A--Oncogenetics Genomics Oncology Research and Treatment via targeted DNA sequencing for known mutations inference against known lab reference or from patient germ-line or carcinoma spec or sequencing RNA Transcriptomeor whole exome

Request for Information (RFI). This is not a solicitation or request for proposals. METATAGS: Oncogenetics Genomics Oncology Research and Treatment via targeted DNA sequencing for known mutations and inference against known laboratory reference or from patient germ-line or carcinoma specimen sequencing RNA-transcriptome or from whole exome The Department of Veterans Affairs, Veterans Health Administration requests information from the research laboratory CLIA-certified profit and non-profit community regarding capabilities to support genomic analysis and testing. Laboratories, contractors, research affiliates and universities are welcomed to furnish to the Contracting Officer below brief responses to the following request for information: Statement of Issue: Advances in the treatment and management of patients with cancer will arise from precise phenotyping and detailed molecular characterization of VA patients and their specimens. The growing capability for detailed genomic analysis of tumor tissue provides vast improvements over current clinical testing models that are rapidly becoming inadequate and outdated. The Veterans Integrated Service Network 1 (VISN 1) has undertaken a program to support the collection and enhanced analysis of clinical and specimen-derived data on all patients seen at VA network hospitals who have a cancer diagnosis. The VA seeks to engage the contractor community with robust, scalable, dynamic, secure, innovative solutions of analyzing samples obtained during regular clinical care - such as tissues from biopsy - using new genomic assay technology. The Department seeks the vendor community to provide emerging technologies to improve oncology care for all patients within the VA healthcare system. The Department recognizes that there is a lack of consensus regarding which method of tumor mutation analysis is most practical, informative and cost-effective. The Department is particularly interested in the following methods: 1. Targeted sequencing of DNA fragments known to harbor mutations in cancer specimens (commonly referred to as a mutation panel). The number of DNA segments sequenced varies by the laboratory and assay performed. Mutations in the DNA can either be inferred against a laboratory 'reference' sequence or can be determined by sequencing of patient germ-line DNA obtained from adjacent normal tissue or peripheral blood. 2. Sequencing of the whole exome of cancer specimens, with mutations identified by comparison against a laboratory 'reference' sequence or germ-line DNA as described above. 3. Sequencing of the cancer specimen RNA or 'transcriptome'. This strategy can be combined with either targeted or whole exome DNA sequencing. The Veterans Administration welcomes information from your enterprise on your present, existing ability to perform enhanced target based oncology testing for veteran patients, including receipt and cataloging of all histopathologic specimens, pathology review to confirm the presence of cancer and determine tissue quality for testing, and extraction of and quality assessment of DNA and possibly RNA, implementation of your recommended testing approach among target or whole exome sequencing and use either of a laboratory reference or germ-line DNA as the comparator for variant calling and also performing whole transcriptome sequencing of tumor samples. Products of the testing returned to the VA include all sequence data including raw test data (FAST-Q, BAM, read quality files and variant call files) and a report of important mutations and their significance to be returned to the medical record. Mutations found in the tumor sample will be annotated so that clinicians can gain an understanding of their meaning. The laboratory shall specify how this annotation will be performed and in particular, what knowledge base will be used to generate the annotations. Due to the rapid evolution of knowledge generation in this field, a VA vendor must be able to demonstrate how the vendor maintains an up-to-date knowledge base and must be able to update annotations of a patient report upon request. Due to innovations, improvements and rapidly declining costs or tumor analysis, it is expected that the preferred testing technology will change over time. In your response to this RFI you are invited to describe how your testing platforms will keep pace with these changes. Please number your response to this RFI such that your answers track to the following questions (1 through 27). 1. Where are the headquarters and laboratory facilities where your laboratory performs work? 2. Is your laboratory CLIA-certified? What is your CLIA certification number? 3. What FDA approved tests and panels is your laboratory currently performing? 4. Please describe the bio-informatics tools that you presently possess. 5. Describe your workflows and capacity for throughput and turn-around 6. Describe your current procedures for UID (Unique Identification) of samples, sample integrity and information integrity. 7. What analytical method is used in your laboratory? What equipment do you presently have in inventory to perform analyses? 8. Describe your ability to produce documentation of sample handling and processing attributes/audit trail, etc. that would address sample mixing and sample error tracking. 9. Describe your ability to electronically return select analysis results in a defined format to VA clinical laboratories (describe native and customizable file formats) 10. What processes do you subcontract out? What analyses do you subcontract out? 11. Describe your present, current information security, IT connectivity and bandwidth capacity? Including your present, current capacity for SFTP, VPN, PKI, including any (DOD, NASA, DHS) NISPOM facility level clearances. 12. Describe any accreditations and formalized affiliations that your laboratory/facility presently, currently possesses. 13. Describe the number of full-time employees you presently employ. (Not part-time personnel, Not sub-contractors, Not independent contractors). 14. Describe any scalable features that your enterprise presently has. 15. Please describe any unique capabilities that your facility has that are beneficial to your clients, including, personnel, equipment, protocols, access to licensing, patented processes, data management, etc. 16. The Department of Veterans Affairs welcomes information from small-business enterprises; please describe your enterprise size, in terms of full-time personnel, gross receipts. 17. What information would you, as laboratory vendor/contractor require from Veterans Health Administration in order to meaningfully respond to a competitive VA solicitation? (Please be as detailed as necessary.) 18. How do you determine suitability of tissue for panel testing? What volume do you require? What is the lowest percent cancer cellularity that you can use? 19. How many individual samples has your laboratory analyzed? 20. What is your method of knowledge curation that allows sample annotation? If recommending a panel test: 21. How may genes should a targeted panel study to be of optimal use for patient care? (Match patients to drugs both FDA approved). 22. How may genes should a targeted panel study to be of optimal use for identifying subjects for drug trials (Match patients to drugs both FDA approved)? 23. What degree of coverage is necessary for panel testing? 24. How often do you reassess and update your test? 25. Describe from your perspective an efficient pricing mechanism such that your Accounts Receivable (AR) department and VA would have visibility into both quantity and type of panels and batches, volume discounts and transparency in pricing. Describe from your experience pricing and invoicing regimes that are efficient, What barriers are there to implementing a non-complex, transparent and efficient pricing and invoicing regime? (You may be as detailed as necessary.) 26. Does your firm/enterprise publish its pricing or rate structures to the web? Do you maintain catalog prices or price lists? 27. Does your firm or enterprise access the Government Purchase Card (GPC) (Credit Card) as a method of payment? In your response to this Request for Information (RFI) please address the foregoing specific items; you may be brief in your response (5 to 10 pages) but be comprehensive. Your response is important for the VHA in formulating any ensuing solicitation so you may elaborator as necessary. You may also draw attention to any salient issues. However, please note: general marketing information, trade literature and general promotional literature are of less interest than your individuated response. Include the name, address, email phone and fax of the person(s) in your Contracting Office or your Office of Grants and Sponsored Programs. Refer to this RFI number on all communications. The Department of Veterans Affairs underscores its interest both in new entrants to federal contracting and in the small business (SB) community who may have interest and present, immediate capacity in genomics. Interested contractors and vendors should monitor this web site (FBO) and Forecast of Opportunities (FCO) for VA requirements. Please respond to the Contracting Officer below within thirty (30) days of this RFI. You may respond either via US Mail (return receipt preferred) or via email. Information provided in response to this RFI does not comprise the basis of any contract or ensuing agreement; information received shall be shared with members of the Government team in order to inform the Acquisition Strategy (basis of the acquisition, set-asides, form of solicitation and model contract vehicle) This RFI and the responses hereto comprise acquisition planning and market research information under FAR Part 7 and Part 10. No media will be returned to any respondents of this RFI. contact@example.gov , John Young, NCO 1 Contracting Mail Stop 90C 623 At wells Avenue, Providence, RI 02909-2472, +1 (555) 000-0000 x 1588. Service Disabled and Veteran-Owned Small Businesses (SDVOSB and VOSB) contracting with VA are to be registered and certified by the Center for Veteran Enterprise (CVE) in Vatic if seeking consideration under PL 109-461 (www.vetbiz.gov - Vendor Information Pages - VIP) All contractors are required to be registered in the System for Award Management (www.sam.gov). Consult your State Procurement Technical Assistance Center (PTAC) for technical assistance with these requirements. (http://www.dla.mil/db/procurem.htm). Link to the VA Forecast of Contracting Opportunities: http://www.vendorportal.ecms.va.gov/eVP/fco/FCO.aspx DISCLAIMER This RFI is issued solely for information and planning purposes only and does not constitute a solicitation. All information received in response to this RFI that is marked as proprietary will be handled accordingly. In accordance with FAR 15.201(e), responses to this notice are not offers and cannot be accepted by the Government to form a binding contract. Responders are solely responsible for all expenses associated with responding to this RFI.