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HelpTest Code LAB3616 Targeted Gene Del/Dup by Array
Additional Codes
Single Gene Deletion/Duplication Analysis
Clinical System Name
Targeted Gene Deletion/Duplication by Array
Description
Deletion/duplication analysis is performed with ThermoFisher’s CytoScan XON array, which provides exon-level resolution for detection of copy number variants.
Requests for targeted gene deletion/duplication testing are primarily limited to genes covered by the SCH gene list.
To request a gene region not on the SCH gene list, please contact the Laboratory Genetic Counselors (206-987-5400, labgc@seattlechildrens.org). In some cases, custom gene requests will be approved after director review.
For targeted testing to be performed by non-SCH lab, please search Lab Test Catalog by gene.
Sample Requirements
Samples MUST have two of the following to be accepted as properly labeled: first & last name, outside medical record number, unique accession number, or date of birth.
Note: For patients who have had a whole blood transfusion, wait 10 days post transfusion to draw for genetic testing. No wait time is necessary for blood or saliva collection if the patient received leuko-reduced red cells or plasma.
Specimen: Whole blood
Container(s): Lavender/EDTA
Preferred Vol: 3 mL
Minimum Vol: 1 mL
Note: Heparin samples (Green tops) are unacceptable.
Specimen: Saliva collected using Oragene Dx OGD-575/675 collection kit.
Container: Oragene Dx OGD-575/675 collection kit
IMPORTANT NOTE: Manufacturer instructions must be followed. Please review link: How to Collect a Saliva Sample for Genetic Testing (Spanish). Contact the lab directly for more information or to obtain a kit - 206-987-2563, ReferenceLabTeam@seattlechildrens.org.
Specimen: Extracted DNA (MUST specify source on requisition)
Preferred: 5µg
Minimum: 2µg
Note: Isolation of nucleic acids for clinical testing must be performed in a CLIA-certified
laboratory or a laboratory meeting equivalent requirements as determined by the CAP
and/or the CMS. DNA concentration minimum 50 µg/mL; 260/280 ratio 1.70-2.00.
Specimen: Tissue
| Fresh frozen tissue | 25-50 mg in a sterile container |
| Skin biopsy |
2-4 mm punch biopsy of skin collected under sterile conditions in a sterile vial, frozen with no media. Also acceptable: refrigerate with 1-3 mL of tissue transport medium. |
Formalin-fixed parafin embeded (FFPE) tissue is NOT acceptable.
Processing Instructions
| Specimen Type | Description |
Temperature |
Storage instructions |
| Whole blood | EDTA or ACD tube | Refrigerate | Molecular Genetics box in CPA refrigerator #2 |
| Extracted DNA | DNA aliquot tube | Refrigerate | Molecular Genetics box in CPA refrigerator #2 |
| Fresh frozen tissue | Frozen aliquot of 25-50 mg tissue | Frozen | M-F 9-1700 call x73872 for pick-up; after hours, weekends & holidays in CPA -70 freezer |
| Skin biopsy | Sterile container | Frozen | M-F 9-1700 call x73872 for pick-up; after hours, weekends & holidays in CPA -70 freezer |
| In medium | Refrigerate | Molecular Genetics box in CPA refrigerator #2 |
Off-site collection: Refrigerate blood samples until ready to ship. Transport saliva, blood or DNA via overnight shipping. Transport fresh frozen tissue on dry ice.
Stability
| Specimen Type | Temperature | Time |
|---|---|---|
| Whole blood, extracted DNA | RT | 3-5 d |
| Whole blood, extracted DNA | 2 - 8 C | 7 d |
|
Saliva, extracted from ORAgene Dx OGD-575/675 |
room temperature or refrigerated | up to 2 weeks |
| Extracted DNA | -20 C or -70 C | years |
Note: Whole blood samples > 7days may be submitted to be assessed by our lab for acceptability for testing.
Availability
| STAT | Performed | TAT |
|---|---|---|
| Contact lab | Monday - Friday | 4-6 weeks |
Performing Laboratory
Seattle Children's Laboratory
Department
Department: Molecular Genetics Laboratory
Phone: 206-987-3872
Lab Client Services: 206-987-2617
Lab Genetic Counselor: LabGC@seattlechildrens.org
CPT Codes
Call or email Lab Client Services, 206-987-2617, labclientservices@seattlechildrens.org, for targeted gene or targeted variant CPT codes.
Methodology
Exon array: Analysis is limited to the targeted regions. Exon-level copy number analysis is performed on genomic DNA using the ThermoFisher Cytoscan Xon Array that includes 6.5 million copy number probes and 300,000 SNP probes. Additional details of this platform can be found at: http://assets.thermofisher.com/TFS-Assets/GSD/brochures/CytoScan_XON_Product_Bulletin%20.pdf
When a copy number change is detected that extends into flanking genes, the genomic coordinates of the full variant will be reported. Copy number variants outside of the targeted genes are not reported. Regions of homozygosity are not routinely reported. In rare cases, exonic copy number variants that encompass a genomic interval under 500 bp may not be detected. The sensitivity of detection of mosaic copy number variants has not been evaluated.
Reference Range
Interpretive report will be provided.