Cargando…
Design and validation of an oligonucleotide microarray for the detection of genomic rearrangements associated with common hereditary cancer syndromes
BACKGROUND: Conventional Sanger sequencing reliably detects the majority of genetic mutations associated with hereditary cancers, such as single-base changes and small insertions or deletions. However, detection of genomic rearrangements, such as large deletions and duplications, requires special te...
Autores principales: | , , , , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2014
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4174268/ https://www.ncbi.nlm.nih.gov/pubmed/25204323 http://dx.doi.org/10.1186/s13046-014-0074-9 |
_version_ | 1782336337532157952 |
---|---|
author | Mancini-DiNardo, Debora Judkins, Thaddeus Woolstenhulme, Nick Burton, Collin Schoenberger, Jeremy Ryder, Matthew Murray, Adam Gutin, Natalia Theisen, Aaron Holladay, Jayson Craft, Jonathan Arnell, Christopher Moyes, Kelsey Roa, Benjamin |
author_facet | Mancini-DiNardo, Debora Judkins, Thaddeus Woolstenhulme, Nick Burton, Collin Schoenberger, Jeremy Ryder, Matthew Murray, Adam Gutin, Natalia Theisen, Aaron Holladay, Jayson Craft, Jonathan Arnell, Christopher Moyes, Kelsey Roa, Benjamin |
author_sort | Mancini-DiNardo, Debora |
collection | PubMed |
description | BACKGROUND: Conventional Sanger sequencing reliably detects the majority of genetic mutations associated with hereditary cancers, such as single-base changes and small insertions or deletions. However, detection of genomic rearrangements, such as large deletions and duplications, requires special technologies. Microarray analysis has been successfully used to detect large rearrangements (LRs) in genetic disorders. METHODS: We designed and validated a high-density oligonucleotide microarray for the detection of gene-level genomic rearrangements associated with hereditary breast and ovarian cancer (HBOC), Lynch, and polyposis syndromes. The microarray consisted of probes corresponding to the exons and flanking introns of BRCA1 and BRCA2 (≈1,700) and Lynch syndrome/polyposis genes MLH1, MSH2, MSH6, APC, MUTYH, and EPCAM (≈2,200). We validated the microarray with 990 samples previously tested for LR status in BRCA1, BRCA2, MLH1, MSH2, MSH6, APC, MUTYH, or EPCAM. Microarray results were 100% concordant with previous results in the validation studies. Subsequently, clinical microarray analysis was performed on samples from patients with a high likelihood of HBOC mutations (13,124), Lynch syndrome mutations (18,498), and polyposis syndrome mutations (2,739) to determine the proportion of LRs. RESULTS: Our results demonstrate that LRs constitute a substantial proportion of genetic mutations found in patients referred for hereditary cancer genetic testing. CONCLUSION: The use of microarray comparative genomic hybridization (CGH) for the detection of LRs is well-suited as an adjunct technology for both single syndrome (by Sanger sequencing analysis) and extended gene panel testing by next generation sequencing analysis. Genetic testing strategies using microarray analysis will help identify additional patients carrying LRs, who are predisposed to various hereditary cancers. |
format | Online Article Text |
id | pubmed-4174268 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-41742682014-09-26 Design and validation of an oligonucleotide microarray for the detection of genomic rearrangements associated with common hereditary cancer syndromes Mancini-DiNardo, Debora Judkins, Thaddeus Woolstenhulme, Nick Burton, Collin Schoenberger, Jeremy Ryder, Matthew Murray, Adam Gutin, Natalia Theisen, Aaron Holladay, Jayson Craft, Jonathan Arnell, Christopher Moyes, Kelsey Roa, Benjamin J Exp Clin Cancer Res Research BACKGROUND: Conventional Sanger sequencing reliably detects the majority of genetic mutations associated with hereditary cancers, such as single-base changes and small insertions or deletions. However, detection of genomic rearrangements, such as large deletions and duplications, requires special technologies. Microarray analysis has been successfully used to detect large rearrangements (LRs) in genetic disorders. METHODS: We designed and validated a high-density oligonucleotide microarray for the detection of gene-level genomic rearrangements associated with hereditary breast and ovarian cancer (HBOC), Lynch, and polyposis syndromes. The microarray consisted of probes corresponding to the exons and flanking introns of BRCA1 and BRCA2 (≈1,700) and Lynch syndrome/polyposis genes MLH1, MSH2, MSH6, APC, MUTYH, and EPCAM (≈2,200). We validated the microarray with 990 samples previously tested for LR status in BRCA1, BRCA2, MLH1, MSH2, MSH6, APC, MUTYH, or EPCAM. Microarray results were 100% concordant with previous results in the validation studies. Subsequently, clinical microarray analysis was performed on samples from patients with a high likelihood of HBOC mutations (13,124), Lynch syndrome mutations (18,498), and polyposis syndrome mutations (2,739) to determine the proportion of LRs. RESULTS: Our results demonstrate that LRs constitute a substantial proportion of genetic mutations found in patients referred for hereditary cancer genetic testing. CONCLUSION: The use of microarray comparative genomic hybridization (CGH) for the detection of LRs is well-suited as an adjunct technology for both single syndrome (by Sanger sequencing analysis) and extended gene panel testing by next generation sequencing analysis. Genetic testing strategies using microarray analysis will help identify additional patients carrying LRs, who are predisposed to various hereditary cancers. BioMed Central 2014-09-11 /pmc/articles/PMC4174268/ /pubmed/25204323 http://dx.doi.org/10.1186/s13046-014-0074-9 Text en © Mancini-DiNardo et al.; licnsee BioMed Central Ltd. 2014 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Mancini-DiNardo, Debora Judkins, Thaddeus Woolstenhulme, Nick Burton, Collin Schoenberger, Jeremy Ryder, Matthew Murray, Adam Gutin, Natalia Theisen, Aaron Holladay, Jayson Craft, Jonathan Arnell, Christopher Moyes, Kelsey Roa, Benjamin Design and validation of an oligonucleotide microarray for the detection of genomic rearrangements associated with common hereditary cancer syndromes |
title | Design and validation of an oligonucleotide microarray for the detection of genomic rearrangements associated with common hereditary cancer syndromes |
title_full | Design and validation of an oligonucleotide microarray for the detection of genomic rearrangements associated with common hereditary cancer syndromes |
title_fullStr | Design and validation of an oligonucleotide microarray for the detection of genomic rearrangements associated with common hereditary cancer syndromes |
title_full_unstemmed | Design and validation of an oligonucleotide microarray for the detection of genomic rearrangements associated with common hereditary cancer syndromes |
title_short | Design and validation of an oligonucleotide microarray for the detection of genomic rearrangements associated with common hereditary cancer syndromes |
title_sort | design and validation of an oligonucleotide microarray for the detection of genomic rearrangements associated with common hereditary cancer syndromes |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4174268/ https://www.ncbi.nlm.nih.gov/pubmed/25204323 http://dx.doi.org/10.1186/s13046-014-0074-9 |
work_keys_str_mv | AT mancinidinardodebora designandvalidationofanoligonucleotidemicroarrayforthedetectionofgenomicrearrangementsassociatedwithcommonhereditarycancersyndromes AT judkinsthaddeus designandvalidationofanoligonucleotidemicroarrayforthedetectionofgenomicrearrangementsassociatedwithcommonhereditarycancersyndromes AT woolstenhulmenick designandvalidationofanoligonucleotidemicroarrayforthedetectionofgenomicrearrangementsassociatedwithcommonhereditarycancersyndromes AT burtoncollin designandvalidationofanoligonucleotidemicroarrayforthedetectionofgenomicrearrangementsassociatedwithcommonhereditarycancersyndromes AT schoenbergerjeremy designandvalidationofanoligonucleotidemicroarrayforthedetectionofgenomicrearrangementsassociatedwithcommonhereditarycancersyndromes AT rydermatthew designandvalidationofanoligonucleotidemicroarrayforthedetectionofgenomicrearrangementsassociatedwithcommonhereditarycancersyndromes AT murrayadam designandvalidationofanoligonucleotidemicroarrayforthedetectionofgenomicrearrangementsassociatedwithcommonhereditarycancersyndromes AT gutinnatalia designandvalidationofanoligonucleotidemicroarrayforthedetectionofgenomicrearrangementsassociatedwithcommonhereditarycancersyndromes AT theisenaaron designandvalidationofanoligonucleotidemicroarrayforthedetectionofgenomicrearrangementsassociatedwithcommonhereditarycancersyndromes AT holladayjayson designandvalidationofanoligonucleotidemicroarrayforthedetectionofgenomicrearrangementsassociatedwithcommonhereditarycancersyndromes AT craftjonathan designandvalidationofanoligonucleotidemicroarrayforthedetectionofgenomicrearrangementsassociatedwithcommonhereditarycancersyndromes AT arnellchristopher designandvalidationofanoligonucleotidemicroarrayforthedetectionofgenomicrearrangementsassociatedwithcommonhereditarycancersyndromes AT moyeskelsey designandvalidationofanoligonucleotidemicroarrayforthedetectionofgenomicrearrangementsassociatedwithcommonhereditarycancersyndromes AT roabenjamin designandvalidationofanoligonucleotidemicroarrayforthedetectionofgenomicrearrangementsassociatedwithcommonhereditarycancersyndromes |