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Table 4 Practical performance comparison between fetal genome recovery methods

From: Haplotype-assisted accurate non-invasive fetal whole genome recovery through maternal plasma sequencing

Category Current study Kitzman et al. Fan et al.
    Trio I1 Trio G1 P1T1 P1T2 P2T3
Gestational week 13 18.5 8.14 9 29 39
Estimated average cff-DNA concentration 5.69% 13%a 6%a 6%a 16%a 30%a
Average sequence depth (fold) 43.91 78a,b 56a,b 52.7 20.8 10.7
Fetal gender Male Male - Female Female Female
Maternal allele       
Predicted rate 100% 91.4% - >99.2%
Predictionaccuracy 95.37% (autosome)
98.45% (ChrX)
- - >99.8%
Paternal allele     
Predicted rate 100% - - 71.60% 72.84% 72.94%
Prediction accuracy 98.57% - - 93.79% 95.84% 96.56%
Accuracy of inferred fetal genotype       
Autosome Paternal-only heterozygous 99.12%, n = 65,409 96.8% 60.3% - - -
  Maternal-only heterozygous 95.84%, n = 66,238 99.3%c 95.7%c - - -
  Biparentally heterozygous 94.90%, n = 41,849 98.7%d 91.3%d - - -
ChrX Maternal-only heterozygous 98.45%, n = 1,932 - - - - -
  1. - = No data
  2. aApproximate.
  3. bNon-duplicate.
  4. cEstimated based on maternal phased sites.
  5. dAccuracy of transmitted maternal allele prediction, estimated based on maternal phased sites.