Loren Data's SAM Daily™

FBO DAILY - FEDBIZOPPS ISSUE OF OCTOBER 19, 2018 FBO #6174
DOCUMENT

Q -- Five Year Single Award IDIQ for SF Anatomic Pathology Lab Testing Services - Attachment

Notice Date

10/17/2018
 

Notice Type

Attachment
 

NAICS

621511 — Medical Laboratories
 

Contracting Office

Department of Veterans Affairs;VA Sierra Pacific Network (VISN 21);VA Northern California HealthCare System;5342 Dudley Blvd, Bldg 209;McClellan CA 95652-2609
 

ZIP Code

95652-2609
 

Solicitation Number

36C26119Q0060
 

Response Due

10/31/2018
 

Archive Date

11/14/2018
 

Point of Contact

brian.trahan@va.gov
 

E-Mail Address

Brian.Trahan@va.gov
(Brian.Trahan@va.gov)
 

Small Business Set-Aside

N/A
 

Description

PERFORMANCE WORK STATEMENT FOR ANATOMIC PATHOLOGY SERVICE LAB TESTING SCHEDULE OF SERVICES Contractor shall provide laboratory services to include specimen packaging and transport of specimens to its laboratories; pre-analytic processing as defined in its Laboratory Testing Manual; performing tests for Special stains and Immunochemical stains, EM Immunofluorescence, and molecular tests. After the sample is collected, received in the Anatomic pathology laboratory, the container is labeled with patient name, accession number along with the completed requisition form with patient information and type of tests. Make sure it has the correct patient name, accession number and proper tests for each request. The tests requested from contractor laboratory such as EM immunofluorescence tests for antibodies to unfixed, frozen sections. Special stains for microorganisms, connective tissue, carbohydrates, pigments, fats and lipids and cytoplasmic granules and nuclear elements. The tests results from Contractor laboratory will be reviewed by Attending Pathologists to finalize diagnosis for VA patients. Place of Performance: Services shall be provided at the outside laboratory. Pricing Instructions: The total cost shall base on number of tests submit to outside laboratories for processing including the courier service cost provides by Contractor. There is an increase of specimens received in Pathology laboratory for processing from other clinical services within the SFVAMC. The tests are submitted to be performed by outside laboratory and accurate results mean increased satisfaction and more effective for our veterans care. There is an increase of specimens received in the anatomic laboratory and these tests are more important for our veterans care. The VA pathologists evaluated the tissue and determine the best type of testing and amount of tissue available to processing. The total monthly cost depends on number of specimens received within the pathology laboratory which is average 10-30 cases a month. 1. SCOPE OF WORK 1. 1 Contractor shall provide laboratory courier services to pick up and transport specimens to its laboratory; preanalytic processing as defined in its laboratory user s manual; analysis, reporting of analytic results, and consultation regarding selection, collection, transportation and result interpretation. See attachment A for a list of additional tests for lab and Eye pathology. This list is not inclusive as patient testing needs change throughout the contract period. Changes can be in volume of tests and test menu. The contractor shall provide the following services: 1.1.2. Provide all necessary supplies, not limited to the following: Requisition forms Specimen containers Dry ice and appropriate container Special instructions Current list of tests with reference ranges and specimen requirements Specimen carriers All forms, including Chain of Custody forms Special media or tubes for viral samples All supplies for special tests (e.g., but not limited to, viral studies) 1.1.3 Provide specimen pick up courier services as defined in the contract. 1.1.4 Transport samples in such a manner as to ensure the integrity of the specimen. 1.1.5 Contractor shall supply any special preservatives required for specimen preservation. 1.1.6 Analyze samples. 1.1.7 Routine test results shall be faxed and reported within 1 to 3 days of specimen testing. 1.1.8 Provide test report summaries by the 3rd workday of each month following the month in which service was delivered. 1.1.9 Consult with Laboratory on test results by telephone as needed. 1.1.10 Provide VAMC Laboratories with a means of communication to permit immediate inquiry regarding the status of pending tests. 1.1.11 Billing and test report summaries shall begin the first day of the month and include the last day of the month. 2. LICENSING AND ACCREDITATION. 2.1. Contractor shall have all licenses, permits, accreditation and certificates required by law. 2.1.1. Contractor shall be accredited by the College of American Pathologists (CAP). 2.1.2. Contractor shall be accredited by Centers for Prevention and Disease Control (CDC) under CLIA if contractor is engaged in interstate commerce. 2.1.3 Laboratory Director shall be a licensed American Board of Pathology certified pathologist or appropriately certified bio-analyst. 3. CHANGES. 3.1. Contractor shall be responsible for assuring all subcontractors have appropriate licensure and accreditation to perform tests that the contractor cannot perform. Contractor shall notify the CO and the COR of any change of subcontract laboratory. Any change shall be submitted to the CO for review and approval. 3.2. If it is deemed that the removal of the test from the test menu is required, due to any changes by the contractor, then it will be communicated by the CO, COR or designee. 3.3. The VA may need to add test to the test list during the contract term without contract modification. This may be due to a change or discontinued test previously done by another laboratory. Requests may be made for pricing, specimen requirements and methodology. The CO, COR or designee will make the final decision on the appropriateness of moving the test to the contractor. 4. PROCEDURE GUIDANCE 4.1. The Contractor shall not introduce new medical procedures and services for specimens provided by VA without prior recommendation to, and approval of, the COR, or authorized laboratory representative. 4.1.1. The Contractor shall ensure that all procedures performed are of current acceptable standard deviation with at least (minimum) daily controls conducted to determine procedure accuracy (per all applicable regulatory agency [RA] guidelines). The standard deviation and daily control records are to be available for review upon request by the Contracting Officer or contracting officer s representative. 4.1.2. The Contractor shall perform repeat tests at no charge to the government if the results do not, in the government requesting physician's opinion; fit the clinical picture of the patient. When requesting these tests, the government requesting physician or representative will explain the conditions of the patient or any discrepancies observed. Repeat tests shall be the same test originally ordered. 4.1.3. The Contractor shall notify the VA COR or designee of instances in which, in the professional judgment of the Contractor, the patient requires services or tests, which were not originally requested. 4.1.4. Tests referred to another laboratory shall be at no additional transfer charge or confirmation charge to the government. 4.1.5. Contractor shall fill out and maintain for specimens the VA provided test request form necessary to meet clinical and administrative requirements of VA at no additional expense to the government. 4.1.6. The Contractor shall contact the VA COR to coordinate the furnishing and delivery of specimen collection and transportation supplies, terminal or data fax and supplies, and the installation of equipment. The Contractor shall provide to the VA facilities the supplies and equipment within two (2) work days after receipt of the delivery order. The VA COR will request replenishment of supplies from the Contractor on an as needed basis. 5. SPECIMEN PICK-UP TIMES. 5.1. Routine. The Contractor shall provide routine scheduled specimen pickup at a time mutually agreed upon by the VA COR but not less than three times a day. The VA COR or designee shall notify the Contractor during weekends (if not already scheduled) and federal holidays, via telephone, when a pick-up courier is required. 6. TEST RESULTS. 6.1. Routine. The Contractor shall provide routine test results to the ordering VA facility within 1 to 3 days following test completion, except when specimens are picked up the day before a weekend or holiday (in which case the results will be provided the following business day). 6.2. Telephone Consultation. The Contractor shall consult with the VA COR, requesting Clinician or designee at the VAMC by telephone as needed. 6.3. The Contractor shall immediately telephone the respective VA COR; requesting Clinician or designee to report Critical Values or test result that may indicate a life threatening condition. SLIDES. 7.1 The Contractor shall return presentative slides, anatomic, hematologic, etc., for quality control review when requested. Quality control slides shall represent duplicate copies original slides prepared by the Contractor from permanent tissue blocks. The Contractor shall provide quality control slides to the participating VAMC or clinics at the same time the contractor submits the final reports. 7.2 The Contractor shall prepare additional blocks and slides, in quantities specified by the participating VAMC for review by pathologists. 7.2.1 For malignant cases, the Contractor shall call results to the submitting VAMC, and prepare paraffin blocks and slides review by the Joint Pathology Center (JPC) or other Government Pathology Organization (GPO). 7.2.2. For benign cases, the Contractor shall prepare slides for review by participating VA. 8. STORAGE OF SPECIMENS. 8.1 The Contractor shall store all specimens as required by regulatory agencies (RA) 8.1.1 Upon request by the VA COR or designee, the Contractor shall provide a copy of the regulatory requirements for each participating RA. 8.1.2. In the absence of RA requirements, the Contractor shall store specimens, after all testing has been completed: clinical specimens seven (7) days, surgical specimens six (6) months, cytology and histopathology slides indefinitely; and paraffin blocks for five (5) years. 9. TEST SAMPLES. 9.1 Upon provision of sample slides by the government, the Contractor shall provide interpretation of sample slides. The sample may include, at a minimum, breast biopsy, thyroid biopsy, mastectomy with nodes, colon resection, lymph node biopsy, and gynecology and non-gynecology cytology. 10. MONTHLY TESTS SUMMARY. 10.1 The Contractor shall provide to each VA a cumulative (year-to-date) and monthly report of all tests received during the month and for all outstanding results. The report will also include turn around statistics, cost per test (including any additional charges) and specimen or testing issues. 11. SERVICE. 11.1 The contractor shall provide telephone number(s) and contact person to be used by the VA facilities to make specimen problem inquiries and problem solving at all times excluding weekends and holidays. 11.1.2 The contractor shall include names and telephone numbers of technical Directors available for consultation. 11.3 Contractor shall assign a specific local account representative to each VA facility. 11.4 Contractor shall advise facility of any changes in methodology, procedure, reference ranges, delays in testing, and any new tests introduced within a timely manner and prior to changes are made. 11.5 In the event that the contractor changes the assay procedure of a critically important component of an assay (e.g., and antibody, purified antigen, etc.), the contractor shall notify the VA COR prior to the intended change and provide documentation that the quality and efficacy of the test will remain unchanged or be improved when desirable for all tests. All new tests shall have CPT codes and LIONC coding. Changes in the assay materials or procedure may be sufficient cause for changing to an alternate contractor for the assay(s) for the duration of the contract at the sole discretion of the CO/COR. 11.5.1. If it is deemed that the removal of the test from the test menu is required, due to any changes by the contractor, then it will be communicated by the CO, COR or designee. 12. TELECOMMUNICATIONS. 12.1 Telecommunications Linkage. Each VA shall receive transmission of the results to a teleprinter located at the hospital site. Contractors shall provide personal computers (PC) or teleprinters at no charge for this service. Any necessary connection/devices shall be the responsibility of the contractor (including one commercial phone line for terminal/datafax connection if required). The transmission of all the completed and/or partial test results shall arrive at the hospital within published TAT except where specified. The contractor is responsible for all supplies required for transmission of test results. The referring VA facility will construct shipping lists on VISTA listing specimens, tests, and other information to openly identify the shipment. The referring VA facility will also transmit electronic messages containing those tests being transported to the receiving Contractor facility. The electronic transmission of orders will include shipping information to enable the VA receiving facility and the Contractor to have shipping information prior to arrival. These orders will be stored in a pending orders file, pending specimen./shipping list arrival. Shipping list will have complete information to allow manual order entry at the referral site, if required. Required information will include: Name of shipping facility Shipping List ID Shipping date/time Referring point of contract Method of shipment carrier, bill no., estimated time of arrival, etc. (if other than the reference lab courier) List of tests with patient demographics similar to VISTA load/worklist Bar code site and specimen ID on shipping list and specimen ID labels Automated order entry will also be possible with the use of a bar code scanner that reads patient demographics in a universal ID number format. The receiving facility (Contractor) shall: Process shipments upon arrival using shipping list Accession specimens into computer from pending orders file Update electronic shipping lists with status of specimens, i.e., received, missing, insufficient quantity, incorrect shipping conditions, improper specimen, etc. Store links to referring site/accession for acknowledge of shipment Receipt, status of testing and results transmission to referring VA facility and update workload, as appropriate Construct electronic messages containing test results and return to VA site Upon receipt of tests, the VA will update the order/accession with test results and allow either automatic release or provide for review before release as well as update workload. Emergencies due to computer malfunction, the Contractor will provide a contingency system to provide a hard copy to each VA facility. The hardware will be placed in a location designated by each VAMC and maintained according to the criteria specified in paragraph 13. TELECOMMUNICATONS with the following additions: Contractor will provide telephone service in the event of transmission or printer degradation Contractor will be responsible for the installation and, if and when necessary, the removal of all telecommunication equipment. This will take place a mutually agreed upon time between the VA facility and the Contractor Hardware(s) that is/are used for storing laboratory data should be sanitized prior to removal from the Clinical Laboratory. 13. TESTING METHODOLOGY & REFERENCE. 13.1 Testing methodology and reference ranges for a test must be defined in the laboratory user manual. 14. FAILURE OF AUTOMATED SYSTEM. 14.1 In case of failure of the automated system, the Contractor shall provide an alternate route of transmission (i.e. telephone, fax, or courier service) to the participating VAMC or clinic, and shall maintains same time frames as the automated system. 15. MAINTENANCE OF AUTOMATED SYSTEM. 15.1 The Contractor shall provide preventive and as-needed maintenance on the terminal system at the facility/clinic at no additional charge to the government. The Contractor shall provide maintenance within 72 hours of notification by the VA COR or designee. 16. CONTRACTOR PERSONNEL. 16.1 The Contractor shall make sure employees have current and valid professional certifications before starting work under this contract. Technologist, medical technicians, and cytotechnologist shall meet personnel qualifications required by Clinical Laboratory Improvement Act (CLIA) '88 Guidelines. Pathologists must have graduated from an approved school of medicine or osteopathy and completed a residency or fellowship in pathology acceptable to the United States Surgeons General must possess a valid license to practice clinical reference laboratory services from a United States (U.S.) jurisdiction; and shall have provided pathology services a minimum of 24 months within the past 36 months and pathology consultation services a minimum of 36 months within the past 48 months. 16.2 The Contractor shall maintain current licenses and certificates and provide copies of such to VA upon reasonable written request. 17.1 PERFORMANCE STANDARDS, QUALITY ASSURANCE (QA) AND QUALITY IMPROVEMENT (QI). 17.1.1 Quality Management/Quality Assurance Surveillance: Contractor performance will be monitored by the government using the standards as outlined in this Performance Work Statement (PWS) and methods of surveillance detailed in the Quality Assurance Surveillance Plan (QASP). The QASP shall be attached to the resultant contract and shall define the methods and frequency of surveillance conducted.   17.1.2 Employee Complaints: The CO will resolve complaints concerning Contractor relations with the Government employees or patients.   The CO is final authority on validating complaints.   In the event that The Contractor is involved and named in a validated patient complaint, the Government reserves the right to refuse acceptance of the services of such personnel.   This does not preclude refusal in the event of incidents involving physical or verbal abuse. 17.1.3 The Government reserves the right to refuse acceptance of any Contractor personnel at any time after performance begins, if personal or professional conduct jeopardizes patient care or interferes with the regular and ordinary operation of the facility.   Breaches of conduct include intoxication or debilitation resulting from drug use, theft, patient abuse, dereliction or negligence in performing directed tasks, or other conduct resulting in formal complaints by patient or other staff members to designated Government representatives.   Standards for conduct shall mirror those prescribed by current federal personnel regulations.   The CO and COR shall deal with issues raised concerning Contractor s conduct.   The final arbiter on questions of acceptability is the CO. 17.1.4 Performance Standards: 17.1.4.1 Measure: Proper labeling of Specimens Performance Requirement: All laboratory staff must handle and perform lab work without labeling errors. Standard: Contrator must handle the specimens properly during the tests processing. Acceptable Quality Level: Satisfactory rating = 100% Surveillance Method: Reviewed at monthly QI meeting Frequency: Every month 17.1.4.2 Measure:   Indication of Specimens Volume Performance Requirement: 10-40 tests per month depending on the specimen availability Standard: Excellent lab work services within the scope of practice 100% of the time Acceptable Quality Level: 100% satisfactory.   Surveillance Method: Review at the monthly QI meeting Frequency: Every month 17.1.4.3 Measure: Quality and TAT of tests results Performance Requirement: Excellent quality of slide staining.. Standard: Accurate diagnosis and turnaround time within 1-5 days. Acceptable Quality Level: Satisfactory rating = 100% during rating period. Surveillance Method: Reviewed at monthly QI meeting Frequency: Every month 17.1.4.4 Measure: Maintains licensing and registration Performance Requirement: Licensing and registration information kept current. Standard: All (100%) licensing for contract laboratory technicians shall be provided as they are renewed. Licensing and registration information kept current. Acceptable Quality Level: All laboratory technicians, licensing, registrations, and certifications must be kept current 100% of the time and proof provided upon renewal. Surveillance Method: Periodic Sampling Frequency: Annually 17.1.4.5 Measure: Privacy, Confidentiality and HIPAA Performance Requirement: Standard: All (100%) contractor technicians and pathologists comply with all laws, regulations, policies and procedures relating to Privacy, Confidentiality and HIPAA Acceptable Quality Level: 100% compliance Surveillance Method: Periodic inspection - Contractor shall provide evidence of annual training required by VANCHCS, reports violations per VA Directive 6500.6. Frequency: Annually 18. HOURS OF OPERATION. 18.1. Normal Hours of Operation. The Contractor shall perform the services required under this contract 8 to 10 hours a day, 5 days a week, 12 months of the year. The Contractor shall provide routine scheduled specimen pickup at a time mutually agreed upon by the VA COR. 19. RECORDS. 19.1 The Contractor shall be responsible for creating, maintaining and disposing of only those government required records that are specifically cited in the work statement or required by the provisions of a mandatory directive listed in section (d) Applicable Publications and Forms. If requested by the VA COR, the Contractor shall provide the original record, or a reproducible copy of any such record, promptly of receipt of the written request. 20. PATIENT LISTS. 20.1 The Contractor shall treat patient lists, no matter how developed, as privileged information. Lists and/or names of patients shall not be disclosed to or revealed in any way for any use outside the participating VAMC without prior written permission by the VA COR or Chief of the Medical Staff. 21. RELEASE OF MEDICAL INFORMATION. 21.1 The Contractor shall not release any medical information obtained during the course of this contract to anyone outside the VA, unless authorized in writing by the VA COR and the patient, as required by applicable law. 22. COLLEGE OF AMERICAN PATHOLOGISTS (CAP). 22.1 All testing facilities providing laboratory services under the contract must possess a valid state license, CLIA license and full accreditation from the College of American Pathologists (CAP). Contractor shall provide evidence of such accreditation upon receipt of a written request. 23. PROFESSIONAL LIABILITY INSURANCE. 23.1 Professional liability insurance shall be by a commercial insurance company in the business of providing the required insurance coverage. The Contractor shall provide a copy of the Insurance Certificate upon receipt of a written request. 24. SAFETY. 24.1 The Contractor shall comply with all applicable OSHA, Federal, State, laws, and regulations as required for performing the type of services required. 25. END OF CONTRACT PERFORMANCE. 25.1 At the end of the period of contract performance, the participating medical treatment facility will notify the Contractor of the quantity of unused supplies and arrange a pick-up time. All Contractor provided equipment shall be disconnected by the Contractor from the VAMC, upon contract expiration and removed within five working days. 26. GENERAL DEFINITIONS. Critical Value. A test result that requires evaluation by a physician or other health care provider as soon as verified. Failure to take appropriate action as a result of a critical value might cause harm or undue suffering for a patient. A list of critical values is to be made available to each VA facility upon request. Frozen Section. A biopsy specimen that is immediately frozen and cut with cryostat; then mounted on a slide, stained, and examined by a pathologist. Frozen sections provide a rapid diagnosis to the physician during surgery. Paraffin Block. A tissue specimen that has been embedded in paraffin wax that the sections can be cut for histologic examination. Reference or Referral Laboratory. The contract laboratory that provides testing, and examination of specimens provided by the medical treatment facility. Reference Value. A range of test values expected for a designated population of individuals. Slides. Glass surface containing biological material to be analyzed. Specimen. A body fluid or tissue sample removed for medical examination and analytical testing. STAT. A designated category of tests that requires immediate processing to expedite results to physicians handling potentially life-threatening cases. Surgical Specimen. A sample or part of an organ or tissue removed during surgery for medical examination and analytical testing. Tests. Diagnostic assays to evaluate a patient's physiological condition. Routine Test - A test that is usually performed at high volume in which the result is required in 24 hours generally. Specialized Test - A test that is performed in low volume but the technology, expense, or time-consuming nature of each test, is such that some delay is expected. However, results should be received within a reasonable amount of time to meet patient care needs. The delay usually occurs to allow tests received from different enters to be batch to make the operation cost-effected. Esoteric Test - A test that is similar to specialized tests, except they can only be done in a few laboratories throughout the country. TAT - The length of elapsed time between pick-up or dispatch of specimen from the contractor s laboratory until the receipt of the completed printed/ electronically transmitted report back in the lab. These definitions apply whether the contractor or a subcontractor performs the test. Special handling - Unusual circumstances may dictate the need for a specimen to be picked up, run out of sequence at a special time, or reported within a shorter than usual time. Overflow - A test usually performed in the VAMC lab, which might be referred to the contractor s laboratory in case of instrument breakdown or other circumstances interfering with the VAMC s ability to analyze the specimens. Proficiency Testing - An assessment of the accuracy of testing by a laboratory based on the analysis of an unknown specimen analyzed by a large number of other labs. The proficiency survey is conducted by an organization or agency authorized by the Department of Health and Human Services to do so. 27. SAMPLE PREPARATION. 27.1 Each VA facility will provide laboratory specimens prepared according to the contractor's laboratory specimens according to industry standards. Contractor shall supply any special preservatives required for specimen preservation. 27.2 Each VA facility is responsible for packaging the specimens and courier transport specimens between SFVMC Pathology laboratory at 4150 Clement Street, San Francisco, CA 94121. Attachment A Additional IPOX and Special stains submitted to Contractor laboratory. MOLECULAR TESTS Molecular test Utility Method Lab Protocol abbreviation in CoPath (Run stain / Process groups) Specimen type Turnaround time 1p/19q deletion Oligodendroglioma FISH Clinical Cancer Genomics Lab 1p19q Formalin-fixed tumor tissue 1-2 weeks ALK rearrangement for lung cancer Non-Small Cell Lung Cancer (NSCLC) FISH Clinical Cancer Genomics Lab ALK FISH FFPE or cytology sample 1-2 weeks ALK rearrangement for lymphoma Anaplastic large cell lymphoma FISH Cytogenetics Lab Contact Cytogenetics to arrange testing     BCR-ABL t(9;22) on fresh tissue CML, ALL, AML FISH Cytogenetics Lab   EDTA, blood, bone marrow aspirate 3-10 days BCR-ABL t(9;22), quantitative CML, ALL, AML RT-PCR Molecular Diagnostics   EDTA, blood, bone marrow aspirate 7-10 days BRAF mutation Thyroid, colon, lung cancer; melanoma; histiocytic diseases Sanger sequencing Clinical Cancer Genomics Lab  BRAF-PCR FFPE or cytology sample 1-2 weeks c-Kit mutation See KIT mutation below c- Myc amplification Medulloblastoma (see IGH-MYC for lymphoma) FISH Clinical Cancer Genomics Lab c-Myc FISH (MYC) Formalin-fixed tumor tissue 1-2 weeks EGFR amplification Glioblastoma FISH Clinical Cancer Genomics Lab EGFRFISH Formalin-fixed tumor tissue 1-2 weeks EGFR mutation Non-small cell lung cancer (NSCLC) Sanger sequencing Clinical Cancer Genomics Lab EGFR FFPE or cytology sample 1-2 weeks EWSR1 rearrangement Ewing sarcoma/PNET; other Ewing family tumors FISH Sendout FISH from Molecular Diagnostics Lab  EWS FFPE or cytology sample 1-2 weeks Extended RAS testing (KRAS, NRAS, BRAF) Colon cancer Sanger sequencing Clinical Cancer Genomics Lab   FFPE or cytology sample 1-2 weeks Flow Cytometry Leukemia/lymphoma Flow Cytometry Immunology   Fresh tissue in RPMI; do not freeze   GNA11 mutation Melanoma Sanger sequencing Clinical Cancer Genomics Lab GNA11 FFPE or cytology sample 1-2 weeks GNAQ mutation Melanoma Sanger sequencing Clinical Cancer Genomics Lab GNAQ FFPE or cytology sample 1-2 weeks Hydatidiform mole genotyping Suspected molar pregnancy PCR and fragment analysis Clinical Cancer Genomics Lab MLR (genotyping only) or MLRp57 (genotyping and p57 IHC) Formalin-fixed tissue.   Both maternal and fetal tissue are required. 1-2 weeks IDH1 mutation Brain tumors, AML Sanger sequencing Clinical Cancer Genomics Lab IDH1PCR for IDH1 only, IDH1,2PCR for both IDH1 and IDH2 FFPE or fresh blood/marrow in EDTA tube 1-2 weeks IDH2 mutation Brain tumors, AML Sanger sequencing Clinical Cancer Genomics Lab IDH2PCR for IDH2 only, IDH1,2PCR for both IDH1 and IDH2 FFPE or fresh blood/marrow in EDTA tube 1-2 weeks IGH-BCL2 t(14;18) translocation Double hit diffuse large B-cell lymphoma FISH Cytogenetics Lab Contact Cytogenetics to arrange testing FFPE or cytology sample   IGH-MYC t(8;14) translocation Double hit diffuse large B-cell lymphoma FISH Cytogenetics Lab Contact Cytogenetics to arrange testing FFPE or cytology sample   IGH 14q32 rearrangement B-cell lymphoma FISH Cytogenetics Lab Contact Cytogenetics to arrange testing FFPE or cytology sample   Isochromosome 17q Medulloblastoma FISH Clinical Cancer Genomics Lab  17q Formalin-fixed tumor tissue 1-2 weeks KIT mutation GI stromal tumors, melanoma, mastocytosis. NOT RECOMMENDED for leukemia. Sanger sequencing Clinical Cancer Genomics Lab KITPCR FFPE or cytology sample 1-2 weeks KRAS mutation (including codons 12, 13, 59, 61, 117, 146) Colon cancer, Lung cancer Sangersequencing Clinical Cancer Genomics Lab  KRAS FFPE or cytology sample 1-2 weeks Melanoma CGH (comparative genomic hybridization) Melanoma Array CGH Dermatopathology Lab   Formalin-fixed tumor tissue   Microsatellite Instability (MSI) Colon, uterine, other Lynch cancers PCR and fragment analysis Clinical Cancer Genomics Lab MSI for PCR+MMR IHC; MSIpcr for PCR only Formalin-fixed tissue.   Both tumor and normal (non-tumor) tissue are required. 1-2 weeks MGMT promoter methylation Brain tumors Bisulfite treatment and sequencing Molecular Diagnostics Lab FFPE 2-3 weeks MLH1 Promoter Methylation Identify sporadic MSI-H tumors with MLH1 hypermethylation Bisulfite treatment and real-time PCR Clinical Cancer Genomics Lab  MLH1METH Formalin-fixed tumor and normal tissue 1-2 weeks MYC (c-Myc) amplification See c-Myc amplification above. (see IGH-MYC for lymphoma) n-MYC amplification Medulloblastoma, Neuroblastoma (see IGH-MYC for lymphoma) FISH Clinical Cancer Genomics Lab MYCN Formalin-fixed tumor tissue 1-2 weeks NRAS mutation (including codons 12, 13, 59, 61) Colon cancer, melanoma Sanger sequencing Clinical Cancer Genomics Lab NRASPCR Formalin-fixed tumor tissue 1-2 weeks PTEN deletion Glioblastoma FISH Clinical Cancer Genomics Lab  PTEN Formalin-fixed tumor tissue 1-2 weeks RAS testing Confirm exactly which test(s) are needed.   May include KRAS, NRAS, BRAF, or all three (Extended RAS).   See entries for each. ROS1 rearrangement Lung cancer FISH Cancer Genetics (formerly Response Genetics) Send block to outside lab     Specimen identification testing Specimen identification PCR of short tandem repeats Clinical Cancer Genomics Lab SID for each block. Contact J.P. Grenert, N Joseph, or CCGL when ordering Formalin-fixed paraffin-embedded tissue or blood 1-2 weeks SYT (SS18) rearrangement Synovial sarcoma FISH Sendout FISH from Molecular Diagnostics Lab SS18 FFPE or cytology sample 1-2 weeks Urovysion Bladder cancer FISH Sendout FISH from Molecular Diagnostics Lab   Urine in Carbowax fixative 1-2 weeks Description Qty. Unit Cost Total Annual Cost Molecular tests, Special stains, EM Immunoflourescence tests (Renal and Derm cases) Monthly 15 30 cases DO NOT PRICE DO NOT PRICE Muscle,collagen connective tissue Congo Red C-myc MDM2 PAX2 Bap.1 Kappa and lambda CKIT Analysis in GISTs FISH DNA Probe FISH Analysis EGFR Mutation Breast IHC/FISH Immunoglobulin G, F (ab)2 Fraction Immunoglobulin M Immunoglobulin A Complement, C3 Complement, C1q Fibrinogen Albumin Kappa, Fc Fraction Dystrophin (muscle) HLA-Dr (tx heart Bx) HLA-abc (tx heart Bx) Complement C4d Collagen type IV, a1, A3, a5 chains
 

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