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Table 2 The details of clinically significant copy number variations in the fetuses with ultrasound anomalies

From: Clinical utility of array comparative genomic hybridisation in prenatal setting

Case number Ultrasound findings aCGH results CNV size CNV classificationa Related syndrome/gene or literature and comments
1 Structural heart anomaly, Hydrops arr[hg19] 1p36.33p36.31(779,727–6,377,318)x1 dn 5,8 Mb P 1p36 deletion syndrome (OMIM#607872)
2 Bilateral radial aplasia arr[hg19] 1q21.1q21.2(145,415,190–145,799,602)x1 mat 385 kb P* TAR syndrome (OMIM#274000)
3 Bilateral radial aplasia arr[hg19] 1q21.1q21.2(145,415,190–145,799,602)x1 385 kb P* TAR syndrome (OMIM#274000)
4 Oral cleft, Contractures of the large joints arr[hg19] 1q21.1q21.2(146,507,518–147,379,946)x1 mat, 4q35.2(189,247,673–190,552,305)x1 pat 872 kb
1,3 Mb
Likely B
1q21.1 deletion syndrome (OMIM#612474), including GJA5 gene
5 Spina bifida, hydrocephalus, polydactyly arr[hg19] 2p25.3p22.1(23,938–41,524,241)x3 41,5 Mb P Derived from maternal balanced translocation
6 Cystic hygroma arr[hg19] 2p16.3(51,109,690–51,251,557) × 1 141,8 kb SF, P** NRXN1 gene (OMIM*600565)
7 IUGR arr[hg19] 2q13(111,442,130–113,065,779) × 1 pat 1,6 Mb VOUS 2q13 deletion syndrome [21, 22]
8 Ventriculomegaly, ACC arr 2q33.3q35(208,814,372–219,814,526)x3 dn 11 Mb P De novo, many genes
9 Upper limb anomalies arr[hg19] 5p13.2(36,952,801–37,024,752)x1 dn 72 kb P CdL syndrome (OMIM#122470)
10 Multiple congenital anomalies arr[hg19] 6p25.3p25.1(206,749–5,507,458) × 3 dn 5,3 Mb P ORPHA1745
11 Ambiguous genitalia (karyotype 46,XY) arr[hg19] 9p24.3(220,253–1,999,170)x1 mat 1,7 Mb P 9p24.3 deletion syndrome, 46,XY sex reversal (OMIM#154230)
12 Multicystic kidney arr[hg19] 15q11.2(22,765,628–23,217,514) × 1 mat 452 kb VOUS 15q11.2 risk factor locus, inherited from the mother with mild learning diffuculties
13 Cystic higroma, IUGR arr[hg19] 15q13.2q13.3(30,653,877–32,861,626) × 3 dn 2,2 Mb LP 8 OMIM genes, DECIPHER cases
14 Pyelectasis, short femur arr[hg19] 16p13.3(1,917,269–2,527,114) × 3 pat 610 kb VOUS Inherited from healthy father
15 Multiple congenital anomalies arr[hg19] 16p13.12p11.2(14,145,698–29,331,350) × 3 dn 15,2 Mb P De novo, many genes
16 IUGR, multicystic kidney arr[hg19] 16p12.2(21,837,492–22,407,931) × 1 mat 570 kb SF, P** 16p12.1 deletion syndrome (OMIM#136570)
17 Multiple congenital anomalies arr[hg19] 16p11.2(29,592,783–30,190,568) × 3 dn 610 kb SF, P** 16p11.2 duplication syndrome (OMIM#614671)
18 Bilateral pes equinovarus arr[hg19] 16p11.2(29,673,954–30,190,568) × 1 pat 516 kb SF, P** 16p11.2 deletion syndrome (OMIM#611913)
19 Vertebral anomalies, scoliosis arr[hg19] 16p11.2(29,673,954–30,190,568) × 1 516 kb SF, P** 16p11.2 deletion syndrome (OMIM#611913)
20 Increased NT arr[hg19] 16q24.1(86,211,031–86,649,743) × 1 dn 439 kb P FOXF1 (OMIM*601089)
21 Occipital meningocele arr[hg19] 18p11.32p11.21(148,963–14,081,887) × 4 dn 13,9 Mb P 18p tetrasomy (OMIM#614290)
22 Increased NT arr[hg19] 20p13(60,747–748,964) × 1, 20q13.13q13.33(47,912,240–62,880,583) × 3 688 kb
15,0 Mb
P Derived from paternal inversion of chromosme 20
23 Bilateral cleft lip and palate arr[hg19] 22q11.21(20,659,547–21,440,514)x3 pat 781 kb SF, P** Atypical 22q11.2 duplication syndrome (OMIM#608363)
24 Hypoplastic nasal bone, cystic formation in abdomen arr[hg19] Xp22.31(6,488,721–8,097,511) × 2 mat (male fetus) 1,6 Mb VOUS Xp22.31 duplication [23]
25 Complex structural heart anomaly arr[hg19] Xq13.3(74,463,757–74,651,249) × 3 (female fetus) 188 kb VOUS ZDHHC15(OMIM*300576)
  1. aP-pathogenic, VOUS –variant of unknown significance, B - benign, SF - secondary finding; P*hypomorphic nucleotide change on the second allele; P**-microdeletion/microduplication with reduced penetrance; IUGR – in utero growth restriction, ACC – agenesis of corpus callosum