Skip to main content

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