Home
HelpTest Code LAB11013 GDX Exome Sequencing
Clinical System Name
GDX Exome Sequencing
Synonyms
Exome; WES; Whole Exome; Whole Exome Sequencing
Description
Exome Sequencing analyzes the nuclear exome at GeneDx.
This test evaluates the protein-coding regions (exons) of ~20,000 genes, which account for approximately ~2% of the human genome. Concurrent mitochondrial genome sequencing and deletion testing can be ordered at GeneDx (see order questions).
Exome sequence analysis is performed on the affected individual (i.e., the proband) and, when submitted together for analysis, biological parental samples, and/or additional biological relatives as needed. Standardly, a report is issued only for the proband. If ordered, the mitochondrial genome sequencing and deletion test results are issued in a separate report.
Sample Requirements
Preferred Specimen: Whole Blood
Container: Lavender top (EDTA)
Preferred Vol: 5.0 mL
Minimum Vol: 3.0 mL
- 1.0 mL may be acceptable for infants. Please contact Send Outs at ext. 7-2563 for confirmation of 1.0 mL minimum volume.
Specimen: Extracted DNA
Container(s): Sterile Plastic Tube
Preferred Vol: 5 µg at a concentration of ≥50 ng/µL AND a volume of ≥100 µL
Alternative Specimen(s): GeneDx can send genetic testing collection kits directly to the family's home address. Please use the EPIC order questions to indicate if kits should be shipped to the family. You DO NOT need to place a seperate "Genetic Test Kit Request" order in EPIC. Please contact Send Outs at referencelabteam@seattlechildrens.org or call us at ext. 7-2563 for additional questions regarding alternative specimen acceptibility.
Processing Instructions
Reject due to:
Spin: N
Aliquot: N
Temp:
- Whole Blood or Extracted DNA: 2 - 8 C
- Buccal Swabs or Saliva Swabs: RT
Storage Location:
- CPA refrigerator, Send Outs rack.
- Send Outs room temperature rack.
Off-Site Collection: Send whole blood refrigerated.
Stability
| Specimen Type | Temperature | Time |
|---|---|---|
| Whole Blood | Room Temp | 3 d |
| Refrigerated | 7 d | |
| Frozen | Unacceptable | |
| Extracted DNA | Room Temp | 3 - 4 d |
| Refrigerated | 1 y | |
| Frozen | Indefinitely | |
| Buccal Swabs | Room Temp | 90 days |
Availability
| STAT | TAT |
| N | 5 - 7 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)
See linked Test Info in the Special Instructions section for details.
If ordered, the mitochondrial genome is analyzed by NGS-CNV and alternative sequencing or other detection methods may be used to analyze or confirm mtDNA variants. Next generation sequencing of the mitochondrial genome can detect mtDNA variants as low as 2% heteroplasmy and large-scale deletions (2 kb or larger) as low as 5% heteroplasmy. However, for large-scale deletions observed at less than 15% heteroplasmy a quantitative value will not be provided. This test is expected to detect greater than 98% of known pathogenic variants and deletions of the mitochondrial genome.
This is a phenotype-driven test of a very large number of genes; therefore, reported results are focused on pathogenic variants, likely pathogenic variants, and variants of uncertain significance in genes related to the clinical information provided.
Reference Range
Interpretive report provided.
Clinical Utility
Exome sequencing can be used to identify the underlying molecular basis of a genetic disorder in an affected individual with:
- A constellation of clinical findings not recognized as part of a known syndrome
- One or more congenital anomalies, dysmorphic features, or birth defects
- Unexplained epilepsy
- Unexplained hypotonia
- Neurodevelopmental disorders including global developmental delay/intellectual disability, with or without dysmorphic features
- A phenotype suggestive of a genetic etiology that does not correspond to a specific condition for which genetic testing is available
- A suspected genetic condition that has a high degree of genetic heterogeneity
- Unresolved genetic testing such as normal karyotyping or microarray analysis, and negative single gene or gene panel sequencing results
Reported diagnostic rates from commercial and academic laboratories have found that WES assays have a ~20-40% positive diagnostic rate, with higher rates being reported from trio analysis (i.e. proband and parents) compared to singleton analysis. Several large studies including those with critically ill infant populations have demonstrated that exome sequencing identifies a causal variant in 25-58% of cases, with a higher yield for cases that specifically include other biological family members.
Common features of mitochondrial disease may include ptosis, external ophthalmoplegia, proximal myopathy, exercise intolerance, cardiomyopathy, sensorineural deafness, optic atrophy, pigmentary retinopathy, diabetes mellitus, encephalopathy, seizures, dementia, migraine, stroke-like episodes, ataxia, spasticity, chorea and dementia.
The combination of full sequence analysis plus deletion testing is expected to identify a mitochondrial DNA variant in approximately 40% of adults and 10-20% of pediatric patients with a primary mitochondrial disorder.
A genetic diagnosis may have implications for treatment, management, recurrence risk, and family member testing.
Send Out Instructions
| Reference Lab Test Name: |
XomeDx (GeneDx) |
| Reference Lab Test Code: |
XomeDx: XomeDx Plus |
| Send-out Instructions: |
This test is interfaced through GeneDx Aura in EPIC. Add specimens to GeneDx pakcing list to trigger order communication to GeneDx. Ship Monday through Friday via FedEx Priority Overnight. Saturday deliveries are accepted. |