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 |