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SNP allele frequency estimation in DNA pools and variance components analysis
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| Zeitschriftentitel: | BioTechniques |
|---|---|
| Personen und Körperschaften: | , , , , , , |
| In: | BioTechniques, 36, 2004, 5, S. 840-845 |
| Format: | E-Article |
| Sprache: | Englisch |
| veröffentlicht: |
Future Science Ltd
|
| Schlagwörter: |
| author_facet |
Downes, Kate Barratt, Bryan J. Akan, Pelin Bumpstead, Sue J. Taylor, Stacey D. Clayton, David G. Deloukas, Panos Downes, Kate Barratt, Bryan J. Akan, Pelin Bumpstead, Sue J. Taylor, Stacey D. Clayton, David G. Deloukas, Panos |
|---|---|
| author |
Downes, Kate Barratt, Bryan J. Akan, Pelin Bumpstead, Sue J. Taylor, Stacey D. Clayton, David G. Deloukas, Panos |
| spellingShingle |
Downes, Kate Barratt, Bryan J. Akan, Pelin Bumpstead, Sue J. Taylor, Stacey D. Clayton, David G. Deloukas, Panos BioTechniques SNP allele frequency estimation in DNA pools and variance components analysis General Biochemistry, Genetics and Molecular Biology Biotechnology |
| author_sort |
downes, kate |
| spelling |
Downes, Kate Barratt, Bryan J. Akan, Pelin Bumpstead, Sue J. Taylor, Stacey D. Clayton, David G. Deloukas, Panos 0736-6205 1940-9818 Future Science Ltd General Biochemistry, Genetics and Molecular Biology Biotechnology http://dx.doi.org/10.2144/04365rr01 <jats:p> The estimation of single nucleotide polymorphism (SNP) allele frequency in pooled DNA samples has been proposed as a cost-effective approach to whole genome association studies. However, the key issue is the allele frequency window in which a genotyping method operates and provides a statistically reliable answer. We assessed the homogeneous mass extend assay and estimated the variance associated with each experimental stage. We report that a relationship between estimated allele frequency and variance might exist, suggesting that high statistical power can be retained at low, as well as high, allele frequencies. Assuming this relationship, the formation of subpools consisting of 100 samples retains an effective sample size greater than 70% of the true sample size, with a savings of 11-fold the cost of an individual genotyping study, regardless of allele frequency. </jats:p> SNP allele frequency estimation in DNA pools and variance components analysis BioTechniques |
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| title |
SNP allele frequency estimation in DNA pools and variance components analysis |
| title_unstemmed |
SNP allele frequency estimation in DNA pools and variance components analysis |
| title_full |
SNP allele frequency estimation in DNA pools and variance components analysis |
| title_fullStr |
SNP allele frequency estimation in DNA pools and variance components analysis |
| title_full_unstemmed |
SNP allele frequency estimation in DNA pools and variance components analysis |
| title_short |
SNP allele frequency estimation in DNA pools and variance components analysis |
| title_sort |
snp allele frequency estimation in dna pools and variance components analysis |
| topic |
General Biochemistry, Genetics and Molecular Biology Biotechnology |
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http://dx.doi.org/10.2144/04365rr01 |
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2004 |
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840-845 |
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<jats:p> The estimation of single nucleotide polymorphism (SNP) allele frequency in pooled DNA samples has been proposed as a cost-effective approach to whole genome association studies. However, the key issue is the allele frequency window in which a genotyping method operates and provides a statistically reliable answer. We assessed the homogeneous mass extend assay and estimated the variance associated with each experimental stage. We report that a relationship between estimated allele frequency and variance might exist, suggesting that high statistical power can be retained at low, as well as high, allele frequencies. Assuming this relationship, the formation of subpools consisting of 100 samples retains an effective sample size greater than 70% of the true sample size, with a savings of 11-fold the cost of an individual genotyping study, regardless of allele frequency. </jats:p> |
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| author | Downes, Kate, Barratt, Bryan J., Akan, Pelin, Bumpstead, Sue J., Taylor, Stacey D., Clayton, David G., Deloukas, Panos |
| author_facet | Downes, Kate, Barratt, Bryan J., Akan, Pelin, Bumpstead, Sue J., Taylor, Stacey D., Clayton, David G., Deloukas, Panos, Downes, Kate, Barratt, Bryan J., Akan, Pelin, Bumpstead, Sue J., Taylor, Stacey D., Clayton, David G., Deloukas, Panos |
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| description | <jats:p> The estimation of single nucleotide polymorphism (SNP) allele frequency in pooled DNA samples has been proposed as a cost-effective approach to whole genome association studies. However, the key issue is the allele frequency window in which a genotyping method operates and provides a statistically reliable answer. We assessed the homogeneous mass extend assay and estimated the variance associated with each experimental stage. We report that a relationship between estimated allele frequency and variance might exist, suggesting that high statistical power can be retained at low, as well as high, allele frequencies. Assuming this relationship, the formation of subpools consisting of 100 samples retains an effective sample size greater than 70% of the true sample size, with a savings of 11-fold the cost of an individual genotyping study, regardless of allele frequency. </jats:p> |
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| spelling | Downes, Kate Barratt, Bryan J. Akan, Pelin Bumpstead, Sue J. Taylor, Stacey D. Clayton, David G. Deloukas, Panos 0736-6205 1940-9818 Future Science Ltd General Biochemistry, Genetics and Molecular Biology Biotechnology http://dx.doi.org/10.2144/04365rr01 <jats:p> The estimation of single nucleotide polymorphism (SNP) allele frequency in pooled DNA samples has been proposed as a cost-effective approach to whole genome association studies. However, the key issue is the allele frequency window in which a genotyping method operates and provides a statistically reliable answer. We assessed the homogeneous mass extend assay and estimated the variance associated with each experimental stage. We report that a relationship between estimated allele frequency and variance might exist, suggesting that high statistical power can be retained at low, as well as high, allele frequencies. Assuming this relationship, the formation of subpools consisting of 100 samples retains an effective sample size greater than 70% of the true sample size, with a savings of 11-fold the cost of an individual genotyping study, regardless of allele frequency. </jats:p> SNP allele frequency estimation in DNA pools and variance components analysis BioTechniques |
| spellingShingle | Downes, Kate, Barratt, Bryan J., Akan, Pelin, Bumpstead, Sue J., Taylor, Stacey D., Clayton, David G., Deloukas, Panos, BioTechniques, SNP allele frequency estimation in DNA pools and variance components analysis, General Biochemistry, Genetics and Molecular Biology, Biotechnology |
| title | SNP allele frequency estimation in DNA pools and variance components analysis |
| title_full | SNP allele frequency estimation in DNA pools and variance components analysis |
| title_fullStr | SNP allele frequency estimation in DNA pools and variance components analysis |
| title_full_unstemmed | SNP allele frequency estimation in DNA pools and variance components analysis |
| title_short | SNP allele frequency estimation in DNA pools and variance components analysis |
| title_sort | snp allele frequency estimation in dna pools and variance components analysis |
| title_unstemmed | SNP allele frequency estimation in DNA pools and variance components analysis |
| topic | General Biochemistry, Genetics and Molecular Biology, Biotechnology |
| url | http://dx.doi.org/10.2144/04365rr01 |