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Table 1 Regions with at least nominal evidence in pSGS (p≤0.05)

From: Pairwise shared genomic segment analysis in three Utah high-risk breast cancer pedigrees

Pedigree (number cases; min. possible sharing)†

Chromosome

Region€

Length (Mb)

pSGS p-value¥

Average cases sharing (range)

SGS

Linkage

1

4*

37,542,764 - 54,575,432

17.0

0.0060

4.78 (3–5)

0.00017

1.19

(n=5; min=3)

7*

16,704,212 - 31,213,647

14.5

0.0050

4.83 (3–5)

0.00010

2.62

 

8

38,344,499 - 122,638,989

83.3

0.0025

4.78 (3–5)

0.000018

1.55

 

10

28,738,098 - 49,576,878

20.8

0.019

4.78 (3–5)

0.0020

1.25

 

14*

66,272,834 - 77,581,481

11.3

0.040

4.78 (3–5)

0.029

1.19

 

16

359,567 - 8,197,462

7.8

0.041

4.76 (3–5)

0.009

1.03

 

17

10,784,088 - 16,883,680

6.1

0.019

4.81 (3–5)

0.0015

1.30

3

2

74,758,934 - 162,960,873

88.2

0.0040

9.41 (6–10)

0.00014

1.66

(n=10; min=5)

4*

47,003,076 - 88,807,556

41.8

0.013

9.44 (5–10)

0.00033

0.89

 

6

31,320,810 - 31,628,733

0.3

0.037

9.60 (7–10)

0.0062

0.19

 

7*

11,358,235 - 96,674,424

85.3

0.0065

9.40 (6–10)

0.00025

1.04

 

12

67,987,630 - 101,376,241

33.4

0.0095

9.44 (6–10)

0.00020

1.27

 

14*

56,883,760 - 99,254,712

42.4

0.0070

9.43 (6–10)

0.00050

0.57

 

17

32,760,735 - 51,072,912

18.3

0.039

9.33 (6–10)

0.0014

0.03

 

18

8,247,249 - 50,460,551

42.2

0.017

9.43 (6–10)

0.0011

1.32

  1. † For each pedigree the total number of cases in the pedigree, and the minimum possible number of cases that can share (i.e. the number of cases sharing cannot go below this value) are shown.
  2. €Coordinates are based on GRCh37/hg19.
  3. ¥Significance based on a LD map from 224 local controls.
  4. *Overlapping regions are indicated by an asterisk.
  5. For pedigree 1, genomewide pSGS thresholds are p=6.5×10-3 and p=3.0×10-4, for suggestive and significance, respectively, and corresponding SGS thresholds are p=1.3×10-4 and p<1.0×10-6.
  6. For pedigree 3, genomewide pSGS thresholds are p=5.0×10-3 and p=2.5×10-4, for suggestive and significance, respectively, and corresponding SGS thresholds are p=3.8×10-5 and p<1.0×10-6.
  7. For linkage, genomewide suggestive and significance LOD thresholds are 1.86 and 3.30, respectively, corresponding to p-values of 1.7×10-3 and 4.9×10-5.
  8. Genomewide suggestive signals are indicated in bold. Borderline genomewide suggestive signals are bold and italicized.