Validation and implementation of targeted capture and sequencing for the detection of actionable mutation, copy number variation, and gene rearrangement in clinical cancer specimens

Journal of Molecular Diagnostics

Volumn 16, Issue 1, 2014, Pages 56-67

  Pritchard, Colin C ^a   Salipante, Stephen J ^a   Koehler, Karen ^a   Smith, Christina ^a   Scroggins, Sheena ^a   Wood, Brent ^a   Wu, David ^a   Lee, Ming K ^b   Dintzis, Suzanne ^a   Adey, Andrew ^a   Liu, Yajuan ^a   Eaton, Keith D ^b   Martins, Renato ^b   Stricker, Kari ^b   Margolin, Kim A ^b   Hoffman, Noah ^a   Churpek, Jane E ^c   Tait, Jonathan F ^a   King, Mary Claire ^a,b   Walsh, Tom ^b  

^a UNIVERSITY OF WASHINGTON   (United States)

^b UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ASXL1 PROTEIN; ATM PROTEIN; BCR ABL PROTEIN; BRCA1 PROTEIN; BREAKPOINT CLUSTER REGION PROTEIN; BREAST CANCER RESISTANCE PROTEIN; CATECHOL METHYLTRANSFERASE; CCAAT ENHANCER BINDING PROTEIN ALPHA; CD135 ANTIGEN; CYTOCHROME P450 1B1; CYTOCHROME P450 2C19; CYTOCHROME P450 2C8; CYTOCHROME P450 2D6; CYTOCHROME P450 3A4; CYTOCHROME P450 3A5; EPIDERMAL GROWTH FACTOR RECEPTOR; GLUTAMATE RECEPTOR 42; ISOCITRATE DEHYDROGENASE 1; ISOCITRATE DEHYDROGENASE 2; JANUS KINASE 2; K RAS PROTEIN; MIXED LINEAGE LEUKEMIA PROTEIN; PLATELET DERIVED GROWTH FACTOR ALPHA RECEPTOR; PROTEIN KINASE B BETA; PROTEIN MCL 1; REACTIVE OXYGEN METABOLITE; SCATTER FACTOR RECEPTOR; SGCZ PROTEIN; TRANSCRIPTION FACTOR RUNX1; UNCLASSIFIED DRUG; URIDINE PHOSPHATE;

ACUTE GRANULOCYTIC LEUKEMIA; ARTICLE; COPY NUMBER VARIATION; GENE DOSAGE; GENE MUTATION; GENE REARRANGEMENT; GENE SEQUENCE; INDEL MUTATION; LIMIT OF DETECTION; MELANOMA; NEOPLASM; POINT MUTATION;

DNA COPY NUMBER VARIATIONS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE REARRANGEMENT; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; LIMIT OF DETECTION; MOLECULAR DIAGNOSTIC TECHNIQUES; MUTATION; NEOPLASMS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

EID: 84890409823     PISSN: 15251578     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmoldx.2013.08.004     Document Type: Article

References (47)

1. D.J. Slamon, B. Leyland-Jones, S. Shak, H. Fuchs, V. Paton, A. Bajamonde, T. Fleming, W. Eiermann, J. Wolter, M. Pegram, J. Baselga, and L. Norton Use of chemotherapy plus a monoclonal antibody against HER2 for metastatic breast cancer that overexpresses HER2 N Engl J Med 344 2001 783 792
2. T.J. Lynch, D.W. Bell, R. Sordella, S. Gurubhagavatula, R.A. Okimoto, B.W. Brannigan, P.L. Harris, S.M. Haserlat, J.G. Supko, F.G. Haluska, D.N. Louis, D.C. Christiani, J. Settleman, and D.A. Haber Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib N Engl J Med 350 2004 2129 2139
3. J.G. Paez, P.A. Janne, J.C. Lee, S. Tracy, H. Greulich, S. Gabriel, P. Herman, F.J. Kaye, N. Lindeman, T.J. Boggon, K. Naoki, H. Sasaki, Y. Fujii, M.J. Eck, W.R. Sellers, B.E. Johnson, and M. Meyerson EGFR mutations in lung cancer: correlation with clinical response to gefitinib therapy Science 304 2004 1497 1500
4. W. Pao, V. Miller, M. Zakowski, J. Doherty, K. Politi, I. Sarkaria, B. Singh, R. Heelan, V. Rusch, L. Fulton, E. Mardis, D. Kupfer, R. Wilson, M. Kris, and H. Varmus EGF receptor gene mutations are common in lung cancers from "never smokers" and are associated with sensitivity of tumors to gefitinib and erlotinib Proc Natl Acad Sci U S A 101 2004 13306 13311
5. P.B. Chapman, A. Hauschild, C. Robert, J.B. Haanen, P. Ascierto, J. Larkin, R. Dummer, C. Garbe, A. Testori, M. Maio, D. Hogg, P. Lorigan, C. Lebbe, T. Jouary, D. Schadendorf, A. Ribas, S.J. O'Day, J.A. Sosman, J.M. Kirkwood, A.M. Eggermont, B. Dreno, K. Nolop, J. Li, B. Nelson, J. Hou, R.J. Lee, K.T. Flaherty, and G.A. McArthur Improved survival with vemurafenib in melanoma with BRAF V600E mutation N Engl J Med 364 2011 2507 2516
6. E.L. Kwak, Y.J. Bang, D.R. Camidge, A.T. Shaw, B. Solomon, R.G. Maki, S.H. Ou, B.J. Dezube, P.A. Janne, D.B. Costa, M. Varella-Garcia, W.H. Kim, T.J. Lynch, P. Fidias, H. Stubbs, J.A. Engelman, L.V. Sequist, W. Tan, L. Gandhi, M. Mino-Kenudson, G.C. Wei, S.M. Shreeve, M.J. Ratain, J. Settleman, J.G. Christensen, D.A. Haber, K. Wilner, R. Salgia, G.I. Shapiro, J.W. Clark, and A.J. Iafrate Anaplastic lymphoma kinase inhibition in non-small-cell lung cancer N Engl J Med 363 2010 1693 1703
7. X. Wei, V. Walia, J.C. Lin, J.K. Teer, T.D. Prickett, J. Gartner, S. Davis, K. Stemke-Hale, M.A. Davies, J.E. Gershenwald, W. Robinson, S. Robinson, S.A. Rosenberg, and Y. Samuels Exome sequencing identifies GRIN2A as frequently mutated in melanoma Nat Genet 43 2011 442 446
8. M.S. Stark, S.L. Woods, M.G. Gartside, V.F. Bonazzi, K. Dutton-Regester, L.G. Aoude, D. Chow, C. Sereduk, N.M. Niemi, N. Tang, J.J. Ellis, J. Reid, V. Zismann, S. Tyagi, D. Muzny, I. Newsham, Y. Wu, J.M. Palmer, T. Pollak, D. Youngkin, B.R. Brooks, C. Lanagan, C.W. Schmidt, B. Kobe, J.P. MacKeigan, H. Yin, K.M. Brown, R. Gibbs, J. Trent, and N.K. Hayward Frequent somatic mutations in MAP3K5 and MAP3K9 in metastatic melanoma identified by exome sequencing Nat Genet 44 2012 165 169
9. S.I. Nikolaev, D. Rimoldi, C. Iseli, A. Valsesia, D. Robyr, C. Gehrig, K. Harshman, M. Guipponi, O. Bukach, V. Zoete, O. Michielin, K. Muehlethaler, D. Speiser, J.S. Beckmann, I. Xenarios, T.D. Halazonetis, C.V. Jongeneel, B.J. Stevenson, and S.E. Antonarakis Exome sequencing identifies recurrent somatic MAP2K1 and MAP2K2 mutations in melanoma Nat Genet 44 2012 133 139
10. R.J. Leary, I. Kinde, F. Diehl, K. Schmidt, C. Clouser, C. Duncan, A. Antipova, C. Lee, K. McKernan, F.M. De La Vega, K.W. Kinzler, B. Vogelstein, L.A. Diaz Jr., and V.E. Velculescu Development of personalized tumor biomarkers using massively parallel sequencing Sci Transl Med 2 2010 20ra14
11. S. Roychowdhury, M.K. Iyer, D.R. Robinson, R.J. Lonigro, Y.M. Wu, X. Cao, S. Kalyana-Sundaram, L. Sam, O.A. Balbin, M.J. Quist, T. Barrette, J. Everett, J. Siddiqui, L.P. Kunju, N. Navone, J.C. Araujo, P. Troncoso, C.J. Logothetis, J.W. Innis, D.C. Smith, C.D. Lao, S.Y. Kim, J.S. Roberts, S.B. Gruber, K.J. Pienta, M. Talpaz, and A.M. Chinnaiyan Personalized oncology through integrative high-throughput sequencing: a pilot study Sci Transl Med 3 2011 111ra121
12. G. Wu, A. Broniscer, T.A. McEachron, C. Lu, B.S. Paugh, J. Becksfort, C. Qu, L. Ding, R. Huether, M. Parker, J. Zhang, A. Gajjar, M.A. Dyer, C.G. Mullighan, R.J. Gilbertson, E.R. Mardis, R.K. Wilson, J.R. Downing, D.W. Ellison, and S.J. Baker Somatic histone H3 alterations in pediatric diffuse intrinsic pontine gliomas and non-brainstem glioblastomas Nat Genet 44 2012 251 253
13. L.E. MacConaill, C.D. Campbell, S.M. Kehoe, A.J. Bass, C. Hatton, L. Niu, M. Davis, K. Yao, M. Hanna, C. Mondal, L. Luongo, C.M. Emery, A.C. Baker, J. Philips, D.J. Goff, M. Fiorentino, M.A. Rubin, K. Polyak, J. Chan, Y. Wang, J.A. Fletcher, S. Santagata, G. Corso, F. Roviello, R. Shivdasani, M.W. Kieran, K.L. Ligon, C.D. Stiles, W.C. Hahn, M.L. Meyerson, and L.A. Garraway Profiling critical cancer gene mutations in clinical tumor samples PLoS One 4 2009 e7887
14. Z. Su, D. Dias-Santagata, M. Duke, K. Hutchinson, Y.L. Lin, D.R. Borger, C.H. Chung, P.P. Massion, C.L. Vnencak-Jones, A.J. Iafrate, and W. Pao A platform for rapid detection of multiple oncogenic mutations with relevance to targeted therapy in non-small-cell lung cancer J Mol Diagn 13 2011 74 84
15. O. Harismendy, R.B. Schwab, L. Bao, J. Olson, S. Rozenzhak, S.K. Kotsopoulos, S. Pond, B. Crain, M.S. Chee, K. Messer, D.R. Link, and K.A. Frazer Detection of low prevalence somatic mutations in solid tumors with ultra-deep targeted sequencing Genome Biol 12 2011 R124
16. N. Wagle, M.F. Berger, M.J. Davis, B. Blumenstiel, M. Defelice, P. Pochanard, M. Ducar, P. Van Hummelen, L.E. Macconaill, W.C. Hahn, M. Meyerson, S.B. Gabriel, and L.A. Garraway High-throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing Cancer Discov 2 2012 82 93
17. H. Beltran, R. Yelensky, G.M. Frampton, K. Park, S.R. Downing, T.Y. Macdonald, M. Jarosz, D. Lipson, S.T. Tagawa, D.M. Nanus, P.J. Stephens, J.M. Mosquera, M.T. Cronin, and M.A. Rubin Targeted next-generation sequencing of advanced prostate cancer identifies potential therapeutic targets and disease heterogeneity Eur Urol 63 2013 920 926
18. C.C. Pritchard, C. Smith, S.J. Salipante, M.K. Lee, A.M. Thornton, A.S. Nord, C. Gulden, S.S. Kupfer, E.M. Swisher, R.L. Bennett, A.P. Novetsky, G.P. Jarvik, O.I. Olopade, P.J. Goodfellow, M.C. King, J.F. Tait, and T. Walsh ColoSeq provides comprehensive lynch and polyposis syndrome mutational analysis using massively parallel sequencing J Mol Diagn 14 2012 357 366
19. H. Li, and R. Durbin Fast and accurate long-read alignment with Burrows-Wheeler transform Bioinformatics 26 2010 589 595
20. H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, and R. Durbin 1000 Genome Project Data Processing Subgroup: The Sequence Alignment/Map format and SAMtools Bioinformatics 25 2009 2078 2079
21. M.A. DePristo, E. Banks, R. Poplin, K.V. Garimella, J.R. Maguire, C. Hartl, A.A. Philippakis, G. del Angel, M.A. Rivas, M. Hanna, A. McKenna, T.J. Fennell, A.M. Kernytsky, A.Y. Sivachenko, K. Cibulskis, S.B. Gabriel, D. Altshuler, and M.J. Daly A framework for variation discovery and genotyping using next-generation DNA sequencing data Nat Genet 43 2011 491 498
22. D.C. Koboldt, Q. Zhang, D.E. Larson, D. Shen, M.D. McLellan, L. Lin, C.A. Miller, E.R. Mardis, L. Ding, and R.K. Wilson VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing Genome Res 22 2012 568 576
23. J.T. Robinson, H. Thorvaldsdottir, W. Winckler, M. Guttman, E.S. Lander, G. Getz, and J.P. Mesirov Integrative genomics viewer Nature Biotechnol 29 2011 24 26
24. K. Ye, M.H. Schulz, Q. Long, R. Apweiler, and Z. Ning Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads Bioinformatics 25 2009 2865 2871
25. J. Wang, C.G. Mullighan, J. Easton, S. Roberts, S.L. Heatley, J. Ma, M.C. Rusch, K. Chen, C.C. Harris, L. Ding, L. Holmfeldt, D. Payne-Turner, X. Fan, L. Wei, D. Zhao, J.C. Obenauer, C. Naeve, E.R. Mardis, R.K. Wilson, J.R. Downing, and J. Zhang CREST maps somatic structural variation in cancer genomes with base-pair resolution Nat Methods 8 2011 652 654
26. J. Li, R. Lupat, K.C. Amarasinghe, E.R. Thompson, M.A. Doyle, G.L. Ryland, R.W. Tothill, S.K. Halgamuge, I.G. Campbell, and K.L. Gorringe CONTRA: copy number analysis for targeted resequencing Bioinformatics 28 2012 1307 1313
27. H. Wickham ggplot2: elegant graphics for data analysis 2009 Springer New York
28. K. Wang, M. Li, and H. Hakonarson ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data Nucleic Acids Res 38 2010 e164
29. G.R. Abecasis, A. Auton, L.D. Brooks, M.A. DePristo, R.M. Durbin, R.E. Handsaker, H.M. Kang, G.T. Marth, and G.A. McVean An integrated map of genetic variation from 1,092 human genomes Nature 491 2012 56 65
30. D.C. Koboldt, K. Chen, T. Wylie, D.E. Larson, M.D. McLellan, E.R. Mardis, G.M. Weinstock, R.K. Wilson, and L. Ding VarScan: variant detection in massively parallel sequencing of individual and pooled samples Bioinformatics 25 2009 2283 2285
31. D.H. Spencer, H.J. Abel, C.M. Lockwood, J.E. Payton, P. Szankasi, T.W. Kelley, S. Kulkarni, J.D. Pfeifer, and E.J. Duncavage Detection of FLT3 internal tandem duplication in targeted. short-read-length, next-generation sequencing data J Mol Diagn 15 2013 81 93
32. M.W. Schmitt, S.R. Kennedy, J.J. Salk, E.J. Fox, J.B. Hiatt, and L.A. Loeb Detection of ultra-rare mutations by next-generation sequencing Proc Natl Acad Sci U S A 109 2012 14508 14513
33. K.P. Ng, A.M. Hillmer, C.T. Chuah, W.C. Juan, T.K. Ko, and A.S. Teo A common BIM deletion polymorphism mediates intrinsic resistance and inferior responses to tyrosine kinase inhibitors in cancer Nat Med 18 2012 521 528
34. J. Shendure Next-generation human genetics Genome Biol 12 2011 408
35. Comprehensive molecular portraits of human breast tumours Nature 490 2012 61 70
36. S. Schnittger, C. Eder, S. Jeromin, T. Alpermann, A. Fasan, V. Grossmann, A. Kohlmann, T. Illig, N. Klopp, H.E. Wichmann, K.A. Kreuzer, C. Schmid, P. Staib, R. Peceny, N. Schmitz, W. Kern, C. Haferlach, and T. Haferlach ASXL1 exon 12 mutations are frequent in AML with intermediate risk karyotype and are independently associated with an adverse outcome Leukemia 27 2013 82 91
37. M.T. Wheeler, S. Zarnegar, and E.M. McNally Zeta-sarcoglycan, a novel component of the sarcoglycan complex, is reduced in muscular dystrophy Hum Mol Genet 11 2002 2147 2154
38. S.N. Quayle, J.Y. Lee, L.W. Cheung, L. Ding, R. Wiedemeyer, R.W. Dewan, E. Huang-Hobbs, L. Zhuang, R.K. Wilson, K.L. Ligon, G.B. Mills, L.C. Cantley, and L. Chin Somatic mutations of PIK3R1 promote gliomagenesis PLoS One 7 2012 e49466
39. L.W. Cheung, B.T. Hennessy, J. Li, S. Yu, A.P. Myers, B. Djordjevic, Y. Lu, K. Stemke-Hale, M.D. Dyer, F. Zhang, Z. Ju, L.C. Cantley, S.E. Scherer, H. Liang, K.H. Lu, R.R. Broaddus, and G.B. Mills High frequency of PIK3R1 and PIK3R2 mutations in endometrial cancer elucidates a novel mechanism for regulation of PTEN protein stability Cancer Discov 1 2011 170 185
40. Y. Shen, Y.M. Zhu, X. Fan, J.Y. Shi, Q.R. Wang, X.J. Yan, Z.H. Gu, Y.Y. Wang, B. Chen, C.L. Jiang, H. Yan, F.F. Chen, H.M. Chen, Z. Chen, J. Jin, and S.J. Chen Gene mutation patterns and their prognostic impact in a cohort of 1185 patients with acute myeloid leukemia Blood 118 2011 5593 5603
41. T.C. Somervaille, and M.L. Cleary Grist for the MLL: how do MLL oncogenic fusion proteins generate leukemia stem cells? Int J Hematol 91 2010 735 741
42. C. Szpirer, M. Molne, R. Antonacci, N.A. Jenkins, P. Finelli, J. Szpirer, M. Riviere, M. Rocchi, D.J. Gilbert, and N.G. Copeland The genes encoding the glutamate receptor subunits KA1 and KA2 (GRIK4 and GRIK5) are located on separate chromosomes in human, mouse, and rat Proc Natl Acad Sci U S A 91 1994 11849 11853
43. K.Y. Choi, K. Chang, J.M. Pickel, J.D. Badger 2nd, and K.W. Roche Expression of the metabotropic glutamate receptor 5 (mGluR5) induces melanoma in transgenic mice Proc Natl Acad Sci U S A 108 2011 15219 15224
44. Z. Song, C.D. He, J. Liu, C. Sun, P. Lu, L. Li, L. Gao, Y. Zhang, Y. Xu, L. Shan, Y. Liu, W. Zou, H. Gao, and W. Gao Blocking glutamate-mediated signalling inhibits human melanoma growth and migration Exp Dermatol 21 2012 926 931
45. J.J. Martino, B.A. Wall, E. Mastrantoni, B.J. Wilimczyk, S.N. La Cava, K. Degenhardt, E. White, and S. Chen Metabotropic glutamate receptor 1 (Grm1) is an oncogene in epithelial cells Oncogene 32 2013 4366 4376
46. M. Neiman, S. Sundling, H. Gronberg, P. Hall, K. Czene, J. Lindberg, and D. Klevebring Library preparation and multiplex capture for massive parallel sequencing applications made efficient and easy PLoS One 7 2012 e48616
47. N. Rohland, and D. Reich Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture Genome Res 22 2012 939 946