Alpha-1-antitrypsin molecular testing in Canada: A seven year, multi-centre comparison

Accurate identification of alpha-1-antitrypsin deficiency requires reliable diagnostic methods. Prior research has shown that serum concentration testing can flag potential cases, but it does not confirm pathogenic variants. No prior work had resolved how different diagnostic protocols compare in detecting rare or complex variants. This gap motivated a multi-centre study to assess protocol comprehensiveness and efficiency. The study aimed to evaluate how variant detection rates differ across diagnostic approaches. It was already known that the ZZ genotype is easily identifiable, but other variants remain less understood. The study focused on how diagnostic strategies impact detection rates of pathogenic and undefined variants. Variability in regional patient demographics may affect protocol performance. The goal was to determine which diagnostic methods best detect rare and compound heterozygous genotypes.

The study aimed to compare the effectiveness of four diagnostic protocols in detecting pathogenic variants of alpha-1-antitrypsin deficiency. It sought to determine which methods most efficiently identify rare and compound genotypes. The specific problem addressed was the variability in protocol design and detection rates across diagnostic centers. The motivation was to identify the most comprehensive and efficient approach for diagnosing A1AT deficiency. The study focused on how different diagnostic steps influence variant detection rates. It aimed to assess whether certain protocols miss rare variants or produce more undefined results. The goal was to inform clinical practice by evaluating protocol performance. The study sought to highlight the trade-offs between detection comprehensiveness and diagnostic clarity.

The study analyzed data from four Canadian clinical laboratories over seven years. Each lab used a distinct diagnostic protocol for A1AT deficiency. The BC-CGID protocol combined serum concentration, genotyping, IEF, and DNA sequencing. The AB-CID protocol used serum concentration, IEF, and DNA sequencing. The ON-CD protocol used serum concentration and DNA sequencing. The QC-G protocol used genotyping alone. Patient data from British Columbia, Alberta, Ontario, and Québec were reviewed. The catchment areas varied in size and ethnic composition. The study compared genotype detection rates relative to the ZZ genotype. It assessed detection rates of pathogenic, undefined, and likely benign variants.

Collectively, 5399 patients were tested, identifying 396 ZZ genotypes. Serum concentration testing efficiently flagged cases for further analysis. The ON-CD protocol detected the highest rate of pathogenic variants at 0.67 per ZZ genotype. It also detected the most undefined and likely benign variants at 0.16 and 0.08 per ZZ, respectively. The F variant was identified only in ON-CD and AB-CID protocols at 0.10 per ZZ. The M_Malton variant was detected as a compound heterozygous genotype in ON-CD and BC-CGID protocols at 0.04 per ZZ. Other protocols detected fewer pathogenic and rare variants. ON-CD had higher detection rates but also more undefined results.

The study found that protocols detecting variants across the full SERPINA1 coding sequence identify more pathogenic and rare variants. ON-CD had the highest detection rates but also higher rates of undefined and likely benign variants. The BC-CGID and AB-CID protocols detected fewer rare variants but produced fewer undefined results. The QC-G protocol had the lowest detection rates for non-ZZ genotypes. The study suggests that comprehensive DNA sequencing improves detection of complex genotypes. It also highlights the trade-off between detection breadth and diagnostic clarity. The findings support the use of protocols that include full coding sequence analysis. The authors propose that detection comprehensiveness should be balanced with diagnostic specificity.