Identification of copy number variations among fetuses with isolated ultrasound soft markers in pregnant women not of advanced maternal age

Liu, Yunyun; Liu, Sha; Liu, Jianlong; Bai, Ting; Jing, Xiaosha; Deng, Cechuan; Xia, Tianyu; Cheng, Jing; Xing, Lingling; Wei, Xiang; Luo, Yuan; Zhou, Quanfang; Xie, Dan; Xiong, Yueyue; Liu, Ling; Zhu, Qian; Liu, Hongqian

doi:10.1186/s13023-024-03066-4

Orphanet Journal of Rare Diseases

Table 2 Details of confirmed fetal CNVs with positive and negative NIPS results

From: Identification of copy number variations among fetuses with isolated ultrasound soft markers in pregnant women not of advanced maternal age

Sample number	Maternal age	Gestational age-weeks	USM	Maternal serum screening	hg19 co-ordinates (NIPS)	Type	Size	Z-score of CNV	Confirmatory method	Confirmatory results	ACMG Classification	Inherited or de novo	Agreement with NIPS	Outcomes
14	31	23 ⁺⁴	EIF	Low-risk	trisomy13	trisomy	–	–	CNV-seq	delXp21.1 (0.32 Mb)	P	NA	Discordant	TOP
38	32	22 ⁺⁴	EIF	Low-risk	chr13:51500000–55999999	Dup	4.5 Mb	2.25	CNV-seq	del15q11.2 (0.36 Mb)	P	NA	Discordant	TOP
39	30	17 ⁺⁴	EIF	NA	chr16:15500000–17999999	Del	2.5 Mb	− 9.22	CNV-seq	del16p13.11p12.3 (2.66 Mb)	P	NA	Concordant	TOP
40	29	23 ⁺⁴	EIF	Low-risk	chr16:15500000–18499999	Dup	3.0 Mb	7.14	CMA	del16p13.11p12.3	P	NA	Concordant	TOP
41	29	17 ⁺⁶	ARSA	NA	chr10:49500000–52499999	Del	3.0 Mb	− 9.95	CNV-seq	del2q37.3 (4.29 Mb) del10q11.22q11.23 (2.57 Mb)	P/VUS	de novo/Mat	Partially concordant	Birth with defects:congenital anorectal malformation, congenital heart disease, mild ventriculomegaly
42	21	24	EIF	NA	chr5:101500000–110999999	Dup	9.5 Mb	8.96	CNV-seq	dup5q21.1q22.1 (9.11 Mb)	VUS	Mat	Concordant	TOP
43	32	23 ⁺³	EIF	Low-risk	chr13:88500000–91999999	Del	3.5 Mb	− 7.54	CNV-seq	del13q31.2q31.3 (2.54 Mb)	VUS	NA	Concordant	Neonates with no phenotypical abnormalities
44	27	25	EIF	NA	chr8:3500000–6999999	Dup	3.5 Mb	6.22	CNV-seq	dup8p23.2 (2.34 Mb)	VUS	Mat	Concordant	Neonates with no phenotypical abnormalities
45	31	22 ⁺³	EIF	Low-risk	chr3:0–2499999	Dup	2.5 Mb	7.24	CNV-seq	dup3p26.3 (1.44 Mb)	VUS	NA	Concordant	Neonates with no phenotypical abnormalities
46	25	26 ⁺⁶	EIF	Low-risk	chr1:100000000–105999999	Dup	6.0 Mb	2.07	CNV-seq	dup1p21.2p21.1 (7.18 Mb)	VUS	NA	Concordant	Neonates with no phenotypical abnormalities
47	24	23 ⁺²	EIF	Low-risk	chr2:78500000–80499999	Dup	2.0 Mb	8.13	CNV-seq	dup2p12 (1.68 Mb)	VUS	Mat	Concordant	Neonates with no phenotypical abnormalities
48	29	27	EIF	Low-risk	chr3:0–3499999	Dup	3.5 Mb	2.73	CMA	dup3p26.3p26.2 (3.24 Mb)	VUS	NA	Concordant	Neonates with no phenotypical abnormalities
49	27	24 ⁺⁵	EIF	Low-risk	chr8:1500000–3999999	Dup	2.5 Mb	4.98	CNV-seq	dup8p23.3p23.2 (2.26 Mb)	VUS	Mat	Concordant	Neonates with no phenotypical abnormalities
50	25	25 ⁺¹	EIF	NA	chr9:116500000–118999999	Dup	2.5 Mb	5.33	CNV-seq	dup9q32q33.1 (1.42 Mb)	VUS	Mat	Concordant	Neonates with no phenotypical abnormalities
51	25	24 ⁺²	EIF	Low-risk	chr5:124500000–126499999	Dup	2.0 Mb	6.45	CNV-seq	dup5q23.2q23.2 (1.25 Mb)	VUS	NA	Concordant	Neonates with no phenotypical abnormalities
52	23	21	EIF	Low-risk	chr4:188500000–190999999 chr9:120000000–124499999	Del, Del	2.5 Mb,4.5 Mb	− 5.65, − 6.42	CMA	del4q35.2, del9q33.1	VUS	NA	Concordant	Neonates with no phenotypical abnormalities
53	32	25 ⁺⁵	EIF	Low-risk	chr6:120500000–122499999	Del	2.0 Mb	− 6.94	CNV-seq	del6q22.31 (1.34 Mb)	VUS	Mat	Concordant	Neonates with no phenotypical abnormalities
54	24	25	EIF	Low-risk	chr21:44000000–46499999	Dup	2.5 Mb	5.83	CNV-seq	dup21q22.3 (2.58 Mb)	VUS	Mat	Concordant	Neonates with no phenotypical abnormalities
55	29	23 ⁺⁶	EIF	NA	chr21:42000000–43999999	Dup	2.0 Mb	7.47	CNV-seq	dup21q22.2q22.3 (1.56 Mb)	VUS	NA	Concordant	Neonates with no phenotypical abnormalities
56	33	18	CPCs	Low-risk	chr14:25000000–26999999	Dup	2.0 Mb	8.22	CMA	dup14q12	VUS	Mat	Concordant	Neonates with no phenotypical abnormalities
57	26	23	EIF, Mild pyelectasis	Low-risk	chr10:2000000–4499999	Dup	2.5 Mb	6.06	CNV-seq	dup10p15.3p15.2 (1.32 Mb)	VUS	Mat	Concordant	Neonates with no phenotypical abnormalities
58	34	25 ⁺¹	SUA	Low-risk	chr18:0–10999999 chr18:29500000–58499999	Del, Dup	11.0 Mb, 29.0 Mb	− 1.49, 1.12	CNV-seq	dup18p11.22p11.21 (1.8 Mb), dup18q12.1q12.1 (1.32 Mb), dup18q21.33q22.1 (4.9 Mb)	VUS	NA	Partially concordant	TOP
59	29	25 ⁺⁵	EICF	Low-risk	chr2:105000000–106999999	Del	2.0 Mb	− 5.45	CMA	del2q12.1q12.2	VUS	Mat	Concordant	TOP
60	29	25 ⁺¹	ARSA	Low-risk	–	–	–	–	CMA	del16p11.2 (0.60 Mb)	P	NA	Discordant	TOP
61	28	16 ⁺⁶	Mild ventriculomegaly	NA	–	–	–	–	CMA	del12q15q22 (26 Mb)	VUS	NA	Discordant	Birth with moderate ventriculomegaly
62	32	17	SUA	NA	–	–	–	–	CMA	dup5q21.3 (1.43 Mb)	VUS	NA	Discordant	Birth with mild ventriculomegaly

NIPS noninvasive prenatal screening, USM ultrasound soft marker, CNV copy number variant, ACMG American College of Medical Genetics and Genomics, EIF echogenic intracardiac focus, CPCs choroid plexus cysts, SUA single umbilical artery, ARSA aberrant right subclavian artery, CMA Chromosomal microarray, P pathogenic, VUS variant of uncertain significance, Mat maternal, TOP termination of pregnancy, NA not applicable

Back to article page

ISSN: 1750-1172

Contact us

Submission enquiries: Access here and click Contact Us
General enquiries: info@biomedcentral.com