AGL gene sequencing is performed using the Genetic Diagnostic Sequencing Test. The Genetic Diagnostic Sequencing Test is intended to detect genetic variants in genes known to be associated with various genetic diseases patient samples. Genetic variant information is used to confirm a clinical or biochemical diagnosis. A specific diagnosis informs medical management and prognosis as well as allowing for appropriate counseling of family members.

[Swedac test name: AGL Genotyping]

Sequence analysis of the gene(s) of interest was performed by next-generation sequencing on the Element AVITI system. Alignment to the human reference genome (GRCh37) is performed and annotated variants are identified in the targeted region.

Variants reviewed have an alternate allele frequency of 20% or higher. A base is considered to have sufficient coverage at 20X and an exon is considered fully covered if all coding bases plus three nucleotides of flanking sequence on either side are covered at 20X or more. This analysis cannot detect variants in regions not analyzed such as promoters or deep intronic regions.

Copy number variation (CNV) analysis detects deletions and duplications; in some instances, due to the size of the exons, sequence complexity, or other factors, not all CNVs may be detected. When reported, copy number variant size is approximate. Actual breakpoint locations may lie outside of the targeted regions.

This assay is not designed to detect mosaicism; possible cases of mosaicism may be investigated at the discretion of the laboratory director. Data analysis is performed using the Revvity Omics AWS NGS (ROAN) Software System version 2.1.