A method for checking genomic integrity in cultured cell lines from snp genotyping data

PLoS ONE

Volumn 11, Issue 5, 2016, Pages

  Danecek, Petr ^a   McCarthy, Shane A ^a   Consortium, HipSci ^a   Durbin, Richard ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ANEUPLOIDY; ARTICLE; CANCER CELL; COPY NUMBER VARIATION; GENE FREQUENCY; GENE FUNCTION; GENE IDENTIFICATION; GENE MUTATION; GENETIC ALGORITHM; GENETIC ANALYSIS; GENOTYPE; HUMAN; HUMAN CELL; PLURIPOTENT STEM CELL; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; SINGLE NUCLEOTIDE POLYMORPHISM; CELL CULTURE; CHROMOSOME DELETION; COMPUTER SIMULATION; GENE DUPLICATION; GENETICS; GENOME; GENOTYPING TECHNIQUE; PROCEDURES; STATISTICS;

CELLS, CULTURED; CHROMOSOME DELETION; COMPUTER SIMULATION; DNA COPY NUMBER VARIATIONS; GENE DUPLICATION; GENE FREQUENCY; GENOME; GENOTYPING TECHNIQUES; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS; STATISTICS AS TOPIC;

EID: 84969808320     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0155014     Document Type: Article

References (19)

1. Gore A, Li Z, Fung HL, Young JE, Agarwal S, Antosiewicz-Bourget J, Canto I, et al. Somatic coding mutations in human induced pluripotent stem cells. Nature. 2011; 471:63-67.
2. Mayshar Y, Ben-David U, Lavon N, Biancotti JC, Yakir B, Clark AT, et al. Identification and Classification of Chromosomal Aberrations in Human Induced Pluripotent Stem Cells. Cell Stem Cell. 2010; 7:521-531. doi: 10.1016/j.stem.2010.07.017 PMID: 20887957
3. Liu P, Kaplan A, Yuan B, Hanna JH, Lupski JR, Reiner O. Passage number is a major contributor to genomic structural variations in mouse iPSCs. Stem Cells. 2014; 32:2657-2667. doi: 10.1002/stem. 1779 PMID: 24965231
4. Ma H, Morey R, O'Neil RC, He Y, Daughtry B, Schultz MD, et al. Abnormalities in human pluripotent cells due to reprogramming mechanisms. Nature. 2014; 511:177-183.
5. Bai Q, Ramirez JM, Becker F, Pantesco V, Lavabre-Bertrand T, Hovatta O, et al. Temporal analysis of genome alterations induced by single-cell passaging in human embryonic stem cells. Stem Cells Dev. 2014;. doi: 10.1089/scd.2014.0292 PMID: 25254421
6. Peiffer DA, Le JM, Steemers FJ, Chang W, Jenniges T, Garcia F, et al. High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping. Genome Res. 2006; 16:1136-1148. doi: 10.1101/gr.5402306 PMID: 16899659
7. Fiegler H, Redon R, Andrews D, Scott C, Andrews R, Carder C, et al. Accurate and reliable highthroughput detection of copy number variation in the human genome. Genome Res. 2006; 16 (12):1566-1574. doi: 10.1101/gr.5630906 PMID: 17122085
8. Olshen AB, Venkatraman ES, Lucito R, Wigler M. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics. 2004; 5(4):557-72. doi: 10.1093/biostatistics/ kxh008 PMID: 15475419
9. Colella S, Yau C, Taylor JM, Mirza G, Butler H, Clouston P, et al. QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data. Nucleic Acids Research. 2007; 35(6):2013-25. doi: 10.1093/nar/gkm076 PMID: 17341461
10. Wang K, Li M, Hadley D, Liu R, Glessner J, Grant SF, et al. PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res. 2007; 17:1665-1674. doi: 10.1101/gr.6861907 PMID: 17921354
11. Tsuang DW, Millard SP, Ely B, Chi P, Wang K, Raskind WH, et al. The effect of algorithms on copy number variant detection. PLoS One. 2010; 5(12):e14456. doi: 10.1371/journal.pone.0014456 PMID: 21209939
12. Xu L, Hou Y, Bickhart DM, Song J, Liu GE. Comparative Analysis of CNV Calling Algorithms: Literature Survey and a Case Study Using Bovine High-Density SNP Data. Microarrays. 2013; 2(3):171-185. doi: 10.3390/microarrays2030171
13. Sun W, Wright FA, Tang Z, Nordgard SH, Van Loo P, Yu T, et al. Integrated Study of Copy Number States and Genotype Calls Using High-Density SNP Arrays. Nucleic Acids Research. 2009; 37 (16):5365-5377. doi: 10.1093/nar/gkp493 PMID: 19581427
14. Yau C, Mouradov D, Jorissen RN, Colella S, Mirza G, Steers G, et al. A statistical approach for detecting genomic aberrations in heterogeneous tumor samples from single nucleotide polymorphism genotyping data. Genome Biol. 2010; 11(9).
15. Li A, Liu Z, Lezon-Geyda K, Sarkar S, Lannin D, Schulz V, et al. GPHMM: an integrated hidden Markov model for identification of copy number alteration and loss of heterozygosity in complex tumor samples using whole genome SNP arrays. Nucleic Acids Research. 2011 Jul; 39(12):4928-4941. doi: 10.1093/ nar/gkr014 PMID: 21398628
16. BCFtools; available from: http://github.com/samtools/bcftools.
17. Galassi M, et al. GNU Scientific Library Reference Manual (3rd Ed.);.
18. Oros KK, Arcand SL, Bayani J, Squire JA, Mes-Masson AM, Tonin PN, et al. cnvPartition: DNA Copy Number and Loss of Heterozygosity Analysis Algorithms. Technical note: Illumina systems and software. 24 June 2013;Pub. No. 970-2007-008.
19. HipSci Consortium http://www.hipsci.org.