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Table 2 Summary of genomic disorder loci CNVs recombination calculations

From: Sex-specific recombination patterns predict parent of origin for recurrent genomic disorders

Locus

CNV type

BED coordinates [7]

# Samples (%)

M:F origin countsa

Del/dup counts

Avg. male recombination rate [106]b

Avg. female recombination rate [106]b

Loge M:F recombination ratio [106]c

1q21.1

Del/Dup

chr1:147101794–147921262

9 (0.46%)

6:3

7/2

0.12331689

0.50839541

− 1.416626

1q21.1 TAR

Del

chr1:145686999–146048495

1 (0.05%)

1:0

1/0

0.15712388

0.77814863

− 1.599883

2q13

Dup

chr2:110625954–112335952

1 (0.05%)

1:0

0/1

0.44854539

1.64377881

− 1.298743

3q29

Del

chr3:195988732–197628732

22 (1.11%)

21:1

22/0

3.1305211

0.27775988

2.422197

5q35

Del

chr5:176290391–177630393

41 (2.07%)

36:5

41/0

1.29955355

0.97941355

0.282822

7q11.23

Del/Dup

chr7:73328061–74727726

618 (31.26%)

296:322

598/20

0.49353554

1.92657023

− 1.361890

8p23.1

Del/Dup

chr8:8235068–12035082

3 (0.15%)

1:2

1/2

0.67201752

1.81857951

− 0.995527

11q13.2q13.4

Del

chr11:67985953–71571306

1 (0.05%)

0:1

1/0

0.8431765

2.23501635

− 0.974828

15q13.3

Del/Dup

chr15:30840505–32190507

6 (0.30%)

5:1

5/1

1.63640726

1.89901039

− 0.148828

15q24 AC

Del

chr15:72670606–75240606

1 (0.05%)

1:0

1/0

0.28479919

0.86129537

− 1.106653

15q24 AD

Del

chr15:72670606–75720604

3 (0.15%)

1:2

3/0

0.27613544

0.82152961

− 1.090277

15q24 BD

Del

chr15:73720606–75720604

1 (0.05%)

0:1

1/0

0.30739967

0.68432207

− 0.800280

15q24 BE

Del

chr15:73720606–77840603

2 (0.10%)

0:2

2/0

0.23485125

0.72623183

− 1.128917

15q25.2

Del

chr15:82513967–84070244

5 (0.25%)

0:5

5/0

0.21225081

0.32633295

− 0.430177

16p11.2

Del/Dup

chr16:29641178–30191178

98 (4.96%)

11:87

79/19

0.06570935

1.28740565

− 2.974798

16p11.2 distal

Del/Dup

chr16:28761178–29101178

4 (0.20%)

0:4

3/1

0.12150949

1.61662624

− 2.600350

16p11.2p12.1

Dup

chr16:21341178–29431178

1 (0.05%)

1:0

0/1

0.5534655

2.68382469

− 1.578799

16p13.11

Del/Dup

chr16:15408642–16198642

2 (0.10%)

1:1

1/1

1.67072378

2.46524529

− 0.389038

17p11.2

Del/Dup

chr17:16805961–20576095

71 (3.59%)

44:27

59/12

0.1888066

1.19115966

− 1.841959

17q11.2

Del

chr17:30838856–31888868

62 (3.14%)

10:52

62/0

0.26024285

1.85442774

− 1.963716

17q12

Del

chr17:36460073–37846263

6 (0.30%

4:2

6/0

0.64750654

3.64754421

− 1.728720

17q21.31

Del/Dup

chr17:45626851–46106851

39 (1.97%)

19:20

35/4

0.38234179

0.98304273

− 0.944338

17q23.1q23.2

Del

chr17:59987857–62227857

2 (0.10%)

0:2

2/0

0.56466054

1.30765625

− 0.839748

22q11.2

Del

chr22:18924718–21111383d

978 (49.47%)

411:567

978/0

1.45946494

3.69205976

− 0.920692

All

Del/Dup

1977 (100%)

870:1107

1913/64

  1. Summarized CNV data. Data are consolidated by locus. BED coordinates correspond to hg38 (LiftOver from hg18 coordinates in Coe et al. [7])
  2. aMale to female CNV parent of origin counts
  3. bAverage male and female recombination rates are the average of the recombination rates calculated for each sample observed for the locus, e.g., 0.123331689 is the average male recombination rate calculated from the male recombination rates of the nine 1q21.1 CNVs
  4. cNatural log-transformed average male to female recombination rate ratio for the locus
  5. dBreakpoints cited by ClinGen for ~ 3.0 Mb LCR22A-LCR22D interval