B--SOURCES SOUGHT DATA ANNOTATION, MAPPING AND CURATION SERVICE

The purpose of this synopsis is to gain knowledge of potential qualified sources who can meet the requirements below and their size classification (large business, small business, 8(a), SDVOSB, etc.), relative to NAICS code 518210. Responses to this synopsis will be used by the Government to make appropriate acquisition decisions. Based on responses to this synopsis, the Government intends to issue a Request for Quotation (RFQ). This notice is not a request for competitive proposals, however; any responsible source who believes it is capable of meeting the requirement may submit a capability statement to the contracting office no later than Wednesday, August 2nd, 2017 at 4 PM, EST. Interest/capability statements may be sent to Lynn Portman at contact@example.gov. No telephone responses will be accepted. Vendors must include company name, address, point of contact, business size, SDVOSB/VOSB status, and capability information. Additionally, the Government is interested in the industry standard pricing. Therefore, vendors must also include a proposed pricing methodology for these services (i.e. flat hourly rate, labor category, etc.). The government is not requesting a formal quote, but instead trying to determine the industry standard for the pricing of the services. This notice is to assist the Government in determining sources capable of performing this work and gather other relevant information on industry norms. A solicitation is not currently available. If a solicitation is issued, all interested parties must respond to that solicitation announcement separately from the responses to this announcement. The Million Veteran Program (MVP) is a national research program initiated in 2011 that is creating a resource of genetic information of one million consented Veteran volunteers (who receive their health care from the VA) linked with information from self-reported survey instruments and their electronic health records. There are 50 Veteran Affairs Medical Centers (VAMCs) enrolling participants into MVP, with the goal of expanding to other VA centers. Currently, over 370,000 participants have fully consented and provided a blood sample to MVP. Thus, VA currently stands at the cutting edge of generating, storing and analyzing large amount of clinical and genomic data and needs resources to ensure data is efficiently used so that the Veterans receive the benefit of the latest technology and research to best meet their health needs. to secure multiple scientific services for the large amount of clinical and genomic data that is being generated to support the VA s Genomic Medicine Program, particularly to forward the objectives of the GMP cornerstone program, the Million Veteran Program. The Veterans Health Administration Office of Research and Development (ORD) requires the service of data annotation, mapping and curation service as well as Scientific Help Desk services to help trouble shoot the genomic analysis tools in the High Performance Computing environment. In the context of such large volumes of data getting the appropriate data for specific analysis such as advising for target based individualized therapy, becomes a challenge. In order to efficiently perform such specific analysis, the MVP data needs to be annotated, mapped to available standard terminologies, metadata collected and organized by developing common data elements and creating ontological representations that is amenable to aggregate queries and curated to assist in developing meaningful associations. Towards this goal an MVP knowledge Ontology Repository needs to be created and vendor service is required for the following tasks: Scientific Help desk manned by genomic analysis experts in the field of GWAS analysis from both genotype data as well as sequence data. Data annotation and associations with reference/standards. Curation of molecular data to develop disease and outcomes association annotation knowledgebase. Terminology mapping and metadata curation for meaningful ontology representation. Advanced statistical analysis for association studies and Molecular pathway analysis The following tasks may be included in a future solicitation. The contractor shall furnish all the necessary services, qualified personnel, expertise or other materials not provided by the government, as needed to perform Task assignments in the following task areas. The qualified personnel required to perform these tasks are projected to include a Bioinformatician, Computational Biologist, Data Scientist, Clinical Informaticist, HPC Expert (Sysadmin), Tech Writer, Statistical Geneticist, Data Modeler. Task 1: Detailed Project Management Plan: The Contractor shall provide a Project Management Plan (PMP) that lays out the Contractor s approach, timeline and tools to be used in execution of the contract. - The PMP should take the form of both a narrative and graphic format that displays the schedule, milestones, risks and resource support. - The PMP shall also include how the Contractor shall coordinate and execute planned, routine, and special data collection reporting requests as identified within the PWS; risk management strategy; communications management strategy; and process for monitoring individual task performance. The initial baseline PMP shall be concurred upon and updated monthly by the vendor PM thereafter. The Contractor shall update and maintain the VA Program Manager (PM) approved PMP throughout the period of performance. The Contractor shall notify the Contracting Officer's Representative (COR) and the VA PM in writing, in advance of any deviation from the approved plan, noting the specific deviation, the rationale for the deviation, and impact if deviation is not approved. Deliverable 1. Detailed Project Management Plan and iterative updates. Task 2: Attend an initial contract kick-off meeting, and as needed meetings through the life of the contract: A kick off meeting will be held at or near the Boston Jamaica Plains Campus of the Department of Veterans Affairs within 14 days after contract award and shall be attended by all staff responsible for this contract. This meeting may take place via teleconference if agreed upon by the VA PD/COR. The contractor shall be required to communicate with VA PM and staff assigned to this project on an as needed basis throughout the life of the contract via an agreed upon method of communication like in-person visit, teleconference or videoconference. Deliverable 2: A kick-off meeting plan, agenda and meeting minutes. Task 3: Monthly Status Reports The Contractor shall provide written Monthly Status Reports that include schedule, milestones, costs and task assignments, expended efforts in each labor categories etc in the past month and plans for the next month. The report should have sufficient information to track all aspects of the tasks being undertaken to enable any necessary mutually agreed upon adjustments. This report does not relieve the contractor of the responsibility to proactively keep the government informed of issues or problems as they occur. Deliverable 3: Monthly Status Report. Task 4. Scientific Help Desk: Currently multiple GWAS studies are being conducted with over 400,000 genotyped samples in multiple disease domains. The contractor shall maintain a scientific help desk during office hours to answer analysts/researcher questions regarding data, statistical analysis and tools. Extensive experience with using the common genomic analysis tools like PLINK, RVTESTS, Eigensoft, Bioconductor, Impute2, GATK, etc is required. The contractor shall document all the issue requests in a ticketing system and track metrics like the average turn around time etc. Deliverable 4: Monthly Help Desk performance report Task 5: Data Annotation/Modelling Model complex MVP data types to capture their inter-relationships and facilitate capture of relevant metadata. The data model shall permit efficient query potentially at the meta data layer and evolving relationship management. The contractor shall support the following efforts either already underway or planned for GenISIS: Develop data models for capturing genomic data annotations. Model capture and upkeep of the changing/evolving genomic data annotations for downstream research purposes. Develop and implement meta-data and meta-thesaurus standards and searchable annotations that would enable uniform concept representations and support translation genomics. Deliverable 5: a) Data annotation models b) Data annotations implementations for research Task 6: HPC System testing services. The contractor shall support efforts to define and manage the GenISIS Data environment by developing testing protocols, and best practices approaches. Activities will include research, and development of appropriate test methodologies to maintain data fidelity and provenance. Deliverable 6: Best Practices document for genomic analysis Task 7: Biostatistics and Bioinformatics Analytics Support The contractor shall provide analytical support services to provide Scientific Help Desk for researchers. The contractor will also support the development of graphical summaries of available data and assist with choices and development of appropriate statistical and computational methodologies for data QA/QC and analytical support for translational genomics. This notice is not a request for competitive proposals, however; any responsible source who believes it is capable of meeting the requirement may submit a capability statement to the contracting office no later than Wednesday, August 2nd, 2017 at 4 PM, EST. Interest/capability statements may be sent to Lynn Portman at contact@example.gov. Vendors must include company name, address, point of contact, business size, SDVOSB/VOSB status, and capability information. Additionally, the Government is interested in the industry standard pricing. Therefore, vendors must also include a proposed pricing methodology for these services (i.e. flat hourly rate, labor category, etc.). No telephone responses will be accepted. This notice is to assist the Government in determining sources capable of performing this work and gather other relevant information on industry norms. A solicitation is not currently available. If a solicitation is issued, all interested parties must respond to that solicitation announcement separately from the responses to this announcement.