Long-read nanopore sequencing resolves a TMEM231 gene conversion event causing Meckel-Gruber syndrome

Area of Science:

• Genetics
• Genomic Medicine
• Molecular Biology

Background:

• Next-generation sequencing (NGS) has advanced genetic testing for rare inherited disorders.
• Short-read sequencing struggles with accurately detecting gene conversion events.
• Meckel-Gruber syndrome (MKS) is an autosomal recessive disorder with significant genetic complexity.

Purpose of the Study:

• To investigate the genetic basis of Meckel-Gruber syndrome in a family with affected fetuses.
• To evaluate the limitations of short-read sequencing in detecting complex genetic variants.
• To demonstrate the utility of long-read sequencing for accurate genetic diagnosis.

Main Methods:

• Targeted next-generation sequencing (NGS) of MKS-associated genes.
• Comparative read-depth analysis to identify potential deletions.
• Single-molecule long-read sequencing for precise variant detection and phasing.
• Parental segregation analysis to confirm variant inheritance patterns.

Main Results:

• Short-read NGS identified a splice donor variant and an apparent deletion in TMEM231.
• Long-read sequencing revealed four missense variants missed by short-read data due to pseudogene mapping.
• Long reads confirmed the trans-arrangement of variants, clarifying the genetic diagnosis.
• Validation of apparent dosage variants is critical to avoid misdiagnosis.

Conclusions:

• Short-read sequencing has limitations in detecting complex variants like gene conversions.
• Long-read sequencing technologies are valuable tools for accurate genetic diagnostics in clinical settings.
• Robust validation of genetic findings is essential for reliable diagnosis of rare inherited disorders.