Re-Analysis on GRCh38 with the MANE Select Transcript Resolves Previously Undetected Biallelic ODAD4 Variants in...

Molecular diagnosis is highly sensitive to the human genome assembly used in a bioinformatics pipeline. Panels designed on GRCh37 (hg19) inherit its exon annotation, whereas transcript standards and interpretation databases are anchored to GRCh38 (hg38); a coding exon absent from GRCh37 can therefore be neither targeted nor analyzed. We describe two unrelated individuals with primary ciliary dyskinesia (PCD) in whom first-line, GRCh37-based panel sequencing was non-diagnostic. Both were re-analyzed on GRCh38 against the Matched Annotation from NCBI and EMBL-EBI (MANE) Select transcript. In Patient 1 (OP-880 II1), trio whole-genome sequencing identified a homozygous frameshift variant (NM_031421.5:c.1157del, p.(Lys386ArgfsTer52)) in exon 9 of ODAD4 (previously TTC25), an exon not represented in GRCh37. In Patient 2 (OP-4121 II1), the panel detected only c.100C>T, p.(Gln34Ter); Sanger sequencing of exon 9 disclosed NM_031421.5:c.1273C>T, p.(Gln425Ter) in trans. Her cilia were immotile on high-speed video microscopy and lacked outer dynein arms on transmission electron microscopy. Two cases cannot establish frequency, but they identify a remediable failure mode: GRCh37-based pipelines miss GRCh38-defined exons, leaving a recessive genotype apparently monoallelic. Re-analysis on GRCh38 against MANE Select transcripts should be reflexive whenever a strong phenotype yields a negative or monoallelic result, including in previously tested individuals.