Retrospective NGS Study in High-risk Hereditary Cancer Patients at Masaryk Memorial Cancer Institute

Česká verzia

Authors: E. Macháčková; J. Hazova; E. Sťahlová Hrabincová; P. Vašíčková; M. Navratilova; M. Svoboda; L. Foretová
Authors place of work: Oddělení epidemiologie a genetiky nádorů, Masarykův onkologický ústav, Brno
Published in the journal: Klin Onkol 2016; 29(Supplementum 1): 35-45
Category: Original Articles
doi: https://doi.org/10.14735/amko2016S35

Summary

Background:
Currently, more than 200 hereditary cancer syndromes have been described, yet, in most countries genetic testing is restricted to a narrow spectrum of genes within a limited group of people tested.

Methods:
For this retrospective study we used the TruSight cancer panel (Illumina) – NGS panel targeting 94 cancer predisposition genes in order to analyze 50 high-risk cancer patients with significant personal and family history of cancer who did not carry mutations in BRCA1, BRCA2, MLH1, MSH2, MSH6, TP53 or APC genes. All pathogenic and potentially pathogenic mutations detected by NGS technology have been confirmed by Sanger sequencing.

Results:
There were several deleterious (frame-shift/nonsense) mutations detected in ATM, BAP1, FANCC, FANCI, PMS2, SBDS, ERCC2, RECQL4 genes. Various pathogenic or potentially pathogenic (missense, predicted splice site, in-frame insertion/deletion) mutations were detected in ATM, BRIP1, CDH1, CHEK2, ERCC2, ERCC3, ERCC4, FANCA, MC1R, MEN1, MRE11A, MUTYH, PALB2, RAD51C, RET, SDHB, STK11. These mutations affect highly conserved protein domains and affect their function as proved by the available functional assays. They were confirmed to be pathogenic as an „Parent No2 “ in serious recessive diseases such as Ataxia telangiectasia or Fanconi anemia. The clinical significance of the majority of detected missense variants still remains to be identified.

Conclusion:
Moderate or low penetrance variants are of limited clinical importance. Panel genetic testing in high-risk individuals with cancer provides important information concerning the cause of the investigated cancer, and may assist in the risk assesment and optimal management of the cancer, as well as in further preventive care.

Key words:
hereditary cancer syndromes – hereditary breast and ovarian cancer syndrome – hereditary nonpolyposis colorectal cancer – high-throughput DNA sequencing – TruSight cancer panel – MiSeq

This work was supported by MH CZ – DRO (MMCI, 00209805) and by the State budget project of CR (OP VaVpI – RECAMO CZ.1.05/2.1.00/03.0101).

The authors declare they have no potential conflicts of interest concerning drugs, products, or services used in the study.

The Editorial Board declares that the manuscript met the ICMJE recommendation for biomedical papers.

Submitted:
20. 8. 2015

Accepted:
22. 9. 2015

Zdroje

1. Vaughn CP, Robles J, Swensen JJ et al. Clinical analysis of PMS2: mutation detection and avoidance of pseudogenes. Hum Mutat 2010; 31(5): 588–593. doi: 10.1002/ humu.21230.

2. Kawakami T, Mitsui T, Kanai M et al. Genetic analysis of Shwachman-diamond syndrome: phenotypic heterogeneity in patients carrying identical SBDS mutations. Tohoku J Exp Med 2005; 206(3): 253–259.

3. Wu Y, Brosh RM. DNA helicase and helicase-nuclease enzymes with a conserved iron-sulfur cluster. Nucleic Acids Res 2012; 40(10): 4247–4260. doi: 10.1093/ nar/ gks039.

4. De Nicolo A, Tancredi M, Lombardi G et al. A novel breast cancer – associated BRIP1 (FANCJ/ BACH1) germ-line mutation impairs protein stability and function. Clin Cancer Res 2008; 14(14): 4672–4680. doi: 10.1158/ 1078-0432.CCR-08-0087.

5. Vaz F, Hanenberg H, Schuster B et al. Mutation of the RAD51C gene in a Fanconi anemia-like disorder. Nat Genet 2010, 42(5): 406–409.

6. Meindl A, Hellebrand H, Wiek C et al. Germline mutations in breast and ovarian cancer pedigrees establish RAD51C as a human cancer susceptibility gene. Nat Genet 2010; 42(5): 410–414. doi: 10.1038/ ng.569.

7. Clague J, Wilhoite G, Adamson A et al. RAD51C germ-line mutations in breast and ovarian cancer cases from high-risk families. PLoS One 2011; 6(9): e25632. doi: 10.1371/ journal.pone.0025632.

8. Janatova M, Soukupova J, Stribrna J et al. Mutation analysis of the RAD51C and RAD51D genes in high-risk ovarian cancer patients and families from the Czech Republic. PLoS One 2015; 10(6): e0127711. doi: 10.1371/ journal.pone.0127711.

9. Huck K, Hanenberg H, Gudowius S et al. Delayed diagnosis and complications of Fanconi anaemia at advanced age – a paradigm. Br J Haematol 2006; 133(2): 188–197.

10. Berwick M, Satagopan JM, Ben-Porat L et al. Genetic heterogeneity among Fanconi anemia heterozygotes and risk of cancer. Cancer Res 2007; 67(19): 9591–9596.

11. Kennedy RD, D’Andrea AD. DNA repair pathways in clinical practice: lessons from pediatric cancer susceptibility syndromes. J Clin Oncol 2006; 24(23): 3799–3808.

12. Lemos MC, Thakker RV. Multiple endocrine neoplasia type 1 (MEN1): analysis of 1336 mutations reported in the first decade following identification of the gene. Hum Mutat 2008; 29(1): 22–32.

13. Wu X, Platt JL, Cascalho M. Dimerization of MLH1 and PMS2 limits nuclear localization of MutLalpha. Mol Cell Biol 2003; 23(9): 3320–3328.

14. Herkert J, Niessen R, Olderode-Berends M et al. Paediatric intestinal cancer and polyposis due to bi-allelic PMS2 mutations: case series, review and follow-up guidelines. Eur J Cancer 2011; 47: 965–982. doi: 10.1016/ j.ejca.2011.01.013.

15. Rahal EA, Henricksen LA, Li Y et al. ATM regulates Mre11-dependent DNA end-degradation and microhomology – mediated end joining. Cell Cycle 2010; 9(14): 2866–2877.

16. Edvadsen H, Tefre T, Jansen L et al. Linkage disequilibrium pattern of the ATM gene in breast cancer patients and controls; association of SNPs and haplotypes to radio-sensitivity and post-lumpectomy local recurrence. Radiat Oncol 2007; 2: 25–33.

17. Testa JR, Cheung M, Pei J et al. Germline BAP1 mutations predispose to malignant mesothelioma. Nat Genet 2011; 43(10): 1022–1025. doi: 10.1038/ ng.912.

18. Janeway KA, Kim SY, Lodish M et al. Defects in succinate dehydrogenase in gastrointestinal stromal tumors lacking KIT and PDGFRA mutations. Proc Natl Acad Sci U S A 2011; 108(1): 314–318. doi: 10.1073/ pnas.1009199108.

19. Plon SE, Eccles D, Easton D et al. Sequence variant classification and reporting: recommendations for improving the interpretation of cancer susceptibility genetic test results. Hum Mutat 2008; 29(11): 1282–1291. doi: 10.1002/ humu.20880.

20. Easton DF, Pharoah PD, Antoniou AC et al. Gene-Panel sequencing and the prediction of breast cancer risk. N Engl J Med 2015; 372: 2243–2257. doi: 10.1056/ NEJMsr1501341.

21. Desai AN, Jere A. Next-generation sequencing: redy for the clinics? Clin Gene 2012; 81(6): 503–510. doi: 10.1111/ j.1399-0004.2012.01865.x.

22. Hollestelle A, Wasielewski M, Martens JW et al. Discovering moderate-risk breast cancer susceptibility genes. Curr Opin Genet Dev 2010; 20(3): 268–276. doi: 10.1016/ j.gde.2010.02.009.

23. Ni Y, Zbuk KM, Sadler T et al. Germline mutations and variants in the succinate dehydrogenase genes in Cowden and Cowden-like syndromes. Am J Hum Genet 2008; 83(2): 261–268. doi: 10.1016/ j.ajhg.2008.07.011.

24. Park JY, Singh TR, Nassar N et al. Breast cancer-associated missense mutants of the PALB2 WD40 domain, which directly binds RAD51C, RAD51 and BRCA2, disrupt DNA repair. Oncogene 2014; 33(40): 4803–4812. doi: 10.1038/ onc.2013.421.

25. Machens A, Spitschak A, Lorenz K et al. Germline RET sequence variation I852M and occult medullary thyroid cancer: harmless polymorphism or causative mutation? Clin Endocrinol 2011; 75(6): 801–805. doi: 10.1111/ j.1365-2265.2011.04158.x.