Lysosomal Storage Disorder Panel with GBA and IDS

The lysosomal storage disorders (LSD) are a diverse group of inherited conditions caused by the defective function of specific lysosomal proteins. It is estimated that there are more than 50 different types. The disease course of these conditions is generally progressive, but the age of onset, nature and severity of symptoms can be variable between the disorders. Common symptoms of lysosomal disorders include hepatosplenomegaly, coarsening of facial features, short stature, corneal clouding, dysostosis multiplex and neurological regression. The combined prevalence of LSDs is estimated to be 1 in 7,000 births.

Sequencing is performed on genomic DNA using a targeted sequence capture method to enrich for the exome. Captured regions are sequenced on a short-read next-generation sequencing (NGS) system. Coverage requirements are based on validation data. An exon is considered fully covered if all coding bases plus three nucleotides of flanking sequence on either side are covered. Alignment to the human reference genome is performed, and annotated variants within the targeted region are identified. Variants are reviewed based on minimum coverage and alternate allele frequency cutoffs defined as per laboratory procedure. Indel and single-nucleotide variants (SNVs) may be confirmed by Sanger sequencing analysis before reporting, based on laboratory requirements.

This assay cannot detect variants in regions that are not targeted, including deep intronic, promoter, or enhancer regions. Exons with nonunique sequences, such as those containing pseudogene regions, are not analyzed in this assay. Copy number variation (CNV) analysis detects deletions and duplications in genes on this panel; however, in some instances, due to exon size, sequence complexity, or other factors, certain CNVs may be difficult to detect and analyze. When reported, copy number variant size is approximate, and actual breakpoint locations may lie outside of the targeted regions. Only CNVs identified in genes included in the panel will be reported. This assay does not interrogate CNVs in mitochondrial DNA. CNV analysis will not detect tandem repeats, balanced alterations (reciprocal translocations, Robertsonian translocations, inversions, and balanced insertions), methylation abnormalities, triploidy, or genomic imbalances in segmentally duplicated regions. This assay is not designed to detect mosaicism; however, possible cases of mosaicism may be detected and reported if laboratory requirements are met.

Primary data analysis is performed using standard FASTQ conversion tools appropriate to the sequencing platform. Secondary analysis is conducted using a high-performance genomic analysis pipeline. Tertiary analysis incorporates established annotation tools together with Revvity Omics' internal software. Copy number variation and absence of heterozygosity assessments are performed using a clinical cytogenomics platform.

For pseudogenes included in this panel -

Long-range PCR was performed to specifically amplify the genomic sequence of the gene of interest from the individual's genomic DNA; sequences from associated pseudogene regions are excluded. Sequencing of the long-range PCR product was performed using short-read next-generation sequencing (NGS). Indel and single-nucleotide variants (SNVs) may be confirmed by Sanger sequencing analysis before reporting, based on laboratory requirements. This analysis cannot detect variants in regions that are not analyzed, such as promoters, deep intronic, or long repetitive regions. This assay is not designed to detect mosaicism; however, possible cases of mosaicism may be detected and reported if laboratory requirements are met.

Copy number variation (CNV) analysis was performed using MLPA (Multiplex Ligation-dependent Probe Amplification). This analysis cannot determine the location or orientation of a duplication. Copy-neutral gene conversion or fusion, complex rearrangements, or large deletions including the entire gene with breakpoint(s) outside the targeted region may not be detected by this assay.