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Cytogenetics Laboratory

The Cytogenetics Laboratory provides the following services:

  • 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
Chromosome Part of a cell that contains genetic information. Except for sperm and eggs, all human cells contain 46 chromosomes. Fluorescence in situ hybridization A laboratory method used to look at genes or chromosomes in cells and tissues with the help of fluorescent dye. It is used to help diagnose diseases such as cancer and to help plan treatment. A laboratory method used to look at genes or chromosomes in cells and tissues. Pieces of DNA that contain a fluorescent dye are made in the laboratory and added to a cell or tissue sample. When these pieces of DNA bind to certain genes or areas on chromosomes in the sample, they light up when viewed under a microscope with a special light. FISH can be used to identify where a specific gene is located on a chromosome, how many copies of the gene are present and any chromosomal abnormalities. It is used to help diagnose diseases such as cancer and to help plan treatment.
SCCA Cytogenetics Laboratory

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 Cytogenetics 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@seattlecca.org or (206) 606-1390 to request additional details of performance characteristics for karyotype analysis.

Anemia A condition in which the number of red blood cells is below normal. B cell A type of white blood cell that makes antibodies. B cells are part of the immune system and develop from stem cells in the bone marrow. Bone marrow The soft, spongy material in the center of your bones that produces all your blood cells, such as white blood cells, red blood cells and platelets. Chromosome Part of a cell that contains genetic information. Except for sperm and eggs, all human cells contain 46 chromosomes. Cytogenetic test The process of analyzing cells in a sample of tissue, blood, bone marrow or amniotic fluid to look for changes in chromosomes, including broken, missing, rearranged or extra chromosomes. The process of analyzing cells in a sample of tissue, blood, bone marrow or amniotic fluid to look for changes in chromosomes, including broken, missing, rearranged or extra chromosomes. Changes in certain chromosomes may be a sign of a genetic disease or condition or some types of cancer. Cytogenetic analysis may be used to help diagnose disease, plan treatment or find out how well treatment is working. Prognosis A statement about the likely outcome of a disease in a patient. Relapse The recurrence (return) of disease after an apparent recovery.
Normal XX (female) karyotype
Normal XX (female) karyotype
Conventional Chromosome Analysis or Karyotyping

Karyotype analysis includes complete chromosome analysis of at least twenty metaphases with at least two cut karyotypes.

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@seattlecca.org or (206) 606-1390 to request additional details of assay performance characteristics such as sensitivity, specificity, and limit of detection.

Bone marrow The soft, spongy material in the center of your bones that produces all your blood cells, such as white blood cells, red blood cells and platelets. Disease progression When the disease is getting worse or spreading. Fluorescence in situ hybridization A laboratory method used to look at genes or chromosomes in cells and tissues with the help of fluorescent dye. It is used to help diagnose diseases such as cancer and to help plan treatment. A laboratory method used to look at genes or chromosomes in cells and tissues. Pieces of DNA that contain a fluorescent dye are made in the laboratory and added to a cell or tissue sample. When these pieces of DNA bind to certain genes or areas on chromosomes in the sample, they light up when viewed under a microscope with a special light. FISH can be used to identify where a specific gene is located on a chromosome, how many copies of the gene are present and any chromosomal abnormalities. It is used to help diagnose diseases such as cancer and to help plan treatment.
FISH
Interphase FISH with a dual color, dual fusion probe set to detect translocation.
Fluorescence in Situ Hybridization (FISH)

FISH often provides important diagnostic and prognostic information, as well as a method for monitoring tumor burden post treatment. 

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@seattlecca.org or (206) 606-1390 to request additional details of assay performance characteristics such as sensitivity, specificity, and limit of detection.

Bone marrow The soft, spongy material in the center of your bones that produces all your blood cells, such as white blood cells, red blood cells and platelets. Chromosome Part of a cell that contains genetic information. Except for sperm and eggs, all human cells contain 46 chromosomes. Metastatic A metastatic cancer is a cancer that has spread to other areas of the body by way of the lymph system or bloodstream. Relapse The recurrence (return) of disease after an apparent recovery.
CGAT data plot with multiple aberrations detected
CGAT data plot with multiple aberrations detected
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.

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@seattlecca.org or (206) 606-1390 to request additional details of assay performance characteristics such as sensitivity, specificity, and limit of detection.

Bone marrow The soft, spongy material in the center of your bones that produces all your blood cells, such as white blood cells, red blood cells and platelets. Fluorescence in situ hybridization A laboratory method used to look at genes or chromosomes in cells and tissues with the help of fluorescent dye. It is used to help diagnose diseases such as cancer and to help plan treatment. A laboratory method used to look at genes or chromosomes in cells and tissues. Pieces of DNA that contain a fluorescent dye are made in the laboratory and added to a cell or tissue sample. When these pieces of DNA bind to certain genes or areas on chromosomes in the sample, they light up when viewed under a microscope with a special light. FISH can be used to identify where a specific gene is located on a chromosome, how many copies of the gene are present and any chromosomal abnormalities. It is used to help diagnose diseases such as cancer and to help plan treatment. Gene The functional and physical unit of heredity passed from parent to offspring. Genes are pieces of DNA, and most genes contain the information for making a specific protein. Gene The functional and physical unit of heredity passed from parent to offspring. Genes are pieces of DNA, and most genes contain the information for making a specific protein. Polymerase chain reaction A laboratory method used to make many copies of a specific piece of DNA from a sample. It allows very small amounts of DNA to be amplified so they can be detected. A laboratory method used to make many copies of a specific piece of DNA from a sample that contains very tiny amounts of that DNA. Polymerase chain reaction allows these pieces of DNA to be amplified so they can be detected. Polymerase chain reaction may be used to look for certain changes in a gene or chromosome, which may help find and diagnose a genetic condition or a disease, such as cancer. It may also be used to look at pieces of the DNA of certain bacteria, viruses or other microorganisms to help diagnose an infection. Prognosis A statement about the likely outcome of a disease in a patient. Refractory In medicine, refractory disease is a disease or condition that does not respond to treatment.
RNA
TRS
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.

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@seattlecca.org or (206) 606-1390 to request additional details.

Biopsy The removal of a sample of tissue or fluid that is examined to see whether cancer is present. This may be done with a large needle or through surgical removal of tissue or fluids.
Fibroblast expansion
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.

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@seattlecca.org or (206) 606-1390 to request additional details

choosing the right test
diagnostics
Choosing the right tests

Clinical cancer genomics is a complex and quickly evolving field.

Our team and philosophy

Team Cyto is 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.

Check the Fred Hutchinson career site for current openings or inquire at cytolab@seattlecca.org.

Clinical trial A type of research study that tests how well new medical approaches work in people. These studies test new methods of screening, prevention, diagnosis or treatment of a disease. Fluorescence in situ hybridization A laboratory method used to look at genes or chromosomes in cells and tissues with the help of fluorescent dye. It is used to help diagnose diseases such as cancer and to help plan treatment. A laboratory method used to look at genes or chromosomes in cells and tissues. Pieces of DNA that contain a fluorescent dye are made in the laboratory and added to a cell or tissue sample. When these pieces of DNA bind to certain genes or areas on chromosomes in the sample, they light up when viewed under a microscope with a special light. FISH can be used to identify where a specific gene is located on a chromosome, how many copies of the gene are present and any chromosomal abnormalities. It is used to help diagnose diseases such as cancer and to help plan treatment. Flow cytometry A laboratory method that measures the number of cells, the percentage of live cells and certain characteristics of cells in a sample of blood, bone marrow or other tissue. A laboratory method that measures the number of cells, the percentage of live cells and certain characteristics of cells (such as size and shape) in a sample of blood, bone marrow or other tissue. The presence of tumor markers, such as antigens, on the surface of the cells is also measured. The cells are stained with a light-sensitive dye, placed in a fluid and then passed one at a time through a beam of light. The measurements are based on how the stained cells react to the beam of light. Flow cytometry is used in basic research and to help diagnose and manage certain diseases, including cancer.