Evaluation of different sources of DNA for use in genome wide studies and forensic application

Habiba S. Al Safar; Fatima H. Abidi; Kamal A. Khazanehdari; Ian R. Dadour; Guan K. Tay

doi:10.1007/s00253-010-2926-3

Evaluation of different sources of DNA for use in genome wide studies and forensic application

Habiba S. Al Safar, Fatima H. Abidi, Kamal A. Khazanehdari, Ian R. Dadour, Guan K. Tay

Biomedical Engineering & Biotechnology

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

8 Scopus citations

Abstract

In the field of epidemiology, Genome-Wide Association Studies (GWAS) are commonly used to identify genetic predispositions of many human diseases. Large repositories housing biological specimens for clinical and genetic investigations have been established to store material and data for these studies. The logistics of specimen collection and sample storage can be onerous, and new strategies have to be explored. This study examines three different DNA sources (namely, degraded genomic DNA, amplified degraded genomic DNA and amplified extracted DNA from FTA card) for GWAS using the Illumina platform. No significant difference in call rate was detected between amplified degraded genomic DNA extracted from whole blood and amplified DNA retrieved from FTA™ cards. However, using unamplified-degraded genomic DNA reduced the call rate to a mean of 42.6% compared to amplified DNA extracted from FTA card (mean of 96.6%). This study establishes the utility of FTA™ cards as a viable storage matrix for cells from which DNA can be extracted to perform GWAS analysis.

Original language	British English
Pages (from-to)	807-815
Number of pages	9
Journal	Applied Microbiology and Biotechnology
Volume	89
Issue number	3
DOIs	https://doi.org/10.1007/s00253-010-2926-3
State	Published - Feb 2011

Keywords

DNA quality
FTA
GWAS

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10.1007/s00253-010-2926-3

Cite this

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title = "Evaluation of different sources of DNA for use in genome wide studies and forensic application",

abstract = "In the field of epidemiology, Genome-Wide Association Studies (GWAS) are commonly used to identify genetic predispositions of many human diseases. Large repositories housing biological specimens for clinical and genetic investigations have been established to store material and data for these studies. The logistics of specimen collection and sample storage can be onerous, and new strategies have to be explored. This study examines three different DNA sources (namely, degraded genomic DNA, amplified degraded genomic DNA and amplified extracted DNA from FTA card) for GWAS using the Illumina platform. No significant difference in call rate was detected between amplified degraded genomic DNA extracted from whole blood and amplified DNA retrieved from FTA{\texttrademark} cards. However, using unamplified-degraded genomic DNA reduced the call rate to a mean of 42.6\% compared to amplified DNA extracted from FTA card (mean of 96.6\%). This study establishes the utility of FTA{\texttrademark} cards as a viable storage matrix for cells from which DNA can be extracted to perform GWAS analysis.",

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note = "Funding Information: Acknowledgements Publication number HA09-0003 of the Centre for Forensic Science at the University of Western Australia, Ms. Alsafar is a Ph.D. scholar at the University of the Western Australia supported by the Dubai Police General Head Quarters in the United Arab Emirates. Funding for this project was provided by the Emirates Foundation, and support was also kindly provided by Ali Ridha, the director of Central Veterinary Research Laboratory (CVRL) in Dubai, United Arab Emirates.",

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AU - Tay, Guan K.

N1 - Funding Information: Acknowledgements Publication number HA09-0003 of the Centre for Forensic Science at the University of Western Australia, Ms. Alsafar is a Ph.D. scholar at the University of the Western Australia supported by the Dubai Police General Head Quarters in the United Arab Emirates. Funding for this project was provided by the Emirates Foundation, and support was also kindly provided by Ali Ridha, the director of Central Veterinary Research Laboratory (CVRL) in Dubai, United Arab Emirates.

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AB - In the field of epidemiology, Genome-Wide Association Studies (GWAS) are commonly used to identify genetic predispositions of many human diseases. Large repositories housing biological specimens for clinical and genetic investigations have been established to store material and data for these studies. The logistics of specimen collection and sample storage can be onerous, and new strategies have to be explored. This study examines three different DNA sources (namely, degraded genomic DNA, amplified degraded genomic DNA and amplified extracted DNA from FTA card) for GWAS using the Illumina platform. No significant difference in call rate was detected between amplified degraded genomic DNA extracted from whole blood and amplified DNA retrieved from FTA™ cards. However, using unamplified-degraded genomic DNA reduced the call rate to a mean of 42.6% compared to amplified DNA extracted from FTA card (mean of 96.6%). This study establishes the utility of FTA™ cards as a viable storage matrix for cells from which DNA can be extracted to perform GWAS analysis.

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Evaluation of different sources of DNA for use in genome wide studies and forensic application

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