Whole Genome Sequencing includes:

• Mean coverage of 40X or greater with complete coverage of more than 99% of the exome, including over 5,400 disease-associated genes
• Analysis of single nucleotide variants (SNVs), deletions, and duplications in coding and non-coding regions of the genome
• Reliable detection of large-scale copy number variants (CNVs), including microdeletions and other gene- and chromosomal-level events
• Mitochondrial genome sequencing and analysis of SNVs as low as 5% heteroplasmy
• Rule-out of short tandem repeat (STR) expansion in more than 30 genes, including those associated with intellectual disability, epilepsy, and neuromuscular and movement disorders
• Spinal Muscular Atrophy (SMA) screening via SMN1 copy number characterization

All variants are analyzed according to American College of Medical Genetics and Genomics (ACMG) guidelines, and pathogenic, likely pathogenic, and variants of uncertain significance (VOUS) are reported. Variant analysis is phenotype-driven to minimize the reporting of VOUS.

Familial testing for VOUS is complimentary for up to two variants in two family members.

Complimentary opt-in for additional reports:

• ACMG Recommended Secondary Findings - pathogenic and likely pathogenic variants in genes recommended for reporting based on well-defined, highly-penetrant phenotypes with clinical actionability
• Pharmacogenetic Variants - select allele haplotypes recommended by the Association for Molecular Pathology pharmacogenomics working group and classified as Clinical Pharmacogenetics Implementation Consortium (CPIC) level A and PharmGKB level 1A
• Carrier Status - 330+ genes associated with disorders whose inheritance pattern is autosomal recessive or X-linked
• Diagnostic findings in all disease-associated genes - pathogenic and likely pathogenic variants are reported in genes associated with disease unrelated to clinical presentation

One complimentary reanalysis is included and can be requested at any time.

Access to raw data is included and available via electronic transfer.

• Genetically heterogeneous disease associated with pathogenic variants in multiple genes
• Clinical features are suggestive of a genetic disorder with a long list of differential diagnoses
• Unclear or atypical presentation of a genetic disorder
• Previous genetic testing did not yield a diagnosis, including exome sequencing

Whole genome sequencing is performed on genomic DNA using 2X150bp reads on Illumina next-generation sequencing (NGS) systems at a mean coverage of 40X. 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 low-coverage regions, if any, is available upon request. Revvity Omics has curated deep intronic pathogenic variants in public databases and these are tagged for identification during analysis. 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. Indels and single nucleotide variants (SNVs) may be confirmed by Sanger sequence analysis before reporting at the director’s discretion. Mitochondrial DNA is sequenced and analyzed using the same pipeline. Genes and/or exons located in pseudogene regions are not covered in this assay. 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. 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, 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 and tandem repeats analysis are 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. SMA testing and repeat expansion disorder screening are performed using in-house bioinformatics tools based on published literature with modification (PMID: 28125085, 32092542, 28887402).