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Utility of the pooling approach as applied to whole genome association scans with high-density Affymetrix microarrays

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Utility of the pooling approach as applied to whole genome association scans with high-density Affymetrix microarrays. / Schosser, Alexandra; Pirlo, Katrina; Gaysina, Darya; Cohen-Woods, Sarah; Schalkwyk, Leonard C; Elkin, Amanda; Korszun, Ania; Gunasinghe, Cerisse; Gray, Joanna; Jones, Lisa; Meaburn, Emma; Farmer, Anne E; Craig, Ian W; McGuffin, Peter.

In: BMC Research Notes, Vol. 3, 274, 01.11.2010, p. 274.

Research output: Contribution to journalArticle

Harvard

Schosser, A, Pirlo, K, Gaysina, D, Cohen-Woods, S, Schalkwyk, LC, Elkin, A, Korszun, A, Gunasinghe, C, Gray, J, Jones, L, Meaburn, E, Farmer, AE, Craig, IW & McGuffin, P 2010, 'Utility of the pooling approach as applied to whole genome association scans with high-density Affymetrix microarrays', BMC Research Notes, vol. 3, 274, pp. 274. https://doi.org/10.1186/1756-0500-3-274

APA

Schosser, A., Pirlo, K., Gaysina, D., Cohen-Woods, S., Schalkwyk, L. C., Elkin, A., Korszun, A., Gunasinghe, C., Gray, J., Jones, L., Meaburn, E., Farmer, A. E., Craig, I. W., & McGuffin, P. (2010). Utility of the pooling approach as applied to whole genome association scans with high-density Affymetrix microarrays. BMC Research Notes, 3, 274. [274]. https://doi.org/10.1186/1756-0500-3-274

Vancouver

Schosser A, Pirlo K, Gaysina D, Cohen-Woods S, Schalkwyk LC, Elkin A et al. Utility of the pooling approach as applied to whole genome association scans with high-density Affymetrix microarrays. BMC Research Notes. 2010 Nov 1;3:274. 274. https://doi.org/10.1186/1756-0500-3-274

Author

Schosser, Alexandra ; Pirlo, Katrina ; Gaysina, Darya ; Cohen-Woods, Sarah ; Schalkwyk, Leonard C ; Elkin, Amanda ; Korszun, Ania ; Gunasinghe, Cerisse ; Gray, Joanna ; Jones, Lisa ; Meaburn, Emma ; Farmer, Anne E ; Craig, Ian W ; McGuffin, Peter. / Utility of the pooling approach as applied to whole genome association scans with high-density Affymetrix microarrays. In: BMC Research Notes. 2010 ; Vol. 3. pp. 274.

Bibtex Download

@article{430fcde510d14c528185b8b9a237937b,
title = "Utility of the pooling approach as applied to whole genome association scans with high-density Affymetrix microarrays",
abstract = "BACKGROUND: We report an attempt to extend the previously successful approach of combining SNP (single nucleotide polymorphism) microarrays and DNA pooling (SNP-MaP) employing high-density microarrays. Whereas earlier studies employed a range of Affymetrix SNP microarrays comprising from 10 K to 500 K SNPs, this most recent investigation used the 6.0 chip which displays 906,600 SNP probes and 946,000 probes for the interrogation of CNVs (copy number variations). The genotyping assay using the Affymetrix SNP 6.0 array is highly demanding on sample quality due to the small feature size, low redundancy, and lack of mismatch probes.FINDINGS: In the first study published so far using this microarray on pooled DNA, we found that pooled cheek swab DNA could not accurately predict real allele frequencies of the samples that comprised the pools. In contrast, the allele frequency estimates using blood DNA pools were reasonable, although inferior compared to those obtained with previously employed Affymetrix microarrays. However, it might be possible to improve performance by developing improved analysis methods.CONCLUSIONS: Despite the decreasing costs of genome-wide individual genotyping, the pooling approach may have applications in very large-scale case-control association studies. In such cases, our study suggests that high-quality DNA preparations and lower density platforms should be preferred.",
author = "Alexandra Schosser and Katrina Pirlo and Darya Gaysina and Sarah Cohen-Woods and Schalkwyk, {Leonard C} and Amanda Elkin and Ania Korszun and Cerisse Gunasinghe and Joanna Gray and Lisa Jones and Emma Meaburn and Farmer, {Anne E} and Craig, {Ian W} and Peter McGuffin",
year = "2010",
month = nov,
day = "1",
doi = "10.1186/1756-0500-3-274",
language = "English",
volume = "3",
pages = "274",
journal = "BMC Research Notes",
issn = "1756-0500",
publisher = "BioMed Central",

}

RIS (suitable for import to EndNote) Download

TY - JOUR

T1 - Utility of the pooling approach as applied to whole genome association scans with high-density Affymetrix microarrays

AU - Schosser, Alexandra

AU - Pirlo, Katrina

AU - Gaysina, Darya

AU - Cohen-Woods, Sarah

AU - Schalkwyk, Leonard C

AU - Elkin, Amanda

AU - Korszun, Ania

AU - Gunasinghe, Cerisse

AU - Gray, Joanna

AU - Jones, Lisa

AU - Meaburn, Emma

AU - Farmer, Anne E

AU - Craig, Ian W

AU - McGuffin, Peter

PY - 2010/11/1

Y1 - 2010/11/1

N2 - BACKGROUND: We report an attempt to extend the previously successful approach of combining SNP (single nucleotide polymorphism) microarrays and DNA pooling (SNP-MaP) employing high-density microarrays. Whereas earlier studies employed a range of Affymetrix SNP microarrays comprising from 10 K to 500 K SNPs, this most recent investigation used the 6.0 chip which displays 906,600 SNP probes and 946,000 probes for the interrogation of CNVs (copy number variations). The genotyping assay using the Affymetrix SNP 6.0 array is highly demanding on sample quality due to the small feature size, low redundancy, and lack of mismatch probes.FINDINGS: In the first study published so far using this microarray on pooled DNA, we found that pooled cheek swab DNA could not accurately predict real allele frequencies of the samples that comprised the pools. In contrast, the allele frequency estimates using blood DNA pools were reasonable, although inferior compared to those obtained with previously employed Affymetrix microarrays. However, it might be possible to improve performance by developing improved analysis methods.CONCLUSIONS: Despite the decreasing costs of genome-wide individual genotyping, the pooling approach may have applications in very large-scale case-control association studies. In such cases, our study suggests that high-quality DNA preparations and lower density platforms should be preferred.

AB - BACKGROUND: We report an attempt to extend the previously successful approach of combining SNP (single nucleotide polymorphism) microarrays and DNA pooling (SNP-MaP) employing high-density microarrays. Whereas earlier studies employed a range of Affymetrix SNP microarrays comprising from 10 K to 500 K SNPs, this most recent investigation used the 6.0 chip which displays 906,600 SNP probes and 946,000 probes for the interrogation of CNVs (copy number variations). The genotyping assay using the Affymetrix SNP 6.0 array is highly demanding on sample quality due to the small feature size, low redundancy, and lack of mismatch probes.FINDINGS: In the first study published so far using this microarray on pooled DNA, we found that pooled cheek swab DNA could not accurately predict real allele frequencies of the samples that comprised the pools. In contrast, the allele frequency estimates using blood DNA pools were reasonable, although inferior compared to those obtained with previously employed Affymetrix microarrays. However, it might be possible to improve performance by developing improved analysis methods.CONCLUSIONS: Despite the decreasing costs of genome-wide individual genotyping, the pooling approach may have applications in very large-scale case-control association studies. In such cases, our study suggests that high-quality DNA preparations and lower density platforms should be preferred.

U2 - 10.1186/1756-0500-3-274

DO - 10.1186/1756-0500-3-274

M3 - Article

C2 - 21040578

VL - 3

SP - 274

JO - BMC Research Notes

JF - BMC Research Notes

SN - 1756-0500

M1 - 274

ER -

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