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A Novel Approach for Determining Cancer Genomic Breakpoints in the Presence of Normal DNA
CDKN2A (encodes p16(INK4A) and p14(ARF)) deletion, which results in both Rb and p53 inactivation, is the most common chromosomal anomaly in human cancers. To precisely map the deletion breakpoints is important to understanding the molecular mechanism of genomic rearrangement and may also be useful f...
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Formato: | Texto |
Lenguaje: | English |
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Public Library of Science
2007
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1847701/ https://www.ncbi.nlm.nih.gov/pubmed/17440616 http://dx.doi.org/10.1371/journal.pone.0000380 |
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author | Liu, Yu-Tsueng Carson, Dennis A. |
author_facet | Liu, Yu-Tsueng Carson, Dennis A. |
author_sort | Liu, Yu-Tsueng |
collection | PubMed |
description | CDKN2A (encodes p16(INK4A) and p14(ARF)) deletion, which results in both Rb and p53 inactivation, is the most common chromosomal anomaly in human cancers. To precisely map the deletion breakpoints is important to understanding the molecular mechanism of genomic rearrangement and may also be useful for clinical applications. However, current methods for determining the breakpoint are either of low resolution or require the isolation of relatively pure cancer cells, which can be difficult for clinical samples that are typically contaminated with various amounts of normal host cells. To overcome this hurdle, we have developed a novel approach, designated Primer Approximation Multiplex PCR (PAMP), for enriching breakpoint sequences followed by genomic tiling array hybridization to locate the breakpoints. In a series of proof-of-concept experiments, we were able to identify cancer-derived CDKN2A genomic breakpoints when more than 99.9% of wild type genome was present in a model system. This design can be scaled up with bioinformatics support and can be applied to validate other candidate cancer-associated loci that are revealed by other more systemic but lower throughput assays. |
format | Text |
id | pubmed-1847701 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2007 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-18477012007-04-18 A Novel Approach for Determining Cancer Genomic Breakpoints in the Presence of Normal DNA Liu, Yu-Tsueng Carson, Dennis A. PLoS One Research Article CDKN2A (encodes p16(INK4A) and p14(ARF)) deletion, which results in both Rb and p53 inactivation, is the most common chromosomal anomaly in human cancers. To precisely map the deletion breakpoints is important to understanding the molecular mechanism of genomic rearrangement and may also be useful for clinical applications. However, current methods for determining the breakpoint are either of low resolution or require the isolation of relatively pure cancer cells, which can be difficult for clinical samples that are typically contaminated with various amounts of normal host cells. To overcome this hurdle, we have developed a novel approach, designated Primer Approximation Multiplex PCR (PAMP), for enriching breakpoint sequences followed by genomic tiling array hybridization to locate the breakpoints. In a series of proof-of-concept experiments, we were able to identify cancer-derived CDKN2A genomic breakpoints when more than 99.9% of wild type genome was present in a model system. This design can be scaled up with bioinformatics support and can be applied to validate other candidate cancer-associated loci that are revealed by other more systemic but lower throughput assays. Public Library of Science 2007-04-18 /pmc/articles/PMC1847701/ /pubmed/17440616 http://dx.doi.org/10.1371/journal.pone.0000380 Text en Liu, Carson. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Liu, Yu-Tsueng Carson, Dennis A. A Novel Approach for Determining Cancer Genomic Breakpoints in the Presence of Normal DNA |
title | A Novel Approach for Determining Cancer Genomic Breakpoints in the Presence of Normal DNA |
title_full | A Novel Approach for Determining Cancer Genomic Breakpoints in the Presence of Normal DNA |
title_fullStr | A Novel Approach for Determining Cancer Genomic Breakpoints in the Presence of Normal DNA |
title_full_unstemmed | A Novel Approach for Determining Cancer Genomic Breakpoints in the Presence of Normal DNA |
title_short | A Novel Approach for Determining Cancer Genomic Breakpoints in the Presence of Normal DNA |
title_sort | novel approach for determining cancer genomic breakpoints in the presence of normal dna |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1847701/ https://www.ncbi.nlm.nih.gov/pubmed/17440616 http://dx.doi.org/10.1371/journal.pone.0000380 |
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