Characterization and Genomic Localization of a SMAD4 Processed Pseudogene.

Area of Science:

• Genetics
• Molecular Biology
• Bioinformatics

Background:

• Clinical diagnostic laboratories routinely analyze patient DNA for hereditary cancer genes using high-throughput sequencing.
• Accurate variant calling is crucial, but rare nonpathogenic variants can interfere with diagnostic results.

Purpose of the Study:

• To investigate a nonpathogenic variant initially identified as a SMAD4 deletion in cancer predisposition testing.
• To characterize the nature and origin of the identified SMAD4 processed gene and its impact on diagnostics.

Main Methods:

• Analysis of a cohort of 2042 cancer-predisposed individuals.
• Whole-genome sequencing and Sanger sequencing of junction PCR products.
• Comparison with reference SMAD4 mRNA sequence.

Main Results:

• Five individuals were found to carry a SMAD4 processed gene, not a pathogenic deletion.
• The SMAD4 processed gene was integrated at a specific locus on chromosome 9 in all affected individuals, indicating a single ancestral retrotransposition event.
• The processed gene has truncated untranslated regions but an unaltered open reading frame.

Conclusions:

• A rare SMAD4 processed gene can be mistaken for a pathogenic deletion in hereditary cancer diagnostics.
• Utilizing RNA-seq aligners in diagnostic assay quality assurance can facilitate the automated recognition of processed pseudogenes, enhancing diagnostic accuracy.