Characterisation of the genomic architecture of human chromosome 17q and evaluation of different methods for haplotype block definition
<p>Abstract</p> <p>Background</p> <p>The selection of markers in association studies can be informed through the use of haplotype blocks. Recent reports have determined the genomic architecture of chromosomal segments through different haplotype block definitions based...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2005-04-01
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| Series: | BMC Genetics |
| Online Access: | http://www.biomedcentral.com/1471-2156/6/21 |
| _version_ | 1818233531416969216 |
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| author | Ollier William Ward Daniel Eyre Stephen Barton Anne Zeggini Eleftheria Worthington Jane John Sally |
| author_facet | Ollier William Ward Daniel Eyre Stephen Barton Anne Zeggini Eleftheria Worthington Jane John Sally |
| author_sort | Ollier William |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>The selection of markers in association studies can be informed through the use of haplotype blocks. Recent reports have determined the genomic architecture of chromosomal segments through different haplotype block definitions based on linkage disequilibrium (LD) measures or haplotype diversity criteria. The relative applicability of distinct block definitions to association studies, however, remains unclear. We compared different block definitions in 6.1 Mb of chromosome 17q in 189 unrelated healthy individuals. Using 137 single nucleotide polymorphisms (SNPs), at a median spacing of 15.5 kb, we constructed haplotype block maps using published methods and additional methods we have developed. Haplotype tagging SNPs (htSNPs) were identified for each map.</p> <p>Results</p> <p>Blocks were found to be shorter and coverage of the region limited with methods based on LD measures, compared to the method based on haplotype diversity. Although the distribution of blocks was highly variable, the number of SNPs that needed to be typed in order to capture the maximum number of haplotypes was consistent.</p> <p>Conclusion</p> <p>For the marker spacing used in this study, choice of block definition is not important when used as an initial screen of the region to identify htSNPs. However, choice of block definition has consequences for the downstream interpretation of association study results.</p> |
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| format | Article |
| id | doaj.art-ecf13177d5ac4d928bea8677e297119d |
| institution | Directory Open Access Journal |
| issn | 1471-2156 |
| language | English |
| last_indexed | 2024-12-12T11:23:40Z |
| publishDate | 2005-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genetics |
| spelling | doaj.art-ecf13177d5ac4d928bea8677e297119d2022-12-22T00:25:58ZengBMCBMC Genetics1471-21562005-04-01612110.1186/1471-2156-6-21Characterisation of the genomic architecture of human chromosome 17q and evaluation of different methods for haplotype block definitionOllier WilliamWard DanielEyre StephenBarton AnneZeggini EleftheriaWorthington JaneJohn Sally<p>Abstract</p> <p>Background</p> <p>The selection of markers in association studies can be informed through the use of haplotype blocks. Recent reports have determined the genomic architecture of chromosomal segments through different haplotype block definitions based on linkage disequilibrium (LD) measures or haplotype diversity criteria. The relative applicability of distinct block definitions to association studies, however, remains unclear. We compared different block definitions in 6.1 Mb of chromosome 17q in 189 unrelated healthy individuals. Using 137 single nucleotide polymorphisms (SNPs), at a median spacing of 15.5 kb, we constructed haplotype block maps using published methods and additional methods we have developed. Haplotype tagging SNPs (htSNPs) were identified for each map.</p> <p>Results</p> <p>Blocks were found to be shorter and coverage of the region limited with methods based on LD measures, compared to the method based on haplotype diversity. Although the distribution of blocks was highly variable, the number of SNPs that needed to be typed in order to capture the maximum number of haplotypes was consistent.</p> <p>Conclusion</p> <p>For the marker spacing used in this study, choice of block definition is not important when used as an initial screen of the region to identify htSNPs. However, choice of block definition has consequences for the downstream interpretation of association study results.</p>http://www.biomedcentral.com/1471-2156/6/21 |
| spellingShingle | Ollier William Ward Daniel Eyre Stephen Barton Anne Zeggini Eleftheria Worthington Jane John Sally Characterisation of the genomic architecture of human chromosome 17q and evaluation of different methods for haplotype block definition BMC Genetics |
| title | Characterisation of the genomic architecture of human chromosome 17q and evaluation of different methods for haplotype block definition |
| title_full | Characterisation of the genomic architecture of human chromosome 17q and evaluation of different methods for haplotype block definition |
| title_fullStr | Characterisation of the genomic architecture of human chromosome 17q and evaluation of different methods for haplotype block definition |
| title_full_unstemmed | Characterisation of the genomic architecture of human chromosome 17q and evaluation of different methods for haplotype block definition |
| title_short | Characterisation of the genomic architecture of human chromosome 17q and evaluation of different methods for haplotype block definition |
| title_sort | characterisation of the genomic architecture of human chromosome 17q and evaluation of different methods for haplotype block definition |
| url | http://www.biomedcentral.com/1471-2156/6/21 |
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