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Table 1 Breast cancer risk association results from logistic regression and mixture models of population training samples

From: Breast cancer risks associated with missense variants in breast cancer susceptibility genes

 

N

Logistic regression model

Mixture model

Risk group

Variantsa

Cases

Controls

ORb

95% CIc

P-value

Missense OR (95% CI)d

αe

95% CIf

ATM

   

Log-likelihood =  − 48,624.97

Log-likelihood =  − 48,624.64

Non-carriers

–

33,351

37,001

1

–

–

 

0

–

Carriers

      

2.16 (1.78–2.63)h

  

Variant outside FAT and PIK domains

714

1259

1443

0.98

(0.91–1.06)

0.67

 

0.0041

(0.001–0.02)

Variant inside FAT or PIK domain and CADD score quintiles 1–4 g

171

317

333

1.10

(0.94–1.29)

0.24

 

0.055

(0.03–0.12)

Variant inside FAT or PIK domain and CADD score quintile 5 g

103

239

162

1.64

(1.33–2.02)

3.1 × 10−6

 

0.54

(0.41–0.68)

BRCA1

   

Log-likelihood =  − 48,652.14

Log-likelihood =  − 48,652.29

Non-carriers

–

34,191

37,996

1

–

–

 

0

–

Carriers

      

10.61 (7.92–14.21)h

  

Variant outside RING and BRCT domains

479

811

856

1.01

(0.92–1.12)

0.79

 

0.0015

(9.4 × 10−5–0.025)

Variant inside RING or BRCT domain and low Helix score

79

120

103

1.18

(0.90–1.55)

0.23

 

1.0 × 10−11

NA

Variant inside RING or BRCT domain and high Helix score

23

63

16

4.94

(2.83–8.61)

1.9 × 10−8

 

0.48

(0.19–0.78)

BRCA2

   

Log-likelihood =  − 48,641.97

Log-likelihood =  − 48,638.78

Non-carriers

–

33,006

36,517

1

–

–

 

0

–

Carriers

      

5.87 (4.75–7.24)h

  

Variant with low Helix score

1160

2062

2323

0.98

(0.92–1.04)

0.47

 

5.1 × 10−5

(2.4 × 10−9–0.52)

Variant with high Helix score

62

114

94

1.28

(0.96–1.70)

0.087

 

0.11

(0.04–0.25)

CHEK2

   

Log-likelihood =  − 48,728.96

Log-likelihood =  − 48,728.70

Non-carriers

–

34,582

38,480

1

–

–

 

0

–

Carriers

      

1.75 (1.47–2.08)i

  

Variant with low Helix score

157

403

363

1.26

(1.08–1.46)

0.0025

 

0.33

(0.25–0.43)

Variant with high Helix score

121

265

177

1.73

(1.42–2.11)

4.7 × 10−8

 

0.95

(0.86–0.98)

PALB2

   

Log-likelihood =  − 48,728.67

Log-likelihood =  − 48,729.17

Non-carriers

–

34,622

38,291

1

–

–

 

0

–

Carriers

424

618

713

0.95

(0.85–1.06)

0.34

4.87 (3.50–6.77)h

1.1 × 10−4

(1.6 × 10−9–0.88)

  1. a Number of unique missense substitutions in population dataset
  2. b Logistic regression odds ratio estimate for missense variant carriers
  3. c 95% confidence interval for logistic regression OR estimate for missense variant carriers
  4. d Mixture model odds ratio and 95% confidence interval for missense variant carriers
  5. e Alpha: estimated proportion of risk associated missense variants
  6. f 95% confidence interval for alpha
  7. g CADD quintiles 1–4 includes all CADD score values ≤ 3.736542; CADD quintile 5 includes all CADD score values > 3.736542
  8. h Missense variant odds ratio constrained to equal odds ratio for protein truncating variants
  9. i Missense variant odds ratio unconstrained
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Genome Medicine

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