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...
Saved in:
| Main Authors: | , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2011-01-01
|
| Series: | PLoS ONE |
| Online Access: | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0021639&type=printable |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849434452031176704 |
|---|---|
| author | Louise J Barber Juan M Rosa Rosa Iwanka Kozarewa Kerry Fenwick Ioannis Assiotis Costas Mitsopoulos David Sims Jarle Hakas Marketa Zvelebil Christopher J Lord Alan Ashworth |
| author_facet | Louise J Barber Juan M Rosa Rosa Iwanka Kozarewa Kerry Fenwick Ioannis Assiotis Costas Mitsopoulos David Sims Jarle Hakas Marketa Zvelebil Christopher J Lord Alan Ashworth |
| author_sort | Louise J Barber |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-41dfd1b52c244a2daed0cc7c2c59e448 |
| institution | Kabale University |
| issn | 1932-6203 |
| language | English |
| publishDate | 2011-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj-art-41dfd1b52c244a2daed0cc7c2c59e4482025-08-20T03:26:38ZengPublic Library of Science (PLoS)PLoS ONE1932-62032011-01-0167e2163910.1371/journal.pone.0021639Comprehensive genomic analysis of a BRCA2 deficient human pancreatic cancer.Louise J BarberJuan M Rosa RosaIwanka KozarewaKerry FenwickIoannis AssiotisCostas MitsopoulosDavid SimsJarle HakasMarketa ZvelebilChristopher J LordAlan AshworthCapan-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.https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0021639&type=printable |
| spellingShingle | Louise J Barber Juan M Rosa Rosa Iwanka Kozarewa Kerry Fenwick Ioannis Assiotis Costas Mitsopoulos David Sims Jarle Hakas Marketa Zvelebil Christopher J Lord Alan Ashworth Comprehensive genomic analysis of a BRCA2 deficient human pancreatic cancer. PLoS ONE |
| title | Comprehensive genomic analysis of a BRCA2 deficient human pancreatic cancer. |
| title_full | Comprehensive genomic analysis of a BRCA2 deficient human pancreatic cancer. |
| title_fullStr | Comprehensive genomic analysis of a BRCA2 deficient human pancreatic cancer. |
| title_full_unstemmed | Comprehensive genomic analysis of a BRCA2 deficient human pancreatic cancer. |
| title_short | Comprehensive genomic analysis of a BRCA2 deficient human pancreatic cancer. |
| title_sort | comprehensive genomic analysis of a brca2 deficient human pancreatic cancer |
| url | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0021639&type=printable |
| work_keys_str_mv | AT louisejbarber comprehensivegenomicanalysisofabrca2deficienthumanpancreaticcancer AT juanmrosarosa comprehensivegenomicanalysisofabrca2deficienthumanpancreaticcancer AT iwankakozarewa comprehensivegenomicanalysisofabrca2deficienthumanpancreaticcancer AT kerryfenwick comprehensivegenomicanalysisofabrca2deficienthumanpancreaticcancer AT ioannisassiotis comprehensivegenomicanalysisofabrca2deficienthumanpancreaticcancer AT costasmitsopoulos comprehensivegenomicanalysisofabrca2deficienthumanpancreaticcancer AT davidsims comprehensivegenomicanalysisofabrca2deficienthumanpancreaticcancer AT jarlehakas comprehensivegenomicanalysisofabrca2deficienthumanpancreaticcancer AT marketazvelebil comprehensivegenomicanalysisofabrca2deficienthumanpancreaticcancer AT christopherjlord comprehensivegenomicanalysisofabrca2deficienthumanpancreaticcancer AT alanashworth comprehensivegenomicanalysisofabrca2deficienthumanpancreaticcancer |