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Int J Mol Epidemiol Genet 2011;2(1):30-35.
Bioinformatics Application Note
Using Fisher’s method with PLINK ‘LD clumped’ output to compare SNP effects
across Genome-wide Association Study (GWAS) datasets
Hui Shi, Christopher Medway, Kristelle Brown, Noor Kalsheker and Kevin Morgan
Human Genetics, School of Molecular Medical Sciences, Queens Medical Centre, University of Nottingham, Nottingham NG7
2UH, UK.
Received September 29, 2010; accepted November 16, 2010; Epub November 25, 2010; published January 1,
2011
Abstract: As the number of publically available GWAS datasets continues to grow, bioinformatic tools which enable routine
manipulation of data are becoming increasingly useful. Meta-analysis using multiple GWAS datasets has become essential to
elucidate novel SNP associations which may not be readily discovered in each GWAS individually due to insufficient power.
Replication of GWAS findings is critical and is the ‘arbiter’ of genuine SNP associations. We have developed an ‘LD aware’
bioinformatics application which allows efficient comparison of SNP effects across multiple GWAS datasets using Fisher’s
combined probability test from PLINK (v1.06) ‘LD clumped’ output. (IJMEG1009006).
Key words: Genome-wide Association Studies (GWAS), Fisher’s method, bioinformatic tools
Full Text PDF
Address all correspondence to:
Professor Kevin Morgan
Professor of Human Genomics and Molecular Genetics
Institute of Genetics, School of Molecular Medical Sciences
A Floor, West Block, Room
1306, Queens Medical Centre
Nottingham NG7 2UH
United Kingdom
Tel: 0115 8230724
E-mail: kevin.morgan@nottingham.ac.uk
Bioinformatics Application Note
Using Fisher’s method with PLINK ‘LD clumped’ output to compare SNP effects
across Genome-wide Association Study (GWAS) datasets
Hui Shi, Christopher Medway, Kristelle Brown, Noor Kalsheker and Kevin Morgan
Human Genetics, School of Molecular Medical Sciences, Queens Medical Centre, University of Nottingham, Nottingham NG7
2UH, UK.
Received September 29, 2010; accepted November 16, 2010; Epub November 25, 2010; published January 1,
2011
Abstract: As the number of publically available GWAS datasets continues to grow, bioinformatic tools which enable routine
manipulation of data are becoming increasingly useful. Meta-analysis using multiple GWAS datasets has become essential to
elucidate novel SNP associations which may not be readily discovered in each GWAS individually due to insufficient power.
Replication of GWAS findings is critical and is the ‘arbiter’ of genuine SNP associations. We have developed an ‘LD aware’
bioinformatics application which allows efficient comparison of SNP effects across multiple GWAS datasets using Fisher’s
combined probability test from PLINK (v1.06) ‘LD clumped’ output. (IJMEG1009006).
Key words: Genome-wide Association Studies (GWAS), Fisher’s method, bioinformatic tools
Full Text PDF
Address all correspondence to:
Professor Kevin Morgan
Professor of Human Genomics and Molecular Genetics
Institute of Genetics, School of Molecular Medical Sciences
A Floor, West Block, Room
1306, Queens Medical Centre
Nottingham NG7 2UH
United Kingdom
Tel: 0115 8230724
E-mail: kevin.morgan@nottingham.ac.uk
