Optimized pipeline of MuTect and GATK tools to improve the detection of somatic single nucleotide polymorphisms in whole-exome sequencing data

BMC Bioinformatics

Volumn 17, Issue , 2016, Pages

  do Valle, Ítalo Faria ^a,b   Giampieri, Enrico ^a   Simonetti, Giorgia ^a   Padella, Antonella ^a   Manfrini, Marco ^a   Ferrari, Anna ^a   Papayannidis, Cristina ^a   Zironi, Isabella ^a   Garonzi, Marianna ^c   Bernardi, Simona ^d   Delledonne, Massimo ^c,e   Martinelli, Giovanni ^a   Remondini, Daniel ^a   Castellani, Gastone ^a  

^a UNIVERSITY OF BOLOGNA   (Italy)

^b MINISTRY OF EDUCATION OF BRAZIL   (Brazil)

^c UNIVERSITY OF VERONA   (Italy)

^d UNIVERSITY OF BRESCIA   (Italy)

^e Personalgenomics   (Italy)

Author keywords

Cancer; Somatic single nucleotide variants; Whole exome sequencing

Indexed keywords

CHEMOTHERAPY; DISEASES; GENES; NUCLEOTIDES; TUMORS;

ACUTE LYMPHOBLASTIC LEUKEMIA; CANCER; GASTROINTESTINAL STROMAL TUMORS; SENSITIVITY AND SPECIFICITY; SINGLE NUCLEOTIDE POLYMORPHISMS; SINGLE NUCLEOTIDES; STANDARD ALGORITHMS; WHOLE EXOME SEQUENCING;

PIPELINES;

ALGORITHM; EVALUATION STUDY; EXOME; GENETICS; GENOMICS; HIGH THROUGHPUT SEQUENCING; HUMAN; MUTATION; NEOPLASM; PROCEDURES; SENSITIVITY AND SPECIFICITY; SINGLE NUCLEOTIDE POLYMORPHISM; SOFTWARE;

ALGORITHMS; EXOME; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MUTATION; NEOPLASMS; POLYMORPHISM, SINGLE NUCLEOTIDE; SENSITIVITY AND SPECIFICITY; SOFTWARE;

EID: 84994452804     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/s12859-016-1190-7     Document Type: Article

References (30)

1. Ding L, Wendl MC, Koboldt DC, Mardis ER. Analysis of next-generation genomic data in cancer: accomplishments and challenges. Hum Mol Genet. 2010;19:188-96.
2. Spencer DH, Tyagi M, Vallania F, Bredemeyer AJ, Pfeifer JD, Mitra RD, Duncavage EJ. Performance of common analysis methods for detecting low-frequency single nucleotide variants in targeted next-generation sequence data. J Mol Diagn. 2014;16:75-88.
3. Xu H, DiCarlo J, Satya RV, Peng Q, Wang Y. Comparison of somatic mutation calling methods in amplicon and whole exome sequence data. BMC Genomics. 2014;15:244.
4. O'Rawe J, Jiang T, Sun G, Wu Y, Wang W, Hu J, Bodily P, Tian L, Hakonarson H, Johnson WE, Wei Z, Wang K, Lyon GJ. Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing. Genome Med. 2013;5:28.
5. Liu B, Morrison CD, Johnson CS, Trump DL, Qin M, Conroy JC, Wang J, Liu S. Computational methods for detecting copy number variations in cancer genome using next generation sequencing: principles and challenges. Oncotarget. 2013;4:1868-81.
6. Pabinger S, Dander A, Fischer M, Snajder R, Sperk M, Efremova M, Krabichler B, Speicher MR, Zschocke J, Trajanoski Z. A survey of tools for variant analysis of next-generation genome sequencing data. Brief Bioinform. 2014;15:256-78.
7. Carson AR, Smith EN, Matsui H, Brækkan SK, Jepsen K, Hansen J-B, Frazer KA. Effective filtering strategies to improve data quality from population-based whole exome sequencing studies. BMC Bioinformatics. 2014;15:125.
8. Bodini M, Ronchini C, Giac L, Russo A, Melloni GEM, Luzi L, Sardella D, Volorio S, Hasan SK, Ottone T, Lavorgna S, Lo-coco F, Candoni A, Fanin R, Toffoletti E, Iacobucci I, Martinelli G, Cignetti A, Tarella C, Bernard L, Pelicci PG, Riva L. Perspectives the hidden genomic landscape of acute myeloid leukemia: subclonal structure revealed by undetected mutations. Blood. 2015;125:600-6.
9. Kim SY, Jacob L, Speed TP. Combining calls from multiple somatic mutation-callers. BMC Bioinformatics. 2014;15:154.
10. Kang G, Yun H, Sun C, Park I, Kwon J, Do I, Hong ME, Van Vrancken M, Park JO, Cho J, Kim K, Sohn TS. Integrated genomic analyses identify frequent gene fusion events and VHL inactivation in gastrointestinal stromal tumors. Oncotarget. 2016;7(6);6538-51.
11. Seo JS, Ju YS, Lee WC, Shin JY, Lee JK, Bleazard T, Lee J, Jung YJ, Kim JO, Shin JY, Yu SB, Kim J, Lee ER, Kang CH, Park IK, Rhee H, Lee SH, Kim JI, Kang JH, Kim YT. The transcriptional landscape and mutational profile of lung adenocarcinoma. Genome Res. 2012;22:2109-19.
12. FASTX-Toolkit http://hannonlab.cshl.edu/fastx_toolkit/.
13. Li H, Durbin R. Fast and accurate short read alignment with burrows-wheeler transform. Bioinformatics. 2009;25:1754-60.
14. Picard Tools http://broadinstitute.github.io/picard/.
15. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011;43:491-8.
16. Cibulskis K, Lawrence MS, Carter SL, Sivachenko A, Jaffe D, Sougnez C, Gabriel S, Meyerson M, Lander ES, Getz G. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol. 2013;31:213-9.
17. Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38:e164.
18. Breese MR, Liu Y. NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets. Bioinformatics. 2013;29:494-6.
19. Hansen NF, Gartner JJ, Mei L, Samuels Y, Mullikin JC. Shimmer: detection of genetic alterations in tumors using next-generation sequence data. Bioinformatics. 2013;29:1498-503.
20. Hansen MC, Nederby L, Roug A, Villesen P, Kjeldsen E, Nyvold CG, Hokland P. Novel scripts for improved annotation and selection of variants from whole exome sequencing in cancer research. MethodsX. 2015;2:145-53.
21. Roberts ND, Kortschak RD, Parker WT, Schreiber AW, Branford S, Scott HS, Glonek G, Adelson DL. A comparative analysis of algorithms for somatic SNV detection in cancer. Bioinformatics. 2013;29:2223-30.
22. Lyon GJ, Wang K. Identifying disease mutations in genomic medicine settings: current challenges and how to accelerate progress. Genome Med. 2012;4:58.
23. Ciriello G, Miller ML, Aksoy BA, Senbabaoglu Y, Schultz N, Sander C. Emerging landscape of oncogenic signatures across human cancers. Nat Genet. 2013;45:1127-33.
24. Kim N, Hong Y, Kwon D, Yoon S. Somatic mutaome profile in human cancer tissues. Genomics Inform. 2013;11:239-44.
25. Lawrence MS, Stojanov P, Polak P, Kryukov GV, Cibulskis K, Sivachenko A, Carter SL, Stewart C, Mermel CH, Roberts SA, Kiezun A, Hammerman PS, McKenna A, Drier Y, Zou L, Ramos AH, Pugh TJ, Stransky N, Helman E, Kim J, Sougnez C, Ambrogio L, Nickerson E, Shefler E, Cortés ML, Auclair D, Saksena G, Voet D, Noble M, DiCara D, et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature. 2013;499:214-8.
26. Kandoth C, McLellan MD, Vandin F, Ye K, Niu B, Lu C, Xie M, Zhang Q, McMichael JF, Wyczalkowski MA, Leiserson MDM, Miller CA, Welch JS, Walter MJ, Wendl MC, Ley TJ, Wilson RK, Raphael BJ, Ding L. Mutational landscape and significance across 12 major cancer types. Nature. 2013;502:333-9.
27. Collisson EA, Campbell JD, Brooks AN, Berger AH, Lee W, Chmielecki J, Beer DG, Cope L, Creighton CJ, Danilova L, Ding L, Getz G, Hammerman PS, Neil Hayes D, Hernandez B, Herman JG, Heymach JV, Jurisica I, Kucherlapati R, Kwiatkowski D, Ladanyi M, Robertson G, Schultz N, Shen R, Sinha R, Sougnez C, Tsao M-S, Travis WD, Weinstein JN, Wigle DA, et al. Comprehensive molecular profiling of lung adenocarcinom. Nature. 2014;511:543-50.
28. Reumers J, De Rijk P, Zhao H, Liekens A, Smeets D, Cleary J, Van Loo P, Van Den Bossche M, Catthoor K, Sabbe B, Despierre E, Vergote I, Hilbush B, Lambrechts D, Del-Favero J. Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing. Nat Biotechnol. 2011;30:61-8.
29. Nakamura K, Oshima T, Morimoto T, Ikeda S, Yoshikawa H, Shiwa Y, Ishikawa S, Linak MC, Hirai A, Takahashi H, Altaf-Ul-Amin M, Ogasawara N, Kanaya S. Sequence-specific error profile of illumina sequencers. Nucleic Acids Res. 2011;39:e90.
30. Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, Bertoni A, Swerdlow HP, Gu Y. A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers. BMC Genomics. 2012;13:341.