Dataset Information

Genetic testing in hereditary breast and ovarian cancer using massive parallel sequencing.

ABSTRACT: High throughput methods such as next generation sequencing are increasingly used in molecular diagnosis. The aim of this study was to develop a workflow for the detection of BRCA1 and BRCA2 mutations using massive parallel sequencing in a 454 GS Junior bench top sequencer. Our approach was first validated in a panel of 23 patients containing 62 unique variants that had been previously Sanger sequenced. Subsequently, 101 patients with familial breast and ovarian cancer were studied. BRCA1 and BRCA2 exon enrichment has been performed by PCR amplification using the BRCA MASTR kit (Multiplicom). Bioinformatic analysis of reads is performed with the AVA software v2.7 (Roche). In total, all 62 variants were detected resulting in a sensitivity of 100%. 71 false positives were called resulting in a specificity of 97.35%. All of them correspond to deletions located in homopolymeric stretches. The analysis of the homopolymers stretches of 6?bp or longer using the BRCA HP kit (Multiplicom) increased the specificity of the detection of BRCA1 and BRCA2 mutations to 99.99%. We show here that massive parallel pyrosequencing can be used as a diagnostic strategy to test for BRCA1 and BRCA2 mutations meeting very stringent sensitivity and specificity parameters replacing traditional Sanger sequencing with a lower cost.

SUBMITTER: Ruiz A

PROVIDER: S-EPMC4098986 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Genetic testing in hereditary breast and ovarian cancer using massive parallel sequencing.

Ruiz Anna A Llort Gemma G Yagüe Carmen C Baena Neus N Viñas Marina M Torra Montse M Brunet Anna A Seguí Miquel A MA Saigí Eugeni E Guitart Miriam M

BioMed research international 20140626

High throughput methods such as next generation sequencing are increasingly used in molecular diagnosis. The aim of this study was to develop a workflow for the detection of BRCA1 and BRCA2 mutations using massive parallel sequencing in a 454 GS Junior bench top sequencer. Our approach was first validated in a panel of 23 patients containing 62 unique variants that had been previously Sanger sequenced. Subsequently, 101 patients with familial breast and ovarian cancer were studied. BRCA1 and BRC ...[more]

PMID: 25136594

Similar Datasets

Project description:Breast, colorectal, ovarian, and endometrial cancers constitute approximately 30% of newly diagnosed cancer cases in Switzerland and affect more than 12,000 individuals annually. Several hundred of these patients are likely to carry known genetic mutations associated with HBOC or LS. Genetic testing for hereditary susceptibility to cancer can prevent many cancer deaths through early identification and engagement in high-risk management care that involves intensive surveillance, chemoprevention and/or prophylactic surgery. However, current rates of genetic testing indicate that many Swiss mutation carriers and their family members do not use cancer genetic services (counseling and/or testing), either due to lack of coordination of care or due to lack of communication about the mutation among family members. Cascade screening identifies and tests family members of a known mutation carrier. It determines whether asymptomatic family members are carriers of the identified mutation and proposes management options to reduce harmful outcomes. Robust evidence of basic science and descriptive population-based studies in Switzerland support the necessity of cascade screening for HBOC and LS. However, translation of this knowledge into public health interventions is lacking. Specific Aims of the CASCADE study are: 1. Survey Index Patients diagnosed with HBOC or LS from clinic-based genetic testing records and determine their cancer status and surveillance practices; needs for coordination of medical care; psychosocial needs; patient-provider and patient-family communication needs; quality of life; willingness to serve as advocates for cancer genetic services for blood relatives. 2. Survey first- and second-degree relatives, and first cousins identified from pedigrees and/or family history records of HBOC and LS Index Patients and determine their cancer and mutation status; cancer surveillance practices; needs for coordination of medical care; barriers and facilitators to using cancer genetic services; psychosocial needs; patient-provider and patient-family communication needs; quality of life; willingness to participate in a study designed to increase use of cancer genetic services. 3. Explore the influence of patient-provider communication about genetic cancer risk on patient-family communication and the acceptability of a family-based communication, coping, and decision support intervention with focus group(s) of mutation carriers and blood relatives.

Dataset Information

Genetic testing in hereditary breast and ovarian cancer using massive parallel sequencing.

Publications

Genetic testing in hereditary breast and ovarian cancer using massive parallel sequencing.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure