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Table 3 Comparison of fetal genome recovery methods

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

Category

Current study

Kitzmanet al.

Fan et al.

Parental haplotype inference

Method for parental haplotype construction

Trio strategy with corresponding grandparents and CHS

Maternal: fosmid-based approach [26]

Paternal: could not be assessed due to lowmolecular weight of saliva DNA

Maternal: single-cell approach [27]

Paternal: not collected

Strategy for fetal genome recovery

Paternalallele

Two different alleles of fetal haplotype, transmitted from the two parents, were reconstructed by a HMM model in one step, including transmitted chromosomes and recombination breakpoints

SBSS

SBSS+ imputation

Maternal allele

 

For maternal-only heterozygous sites, they used AIEto determine whole-block transitions and HMM to identify assembly errors and recombination breakpoints. For biparentally heterozygous sites, maternal alleles were determined by maternal-only heterozygous sites within the same block

Allele imbalance estimated by counting nucleotides specific to each of the two maternal alleles

Recovery of fetal genome

Genotype

Yes

Yes

Yes

Haplotype

Yes

No

No

De-novo mutation

No

Yes

No