Table 1

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

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.

Coordinates are based on GRCh37/hg19.

¥Significance based on a LD map from 224 local controls.

*Overlapping regions are indicated by an asterisk.

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.

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.

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.

Genomewide suggestive signals are indicated in bold. Borderline genomewide suggestive signals are bold and italicized.

Cai et al.

Cai et al. BMC Genomics 2012 13:676   doi:10.1186/1471-2164-13-676

Open Data