Joubert and Meckel-Gruber Syndromes Panel

Joubert syndrome is a disorder that affects many parts of the body. The hallmark feature of Joubert syndrome is a combination of brain abnormalities known as the molar tooth sign. Other characteristics include low muscle tone, ataxia, fast or slow breathing, abnormal eye movements, delayed development, and intellectual disability. Joubert syndrome affects 1 in 80,000 and 1 in 100,000 newborns and can be caused by mutations in many genes (NIH, genetics home reference). Meckel-Gruber syndrome is a disorder with severe signs and symptoms. The most common features include enlarged kidneys with fluid-filled cysts, an occipital encephalocele, and the presence of extra fingers and toes. Because of their serious health problems, most individuals with Meckel-Gruber syndrome die before or shortly after birth. Meckel-Gruber syndrome affects 1 in 13,250 to 1 in 140,000 people worldwide and may be more common in certain populations. Meckel-Gruber syndrome can be caused by mutations in one of at least eight genes.

Sequencing is performed on genomic DNA using an Agilent targeted sequence capture method to enrich for the genes on this panel. Direct sequencing of the amplified captured regions was performed using 2X100bp 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. Low coverage regions, if any, are limited to ~1% or less of the nucleotides in the test unless a pathogenic variant explaining the phenotype is discovered. A list of these regions is available upon request. Alignment to the human reference genome (hg19) is performed, and annotated variants are identified in the targeted region. Variants are called at a minimum coverage of 8X and an alternate allele frequency of 20% or higher. Single nucleotide variants (SNVs) meeting internal quality assessment guidelines are confirmed by Sanger sequence analysis for records after results are reported. Indels and SNVs are confirmed by Sanger sequence analysis before reporting at the director's 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, sequencing complexity, or other factors, not all CNVs may be analyzed and/or may be difficult to detect. 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 DRAGEN Bio-IT Platform v.3.4.12. Secondary and tertiary data analysis is performed using PerkinElmer’s internal ODIN v.1.01 software for SNVs and Biodiscovery’s NxClinical v.6.1 or Illumina DRAGEN Bio-IT Platform v.3.4.12 for CNV and the absence of heterozygosity (AOH). Genes and/or exons located in pseudogene regions are not covered in this assay.