Fah Sathirapongsasuti, Hane Lee, +5 authors, Stanley F Nelson.
Bioinformatics, 2011 Aug 11; 27(19). PMID: 21828086    Free PMC article.
Highly Cited.
Cell of origin strongly influences genetic selection in a mouse model of T-ALL.
Katherine E Berquam-Vrieze, Kishore Nannapaneni, +10 authors, Adam J Dupuy.
Blood, 2011 Aug 11; 118(17). PMID: 21828136    Free PMC article.
Hunger artists: yeast adapted to carbon limitation show trade-offs under carbon sufficiency.
Jared W Wenger, Jeffrey Piotrowski, +3 authors, Frank Rosenzweig.
PLoS Genet, 2011 Aug 11; 7(8). PMID: 21829391    Free PMC article.
Selective genomic copy number imbalances and probability of recurrence in early-stage breast cancer.
Patricia A Thompson, Abenaa M Brewster, +12 authors, Melissa L Bondy.
PLoS One, 2011 Aug 23; 6(8). PMID: 21858162    Free PMC article.
Mirror extreme BMI phenotypes associated with gene dosage at the chromosome 16p11.2 locus.
Sébastien Jacquemont, Alexandre Reymond, +178 authors, Philippe Froguel.
Nature, 2011 Sep 02; 478(7367). PMID: 21881559    Free PMC article.
Highly Cited.
Losing balance: Hardy-Weinberg disequilibrium as a marker for recurrent loss-of-heterozygosity in cancer.
Katherine Wilkins, Thomas LaFramboise.
Hum Mol Genet, 2011 Sep 17; 20(24). PMID: 21920941    Free PMC article.
A model-based circular binary segmentation algorithm for the analysis of array CGH data.
Fang-Han Hsu, Hung-I H Chen, +5 authors, Yidong Chen.
BMC Res Notes, 2011 Oct 12; 4. PMID: 21985277    Free PMC article.
Chipster: user-friendly analysis software for microarray and other high-throughput data.
M Aleksi Kallio, Jarno T Tuimala, +6 authors, Eija I Korpelainen.
BMC Genomics, 2011 Oct 18; 12. PMID: 21999641    Free PMC article.
Highly Cited.
Subtype and pathway specific responses to anticancer compounds in breast cancer.
Laura M Heiser, Anguraj Sadanandam, +40 authors, Paul T Spellman.
Proc Natl Acad Sci U S A, 2011 Oct 18; 109(8). PMID: 22003129    Free PMC article.
Highly Cited.
Allele-specific copy number analysis of tumor samples with aneuploidy and tumor heterogeneity.
Markus Rasmussen, Magnus Sundström, +5 authors, Anders Isaksson.
Genome Biol, 2011 Oct 26; 12(10). PMID: 22023820    Free PMC article.
Improved Statistical Analysis for Array CGH-Based DNA Copy Number Aberrations.
Hongmei Jiang, Zhong-Zheng Zhu, +2 authors, Lifang Hou.
Cancer Inform, 2011 Nov 16; 10. PMID: 22084565    Free PMC article.
Prognostic classification of pediatric medulloblastoma based on chromosome 17p loss, expression of MYCC and MYCN, and Wnt pathway activation.
Ae Kyung Park, Seung-Jun Lee, +13 authors, Woong-Yang Park.
Neuro Oncol, 2011 Nov 18; 14(2). PMID: 22090452    Free PMC article.
Heritable epigenetic variation among maize inbreds.
Steve R Eichten, Ruth A Swanson-Wagner, +10 authors, Nathan M Springer.
PLoS Genet, 2011 Nov 30; 7(11). PMID: 22125494    Free PMC article.
Identification of tumor suppressors and oncogenes from genomic and epigenetic features in ovarian cancer.
Kazimierz O Wrzeszczynski, Vinay Varadan, +6 authors, Robert Lucito.
PLoS One, 2011 Dec 17; 6(12). PMID: 22174824    Free PMC article.
Whole genome sequencing of matched primary and metastatic acral melanomas.
Samra Turajlic, Simon J Furney, +13 authors, Richard Marais.
Genome Res, 2011 Dec 21; 22(2). PMID: 22183965    Free PMC article.
GSVD comparison of patient-matched normal and tumor aCGH profiles reveals global copy-number alterations predicting glioblastoma multiforme survival.
Cheng H Lee, Benjamin O Alpert, Preethi Sankaranarayanan, Orly Alter.
PLoS One, 2012 Feb 01; 7(1). PMID: 22291905    Free PMC article.
cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate.
Günter Klambauer, Karin Schwarzbauer, +4 authors, Sepp Hochreiter.
Nucleic Acids Res, 2012 Feb 04; 40(9). PMID: 22302147    Free PMC article.
Highly Cited.
Genomic complexity and AKT dependence in serous ovarian cancer.
Aphrothiti J Hanrahan, Nikolaus Schultz, +18 authors, David B Solit.
Cancer Discov, 2012 Feb 14; 2(1). PMID: 22328975    Free PMC article.
Submicroscopic chromosomal copy number variations identified in children with hypoplastic left heart syndrome.
Ashleigh R Payne, Sheng-Wei Chang, +2 authors, Vidu Garg.
Pediatr Cardiol, 2012 Feb 22; 33(5). PMID: 22349727
A whole-genome massively parallel sequencing analysis of BRCA1 mutant oestrogen receptor-negative and -positive breast cancers.
Rachael Natrajan, Alan Mackay, +30 authors, Jorge S Reis-Filho.
J Pathol, 2012 Mar 01; 227(1). PMID: 22362584    Free PMC article.
The consequences of chromosomal aneuploidy on the transcriptome of cancer cells.
Thomas Ried, Yue Hu, +3 authors, Jordi Camps.
Biochim Biophys Acta, 2012 Mar 20; 1819(7). PMID: 22426433    Free PMC article.
Review.
Genetic association studies of copy-number variation: should assignment of copy number states precede testing?
Patrick Breheny, Prabhakar Chalise, +2 authors, Brooke L Fridley.
PLoS One, 2012 Apr 12; 7(4). PMID: 22493684    Free PMC article.
Prediction of cytogenetic abnormalities with gene expression profiles.
Yiming Zhou, Qing Zhang, +9 authors, John D Shaughnessy.
Blood, 2012 Apr 13; 119(21). PMID: 22496154    Free PMC article.
Using the R Package crlmm for Genotyping and Copy Number Estimation.
Robert B Scharpf, Rafael A Irizarry, +2 authors, Ingo Ruczinski.
J Stat Softw, 2012 Apr 24; 40(12). PMID: 22523482    Free PMC article.
Genome-wide copy number analysis of single cells.
Timour Baslan, Jude Kendall, +10 authors, James Hicks.
Nat Protoc, 2012 May 05; 7(6). PMID: 22555242    Free PMC article.
Highly Cited.
Identity by descent mapping of founder mutations in cancer using high-resolution tumor SNP data.
Eric Letouzé, Aliou Sow, +6 authors, Aurélien de Reyniès.
PLoS One, 2012 May 09; 7(5). PMID: 22567117    Free PMC article.
Improved multiplex ligation-dependent probe amplification analysis identifies a deleterious PMS2 allele generated by recombination with crossover between PMS2 and PMS2CL.
Annekatrin Wernstedt, Emanuele Valtorta, +9 authors, Katharina Wimmer.
Genes Chromosomes Cancer, 2012 May 16; 51(9). PMID: 22585707    Free PMC article.
Relax with CouchDB--into the non-relational DBMS era of bioinformatics.
Ganiraju Manyam, Michelle A Payton, +2 authors, Kevin R Coombes.
Genomics, 2012 May 23; 100(1). PMID: 22609849    Free PMC article.
Characterization of whole genome amplified (WGA) DNA for use in genotyping assay development.
Tao Han, Ching-Wei Chang, +8 authors, James C Fuscoe.
BMC Genomics, 2012 Jun 05; 13. PMID: 22655855    Free PMC article.
Comparative genomic analysis of primary versus metastatic colorectal carcinomas.
Efsevia Vakiani, Manickam Janakiraman, +13 authors, David B Solit.
J Clin Oncol, 2012 Jun 06; 30(24). PMID: 22665543    Free PMC article.
Highly Cited.
Statistical model-based testing to evaluate the recurrence of genomic aberrations.
Atushi Niida, Seiya Imoto, Teppei Shimamura, Satoru Miyano.
Bioinformatics, 2012 Jun 13; 28(12). PMID: 22689750    Free PMC article.
Change-point analysis of paired allele-specific copy number variation data.
Yinglei Lai.
J Comput Biol, 2012 Jun 16; 19(6). PMID: 22697241    Free PMC article.
Identification and validation of copy number variants using SNP genotyping arrays from a large clinical cohort.
Armand Valsesia, Brian J Stevenson, +7 authors, Sven Bergmann.
BMC Genomics, 2012 Jun 19; 13. PMID: 22702538    Free PMC article.
DNA methylation analyses of urothelial carcinoma reveal distinct epigenetic subtypes and an association between gene copy number and methylation status.
Martin Lauss, Mattias Aine, +11 authors, Mattias Höglund.
Epigenetics, 2012 Jun 19; 7(8). PMID: 22705924    Free PMC article.
Amplified loci on chromosomes 8 and 17 predict early relapse in ER-positive breast cancers.
Erhan Bilal, Kristen Vassallo, +8 authors, Shridar Ganesan.
PLoS One, 2012 Jun 22; 7(6). PMID: 22719901    Free PMC article.
STAR RNA-binding protein Quaking suppresses cancer via stabilization of specific miRNA.
An-Jou Chen, Ji-Hye Paik, +14 authors, Ronald A Depinho.
Genes Dev, 2012 Jul 04; 26(13). PMID: 22751500    Free PMC article.
Clonal relatedness between lobular carcinoma in situ and synchronous malignant lesions.
Victor P Andrade, Irina Ostrovnaya, +7 authors, Tari A King.
Breast Cancer Res, 2012 Jul 11; 14(4). PMID: 22776144    Free PMC article.
Expression and function of the protein tyrosine phosphatase receptor J (PTPRJ) in normal mammary epithelial cells and breast tumors.
Chanel E Smart, Marjan E Askarian Amiri, +17 authors, Stuart Kellie.
PLoS One, 2012 Jul 21; 7(7). PMID: 22815804    Free PMC article.
A global view of the oncogenic landscape in nasopharyngeal carcinoma: an integrated analysis at the genetic and expression levels.
Chunfang Hu, Wenbin Wei, +14 authors, John R Arrand.
PLoS One, 2012 Jul 21; 7(7). PMID: 22815911    Free PMC article.
TAGCNA: a method to identify significant consensus events of copy number alterations in cancer.
Xiguo Yuan, Junying Zhang, +4 authors, Yue Wang.
PLoS One, 2012 Jul 21; 7(7). PMID: 22815924    Free PMC article.
Integrative genome-wide expression profiling identifies three distinct molecular subgroups of renal cell carcinoma with different patient outcome.
Manfred Beleut, Philip Zimmermann, +7 authors, Holger Moch.
BMC Cancer, 2012 Jul 25; 12. PMID: 22824167    Free PMC article.
Genome-wide identification of significant aberrations in cancer genome.
Xiguo Yuan, Guoqiang Yu, +7 authors, Yue Wang.
BMC Genomics, 2012 Jul 31; 13. PMID: 22839576    Free PMC article.
Copy-number-aware differential analysis of quantitative DNA sequencing data.
Mark D Robinson, Dario Strbenac, +4 authors, Susan J Clark.
Genome Res, 2012 Aug 11; 22(12). PMID: 22879430    Free PMC article.
Germline copy number variation and ovarian cancer survival.
Brooke L Fridley, Prabhakar Chalise, +14 authors, Ellen L Goode.
Front Genet, 2012 Aug 15; 3. PMID: 22891074    Free PMC article.
Recurrent R-spondin fusions in colon cancer.
Somasekar Seshagiri, Eric W Stawiski, +24 authors, Frederic J de Sauvage.
Nature, 2012 Aug 17; 488(7413). PMID: 22895193    Free PMC article.
Highly Cited.
Reconstructing DNA copy number by joint segmentation of multiple sequences.
Zhongyang Zhang, Kenneth Lange, Chiara Sabatti.
BMC Bioinformatics, 2012 Aug 18; 13. PMID: 22897923    Free PMC article.
Getting DNA copy numbers without control samples.
Maria Ortiz-Estevez, Ander Aramburu, Angel Rubio.
Algorithms Mol Biol, 2012 Aug 18; 7(1). PMID: 22898240    Free PMC article.
Identification of molecular pathway aberrations in uterine serous carcinoma by genome-wide analyses.
Elisabetta Kuhn, Ren-Chin Wu, +16 authors, Ie-Ming Shih.
J Natl Cancer Inst, 2012 Aug 28; 104(19). PMID: 22923510    Free PMC article.
Highly Cited.
Inferring transcriptional and microRNA-mediated regulatory programs in glioblastoma.
Manu Setty, Karim Helmy, +7 authors, Christina S Leslie.
Mol Syst Biol, 2012 Aug 30; 8. PMID: 22929615    Free PMC article.
Loss-of-heterozygosity on chromosome 19q in early-stage serous ovarian cancer is associated with recurrent disease.
Ingiridur Skirnisdottir, Markus Mayrhofer, +2 authors, Anders Isaksson.
BMC Cancer, 2012 Sep 13; 12. PMID: 22967087    Free PMC article.
A high-throughput computational framework for identifying significant copy number aberrations from array comparative genomic hybridisation data.
Ian Roberts, Stephanie A Carter, +4 authors, Nicholas Coleman.
Adv Bioinformatics, 2012 Sep 26; 2012. PMID: 23008709    Free PMC article.
High-resolution whole-genome analysis of skull base chordomas implicates FHIT loss in chordoma pathogenesis.
Roberto Jose Diaz, Mustafa Guduk, +9 authors, James T Rutka.
Neoplasia, 2012 Sep 29; 14(9). PMID: 23019410    Free PMC article.
Genome and transcriptome sequencing of lung cancers reveal diverse mutational and splicing events.
Jinfeng Liu, William Lee, +31 authors, Zemin Zhang.
Genome Res, 2012 Oct 04; 22(12). PMID: 23033341    Free PMC article.
Highly Cited.
Interpreting genomic data via entropic dissection.
Rajeev K Azad, Jing Li.
Nucleic Acids Res, 2012 Oct 06; 41(1). PMID: 23036836    Free PMC article.
Digital transcriptome profiling of normal and glioblastoma-derived neural stem cells identifies genes associated with patient survival.
Pär G Engström, Diva Tommei, +3 authors, Paul Bertone.
Genome Med, 2012 Oct 11; 4(10). PMID: 23046790    Free PMC article.
GWASTools: an R/Bioconductor package for quality control and analysis of genome-wide association studies.
Stephanie M Gogarten, Tushar Bhangale, +13 authors, Cathy C Laurie.
Bioinformatics, 2012 Oct 12; 28(24). PMID: 23052040    Free PMC article.
Modeling read counts for CNV detection in exome sequencing data.
Michael I Love, Alena Myšičková, +3 authors, Stefan A Haas.
Stat Appl Genet Mol Biol, 2011 Jan 01; 10(1). PMID: 23089826    Free PMC article.
Combined analysis of genome-wide expression and copy number profiles to identify key altered genomic regions in cancer.
Celia Fontanillo, Sara Aibar, Jose Manuel Sanchez-Santos, Javier De Las Rivas.
BMC Genomics, 2012 Nov 01; 13 Suppl 5. PMID: 23095915    Free PMC article.
Genomic aberrations in normal tissue adjacent to HER2-amplified breast cancers: field cancerization or contaminating tumor cells?
Anguraj Sadanandam, Aseem Lal, +6 authors, Christopher C Benz.
Breast Cancer Res Treat, 2012 Oct 30; 136(3). PMID: 23104223    Free PMC article.
Detection limits of DNA copy number alterations in heterogeneous cell populations.
Oscar Krijgsman, Daniëlle Israeli, +8 authors, Bauke Ylstra.
Cell Oncol (Dordr), 2012 Nov 03; 36(1). PMID: 23117839
Current analysis platforms and methods for detecting copy number variation.
Wenli Li, Michael Olivier.
Physiol Genomics, 2012 Nov 08; 45(1). PMID: 23132758    Free PMC article.
Review.
Piecewise polynomial representations of genomic tracks.
Maxime Tarabichi, Vincent Detours, Tomasz Konopka.
PLoS One, 2012 Nov 21; 7(11). PMID: 23166601    Free PMC article.
Fast detection of de novo copy number variants from SNP arrays for case-parent trios.
Robert B Scharpf, Terri H Beaty, +3 authors, Ingo Ruczinski.
BMC Bioinformatics, 2012 Dec 14; 13. PMID: 23234608    Free PMC article.
A discovery resource of rare copy number variations in individuals with autism spectrum disorder.
Aparna Prasad, Daniele Merico, +12 authors, Stephen W Scherer.
G3 (Bethesda), 2013 Jan 01; 2(12). PMID: 23275889    Free PMC article.
Highly Cited.
Estimation of copy number alterations from exome sequencing data.
Rafael Valdés-Mas, Silvia Bea, +2 authors, Xose S Puente.
PLoS One, 2013 Jan 04; 7(12). PMID: 23284693    Free PMC article.
Comparative analysis of methods for identifying recurrent copy number alterations in cancer.
Xiguo Yuan, Junying Zhang, +2 authors, Yue Wang.
PLoS One, 2013 Jan 04; 7(12). PMID: 23285074    Free PMC article.
Major chromosomal breakpoint intervals in breast cancer co-localize with differentially methylated regions.
Man-Hung Tang, Vinay Varadan, +3 authors, James Hicks.
Front Oncol, 2013 Jan 08; 2. PMID: 23293768    Free PMC article.
The genomic landscape of hypodiploid acute lymphoblastic leukemia.
Linda Holmfeldt, Lei Wei, +60 authors, Charles G Mullighan.
Nat Genet, 2013 Jan 22; 45(3). PMID: 23334668    Free PMC article.
Highly Cited.
Genome wide analysis of chromosomal alterations in oral squamous cell carcinomas revealed over expression of MGAM and ADAM9.
Vui King Vincent-Chong, Arif Anwar, +15 authors, Rosnah Binti Zain.
PLoS One, 2013 Feb 14; 8(2). PMID: 23405089    Free PMC article.
Copynumber: Efficient algorithms for single- and multi-track copy number segmentation.
Gro Nilsen, Knut Liestøl, +9 authors, Ole Christian Lingjaerde.
BMC Genomics, 2013 Feb 28; 13. PMID: 23442169    Free PMC article.
Highly Cited.
Molecular subtypes in head and neck cancer exhibit distinct patterns of chromosomal gain and loss of canonical cancer genes.
Vonn Walter, Xiaoying Yin, +22 authors, D Neil Hayes.
PLoS One, 2013 Mar 02; 8(2). PMID: 23451093    Free PMC article.
Highly Cited.
Genomic distribution of maize facultative heterochromatin marked by trimethylation of H3K27.
Irina Makarevitch, Steven R Eichten, +6 authors, Nathan M Springer.
Plant Cell, 2013 Mar 07; 25(3). PMID: 23463775    Free PMC article.
Clinical and biological relevance of genomic heterogeneity in chronic lymphocytic leukemia.
Daphne R Friedman, Joseph E Lucas, J Brice Weinberg.
PLoS One, 2013 Mar 08; 8(2). PMID: 23468975    Free PMC article.
Advances in biotechnology and informatics to link variation in the genome to phenotypes in plants and animals.
R Appels, R Barrero, M Bellgard.
Funct Integr Genomics, 2013 Mar 16; 13(1). PMID: 23494190    Free PMC article.
Review.
Bivariate segmentation of SNP-array data for allele-specific copy number analysis in tumour samples.
David Mosén-Ansorena, Ana María Aransay.
BMC Bioinformatics, 2013 Mar 19; 14. PMID: 23497144    Free PMC article.
Exome profiling of primary, metastatic and recurrent ovarian carcinomas in a BRCA1-positive patient.
Jian Zhang, Yuhao Shi, +6 authors, Jacek Majewski.
BMC Cancer, 2013 Mar 26; 13. PMID: 23522120    Free PMC article.
Patchwork: allele-specific copy number analysis of whole-genome sequenced tumor tissue.
Markus Mayrhofer, Sebastian DiLorenzo, Anders Isaksson.
Genome Biol, 2013 Mar 28; 14(3). PMID: 23531354    Free PMC article.
The genomic and transcriptomic landscape of a HeLa cell line.
Jonathan J M Landry, Paul Theodor Pyl, +11 authors, Lars M Steinmetz.
G3 (Bethesda), 2013 Apr 04; 3(8). PMID: 23550136    Free PMC article.
Highly Cited.
Rare genomic structural variants in complex disease: lessons from the replication of associations with obesity.
Robin G Walters, Lachlan J M Coin, +28 authors, Alexandra I F Blakemore.
PLoS One, 2013 Apr 05; 8(3). PMID: 23554873    Free PMC article.
CNVrd, a read-depth algorithm for assigning copy-number at the FCGR locus: population-specific tagging of copy number variation at FCGR3B.
Hoang tan Nguyen, Tony R Merriman, Michael A Black.
PLoS One, 2013 May 07; 8(4). PMID: 23646200    Free PMC article.
The mutational landscape of adenoid cystic carcinoma.
Allen S Ho, Kasthuri Kannan, +35 authors, Timothy A Chan.
Nat Genet, 2013 May 21; 45(7). PMID: 23685749    Free PMC article.
Highly Cited.
Learning smoothing models of copy number profiles using breakpoint annotations.
Toby Dylan Hocking, Gudrun Schleiermacher, +5 authors, Jean-Philippe Vert.
BMC Bioinformatics, 2013 May 24; 14. PMID: 23697330    Free PMC article.
Targeted next-generation sequencing of head and neck squamous cell carcinoma identifies novel genetic alterations in HPV+ and HPV- tumors.
Matthias Lechner, Garrett M Frampton, +17 authors, Chris Boshoff.
Genome Med, 2013 May 31; 5(5). PMID: 23718828    Free PMC article.
Target inference from collections of genomic intervals.
Alexander Krasnitz, Guoli Sun, Peter Andrews, Michael Wigler.
Proc Natl Acad Sci U S A, 2013 Jun 08; 110(25). PMID: 23744040    Free PMC article.
The Growing Importance of CNVs: New Insights for Detection and Clinical Interpretation.
Armand Valsesia, Aurélien Macé, +2 authors, Zoltán Kutalik.
Front Genet, 2013 Jun 12; 4. PMID: 23750167    Free PMC article.
A survey of intragenic breakpoints in glioblastoma identifies a distinct subset associated with poor survival.
Siyuan Zheng, Jun Fu, +15 authors, Roel G W Verhaak.
Genes Dev, 2013 Jun 26; 27(13). PMID: 23796897    Free PMC article.
New rapid scheme for distinguishing the subspecies of the Mycobacterium abscessus group and identifying Mycobacterium massiliense isolates with inducible clarithromycin resistance.
Shamira J Shallom, Paul J Gardina, +9 authors, Adrian M Zelazny.
J Clin Microbiol, 2013 Jun 28; 51(9). PMID: 23804391    Free PMC article.
Two Distinct Categories of Focal Deletions in Cancer Genomes.
Megha Rajaram, Jianping Zhang, +20 authors, R Scott Powers.
PLoS One, 2013 Jun 28; 8(6). PMID: 23805207    Free PMC article.
Detailed Analysis of Focal Chromosome Arm 1q and 6p Amplifications in Urothelial Carcinoma Reveals Complex Genomic Events on 1q, and SOX4 as a Possible Auxiliary Target on 6p.
Pontus Eriksson, Mattias Aine, +3 authors, Mattias Höglund.
PLoS One, 2013 Jul 05; 8(6). PMID: 23825644    Free PMC article.
Integrated high-resolution array CGH and SKY analysis of homozygous deletions and other genomic alterations present in malignant mesothelioma cell lines.
Geula Klorin, Ester Rozenblum, +6 authors, Anna V Roschke.
Cancer Genet, 2013 Jul 09; 206(5). PMID: 23830731    Free PMC article.
Dissecting the gray zone between follicular lymphoma and marginal zone lymphoma using morphological and genetic features.
Oscar Krijgsman, Patricia Gonzalez, +10 authors, Daphne de Jong.
Haematologica, 2013 Jul 16; 98(12). PMID: 23850804    Free PMC article.
Loss of heterozygosity and copy number alterations in flow-sorted bulky cervical cancer.
Sabrina A H M van den Tillaart, Wim E Corver, +5 authors, Jan Oosting.
PLoS One, 2013 Jul 23; 8(7). PMID: 23874418    Free PMC article.
Epigenetic and genetic influences on DNA methylation variation in maize populations.
Steven R Eichten, Roman Briskine, +10 authors, Nathan M Springer.
Plant Cell, 2013 Aug 08; 25(8). PMID: 23922207    Free PMC article.
Highly Cited.
Comparative oncogenomic analysis of copy number alterations in human and zebrafish tumors enables cancer driver discovery.
GuangJun Zhang, Sebastian Hoersch, +8 authors, Jacqueline A Lees.
PLoS Genet, 2013 Sep 07; 9(8). PMID: 24009526    Free PMC article.
A recurrent germline PAX5 mutation confers susceptibility to pre-B cell acute lymphoblastic leukemia.
Sohela Shah, Kasmintan A Schrader, +67 authors, Kenneth Offit.
Nat Genet, 2013 Sep 10; 45(10). PMID: 24013638    Free PMC article.
Highly Cited.
Transmission disequilibrium of small CNVs in simplex autism.
Niklas Krumm, Brian J O'Roak, +7 authors, Evan E Eichler.
Am J Hum Genet, 2013 Sep 17; 93(4). PMID: 24035194    Free PMC article.
Genome-wide copy-number analyses reveal genomic abnormalities involved in transformation of follicular lymphoma.
Alyssa Bouska, Timothy W McKeithan, +24 authors, Wing-Chung Chan.
Blood, 2013 Sep 17; 123(11). PMID: 24037725    Free PMC article.
THE SCREENING AND RANKING ALGORITHM TO DETECT DNA COPY NUMBER VARIATIONS.
Yue S Niu, Heping Zhang.
Ann Appl Stat, 2013 Sep 27; 6(3). PMID: 24069112    Free PMC article.
Pan-cancer patterns of somatic copy number alteration.
Travis I Zack, Stephen E Schumacher, +15 authors, Rameen Beroukhim.
Nat Genet, 2013 Sep 28; 45(10). PMID: 24071852    Free PMC article.
Highly Cited.
Concurrent gene signatures for han chinese breast cancers.
Chi-Cheng Huang, Shih-Hsin Tu, +5 authors, Eric Y Chuang.
PLoS One, 2013 Oct 08; 8(10). PMID: 24098497    Free PMC article.
High expression of ZNF703 independent of amplification indicates worse prognosis in patients with luminal B breast cancer.
Inga Reynisdottir, Adalgeir Arason, +14 authors, Rosa Bjork Barkardottir.
Cancer Med, 2013 Oct 25; 2(4). PMID: 24156016    Free PMC article.
Phenotypic and genotypic convergences are influenced by historical contingency and environment in yeast.
Aymé Spor, Daniel J Kvitek, +7 authors, Delphine Sicard.
Evolution, 2013 Oct 30; 68(3). PMID: 24164389    Free PMC article.
New combined serum creatinine and cystatin C quadratic formula for GFR assessment in children.
Hassib Chehade, Francois Cachat, +5 authors, Eric Girardin.
Clin J Am Soc Nephrol, 2013 Nov 10; 9(1). PMID: 24202134    Free PMC article.
Novel genes associated with colorectal cancer are revealed by high resolution cytogenetic analysis in a patient specific manner.
Hisham Eldai, Sathish Periyasamy, +9 authors, Mohammad Azhar Aziz.
PLoS One, 2013 Nov 10; 8(10). PMID: 24204606    Free PMC article.
Identification of a neuronal transcription factor network involved in medulloblastoma development.
Maria Lastowska, Hani Al-Afghani, +14 authors, Michael S Jackson.
Acta Neuropathol Commun, 2013 Nov 21; 1. PMID: 24252690    Free PMC article.
BET bromodomain inhibition of MYC-amplified medulloblastoma.
Pratiti Bandopadhayay, Guillaume Bergthold, +22 authors, Yoon-Jae Cho.
Clin Cancer Res, 2013 Dec 04; 20(4). PMID: 24297863    Free PMC article.
Highly Cited.
Evaluation of calling algorithms for array-CGH.
Siddharth Roy, Alison Motsinger Reif.
Front Genet, 2013 Dec 04; 4. PMID: 24298279    Free PMC article.
Mutational analysis reveals the origin and therapy-driven evolution of recurrent glioma.
Brett E Johnson, Tali Mazor, +31 authors, Joseph F Costello.
Science, 2013 Dec 18; 343(6167). PMID: 24336570    Free PMC article.
Highly Cited.
Molecular specificity, convergence and constraint shape adaptive evolution in nutrient-poor environments.
Jungeui Hong, David Gresham.
PLoS Genet, 2014 Jan 15; 10(1). PMID: 24415948    Free PMC article.
SegAnnDB: interactive Web-based genomic segmentation.
Toby D Hocking, Valentina Boeva, +9 authors, Jean-Philippe Vert.
Bioinformatics, 2014 Feb 05; 30(11). PMID: 24493034    Free PMC article.
Whole-genome sequencing reveals complex mechanisms of intrinsic resistance to BRAF inhibition.
S Turajlic, S J Furney, +9 authors, R Marais.
Ann Oncol, 2014 Feb 08; 25(5). PMID: 24504448    Free PMC article.
RB1 gene inactivation by chromothripsis in human retinoblastoma.
Justina McEvoy, Panduka Nagahawatte, +24 authors, Michael A Dyer.
Oncotarget, 2014 Feb 11; 5(2). PMID: 24509483    Free PMC article.
A genome-wide study of de novo deletions identifies a candidate locus for non-syndromic isolated cleft lip/palate risk.
Samuel G Younkin, Robert B Scharpf, +5 authors, Ingo Ruczinski.
BMC Genet, 2014 Feb 18; 15. PMID: 24528994    Free PMC article.
SPARSE INTEGRATIVE CLUSTERING OF MULTIPLE OMICS DATA SETS.
Ronglai Shen, Sijian Wang, Qianxing Mo.
Ann Appl Stat, 2014 Mar 04; 7(1). PMID: 24587839    Free PMC article.
Identification of genomic alterations in oesophageal squamous cell cancer.
Yongmei Song, Lin Li, +43 authors, Qimin Zhan.
Nature, 2014 Mar 29; 509(7498). PMID: 24670651
Highly Cited.
FISH Oracle 2: a web server for integrative visualization of genomic data in cancer research.
Malte Mader, Ronald Simon, Stefan Kurtz.
J Clin Bioinforma, 2014 Apr 02; 4(1). PMID: 24684958    Free PMC article.
Recurrent epimutations activate gene body promoters in primary glioblastoma.
Raman P Nagarajan, Bo Zhang, +12 authors, Joseph F Costello.
Genome Res, 2014 Apr 09; 24(5). PMID: 24709822    Free PMC article.
Expression profiling of primary and metastatic ovarian tumors reveals differences indicative of aggressive disease.
Alexander S Brodsky, Andrew Fischer, +9 authors, Laurent Brard.
PLoS One, 2014 Apr 16; 9(4). PMID: 24732363    Free PMC article.
Genome-wide analysis of copy number variation identifies candidate gene loci associated with the progression of non-alcoholic fatty liver disease.
Shamsul Mohd Zain, Rosmawati Mohamed, +10 authors, Zahurin Mohamed.
PLoS One, 2014 Apr 20; 9(4). PMID: 24743702    Free PMC article.
Integrated genomic characterization of adrenocortical carcinoma.
Guillaume Assié, Eric Letouzé, +31 authors, Jérôme Bertherat.
Nat Genet, 2014 Apr 22; 46(6). PMID: 24747642
Highly Cited.
Focal adhesion kinase: an alternative focus for anti-angiogenesis therapy in ovarian cancer.
Rebecca L Stone, Keith A Baggerly, +14 authors, Anil K Sood.
Cancer Biol Ther, 2014 Apr 24; 15(7). PMID: 24755674    Free PMC article.
An ANOCEF genomic and transcriptomic microarray study of the response to irinotecan and bevacizumab in recurrent glioblastomas.
Julien Laffaire, Anna Luisa Di Stefano, +11 authors, François Ducray.
Biomed Res Int, 2014 May 08; 2014. PMID: 24804210    Free PMC article.
A HIERARCHICAL BAYESIAN MODEL FOR INFERENCE OF COPY NUMBER VARIANTS AND THEIR ASSOCIATION TO GENE EXPRESSION.
Alberto Cassese, Michele Guindani, +2 authors, Marina Vannucci.
Ann Appl Stat, 2014 May 17; 8(1). PMID: 24834139    Free PMC article.
A community effort to assess and improve drug sensitivity prediction algorithms.
James C Costello, Laura M Heiser, +20 authors, Gustavo Stolovitzky.
Nat Biotechnol, 2014 Jun 02; 32(12). PMID: 24880487    Free PMC article.
Highly Cited.
Novel somatic and germline mutations in intracranial germ cell tumours.
Linghua Wang, Shigeru Yamaguchi, +23 authors, Ching C Lau.
Nature, 2014 Jun 05; 511(7508). PMID: 24896186    Free PMC article.
SOX2 controls tumour initiation and cancer stem-cell functions in squamous-cell carcinoma.
Soufiane Boumahdi, Gregory Driessens, +14 authors, Cédric Blanpain.
Nature, 2014 Jun 10; 511(7508). PMID: 24909994
Highly Cited.
biomvRhsmm: genomic segmentation with hidden semi-Markov model.
Yang Du, Eduard Murani, Siriluck Ponsuksili, Klaus Wimmers.
Biomed Res Int, 2014 Jul 06; 2014. PMID: 24995333    Free PMC article.
Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data.
Valentina Boeva, Tatiana Popova, +10 authors, Jean-François Laes.
Bioinformatics, 2014 Jul 14; 30(24). PMID: 25016581    Free PMC article.
Insights into the effects of long-term artificial selection on seed size in maize.
Candice N Hirsch, Sherry A Flint-Garcia, +10 authors, Shawn M Kaeppler.
Genetics, 2014 Jul 20; 198(1). PMID: 25037958    Free PMC article.
Outcomes of children with BCR-ABL1–like acute lymphoblastic leukemia treated with risk-directed therapy based on the levels of minimal residual disease.
Kathryn G Roberts, Deqing Pei, +16 authors, Ching-Hon Pui.
J Clin Oncol, 2014 Jul 23; 32(27). PMID: 25049327    Free PMC article.
Highly Cited.
Remodeling of the methylation landscape in breast cancer metastasis.
Marsha Reyngold, Sevin Turcan, +7 authors, Timothy A Chan.
PLoS One, 2014 Aug 02; 9(8). PMID: 25083786    Free PMC article.
Identification of copy number variants from exome sequence data.
Pubudu Saneth Samarakoon, Hanne Sørmo Sorte, +7 authors, Robert Lyle.
BMC Genomics, 2014 Aug 12; 15. PMID: 25102989    Free PMC article.
SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization.
Yi Qiao, Aaron R Quinlan, +3 authors, Gabor T Marth.
Genome Biol, 2014 Aug 28; 15(8). PMID: 25160522    Free PMC article.
Systems consequences of amplicon formation in human breast cancer.
Koichiro Inaki, Francesca Menghi, +16 authors, Edison T Liu.
Genome Res, 2014 Sep 05; 24(10). PMID: 25186909    Free PMC article.
Performance evaluation of DNA copy number segmentation methods.
Morgane Pierre-Jean, Guillem Rigaill, Pierre Neuvial.
Brief Bioinform, 2014 Sep 10; 16(4). PMID: 25202135    Free PMC article.
DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly.
Ilari Scheinin, Daoud Sie, +12 authors, Bauke Ylstra.
Genome Res, 2014 Sep 23; 24(12). PMID: 25236618    Free PMC article.
Highly Cited.
Clonal evolution revealed by whole genome sequencing in a case of primary myelofibrosis transformed to secondary acute myeloid leukemia.
E K Engle, D A C Fisher, +6 authors, S T Oh.
Leukemia, 2014 Sep 26; 29(4). PMID: 25252869    Free PMC article.
Population structure and comparative genome hybridization of European flor yeast reveal a unique group of Saccharomyces cerevisiae strains with few gene duplications in their genome.
Jean-Luc Legras, Claude Erny, Claudine Charpentier.
PLoS One, 2014 Oct 02; 9(10). PMID: 25272156    Free PMC article.
Is there an age cutoff to apply adult formulas for GFR estimation in children?
Antonio Azzi, Francois Cachat, +4 authors, Hassib Chehade.
J Nephrol, 2014 Oct 08; 28(1). PMID: 25286987
A bayesian integrative model for genetical genomics with spatially informed variable selection.
Alberto Cassese, Michele Guindani, Marina Vannucci.
Cancer Inform, 2014 Oct 08; 13(Suppl 2). PMID: 25288877    Free PMC article.
ExomeAI: detection of recurrent allelic imbalance in tumors using whole-exome sequencing data.
Javad Nadaf, Jacek Majewski, Somayyeh Fahiminiya.
Bioinformatics, 2014 Oct 10; 31(3). PMID: 25297069    Free PMC article.
TP53 mutational status is a potential marker for risk stratification in Wilms tumour with diffuse anaplasia.
Mariana Maschietto, Richard D Williams, +8 authors, Kathy Pritchard-Jones.
PLoS One, 2014 Oct 15; 9(10). PMID: 25313908    Free PMC article.
Angiomatous meningiomas have a distinct genetic profile with multiple chromosomal polysomies including polysomy of chromosome 5.
Malak S Abedalthagafi, Parker H Merrill, +14 authors, Sandro Santagata.
Oncotarget, 2014 Oct 28; 5(21). PMID: 25347344    Free PMC article.
Investigating genomic structure using changept: A Bayesian segmentation model.
Manjula Algama, Jonathan M Keith.
Comput Struct Biotechnol J, 2014 Oct 29; 10(17). PMID: 25349679    Free PMC article.
Review.
Comprehensive characterization of the genomic alterations in human gastric cancer.
Juan Cui, Yanbin Yin, +15 authors, Ying Xu.
Int J Cancer, 2014 Nov 26; 137(1). PMID: 25422082    Free PMC article.
Allele-specific copy number profiling by next-generation DNA sequencing.
Hao Chen, John M Bell, +2 authors, Nancy R Zhang.
Nucleic Acids Res, 2014 Dec 06; 43(4). PMID: 25477383    Free PMC article.
Impact of centralization on aCGH-based genomic profiles for precision medicine in oncology.
F Commo, C Ferté, +3 authors, J Guinney.
Ann Oncol, 2014 Dec 30; 26(3). PMID: 25538175    Free PMC article.
Modified screening and ranking algorithm for copy number variation detection.
Feifei Xiao, Xiaoyi Min, Heping Zhang.
Bioinformatics, 2014 Dec 30; 31(9). PMID: 25542927    Free PMC article.
Focal chromosomal copy number aberrations identify CMTM8 and GPR177 as new candidate driver genes in osteosarcoma.
Joeri Both, Oscar Krijgsman, +4 authors, Theo J M Hulsebos.
PLoS One, 2015 Jan 01; 9(12). PMID: 25551557    Free PMC article.
Integrative genomic and transcriptomic characterization of matched primary and metastatic liver and colorectal carcinoma.
Stephanie Roessler, Guoling Lin, +9 authors, Xin Wei Wang.
Int J Biol Sci, 2015 Jan 02; 11(1). PMID: 25552933    Free PMC article.
Copy number variation analysis based on AluScan sequences.
Jian-Feng Yang, Xiao-Fan Ding, +22 authors, Hong Xue.
J Clin Bioinforma, 2015 Jan 06; 4(1). PMID: 25558350    Free PMC article.
Directed targeting of chromatin to the nuclear lamina is mediated by chromatin state and A-type lamins.
Jennifer C Harr, Teresa Romeo Luperchio, +3 authors, Karen L Reddy.
J Cell Biol, 2015 Jan 07; 208(1). PMID: 25559185    Free PMC article.
Highly Cited.
BCL11A is a triple-negative breast cancer gene with critical functions in stem and progenitor cells.
Walid T Khaled, Song Choon Lee, +15 authors, Pentao Liu.
Nat Commun, 2015 Jan 13; 6. PMID: 25574598    Free PMC article.
Highly Cited.
Integrated genome and transcriptome sequencing of the same cell.
Siddharth S Dey, Lennart Kester, +2 authors, Alexander van Oudenaarden.
Nat Biotechnol, 2015 Jan 20; 33(3). PMID: 25599178    Free PMC article.
Highly Cited.
Deep sequencing of multiple regions of glial tumors reveals spatial heterogeneity for mutations in clinically relevant genes.
Akash Kumar, Evan A Boyle, +14 authors, Jay Shendure.
Genome Biol, 2015 Jan 23; 15(12). PMID: 25608559    Free PMC article.
Multi-omics analysis defines core genomic alterations in pheochromocytomas and paragangliomas.
Luis Jaime Castro-Vega, Eric Letouzé, +19 authors, Anne-Paule Gimenez-Roqueplo.
Nat Commun, 2015 Jan 28; 6. PMID: 25625332    Free PMC article.
Highly Cited.
Evolution of DNA repair defects during malignant progression of low-grade gliomas after temozolomide treatment.
Hinke F van Thuijl, Tali Mazor, +21 authors, Joseph F Costello.
Acta Neuropathol, 2015 Mar 01; 129(4). PMID: 25724300    Free PMC article.
Highly Cited.
Robust BRCA1-like classification of copy number profiles of samples repeated across different datasets and platforms.
Philip C Schouten, Anita Grigoriadis, +23 authors, Sabine C Linn.
Mol Oncol, 2015 Apr 01; 9(7). PMID: 25825120    Free PMC article.
Optimizing sparse sequencing of single cells for highly multiplex copy number profiling.
Timour Baslan, Jude Kendall, +15 authors, James Hicks.
Genome Res, 2015 Apr 11; 25(5). PMID: 25858951    Free PMC article.
Interactive analysis of large cancer copy number studies with Copy Number Explorer.
Scott Newman.
Bioinformatics, 2015 May 10; 31(17). PMID: 25957352    Free PMC article.
Excess of rare, inherited truncating mutations in autism.
Niklas Krumm, Tychele N Turner, +10 authors, Evan E Eichler.
Nat Genet, 2015 May 12; 47(6). PMID: 25961944    Free PMC article.
Highly Cited.
Minimal evidence for consistent changes in maize DNA methylation patterns following environmental stress.
Steven R Eichten, Nathan M Springer.
Front Plant Sci, 2015 May 23; 6. PMID: 25999972    Free PMC article.
The fitness consequences of aneuploidy are driven by condition-dependent gene effects.
Anna B Sunshine, Celia Payen, +3 authors, Maitreya J Dunham.
PLoS Biol, 2015 May 27; 13(5). PMID: 26011532    Free PMC article.
Reconstructing breakage fusion bridge architectures using noisy copy numbers.
Shay Zakov, Vineet Bafna.
J Comput Biol, 2015 May 29; 22(6). PMID: 26020441    Free PMC article.
Dynamic changes in replication timing and gene expression during lineage specification of human pluripotent stem cells.
Juan Carlos Rivera-Mulia, Quinton Buckley, +14 authors, David M Gilbert.
Genome Res, 2015 Jun 10; 25(8). PMID: 26055160    Free PMC article.
Highly Cited.
Copy number variant analysis from exome data in 349 patients with epileptic encephalopathy.
Epilepsy Phenome/Genome Project Epi4K Consortium.
Ann Neurol, 2015 Jun 13; 78(2). PMID: 26068938    Free PMC article.
Quantitative assessment of single-cell whole genome amplification methods for detecting copy number variation using hippocampal neurons.
Luwen Ning, Zhoufang Li, +10 authors, Jiankui He.
Sci Rep, 2015 Jun 20; 5. PMID: 26091148    Free PMC article.
Progesterone receptor modulates ERα action in breast cancer.
Hisham Mohammed, I Alasdair Russell, +22 authors, Jason S Carroll.
Nature, 2015 Jul 15; 523(7560). PMID: 26153859    Free PMC article.
Highly Cited.
Detection of Genomic Structural Variants from Next-Generation Sequencing Data.
Lorenzo Tattini, Romina D'Aurizio, Alberto Magi.
Front Bioeng Biotechnol, 2015 Jul 15; 3. PMID: 26161383    Free PMC article.
Highly Cited. Review.
Combined Analysis of SNP Array Data Identifies Novel CNV Candidates and Pathways in Ependymoma and Mesothelioma.
Gabriel Wajnberg, Benilton S Carvalho, Carlos G Ferreira, Fabio Passetti.
Biomed Res Int, 2015 Jul 18; 2015. PMID: 26185765    Free PMC article.
Paired exome analysis of Barrett's esophagus and adenocarcinoma.
Matthew D Stachler, Amaro Taylor-Weiner, +20 authors, Adam J Bass.
Nat Genet, 2015 Jul 21; 47(9). PMID: 26192918    Free PMC article.
Highly Cited.
Acquirement of DNA copy number variations in non-small cell lung cancer metastasis to the brain.
Fang Li, Libo Sun, Sixun Zhang.
Oncol Rep, 2015 Aug 12; 34(4). PMID: 26259861    Free PMC article.
A Single-Array-Based Method for Detecting Copy Number Variants Using Affymetrix High Density SNP Arrays and its Application to Breast Cancer.
Ming Li, Yalu Wen, Wenjiang Fu.
Cancer Inform, 2014 Jan 01; 13(Suppl 4). PMID: 26279618    Free PMC article.
Exome sequencing of desmoplastic melanoma identifies recurrent NFKBIE promoter mutations and diverse activating mutations in the MAPK pathway.
A Hunter Shain, Maria Garrido, +20 authors, Boris C Bastian.
Nat Genet, 2015 Sep 08; 47(10). PMID: 26343386    Free PMC article.
Highly Cited.
NF2 Loss Promotes Oncogenic RAS-Induced Thyroid Cancers via YAP-Dependent Transactivation of RAS Proteins and Sensitizes Them to MEK Inhibition.
Maria E R Garcia-Rendueles, Julio C Ricarte-Filho, +16 authors, James A Fagin.
Cancer Discov, 2015 Sep 12; 5(11). PMID: 26359368    Free PMC article.
Comprehensive genetic exploration of skeletal dysplasia using targeted exome sequencing.
Jun-Seok Bae, Nayoung K D Kim, +16 authors, Tae-Joon Cho.
Genet Med, 2015 Sep 25; 18(6). PMID: 26402641
The genomic landscape of juvenile myelomonocytic leukemia.
Elliot Stieglitz, Amaro N Taylor-Weiner, +44 authors, Mignon L Loh.
Nat Genet, 2015 Oct 13; 47(11). PMID: 26457647    Free PMC article.
Highly Cited.
An Integrative Analysis to Identify Driver Genes in Esophageal Squamous Cell Carcinoma.
Genta Sawada, Atsushi Niida, +26 authors, Koshi Mimori.
PLoS One, 2015 Oct 16; 10(10). PMID: 26465158    Free PMC article.
A definitive haplotype map of structural variations determined by microarray analysis of duplicated haploid genomes.
Tomoko Tahira, Koji Yahara, +4 authors, Kenshi Hayashi.
Genom Data, 2015 Oct 21; 2. PMID: 26484070    Free PMC article.
The distribution and impact of common copy-number variation in the genome of the domesticated apple, Malus x domestica Borkh.
James Boocock, David Chagné, Tony R Merriman, Michael A Black.
BMC Genomics, 2015 Oct 27; 16. PMID: 26493398    Free PMC article.
Polycomb Repressor Complex 1 Member, BMI1 Contributes to Urothelial Tumorigenesis through p16-Independent Mechanisms.
Lia E De Faveri, Carolyn D Hurst, +4 authors, Emma J Chapman.
Transl Oncol, 2015 Oct 27; 8(5). PMID: 26500029    Free PMC article.
Ectopic lymphoid structures function as microniches for tumor progenitor cells in hepatocellular carcinoma.
Shlomi Finkin, Detian Yuan, +18 authors, Eli Pikarsky.
Nat Immunol, 2015 Oct 27; 16(12). PMID: 26502405    Free PMC article.
Highly Cited.
Outcome of children with hypodiploid ALL treated with risk-directed therapy based on MRD levels.
Charles G Mullighan, Sima Jeha, +20 authors, Ching-Hon Pui.
Blood, 2015 Nov 04; 126(26). PMID: 26527677    Free PMC article.
Statistical Approach to Decreasing the Error Rate of Noninvasive Prenatal Aneuploid Detection caused by Maternal Copy Number Variation.
Han Zhang, Yang-Yu Zhao, +13 authors, Jie Qiao.
Sci Rep, 2015 Nov 05; 5. PMID: 26534864    Free PMC article.
De novo identification of replication-timing domains in the human genome by deep learning.
Feng Liu, Chao Ren, +3 authors, Wenjie Shu.
Bioinformatics, 2015 Nov 08; 32(5). PMID: 26545821    Free PMC article.
RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome.
Qing Li, Jonathan I Gent, +11 authors, Nathan M Springer.
Proc Natl Acad Sci U S A, 2015 Nov 11; 112(47). PMID: 26553984    Free PMC article.
Highly Cited.
Associations between circulating carotenoids, genomic instability and the risk of high-grade prostate cancer.
Tobias Nordström, Erin L Van Blarigan, +7 authors, Pamela L Paris.
Prostate, 2015 Nov 21; 76(4). PMID: 26585352    Free PMC article.
Delineation of MGMT Hypermethylation as a Biomarker for Veliparib-Mediated Temozolomide-Sensitizing Therapy of Glioblastoma.
Shiv K Gupta, Sani H Kizilbash, +16 authors, Jann N Sarkaria.
J Natl Cancer Inst, 2015 Nov 29; 108(5). PMID: 26615020    Free PMC article.
Penalized weighted low-rank approximation for robust recovery of recurrent copy number variations.
Xiaoli Gao.
BMC Bioinformatics, 2015 Dec 15; 16. PMID: 26652207    Free PMC article.
Chromosomal copy number alterations and HPV integration in cervical precancer and invasive cancer.
Clara Bodelon, Svetlana Vinokurova, +16 authors, Nicolas Wentzensen.
Carcinogenesis, 2015 Dec 15; 37(2). PMID: 26660085    Free PMC article.
Identifying rhesus macaque gene orthologs using heterospecific human CNV probes.
Jillian Ng, Joseph N Fass, +2 authors, Sree Kanthaswamy.
Genom Data, 2015 Dec 24; 6. PMID: 26697375    Free PMC article.
A distinctive oral phenotype points to FAM20A mutations not identified by Sanger sequencing.
James A Poulter, Claire E L Smith, +9 authors, Alan J Mighell.
Mol Genet Genomic Med, 2016 Jan 08; 3(6). PMID: 26740946    Free PMC article.
Clinical impact of ABL1 kinase domain mutations and IKZF1 deletion in adults under age 60 with Philadelphia chromosome-positive (Ph+) acute lymphoblastic leukemia (ALL): molecular analysis of CALGB (Alliance) 10001 and 9665.
Rebecca DeBoer, Gregory Koval, +9 authors, Wendy Stock.
Leuk Lymphoma, 2016 Feb 20; 57(10). PMID: 26892479    Free PMC article.
Characterization of novel low passage primary and metastatic colorectal cancer cell lines.
Arnoud Boot, Jaap van Eendenburg, +6 authors, Tom van Wezel.
Oncotarget, 2016 Feb 20; 7(12). PMID: 26894854    Free PMC article.
Characterization of FGFR1 Locus in sqNSCLC Reveals a Broad and Heterogeneous Amplicon.
Claire Rooney, Catherine Geh, +12 authors, Elaine Kilgour.
PLoS One, 2016 Feb 26; 11(2). PMID: 26905262    Free PMC article.
An integrated analysis tool for analyzing hybridization intensities and genotypes using new-generation population-optimized human arrays.
Mei-Chu Huang, Tzu-Po Chuang, +4 authors, Hsin-Chou Yang.
BMC Genomics, 2016 Apr 01; 17. PMID: 27029637    Free PMC article.
Integrated multi-omics analysis of oligodendroglial tumours identifies three subgroups of 1p/19q co-deleted gliomas.
Aurélie Kamoun, Ahmed Idbaih, +14 authors, POLA network.
Nat Commun, 2016 Apr 20; 7. PMID: 27090007    Free PMC article.
Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq.
Itay Tirosh, Benjamin Izar, +34 authors, Levi A Garraway.
Science, 2016 Apr 29; 352(6282). PMID: 27124452    Free PMC article.
Highly Cited.
Application of single-cell RNA sequencing in optimizing a combinatorial therapeutic strategy in metastatic renal cell carcinoma.
Kyu-Tae Kim, Hye Won Lee, +10 authors, Woong-Yang Park.
Genome Biol, 2016 May 04; 17. PMID: 27139883    Free PMC article.
Highly Cited.
Fast Bayesian Inference of Copy Number Variants using Hidden Markov Models with Wavelet Compression.
John Wiedenhoeft, Eric Brugel, Alexander Schliep.
PLoS Comput Biol, 2016 May 14; 12(5). PMID: 27177143    Free PMC article.
Analysis of Paired Primary-Metastatic Hormone-Receptor Positive Breast Tumors (HRPBC) Uncovers Potential Novel Drivers of Hormonal Resistance.
Luis Manso, Silvana Mourón, +8 authors, Miguel Quintela-Fandino.
PLoS One, 2016 May 20; 11(5). PMID: 27195705    Free PMC article.
Stepwise Signal Extraction via Marginal Likelihood.
Chao Du, Chu-Lan Michael Kao, S C Kou.
J Am Stat Assoc, 2016 May 24; 111(513). PMID: 27212739    Free PMC article.
FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing.
Ronglai Shen, Venkatraman E Seshan.
Nucleic Acids Res, 2016 Jun 09; 44(16). PMID: 27270079    Free PMC article.
Highly Cited.
Distinct evolution and dynamics of epigenetic and genetic heterogeneity in acute myeloid leukemia.
Sheng Li, Francine E Garrett-Bakelman, +30 authors, Christopher E Mason.
Nat Med, 2016 Jun 21; 22(7). PMID: 27322744    Free PMC article.
Highly Cited.
Chronic p53-independent p21 expression causes genomic instability by deregulating replication licensing.
Panagiotis Galanos, Konstantinos Vougas, +24 authors, Vassilis G Gorgoulis.
Nat Cell Biol, 2016 Jun 21; 18(7). PMID: 27323328    Free PMC article.
Highly Cited.
Clonal relationships between lobular carcinoma in situ and other breast malignancies.
Colin B Begg, Irina Ostrovnaya, +9 authors, Tari A King.
Breast Cancer Res, 2016 Jun 24; 18(1). PMID: 27334989    Free PMC article.
Analyzing tumor heterogeneity and driver genes in single myeloid leukemia cells with SBCapSeq.
Karen M Mann, Justin Y Newberg, +18 authors, Michael B Mann.
Nat Biotechnol, 2016 Aug 02; 34(9). PMID: 27479497    Free PMC article.
Elucidating Genomic Characteristics of Lung Cancer Progression from In Situ to Invasive Adenocarcinoma.
Chanida Vinayanuwattikun, Florence Le Calvez-Kelm, +11 authors, Ghislaine Scelo.
Sci Rep, 2016 Aug 23; 6. PMID: 27545006    Free PMC article.
Gain- and Loss-of-Function Mutations in the Breast Cancer Gene GATA3 Result in Differential Drug Sensitivity.
Barbara Mair, Tomasz Konopka, +6 authors, Sebastian M B Nijman.
PLoS Genet, 2016 Sep 03; 12(9). PMID: 27588951    Free PMC article.
Kernel-Based Aggregation of Marker-Level Genetic Association Tests Involving Copy-Number Variation.
Yinglei Li, Patrick Breheny.
Microarrays (Basel), 2013 Jan 01; 2(3). PMID: 27605192    Free PMC article.
Aurora kinase-A overexpression in mouse mammary epithelium induces mammary adenocarcinomas harboring genetic alterations shared with human breast cancer.
Warapen Treekitkarnmongkol, Hiroshi Katayama, +9 authors, Subrata Sen.
Carcinogenesis, 2016 Sep 15; 37(12). PMID: 27624071    Free PMC article.
CNARA: reliability assessment for genomic copy number profiles.
Ni Ai, Haoyang Cai, Caius Solovan, Michael Baudis.
BMC Genomics, 2016 Oct 14; 17(1). PMID: 27733115    Free PMC article.
Condensin II mutation causes T-cell lymphoma through tissue-specific genome instability.
Jessica Woodward, Gillian C Taylor, +16 authors, Andrew J Wood.
Genes Dev, 2016 Nov 01; 30(19). PMID: 27737961    Free PMC article.
The Impact of Environmental and Endogenous Damage on Somatic Mutation Load in Human Skin Fibroblasts.
Natalie Saini, Steven A Roberts, +14 authors, Dmitry A Gordenin.
PLoS Genet, 2016 Oct 28; 12(10). PMID: 27788131    Free PMC article.
DNA methylation signature (SAM40) identifies subgroups of the Luminal A breast cancer samples with distinct survival.
Thomas Fleischer, Jovana Klajic, +15 authors, Vessela N Kristensen.
Oncotarget, 2016 Dec 03; 8(1). PMID: 27911866    Free PMC article.
Early dissemination seeds metastasis in breast cancer.
Hedayatollah Hosseini, Milan M S Obradović, +24 authors, Christoph A Klein.
Nature, 2016 Dec 16; 540(7634). PMID: 27974799    Free PMC article.
Highly Cited.
An mRNA Gene Expression-Based Signature to Identify FGFR1-Amplified Estrogen Receptor-Positive Breast Tumors.
Jingqin Luo, Shuzhen Liu, +11 authors, Matthew J Ellis.
J Mol Diagn, 2016 Dec 21; 19(1). PMID: 27993329    Free PMC article.
The epigenetic landscape of Alu repeats delineates the structural and functional genomic architecture of colon cancer cells.
Mireia Jordà, Anna Díez-Villanueva, +6 authors, Miguel A Peinado.
Genome Res, 2016 Dec 22; 27(1). PMID: 27999094    Free PMC article.
p120-catenin prevents multinucleation through control of MKLP1-dependent RhoA activity during cytokinesis.
Robert A H van de Ven, Jolien S de Groot, +11 authors, Patrick W B Derksen.
Nat Commun, 2016 Dec 23; 7. PMID: 28004812    Free PMC article.
GenomeCAT: a versatile tool for the analysis and integrative visualization of DNA copy number variants.
Katrin Tebel, Vivien Boldt, +3 authors, Reinhard Ullmann.
BMC Bioinformatics, 2017 Jan 08; 18(1). PMID: 28061750    Free PMC article.
THE SCREENING AND RANKING ALGORITHM FOR CHANGE-POINTS DETECTION IN MULTIPLE SAMPLES.
Chi Song, Xiaoyi Min, Heping Zhang.
Ann Appl Stat, 2017 Jan 17; 10(4). PMID: 28090239    Free PMC article.
Genomic structural variations for cardiovascular and metabolic comorbidity.
Maria S Nazarenko, Aleksei A Sleptcov, +7 authors, Valery P Puzyrev.
Sci Rep, 2017 Jan 26; 7. PMID: 28120895    Free PMC article.
The subclonal structure and genomic evolution of oral squamous cell carcinoma revealed by ultra-deep sequencing.
Siavosh Tabatabaeifar, Mads Thomassen, +3 authors, Jens A Sørensen.
Oncotarget, 2017 Feb 06; 8(10). PMID: 28157713    Free PMC article.
DNA copy number profiling using single-cell sequencing.
Xuefeng Wang, Hao Chen, Nancy R Zhang.
Brief Bioinform, 2017 Feb 06; 19(5). PMID: 28159966    Free PMC article.
Whole-genome single-cell copy number profiling from formalin-fixed paraffin-embedded samples.
Luciano G Martelotto, Timour Baslan, +20 authors, Jorge S Reis-Filho.
Nat Med, 2017 Feb 07; 23(3). PMID: 28165479    Free PMC article.
Highly Cited.
Diversity and regulatory impact of copy number variation in the primate Macaca fascicularis.
Andreas R Gschwind, Anjali Singh, +2 authors, Tobias Heckel.
BMC Genomics, 2017 Feb 12; 18(1). PMID: 28183275    Free PMC article.
Gene expression profiling of patient-derived pancreatic cancer xenografts predicts sensitivity to the BET bromodomain inhibitor JQ1: implications for individualized medicine efforts.
Benjamin Bian, Martin Bigonnet, +25 authors, Juan Iovanna.
EMBO Mol Med, 2017 Mar 10; 9(4). PMID: 28275007    Free PMC article.
The Mutational Landscape of Circulating Tumor Cells in Multiple Myeloma.
Yuji Mishima, Bruno Paiva, +23 authors, Irene M Ghobrial.
Cell Rep, 2017 Apr 06; 19(1). PMID: 28380360    Free PMC article.
Genome wide profiling in oral squamous cell carcinoma identifies a four genetic marker signature of prognostic significance.
Vui King Vincent-Chong, Iman Salahshourifar, +11 authors, Rosnah Binti Zain.
PLoS One, 2017 Apr 07; 12(4). PMID: 28384287    Free PMC article.
Genome and transcriptome profiling of fibrolamellar hepatocellular carcinoma demonstrates p53 and IGF2BP1 dysregulation.
Eric C Sorenson, Raya Khanin, +11 authors, Ronald P DeMatteo.
PLoS One, 2017 May 10; 12(5). PMID: 28486549    Free PMC article.
The genomic road to invasion-examining the similarities and differences in the genomes of associated oral pre-cancer and cancer samples.
Henry M Wood, Catherine Daly, +10 authors, Caroline Conway.
Genome Med, 2017 Jun 09; 9(1). PMID: 28592326    Free PMC article.
Novel near-diploid ovarian cancer cell line derived from a highly aneuploid metastatic ovarian tumor.
Ester Rozenblum, Jose R Sotelo-Silveira, +11 authors, Anna V Roschke.
PLoS One, 2017 Aug 09; 12(8). PMID: 28787462    Free PMC article.
Genomic comparison of esophageal squamous cell carcinoma and its precursor lesions by multi-region whole-exome sequencing.
Xi-Xi Chen, Qian Zhong, +17 authors, Mu-Sheng Zeng.
Nat Commun, 2017 Sep 14; 8(1). PMID: 28900112    Free PMC article.
Contralateral breast cancers: Independent cancers or metastases?
Colin B Begg, Irina Ostrovnaya, +13 authors, Jorge S Reis-Filho.
Int J Cancer, 2017 Sep 19; 142(2). PMID: 28921573    Free PMC article.
Integrated molecular analysis of Tamoxifen-resistant invasive lobular breast cancer cells identifies MAPK and GRM/mGluR signaling as therapeutic vulnerabilities.
Hillary Stires, Mary M Heckler, +10 authors, Rebecca B Riggins.
Mol Cell Endocrinol, 2017 Sep 25; 471. PMID: 28935545    Free PMC article.
Genomic Heterogeneity as a Barrier to Precision Medicine in Gastroesophageal Adenocarcinoma.
Eirini Pectasides, Matthew D Stachler, +54 authors, Daniel V Catenacci.
Cancer Discov, 2017 Oct 06; 8(1). PMID: 28978556    Free PMC article.
Highly Cited.
ALLELE-SPECIFIC COPY NUMBER ESTIMATION BY WHOLE EXOME SEQUENCING.
Hao Chen, Yuchao Jiang, +2 authors, Nancy Zhang.
Ann Appl Stat, 2017 Oct 11; 11(2). PMID: 28989557    Free PMC article.
Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors.
Viktor A Adalsteinsson, Gavin Ha, +54 authors, Matthew Meyerson.
Nat Commun, 2017 Nov 08; 8(1). PMID: 29109393    Free PMC article.
Highly Cited.
Integrative analysis of genome-wide gene copy number changes and gene expression in non-small cell lung cancer.
Verena Jabs, Karolina Edlund, +10 authors, Patrick Micke.
PLoS One, 2017 Nov 08; 12(11). PMID: 29112949    Free PMC article.
Mutations in EMT-Related Genes in ALK Positive Crizotinib Resistant Non-Small Cell Lung Cancers.
Jiacong Wei, Anthonie J van der Wekken, +7 authors, Klaas Kok.
Cancers (Basel), 2018 Jan 05; 10(1). PMID: 29300322    Free PMC article.
Integrative molecular network analysis identifies emergent enzalutamide resistance mechanisms in prostate cancer.
Carly J King, Josha Woodward, +9 authors, Joshi J Alumkal.
Oncotarget, 2018 Jan 18; 8(67). PMID: 29340039    Free PMC article.
CINdex: A Bioconductor Package for Analysis of Chromosome Instability in DNA Copy Number Data.
Lei Song, Krithika Bhuvaneshwar, +4 authors, Yuriy Gusev.
Cancer Inform, 2018 Jan 19; 16. PMID: 29343938    Free PMC article.
The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution.
Jeramiah J Smith, Nataliya Timoshevskaya, +21 authors, Chris T Amemiya.
Nat Genet, 2018 Jan 24; 50(2). PMID: 29358652    Free PMC article.
Highly Cited.
Near-tetraploid cancer cells show chromosome instability triggered by replication stress and exhibit enhanced invasiveness.
Darawalee Wangsa, Isabel Quintanilla, +12 authors, Jordi Camps.
FASEB J, 2018 Feb 18; 32(7). PMID: 29452566    Free PMC article.
Integrative genomic profiling of large-cell neuroendocrine carcinomas reveals distinct subtypes of high-grade neuroendocrine lung tumors.
Julie George, Vonn Walter, +59 authors, Roman K Thomas.
Nat Commun, 2018 Mar 15; 9(1). PMID: 29535388    Free PMC article.
Highly Cited.
iSeg: an efficient algorithm for segmentation of genomic and epigenomic data.
Senthil B Girimurugan, Yuhang Liu, +4 authors, Jinfeng Zhang.
BMC Bioinformatics, 2018 Apr 13; 19(1). PMID: 29642840    Free PMC article.
Whole-exome sequencing of cell-free DNA and circulating tumor cells in multiple myeloma.
S Manier, J Park, +20 authors, I M Ghobrial.
Nat Commun, 2018 Apr 29; 9(1). PMID: 29703982    Free PMC article.
Highly Cited.
GEMiCCL: mining genotype and expression data of cancer cell lines with elaborate visualization.
Inhae Jeong, Namhee Yu, +5 authors, Sanghyuk Lee.
Database (Oxford), 2018 May 05; 2018. PMID: 29726944    Free PMC article.
Novel variants identified with next-generation sequencing in Polish patients with cone-rod dystrophy.
Anna Wawrocka, Anna Skorczyk-Werner, +10 authors, Maciej R Krawczynski.
Mol Vis, 2018 May 18; 24. PMID: 29769798    Free PMC article.
Distinct epigenetic landscapes underlie the pathobiology of pancreatic cancer subtypes.
Gwen Lomberk, Yuna Blum, +30 authors, Raul Urrutia.
Nat Commun, 2018 May 19; 9(1). PMID: 29773832    Free PMC article.
Highly Cited.
Dual origin of relapses in retinoic-acid resistant acute promyelocytic leukemia.
Jacqueline Lehmann-Che, Cécile Bally, +11 authors, Hugues de Thé.
Nat Commun, 2018 May 26; 9(1). PMID: 29795382    Free PMC article.
Dynamics of multiple resistance mechanisms in plasma DNA during EGFR-targeted therapies in non-small cell lung cancer.
Dana Wai Yi Tsui, Muhammed Murtaza, +15 authors, Nitzan Rosenfeld.
EMBO Mol Med, 2018 Jun 01; 10(6). PMID: 29848757    Free PMC article.
Using low-coverage whole genome sequencing technique to analyze the chromosomal copy number alterations in the exfoliative cells of cervical cancer.
Tong Ren, Jing Suo, +4 authors, Jing He Lang.
J Gynecol Oncol, 2018 Jul 20; 29(5). PMID: 30022638    Free PMC article.
Genome-wide copy number analyses of samples from LACE-Bio project identify novel prognostic and predictive markers in early stage non-small cell lung cancer.
Federico Rotolo, Chang-Qi Zhu, +10 authors, Ming-Sound Tsao.
Transl Lung Cancer Res, 2018 Jul 28; 7(3). PMID: 30050779    Free PMC article.
Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting.
Francesco Iorio, Fiona M Behan, +13 authors, Mathew J Garnett.
BMC Genomics, 2018 Aug 15; 19(1). PMID: 30103702    Free PMC article.
KMT2C Mutations in Diffuse-Type Gastric Adenocarcinoma Promote Epithelial-to-Mesenchymal Transition.
Soo-Jeong Cho, Changhwan Yoon, +10 authors, Sam S Yoon.
Clin Cancer Res, 2018 Aug 16; 24(24). PMID: 30108106    Free PMC article.
Copy number variation is associated with gene expression change in archaea.
Keely A Dulmage, Cynthia L Darnell, Angie Vreugdenhil, Amy K Schmid.
Microb Genom, 2018 Aug 25; 4(9). PMID: 30142055    Free PMC article.
Genomic region detection via Spatial Convex Clustering.
John Nagorski, Genevera I Allen.
PLoS One, 2018 Sep 12; 13(9). PMID: 30204756    Free PMC article.
Recurrent WNT pathway alterations are frequent in relapsed small cell lung cancer.
Alex H Wagner, Siddhartha Devarakonda, +27 authors, Ramaswamy Govindan.
Nat Commun, 2018 Sep 19; 9(1). PMID: 30224629    Free PMC article.
Long-read sequencing identified a causal structural variant in an exome-negative case and enabled preimplantation genetic diagnosis.
Hefan Miao, Jiapeng Zhou, +8 authors, Qianjun Zhang.
Hereditas, 2018 Oct 04; 155. PMID: 30279644    Free PMC article.
Tumor mutational burden is a determinant of immune-mediated survival in breast cancer.
Alexandra Thomas, Eric D Routh, +17 authors, Lance D Miller.
Oncoimmunology, 2018 Nov 06; 7(10). PMID: 30386679    Free PMC article.
Highly Cited.
Genomic subtyping and therapeutic targeting of acute erythroleukemia.
Ilaria Iacobucci, Ji Wen, +45 authors, Charles G Mullighan.
Nat Genet, 2019 Mar 31; 51(4). PMID: 30926971    Free PMC article.
Highly Cited.
Molecular Classification of Epithelial Ovarian Cancer Based on Methylation Profiling: Evidence for Survival Heterogeneity.
Clara Bodelon, J Keith Killian, +11 authors, Nicolas Wentzensen.
Clin Cancer Res, 2019 May 31; 25(19). PMID: 31142506    Free PMC article.
Genomic landscape of neutrophilic leukemias of ambiguous diagnosis.
Haijiao Zhang, Beth Wilmot, +29 authors, Jeffrey W Tyner.
Blood, 2019 Aug 02; 134(11). PMID: 31366621    Free PMC article.
Repair of multiple simultaneous double-strand breaks causes bursts of genome-wide clustered hypermutation.
Cynthia J Sakofsky, Natalie Saini, +6 authors, Dmitry A Gordenin.
PLoS Biol, 2019 Oct 01; 17(9). PMID: 31568516    Free PMC article.
Integrated molecular characterization of chondrosarcoma reveals critical determinants of disease progression.
Rémy Nicolle, Mira Ayadi, +17 authors, Gonzague de Pinieux.
Nat Commun, 2019 Oct 13; 10(1). PMID: 31604924    Free PMC article.
Characterization of genetic subclonal evolution in pancreatic cancer mouse models.
Noushin Niknafs, Yi Zhong, +6 authors, Rachel Karchin.
Nat Commun, 2019 Nov 30; 10(1). PMID: 31780749    Free PMC article.
Clonal copy-number mosaicism in autoreactive T lymphocytes in diabetic NOD mice.
Maha Alriyami, Luc Marchand, +3 authors, Constantin Polychronakos.
Genome Res, 2019 Nov 07; 29(12). PMID: 31694869    Free PMC article.
Forty-five patient-derived xenografts capture the clinical and biological heterogeneity of Wilms tumor.
Andrew J Murphy, Xiang Chen, +21 authors, Andrew M Davidoff.
Nat Commun, 2019 Dec 22; 10(1). PMID: 31862972    Free PMC article.
Concordance of copy number abnormality detection using SNP arrays and Multiplex Ligation-dependent Probe Amplification (MLPA) in acute lymphoblastic leukaemia.
Matthew Bashton, Robin Hollis, +5 authors, Amir Enshaei.
Sci Rep, 2020 Jan 09; 10(1). PMID: 31913349    Free PMC article.
CNApp, a tool for the quantification of copy number alterations and integrative analysis revealing clinical implications.
Sebastià Franch-Expósito, Laia Bassaganyas, +8 authors, Jordi Camps.
Elife, 2020 Jan 16; 9. PMID: 31939734    Free PMC article.
Recurring genomic structural variation leads to clonal instability and loss of productivity.
Arpan A Bandyopadhyay, Sofie A O'Brien, +3 authors, Wei-Shou Hu.
Biotechnol Bioeng, 2018 Aug 26; 116(1). PMID: 30144379    Free PMC article.
Detection of de novo copy number deletions from targeted sequencing of trios.
Jack M Fu, Elizabeth J Leslie, +5 authors, Ingo Ruczinski.
Bioinformatics, 2018 Aug 08; 35(4). PMID: 30084993    Free PMC article.
Identification of paternal uniparental disomy on chromosome 22 and a de novo deletion on chromosome 18 in individuals with orofacial clefts.
Ganiyu O Oseni, Deepti Jain, +26 authors, Azeez Butali.
Mol Genet Genomic Med, 2018 Aug 25; 6(6). PMID: 30141273    Free PMC article.
Integrated Genomic, Epigenomic, and Expression Analyses of Ovarian Cancer Cell Lines.
Eniko Papp, Dorothy Hallberg, +15 authors, Robert B Scharpf.
Cell Rep, 2018 Nov 30; 25(9). PMID: 30485824    Free PMC article.
G-quadruplex DNA drives genomic instability and represents a targetable molecular abnormality in ATRX-deficient malignant glioma.
Yuxiang Wang, Jie Yang, +8 authors, Jason T Huse.
Nat Commun, 2019 Feb 28; 10(1). PMID: 30808951    Free PMC article.
Highly Cited.
Noninvasive prenatal testing for fetal subchromosomal copy number variations and chromosomal aneuploidy by low-pass whole-genome sequencing.
Dongyi Yu, Kai Zhang, +14 authors, Yang Du.
Mol Genet Genomic Med, 2019 Apr 21; 7(6). PMID: 31004415    Free PMC article.
Predisposition to childhood acute lymphoblastic leukemia caused by a constitutional translocation disrupting ETV6.
Tekla Järviaho, Benedicte Bang, +7 authors, Ann Nordgren.
Blood Adv, 2019 Sep 15; 3(18). PMID: 31519648    Free PMC article.
Network-based analysis of prostate cancer cell lines reveals novel marker gene candidates associated with radioresistance and patient relapse.
Michael Seifert, Claudia Peitzsch, +3 authors, Anna Dubrovska.
PLoS Comput Biol, 2019 Nov 05; 15(11). PMID: 31682594    Free PMC article.
Development of a Precision Medicine Workflow in Hematological Cancers, Aalborg University Hospital, Denmark.
Julie S Bødker, Mads Sønderkær, +14 authors, Martin Bøgsted.
Cancers (Basel), 2020 Feb 06; 12(2). PMID: 32013121    Free PMC article.
An accurate and powerful method for copy number variation detection.
Feifei Xiao, Xizhi Luo, +5 authors, Heping Zhang.
Bioinformatics, 2019 Jan 17; 35(17). PMID: 30649252    Free PMC article.
Relapse-Fated Latent Diagnosis Subclones in Acute B Lineage Leukemia Are Drug Tolerant and Possess Distinct Metabolic Programs.
Stephanie M Dobson, Laura García-Prat, +30 authors, John E Dick.
Cancer Discov, 2020 Feb 23; 10(4). PMID: 32086311    Free PMC article.
Genetic characterization of a unique neuroendocrine transdifferentiation prostate circulating tumor cell-derived eXplant model.
Vincent Faugeroux, Emma Pailler, +19 authors, Françoise Farace.
Nat Commun, 2020 Apr 22; 11(1). PMID: 32313004    Free PMC article.
Functional Enhancers Shape Extrachromosomal Oncogene Amplifications.
Andrew R Morton, Nergiz Dogan-Artun, +16 authors, Peter C Scacheri.
Cell, 2019 Nov 26; 179(6). PMID: 31761532    Free PMC article.
Integrated Computational Pipeline for Single-Cell Genomic Profiling.
Lubomir Chorbadjiev, Jude Kendall, +4 authors, Alexander Krasnitz.
JCO Clin Cancer Inform, 2020 May 21; 4. PMID: 32432904    Free PMC article.
Decoding the evolutionary response to prostate cancer therapy by plasma genome sequencing.
Naveen Ramesh, Emi Sei, +7 authors, Nicholas E Navin.
Genome Biol, 2020 Jul 08; 21(1). PMID: 32631448    Free PMC article.
Quantitative characterization of tumor cell-free DNA shortening.
Juntang Guo, Kefeng Ma, +6 authors, Jin Huang.
BMC Genomics, 2020 Jul 12; 21(1). PMID: 32650715    Free PMC article.
Molecular Characterization of Astrocytoma Progression Towards Secondary Glioblastomas Utilizing Patient-Matched Tumor Pairs.
Michael Seifert, Gabriele Schackert, +3 authors, Barbara Klink.
Cancers (Basel), 2020 Jul 02; 12(6). PMID: 32604718    Free PMC article.
Characterization of a head and neck cancer-derived cell line panel confirms the distinct TP53-proficient copy number-silent subclass.
Anne M van Harten, Jos B Poell, +5 authors, Ruud H Brakenhoff.
Oral Oncol, 2019 Sep 22; 98. PMID: 31541927    Free PMC article.
Cross-species oncogenic signatures of breast cancer in canine mammary tumors.
Tae-Min Kim, In Seok Yang, +10 authors, Sangwoo Kim.
Nat Commun, 2020 Jul 19; 11(1). PMID: 32680987    Free PMC article.
Identification and Characterization of the Copy Number Dosage-Sensitive Genes in Colorectal Cancer.
Zhiqiang Chang, Xinxin Liu, Wenyuan Zhao, Yan Xu.
Mol Ther Methods Clin Dev, 2020 Aug 11; 18. PMID: 32775488    Free PMC article.
Mutational landscape and patterns of clonal evolution in relapsed pediatric acute lymphoblastic leukemia.
Esmé Waanders, Zhaohui Gu, +40 authors, Charles G Mullighan.
Blood Cancer Discov, 2020 Aug 15; 1(1). PMID: 32793890    Free PMC article.
Genomic characterization of malignant progression in neoplastic pancreatic cysts.
Michaël Noë, Noushin Niknafs, +35 authors, Laura D Wood.
Nat Commun, 2020 Aug 17; 11(1). PMID: 32796935    Free PMC article.
A novel algorithm comprehensively characterizes human RH genes using whole-genome sequencing data.
Ti-Cheng Chang, Kelly M Haupfear, +10 authors, Yan Zheng.
Blood Adv, 2020 Sep 12; 4(18). PMID: 32915977    Free PMC article.
Identification of portal vein tumor thrombus with an independent clonal origin in hepatocellular carcinoma via multi-omics data analysis.
Shupeng Liu, Zaixin Zhou, +5 authors, Shanrong Liu.
Cancer Biol Med, 2019 May 24; 16(1). PMID: 31119055    Free PMC article.
Bioinformatics Analysis for Circulating Cell-Free DNA in Cancer.
Chiang-Ching Huang, Meijun Du, Liang Wang.
Cancers (Basel), 2019 Jun 20; 11(6). PMID: 31212602    Free PMC article.
Review.
Evolution from adherent to suspension: systems biology of HEK293 cell line development.
Magdalena Malm, Rasool Saghaleyni, +9 authors, Johan Rockberg.
Sci Rep, 2020 Nov 06; 10(1). PMID: 33149219    Free PMC article.
Single-Cell Analysis of Circulating Tumor Cells.
Jana- A Thiele, Pavel Pitule, James Hicks, Peter Kuhn.
Methods Mol Biol, 2019 Jan 17; 1908. PMID: 30649733    Free PMC article.
REDBot: Natural language process methods for clinical copy number variation reporting in prenatal and products of conception diagnosis.
Mengmeng Liu, Yunshan Zhong, +9 authors, Fuli Yu.
Mol Genet Genomic Med, 2020 Sep 23; 8(11). PMID: 32961042    Free PMC article.
Cross-species genomics identifies DLG2 as a tumor suppressor in osteosarcoma.
Yang W Shao, Geoffrey A Wood, +9 authors, Rama Khokha.
Oncogene, 2018 Aug 11; 38(2). PMID: 30093633    Free PMC article.
DBS: a fast and informative segmentation algorithm for DNA copy number analysis.
Jun Ruan, Zhen Liu, +3 authors, Guoqiang Yu.
BMC Bioinformatics, 2019 Jan 05; 20(1). PMID: 30606105    Free PMC article.
Fuzzy methods for the detection of copy number variations in comparative genomic hybridization arrays.
Ahmad AlShibli, Hassan Mathkour.
Saudi J Biol Sci, 2020 Dec 12; 27(12). PMID: 33304176    Free PMC article.
Comparative genomic analysis of primary tumors and paired brain metastases in lung cancer patients by whole exome sequencing: a pilot study.
Pascale Tomasini, Fabrice Barlesi, +7 authors, Philippe Metellus.
Oncotarget, 2021 Jan 06; 11(50). PMID: 33400739    Free PMC article.
Genomic Adaption and Mutational Patterns in a HaCaT Subline Resistant to Alkylating Agents and Ionizing Radiation.
Reinhard Ullmann, Benjamin Valentin Becker, +9 authors, Harry Scherthan.
Int J Mol Sci, 2021 Jan 28; 22(3). PMID: 33498964    Free PMC article.
Survival outcomes are associated with genomic instability in luminal breast cancers.
Lydia King, Andrew Flaus, Emma Holian, Aaron Golden.
PLoS One, 2021 Feb 04; 16(2). PMID: 33534788    Free PMC article.
Telomeres reforged with non-telomeric sequences in mouse embryonic stem cells.
Chuna Kim, Sanghyun Sung, +11 authors, Junho Lee.
Nat Commun, 2021 Feb 19; 12(1). PMID: 33597549    Free PMC article.
Statistical Considerations on NGS Data for Inferring Copy Number Variations.
Jie Chen.
Methods Mol Biol, 2021 Feb 20; 2243. PMID: 33606251
Review.
A novel homozygous nonsense mutation in zona pellucida 1 (ZP1) causes human female empty follicle syndrome.
Jing Wang, Xiaoyu Yang, +8 authors, Xiang Ma.
J Assist Reprod Genet, 2021 Mar 06; 38(6). PMID: 33665726    Free PMC article.
Targeted next-generation sequencing panel screening of 668 Chinese patients with non-obstructive azoospermia.
Miao An, Yidong Liu, +5 authors, Mujun Lu.
J Assist Reprod Genet, 2021 Mar 18;. PMID: 33728612
Breast tumours maintain a reservoir of subclonal diversity during expansion.
Darlan C Minussi, Michael D Nicholson, +24 authors, Nicholas E Navin.
Nature, 2021 Mar 26; 592(7853). PMID: 33762732    Free PMC article.
Detecting rare copy number variants from Illumina genotyping arrays with the CamCNV pipeline: Segmentation of z-scores improves detection and reliability.
Joe Dennis, Logan Walker, +2 authors, Douglas F Easton.
Genet Epidemiol, 2020 Oct 07; 45(3). PMID: 33020983    Free PMC article.
Mapping the micro-proteome of the nuclear lamina and lamina-associated domains.
Xianrong Wong, Jevon A Cutler, +4 authors, Karen L Reddy.
Life Sci Alliance, 2021 Mar 25; 4(5). PMID: 33758005    Free PMC article.
13q12.2 deletions and FLT3 overexpression in acute leukemias.
Caroline Pires Poubel, Mariana Boroni, Mariana Emerenciano.
Blood Adv, 2021 Apr 21; 5(8). PMID: 33877294    Free PMC article.
Genome-wide copy number variations in a large cohort of bantu African children.
Feyza Yilmaz, Megan Null, +8 authors, Tamim H Shaikh.
BMC Med Genomics, 2021 May 19; 14(1). PMID: 34001112    Free PMC article.
Multi-site tumor sampling highlights molecular intra-tumor heterogeneity in malignant pleural mesothelioma.
Clément Meiller, François Montagne, +19 authors, Didier Jean.
Genome Med, 2021 Jul 16; 13(1). PMID: 34261524    Free PMC article.
CIRCNV: Detection of CNVs Based on a Circular Profile of Read Depth from Sequencing Data.
Hai-Yong Zhao, Qi Li, +3 authors, Xi-Guo Yuan.
Biology (Basel), 2021 Jul 03; 10(7). PMID: 34202028    Free PMC article.
Genomic and Transcriptomic Profiling of Combined Hepatocellular and Intrahepatic Cholangiocarcinoma Reveals Distinct Molecular Subtypes.
Ruidong Xue, Lu Chen, +32 authors, Ning Zhang.
Cancer Cell, 2019 May 28; 35(6). PMID: 31130341    Free PMC article.
Highly Cited.
Comparison of the oncogenomic landscape of canine and feline hemangiosarcoma shows novel parallels with human angiosarcoma.
Kim Wong, Latasha Ludwig, +3 authors, Louise van der Weyden.
Dis Model Mech, 2021 Jul 24; 14(7). PMID: 34296746    Free PMC article.
LiquidCNA: Tracking subclonal evolution from longitudinal liquid biopsies using somatic copy number alterations.
Eszter Lakatos, Helen Hockings, +3 authors, Trevor A Graham.
iScience, 2021 Aug 18; 24(8). PMID: 34401670    Free PMC article.