Comparison of targeted next-generation sequencing and Sanger sequencing for the detection of PIK3CA mutations in breast cancer

BMC Clinical Pathology

Volumn 15, Issue 1, 2015, Pages

  Arsenic, Ruza ^a   Treue, Denise ^a   Lehmann, Annika ^a   Hummel, Michael ^a   Dietel, Manfred ^a   Denkert, Carsten ^a   Budczies, Jan ^a  

^a CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

Author keywords

Breast cancer; Next generation sequencing; PIK3CA; Sanger sequencing

Indexed keywords

EPIDERMAL GROWTH FACTOR RECEPTOR 2; HORMONE RECEPTOR;

ADULT; AGED; ARTICLE; BREAST CARCINOMA; CANCER GRADING; CARCINOGENESIS; COHORT ANALYSIS; EXON; FEMALE; GENE FREQUENCY; GENE IDENTIFICATION; GENE MUTATION; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC VARIABILITY; HUMAN; HUMAN TISSUE; INTERMETHOD COMPARISON; LYMPH NODE; MAJOR CLINICAL STUDY; NEXT GENERATION SEQUENCING; ONCOGENE; OVERALL SURVIVAL; PIK3CA GENE; SANGER SEQUENCING; SEQUENCE ANALYSIS; VERY ELDERLY;

EID: 84960111823     PISSN: None     EISSN: 14726890     Source Type: Journal    
DOI: 10.1186/s12907-015-0020-6     Document Type: Article

References (62)

1. Chan M, Ji SM, Yeo ZH, Gan L, Yap E, Yap, YS et al. Development of a next-generation sequencing method for BRCA mutation screening a comparison between a high-throughput and a benchtop platform. J Mol Diagn. 2012;14(6):602-12.
2. Chou LS, Liu CS-J, Boese B, Zhan X, Mao R. DNA Sequence Capture and Enrichment by Microarray Followed by Next-Generation Sequencing for Targeted Resequencing: Neurofibromatosis Type 1 Gene as a Model. Clin Chem. 2010;56(1):62-72.
3. De Leeneer, KHellemans J, De Schrivjer J, Baetens M, Poppe B., Van Criekinge W, et al. Massive parallel amplicon sequencing of the breast cancer genes BRCA1 and BRCA2: opportunities, challenges, and limitations. Hum Mutat. 2011;32(3):335-44.
4. Goossens D, Moens LN, Nelis E, Lenaerts AS, Glassee W, Kalbe A, et al. Simultaneous mutation and copy number variation (CNV) detection by multiplex PCR-based GS-FLX sequencing. Hum Mutat. 2009;30(3):472-6.
5. Hernan I, Borràs E, de Sousa Dias M, Gamundi MJ, Mañé B, Llort G, et al. Detection of genomic variations in BRCA1 and BRCA2 genes by long-range PCR and next-generation sequencing. J Mol Diagn. 2012;14(3):286-93.
6. Mamanova L, Coffey AJ, Scott CE, Kozarewa I, Turner EH, Kumar A, et al. Target-enrichment strategies for next-generation sequencing. Nat Methods. 2010;7(2):111-8.
7. Ozcelik H, Shi X, Chang MC, Tram E, Vlasschaert M, Di Nicola N, et al. Long-range PCR and next-generation sequencing of BRCA1 and BRCA2 in breast cancer. J Mol Diagn. 2012;14(5):467-75.
8. Pritchard CC, Smith C, Salipante SJ, Lee MK, Thornton AM, Nord AS, et al. ColoSeq provides comprehensive lynch and polyposis syndrome mutational analysis using massively parallel sequencing. J Mol Diagn. 2012;14(4):357-66.
9. Walsh T, Lee MK, Casadei S, Thornton AM, Stray SM, Pennil C, et al. Detection of inherited mutations for breast and ovarian cancer using genomic capture and massively parallel sequencing. Proc Natl Acad Sci U S A. 2010;107(28):12629-33.
10. Walsh T, Casadei S, Lee MK, Pennil CC, Nord AS, Thornton AM, et al. Mutations in 12 genes for inherited ovarian, fallopian tube, and peritoneal carcinoma identified by massively parallel sequencing. Proc Natl Acad Sci U S A. 2011;108(44):18032-7.
11. Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W, Davey M, et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature. 2011;475(7356):348-52.
12. Voelkerding KV, Dames SA, Durtschi JD. Next-generation sequencing: from basic research to diagnostics. Clin Chem. 2009;55(4):641-58.
13. Hanahan D, Weinberg RA. The hallmarks of cancer. Cell. 2000;100(1):57-70.
14. Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell. 2011;144(5):646-74.
15. MacConaill LE. Existing and emerging technologies for tumor genomic profiling. J Clin Oncol. 2013;31(15):1815-24.
16. Bustin SA. Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J Mol Endocrinol. 2000;25(2):169-93.
17. Meyerson M, Gabriel S, Getz G. Advances in understanding cancer genomes through second-generation sequencing. Nat Rev Genet. 2010;11(10):685-96.
18. Forbes SA, Bindal N, Bamford S, Cole C, Kok CY, Beare D, et al. COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res. 2011;39(Database issue):D945-50.
19. Robbins DE, Grüneberg A, Deus HF, Tanik MM, Almeida SJ. A self-updating road map of The Cancer Genome Atlas. Bioinformatics. 2013;29(10):1333-40.
20. Chandarlapaty S, Sakr RA, Giri D, Patil S, Heguy A, Morrow M, et al. Frequent mutational activation of the PI3K-AKT pathway in trastuzumab-resistant breast cancer. Clin Cancer Res. 2012;18(24):6784-91.
21. Cizkova M, Cizkova M, Dujaric ME, Lehmann-Che J, Scott V, Tembo O, et al. Outcome impact of PIK3CA mutations in HER2-positive breast cancer patients treated with trastuzumab. Br J Cancer. 2013;108(9):1807-9.
22. Jensen JD, Knoop A, Laenkholm AV, Grauslund M, Jensen MB, Santoni-Rugiu E, et al. PIK3CA mutations, PTEN, and pHER2 expression and impact on outcome in HER2-positive early-stage breast cancer patients treated with adjuvant chemotherapy and trastuzumab. Ann Oncol. 2012;23(8):2034-42.
23. Bai X, Zhang E, Ye H, Nandakumar V, Wang Z, Chen L, et al. PIK3CA and TP53 gene mutations in human breast cancer tumors frequently detected by ion torrent DNA sequencing. PLoS One. 2014;9(6):e99306.
24. Frierson Jr HF, Wolber RA, Berean KW, Franquemont DW, Gaffey MJ, Boyd JC, et al. Interobserver reproducibility of the Nottingham modification of the Bloom and Richardson histologic grading scheme for infiltrating ductal carcinoma. Am J Clin Pathol. 1995;103(2):195-8.
25. Hammond ME, Hayes DF, Dowsett M, Allred DC, Hagerty KL, Badve S, et al. American Society of Clinical Oncology/College of American Pathologists guideline recommendations for immunohistochemical testing of estrogen and progesterone receptors in breast cancer. Arch Pathol Lab Med. 2010;134(6):907-22.
26. Wolff AC, Hammond ME, Hicks DG, Dowsett M, McShane LM, Allison KH, et al. Recommendations for human epidermal growth factor receptor 2 testing in breast cancer: American Society of Clinical Oncology/College of American Pathologists clinical practice guideline update. Arch Pathol Lab Med. 2014;138(2):241-56.
27. A.E. beeswarm: The bee swarm plot, an alternative to stripchart. R package version 0.1.6. 2013. http://CRAN.R-project.org/package=beeswarm.
28. R.C.T. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. 2014. URL http://www.R-project.org/.
29. Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA, et al. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov. 2012;2(5):401-4.
30. Fokkema IF, Taschner PE, Schaafsma GC, Celli J, Laros JF, den Dunnen JT, et al. LOVD v. 2.0: the next generation in gene variant databases. Hum Mutat. 2011;32(5):557-63.
31. Kohlmann A, Klein HU, Weissmann S, Bresolin S, Chaplin T, Cuppens H, et al. The Interlaboratory RObustness of Next-generation sequencing (IRON) study: a deep sequencing investigation of TET2, CBL and KRAS mutations by an international consortium involving 10 laboratories. Leukemia. 2011;25(12):1840-8.
32. Cleator SJ, Powles TJ, Dexter T, Fulford L, Mackay A, Smith IE, et al. The effect of the stromal component of breast tumours on prediction of clinical outcome using gene expression microarray analysis. Breast Cancer Res. 2006;8(3):R32.
33. Buttitta F, Felicioni L, Del Grammastro M, Filice G, Di Lorito A, Malatesta S, et al. Effective assessment of egfr mutation status in bronchoalveolar lavage and pleural fluids by next-generation sequencing. Clin Cancer Res. 2013;19(3):691-8.
34. Moskalev EA, Stöhr R, Rieker R, Hebele S, Fuchs F, Sirbu H, et al. Increased detection rates of EGFR and KRAS mutations in NSCLC specimens with low tumour cell content by 454 deep sequencing. Virchows Arch. 2013;462(4):409-19.
35. Chin ELH, C da Silva, M Hegde. Assessment of clinical analytical sensitivity and specificity of next-generation sequencing for detection of simple and complex mutations. BMC Genet. 2013;14:14-6
36. Guan YF, Hu H, Peng Y, Gong Y, Yi Y, Shao L, et al. Detection of inherited mutations for hereditary cancer using target enrichment and next generation sequencing. Fam Cancer. 2015;14(1):9-18.
37. Hadd AG, Houghton J, Choudhary A, Sah S, Chen L, Marko AC, et al. Targeted, high-depth, next-generation sequencing of cancer genes in formalin-fixed, paraffin-embedded and fine-needle aspiration tumor specimens. J Mol Diagn. 2013;15(2):234-47.
38. Lin MT, Mosier Sl, Thiess M, Beierel KF, Debeljak M, Tseng LH, et al. Clinical Validation of KRAS, BRAF, and EGFR mutation detection using next-generation sequencing. Am J Clin Pathol. 2014;141(6):856-66.
39. Nijman IJ, van Montfrans JM, Hoogstraat M, Boes ML, van de Corput L, Renner ED, et al. Targeted next-generation sequencing: a novel diagnostic tool for primary immunodeficiencies. J Allergy Clin Immunol. 2014;133(2):529-34.
40. Barbareschi M, Buttitta F, Felicioni L, Cotrupi S, Barassi F, Del Grammastro M, et al. Different prognostic roles of mutations in the helical and kinase domains of the PIK3CA gene in breast carcinomas. Clin Cancer Res. 2007;13(20):6064-9.
41. Lai YL, Mau BL, Cheng WH, Chen HM, Chiu HH, Tzen CY. et al. PIK3CA exon 20 mutation is independently associated with a poor prognosis in breast cancer patients. Ann Surg Oncol. 2008;15(4):1064-9.
42. Li SY, Rong M, Grieu F, Iacopetta B. PIK3CA mutations in breast cancer are associated with poor outcome. Breast Cancer Res Treat. 2006;96(1):91-5.
43. Mangone FR, Bobrovnitchaia IG, Salaorni S, Manuli E, Nagai MA.PIK3CA exon 20 mutations are associated with poor prognosis in breast cancer patients. Clinics (Sao Paulo). 2012;67(11):1285-90.
44. Saal LH, Holm K, Maurer M, Memeo L, Su T, Wang X, et al. PIK3CA mutations correlate with hormone receptors, node metastasis, and ERBB2, and are mutually exclusive with PTEN loss in human breast carcinoma. Cancer Res. 2005;65(7):2554-9.
45. Koboldt DC, Fulton RS, McLellan, MD, Schmidt H, Kalicki-Veizer J, McMichael, JF, et al. Comprehensive molecular portraits of human breast tumours. Nature. 2012;490(7418):61-70.
46. Rohlin A, Wernersson J, Engwall Y, Wiklund L, Bjoerk J, Nordling M, et al. Parallel sequencing used in detection of mosaic mutations: comparison with four diagnostic DNA screening techniques. Hum Mutat. 2009;30(6):1012-20.
47. Walsh T, Casadei S, Coats KH, Swisher E, Stray SM, Higgins J, et al. Spectrum of mutations in BRCA1, BRCA2, CHEK2, and TP53 in families at high risk of breast cancer. JAMA. 2006;295(12):1379-88.
48. Arsenic R, Lehmann A, Budczies J, Koch I, Prinzler J, Kleine-Tebbe A, et al. Analysis of PIK3CA mutations in breast cancer subtypes. Appl Immunohistochem Mol Morphol. 2014;22(1):50-6.
49. Ikenoue T, Kanai F, Hikiba Y, Obata T, Tanaka Y, Imamura J, et al. Functional analysis of PIK3CA gene mutations in human colorectal cancer. Cancer Res. 2005;65(11):4562-7.
50. Gymnopoulos M, Elsliger MA, Vogt PK. Rare cancer-specific mutations in PIK3CA show gain of function. Proc Natl Acad Sci U S A. 2007;104(13):5569-74.
51. Boyault S, Drouet Y, Navarro C, Bachelot T, Lasset C, Treilleux I, et al. Mutational characterization of individual breast tumors: TP53 and PI3K pathway genes are frequently and distinctively mutated in different subtypes. Breast Cancer Res Treat. 2012;132(1):29-39.
52. Kalinsky K, Jacks LM, Heguy A, Patil S, Drobnjak M, Bhanot UK, et al. PIK3CA mutation associates with improved outcome in breast cancer. Clin Cancer Res. 2009;15(16):5049-59.
53. Dunlap J, Le C, Shukla A, Patterson J, Presnell A, Heinrich MC, et al. Phosphatidylinositol-3-kinase and AKT1 mutations occur early in breast carcinoma. Breast Cancer Res Treat. 2010;120(2):409-18.
54. Hutter RV. Pathological parameters useful in predicting prognosis for patients with breast cancer. Monogr Pathol. 1984;25:175-85.
55. McGuire WL, Clark, GM, Dressler LG and Owens, MA. Role of steroid hormone receptors as prognostic factors in primary breast cancer. NCI Monogr. 1986;1:19-23.
56. Huang YE, Iijima M, Parent CA, Funamoto S, Firtel RA,Devreotes P, et al. Receptor-mediated regulation of PI3Ks confines PI(3,4,5)P3 to the leading edge of chemotaxing cells. Mol Biol Cell. 2003;14(5):1913-22.
57. Cizkova M, Susini A, Vacher S, Cizeron-Clairac G, Andrieu C, Driouch K, et al. PIK3CA mutation impact on survival in breast cancer patients and in ER alpha, PR and ERBB2-based subgroups. Breast Cancer Res. 2012;14(1):R28.
58. Baselga J, Cortés J, Im SA, Clark E, Ross G, Kiermaier A, et al. Biomarker analyses in CLEOPATRA: a phase III, placebo-controlled study of pertuzumab in human epidermal growth factor receptor 2-positive, first-line metastatic breast cancer. J Clin Oncol. 2014;32(33):3753-61.
59. Joensuu H, Kellokumpu-Lehtinen PL, Bono P, Alanko T, Kataja V, Asola R, et al. Adjuvant docetaxel or vinorelbine with or without trastuzumab for breast cancer. N Engl J Med. 2006;354(8):809-20.
60. Loi S, Michiels S, Lambrechts D, Fumagalli D, Claes B, Kellokumpu-Lehtinen PL, et al. Somatic mutation profiling and associations with prognosis and trastuzumab benefit in early breast cancer. J Natl Cancer Inst. 2013;105(13):960-7.
61. Fu X, Osborne CK, Schiff R. Biology and therapeutic potential of PI3K signaling in ER+/HER2-negative breast cancer. Breast. 2013;22 Suppl 2:S12-8.
62. Harle A, Lion M, Lozano N, Merlin JL. Clinical, diagnostic significance and theranostic interest of PIK3CA gene mutations in breast cancer. Bull Cancer. 2013;100(10):947-54.