A rapid conditional enumeration haplotyping method in pedigrees
<p>Abstract</p> <p>Haplotyping in pedigrees provides valuable information for genetic studies (<it>e.g.</it>, linkage analysis and association study). In order to identify a set of haplotype configurations with the highest likelihoods for a large pedigree with a large n...
| Main Authors: | , |
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| Format: | Article |
| Language: | deu |
| Published: |
BMC
2008-01-01
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| Series: | Genetics Selection Evolution |
| Subjects: | |
| Online Access: | http://www.gsejournal.org/content/40/1/25 |
| _version_ | 1819030988837093376 |
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| author | Hoeschele Ina Gao Guimin |
| author_facet | Hoeschele Ina Gao Guimin |
| author_sort | Hoeschele Ina |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Haplotyping in pedigrees provides valuable information for genetic studies (<it>e.g.</it>, linkage analysis and association study). In order to identify a set of haplotype configurations with the highest likelihoods for a large pedigree with a large number of linked loci, in our previous work, we proposed a conditional enumeration haplotyping method which sets a threshold for the conditional probabilities of the possible ordered genotypes at every unordered individual-marker to delete some ordered genotypes with low conditional probabilities and then eliminate some haplotype configurations with low likelihoods. In this article we present a rapid haplotyping algorithm based on a modification of our previous method by setting an additional threshold for the ratio of the conditional probability of a haplotype configuration to the largest conditional probability of all haplotype configurations in order to eliminate those configurations with relatively low conditional probabilities. The new algorithm is much more efficient than our previous method and the widely used software SimWalk2.</p> |
| first_indexed | 2024-12-21T06:38:54Z |
| format | Article |
| id | doaj.art-f467d42e653f477c81f8759f8b6d6e4a |
| institution | Directory Open Access Journal |
| issn | 0999-193X 1297-9686 |
| language | deu |
| last_indexed | 2024-12-21T06:38:54Z |
| publishDate | 2008-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Genetics Selection Evolution |
| spelling | doaj.art-f467d42e653f477c81f8759f8b6d6e4a2022-12-21T19:12:48ZdeuBMCGenetics Selection Evolution0999-193X1297-96862008-01-01401253610.1186/1297-9686-40-1-25A rapid conditional enumeration haplotyping method in pedigreesHoeschele InaGao Guimin<p>Abstract</p> <p>Haplotyping in pedigrees provides valuable information for genetic studies (<it>e.g.</it>, linkage analysis and association study). In order to identify a set of haplotype configurations with the highest likelihoods for a large pedigree with a large number of linked loci, in our previous work, we proposed a conditional enumeration haplotyping method which sets a threshold for the conditional probabilities of the possible ordered genotypes at every unordered individual-marker to delete some ordered genotypes with low conditional probabilities and then eliminate some haplotype configurations with low likelihoods. In this article we present a rapid haplotyping algorithm based on a modification of our previous method by setting an additional threshold for the ratio of the conditional probability of a haplotype configuration to the largest conditional probability of all haplotype configurations in order to eliminate those configurations with relatively low conditional probabilities. The new algorithm is much more efficient than our previous method and the widely used software SimWalk2.</p>http://www.gsejournal.org/content/40/1/25haplotypingpedigreeconditional probabilitylikelihood |
| spellingShingle | Hoeschele Ina Gao Guimin A rapid conditional enumeration haplotyping method in pedigrees Genetics Selection Evolution haplotyping pedigree conditional probability likelihood |
| title | A rapid conditional enumeration haplotyping method in pedigrees |
| title_full | A rapid conditional enumeration haplotyping method in pedigrees |
| title_fullStr | A rapid conditional enumeration haplotyping method in pedigrees |
| title_full_unstemmed | A rapid conditional enumeration haplotyping method in pedigrees |
| title_short | A rapid conditional enumeration haplotyping method in pedigrees |
| title_sort | rapid conditional enumeration haplotyping method in pedigrees |
| topic | haplotyping pedigree conditional probability likelihood |
| url | http://www.gsejournal.org/content/40/1/25 |
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