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Table 2 Functional Annotation of CNV Regions in the Qatari Genetic Subpopulationsa

From: Copy number variations in the genome of the Qatari population

   Total number Nongenic Genic miRNA Genic affecting Mendelian disease genes # Mendelian genes affected Overlap DGV Novel Novel genic Promoter site Transcription factor binding site
Q1 –  0 – homozygous deletions 341 228 113 2 8 8 322 19 7 20 127
   1 – heterozygous deletions 3,316 2,151 1,165 19 76 83 3,091 225 97 248 1,321
   3 – duplication 2,161 1,121 1,040 196 182 223 2,045 116 48 509 980
   4 – amplification 463 290 173 12 18 18 445 18 5 54 145
Sub-total Q1 6,281 3,790 2,491 229 284 332 5,903 378 157 831 2,573
Q2 –  0 – homozygous deletions 293 183 110 1 11 11 287 6 1 14 109
   1 – heterozygous deletions 2,470 1,598 872 15 65 70 2,350 120 53 172 879
   3 – duplication 1,760 913 847 156 124 157 1,694 66 28 409 748
   4 – amplification 434 268 166 11 17 17 422 12 5 52 143
Sub-total Q2 4,957 2,962 1,995 183 217 255 4,753 204 87 647 1,879
Q3 –  0 – homozygous deletions 267 174 93 0 18 8 262 5 2 16 101
   1 – heterozygous deletions 2,858 1,902 956 13 61 65 2,726 132 45 176 1,046
   3 – duplication 1,835 977 858 148 122 141 1,754 81 29 407 772
   4 – amplification 462 284 178 19 23 24 443 19 9 61 146
Sub-total Q3 5,422 3,337 2,085 180 224 238 5,185 237 85 660 2,065
Total 16,660 10,089 6,571 592 725 825 15,841 819 329 2,138 6,517
  1. aCNVRs were annotated as described in Methods. Distribution of CNVs is summarized by CN class within each subpopulation and by functional class including: Total number = all CNVRs detected; nongenic = CNVRs that do not overlap coding regions; genic = CNVRs that overlap genes; miRNA = CNVRs that overlap microRNAs; Mendelian disease genes = CNVRs that include at least 1 known Mendelian disease gene; DGV = CNVRs that overlap a known CNV from the database of genomic variants; novel = CNVRs that do not overlap known CNVs and are unique to Qataris; novel genic = the subset of novel CNVRs that overlap at least 1 gene; promoter site = CNVRs that overlap promoter elements; transcription factor site = CNVRs that overlap at least 1 transcription factor site. Total for each subpopulation is a sum of deletions and duplications in each subpopulation