Long-read genome and RNA sequencing resolve a pathogenic intronic germline LINE-1 insertion in APC

Area of Science:

• Genomics
• Molecular Biology
• Human Genetics

Background:

• Familial Adenomatous Polyposis (FAP) is a hereditary condition linked to the APC tumor suppressor gene.
• Previous diagnostic methods like gene panels and exome sequencing failed to confirm FAP in a multigenerational family.

Purpose of the Study:

• To identify the genetic cause of FAP in a family where standard sequencing failed.
• To demonstrate the utility of long-read genome sequencing for complex genetic variants.

Main Methods:

• Long-read (PacBio) and short-read (Illumina) genome sequencing were employed.
• Short-read RNA sequencing and targeted RNA analysis were performed.
• Variant segregation analysis was conducted across multiple family members.

Main Results:

• A 6kb LINE-1 element insertion within an APC intron was identified using long-read sequencing.
• This insertion caused aberrant splicing, leading to a pseudo-exon and premature stop codon.
• The identified variant segregated with the FAP phenotype in the family.

Conclusions:

• Long-read genome sequencing is effective in resolving complex intronic variants missed by short-read technologies.
• Combined DNA and RNA sequencing approaches are valuable for diagnosing unsolved hereditary diseases like FAP.
• This study highlights the importance of advanced sequencing for accurate genetic diagnosis.