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Table 6 Mendel's gamete competition analysis P-values for three data sets (Dutch, Finn 1 and Finn 2) analyzed separately and combined using the a) one-to-one and b) lumped alignment formats.

From: Merging microsatellite data: enhanced methodology and software to combine genotype data for linkage and association analysis

a)

Gamete Competition (GC) P-value

1:1 Format Results: GC P-value and Pr(A1)

Locus

Dutch (D)

Finn 1 (F1)

Finn 2 (F2)

i) D-F1-F2

ii) F1-F2

iii) D-F1

iv) D-F2

D11S1984

0.118

0.191

0.717

0.314 (0.59)

0.689 (0.89)

0.188 (0.65)

0.487 (0.99)

D11S2362

0.318

0.442

0.169

0.127 (0.77)

0.181 (0.57)

0.914 (0.55)

0.057 (0.89)

D11S1999

0.665

0.760

0.965

0.790 (0.90)

0.925 (0.82)

0.636 (0.61)

0.900 (0.64)

D11S1981

0.235

0.477

0.675

0.781 (0.40)

0.801 (0.54)

0.548 (0.44)

0.796 (0.61)

D11S1392

0.614

0.599

0.102

0.068 (1.00)

0.140 (1.00)

0.827 (1.00)

0.035 (1.00)

D11S2002

0.424

0.987

0.038

0.022 (0.27)

0.011 (0.97)

0.468 (1.00)

0.032 (0.97)

D11S2000

0.843

0.373

0.132

0.694 (0.22)

0.409 (0.49)

0.889 (0.65)

0.414 (0.52)

D11S1998

0.090

0.016

0.859

0.044 (0.65)

0.273 (0.94)

0.010 (0.94)

0.148 (0.58)

D11S4464

0.467

0.132

0.302

0.102 (0.30)

0.142 (0.86)

0.080 (0.27)

0.289 (0.88)

D11S912

0.567

0.099

0.559

0.366 (0.69)

0.286 (0.42)

0.572 (0.96)

0.557 (0.42)

b)

Gamete Competition (GC) P-value

Lumped Format Results: GC P-value and Pr(A1)

Locus

Dutch (D)

Finn 1 (F1)

Finn 2 (F2)

i) D-F1-F2

ii) F1-F2

iii) D-F1

iv) D-F2

D11S1984

0.118

0.191

0.717

0.388 (0.97)

0.508 (0.73)

0.255 (0.62)

0.511 (0.96)

D11S2362

0.318

0.442

0.169

0.137 (0.32)

0.248 (0.32)

0.870 (0.29)

0.050 (0.43)

D11S1999

0.665

0.760

0.965

0.620 (0.64)

0.925 (0.87)

0.542 (0.32)

0.755 (0.71)

D11S1981

0.235

0.477

0.675

0.790 (0.17)

0.438 (0.48)

0.565 (0.27)

0.848 (0.65)

D11S1392

0.614

0.599

0.102

0.068 (0.97)

0.140 (0.93)

0.827 (0.98)

0.035 (0.97)

D11S2002

0.424

0.987

0.038

0.030 (0.34)

0.109 (0.73)

0.264 (0.52)

0.020 (0.67)

D11S2000

0.843

0.373

0.132

0.459 (0.07)

0.496 (0.38)

0.861 (0.55)

0.478 (0.16)

D11S1998

0.090

0.016

0.859

0.044 (0.52)

0.273 (0.93)

0.010 (0.87)

0.173 (0.50)

D11S4464

0.467

0.132

0.302

0.101 (0.40)

0.230 (0.45)

0.082 (0.25)

0.246 (0.84)

D11S912

0.567

0.099

0.559

0.498 (0.57)

0.415 (0.42)

0.572 (0.67)

0.606 (0.19)

  1. The posterior probability of the top alignment for each marker is included in parentheses. Marker D11S2002 is emphasized because its association significance improved in the one-to-one merge of the two Finnish data sets. This marker was recently discovered to have the strongest linkage among these markers to familial dyslipidemia in a larger fine-mapping analysis.
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BMC Bioinformatics

ISSN: 1471-2105

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