Detection of inherited mutations for breast and ovarian cancer using genomic capture and massively parallel sequencing

Tom Walsh, Ming K. Lee, Silvia Casadei, Anne M. Thornton, Sunday M. Stray, Christopher Pennil, Alexander Nord, Jessica B. Mandell, Elizabeth M. Swisher, Mary Claire King

Research output: Contribution to journalArticle

326 Citations (Scopus)

Abstract

Inherited loss-of-function mutations in the tumor suppressor genes BRCA1, BRCA2, and multiple other genes predispose to high risks of breast and/or ovarian cancer. Cancer-associated inherited mutations in these genes are collectively quite common, but individually rare or even private. Genetic testing for BRCA1 and BRCA2 mutations has become an integral part of clinical practice, but testing is generally limited to these two genes and to women with severe family histories of breast or ovarian cancer. To determine whether massively parallel, "next-generation" sequencing would enable accurate, thorough, and cost-effective identification of inherited mutations for breast and ovarian cancer, we developed a genomic assay to capture, sequence, and detect all mutations in 21 genes, including BRCA1 and BRCA2, with inherited mutations that predispose to breast or ovarian cancer. Constitutional genomic DNA from subjects with known inherited mutations, ranging in size from 1 to >100,000 bp, was hybridized to custom oligonucleotides and then sequenced using a genome analyzer. Analysis was carried out blind to the mutation in each sample. Average coverage was >1200 reads per base pair. After filtering sequences for quality and number of reads, all single-nucleotide substitutions, small insertion and deletion mutations, and large genomic duplications and deletions were detected. There were zero false-positive calls of nonsense mutations, frameshift mutations, or genomic rearrangements for any gene in any of the test samples. This approach enables widespread genetic testing and personalized risk assessment for breast and ovarian cancer.

Original languageEnglish (US)
Pages (from-to)12629-12633
Number of pages5
JournalProceedings of the National Academy of Sciences of the United States of America
Volume107
Issue number28
DOIs
StatePublished - Jul 13 2010
Externally publishedYes

Fingerprint

High-Throughput Nucleotide Sequencing
Ovarian Neoplasms
Breast Neoplasms
Mutation
Genetic Testing
INDEL Mutation
BRCA2 Gene
BRCA1 Gene
Genes
Frameshift Mutation
Gene Rearrangement
Nonsense Codon
Tumor Suppressor Genes
Oligonucleotides
Base Pairing
Nucleotides
Genome
Costs and Cost Analysis
DNA

Keywords

  • BRCA1
  • BRCA2
  • Genetic testing
  • Genomics
  • Next-generation sequencing

ASJC Scopus subject areas

  • General

Cite this

Detection of inherited mutations for breast and ovarian cancer using genomic capture and massively parallel sequencing. / Walsh, Tom; Lee, Ming K.; Casadei, Silvia; Thornton, Anne M.; Stray, Sunday M.; Pennil, Christopher; Nord, Alexander; Mandell, Jessica B.; Swisher, Elizabeth M.; King, Mary Claire.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 107, No. 28, 13.07.2010, p. 12629-12633.

Research output: Contribution to journalArticle

Walsh, Tom ; Lee, Ming K. ; Casadei, Silvia ; Thornton, Anne M. ; Stray, Sunday M. ; Pennil, Christopher ; Nord, Alexander ; Mandell, Jessica B. ; Swisher, Elizabeth M. ; King, Mary Claire. / Detection of inherited mutations for breast and ovarian cancer using genomic capture and massively parallel sequencing. In: Proceedings of the National Academy of Sciences of the United States of America. 2010 ; Vol. 107, No. 28. pp. 12629-12633.
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