This test analyzes 7 genes that have been associated with Joubert and Aicardi-Goutieres Syndrome
|Turn-Around-Time (TAT)*||2 - 3 weeks|
|Acceptable Sample Types||
Whole Blood (EDTA)
Dried Blood Spots
|Acceptable Billing Types||
Self (patient) Payment
|Self (patient) Price||$250.00|
|CPT Codes**||81479 (x2)|
This panel analyzes 7 genes that have been associated with Aicardi- Goutieres Syndrome and/or disorders associated with Aicardi- Goutieres Syndrome. Both sequencing and deletion/duplication (CNV) analysis will be performed on the coding regions of all genes included (unless otherwise marked). All analysis is performed utilizing Next Generation Sequencing (NGS) technology. CNV analysis is designed to detect the majority of deletions and duplications of three exons or greater in size. Smaller CNV events may also be detected and reported, but additional follow-up testing is recommended if a smaller CNV is suspected. All variants are classified according to ACMG guidelines.
This panel may be appropriate for individuals with a clinical suspicion of Aicardi-Goutieres Syndrome and/or for individuals with a family history of Joubert and Aicardi-Goutieres Syndrome.
Aicardi-Goutieres is a disorder that mainly affects the brain, the immune system, and the skin. Many newborns with this condition are born with an enlarged liver and spleen, elevated blood levels of liver enzymes, a shortage of blood platelets, and neurological abnormalities. This combination of signs and symptoms is typically associated with the immune system's response to a viral infection no actual infection is found and for this reason, this condition may be referred to as a "mimic of congenital infection." Most individuals with Aicardi-Goutieres syndrome experience an episode of severe brain dysfunction typically lasting for several months. As a result of the severe neurological problems associated with this condition, most people with this disorder do not survive past childhood, however, some affected individuals may develop the condition later or have milder neurological problems live into adulthood. This is a rare syndrome and the prevalence is unknown. Aicardi-Goutieres can be caused by mutations in several 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.
EDTA (purple top)
Infants (< 2-years): 2 to 3 mL; Children (>2-years): 3 to 5 mL; Older children and adults: Minimum 5mL. The blood tube should be inverted several times immediately after blood collection to prevent coagulation.
Clotted or hemolyzed samples are not accepted.
Required DNA Quantity by Test Type*:
- Next Generation Sequencing (NGS): Send >1000 ng total gDNA @ >15 ng/μL. Please ship samples in 10mM Tris. Do not use EDTA.
- Sanger Sequencing: Send >500 ng total gDNA @ >15 ng/μL (varies by the size of the gene and the variants requested).
- Non-Sanger Sequencing Tests: Send >500 ng total gDNA @ >15 ng/μL.
- Research Laboratories: DNA extracted in research laboratories is not acceptable. Only under exceptional circumstances (e.g., proband not available) will DNA extracted in a research laboratory be accepted for clinical testing. Additional testing (e.g., of other family members) may be required to confirm results.
- Laboratories outside the United States: Non-US laboratories are not subject to CLIA regulations and will be reviewed on a case-by-case basis. Please call to speak with a laboratory genetic counselor prior to submitting a DNA sample from any non-CLIA certified laboratory.
- Special Notes: If extracted DNA is submitted, information regarding the method used for extraction should be sent along with the sample.
Dried blood spot card
Follow kit instructions. Briefly, allow blood to saturate card until indicated areas are filled and blood has soaked through card. Air dry card at ambient temperature for at least 3 hours.
- NBS: Please contact PKIG to request the StepOne® kit.
- Gene Sequencing: Please contact PKIG to request the DBS collection kit.
- For pre-punched DBS: The required minimum 6 punches with 3.2 mm or 4 punches 4.75 mm.
Oragene™ Saliva Collection Kit or ORAcollect-Dx kit
Collect saliva on an Oragene™ Saliva Collection Kit ORAcollect-Dx kit according to the manufacturer’s instructions.
Please contact PerkinElmer to request the saliva collection kit for patients that cannot provide a blood sample as whole blood is the preferred sample.