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Table 3 Discrepant results of fetal CNVs detected by NIPS and CMA

From: Clinical evaluation of non-invasive prenatal screening for the detection of fetal genome-wide copy number variants

Case

NIPS

Prenatal diagnosis

Pregnancy outcome

Result

Size (Mb)

Z-score

Fetal fraction

Unique reads (Mb)

Result

Size (Mb)

Syndrome

Type

1

gain(2q14.1-q21.1)(114,500,000–130,999,999)

16.5

11.15

10.05

3.03

arr[GRCh37] 2q31.1q33.3(175,042,562–206,347,968)x2hmz

31.0

LOH

Birth

gain(2q35-q37.3)(216,500,000–237,999,999)

21.5

arr[GRCh37] 2q11.1q13(95,550,957–114,045,382) × 2 hmz

18.5

LOH

gain(2p25.3-p24.1)(500,000–20,499,999)

20.0

arr[GRCh37] 2p15p11.2(62,680,101–87,053,152) × 2 hmz

24.4

LOH

2

gain(5p15.33)(0–1,999,999)

2.0

0.71

13.97

3.86

arr[GRCh37] 5p13.2p13.1(36,902,395–38,963,081) × 3

2.0

5p13 microduplication syndrome

P

TOP

3

gain(9q33.3-q34.3)(129,000,000–140,499,999)

11.5

4.62

8.67

2.48

arr[GRCh37] 9q31.1q33.1(107,923,508–121,624,320) × 3

13.7

VUS

Birth

4

gain(16q23.1)(76,000,000–78,999,999)

3.0

4.18

10.23

2.16

arr[GRCh37] 16q23.1q24.3(78,969,980–90,146,366) × 2 hmz

11.0

LOH

Birth

arr[GRCh37] 16p13.3p12.3(94,807–19,500,124) × 2 hmz

19.0

LOH

5

gain(16q23.1)(76,500,000–78,499,999)

2.0

0.47

13.58

2.82

arr[GRCh37] 16p13.11(14,900,042–16,278,133) × 3

1.4

LP

TOP

  1. LOH Loss of heterozygosity, P Pathogenic, LP Likely pathogenic, VUS Variants of uncertain significance, TOP Termination of pregnancy, Genome build GRCh37