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Table 1 Description of the three twin pairs and corresponding sequencing statistics

From: Whole genome and exome sequencing of monozygotic twins discordant for Crohn’s disease

  Twin pair 1 Twin pair 2 Twin pair 3
Sex Female Female Female
Age of onset in affected twin 45 19 12
Year of birth 1944 1962 1974
Recruited 2007 2007 2006
Last recontact 2008 2007 2012
  Genomes Exomes Exomes
  Blood CD Biopsy CD Blood healthy Biopsy healthy Blood CD Biopsy CD Blood healthy Biopsy healthy Blood CD Blood healthy Blood CD Blood healthy
Gb coverage 126.70 124.02 143.82 110.28 3.44 3.16 2.47 3.50 3.33 3.29 2.86 2.21
Average coverage 41.92 41.03 47.58 36.49 55.36 50.83 39.81 56.34 72.29 71.58 62.22 47.88
% of genome/exome covered:             
≥ 1× 93.12 93.05 93.04 93.03 97.10 97.17 96.25 96.97 97.28 97.16 96.64 95.36
≥ 8× 90.46 88.95 88.77 90.49 91.48 90.72 89.11 91.82 90.13 89.87 88.91 85.25
≥ 20× 73.29 65.11 67.26 80.82 83.37 79.47 76.78 84.72 80.39 79.87 78.27 71.02
Total number of variants 3,064,772 3,053,010 3,055,001 3,081,680 44,890 44,357 44,928 44,920 29,180 28,985 28,407 27,465
Ti/Tv ratio 2.1 2.1 2.1 2.1 2.6 2.6 2.6 2.6 2.7 2.7 2.7 2.8
NS/S ratio 0.9 0.9 0.9 0.9 0.8 0.8 0.8 0.8 0.9 0.9 0.9 0.9
Total number of SNVs 2,894,614 2,878,835 2,877,807 2,911,350 44,377 43,846 44,426 44,406 28,663 28,542 27,947 27,185
Total number of InDels 170,158 174,175 177,194 170,330 514 512 503 515 517 443 460 280
Synonymous SNVs 9,655 9,630 9,658 9,625 10,168 10,046 10,163 10,205 8,977 8,920 8,678 8,457
Missense SNVs 8,443 8,414 8,425 8,413 8,600 8,488 8,588 8,618 7,668 7,639 7,562 7,369
Nonsense SNVs 64 66 63 65 57 56 57 57 56 58 58 54
Non-frameshift InDels 77 76 78 78 208 208 201 209 205 182 169 111
Frameshift InDels 53 48 54 48 144 142 141 143 296 246 273 162
Stopgain InDels 0 0 0 0 3 3 3 3 0 0 0 0
Splice-site variants 55 56 56 58 96 96 96 98 45 45 49 34
Variants in UTR 208,685 207,740 207,924 209,726 23,714 23,446 23,770 23,685 1,253 1,241 1,195 1,143
Intronic variants 956,711 953,878 954,959 962,132 1,659 1,635 1,667 1,659 10,154 10,127 9,836 9,573
Intergenic variants 1,881,029 1,873,102 1,873,784 1,891,535 242 238 243 244 526 527 587 562
Novel SNVs 54,823 (1.9%) 54,251 (1.9%) 54,372 (1.9%) 55,243 (1.9%) 988 (2.2%) 988 (2.3%) 960 (2.2%) 995 (2.2%) 2,009 (7.0%) 2,023 (7.1%) 1,802 (6.4%) 1,724 (6.3%)
Damaging SNV predictions             
HGMD 57 59 55 59 61 61 61 61 44 43 40 41
SIFT 697 689 697 695 685 686 683 689 674 670 645 630
PolyPhen2 734 731 728 733 765 764 755 767 653 651 648 639
Grantham score 1,442 1,437 1,445 1,439 1,496 1,499 1,477 1,501 1,356 1,355 1,372 1,327
PhyloP 7,753 7,728 7,730 7,757 1,854 1,855 1,837 1,859 1,968 1,964 1,957 1,892
  1. Coverage and variant calls for exomes refer to the corresponding exome target. Ti/Tv ratio: transition/transversion ratio of SNVs; NS/S ratio: nonsynonymous to synonymous ratio of SNVs; SNVs not in dbSNP132 for TP1 (hg19) and dbSNP130 for TP2 and TP3 (hg18) are defined as novel. SNVs predicted to be damaging: “DM” in HGMD (Human Gene Mutation Database Professional, version 2013.3), missense SNVs called as “deleterious” by SIFT, “probably damaging” by PolyPhen2, grantham score above 100 or positions with a phyloP value above 2.5.