Clinical Cancer Genomics Laboratory Services
Fred Hutch Clinical Cancer Genomics Laboratory (formerly Cytogenetics Lab)
Phone: 206.606.1390
Email: cytolab@fredhutch.org
- Conventional chromosome analysis or karyotyping
- Fluorescence in Situ Hybridization (FISH)
- Chromosome Genomic Array Testing (CGAT)
- Targeted RNA Sequencing (TRS)
- Fibroblast expansion for germline genetic testing
- Review of outside reports to advise clinicians
- Collaboration with researchers for sample processing and analysis
Services Information
Conventional Chromosome Analysis or Karyotyping
Karyotype analysis includes complete chromosome analysis of at least twenty metaphases with at least two cut karyotypes. The presence or absence of an acquired clonal chromosomal abnormality may aid in defining diagnosis and prognosis, treatment response, and relapse, or evaluate for secondary hematologic malignancy. Chromosome analysis on potential donors may also be requested to rule out a genetic clonal process.
Bone marrow is the preferred specimen for karyotype analysis for hematologic disorders, but peripheral blood may be used if spontaneously dividing cells are present (e.g., >5% blasts in the periphery) or for certain diseases as follows:
- Chronic lymphocytic leukemia - peripheral blood may be studied instead of bone marrow if abnormal cells are present. CLL samples are often stimulated with B cell mitogens because the tumor cells in this disease of B cell origin are well differentiated.
- Agnogenic myeloid metaplasia (AMM) and myelofibrosis - dividing cells for cytogenetic analysis may be obtained from unstimulated peripheral blood when a sufficient bone marrow aspirate cannot be obtained, even if <5% peripheral blasts are present.
The Clinical Cancer Genomics Laboratory does not perform fragility testing for Fanconi Anemia (also known as a breakage study). This test will be sent out by UW Medicine as a reference test.
Please contact the laboratory at cytolab@fredhutch.org or 206.606.1390 to request additional details of performance characteristics for karyotype analysis.
Fluorescence in Situ Hybridization (FISH)
FISH often provides important diagnostic and prognostic information, as well as a method for monitoring tumor burden post treatment. FISH testing identifies abnormalities that are specific to the particular assay and generally will not detect clonal evolution associated with disease progression. Both metaphase and interphase cells can be examined by FISH.
Suitable specimen types include fresh bone marrow, fresh peripheral blood, MACS and FACS enriched fractions, CSF, stored cell pellets from prior cytogenetic studies, and some archived tissue sections.
The laboratory offers an extensive menu of probes to thoroughly assess patients with hematology disorders. Please contact the laboratory at cytolab@fredhutch.org or 206.606.1390 to request additional details of assay performance characteristics such as sensitivity, specificity, and limit of detection.
Chromosome Genomic Array Testing (CGAT)
Chromosomal genomic array testing (CGAT) offers high resolution for detecting chromosome abnormalities including copy number gains and losses [collectively referred to as copy number aberrations (CNAs)], as well as copy-neutral loss of heterozygosity (cnLOH) when single-nucleotide polymorphisms (SNPs) are incorporated in the array design.
Its clinical utility in hematological malignancies and solid tumors has also been reported in literature with increasing contribution to clinical care. Our lab uses the CytoScan™ HD Array, which contains 2.6 million markers including 750,000 SNPs. We report copy number aberrations at 100 Kb resolution and copy-neutral loss of heterozygosity at 10 Mb resolution. Whole-arm copy neutral LOH is usually clinically significant.
Suitable specimen types include fresh bone marrow, fresh peripheral blood, MACS and FACS enriched fractions, and frozen solid tumors. The lab uses OncoScan™ FFPE to obtain similar CGAT results on formalin fixed, paraffin embedded samples.
Genomic array analysis is best for new diagnosis, relapse, or metastatic samples with clonal disease burden above 20%; therefore, it is not intended for minimal residual disease detection. Any detectable CNA or cnLOH events are considered clonal abnormalities unless they are constitutional in nature. Paired sample analysis can help distinguish somatic from constitutional abnormalities in cancer samples. Known copy number variants of no clinical significance for the patient’s malignancy are not reported. This test cannot detect balanced rearrangements, euploid changes, and nucleotide base pair changes, including point mutations and small insertion/deletions (indels). This method also cannot distinguish abnormalities belonging to different clones.
Please contact the laboratory at cytolab@fredhutch.org or 206.606.1390 to request additional details of assay performance characteristics such as sensitivity, specificity, and limit of detection.
Targeted RNA Sequencing (TRS)
This NGS-based technology is targeted RNA sequencing, where RNA extracted from the patient sample is reverse transcribed into cDNA, which is PCR amplified to generate enriched libraries that are then sequenced and analyzed for fusion identification. An appropriate panel of PCR primers is used to amplify and enrich for 72 relevant targets; FusionPlex® Heme v2 (ArcherDX) is our validated panel for hematology samples.
The assay is intended for cancer patients at diagnosis and refractory/relapse. The test assesses multiple oncogenic fusions in a single test. Ascertainments of these fusions aid in the appropriate diagnosis, prognosis, and therapy selection for the disease per WHO classification, National Comprehensive Cancer Network (NCCN) guidelines, as well as emerging evidences from the literature. Many of these fusions, despite being in international/national guidelines, are either not included in or detectable by standard diagnostic workup strategies such as RT-PCR or FISH panels. Examples include NTRK fusions, cryptic ALK gene fusions, cryptic rearrangement in myeloid and lymphoid neoplasms with eosinophilia, and sentinel fusions that classify Philadelphia-like acute lymphoblastic leukemia (Ph-like ALL).
This assay is not quantitative and cannot detect fusions between genes or exons that are not on the panel, rearrangements between genomic loci that do not produce fusion transcript, copy number aberrations, loss of heterozygosity, point mutations, or small insertion/deletions (indels). In addition, the assay is not a functional study. Therefore, both the oncogenic fusion and its reciprocal transcript may be reported.
Suitable specimen types include fresh bone marrow, fresh peripheral blood, and fixed cell pellets from karyotyping and FISH preparations.
The panel targets the following genes:
ABL1, ABL2, ALK, BCL11B, BCL2, BCL6, BCR, BIRC3, CBFB, CCND1, CCND3, CDK6, CHD1, CHIC2, CIITA, CREBBP, CRLF2, CSF1R, DEK, DUSP22, EBF1, EIF4A1, EPOR, ERG, ETV6, FGFR1, GLIS2, IKZF1, IKZF2, IKZF3, JAK2, KAT6A, KLF2, KMT2A, MALT1, MECOM, MKL1, MLF1, MLLT10, MLLT4, MYC, MYH11, NF1, NFKB2, NOTCH1, NTRK3, NUP214, NUP98, P2RY8, PAG1, PAX5, PDCD1LG2, PDGFRA, PDGFRB, PICALM, PML, PRDM16, PTK2B, RARA, RBM15, ROS1, RUNX1, RUNX1T1, SEMA6A, SETD2, STIL, TAL1, TCF3, TFG, TP63, TYK2, ZCCHC7
Please contact the laboratory at cytolab@fredhutch.org or 206.606.1390 to request additional details of assay performance characteristics such as sensitivity, specificity, and limit of detection.
Fibroblast Expansion
Human fibroblasts from a skin punch biopsy can be cultured for specialized testing for constitutional genetic abnormalities or disease-related genotypes and phenotypes. In addition, cultured fibroblast cells can be cryopreserved for potential future studies.
The laboratory works closely with the clinical genetics and genetic counseling service to prepare appropriate samples for testing. Please contact the laboratory at cytolab@fredhutch.org or 206.606.1390 to request additional details.
Choosing the Right Tests
Clinical cancer genomics is a complex and quickly evolving field. Knowing the best test to run in any given clinical situation is extremely challenging. To overcome this obstacle, and to ensure equity of care, our institution uses standardized testing algorithms for case management of hematology disorders.
The laboratory works closely with the other contributing laboratories to ensure proper testing, sample allocation, and interpretation. Please contact the laboratory at cytolab@fredhutch.org or 206.606.1390 to request additional details
Our Team and Philosophy
We are a group of 30+ talented and passionate techs, directors, and support staff. All our cancer genomic technologists performing case analyses hold either CG(ASCP), MB(ASCP), or equivalent international certification.
Meaningful Clinical Impact
We take immense pride knowing the extra efforts we take to ensure the right results contribute to higher patient survival rates at an institution where revolutionary leukemia treatments were pioneered.
Patient-Focused Collaboration
- Karyotype and FISH reported together for cohesive interpretation
- Mindful triaging of case priorities to match clinical needs
- Tight collaboration with flow cytometry and pathology labs to ensure proper testing, sample allocation, and interpretation
- Comprehensive hematology testing algorithms to ensure the right tests are done at the right time
- Tailored sample processing via MACS, FACS, and culturing to elucidate the most challenging cases, including multiple diseases
Career Enrichment and Work/Life Balance
- Karyotyping, FISH, genomic array, and other cancer genomic testing integrated to allow for cross training and career advancement opportunities
- Techs at all levels may engage in assay improvement and development, as well as contribute to publications
- Best in-class benefits
- Paid CE time
- Flexible schedules are the norm, including limited remote work
- Promotions and pay based on merit system, not a union formula
Environment
- New, light-filled building designed just for labs
- Clean separation of wet bench and analysis space
- Ergonomic sit-stand desks, spacious FISH microscope room, ample wet bench space
- Complimentary on-site gym and roof top terrace
- On the edge of downtown on Lake Union with excellent transit options and walkability
Joining Our Team
We’re expanding significantly in 2022-2023 for the NCI MyeloMatch clinical trial that will redefine best genetic diagnostic practices to inform the most effective induction regimen for acute myeloid leukemia patients.
View the Fred Hutch career site for current openings or inquire at cytolab@fredhutch.org.