Software for tag single nucleotide polymorphism selection
<p>Abstract</p> <p>This paper reviews the theoretical basis for single nucleotide polymorphism (SNP) tagging and considers the use of current software made freely available for this task. A distinction between haplotype block-based and non-block-based approaches yields two classes...
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| Format: | Article |
| Language: | English |
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BMC
2005-06-01
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| Series: | Human Genomics |
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| Online Access: | http://www.humgenomics.com/content/2/2/144 |
| _version_ | 1817992411567095808 |
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| author | Stram Daniel O |
| author_facet | Stram Daniel O |
| author_sort | Stram Daniel O |
| collection | DOAJ |
| description | <p>Abstract</p> <p>This paper reviews the theoretical basis for single nucleotide polymorphism (SNP) tagging and considers the use of current software made freely available for this task. A distinction between haplotype block-based and non-block-based approaches yields two classes of procedures. Analysis of two different sets of SNP genotype data from the HapMap is used to judge the practical aspects of using each of the programs considered, as well as to make some general observations about the performance of the programs in finding optimal sets of tagging SNPs. Pairwise <it>R</it><sup>2 </sup>methods, while the simplest of those considered, do tend to pick more tagging SNPs than are strictly needed to predict unmeasured (non-tagging) SNPs, since a combination of two or more tagging SNPs can form a prediction of SNPs that have no direct (pairwise) surrogate. Block-based methods that exploit the linkage disequilibrium structure within haplotype blocks exploit this sort of redundancy, but run a risk of over-fitting if used without some care. A compromise approach which eliminates the need first to analyse block structure, but which still exploits simple relationships between SNPs, appears promising.</p> |
| first_indexed | 2024-04-14T01:25:56Z |
| format | Article |
| id | doaj.art-0a586a5cbcae43dca1b825e0e7dcccb9 |
| institution | Directory Open Access Journal |
| issn | 1479-7364 |
| language | English |
| last_indexed | 2024-04-14T01:25:56Z |
| publishDate | 2005-06-01 |
| publisher | BMC |
| record_format | Article |
| series | Human Genomics |
| spelling | doaj.art-0a586a5cbcae43dca1b825e0e7dcccb92022-12-22T02:20:26ZengBMCHuman Genomics1479-73642005-06-012214415110.1186/1479-7364-2-2-144Software for tag single nucleotide polymorphism selectionStram Daniel O<p>Abstract</p> <p>This paper reviews the theoretical basis for single nucleotide polymorphism (SNP) tagging and considers the use of current software made freely available for this task. A distinction between haplotype block-based and non-block-based approaches yields two classes of procedures. Analysis of two different sets of SNP genotype data from the HapMap is used to judge the practical aspects of using each of the programs considered, as well as to make some general observations about the performance of the programs in finding optimal sets of tagging SNPs. Pairwise <it>R</it><sup>2 </sup>methods, while the simplest of those considered, do tend to pick more tagging SNPs than are strictly needed to predict unmeasured (non-tagging) SNPs, since a combination of two or more tagging SNPs can form a prediction of SNPs that have no direct (pairwise) surrogate. Block-based methods that exploit the linkage disequilibrium structure within haplotype blocks exploit this sort of redundancy, but run a risk of over-fitting if used without some care. A compromise approach which eliminates the need first to analyse block structure, but which still exploits simple relationships between SNPs, appears promising.</p>http://www.humgenomics.com/content/2/2/144haplotypesSNP tagginglinkage disequilibriumdisease association studies |
| spellingShingle | Stram Daniel O Software for tag single nucleotide polymorphism selection Human Genomics haplotypes SNP tagging linkage disequilibrium disease association studies |
| title | Software for tag single nucleotide polymorphism selection |
| title_full | Software for tag single nucleotide polymorphism selection |
| title_fullStr | Software for tag single nucleotide polymorphism selection |
| title_full_unstemmed | Software for tag single nucleotide polymorphism selection |
| title_short | Software for tag single nucleotide polymorphism selection |
| title_sort | software for tag single nucleotide polymorphism selection |
| topic | haplotypes SNP tagging linkage disequilibrium disease association studies |
| url | http://www.humgenomics.com/content/2/2/144 |
| work_keys_str_mv | AT stramdanielo softwarefortagsinglenucleotidepolymorphismselection |