Novel ITPA variants identified by whole genome sequencing and RNA sequencing

Area of Science:

• Genetics
• Genomics
• Molecular Biology

Background:

• Most rare diseases have genetic origins, necessitating accurate genetic diagnoses for effective management and counseling.
• Whole-exome sequencing (WES) is a common genetic diagnostic tool, but it frequently leaves cases undiagnosed.

Purpose of the Study:

• To identify pathogenic variants in an unsolved rare disease case that remained undiagnosed by WES.
• To evaluate the combined utility of whole genome sequencing (WGS) and RNA sequencing (RNA-seq) for diagnosing complex genetic conditions.

Main Methods:

• Whole-exome sequencing (WES) was initially performed.
• Whole genome sequencing (WGS) and RNA sequencing (RNA-seq) were subsequently employed to analyze the unsolved case.
• Breakpoint analysis was conducted to elucidate the mechanism of a novel deletion.

Main Results:

• RNA sequencing revealed aberrant splicing in exons 4 and 6 of the ITPA gene.
• Whole genome sequencing identified a novel splicing donor variant (c.263+1G>A) and a heterozygous deletion encompassing exon 6 in ITPA.
• The deletion was found to result from Alu element recombination, causing developmental and epileptic encephalopathies in the proband.

Conclusions:

• The combination of WGS and RNA-seq offers a powerful strategy for diagnosing rare genetic diseases that are refractory to WES.
• This integrated approach can uncover complex variants, including splicing defects and deletions, leading to definitive diagnoses.
• Accurate genetic diagnosis through advanced sequencing techniques is crucial for understanding and managing rare inherited disorders.