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Table 1 Copy Number Variations in the Qatari Populationa

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

Parameter Total by parameter Homozygous deletions (CN 0) Heterozygous deletions (CN 1) Total deletions Duplications (CN 3) Amplifications (CN 4+) Total duplications/amplifications Total polymorphic CNVRs Total size of all non-overlapping CNVRs in the subpopulation
Array Data
QSNP 56,135 7,435 23,497 30,932 16,767 8,436 25,203 - -
CNVPart 16,895 1,026 3,906 4,932 9,527 2,436 11,963 - -
Sequencing Data
cn.MOPS 100,026 2,097 32,098 34,195 50,080 15,751 65,831 - -
IL-NGS 363,833 - 49,177 49,177 213,435 101,221 314,656 - -
Total CNVs by CN Class 536,889 10,558 108,678 119,236 289,809 127,844 417,653 - -
CNVs per individual
Average/individual 1,824 120 628 748 801 275 1,076 - -
Median/individual 1,815 121 622 743 801 271 1,072 - -
Average size by class/individual 29,934,170 1,131,273 5,928,199 7,059,472 18,400,102 4,474,596 22,874,698 - -
Median size by class/individual 27,911,587 1,087,616 5,787,942 6,875,558 16,889,655 4,146,374 21,036,029 - -
CNV Regions (CNVRs) by genetic subpopulation
Q1 5,241 149 2,534 2,683 1,480 270 1,750 808 85,705,083
Q2 4,176 116 1,909 2,025 1,242 273 1,515 636 65,814,099
Q3 4,641 101 2,283 2,384 1,316 304 1,620 637 65,851,402
Total across subpopulations 14,058 366 6,726 7,092 4,038 847 4,885 2,081 -
Average size of CNVRs within each class 15,462 4,187 8,604 8,376 20,101 10,669 18,457 32,561 -
  1. aFour different algorithms were applied to detect CNVs in 97 individuals. For analysis of the Illumina Omni2.5 M Array Data, QuantiSNP (QSNP) [27] and Illumina’s cnvPartition (CNVPart) were used; for next-generation-sequencing (NGS) genomic data, cn.MOPS (CNMOPS) [28] was used with additional CNV calls provided by Illumina’s genome-sequencing service (IL-NGS). Shown are the numbers of CNVs detected by each algorithm in each copy number class, along with the total number of CNVs detected by copy number (CN) class and by CNV platform. CN (Copy number) class 0 = homozygous deletions; CN 1 = heterozygous deletions; CN 3 = single-allele duplication; CN 4 + = amplifications. Total deletions and duplications are a sum of CN classes 0, 1 and 3, 4+, respectively. Total CNVs and size are shown by platform and by class. As expected, array-based methods generated fewer but larger CNVs, whereas NGS based methods generated more but, on the average, smaller CNVs. The number of CNVs per individual is shown for the average and median individual amongst 97 individuals who passed the QC. CNV counts are shown by CN class. Additionally, the size of genomic content that is altered by CNVs in each CN class in the average and median individuals are provided. As described in Methods, these CNVs were merged across individuals within the same subpopulation to arrive at subpopulation level CNV Regions (CNVRs). The number of CNVRs within each subpopulation is given for each CN class, and the size of the average CNVR within each class is also shown. Within a population, there are sites that sometimes contain both deletions and duplications in different individuals; these are tallied in a column labeled ‘polymorphic’ CNVRs and represent about 15 % of all CNVRs within a given population. Finally, the total size of all non-overlapping CNV regions within each subpopulation is shown in the last column. The 3 genetic subpopulations are Q1 (Bedouin ancestry, n = 57), Q2 (Persian/South Asian ancestry, n = 20), and Q3 (African ancestry, n = 20)