IDUA Gene Test

Mucopolysaccharidosis type I is a disease associated with the accumulation of complex carbohydrates in various tissues caused by a lysosomal storage disorder. The disease is separated into severe and attenuated forms. The severe form has an age of onset in infancy and the attenuated form has an age of onset in childhood. Both forms show symptoms of a large head, hydrocephalus, distinctive facial features, hepatosplenomegaly, an enlarged tongue, umbilical and inguinal hernias, clouded corneas, hearing loss, weakness in the hands and fingers, and spinal stenosis. The severe form of the disease can also include symptoms of developmental regression, intellectual decline, rapid disease progression, and a life expectancy of late childhood. The attenuated form of the disease can include symptoms of intellectual disability and typically live into adulthood. The incidence of mucopolysaccharidosis type I is estimated to be ~ 1 in 100,000.

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.