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Test Code LAB1899 RNA Heme Fusion Panel

Description

Gene fusions caused by chromosomal rearrangements are common in pediatric leukemias. The RNA heme fusion panel is a customized assay designed to detect gene fusions involving select exons in genes that are recurrent fusion partners in pediatric lymphoblastic and myeloid leukemias (ALL and AML) using anchored multiplex PCR and next generation sequencing (Archer® Fusion Plex).

 

There are 59 genes in version 6 of this targeted panel:  ABL1, ABL2, AFF1, ALK, BCL11B, BCL2, BCL6, BCOR, BCR, BLNK, CBFA2T3, CBFB, CREBBP, CRLF2, CSF1R, EPOR, ERG, ETV6, FGFR1, FLT3, FUS, GLIS2, HLF, HOXA9, IKZF1, IRF4, JAK2, KAT6A, KMT2A, MECOM, MEF2D, MKL1, MLLT10, MYB, MYC, MYCN, MYH11, NTRK3, NUP214, NUP98, NUTM1, PAX5, PDGFRA, PDGFRB, PTK2B, RANBP17, RARA, RUNX1, SPI1, SSBP2, TAL1, TCF3, TLX1, TLX3, TYK2, UBTF, ZCCHC7, ZNF362, ZNF384

 

Comments including limitations: This test detects fusions involving the targeted exons in genes listed above regardless of the fusion partner.

 

Note: This test is not designed to detect rearrangements involving immunoglobulin loci (IGH, IGK, IGL) and cannot reliably detect rearrangements involving MYC due to highly variable breakpoint heterogeneity. First line diagnostic testing for immunoglobulin and MYC rearrangements can be performed using FISH. The following genes known to be involved in fusions in Ph-like ALL are included in this panel: ABL1, ABL2, CRLF2*(except IGH-CRLF2), CSF1R, EPOR, FGFR1, JAK2, PDGFRA, PDGFRB, PTK2B.  This test does not detect non-fusion alterations (point mutations, indels, etc) in genes. Testing for a single gene fusion involving any of the genes included in this panel is also available.

Sample Requirements

Specimen Type:  Bone Marrow, leukemic peripheral blood: 

  • Blast percentage should be > 20%; test is not to be used for minimal residual disease detection
  • Specimen should be received within 24 hours of collection
  • Specimen should be room temperature or refrigerated

Bone Marrow:  1 to 2 mL bone marrow in lavender top (EDTA) or green top (sodium heparin) tube.

 

Leukemic Blood:  3-4 mL blood in lavender top (EDTA) or green top (sodium heparin) tube.

 

Unacceptable:  samples more than 24 hours old

 

 

Processing Instructions

Reject due to:  n/a - send to lab

Spin: N

Aliquot: N

Temp: RT

 

Bone marrows follow standard bone marrow processing:

Days: Transport specimen to 4th floor Cell Markers Lab (tube station # 181).

Eves/Nights/Weekends: Store specimen with other bone marrow samples in the Cell Markers RT box in CPA.　

 

Off-site collection - Bone Marrow: See Bone Marrow Aspirate listing for complete instructions. Off-site providers should fill out the 'Seattle Children's Bone Marrow/Malignancy requisition" (off-site collection) which includes morphology, flow, and cytogenetics requisition. Specimen must reach Children's Laboratory within 24 hours of collection. Samples received after 3 pm will be set up the following day.

 

Leukemic peripheral blood specimens:

Days (07:30-17:00): Transport specimen to 4th floor Cytogenetics (tube station #181).

Eves/Nights (17:00-07:30) & Weekends: Store specimen in the Cytogenetics RT box in CPA. 

Please call Cytogenetics 206-987-1008 to notify them. If no answer, email Cytogenetics team, LabCytogenetics@seattlechildrens.org, to notify them.

Availability

STAT Performed TAT
N   4 - 6 w

Performing Laboratory

Seattle Children's Hospital

Methodology

Method:  The Archer® Fusion Plex®   is a targeted Next Generation Sequencing assay designed to detect gene fusion abnormalites. 

Clinical Utility

Many leukemias demonstrate chromosomal translocations that result in fusion genes that can drive leukemia proliferation. This NGS-based panel provides a comprehensive and efficient test for assessing leukemic bone marrows and peripheral bloods for fusions involving the aforementioned genes. Many of these fusions are cryptic and may not be detectable by karyotype and/or fluorescence in situ hybridization. Even when a rearrangement is detected by cytogenetic testing, this test confirms the specific genes involved, characterizes breakpoints at the exon level, and demonstrates expression of the fusion at the RNA level. Some of the identified fusions may aid in risk stratification and/or guidance of possible targeted therapies.