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Clinical Cytogenetics Laboratory

Summary:

"The OHSU Clinical Cytogenetics Laboratory specializes in high-resolution chromosome analysis. Emphasis has consistently focused on the highest quality preparations in order to provide the patient with the most accurate diagnosis."

Certifications: CLIA; CAP; American Board of Medical Genetics; Clinical Cytogenetics; Medical Genetics

Affiliations:

People:

    Member: Wilcox, Kim
    Role: Systems Admin, Laboratory Services

Resources:

Protocols

  • Williams Syndrome detection using FISH protocol ( Protocol )

    Fluorescent In-Situ Hybridization methods combine both molecular and cytogenetic techniques. They are employed to delineate subtle syndrome related chromosome defects. Williams syndrome probes are used to examine chromosome 7 for deletion of the elastin gene.

Services

  • Abortus, stillbirth, and neonatal death specimen chromosomal analysis ( Material analysis service )

  • Amniotic fluid chromosomal analysis ( Material analysis service )

    "Specimen Requirements:
    18-24 mL of amniotic fluid. Discard or separately collect first one or two mL fluid (can be used for AFP). If fluid bloody, add 0.5 mL sodium heparin (1000 units/mL) to each 10 mL of fluid and mix well. Keep at room temperature. Prior to sending a sample, please call the laboratory: (503) 494-5400. After hours, contact the Paging Operator at (503) 494-8211 and ask for the Cytogeneticist on call."

  • Angelman genetic diagnostic testing ( Material analysis service )

    "Reference Range:
    Angelman Syndrome is linked to the functional loss of imprinted genes located in the maternally derived 15q 11-q13 region. In 75% of these cases this is the result of a maternal deletion of the 15q 11-q13 region; paternal uniparental disomy accounts for another 3-7% of cases.

    Comments:
    Fluorescent In-Situ Hybridization methods combine molecular and cytogenetic techniques. They are employed to delineate subtle syndrome related chromosome defects. Multiple chromosome 15 probes are used for the detection of deletion in the Prader-Willi/Angelman Syndrome region. Please use the Cytogenetics Laboratory Request Forms available on the wards or from the Cytogenetics Lab. Please include detailed clinical information related to the reason for referral to cytogenetics."

  • BCR-ABL RNA Quantitative PCR ( Material analysis service )

    Specimen Requirements:
    620-30 mL peripheral whole blood, LAVENDER top tube. Deliver to the lab within 4 hours of draw, OR mix with RPMI/10% FBS stabilization media and deliver to the lab within 24 hours of draw. Keep cold.

  • Blood chromosomal analysis ( Material analysis service )

    "Specimen Requirements:
    3-5 mL drawn into a GREEN top sodium heparin vacutainer or into a pre-heparinized plastic syringe (use 0.2 cc sodium heparin, 1000 unit/mL). Do NOT use lithium heparin. 1-2 mL usually adequate from infants/small children. Keep at room temperature. Prior to sending a sample, please call the laboratory for specific instructions: (503) 494-5400. After hours, contact the Paging Operator at (503) 494-8211 and ask for the Cytogeneticist on call.

    Comments:
    This is the routine, high-resolution blood chromosome study."

  • Blood chromosomal analysis, high resolution ( Material analysis service )

    "Specimen Requirements:
    3-5 mL drawn into a GREEN top sodium heparin vacutainer or into a pre-heparinized plastic syringe (use 0.2 mL sodium heparin, 1000 unit/mL). Do NOT use lithium heparin. 1-2 mL usually adequate from infants/small children. Keep at room temperature. Prior to sending a sample, please call the laboratory for specific instructions: (503) 494-5400. After hours, contact the Paging Operator at (503) 494-8211 and ask for the Cytogeneticist on call.

    Comments:
    Focused, maximum-resolution study for extremely small deletions or rearrangements."

  • Bone marrow chromosomal analysis ( Material analysis service )

    Specimen Requirements:
    1-2 mL of sodium-heparinized bone marrow in Cytogenetics transport medium (5 mL RPMI 1640 with fetal bovine serum), or in GREEN top sodium heparin vacutainer. Keep at room temperature. Prior to sending a sample, please call the laboratory for specific instructions: (503) 494-5400. After hours, contact the Paging Operator at (503) 494-8211 and ask for the Cytogeneticist on call.

    Comments:
    Used for neoplasia cytogenetics."

  • Chorionic villus sample chromosomal analysis ( Material analysis service )

  • Chromosome breakage study ( Material analysis service )

    Used primarily for diagnosis of Fanconi anemia, done on blood samples.

    "Specimen Requirements:
    5-10 mL peripheral blood drawn into a GREEN top sodium heparin vacutainer or into a pre-heparinized plastic syringe (use 0.2 mL sodium heparin, 1000 unit/mL). Do NOT use lithium heparin. Keep at room temperature. Prior to sending a sample, please call the laboratory for specific instructions: (503) 494-5400. After hours, contact the Paging Operator at (503) 494-8211 and ask for the Cytogeneticist on call."

  • Cystic hygroma fluid chromosomal analysis ( Material analysis service )

  • DiGeorge/velocardiofacial syndrome screening ( Material analysis service )

    "Specimen Requirements:
    For blood specimens: 3-5 mL drawn into a GREEN top sodium heparin vacutainer or into a pre-heparinized plastic syringe (use 0.2 mL sodium heparin, 1000 unit/mL). Do NOT use lithium heparin. 1-2 cc usually adequate for infants/small children. Keep at room temperature. Prior to sending a sample, please call the laboratory for specific instructions: (503) 494-5400. After hours, contact the Paging Operator at (503) 494-8211 and ask for the Cytogeneticist on call.

    Pediatric Specimen Requirements:
    1-2 mL whole blood in GREEN top sodium hepartin.

    Comments:
    Fluorescent In-Situ Hybridization methods combine molecular and cytogenetic techniques. They are employed to delineate subtle syndrome related chromosome defects. Chromosome 22 specific probes are used for detection of deletion in the DiGeorge/Velocardiofacial region."

  • Fibroblast chromosomal analysis ( Material analysis service )

    "Specimen Requirements:
    Skin samples or other tissue at least 2 cubic millimeters in size. Handle specimens aseptically; collect in Cytogenetics Tissue Transport Medium, sterile Ringer's solution, or in sterile normal saline. Send to laboratory immediately. Keep at room temperature. Prior to sending a sample, please call the laboratory for specific instructions: (503) 494-5400. After hours, contact the Paging Operator at (503) 494-8211 and ask for the Cytogeneticist on call."

  • Fibroblast culture and storage ( Material storage service )

    "Specimen Requirements:
    A sterile skin biopsy, preferably obtained from the lower, inner arm after thorough skin sterilization with alcohol, (not betadine). Sample must be put into tissue culture media which can be obtained in advance from this lab; contact 503-494-5400. Post mortem samples may be viable. DO NOT FREEZE SPECIMEN. In urgent cases, samples can be put into sterile but non-bacteriostatic saline for a few hours.

    Pediatric Specimen
    Requirements:
    3 mm punch biopsy."

  • Fibroblast retrieval from storage ( Material processing service )

    "Retrieval of stored fibroblasts for futher culturing, testing or referral or to grow fibroblasts from T25's received for testing or referral."

  • Fluorescent in-situ hybridization (FISH) ( Material analysis service )

    "Fluorescent In-Situ Hybridization methods are employed, in conjunction with routine cytogenetics, to delineate subtle syndrome related chromosome defects, and also to identify the nature/origin of components of translocations, duplications, marker chromosomes not determined by routine cytogenetic techniques."

  • HER2 testing by FISH ( Material analysis service )

    "Specimen Requirements:
    Parraffin block containing invasive tumor, or 5 unstained slides.
    Formalin-fixed, paraffin embedded tissue sections are tested with PathVysionTM HER2 (FDA-approved method)."

  • Kallman Syndrome (X-linked) testing ( Material analysis service )

    "Specimen Requirements:
    For blood specimens: 3-5 mL drawn into a GREEN top sodium heparin vacutainer or into a pre-heparinized plastic syringe (use 0.2 mL sodium heparin, 1000 unit/mL). Do NOT use lithium heparin. 1-2 cc usually adequate for infants/small children. Keep at room temperature. Prior to sending a sample, please call the laboratory for specific instructions: (503) 494-5400. After hours, contact the Paging Operator at (503) 494-8211 and ask for the Cytogeneticist on call.

    Comments:
    Fluorescent In-Situ hybridization methods are employed, in conjunction with routine cytogenetics, to delineate subtle syndrome related chromosome defects, and also to identify the nature/origin of components of translocations, duplications, marker chromosomes not determined by routine cytogenetic techniques. The Kallman Syndrome probe used detects the X-chromosome deletion type. Please use the Cytogenetics Laboratory Request Forms available on the wards or from the Cytogenetics Lab. Please include detailed clinical information related to the reason for referral to cytogenetics."

  • Lymphoma complete surface marker panel ( Material analysis service )

    "Specimen Requirements:
    PERIPHERAL BLOOD: 10 mL blood, GREEN top tube; 2 mL heparinized blood, minimum. Keep at room temperature. Label as "Perishable Specimen" and deliver to laboratory immediately after collection.

    BONE MARROW OR BODY FLUID: 0.1 mL heparin in syringe prior to draw; 2 mLspecimen minimum. Keep at room temperature. Transfer to RPMI tube, if available, and mix. If no RPMI, transfer to red top tube and send within 24 hours. Include current, air-dried peripheral blood and BM aspirate smear on specimen.

    LYMPH NODE OR SOLID TUMOR: Tissue - Include slides of previous pertinent biopsies, if available.
    1. Fresh: Preferred, but must be received within 6 hours. Send as much as possible (minimum 0.5 x 0.5 cm) avoiding any necrotic area. Transfer to RPMI tube and keep at room temperature. If no RPMI or other tissue culture medium is available, use sterile saline.
    2. Frozen: When delivery within 6 hours is not possible. If unsure of delivery, send fresh and frozen. Snap freeze a 2-4 mm slice in O.C.T. freezing medium with either liquid nitrogen or alcohol and dry ice. Keep on dry ice or in -70C freezer. Ship on dry ice."

  • Microarray comparative genomic hybridization ( Material analysis service )

    "Specimen Requirements:
    3-5 mL blood, GREEN top (sodium heparin) AND PURPLE top (EDTA) tube.
    For requisition slips

    Pediatric Specimen Requirements:
    Minimum draw for neonates is 1 mL blood, GREEN top (sodium heparin) tube and 2 mL blood, LAVENDER top tube.

    Comments:
    Microarray comparative genomic hybridization (array CGH, or aCGH) is a cutting-edge, revolutionary analytic tool to aid in the diagnosis of patients with developmental delay, mental retardation, autism and birth defects. Array CGH detects genomic imbalance, ie. gains and losses of genetic material. Contact us for a complete list of disorders detected. Also, please contact us to discuss the advantages and limitations of the test and whether it is appropriate for your needs.

    All abnormalities identified by aCGH are confirmed through fluorescent in situ hybridization (FISH) analysis when possible. Analysis of parental blood may be required for interpretation, which will come at no charge. A comprehensive interpretation performed by a provider certified by the American Board of Medical Genetics (ABMG) in Clinical Cytogenetics and/or in Clinical Genetics is included, as well as any recommendations for genetic counseling."

  • Miller-Dieker lissencephaly syndrome testing ( Material analysis service )

    "Specimen Requirements:
    For blood specimens: 3-5 mL drawn into a GREEN top sodium heparin vacutainer or into a pre-heparinized plastic syringe (use 0.2 mL sodium heparin, 1000 unit/mL). Do NOT use lithium heparin. 1-2 cc usually adequate for infants/small children. Keep at room temperature. Prior to sending a sample, please call the laboratory for specific instructions: (503) 494-5400. After hours, contact the Paging Operator at (503) 494-8211 and ask for the Cytogeneticist on call.

    Comments:
    Fluorescent In-Situ Hybridization methods combine molecular and cytogenetic techniques. They are employed to delineate subtle syndrome related chromosome defects. The Miller-Dieker Syndrome probe is used to examine chromosome 17 for deletion of the region felt to be responsible for lissencephaly. Please use the Cytogenetics Laboratory Request Forms available on the wards or from the Cytogenetics Lab. Please include detailed clinical information related to the reason for referral to cytogenetics."

  • Neoplastic tissue chromosomal analysis ( Material analysis service )

  • Pleural fluid chromosomal analysis ( Material analysis service )

  • Prader-Willi diagnostic testing ( Material analysis service )

    "Specimen Requirements:
    5 mL whole blood in ACD (acid citrate dextrose) solution A or B.
    3-5 mL blood, GREEN top (sodium heparin) tube.
    For requisition slips

    Reference Range:
    PWS is associated with the functional loss of imprinted genes located in the paternally derived 15q 11-q13 region. This is most commonly the result of either a paternal deletion of the 15q 11-q13 region (75% of cases) or maternal uniparental disomy for chromosome 15 (25% of cases).

    Comments:
    Fluorescent In-Situ Hybridization methods combine molecular and cytogenetic techniques. They are employed to delineate subtle syndrome related chromosome defects. Multiple chromosome 15 probes are used for the detection of deletion in the Prader-Willi/Angelman Syndrome region."

  • Tissue culture for biochemical/DNA testing ( Material production service )

    Establishing culture from clinical samples.

  • Unstimulated peripheral blood chromosomal analysis ( Material analysis service )

    "Used for neoplastic disorders in which marrow cannot be obtained, and circulating blasts are present; or for STAT newborn chromosome analysis when bone marrow is not available."

  • Williams syndrome screening ( Material analysis service )

    "Specimen Requirements:
    For blood specimens: 3-5 mL drawn into a GREEN top sodium heparin vacutainer or into a pre-heparinized plastic syringe (use 0.2 mL sodium heparin, 1000 unti/mL).
    Do NOT use lithium heparin. 1-2 mL usually adequate for infants/small children.
    Keep at room temperature.

    Comments:
    Fluorescent In-Situ Hybridization methods combine both molecular and cytogenetic techniques. They are employed to delineate subtle syndrome related chromosome defects. Williams syndrome probes are used to examine chromosome 7 for deletion of the elastin gene."

Software

  • Elekta AB PowerPath ( Software )

    The PowerPath LIS (laboratory information system) "offers a powerful solution for managing laboratory workflow, providing the tools required to accurately and efficiently manage and communicate anatomic pathology diagnoses. The results are improved patient care, the potential for increased revenue and cost savings, better productivity and a truly paperless workflow.

    The PowerPath user interface provides a case-centric view that enables quick access to requisition data, case history, concurrent cases and billing information. When combined with fast, accurate results entry, PowerPath helps reduce case turnaround time."

  • Epic ( Software )

    Electronic medical record system.


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Last updated: 2012-08-17T14:37:58.185-05:00

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The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016