Saliva-derived DNA performs well in large-scale, high-density single-nucleotide polymorphism microarray studies

Melanie Bahlo; Jim Stankovich; Simon J. Foote; Lyn R. Griffiths; Trevor J. Kilpatrick; Jeanette Lechner-Scott; Pablo Moscato; Victoria M. Perreau; Rodney J. Scott; Graeme J. Stewart; James Wiley; Glynnis Clarke; Patrick Danoy; Mathew B. Cox; Peter A. Csurhes; Joanne L. Dickinson; Karen Drysdale; Judith Field; Judith M. Greer; Preethi Guru; Johanna Hadler; Ella Hoban; Brendan J. McMorran; Peter F. Hickey; Cathy J. Jensen; Laura J. Johnson; Ruth McCallum; Marilyn Merriman; Tony Merriman; Andrea Polanowski; Karena Pryce; Lotfi Tajouri; Lucy Whittock; Ella J. Wilkins; Bruce V. Taylor; Brian L. Browning; Devindri Perera; Helmut Butzkueven; William M. Carroll; Caron Chapman; Allan G. Kermode; Mark Marriott; Deborah Mason; Robert N. Heard; Michael P. Pender; Sharon R. Browning; Mark Slee; Niall Tubridy; Ernest Willoughby; Matthew A. Brown; Justin P. Rubio; David R. Booth; Simon A. Broadley

doi:10.1158/1055-9965.EPI-09-0812

Saliva-derived DNA performs well in large-scale, high-density single-nucleotide polymorphism microarray studies

Melanie Bahlo, Jim Stankovich, Simon J. Foote, Lyn R. Griffiths, Trevor J. Kilpatrick, Jeanette Lechner-Scott, Pablo Moscato, Victoria M. Perreau, Rodney J. Scott, Graeme J. Stewart, James Wiley, Glynnis Clarke, Patrick Danoy, Mathew B. Cox, Peter A. Csurhes, Joanne L. Dickinson, Karen Drysdale, Judith Field, Judith M. Greer, Preethi GuruJohanna Hadler, Ella Hoban, Brendan J. McMorran, Peter F. Hickey, Cathy J. Jensen, Laura J. Johnson, Ruth McCallum, Marilyn Merriman, Tony Merriman, Andrea Polanowski, Karena Pryce, Lotfi Tajouri, Lucy Whittock, Ella J. Wilkins, Bruce V. Taylor, Brian L. Browning, Devindri Perera, Helmut Butzkueven, William M. Carroll, Caron Chapman, Allan G. Kermode, Mark Marriott, Deborah Mason, Robert N. Heard, Michael P. Pender, Sharon R. Browning, Mark Slee, Niall Tubridy, Ernest Willoughby, Matthew A. Brown, Justin P. Rubio, David R. Booth, Simon A. Broadley

Research output: Contribution to journal › Article › peer-review

46 Citations (Scopus)

Abstract

As of June 2009, 361 genome-wide association studies (GWAS) had been referenced by the HuGE database. GWAS require DNA from many thousands of individuals, relying on suitable DNA collections. We recently performed a multiple sclerosis (MS) GWAS where a substantial component of the cases (24%) had DNA derived from saliva. Genotyping was done on the Illumina genotyping platform using the Infinium Hap370CNV DUO microarray. Additionally, we genotyped 10 individuals in duplicate using both salivaand blood-derived DNA. The performance of blood- versus saliva-derived DNA was compared using genotyping call rate, which reflects both the quantity and quality of genotyping per sample and the "GCScore," an Illumina genotyping quality score, which is a measure of DNA quality. We also compared genotype calls and GCScores for the 10 sample pairs. Call rates were assessed for each sample individually. For the GWAS samples, we compared data according to source of DNA and center of origin. We observed high concordance in genotyping quality and quantity between the paired samples and minimal loss of quality and quantity of DNA in the saliva samples in the large GWAS sample, with the blood samples showing greater variation between centers of origin. This large data set highlights the usefulness of saliva DNA for genotyping, especially in high-density single-nucleotide polymorphism microarray studies such as GWAS.

Original language	English
Pages (from-to)	794-798
Number of pages	5
Journal	Cancer Epidemiology Biomarkers and Prevention
Volume	19
Issue number	3
DOIs	https://doi.org/10.1158/1055-9965.EPI-09-0812
Publication status	Published - 2010
Externally published	Yes

Keywords

DNA
saliva
genome-wide
association
SNP chip

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10.1158/1055-9965.EPI-09-0812

Cite this

Bahlo, M., Stankovich, J., Foote, S. J., Griffiths, L. R., Kilpatrick, T. J., Lechner-Scott, J., Moscato, P., Perreau, V. M., Scott, R. J., Stewart, G. J., Wiley, J., Clarke, G., Danoy, P., Cox, M. B., Csurhes, P. A., Dickinson, J. L., Drysdale, K., Field, J., Greer, J. M., ... Broadley, S. A. (2010). Saliva-derived DNA performs well in large-scale, high-density single-nucleotide polymorphism microarray studies. Cancer Epidemiology Biomarkers and Prevention, 19(3), 794-798. https://doi.org/10.1158/1055-9965.EPI-09-0812

@article{54b8c8cc829b4c69b1e22e353dca90fa,

title = "Saliva-derived DNA performs well in large-scale, high-density single-nucleotide polymorphism microarray studies",

abstract = "As of June 2009, 361 genome-wide association studies (GWAS) had been referenced by the HuGE database. GWAS require DNA from many thousands of individuals, relying on suitable DNA collections. We recently performed a multiple sclerosis (MS) GWAS where a substantial component of the cases (24%) had DNA derived from saliva. Genotyping was done on the Illumina genotyping platform using the Infinium Hap370CNV DUO microarray. Additionally, we genotyped 10 individuals in duplicate using both salivaand blood-derived DNA. The performance of blood- versus saliva-derived DNA was compared using genotyping call rate, which reflects both the quantity and quality of genotyping per sample and the {"}GCScore,{"} an Illumina genotyping quality score, which is a measure of DNA quality. We also compared genotype calls and GCScores for the 10 sample pairs. Call rates were assessed for each sample individually. For the GWAS samples, we compared data according to source of DNA and center of origin. We observed high concordance in genotyping quality and quantity between the paired samples and minimal loss of quality and quantity of DNA in the saliva samples in the large GWAS sample, with the blood samples showing greater variation between centers of origin. This large data set highlights the usefulness of saliva DNA for genotyping, especially in high-density single-nucleotide polymorphism microarray studies such as GWAS.",

keywords = "DNA, saliva, genome-wide, association, SNP chip",

author = "Melanie Bahlo and Jim Stankovich and Foote, {Simon J.} and Griffiths, {Lyn R.} and Kilpatrick, {Trevor J.} and Jeanette Lechner-Scott and Pablo Moscato and Perreau, {Victoria M.} and Scott, {Rodney J.} and Stewart, {Graeme J.} and James Wiley and Glynnis Clarke and Patrick Danoy and Cox, {Mathew B.} and Csurhes, {Peter A.} and Dickinson, {Joanne L.} and Karen Drysdale and Judith Field and Greer, {Judith M.} and Preethi Guru and Johanna Hadler and Ella Hoban and McMorran, {Brendan J.} and Hickey, {Peter F.} and Jensen, {Cathy J.} and Johnson, {Laura J.} and Ruth McCallum and Marilyn Merriman and Tony Merriman and Andrea Polanowski and Karena Pryce and Lotfi Tajouri and Lucy Whittock and Wilkins, {Ella J.} and Taylor, {Bruce V.} and Browning, {Brian L.} and Devindri Perera and Helmut Butzkueven and Carroll, {William M.} and Caron Chapman and Kermode, {Allan G.} and Mark Marriott and Deborah Mason and Heard, {Robert N.} and Pender, {Michael P.} and Browning, {Sharon R.} and Mark Slee and Niall Tubridy and Ernest Willoughby and Brown, {Matthew A.} and Rubio, {Justin P.} and Booth, {David R.} and Broadley, {Simon A.}",

year = "2010",

doi = "10.1158/1055-9965.EPI-09-0812",

language = "English",

volume = "19",

pages = "794--798",

journal = "Cancer Epidemiology Biomarkers and Prevention",

issn = "1055-9965",

publisher = "American Association for Cancer Research",

number = "3",

}

Bahlo, M, Stankovich, J, Foote, SJ, Griffiths, LR, Kilpatrick, TJ, Lechner-Scott, J, Moscato, P, Perreau, VM, Scott, RJ, Stewart, GJ, Wiley, J, Clarke, G, Danoy, P, Cox, MB, Csurhes, PA, Dickinson, JL, Drysdale, K, Field, J, Greer, JM, Guru, P, Hadler, J, Hoban, E, McMorran, BJ, Hickey, PF, Jensen, CJ, Johnson, LJ, McCallum, R, Merriman, M, Merriman, T, Polanowski, A, Pryce, K, Tajouri, L, Whittock, L, Wilkins, EJ, Taylor, BV, Browning, BL, Perera, D, Butzkueven, H, Carroll, WM, Chapman, C, Kermode, AG, Marriott, M, Mason, D, Heard, RN, Pender, MP, Browning, SR, Slee, M, Tubridy, N, Willoughby, E, Brown, MA, Rubio, JP, Booth, DR & Broadley, SA 2010, 'Saliva-derived DNA performs well in large-scale, high-density single-nucleotide polymorphism microarray studies', Cancer Epidemiology Biomarkers and Prevention, vol. 19, no. 3, pp. 794-798. https://doi.org/10.1158/1055-9965.EPI-09-0812

TY - JOUR

T1 - Saliva-derived DNA performs well in large-scale, high-density single-nucleotide polymorphism microarray studies

AU - Bahlo, Melanie

AU - Stankovich, Jim

AU - Foote, Simon J.

AU - Griffiths, Lyn R.

AU - Kilpatrick, Trevor J.

AU - Lechner-Scott, Jeanette

AU - Moscato, Pablo

AU - Perreau, Victoria M.

AU - Scott, Rodney J.

AU - Stewart, Graeme J.

AU - Wiley, James

AU - Clarke, Glynnis

AU - Danoy, Patrick

AU - Cox, Mathew B.

AU - Csurhes, Peter A.

AU - Dickinson, Joanne L.

AU - Drysdale, Karen

AU - Field, Judith

AU - Greer, Judith M.

AU - Guru, Preethi

AU - Hadler, Johanna

AU - Hoban, Ella

AU - McMorran, Brendan J.

AU - Hickey, Peter F.

AU - Jensen, Cathy J.

AU - Johnson, Laura J.

AU - McCallum, Ruth

AU - Merriman, Marilyn

AU - Merriman, Tony

AU - Polanowski, Andrea

AU - Pryce, Karena

AU - Tajouri, Lotfi

AU - Whittock, Lucy

AU - Wilkins, Ella J.

AU - Taylor, Bruce V.

AU - Browning, Brian L.

AU - Perera, Devindri

AU - Butzkueven, Helmut

AU - Carroll, William M.

AU - Chapman, Caron

AU - Kermode, Allan G.

AU - Marriott, Mark

AU - Mason, Deborah

AU - Heard, Robert N.

AU - Pender, Michael P.

AU - Browning, Sharon R.

AU - Slee, Mark

AU - Tubridy, Niall

AU - Willoughby, Ernest

AU - Brown, Matthew A.

AU - Rubio, Justin P.

AU - Booth, David R.

AU - Broadley, Simon A.

PY - 2010

Y1 - 2010

N2 - As of June 2009, 361 genome-wide association studies (GWAS) had been referenced by the HuGE database. GWAS require DNA from many thousands of individuals, relying on suitable DNA collections. We recently performed a multiple sclerosis (MS) GWAS where a substantial component of the cases (24%) had DNA derived from saliva. Genotyping was done on the Illumina genotyping platform using the Infinium Hap370CNV DUO microarray. Additionally, we genotyped 10 individuals in duplicate using both salivaand blood-derived DNA. The performance of blood- versus saliva-derived DNA was compared using genotyping call rate, which reflects both the quantity and quality of genotyping per sample and the "GCScore," an Illumina genotyping quality score, which is a measure of DNA quality. We also compared genotype calls and GCScores for the 10 sample pairs. Call rates were assessed for each sample individually. For the GWAS samples, we compared data according to source of DNA and center of origin. We observed high concordance in genotyping quality and quantity between the paired samples and minimal loss of quality and quantity of DNA in the saliva samples in the large GWAS sample, with the blood samples showing greater variation between centers of origin. This large data set highlights the usefulness of saliva DNA for genotyping, especially in high-density single-nucleotide polymorphism microarray studies such as GWAS.

AB - As of June 2009, 361 genome-wide association studies (GWAS) had been referenced by the HuGE database. GWAS require DNA from many thousands of individuals, relying on suitable DNA collections. We recently performed a multiple sclerosis (MS) GWAS where a substantial component of the cases (24%) had DNA derived from saliva. Genotyping was done on the Illumina genotyping platform using the Infinium Hap370CNV DUO microarray. Additionally, we genotyped 10 individuals in duplicate using both salivaand blood-derived DNA. The performance of blood- versus saliva-derived DNA was compared using genotyping call rate, which reflects both the quantity and quality of genotyping per sample and the "GCScore," an Illumina genotyping quality score, which is a measure of DNA quality. We also compared genotype calls and GCScores for the 10 sample pairs. Call rates were assessed for each sample individually. For the GWAS samples, we compared data according to source of DNA and center of origin. We observed high concordance in genotyping quality and quantity between the paired samples and minimal loss of quality and quantity of DNA in the saliva samples in the large GWAS sample, with the blood samples showing greater variation between centers of origin. This large data set highlights the usefulness of saliva DNA for genotyping, especially in high-density single-nucleotide polymorphism microarray studies such as GWAS.

KW - DNA

KW - saliva

KW - genome-wide

KW - association

KW - SNP chip

U2 - 10.1158/1055-9965.EPI-09-0812

DO - 10.1158/1055-9965.EPI-09-0812

M3 - Article

C2 - 20200434

SN - 1055-9965

VL - 19

SP - 794

EP - 798

JO - Cancer Epidemiology Biomarkers and Prevention

JF - Cancer Epidemiology Biomarkers and Prevention

IS - 3

ER -

Saliva-derived DNA performs well in large-scale, high-density single-nucleotide polymorphism microarray studies

Abstract

Keywords

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