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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)
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BMC Genomics

ISSN: 1471-2164

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