Table 3 Single gene and polygenic segregation analysis results

From: Estimating single nucleotide polymorphism associations using pedigree data: applications to breast cancer

  

Single gene model

Polygenic model

SNP

Pedigrees

RAF (s.e.) a

HR (95% CI) b

P -value

logL

AIC

RAF (s.e.) a

HR (95% CI) b

P -value

VE (%)

σ R 2

logL

AIC

rs2981582

1626

0.400 (0.008)

1.20 (1.13–1.27)

6.75 × 10−10

−5904.28

11812.56

0.400 (0.008)

1.26 (1.17–1.36)

9.04 × 10−10

1.62

1.637

−5903.33

11810.67

rs1975930

1549

0.113 (0.005)

0.85 (0.77–0.94)

0.002

−2803.64

5611.28

0.113 (0.005)

0.82 (0.72–0.93)

0.002

0.41

1.657

−2804.21

5612.41

rs10941679

1505

0.257 (0.010)

1.09 (1.00–1.19)

0.039

−1480.82

2965.63

0.255 (0.010)

1.13 (1.02–1.26)

0.023

0.38

1.658

−1480.57

2965.14

rs3803662

1606

0.268 (0.007)

1.16 (1.09–1.23)

2.41 × 10−6

−5203.61

10411.22

0.269 (0.007)

1.20 (1.11–1.30)

3.92 × 10−6

0.87

1.650

−5202.84

10409.68

rs2046210

1608

0.348 (0.007)

1.08 (1.02–1.14)

0.011

−5675.98

11355.96

0.349 (0.007)

1.09 (1.01–1.18)

0.028

0.21

1.661

−5676.56

11357.13

rs614367

1627

0.152 (0.005)

1.12 (1.04–1.20)

0.002

−3941.45

7886.89

0.152 (0.005)

1.15 (1.05–1.27)

0.003

0.35

1.658

−3940.83

7885.65

rs10509168

1628

0.466 (0.008)

0.90 (0.85–0.96)

0.001

−5958.28

11920.57

0.464 (0.008)

0.89 (0.83–0.96)

0.002

0.39

1.658

−5959.16

11922.32

rs1292011

1455

0.434 (0.011)

0.97 (0.90–1.04)

0.349

−2177.39

4358.78

0.433 (0.011)

0.96 (0.87–1.06)

0.400

0.05

1.663

−2177.43

4358.85

rs13387042

1598

0.489 (0.008)

1.18 (1.11–1.25)

3.84 × 10−8

−5904.92

11813.85

0.489 (0.008)

1.23 (1.14–1.32)

1.08 × 10−7

1.25

1.643

−5905.31

11814.62

rs13281615

1608

0.401 (0.008)

1.09 (1.03–1.16)

0.002

−5585.14

11174.29

0.402 (0.008)

1.12 (1.04–1.20)

0.004

0.36

1.658

−5585.28

11174.56

rs865686

1547

0.386 (0.008)

0.95 (0.90–1.01)

0.112

−5397.41

10798.83

0.387 (0.008)

0.93 (0.86–1.01)

0.069

0.15

1.662

−5397.31

10798.63

rs11249433

1609

0.414 (0.008)

1.05 (1.00–1.12)

0.072

−5949.54

11903.07

0.415 (0.008)

1.05 (0.98–1.13)

0.174

0.08

1.663

−5950.01

11904.01

rs2823093

1549

0.261 (0.007)

0.95 (0.89–1.02)

0.164

−4882.64

9769.28

0.260 (0.007)

0.95 (0.87–1.04)

0.249

0.06

1.663

−4882.86

9769.72

rs3817198

1607

0.337 (0.007)

1.02 (0.96–1.08)

0.489

−5451.60

10907.21

0.338 (0.007)

1.02 (0.94–1.10)

0.678

0.01

1.664

−5451.68

10907.36

rs889312

1605

0.283 (0.007)

1.07 (1.01–1.14)

0.023

−5181.52

10367.04

0.283 (0.007)

1.09 (1.01–1.18)

0.028

0.20

1.661

−5181.43

10366.87

rs1011970

1628

0.172 (0.006)

1.02 (0.95–1.10)

0.544

−4031.16

8066.33

0.171 (0.006)

1.03 (0.94–1.14)

0.499

0.02

1.664

−4031.11

8066.21

rs17468277

1609

0.141 (0.005)

0.88 (0.80–0.96)

0.004

−3351.37

6706.75

0.141 (0.005)

0.84 (0.75–0.94)

0.002

0.40

1.657

−3351.03

6706.07

rs999737

1566

0.743 (0.007)

1.10 (1.02–1.17)

0.008

−4767.76

9539.52

0.743 (0.007)

1.12 (1.03–1.22)

0.008

0.29

1.659

−4767.38

9538.76

rs2380205

1599

0.412 (0.010)

1.05 (0.98–1.13)

0.141

−2370.80

4745.61

0.412 (0.010)

1.07 (0.98–1.17)

0.156

0.12

1.662

−2370.65

4745.29

rs4973768

1607

0.462 (0.008)

1.09 (1.03–1.15)

0.005

−5904.62

11813.24

0.462 (0.008)

1.12 (1.04–1.21)

0.003

0.38

1.658

−5904.53

11813.06

rs6504950

1609

0.288 (0.007)

0.98 (0.92–1.05)

0.578

−5224.70

10453.40

0.289 (0.007)

0.97 (0.89–1.05)

0.432

0.03

1.664

−5224.80

10453.61

rs2363956

1548

0.508 (0.008)

1.02 (0.96–1.08)

0.515

−5362.61

10729.23

0.508 (0.008)

1.02 (0.95–1.11)

0.533

0.02

1.664

−5362.60

10729.20

rs8170

1549

0.182 (0.006)

1.04 (0.97–1.12)

0.241

−4063.20

8130.40

0.182 (0.006)

1.06 (0.96–1.16)

0.233

0.06

1.663

−4063.24

8130.48

rs12662670

1549

0.076 (0.004)

1.18 (1.08–1.29)

3.64 × 10−4

−2573.28

5150.57

0.077 (0.004)

1.20 (1.06–1.36)

0.003

0.34

1.659

−2574.68

5153.35

  1. Abbreviations: AIC=Akaike Information Criterion (Akaike, 1974); CI=confidence interval; HR=hazard ratio; logL=model maximum log-likelihood; RAF=risk allele frequency; VE=percentage of the total polygenic variance explained by the locus of interest; σR2=residual polygenic variance.
  2. The total polygenic variance estimated by a previous segregation analysis was σP2=1.6641 (Antoniou et al, 2002).
  3. aRAF is the maximum likelihood estimate of the risk allele frequency from the segregation analysis model.
  4. bPer-allele HR is reported such that the effect allele is the same as those from the population-based studies (Supplementary Table 1).
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