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HelpTest Code LAB2824 Autism/ID Xpanded Panel
Clinical System Name
Autism/ID Xpanded Panel
Synonyms
Autism
Intellectual Disability Panel
A/ID
Sample Requirements
Preferred sample is whole blood
Specimen: Whole Blood
Container(s): Lavender/EDTA
Preferred Vol: 5 mL
Minimum Vol: 2 mL (1mL is acceptable for infants)
Specimen: DNA
Container(s): Sterile plastic tube
Preferred Vol: 5 µg of purified DNA at a concentration of ≥50 ng/µL AND a volume of ≥100 µL
Specimen: Buccal Swabs
Container(s): Oragene Dx OGD-100 collection kit
Information about alternate specimen collection kits can be found here on LabMan.
Dried blood spots are also accepted.
Processing Instructions
Reject due to:
Spin: N
Aliquot: N
Temp: 2 - 4 C
Storage location: Refrigerate in CPA refrigerator Sendouts rack. Samples drawn on a Friday can be refrigerated until Monday shipment. Samples drawn on a Friday before a Monday holiday must have DNA extraction.
Off-site collection: Send whole blood refrigerated.
Stability
| Specimen Type | Temperature | Time |
|---|---|---|
| Whole Blood | Room temp | 3 d |
| Whole Blood | Refrigerated | 7 d |
| Whole Blood | Frozen | N |
| Extracted DNA | Room temp | 3-4 d |
| Extracted DNA | Refrigerated | 1 y |
| Extracted DNA | Frozen | Indefinitely |
Availability
| STAT | Performed | TAT |
|---|---|---|
| N | 6 w |
Performing Laboratory
GeneDX
207 Perry Parkway
Gaithersburg, MD 20877
Phone number: (301) 519-2100
Department
Department: Send Outs/Genetic
Phone Number: (206) 987-2563
Methodology
Method: Next-generation sequencing with CNV calling (NGS-CNV)
Please note that while the Autism/ID Xpanded Panel captures and sequences the whole exome, analysis is targeted to the specific phenotype-driven gene list for this panel. The Autism/ID Xpanded Panel gene list includes 2300+ genes. The list was developed by searching for genes associated with autism and/or intellectual disability in multiple sources, including OMIM, HGMD, and Human Phenotype Ontology (HPO) terms. This list undergoes continual review and curation by GeneDx experts. During this review, genes are added to the list using GeneDx data from clinical ES done on patients with ASD or ID. Additionally, genes may be removed from the panel if they are found to be weakly or questionably associated with ASD/ID. In rare situations, genes are removed from the panel if they are expected to be low yield for this phenotype but contain an inherent high risk for incidental findings. The gene list is routinely updated.
Data are filtered and analyzed to identify sequence variants and most deletions and duplications involving three or more coding exons. Smaller deletions or duplications may not be reliably identified.
The average coverage of all genes on the panel is greater than 98% at 10X (with a depth of 10 or more reads). The coverage of each gene on the panel for a specific patient may vary, and the actual coverage for each gene is included in the final report.
Some types of genetic disorders, such as those due to nucleotide repeat expansion/contraction, abnormal DNA methylation, and other mechanisms may not be detectable with this test. Additionally, small sections of a few individual genes have inherent sequence properties that yield suboptimal data and variants in those regions may not be reliably detected. For example, the CGG repeat expansions in FMR1 causing fragile X syndrome, the polyalanine repeat expansions in ARX, and abnormal methylation of UBE3A causing Angelman syndrome would not be detectable by this Autism/ID Xpanded Panel.
Variants of uncertain significance, likely benign and benign variants, if present, are not routinely reported.
Reference Range
Interpretive report is provided
Send Out Instructions
| Reference Test Name: |
Autism/ID Xpanded Panel |
| Reference Test Number: | 952 |
| Instructions: | GeneDx accepts Saturday delivery. Whole blood specimens may be stored refrigerated for up to 7 days prior to shipping. Ship overnight via FedEx M - F, ambient temperature. |
Special Instructions
Clinical Utility
Autism spectrum disorders and intellectual disability (intellectual developmental disorder) are clinically and genetically heterogeneous and are often co-morbid disorders. The cause of ASD and/or ID can be difficult to discern as there are many genes known to cause these neurodevelopmental disorders.
The clinical sensitivity of the Autism/ID Xpanded Panel depends in part on the patient’s clinical phenotype. Previous ES studies have reported identification of a definitive pathogenic variant in 14-33% of individuals who have neurodevelopmental phenotypes such as ASD, ID and/or developmental delay. However, the clinical sensitivity of analysis of the genes included on the panel depends on the clinical phenotype. It has been demonstrated that the yield of WES testing is higher with a Trio approach compared to a Proband-only approach. The sensitivity of this test is expected to be comparable to trio-based exome sequencing since it uses a trio approach to test a comprehensive list of genes previously associated with ASD and/or ID. The clinical sensitivity is expected to be significantly lower for singleton testing when only the affected proband is tested.
In some cases, confirmation of the molecular genetic cause of ASD and/or ID may have implications for treatment, management, and eligibility for needed services.
Description
The Autism/ID Xpanded Panel uses a trio approach that includes concurrent analysis of the affected proband and both parents, which increases the likelihood of identifying a definitive genetic explanation for ASD and/or ID.
The Autism/ID Xpanded Panel is based on whole exome capture, Next Generation sequencing (NGS), and targeted analysis of a comprehensive list of 2300+ genes currently associated with ASD and/or ID. The design of the panel allows for a comprehensive, dynamic gene list that is updated regularly to ensure inclusion of genes recently associated with ASD and/or ID.