Performance evaluation for rapid detection of pan-cancer microsatellite instability with MANTIS

Oncotarget

Volumn 8, Issue 5, 2017, Pages 7452-7463

  Kautto, Esko A ^a   Bonneville, Russell ^a   Miya, Jharna ^a   Yu, Lianbo ^b   Krook, Melanie A ^a   Reeser, Julie W ^a   Roychowdhury, Sameek ^a,b  

^a OHIO STATE UNIVERSITY   (United States)

^b OHIO STATE UNIVERSITY   (United States)

Author keywords

Computational biology; Microsatellite instability; Next generation sequencing

Indexed keywords

ACCURACY; ARTICLE; CLINICAL PRACTICE; CONTROLLED STUDY; DATA ANALYSIS SOFTWARE; GENE LOCUS; GENE TARGETING; IMMUNOHISTOCHEMISTRY; INTERMETHOD COMPARISON; MICROSATELLITE INSTABILITY; MISMATCH REPAIR; NEXT GENERATION SEQUENCING; POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; ALGORITHM; BIOLOGY; COMPARATIVE STUDY; GENETIC PREDISPOSITION; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; NEOPLASM; PATHOLOGY; PHENOTYPE; PREDICTIVE VALUE; PROCEDURES; REPRODUCIBILITY; WORKFLOW;

TUMOR MARKER;

ALGORITHMS; BIOMARKERS, TUMOR; COMPUTATIONAL BIOLOGY; GENETIC LOCI; GENETIC PREDISPOSITION TO DISEASE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MICROSATELLITE INSTABILITY; NEOPLASMS; PHENOTYPE; PREDICTIVE VALUE OF TESTS; REPRODUCIBILITY OF RESULTS; WORKFLOW;

EID: 85018935189     PISSN: None     EISSN: 19492553     Source Type: Journal    
DOI: 10.18632/oncotarget.13918     Document Type: Article

References (36)

1. Kelkar YD, Strubczewski N, Hile SE, Chiaromonte F, Eckert KA and Makova KD. What is a microsatellite: a computational and experimental definition based upon repeat mutational behavior at A/T and GT/AC repeats. Genome Biol Evol. 2010; 2:620-635
2. Shia J. Evolving approach and clinical significance of detecting DNA mismatch repair deficiency in colorectal carcinoma. Semin Diagn Pathol. 2015; 32(5):352-361
3. Aaltonen LA, Peltomäki P, Leach FS, Sistonen P, Pylkkänen L, Mecklin JP, Järvinen H, Powell SM, Jen J and Hamilton SR. Clues to the pathogenesis of familial colorectal cancer. Science. 1993; 260(5109):812-816
4. Armaghany T, Wilson JD, Chu Q and Mills G. Genetic alterations in colorectal cancer. Gastrointest Cancer Res. 2012; 5(1):19-27
5. Dudley JC, Lin MT, Le DT and Eshleman JR. Microsatellite Instability as a Biomarker for PD-1 Blockade. Clin Cancer Res. 2016; 22(4):813-820
6. Le DT, Uram JN, Wang H, Bartlett BR, Kemberling H, Eyring AD, Skora AD, Luber BS, Azad NS, Laheru D, Biedrzycki B, Donehower RC, Zaheer A, et al. PD-1 Blockade in Tumors with Mismatch-Repair Deficiency. N Engl J Med. 2015; 372(26):2509-2520
7. Boland CR, Thibodeau SN, Hamilton SR, Sidransky D, Eshleman JR, Burt RW, Meltzer SJ, Rodriguez-Bigas MA, Fodde R, Ranzani GN and Srivastava S. A National Cancer Institute Workshop on Microsatellite Instability for cancer detection and familial predisposition: development of international criteria for the determination of microsatellite instability in colorectal cancer. Cancer Res. 1998; 58(22):5248-5257
8. Salipante SJ, Scroggins SM, Hampel HL, Turner EH and Pritchard CC. Microsatellite instability detection by next generation sequencing. Clin Chem. 2014; 60(9):1192-1199
9. Niu B, Ye K, Zhang Q, Lu C, Xie M, McLellan MD, Wendl MC and Ding L. MSIsensor: microsatellite instability detection using paired tumor-normal sequence data. Bioinformatics. 2014; 30(7):1015-1016
10. Faulkner RD, Seedhouse CH, Das-Gupta EP and Russell NH. BAT-25 and BAT-26, two mononucleotide microsatellites, are not sensitive markers of microsatellite instability in acute myeloid leukaemia. Br J Haematol. 2004; 124(2):160-165
11. Hempelmann JA, Scroggins SM, Pritchard CC and Salipante SJ. MSIplus for Integrated Colorectal Cancer Molecular Testing by Next-Generation Sequencing. J Mol Diagn. 2015; 17(6):705-714
12. Alhopuro P, Sammalkorpi H, Niittymäki I, Biström M, Raitila A, Saharinen J, Nousiainen K, Lehtonen HJ, Heliövaara E, Puhakka J, Tuupanen S, Sousa S, Seruca R, et al. Candidate driver genes in microsatellite-unstable colorectal cancer. Int J Cancer. 2012; 130(7):1558-1566
13. Kim TM, Laird PW and Park PJ. The landscape of microsatellite instability in colorectal and endometrial cancer genomes. Cell. 2013; 155(4):858-868
14. Hause RJ, Pritchard CC, Shendure J and Salipante SJ. Classification and characterization of microsatellite instability across 18 cancer types. Nat Med. 2016; 22(11):1342-1350
15. Huang MN, McPherson JR, Cutcutache I, Teh BT, Tan P and Rozen SG. MSIseq: Software for Assessing Microsatellite Instability from Catalogs of Somatic Mutations. Sci Rep. 2015; 5:13321
16. Stadler ZK, Battaglin F, Middha S, Hechtman JF, Tran C, Cercek A, Yaeger R, Segal NH, Varghese AM, Reidy-Lagunes DL, Kemeny NE, Salo-Mullen EE, Ashraf A, et al. Reliable Detection of Mismatch Repair Deficiency in Colorectal Cancers Using Mutational Load in Next-Generation Sequencing Panels. J Clin Oncol. 2016; 34(18):2141-2147
17. Lu Y, Soong TD and Elemento O. A novel approach for characterizing microsatellite instability in cancer cells. PLoS One. 2013; 8(5):e63056
18. Zhang X and Li J. Era of universal testing of microsatellite instability in colorectal cancer. World J Gastrointest Oncol. 2013; 5(2):12-19
19. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, et al. Initial sequencing and analysis of the human genome. Nature. 2001; 409(6822):860-921
20. Quinlan AR and Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010; 26(6):841-842
21. Benjamini Y and Hochberg Y. Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society Series B (Methodological). 1995; 57(1):289-300
22. Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK and Ding L. VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics. 2009; 25(17):2283-2285
23. 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. 2012; 22(3):568-576
24. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R and Subgroup GPDP. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25(16):2078-2079
25. Tóth G, Gáspári Z and Jurka J. Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res. 2000; 10(7):967-981
26. Network TCGAR. Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012; 487(7407):330-337
27. Network TCGAR. Integrated genomic characterization of endometrial carcinoma. Nature. 2013; 497(7447):67-73
28. The Cancer Genome Atlas Research N. Comprehensive molecular characterization of gastric adenocarcinoma. Nature. 2014; 513(7517):202-209
29. The Cancer Genome Atlas Research N, Weinstein JN, Collisson EA, Mills GB, Shaw KRM, Ozenberger BA, Ellrott K, Shmulevich I, Sander C and Stuart JM. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet. 2013; 45(10):1113-1120
30. Robinson D, Van Allen EM, Wu YM, Schultz N, Lonigro RJ, Mosquera JM, Montgomery B, Taplin ME, Pritchard CC, Attard G, Beltran H, Abida W, Bradley RK, et al. Integrative clinical genomics of advanced prostate cancer. Cell. 2015; 161(5):1215-1228
31. Wilks C, Cline MS, Weiler E, Diehkans M, Craft B, Martin C, Murphy D, Pierce H, Black J, Nelson D, Litzinger B, Hatton T, Maltbie L, et al. The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data. Database (Oxford). 2014; 2014
32. Mailman MD, Feolo M, Jin Y, Kimura M, Tryka K, Bagoutdinov R, Hao L, Kiang A, Paschall J, Phan L, Popova N, Pretel S, Ziyabari L, et al. The NCBI dbGaP database of genotypes and phenotypes. Nat Genet. 2007; 39(10):1181-1186
33. Leinonen R, Sugawara H, Shumway M and Collaboration INSD. The sequence read archive. Nucleic Acids Res. 2011; 39(Database issue):D19-21
34. Li H and Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):1754-1760
35. Tange O. (2011). GNU Parallel-The Command-Line Power Tool. ;login: The USENIX Magazine, pp. 42-47
36. Newcombe RG. Two-sided confidence intervals for the single proportion: comparison of seven methods. Stat Med. 1998; 17(8):857-872