Haplotype Phasing of Biallelic WNT10B Variants Using Long-Read Sequencing in Split-Hand/Foot Malformation Syndrome

Area of Science:

• Genetics
• Developmental Biology
• Medical Science

Background:

• Split-hand/foot malformation (SHFM) is a congenital limb defect with diverse genetic causes.
• WNT10B gene variants are associated with autosomal recessive SHFM.
• Genetic heterogeneity complicates diagnosis and understanding of SHFM.

Purpose of the Study:

• To identify the genetic basis of SHFM in a patient with unrelated parents.
• To characterize novel WNT10B variants using advanced sequencing techniques.
• To demonstrate the utility of long-read sequencing for variant phasing in recessive disorders.

Main Methods:

• Whole-genome sequencing using long-read PacBio technology.
• Identification and characterization of compound heterozygous missense variants in the WNT10B gene.
• Haplotype phasing to determine variant allelic status without parental DNA.

Main Results:

• A patient was diagnosed as a compound heterozygote for two WNT10B missense variants: p.(Arg332Trp) and a novel variant, p.(Phe213Cys).
• Long-read sequencing enabled successful phasing, confirming the variants were on different alleles.
• The p.(Phe213Cys) variant was novel and not found in population databases like gnomAD.

Conclusions:

• WNT10B variants can cause autosomal recessive SHFM through compound heterozygosity.
• Long-read haplotype phasing is a valuable tool for diagnosing recessive genetic conditions, especially when parental samples are unavailable.
• This study expands the known genetic spectrum of SHFM and highlights WNT10B's role.