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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