Detection of inherited mutations for hereditary cancer using target enrichment and next generation sequencing

Familial Cancer

Volumn 14, Issue 1, 2015, Pages 9-18

  Guan, Yanfang ^a,b,j   Hu, Hong ^c   Peng, Yin ^b,g,i   Gong, Yuhua ^a,b,j   Yi, Yuting ^a,b,j   Shao, Libin ^b   Liu, Tengfei ^b   Li, Gairui ^b   Wang, Rongjiao ^b   Dai, Pingping ^a,b,j   Bignon, Yves Jean ^d,e   Xiao, Zhe ^b   Yang, Ling ^a,b,j   Mu, Feng ^b,f   Xiao, Liang ^g   Xie, Zeming ^h   Yan, Wenhui ^c   Xu, Nan ^c   Zhou, Dongxian ^c   Yi, Xin ^a,b,j  

^a Binhai Genomics Institute   (China)

^b BGI SHENZHEN   (China)

^c SHENZHEN PEOPLE'S HOSPITAL   (China)

^d UNIVERSITÉ CLERMONT AUVERGNE   (France)

^e CENTRE JEAN PERRIN   (France)

^f BGI Beijing ^*  (China)

^g THE FIRST AFFILIATED HOSPITAL OF SHENZHEN UNIVERSITY   (China)

^h SUN YAT SEN UNIVERSITY CANCER CENTER   (China)

ⁱ SUN YAT SEN UNIVERSITY   (China)

^j Tianjin Translational Genomics Center   (China)

more..

Author keywords

Familial cancer; Genetic testing; Hereditary cancer; NGS; Target enrichment

Indexed keywords

BRCA1 PROTEIN; BRCA2 PROTEIN; EPITHELIAL CELL ADHESION MOLECULE; GENOMIC DNA;

ARTICLE; BREAST CANCER; CANCER DIAGNOSIS; CANCER RISK; CANCER SUSCEPTIBILITY; COLON CANCER; COLORECTAL CANCER; CONTROLLED STUDY; COPY NUMBER VARIATION; DATA BASE; DIAGNOSTIC ACCURACY; DIAGNOSTIC TEST ACCURACY STUDY; DNA BASE COMPOSITION; DNA FLANKING REGION; DNA HYBRIDIZATION; EXON; FAMILIAL CANCER; FRAMESHIFT MUTATION; GENE LOCATION; GENE MUTATION; GENETIC ASSOCIATION; GENETIC SCREENING; HEREDITARY NONPOLYPOSIS COLORECTAL CANCER; HETEROZYGOSITY; HOMOZYGOSITY; HUMAN; INDEL MUTATION; INTRON; KIDNEY CARCINOMA; MAJOR CLINICAL STUDY; MISSENSE MUTATION; MULTIPLE CANCER; MULTIPLEX LIGATION DEPENDENT PROBE AMPLIFICATION; NEUROBLASTOMA; NEXT GENERATION SEQUENCING; NONSENSE MUTATION; NUCLEIC ACID BASE SUBSTITUTION; PHEOCHROMOCYTOMA; PRIORITY JOURNAL; PROSTATE CANCER; PSEUDOGENE; RETINOBLASTOMA; SENSITIVITY AND SPECIFICITY; THYROID CARCINOMA; UTERUS CANCER; GENETIC PREDISPOSITION; GENETICS; HIGH THROUGHPUT SEQUENCING; NEOPLASM; NUCLEOTIDE SEQUENCE; PROCEDURES;

DNA MUTATIONAL ANALYSIS; GENETIC PREDISPOSITION TO DISEASE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; NEOPLASMS; SENSITIVITY AND SPECIFICITY;

EID: 84941648621     PISSN: 13899600     EISSN: 15737292     Source Type: Journal    
DOI: 10.1007/s10689-014-9749-9     Document Type: Article

References (23)

1. Garber JE, Offit K (2005) Hereditary cancer predisposition syndromes. J Clin Oncol 23(2):276–292
2. Nagy R, Sweet K, Eng C (2004) Highly penetrant hereditary cancer syndromes. Oncogene 23(38):6445–6470
3. Daly MB, Axilbund JE, Bryant E, Buys S, Eng C, Friedman S, Esserman LJ, Farrell CD, Ford JM, Garber JE, Jeter JM, Kohlmann W, Lynch PM, Marcom PK, Nabell LM, Offit K, Osarogiagbon RU, Pasche B, Reiser G, Sutphen R, Weitzel JN (2006) Genetic/familial high-risk assessment: breast and ovarian. J Natl Compr Canc Netw 4(2):156–176
4. Frank TS, Manley SA, Olopade OI, Cummings S, Garber JE, Bernhardt B, Antman K, Russo D, Wood ME, Mullineau L, Isaacs C, Peshkin B, Buys S, Venne V, Rowley PT, Loader S, Offit K, Robson M, Hampel H, Brener D, Winer EP, Clark S, Weber B, Strong LC, Thomas A et al (1998) Sequence analysis of BRCA1 and BRCA2: correlation of mutations with family history and ovarian cancer risk. J Clin Oncol 16(7):2417–2425
5. Ayme S, Matthijs G, Soini S (2008) Patenting and licensing in genetic testing: recommendations of the European society of human genetics. EJHG 16(Suppl 1):S10–S19
6. Osorio A, Barroso A, Martinez B, Cebrian A, San Roman JM, Lobo F, Robledo M, Benitez J (2000) Molecular analysis of the BRCA1 and BRCA2 genes in 32 breast and/or ovarian cancer Spanish families. Br J Cancer 82(7):1266–1270
7. Chan M, Ji SM, Yeo ZX, Gan L, Yap E, Yap YS, Ng R, Tan PH, Ho GH, Ang P, Lee AS (2012) Development of a next-generation sequencing method for BRCA mutation screening: a comparison between a high-throughput and a benchtop platform. J Mol Diagn 14(6):602–612
8. De Leeneer K, Hellemans J, De Schrijver J, Baetens M, Poppe B, Van Criekinge W, De Paepe A, Coucke P, Claes K (2011) Massive parallel amplicon sequencing of the breast cancer genes BRCA1 and BRCA2: opportunities, challenges, and limitations. Hum Mutat 32(3):335–344
9. Hernan I, Borras E, de Sousa Dias M, Gamundi MJ, Mane B, Llort G, Agundez JA, Blanca M, Carballo M (2012) Detection of genomic variations in BRCA1 and BRCA2 genes by long-range PCR and next-generation sequencing. J Mol Diagn 14(3):286–293
10. Ozcelik H, Shi X, Chang MC, Tram E, Vlasschaert M, Di Nicola N, Kiselova A, Yee D, Goldman A, Dowar M, Sukhu B, Kandel R, Siminovitch K (2012) Long-range PCR and next-generation sequencing of BRCA1 and BRCA2 in breast cancer. J Mol Diagn 14(5):467–475
11. Pritchard CC, Smith C, Salipante SJ, Lee MK, Thornton AM, Nord AS, Gulden C, Kupfer SS, Swisher EM, Bennett RL, Novetsky AP, Jarvik GP, Olopade OI, Goodfellow PJ, King MC, Tait JF, Walsh T (2012) ColoSeq provides comprehensive lynch and polyposis syndrome mutational analysis using massively parallel sequencing. J Mol Diagn 14(4):357–366
12. Walsh T, Lee MK, Casadei S, Thornton AM, Stray SM, Pennil C, Nord AS, Mandell JB, Swisher EM, King MC (2010) Detection of inherited mutations for breast and ovarian cancer using genomic capture and massively parallel sequencing. Proc Natl Acad Sci USA 107(28):12629–12633
13. Mamanova L, Coffey AJ, Scott CE, Kozarewa I, Turner EH, Kumar A, Howard E, Shendure J, Turner DJ (2010) Target-enrichment strategies for next-generation sequencing. Nat Methods 7(2):111–118
14. Goossens D, Moens LN, Nelis E, Lenaerts AS, Glassee W, Kalbe A, Frey B, Kopal G, De Jonghe P, De Rijk P, Del-Favero J (2009) Simultaneous mutation and copy number variation (CNV) detection by multiplex PCR-based GS-FLX sequencing. Hum Mutat 30(3):472–476
15. Chou LS, Liu CS, Boese B, Zhang X, Mao R (2010) DNA sequence capture and enrichment by microarray followed by next-generation sequencing for targeted resequencing: neurofibromatosis type 1 gene as a model. Clin Chem 56(1):62–72
16. Walsh T, Casadei S, Coats KH, Swisher E, Stray SM, Higgins J, Roach KC, Mandell J, Lee MK, Ciernikova S, Foretova L, Soucek P, King MC (2006) Spectrum of mutations in BRCA1, BRCA2, CHEK2, and TP53 in families at high risk of breast cancer. JAMA 295(12):1379–1388
17. Michils G, Hollants S, Dehaspe L, Van Houdt J, Bidet Y, Uhrhammer N, Bignon YJ, Vermeesch JR, Cuppens H, Matthijs G (2012) Molecular analysis of the breast cancer genes BRCA1 and BRCA2 using amplicon-based massive parallel pyrosequencing. J Mol Diagn 14(6):623–630
18. Richards CS, Bale S, Bellissimo DB, Das S, Grody WW, Hegde MR, Lyon E, Ward BE (2008) ACMG recommendations for standards for interpretation and reporting of sequence variations: revisions 2007. Genet Med 10(4):294–300. doi:10.1097/GIM.0b013e31816b5cae
19. Yap HL, Chieng WS, Lim JR, Lim RS, Soo R, Guo J, Lee SC (2009) Recurring MLH1 deleterious mutations in unrelated Chinese Lynch syndrome families in Singapore. Fam Cancer 8(2):85–94. doi:10.1007/s10689-008-9209-5
20. Tommiska J, Seal S, Renwick A, Barfoot R, Baskcomb L, Jayatilake H, Bartkova J, Tallila J, Kaare M, Tamminen A, Heikkila P, Evans DG, Eccles D, Aittomaki K, Blomqvist C, Bartek J, Stratton MR, Nevanlinna H, Rahman N (2006) Evaluation of RAD50 in familial breast cancer predisposition. Int J Cancer 118(11):2911–2916. doi:10.1002/ijc.21738
21. Armes JE, Hammet F, de Silva M, Ciciulla J, Ramus SJ, Soo WK, Mahoney A, Yarovaya N, Henderson MA, Gish K, Hutchins AM, Price GR, Venter DJ (2004) Candidate tumor-suppressor genes on chromosome arm 8p in early-onset and high-grade breast cancers. Oncogene 23(33):5697–5702
22. Peltomaki P (2005) Lynch syndrome genes. Fam Cancer 4(3):227–232. doi:10.1007/s10689-004-7993-0
23. Ewald IP, Ribeiro PL, Palmero EI, Cossio SL, Giugliani R, Ashton-Prolla P (2009) Genomic rearrangements in BRCA1 and BRCA2: a literature review. Genet Mol Biol 32(3):437–446