Sign in →

Test Code LAB3616 Targeted Gene Del/Dup by Array

Important Note

This request is for testing to be performed by Seattle Children's Molecular Genetics Lab only.  Please review the Gene List for appropriate use of this test. If the targeted gene is not on the list, contact the Laboratory Genetic Counselors (206-987-5400, for approval of testing prior to submitting samples.

Additional Codes

Single Gene Deletion/Duplication Analysis

Clinical System Name

Targeted Gene Deletion/Duplication by Array


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,  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,


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.DO NOT use formaldehyde, formalin, alcohol, 5% dextrose or medium buffered with bicarbonate.


Formalin-fixed parafin embeded (FFPE) tissue is NOT acceptable.

Processing Instructions

Specimen Type Description


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.


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.


STAT Performed TAT
Contact lab Monday - Friday 4-6 weeks


Performing Laboratory

Seattle Children's Laboratory


Department:  Molecular Genetics Laboratory

Phone: 206-987-3872

Lab Client Services: 206-987-2617

Lab Genetic Counselor:

CPT Codes

Call or email Lab Client Services, 206-987-2617,, for targeted gene or targeted variant CPT codes.


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:


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. 


Molecular Genetics