Table 2 NIPS cSMART assay results for concordant (selected) and discordant samples

From: A quantitative cSMART assay for noninvasive prenatal screening of autosomal recessive nonsyndromic hearing loss caused by GJB2 and SLC26A4 mutations

Sample

cSMART assay

NIPS

IPS

 

Parental mutations

Mutation/Total reads

Mutation ratio

FF (%)

Input cfDNA per assay (ng)

GA (w)

  

Selected concordant samples for each of the seven possible fetal genotypes

 K002

c.2168A>G (M+P)

883/1738

50.81%

8.86

25.64

21

c.2168A>G (het) (A1a1)

c.2168A>G (het) (A1a1)

 K015

c.235delC (M+P)

914/1973

46.33%

8.01

29.89

17

Normal (hom) (A1A1)

Normal (hom) (A1A1)

 K019

c.919-2A>G (M+P)

953/1699

56.09%

11.09

32.93

19

c.919-2A>G (hom) (a1a1)

c.919-2A>G (hom) (a1a1)

 K029

c.589G>A (M)

1529/3048

50.16%

6.35

50.63

19

c.589G>A (het) c.2168A>G (het) (a1a2)

c.589G>A (het) c.2168A>G (het) (a1a2)

 

c.2168A>G (P)

60/2643

2.27%

     

 K062

c.299_300delAT (M)

876/1750

50.06%

10.82

15.23

19

c.299_300delAT (het) (a1A2)

c.299_300delAT (het) (a1A2)

 

c.235delC (P)

0/1545

0.00%

     

 K075

c.919-2A>G (M)

781/1734

45.04%

12.01

36.25

18

c.1544+9C>T (het) (A1a2)

c.1544+9C>T (het) (A1a2)

 

c.1544+9C>T (P)

33/687

4.80%

     

 K080

c.299_300delAT (M)

891/1942

45.88%

10.07

33.94

19

Normal (hom) (A1A2)

Normal (hom) (A1A2)

 

c.176del16 (P)

0/972

0.00%

     

Discordant samples (n=7)

 K005

c.919-2A>G (M)

580/1069

54.26%

8.21

24.38

17

c.919-2A>G (hom) (a1a1)

c.919-2A>G (het) (a1A2)

 

c.2168A>G (P)

0/992

0.00%

     

 K050

c.427C>T (M)

935/1999

46.77%

5.49

36.65

18

c.299_300delAT (het) (A1a2)

c.427C>T (het) c.299_300delAT (het) (a1a2)

 

c.299_300delAT (P)

41/2016

2.03%

     

 K052

c.919-2A>G (M)

1161/2241

51.81%

5.87

31.39

18

c.919-2A>G (hom) (a1a1)

c.919-2A>G (het) (a1A2)

 

c.1174A>T (P)

0/1663

0.00%

     

 K074

c.235delC (M)

442/943

46.87%

5.00

25.19

18

c.299_300delAT (het) (A1a2)

c.299_300delAT (het) c.235delC (het) (a1a2)

 

c.299_300delAT (P)

36/1448

2.49%

     

 K078

c.299_300delAT (M)

847/1735

48.82%

5.52

44.15

17

c.299_300delAT (het) (a1A2)

Normal (hom) (A1A2)

 

c.235delC (P)

1/1631

0.06%

     

 K095

c.299_300delAT (M)

598/1101

54.31%

9.75

27.78

17

c.299_300delAT (hom) (a1a1)

c.299_300delAT (het) (a1A2)

 

c.235delC (P)

0/877

0.00%

     

 K097

c.1327G>C (M)

808/1703

47.45%

5.24

26.00

17

c.919-2A>G (het) (A1a2)

c.1327G>C (het) c.919-2A>G (het) (a1a2)

 

c.919-2A>G (P)

39/1908

2.04%

     
  1. cfDNA, cell-free DNA; cSMART, circulating single-molecule amplification and resequencing technology; FF, fetal DNA fraction; GA, gestational age; het, heterozygous; hom, homozygous; IPS, invasive prenatal screening; M, maternal; NIPS, noninvasive prenatal screening; P, paternal.
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