Comprehensive genomic analysis of a BRCA2 deficient human pancreatic cancer

Capan-1 is a well-characterised BRCA2-deficient human cell line isolated from a liver metastasis of a pancreatic adenocarcinoma. Here we report a genome-wide assessment of structural variations and high-depth exome characterization of single nucleotide variants and small insertion/deletions in Capan...

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Bibliographic Details
Published in:PloS one 2011-07, Vol.6 (7), p.e21639-e21639
Main Authors: Barber, Louise J, Rosa Rosa, Juan M, Kozarewa, Iwanka, Fenwick, Kerry, Assiotis, Ioannis, Mitsopoulos, Costas, Sims, David, Hakas, Jarle, Zvelebil, Marketa, Lord, Christopher J, Ashworth, Alan
Format: Article
Language:English
Subjects:
Adenocarcinoma
Adenocarcinoma - genetics
Adenocarcinoma - pathology
Analysis
Biology
BRCA2 protein
BRCA2 Protein - deficiency
BRCA2 Protein - genetics
Breast cancer
Cancer genetics
Cancer therapies
Cell Line, Tumor
Cells (Biology)
Chromosome Mapping
Comparative Genomic Hybridization
Deoxyribonucleic acid
DNA
DNA repair
Evolution & development
Genetic aspects
Genome, Human - genetics
Genomes
Genomic analysis
Genomics
Genomics - methods
Humans
Insertion
Liver
Medical research
Medicine
Metastases
Metastasis
Minority & ethnic groups
Mutation
Pancreatic cancer
Pancreatic Neoplasms - genetics
Pancreatic Neoplasms - pathology
Proteins
Sequence Analysis, DNA - methods
Tumors
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Summary:Capan-1 is a well-characterised BRCA2-deficient human cell line isolated from a liver metastasis of a pancreatic adenocarcinoma. Here we report a genome-wide assessment of structural variations and high-depth exome characterization of single nucleotide variants and small insertion/deletions in Capan-1. To identify potential somatic and tumour-associated variations in the absence of a matched-normal cell line, we devised a novel method based on the analysis of HapMap samples. We demonstrate that Capan-1 has one of the most rearranged genomes sequenced to date. Furthermore, small insertions and deletions are detected more frequently in the context of short sequence repeats than in other genomes. We also identify a number of novel mutations that may represent genetic changes that have contributed to tumour progression. These data provide insight into the genomic effects of loss of BRCA2 function.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0021639