Whole Exome Sequencing of Formalin-Fixed Paraffin-Embedded (FFPE) Prostate Cancer Biopsies
Contracting Office Address
Department of Health and Human Services, National Institutes of Health, National Cancer Institute, Office of Acquisitions, 9609 Medical Center Drive, Room 1E134, Bethesda, MD 20892, UNITED STATES
Description
The National Cancer Institute (NCI), Center for Cancer Research (CCR), Radiation Oncology Branch (ROB) plans to procure on a sole source basis custom whole exome sequencing from Genewiz, LLC, 115 Corporate Blvd, South Plainfield, NJ 07080-2409.
This acquisition will be processed in accordance with the simplified acquisition procedures as authorized by FAR Part 13.106-1 (b) (1) and is exempt from the requirements of FAR Part 6. The North American Industry Classification System Code is 541380 and the business size standard is $15.0 million.
Only one award will be made as a result of this solicitation. This will be awarded as a firm fixed price type contract.
The period of performance shall be August 1, 2018 through September 1, 2018.
It has been determined there are no opportunities to acquire green products or services for this procurement.
BACKGROUND
The CCR, ROB research goal is to understand the molecular events that drive radiation therapy resistance in prostate cancer. Blood derived genomic DNA will be exome sequenced at high coverage (50-100x) (n=29). Tissue from targeted biopsies will be enriched for tumor, genomic DNA extracted, and exome sequenced at very high depth (200-300x target coverage). Somatic point mutations, insertions/deletions, and copy number alterations will be identified. (n=60). Tissue from normal tissue where available will be sequenced to serve as a "panel of normals" (required for eliminating false positives) at moderate depth (50-100x), (n=21). The ROB has conducted a preliminary feasibility study using two sets of patient samples to determine if adequate yields of tumor can be obtained from baseline biopsies for sequencing and microarray, and to optimize sequencing output for coverage needed.
OBJECTIVE
The CCR, ROB research goal is to understand the molecular events that drive radiation therapy resistance in prostate cancer. The purpose of this project is to assess genetic changes found in pre-treatment prostate biopsies to determine biological predictors and factors for radiation resistance. Whole Exome Sequencing will be performed on normal and tumor biopsies acquired prior to radiation therapy.
SCOPE
This will encompass custom whole exome sequencing. One hundred and ten homo (110) sapiens samples of double stranded genomic DNA will be sequenced by Illumina HiSeq configuration. The estimated output is approximately 350M raw paired-end reads per lane with a quality guarantee of >80% of bases > Q30. Reports will be delivered as FASTQ files.
CONTRACT REQUIREMENTS/ AND PERSONNEL QUALIFICATIONS
The Contractor shall:
Generate a sequencing library for each sample. Perform exome sequencing with 5gb to 60 gb output (gb = 1 billion sequenced bases), equivalent to 50X - 200X for each sample. Sample output needed will be specified for each sample individually.
Reports - The Government will receive regular updates including QC reports and sequencing metrics.
QUALITY ASSURANCE
Contractor Quality Requirements
Tests - Contractor shall use existing knowledge of acceptable libraries and sequencing output to verify that quality is maintained.
Supervision - This should be limited to avoid employee/employer relationships.
There is no potential conflict of interest on this point.
GOVERNMENT QUALITY ASSURANCE
Inspection Criteria - The Government will download FASTQ files by secure FTP/GLOBUS.
Acceptance Criteria - The Government will perform sequence alignment and contamination checks to verify that the sequence reads are genuine and authentic. The Government will assess data delivery to determine that specified sequencing output (in gb) is delivered for each sample as required.
PLACE OF PERFORMANCE
At the Contractor's Facility.
REPORT(S)/DELIVERABLES AND DELIVERY SCHEDULE
All deliverables will be sent to the NCI Technical Point of Contact.
Deliverables: Quality report, FASTQ files. The Government will receive one or more pairs of FASTQ files for each sample to be sequenced. FASTQ file pairs will contain 5-60gb of sequencing output, as indicated for each sample submitted.
GeneWiz is a sequencing facility with the instrumentation needed to sequence 110 samples at very high depth in the time frame needed. GeneWiz is the only known vendor to have performed a previous pilot study in collaboration with the Government that demonstrated their ability of this project. A comprehensive and robust pilot study from a previous procurement was performed in collaboration with GeneWiz on normal biopsy material to determine optimal input and sequencing requirements to achieve 100-200x coverage needed to effectively analyze genomic alterations in these samples. This pilot study is specific to GeneWiz instrumentation and selecting another Contractor would require the unfeasible task of repeating the pilot study. This is a large sequencing project with 110 different precious pre-treatment patient samples which cannot be replaced. Therefore, this requirement is for continuity of service. GeneWiz has previously performed studies with samples from this study to determine if adequate quality and quantity of DNA could be obtained for informative whole exome sequencing using their materials and hardware. The samples tested for this ongoing project are low abundance/concentration and quality is impacted from the extraction from paraffin embedded tissue. GeneWiz previously sequenced several samples that are included in this project to clarify the depth of sequencing required to provide useful data. This data will be integrated with that of additional samples included in this requirement. It is vital that the sequencing conditions be maintained between the previously sequenced samples and the samples tested through this requirement.
This notice is not a request for competitive quotation. However, if any interested party, especially small businesses, believes it can meet the above requirement, it may submit a capability statement, proposal, or quotation, which shall be considered by the agency. The statement of capabilities and any other information furnished must be in writing and must contain material in sufficient detail to allow NCI to determine if the party can perform the requirement. Responses must be received in the contracting office by 5:00 PM EST, on
June 26, 2018. All responses and questions can be emailed to Kimesha Leake, Contracting Officer via electronic mail at kimesha.leake@nih.gov. A determination by the Government not to compete this proposed requirement based upon responses to this notice is solely within the discretion of the Government. Information received will be considered solely for the purpose of determining whether to conduct a competitive procurement. In order to receive an award, contractors must be registered and have valid certification in the System for Award Management (SAM) through sam.gov. Reference: N02RC82577-24 on all correspondence.
Kimesha Leake, Contracting Officer, Phone 2402765669, Email kimesha.leake@nih.gov - Reyes Rodriguez, Contracting Officer, Phone 240-276-5442, Email reyes.rodriguez@nih.gov
