A three-caller pipeline for variant analysis of cancer whole-exome sequencing data

Liu,Ze‑Kun; Shang,Yu‑Kui; Chen,Zhi‑Nan; Bian,Huijie

doi:10.3892/mmr.2017.6336

May-2017 Volume 15 Issue 5

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May-2017 Volume 15 Issue 5

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Article Open Access

A three-caller pipeline for variant analysis of cancer whole-exome sequencing data

Authors:
- Ze‑Kun Liu
- Yu‑Kui Shang
- Zhi‑Nan Chen
- Huijie Bian
View Affiliations / Copyright

Affiliations: Department of Cell Biology and National Translational Science Center for Molecular Medicine, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China

Copyright: © Liu et al. This is an open access article distributed under the terms of Creative Commons Attribution License.
Pages: 2489-2494
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Published online on: March 16, 2017

https://doi.org/10.3892/mmr.2017.6336
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Abstract

Rapid advancements in next generation sequencing (NGS) technologies, coupled with the dramatic decrease in cost, have made NGS one of the leading approaches applied in cancer research. In addition, it is increasingly used in clinical practice for cancer diagnosis and treatment. Somatic (cancer‑only) single nucleotide variants and small insertions and deletions (indels) are the simplest classes of mutation, however, their identification in whole exome sequencing data is complicated by germline polymorphisms, tumor heterogeneity and errors in sequencing and analysis. An increasing number of software and methodological guidelines are being published for the analysis of sequencing data. Usually, the algorithms of MuTect, VarScan and Genome Analysis Toolkit are applied to identify the variants. However, one of these algorithms alone results in incomplete genomic information. To address this issue, the present study developed a systematic pipeline for analyzing the whole exome sequencing data of hepatocellular carcinoma (HCC) using a combination of the three algorithms, named the three‑caller pipeline. Application of the three‑caller pipeline to the whole exome data of HCC, improved the detection of true positive mutations and a total of 75 tumor‑specific somatic variants were identified. Functional enrichment analysis revealed the mutations in the genes encoding cell adhesion and regulation of Ras GTPase activity. This pipeline provides an effective approach to identify variants from NGS data for subsequent functional analyses.

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1	Lengauer C, Kinzler KW and Vogelstein B: Genetic instabilities in human cancers. Nature. 396:643–649. 1998. View Article : Google Scholar : PubMed/NCBI
2	Bass AJ, Lawrence MS, Brace LE, Ramos AH, Drier Y, Cibulskis K, Sougnez C, Voet D, Saksena G, Sivachenko A, et al: Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion. Nat Genet. 43:964–968. 2011. View Article : Google Scholar : PubMed/NCBI
3	Chapman MA, Lawrence MS, Keats JJ, Cibulskis K, Sougnez C, Schinzel AC, Harview CL, Brunet JP, Ahmann GJ, Adli M, et al: Initial genome sequencing and analysis of multiple myeloma. Nature. 471:467–472. 2011. View Article : Google Scholar : PubMed/NCBI
4	Jia D, Dong R, Jing Y, Xu D, Wang Q, Chen L, Li Q, Huang Y, Zhang Y, Zhang Z, et al: Exome sequencing of hepatoblastoma reveals novel mutations and cancer genes in the Wnt pathway and ubiquitin ligase complex. Hepatology. 60:1686–1696. 2014. View Article : Google Scholar : PubMed/NCBI
5	Biesecker LG and Green RC: Diagnostic clinical genome and exome sequencing. N Engl J Med. 371:11702014.PubMed/NCBI
6	Cancer Genome Atlas Research Network. Hammerman PS, Lawrence MS, Voet D, Jing R, Cibulskis K, Sivachenko A, Stojanov P, McKenna A, Lander ES, et al: Comprehensive genomic characterization of squamous cell lung cancers. Nature. 489:519–525. 2012. View Article : Google Scholar : PubMed/NCBI
7	Cancer Genome Atlas Network. Muzny DM, Bainbridge MN, Chang K, Dinh HH, Drummond JA, Fowler G, Kovar CL, Lewis LR, Morgan MB, et al: Comprehensive molecular characterization of human colon and rectal cancer. Nature. 487:330–337. 2012. View Article : Google Scholar : PubMed/NCBI
8	Cancer Genome Atlas Network. Koboldt DC, Fulton RS, McLellan MD, Schmidt H, Kalicki-Veizer J, McMichael JF, Fulton LL, Dooling DJ, Ding L, et al: Comprehensive molecular portraits of human breast tumours. Nature. 490:61–70. 2012. View Article : Google Scholar : PubMed/NCBI
9	Litchfield K, Summersgill B, Yost S, Sultana R, Labreche K, Dudakia D, Renwick A, Seal S, Al-Saadi R, Broderick P, et al: Whole-exome sequencing reveals the mutational spectrum of testicular germ cell tumours. Nat Commun. 6:59732015. View Article : Google Scholar : PubMed/NCBI
10	Zhang Z: Genomic landscape of liver cancer. Nat Genet. 44:1075–1077. 2012. View Article : Google Scholar : PubMed/NCBI
11	Kan Z, Zheng H, Liu X, Li S, Barber TD, Gong Z, Gao H, Hao K, Willard MD, Xu J, et al: Whole-genome sequencing identifies recurrent mutations in hepatocellular carcinoma. Genome Res. 23:1422–1433. 2013. View Article : Google Scholar : PubMed/NCBI
12	Wang Q, Jia P, Li F, Chen H, Ji H, Hucks D, Dahlman KB, Pao W and Zhao Z: Detecting somatic point mutations in cancer genome sequencing data: A comparison of mutation callers. Genome Med. 5:912013. View Article : Google Scholar : PubMed/NCBI
13	Gerlinger M, Rowan AJ, Horswell S, Larkin J, Endesfelder D, Gronroos E, Martinez P, Matthews N, Stewart A, Tarpey P, et al: Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med. 366:883–892. 2012. View Article : Google Scholar : PubMed/NCBI
14	Cibulskis K, Lawrence MS, Carter SL, Sivachenko A, Jaffe D, Sougnez C, Gabriel S, Meyerson M, Lander ES and Getz G: Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol. 31:213–219. 2013. View Article : Google Scholar : PubMed/NCBI
15	Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L and Wilson RK: Varscan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 22:568–576. 2012. View Article : Google Scholar : PubMed/NCBI
16	McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M and DePristo MA: The genome analysis toolkit: A mapreduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20:1297–1303. 2010. View Article : Google Scholar : PubMed/NCBI
17	Mardis ER: Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet. 9:387–402. 2008. View Article : Google Scholar : PubMed/NCBI
18	Metzker ML: Sequencing technologies-the next generation. Nat Rev Genet. 11:31–46. 2010. View Article : Google Scholar : PubMed/NCBI
19	Dohm JC, Lottaz C, Borodina T and Himmelbauer H: Substantial biases inultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res. 36:e1052008. View Article : Google Scholar : PubMed/NCBI
20	Nielsen R, Paul JS, Albrechtsen A and Song YS: Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet. 12:443–451. 2011. View Article : Google Scholar : PubMed/NCBI
21	Li H and Durbin R: Fast and accurate long-read alignment with burrows-wheeler transform. Bioinformatics. 26:589–595. 2010. View Article : Google Scholar : PubMed/NCBI
22	Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G and Durbin R: 1000 Genome Project Data Processing Subgroup: The sequence alignment/map format and SAMtools. Bioinformatics. 25:2078–2079. 2009. View Article : Google Scholar : PubMed/NCBI
23	Ramos AH, Lichtenstein L, Gupta M, Lawrence MS, Pugh TJ, Saksena G, Meyerson M and Getz G: Oncotator: Cancer variant annotation tool. Hum Mutat. 36:E2423–E2429. 2015. View Article : Google Scholar : PubMed/NCBI
24	Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G and Mesirov JP: Integrative genomics viewer. Nat Biotechnol. 29:24–26. 2011. View Article : Google Scholar : PubMed/NCBI
25	da Huang W, Sherman BT and Lempicki RA: Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 4:44–57. 2009. View Article : Google Scholar : PubMed/NCBI
26	Totoki Y, Tatsuno K, Yamamoto S, Arai Y, Hosoda F, Ishikawa S, Tsutsumi S, Sonoda K, Totsuka H, Shirakihara T, et al: High-resolution characterization of a hepatocellular carcinoma genome. Nat Genet. 43:464–469. 2011. View Article : Google Scholar : PubMed/NCBI
27	Lawrence MS, Stojanov P, Polak P, Kryukov GV, Cibulskis K, Sivachenko A, Carter SL, Stewart C, Mermel CH, Roberts SA, et al: Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature. 499:214–218. 2013. View Article : Google Scholar : PubMed/NCBI
28	Kwon SM, Cho H, Choi JH, Jee BA, Jo Y and Woo HG: Perspectives of integrative cancer genomics in next generation sequencing era. Genomics Inform. 10:69–73. 2012. View Article : Google Scholar : PubMed/NCBI

Journals

International Journal of Molecular Medicine

International Journal of Oncology

Molecular Medicine Reports

Oncology Reports

Experimental and Therapeutic Medicine

Oncology Letters

Biomedical Reports

Molecular and Clinical Oncology

World Academy of Sciences Journal

International Journal of Functional Nutrition

International Journal of Epigenetics

Medicine International

A three-caller pipeline for variant analysis of cancer whole-exome sequencing data

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Abstract

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