Lymphoid Gene Panel by NGS
General Information
Lab Name
Lymphoid Gene Panel by NGS
Lab Code
HCAPL
Epic Name
Lymphoid Gene Panel by NGS
Description
This assay is a multiplexed gene sequencing panel designed to detect mutations associated with hematologic lymphoid disorders. Purified genomic DNA is enzymatically sheared and targeted sequences are isolated by hybrid capture probes and sequenced by using an Illumina NGS platform. This assay will not detect variants if present in only a small proportion of cells in the sample. This assay is not intended for post-treatment disease monitoring nor comprehensive germline evaluation and is not validated to detect all classes of genomic alterations, such as large structural events including fusions and copy alterations.
If lymphoid-panel testing is not desired, single-gene testing (such as for TP53 or EZH2) can be requested and performed (HCAPSG).
SNV
Limit of Detection: 3%
Limit of Quantification: 4%
Precision near LOD (CV): 20%
Accuracy: 100% of expected variants
INDELS
Limit of Detection: 3%
Limit of Quantification: Qualitative Only
Precision near LOD (CV): 20%
Accuracy: 98% of expected insertions/deletions
Hematopathology test request form can be found at Request Form
Synonyms
ALK (exons 01-29), ASXL1 (exons 01-12), ATM (exons 02-63), BCL2 (exons 02-03), BCOR (exons 02-15), BIRC3 (exons 03-10), BRAF (exons 01-18), BTK (exons 02-19), CARD11 (exons 02-25), CCND1 (exons 01-05), CD19 (exons 01-15), CD274 (exons 02-07), CD74 (exons 01-09), CD79B (exons 01-06), CDKN2A (exons 01-03), CXCR4 (exons 01-02), DNMT3A (exons 02-23), EP300 (exons 01-31), EZH2 (exons 02-20), FBXW7 (exons 02-12), Hematologic disorders, Hematologic malignancy, HRAS (exons 02-06), IDH1 (exons 03-10), IDH2 (exons 01-11), KMT2D (exons 01-54), KRAS (exons 02-05), Leukemia, Lymphoma, MAP2K1 (exons 01-11), MYC (exons 01-03), MYD88 (exons 01-05), Next-Generation Sequencing, NGS, NOTCH1 (exons 01-34), NOTCH2 (exons 01-22), NRAS (exons 02-05), PLCG2 (exons 02-33), RHOA (exons 02-05), SF3B1 (exons 01-25), STAT3 (exons 02-24), STAT5B (exons 02-19), STAT6 (exons 02-22), TCF3 (exons 02-19), TET2 (exons 02-11), TNFAIP3 (exons 02-09), TNFRSF14 (exons 01-08), TP53 (exons 02-11), XPO1 (exons 02-25)
Components
| Code | Name |
|---|---|
| HCAPLS | Lymphoid Gene Panel Specimen Description |
| HCAPLR | Lymphoid Gene Panel Result |
| HCAPLI | Lymphoid Gene Panel Interpretation |
| HCREV | Results Reviewed by: |
| HCAPLM | Lymphoid Gene Panel Method |
| HCLGRN | Lymphoid Gene Panel Case Number |
Interpretation
Method
Next-Generation Sequencing
Reference Range
See individual componentsGuidelines
Ordering & Collection
Specimen Type
Collection
Preferred:
Blood: 6mL in Lavender Top (EDTA)
Bone Marrow: 1-2mL in Lavender Top (EDTA)
Tissue, Fluids or Sorted cells: Sterile container in RPMI
Formalin-fixed paraffin embedded tissue (FFPE/PET) block
Slides: 10 unstained
Accepted:
Green Tops (Heparin), while green tops are accepted for testing, there is documentation that heparin can interfere with some PCR assays.
Extracted DNA from CLIA certified laboratory.
Formalin-fixed paraffin embedded tissue (FFPE/PET)
Tissue from curls cut from FFPE/PET blocks or stained cover-slipped slides
Unacceptable:
Specimens received beyond stability limit.
Specimens with low volume or inadequate WBC
Decalcified or unacceptable fixatives
Forms & Requisitions
Handling Instructions
- Deliver samples to Hematopathology as soon as possible.
- If sample is older than 48 hours, please store at 2-6°C upon receipt and send refrigerated.
- Samples stored at room temperature or refrigerated older than 7 days will be rejected.
- Frozen samples should be shipped on dry ice.
Quantity
requested: Blood: 6mL EDTA/BMA: 1-2mL EDTA/Tissue Blocks: Adequate size to cut 10-20 curls/Slides: 10 unstained
minimum: Blood: 1mL EDTA/ BMA: 0.5mL EDTA/Tissue Blocks: 5 curls/Slides: 5 slides
Processing
Send specimens to Hematopathology – Molecular department for processing.
The stability limit for Blood and Bone Marrow is 7 days, samples beyond this limit will be rejected.
Blood and BMA must arrive in lab by 7am and tissue by 12pm Friday to be included on Monday run.
Performance
LIS Dept Code
Molecular Hematopathology (MHP)
Performing Location(s)
| Other |
Hematopathology, Molecular
206-606-7060 UW Hematopathology Laboratory, G7-800 |
Hematopathology, Molecular hours: |
|---|
Frequency
Monday: Results within 12 - 14 days from start of testing. Cases requiring repeat testing, review, or addressing other considerations may have a delay of ~ 12 additional days.
Available STAT?
No