A cancer cell-line titration series for evaluating somatic classification

BMC Research Notes

Volumn 8, Issue 1, 2015, Pages

  Denroche, Robert E ^a   Mullen, Laura ^a   Timms, Lee ^a   Beck, Timothy ^a   Yung, Christina K ^a   Stein, Lincoln ^a,b   McPherson, John D ^a,b   Brown, Andrew M K ^a  

^a ONTARIO INSTITUTE FOR CANCER RESEARCH   (Canada)

^b UNIVERSITY OF TORONTO   (Canada)

Author keywords

Cancer bioinformatics; Normal contamination; Somatic mutation calling; Tumour cellularity; Whole exome sequencing dataset

Indexed keywords

DNA;

ALGORITHM; BIOLOGY; DNA MUTATIONAL ANALYSIS; EXOME; GENE FREQUENCY; GENE LIBRARY; GENETIC VARIATION; GENETICS; HUMAN; INDEL MUTATION; MUTATION; NEOPLASM; NUCLEIC ACID DATABASE; PANCREAS CARCINOMA; PANCREAS TUMOR; SINGLE NUCLEOTIDE POLYMORPHISM; SOFTWARE; TUMOR CELL LINE;

ALGORITHMS; CARCINOMA, PANCREATIC DUCTAL; CELL LINE, TUMOR; COMPUTATIONAL BIOLOGY; DATABASES, NUCLEIC ACID; DNA MUTATIONAL ANALYSIS; DNA, NEOPLASM; EXOME; GENE FREQUENCY; GENE LIBRARY; GENETIC VARIATION; HUMANS; INDEL MUTATION; MUTATION; NEOPLASMS; PANCREATIC NEOPLASMS; POLYMORPHISM, SINGLE NUCLEOTIDE; SOFTWARE;

EID: 84955668238     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/s13104-015-1803-7     Document Type: Article

References (23)

1. Ley TJ, Mardis ER, Ding L, Fulton B, McLellan MD, Chen K, et al. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature. 2008;456:66-72.
2. Jones SJM, Laskin J, Li YY, Griffith OL, An J, Bilenky M, et al. Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors. Genome Biol. 2010. doi: 10.1186/gb-2010-11-8-r82.
3. Shah SP, Morin RD, Khattra J, Prentice L, Pugh T, Burleigh A, et al. Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature. 2009;461:809-13.
4. Roth A, Ding J, Morin R, Crisan A, Ha G, Giuliany R, et al. JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data. Bioinformatics. 2012;28:907-13.
5. Cibulskis K, Lawrence MS, Carter SL, Sivachenko A, Jaffe D, Sougnez C, et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol. 2013;31:213-9.
6. Larson DE, Harris CC, Chen K, Koboldt DC, Abbott TE, Dooling DJ, et al. SomaticSniper: identification of somatic point mutations in whole genome sequencing data. Bioinformatics. 2012;28:311-7.
7. Saunders CT, Wong WSW, Swamy S, Becq J, Murray LJ, Cheetham RK. Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs. Bioinformatics. 2012;28:1811-7.
8. Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 2012;22:568-76.
9. Stead LF, Sutton KM, Taylor GR, Quirke P, Rabbitts P. accurately identifying low-allelic fraction variants in single samples with next-generation sequencing: applications in tumor subclone resolution. Hum Mutat. 2013;34:1432-8.
10. Li H. Towards better understanding of artifacts in variant calling from high-coverage samples. Bioinformatics. 2014;30:2843-51.
11. Wang Q, Jia P, Li F, Chen C, Ji H, Hucks D, et al. Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers. Genome Med. 2013. doi: 10.1186/gm495.
12. Ewing AD. Cancer Genomics Hub TCGA Mutation Calling Benchmark 4 Datasets - UC Santa Cruz. 2013. https://cghub.ucsc.edu/datasets/benchmark-download.html. Accessed 3 Jul 2015.
13. Boutros PC, Ewing AD, Ellrott K, Norman TC, Dang KK, Hu Y. Global optimization of somatic variant identification in cancer genomes with a global community challenge. Nat Genet. 2014;46:318-9.
14. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754-60.
15. Novocraft Technologies Sdn Bhd. http://www.novocraft.com. 2014. Accessed 3 Jul 2015.
16. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011;43:491-8.
17. Alioto TS, Derdak S, Beck TA, Boutros PC, Bower L, Buchhalter I, et al. A Comprehensive Assessment of Somatic Mutation Calling in Cancer Genomes. bioRxiv. 2014. doi: 10.1101/012997.
18. Costello M, Pugh TJ, Fennell TJ, Stewart C, Lichtenstein L, Meldrim JC, et al. Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation. Nucleic Acids Res. 2013. doi: 10.1093/nar/gks1443.
19. Conway T, Wazny J, Bromage A, Tymms M, Sooraj D, Williams ED, et al. Xenome - a tool for classifying reads from xenograft samples. Bioinformatics. 2012;28:i172-8.
20. EMBL-EBI European Genome-phenome Archive. http://www.ebi.ac.uk/ega/. 2015. Accessed 3 Jul 2015.
21. ICGC Data Access Compliance Office. https://icgc.org/daco/. 2014. Accessed 3 Jul 2015.
22. Picard Tools - By Broad Institute. http://broadinstitute.github.io/picard. 2015. Accessed 3 Jul 2015.
23. Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, et al. Integrative genomics viewer. Nat Biotechnol. 2011;29:24-6.