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HelpTest Code LAB3617 Targeted Gene Next-Generation Sequencing
Clinical System Name
Targeted Gene Sequencing by NGS
Description
This test is limited to requests for targeted gene sequencing to be performed at Seattle Children's Hospital Molecular Genetics Lab. For genes covered by SCH Next-Generation Sequencing Panels see the complete gene list.
Please contact the Laboratory Genetic Counselors (206-987-5400, labgc@seattlechildrens.org) if you have questions.
For targeted variant 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.
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
If both frozen tissue and FFPE tissue are available, frozen tissue is preferred.
| Fresh frozen tissue (-70C) | 25-50 mg in a sterile container. A copy of the pathology report is recommended. |
| 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, or 5% dextrose. |
| FFPE (Formalin-Fixed Paraffin-Embedded) Slides or Scrolls |
10 scrolls or 10 unstained, non-baked slides of freshly cut sections of FFPE tissue, each with a thickness of 10 microns. Please also include one slide at 4-micron thickness stained with hematoxylin-and-eosin.
Minimum acceptable tissue area is 10 square millimeters (total of 1 cubic millimeter of tissue). Tissue sections should contain as much lesional tissue as possible. A copy of the pathology report is required. Note that deletion/duplication analysis cannot be performed on FFPE tissue at this time. |
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 (-70C) | M-F 9-1700 call x73872 for pick-up; after hours, weekends & holidays in CPA -70 freezer |
| Skin biopsy | Sterile container (no media) | Frozen (-70C) | 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 | |
| Slides or scrolls | Glass slides or sterile tube | Room temp | Place in CPA Cytogenetics room temp box with requisition |
Off-site collection: Refrigerate blood samples until ready to ship. Transport blood, DNA, slides or scrolls at room temperature via overnight shipping. Transport fresh frozen tissue on dry ice.
Stability
| Specimen Type | Temperature | Time |
|---|---|---|
| Tissue - Fresh Frozen | -70 C | years |
| Tissue - FFPE Slides | RT | years |
| Whole blood | RT | 3-5 d |
| Whole blood | 2 - 8 C |
7 d |
|
Saliva fresh or extracted from ORAgene Dx OGD-575/675 |
refrigerated or room temp | up to 2 weeks |
| Extracted DNA | RT, refrig or frozen | stable |
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 | 4-8 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
Method: Next Generation Sequencing technology using an Illumina NextSeq instrument. Target region includes coding exons and a minimum of 10 bp of flanking intron boundaries of the genes tested. Target enrichment performed using a custom Integrated DNA Technologies (IDT) panel. Deletion/duplication analysis is performed with ThermoFisher’s CytoScan XON array, which provides exon-level resolution for detection of copy number variants.
Average coverage >1,000x, depth of coverage for all target regions is at least 20x. Recurrent hotspot variants can be detected at lower levels of mosaicism (≥1%) but sensitivity will be affected by DNA quality and quantity.
See Description above for reported gene set of each panel
Limitations:
NGS: This method can detect single nucleotide variants, small deletions, and small insertions in the regions targeted. Some exons cannot be efficiently captured due to sequence homology or sequence properties. This method will not detect large insertions and deletions, complex indels, structural variants, or copy number variants. Variants located outside of targeted regions will not be detected. Mosaic variants present at <20% may not be reliably detected, and detection sensitivity of mosaic variants is dependent on the nature of the variant. Recurrent hotspot variants can be detected at lower levels of mosaicism (≥1%) but sensitivity will be affected by DNA quality and quantity.
Reference Range
Interpretive report will be provided. Variants are not reported if they are considered benign or likely benign.