GLB1 Gene Test

Mucopolysaccharidosis type IVB is a disease associated with progressive skeletal disease. Age of onset is typically in early childhood with symptoms that include, but are not limited to, short stature, knock knees, skeletal abnormalities of the ribs, chest, spine, hips, and wrists, hypermobile joints, and/or restricted joint movement. Affected individuals have distinct coarse facial features. Life expectancy is reduced, with more severe forms causing death in late childhood. The incidence of mucopolysaccharidosis type IVB is estimated to be ~ 1 in 200,000. GM1-gangliosidosis is a disease that causes progressive central nervous system dysfunction. There are three types: infantile; type II is subdivided into late-infantile form and juvenile form; and type III is adult or chronic form. Affected infants lose skills they previously acquired, have profound intellectual disabilities, hepatosplenomegaly, skeletal abnormalities, and seizures. Type II and III are milder forms, but symptoms overlap between all three types. GM1 gangliosidosis is estimated to affect 1 in 100,000 to 1 in 200,000 births. Type III is more common is those if Japanese ancestry.

Sequencing is performed on genomic DNA using an Agilent targeted sequence capture method to enrich for the exome. Direct sequencing of the amplified captured regions was performed using 2X150bp reads on Illumina next generation sequencing (NGS) systems. 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. A list of these regions, if any, is available upon request. Alignment to the human reference genome (GRCh37) is performed and annotated variants are identified in the targeted region. Variants reviewed have a minimum coverage of 8X and an alternate allele frequency of 20% or higher. Indel and single nucleotide variants (SNVs) may be confirmed by Sanger sequence analysis before reporting at director discretion. This assay cannot detect variants in regions of the exome that are not covered, such as deep intronic, promoter and enhancer regions, areas containing large numbers of tandem repeats, and variants in mitochondrial DNA. 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 analyzed or may be difficult to detect. When reported, copy number variant size is approximate. Actual breakpoint locations may lie outside of the targeted regions. CNV analysis will not detect tandem repeats, balanced alterations (reciprocal translocations, Robertsonian translocations, inversions, and balanced insertions), methylation abnormalities, triploidy, and genomic imbalances in segmentally duplicated regions. This assay is not designed to detect mosaicism; possible cases of mosaicism may be investigated at the discretion of the laboratory director. Primary data analysis is performed using Illumina bcl2fastq converter v2.19. Secondary analysis is performed using Illumina DRAGEN Bio-IT Platform v.3.10.8. Tertiary data analysis is performed using SnpEff v5.0 and Revvity Omics’ internal ODIN v.1.01 software. CNV and absence of heterozygosity are assessed using BioDiscovery’s NxClinical v6.1 software.