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Table 1 Comparison of PLINK (A) and LEM (B) data format and example data for three hypothetical case-parent triads

From: MI-GWAS: a SAS platform for the analysis of inherited and maternal genetic effects in genome-wide association studies using log-linear models

(A)

PLINK Genotype Data for 5 SNPs

Family Number

Individual ID

Paternal ID

Maternal ID

Sex a

Phenotype b

SNP 1 c

SNP 2 c

SNP 3 c

SNP 4 c

SNP 5 c

1001

1001-A

1001-C

1001-B

1

1

1

1

0

0

1

1

1

1

1

2

1001

1001-B

0

0

2

0

1

1

1

1

1

2

1

1

1

1

1001

1001-C

0

0

1

0

1

1

1

2

1

1

1

1

0

0

1002

1002-A

1002-C

1002-B

2

1

0

0

2

2

1

2

1

1

1

2

1002

1002-B

0

0

2

0

2

2

1

2

0

0

1

1

1

1

1002

1002-C

0

0

1

0

1

1

2

2

1

1

1

2

2

2

1003

1003-A

0

1003-B

2

1

1

2

1

2

1

1

1

1

1

1

1003

1003-B

0

0

2

0

1

1

1

2

1

1

0

0

1

1

(B)

LEM Data File for SNP 1

Mother's Genotype d

Father's Genotype d

Case's Genotype d

1

1

1

3

1

0

1

0

2

  1. a 1 = male, 2 = female
  2. b 1 = unaffected, 2 = affected
  3. c 0 = allele missing, 1 = allele 1, 2 = allele 2
  4. d 0 = genotype missing, 1 = no high-risk alleles present, 2 = one high-risk alleles present, 3 = two high-risk alleles present
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BMC Bioinformatics

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