Heme Single Gene by NGS

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General Information

Lab Name
Heme Single Gene by NGS
Lab Code
HCAPSG
Epic Ordering
Heme Single Gene by NGS
Description

This assay is intented to detect single gene mutations associated with hematologic 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 comprehesive germline evaluation and is not validated to detect all classes of genomic alterations, such as large structural events including fusions and copy alterations.

If indicated, panel-based testing can be performed for myeloid-focused genes (HCAPMY) or lymphoid-focused genes (HCAPL), or both myeloid and lymphoid-panels can be ordered together (HCAPA).

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

Forms & Requisitions

Requisition

Synonyms
ABL1 exons (01-11), ALK exons (01-29), ANKRD26 exons (01-34), ASXL1 exons (01-12), ATM exons (02-63), BCL2 exons(02-03), BCOR exons (02-15), BCORL1 exons (01-12), BIRC3 exons (03-10), BRAF exons (01-18), BTK exons (02-19), CARD11 exons (02-25), CBL exons (01-16), CBLB exons (01-19), CCND1 exons (01-05), CD19 exons (01-15), CD274 exons (02-07), CD33 exons (01-07), CD74 exons (01-09), CD79B exons (01-06), CDC25A exons (01-15), CDKN2A exons (01-03), CRLF2 exons (01-05), CSF3R exons (03-17), CXCR4 exons (01-02), DDX41 exons (01-17), DNMT3A exons (02-23), EGFR exons(01-28), EP300 exons (01-31), ERBB2_exons (1-27), ETNK1 exons (01-08), ETV6 exons (01-08), EZH2 exons (02-20), FBXW7 exons (02-12), FGFR1 exons (02-18), FLT3 exons(01-24), GATA1 exons (01-06), GATA2 exons (02-06), HRAS exons (02-06), IDH1 exons (03-10), IDH2 exons (01-11), IKZF1 exons (02-07), JAK2 exons (03-25), KIT exons (01-21), KMT2A exons (01-36), KMT2D exons (01-54), KRAS exons (02-05), MAP2K1 exons (01-11), MPL exons (01-12), MYC exons(01-03), MYD88 exons (01-05), NF1 exons (01-57), NOTCH1 exons (01-34), NOTCH2 exons(01-22), NPM1 exons (01-11), NRAS exons (02-05), PDGFRA exons (02-23), PDGFRB exons (02-23), PHF6 exons (02-10), PLCG2 exons (02-33), PML exons (01-08), PPM1D exons (01-06), PTEN exons (01-09), PTPN11 exons (01-15), RAD21 exons (02-14), RARA exons (02-09), RB1 exons (01-27), RHOA exons (02-05), RUNX1 exons (01-09), SAMD9 exons (01-03), SAMD9L exons (05), SETBP1 exons (02-06), SF3B1 exons (01-25), SH2B3 exons (02-08), SMC1A exons (01-25), SMC3 exons (01-29), SRSF2 exons (01-02), STAG2 exons (02-33), 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), U2AF1 exons(01-08), WT1 exons(01-10), XPO1 exons(02-25), ZRSR2 exons(01-11, Hematologic malignancy, Leukemia, Hematologic disorders, Next-Generation Sequencing, NGS, AML, Lymphoma
Components

Interpretation

Method

Next-Generation Sequencing

Reference Range
See individual components

Ordering & Collection

Specimen Type
Blood, Bone Marrow, Tissue - Fresh, frozen or FFPE/PET (Blocks), Fluids, Slides, Sorted Cells
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

Requisition

Handling Instructions

Samples should be transported at RT and arrive in lab within 48 hours.

If sample is expected to arrive in the HP lab beyond 48 hours, store and transport at 2 – 6˚C.

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

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
Seattle Cancer Care Alliance
825 Eastlake Avenue E.
Seattle, WA 98109

Frequency
Monday: Results within 12 - 14 days from start of testing.
Available STAT?
No

Billing & Coding

CPT codes
Billing Comments

For additional test/billing information, see following page: Heme Single Gene by NGS CPT codes.

LOINC
35474-6