Bayesian estimation of genomic copy number with single nucleotide polymorphism genotyping arrays
<p>Abstract</p> <p>Background</p> <p>The identification of copy number aberration in the human genome is an important area in cancer research. We develop a model for determining genomic copy numbers using high-density single nucleotide polymorphism genotyping microarray...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2010-12-01
|
| Series: | BMC Research Notes |
| Online Access: | http://www.biomedcentral.com/1756-0500/3/350 |
| _version_ | 1818494213831000064 |
|---|---|
| author | Davis Caleb Vannucci Marina Wang Jian Villagran Alejandro Guo Beibei Man Tsz-Kwong Lau Ching Guerra Rudy |
| author_facet | Davis Caleb Vannucci Marina Wang Jian Villagran Alejandro Guo Beibei Man Tsz-Kwong Lau Ching Guerra Rudy |
| author_sort | Davis Caleb |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>The identification of copy number aberration in the human genome is an important area in cancer research. We develop a model for determining genomic copy numbers using high-density single nucleotide polymorphism genotyping microarrays. The method is based on a Bayesian spatial normal mixture model with an unknown number of components corresponding to true copy numbers. A reversible jump Markov chain Monte Carlo algorithm is used to implement the model and perform posterior inference.</p> <p>Results</p> <p>The performance of the algorithm is examined on both simulated and real cancer data, and it is compared with the popular CNAG algorithm for copy number detection.</p> <p>Conclusions</p> <p>We demonstrate that our Bayesian mixture model performs at least as well as the hidden Markov model based CNAG algorithm and in certain cases does better. One of the added advantages of our method is the flexibility of modeling normal cell contamination in tumor samples.</p> |
| first_indexed | 2024-12-10T18:03:37Z |
| format | Article |
| id | doaj.art-f31eb235f5b442448f51642756ebb76b |
| institution | Directory Open Access Journal |
| issn | 1756-0500 |
| language | English |
| last_indexed | 2024-12-10T18:03:37Z |
| publishDate | 2010-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Research Notes |
| spelling | doaj.art-f31eb235f5b442448f51642756ebb76b2022-12-22T01:38:42ZengBMCBMC Research Notes1756-05002010-12-013135010.1186/1756-0500-3-350Bayesian estimation of genomic copy number with single nucleotide polymorphism genotyping arraysDavis CalebVannucci MarinaWang JianVillagran AlejandroGuo BeibeiMan Tsz-KwongLau ChingGuerra Rudy<p>Abstract</p> <p>Background</p> <p>The identification of copy number aberration in the human genome is an important area in cancer research. We develop a model for determining genomic copy numbers using high-density single nucleotide polymorphism genotyping microarrays. The method is based on a Bayesian spatial normal mixture model with an unknown number of components corresponding to true copy numbers. A reversible jump Markov chain Monte Carlo algorithm is used to implement the model and perform posterior inference.</p> <p>Results</p> <p>The performance of the algorithm is examined on both simulated and real cancer data, and it is compared with the popular CNAG algorithm for copy number detection.</p> <p>Conclusions</p> <p>We demonstrate that our Bayesian mixture model performs at least as well as the hidden Markov model based CNAG algorithm and in certain cases does better. One of the added advantages of our method is the flexibility of modeling normal cell contamination in tumor samples.</p>http://www.biomedcentral.com/1756-0500/3/350 |
| spellingShingle | Davis Caleb Vannucci Marina Wang Jian Villagran Alejandro Guo Beibei Man Tsz-Kwong Lau Ching Guerra Rudy Bayesian estimation of genomic copy number with single nucleotide polymorphism genotyping arrays BMC Research Notes |
| title | Bayesian estimation of genomic copy number with single nucleotide polymorphism genotyping arrays |
| title_full | Bayesian estimation of genomic copy number with single nucleotide polymorphism genotyping arrays |
| title_fullStr | Bayesian estimation of genomic copy number with single nucleotide polymorphism genotyping arrays |
| title_full_unstemmed | Bayesian estimation of genomic copy number with single nucleotide polymorphism genotyping arrays |
| title_short | Bayesian estimation of genomic copy number with single nucleotide polymorphism genotyping arrays |
| title_sort | bayesian estimation of genomic copy number with single nucleotide polymorphism genotyping arrays |
| url | http://www.biomedcentral.com/1756-0500/3/350 |
| work_keys_str_mv | AT daviscaleb bayesianestimationofgenomiccopynumberwithsinglenucleotidepolymorphismgenotypingarrays AT vannuccimarina bayesianestimationofgenomiccopynumberwithsinglenucleotidepolymorphismgenotypingarrays AT wangjian bayesianestimationofgenomiccopynumberwithsinglenucleotidepolymorphismgenotypingarrays AT villagranalejandro bayesianestimationofgenomiccopynumberwithsinglenucleotidepolymorphismgenotypingarrays AT guobeibei bayesianestimationofgenomiccopynumberwithsinglenucleotidepolymorphismgenotypingarrays AT mantszkwong bayesianestimationofgenomiccopynumberwithsinglenucleotidepolymorphismgenotypingarrays AT lauching bayesianestimationofgenomiccopynumberwithsinglenucleotidepolymorphismgenotypingarrays AT guerrarudy bayesianestimationofgenomiccopynumberwithsinglenucleotidepolymorphismgenotypingarrays |