IMPACT: A whole-exome sequencing analysis pipeline for integrating molecular profiles with actionable therapeutics in clinical samples

Journal of the American Medical Informatics Association

Volumn 23, Issue 4, 2016, Pages 721-730

  Hintzsche, Jennifer ^a   Kim, Jihye ^a,b   Yadav, Vinod ^a   Amato, Carol ^a   Robinson, Steven E ^a   Seelenfreund, Eric ^a   Shellman, Yiqun ^a,b   Wisell, Joshua ^a,b   Applegate, Allison ^a   McCarter, Martin ^b   Box, Neil ^a,b   Tentler, John ^a,b   De, Subhajyoti ^a,b,c   Robinson, William A ^a,b   Tan, Aik Choon ^a,b,c  

^a UNIVERSITY OF COLORADO SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF COLORADO   (United States)

^c Global Health and Health Disparities   (United States)

Author keywords

Bioinformatics; Cancer; Personalized medicine; Therapeutics; Whole exome sequencing

Indexed keywords

AFATINIB; B RAF KINASE; BETA CATENIN; CABOZANTINIB; CETUXIMAB; CRIZOTINIB; CYCLIN DEPENDENT KINASE INHIBITOR 2A; DABRAFENIB; DASATINIB; EPIDERMAL GROWTH FACTOR RECEPTOR; ERLOTINIB; GEFITINIB; IBRUTINIB; IMATINIB; LAPATINIB; MITOGEN ACTIVATED PROTEIN KINASE KINASE; OSIMERTINIB; PANITUMUMAB; PEPTIDES AND PROTEINS; PIK3CA PROTEIN; PROTEIN KINASE LKB1; REGORAFENIB; SORAFENIB; STEM CELL FACTOR; TRAMETINIB; TUMOR MARKER; UNCLASSIFIED DRUG; VANDETANIB; VEMURAFENIB; VISMODEGIB;

ARTICLE; BIOINFORMATICS; CANCER COMBINATION CHEMOTHERAPY; CANCER PATIENT; CANCER RECURRENCE; CANCER RESISTANCE; CLONAL VARIATION; CONTROLLED STUDY; COPY NUMBER VARIATION; FOOD AND DRUG ADMINISTRATION; GENE DELETION; GENETIC ASSOCIATION; GENETIC HETEROGENEITY; HUMAN; HUMAN TISSUE; INTEGRATING MOLECULAR PROFILES WITH ACTIONABLE THERAPEUTICS ANALYSIS; LUNG ADENOCARCINOMA; MELANOMA; METHODOLOGY; MOLECULARLY TARGETED THERAPY; ONCOGENE H RAS; ONCOGENE K RAS; ONCOGENE N RAS; PERSONALIZED MEDICINE; PREDICTIVE VALUE; SEQUENCE ANALYSIS; SOMATIC MUTATION; VALIDATION STUDY; WHOLE EXOME SEQUENCING; ADENOCARCINOMA; BIOLOGY; DNA MUTATIONAL ANALYSIS; DRUG RESISTANCE; EXOME; GENETICS; LUNG TUMOR; MUTATION; PROTO ONCOGENE;

ADENOCARCINOMA; COMPUTATIONAL BIOLOGY; DNA COPY NUMBER VARIATIONS; DNA MUTATIONAL ANALYSIS; DRUG RESISTANCE, NEOPLASM; EXOME; GENES, ERBB-1; HUMANS; LUNG NEOPLASMS; MELANOMA; MUTATION; PRECISION MEDICINE;

EID: 84981240762     PISSN: 10675027     EISSN: 1527974X     Source Type: Journal    
DOI: 10.1093/jamia/ocw022     Document Type: Article

References (32)

1. Karczewski KJ, Fernald GH, Martin AR, Snyder M, Tatonetti NP, Dudley JT. STORMSeq: an open-source, user-friendly pipeline for processing personal genomics data in the cloud. PLoS ONE. 2014;9:e84860.
2. Fischer M, Snajder R, Pabinger S, et al. SIMPLEX: cloud-enabled pipeline for the comprehensive analysis of exome sequencing data. PLoS ONE. 2012;7:e41948.
3. Challis D, Yu J, Evani US, et al. An integrative variant analysis suite for whole exome next-generation sequencing data. BMC Bioinformatics. 2012;13:8.
4. Gao X, Xu J, Starmer J. Fastq2vcf: a concise and transparent pipeline for whole-exome sequencing data analyses. BMC Res Notes. 2015;8:72.
5. D'Antonio M, D'Onorio De Meo P, Paoletti D, et al. WEP: a high-performance analysis pipeline for whole-exome data. BMC Bioinformatics. 2013;14(Suppl 7):S11.
6. Coutant S, Cabot C, Lefebvre A, et al. EVA: Exome Variation Analyzer, an efficient and versatile tool for filtering strategies in medical genomics. BMC Bioinformatics. 2012;13(Suppl 14):S9.
7. Pabinger S, Dander A, Fischer M, et al. A survey of tools for variant analysis of next-generation genome sequencing data. Brief Bioinformatics. 2014;15:256-278.
8. Nam J-Y, Kim NKD, Kim SC, et al. Evaluation of somatic copy number estimation tools for whole-exome sequencing data. Brief Bioinformatics. 2015. doi: 10.1093/bib/bbv055.
9. Daneshjou R, Zappala Z, Kukurba K, et al. PATH-SCAN: a reporting tool for identifying clinically actionable variants. Pac Symp Biocomput. 2014:229-240.
10. Dorschner MO, Amendola LM, Turner EH, et al. Actionable, pathogenic incidental findings in 1,000 participants' exomes. Am J Hum Genet. 2013;93:631-640.
11. Amendola LM, Dorschner MO, Robertson PD, et al. Actionable exomic incidental findings in 6503 participants: challenges of variant classification. Genome Res. 2015;25:305-315.
12. Cancer Genome Atlas Research Network. Comprehensive molecular profiling of lung adenocarcinoma. Nature. 2014;511:543-550.
13. Li H, Durbin R. Fast and accurate short read alignment with BurrowsWheeler transform. Bioinformatics. 2009;25:1754-1760.
14. Li H, Durbin R. Fast and accurate long-read alignment with BurrowsWheeler transform. Bioinformatics. 2010;26:589-595.
15. Li H, Handsaker B, Wysoker A, et al.; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25:2078-2079.
16. Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010; 38(16): e164.
17. Genomes Project Consortium, Abecasis GR, Altshuler D, Auton A, et al. A map of human genome variation from population-scale sequencing. Nature 2010;467:1061-1073.
18. Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc. 2009;4:1073-1081.
19. Adzhubei IA, Schmidt S, Peshkin L, et al. A method and server for predicting damaging missense mutations. Nature Methods. 2010;7:248-249.
20. Shihab HA, Gough J, Cooper DN, et al. Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models. Hum Mutat. 2013;34:57-65.
21. Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genetics. 2014;46:310-315.
22. Cooper GM, Stone EA, Asimenos G, et al.; NISC Comparative Sequencing Program,. Distribution and intensity of constraint in mammalian genomic sequence. Genome Res. 2005;15:901-913.
23. Schwarz JM, Rodelsperger C, Schuelke M, Seelow D. MutationTaster evaluates disease-causing potential of sequence alterations. Nat Methods. 2010;7:575-576.
24. Koboldt DC, Zhang Q, Larson DE, et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 2012;22:568-576.
25. Yoo M, Shin J, Kim J, et al. DSigDB: drug signatures database for gene set analysis. Bioinformatics. 2015; 31(18): 3069-3071.
26. Mroz EA, Tward AD, Hammon RJ, Ren Y, Rocco JW. Intra-tumor genetic heterogeneity and mortality in head and neck cancer: analysis of data from the Cancer Genome Atlas. PLoS Med. 2015;12(2): e1001786.
27. Yadav VK, De S. An assessment of computational methods for estimating purity and clonality using genomic data derived from heterogeneous tumor tissue samples. Brief Bioinformatics. 2015;16:232-241.
28. Smirnov N. Table for estimating the goodness of fit of empirical distributions. Ann Mathematical Stat. 1948; 19(2): 279-281.
29. Cross DAE, Ashton SE, Ghiorghiu S, et al. AZD9291, an irreversible EGFR TKI, overcomes T790M-mediated resistance to EGFR inhibitors in lung cancer. CancerDiscov. 2014;4:1046-1061.
30. Nazarian R, Shi H, Wang Q, et al. Melanomas acquire resistance to B-RAF(V600E) inhibition by RTK or N-RAS upregulation. Nature. 2010;468: 973-977.
31. Hauschild A, Grob JJ, Demidov LV, et al. Dabrafenib in BRAF-mutated metastatic melanoma: a multicentre, open-label, phase 3 randomised controlled trial. Lancet. 2012;380:358-365.
32. Menzies AM, Long GV. Dabrafenib and trametinib, alone and in combination for BRAF-mutant metastatic melanoma. Clin Cancer Res. 2014;20: 2035-2043.