Genetic Epidemiology, Translational Neurogenomics, Psychiatric Genetics and Statistical Genetics Laboratories investigate the pattern of disease in families, particularly identical and non-identical twins, to assess the relative importance of genes and environment in a variety of important health problems.
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PMID
18276640
TITLE
Highly cost-efficient genome-wide association studies using DNA pools and dense SNP arrays.
ABSTRACT
Genome-wide association (GWA) studies to map genes for complex traits are powerful yet costly. DNA-pooling strategies have the potential to dramatically reduce the cost of GWA studies. Pooling using Affymetrix arrays has been proposed and used but the efficiency of these arrays has not been quantified. We compared and contrasted Affymetrix Genechip HindIII and Illumina HumanHap300 arrays on the same DNA pools and showed that the HumanHap300 arrays are substantially more efficient. In terms of effective sample size, HumanHap300-based pooling extracts >80% of the information available with individual genotyping (IG). In contrast, Genechip HindIII-based pooling only extracts approximately 30% of the available information. With HumanHap300 arrays concordance with IG data is excellent. Guidance is given on best study design and it is shown that even after taking into account pooling error, one stage scans can be performed for >100-fold reduced cost compared with IG. With appropriately designed two stage studies, IG can provide confirmation of pooling results whilst still providing approximately 20-fold reduction in total cost compared with IG-based alternatives. The large cost savings with Illumina HumanHap300-based pooling imply that future studies need only be limited by the availability of samples and not cost.
DATE PUBLISHED
2008 Apr
HISTORY
PUBSTATUS PUBSTATUSDATE
aheadofprint 2008/02/14
pubmed 2008/02/16 09:00
medline 2008/05/09 09:00
entrez 2008/02/16 09:00
AUTHORS
NAME COLLECTIVENAME LASTNAME FORENAME INITIALS AFFILIATION AFFILIATIONINFO
Macgregor S Macgregor Stuart S Genetic Epidemiology, Queensland Institute of Medical Research, Brisbane, Australia. stuart.macgregor@qims.edu.au
Zhao ZZ Zhao Zhen Zhen ZZ
Henders A Henders Anjali A
Nicholas MG Nicholas Martin G MG
Montgomery GW Montgomery Grant W GW
Visscher PM Visscher Peter M PM
INVESTIGATORS
JOURNAL
VOLUME: 36
ISSUE: 6
TITLE: Nucleic acids research
ISOABBREVIATION: Nucleic Acids Res.
YEAR: 2008
MONTH: Apr
DAY:
MEDLINEDATE:
SEASON:
CITEDMEDIUM: Internet
ISSN: 1362-4962
ISSNTYPE: Electronic
MEDLINE JOURNAL
MEDLINETA: Nucleic Acids Res
COUNTRY: England
ISSNLINKING: 0305-1048
NLMUNIQUEID: 0411011
PUBLICATION TYPE
PUBLICATIONTYPE TEXT
Comparative Study
Evaluation Studies
Journal Article
Research Support, Non-U.S. Gov't
COMMENTS AND CORRECTIONS
REFTYPE REFSOURCE REFPMID NOTE
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GRANTS
GENERAL NOTE
KEYWORDS
MESH HEADINGS
DESCRIPTORNAME QUALIFIERNAME
Female
Gene Frequency
Genome, Human
Genomics methods
Genotype methods
Humans methods
Oligonucleotide Array Sequence Analysis methods
Polymorphism, Single Nucleotide methods
Sequence Analysis, DNA economics
SUPPLEMENTARY MESH
GENE SYMBOLS
CHEMICALS
OTHER ID's
OTHERID SOURCE
PMC2346606 NLM