SPECIAL NOTICE
Q -- Evaluation of Methods for Ascertainment of Microbial Communities in Oral and Fecal Samples
- Notice Date
- 7/17/2020 8:41:16 AM
- Notice Type
- Special Notice
- NAICS
- 541380
— Testing Laboratories
- Contracting Office
- NIH National Cancer Institute Rockville MD 20850 USA
- ZIP Code
- 20850
- Solicitation Number
- 75N91020Q00090
- Response Due
- 7/24/2020 10:00:00 AM
- Archive Date
- 08/08/2020
- Point of Contact
- Adam Hernandez, Phone: 240-276-5633
- E-Mail Address
-
adam.hernandez@nih.gov
(adam.hernandez@nih.gov)
- Description
- The U.S. Department of Health and Human Services (DHHS), National Institutes of Health (NIH), National Cancer Institute (NCI), Division of Cancer Epidemiology and Genetics (DCEG), Metabolic Epidemiology Branch (MEB) intends to procure, on a sole source basis, the evaluation of methods for ascertainment of microbial communities in oral and fecal samples from Diversigen, Inc., 2450 Holcombe Blvd, Ste 10, Houston, TX, 77021-2040, United States. The response close date of the notice for this requirement is in accordance with FAR 5.203(b). This acquisition will be processed under FAR Part 12 � Acquisition for Commercial Items and will be made pursuant to the authority in FAR Part 13.106-1(b)(1); and is exempt from the requirements of FAR Part 6. The North American Industry Classification System (NAICS) code is 541380 and the business size standard is $16.5 million. 1.0 BACKGROUND The human microbiome has been found to be associated with many health outcomes, including various types of cancer. Most of the studies in the Metabolic Epidemiology Branch (MEB) to date have used amplicon sequencing targeting the 16S rRNA gene to study the bacteria found in oral and fecal specimens, but methods are available to target the fungal component (ITS gene sequencing) and all microbes in a sample (shotgun metagenomic sequencing). To move forward using these new technologies, MEB must evaluate these methods using multiple sample types and study populations. 1.1 OBJECTIVE The U.S. Department of Health and Human Services (DHHS), National Institutes of Health (NIH), National Cancer Institute (NCI), Division of Cancer Epidemiology and Genetics (DCEG), Metabolic Epidemiology Branch (MEB) requires the evaluation of methods for ascertainment of microbial communities in oral and fecal samples. The purpose of this study is to evaluate methods used to measure microbial communities in oral and fecal samples. Three different methods shall be used to measure microbiota: 16S rRNA gene sequencing to measure bacteria; ITS gene sequencing to measure fungi; and shotgun metagenomic sequencing to characterize the whole microbial community. 2.0 SCOPE The Metabolic Epidemiology Branch (MEB) shall send 184 oral specimens, and 240 extracted DNA specimens (including extracted DNA from fecal samples) to the Contractor within 60 days after the purchase order award. DNA extraction shall be performed on the 184 oral specimens. 16S rRNA gene sequencing shall be performed on the extracted DNA from the 184 oral specimens. ITS2 gene sequencing shall be performed on the extracted DNA from the 184 oral specimens and an additional 192 aliquots of previously extracted DNA. Shotgun sequencing shall be conducted using the 184 oral specimens and the 240 extracted DNA specimens from oral and fecal samples. The sequencing data shall be processed bioinformatically and residual extracted DNA returned to the NCI. 3.0 CONTRACT REQUIREMENTS/ AND PERSONNEL QUALIFICATIONS The contractor shall perform the following tasks: 3.1 Extract DNA from 184 oral wash and/or buccal cell specimens using the QIAGEN (MoBio) PowerSoil Pro DNA isolation kit. If at least 90% of samples pass quality control (QC), defined as at least 16,000 16S rRNA gene copies/mL or at least 1 ng of DNA/mL for 16S rRNA gene sequencing or whole-genome shotgun sequencing, respectively, the samples shall proceed for the downstream analyses. 3.2 Conduct polymerase chain reaction (PCR) amplification and sequencing of the V4 region of the 16S rRNA gene of the extracted DNA from the 184 samples from Task #3.1. Sequencing should be conducted on the Illumina MiSeq with 2x250 paired-end reads. A mean read depth of at least 50,000 sequences per sample should be achieved and at least 90% of samples should contain at least 20,000 reads, excluding samples which failed prior quality control. 3.3 Conduct PCR amplification and sequencing of the ITS2 gene of the extracted DNA from the 184 samples from Task #3.1 and from 192 aliquots of extracted DNA generated at NCI from buccal cell specimens. Sequencing should be conducted on the Illumina MiSeq with 2x250 paired-end reads. A mean read depth of at least 50,000 sequences per sample should be achieved and at least 90% of samples should contain at least 20,000 reads, excluding samples which failed prior quality control. 3.4 Conduct whole-genome shotgun sequencing of the extracted DNA from the 184 samples from Task #3.1, the 192 aliquots of extracted DNA described in Task #3.3, and 48 aliquots of extracted DNA generated at NCI from fecal specimens. Sequencing should be conducted on the Illumina HiSeq with 2x150 paired-end reads. A mean read depth of at least 10 million sequences per sample should be achieved and at least 90% of samples should contain at least 4 million reads, excluding samples failing prior QC. Bioinformatic processing of the data should also provide human host DNA removal. 3.5 Provide a report which contains the following items: 1) raw FASTQ data; 2) trimmed, adaptor-removed FASTA data; 3) a quality-control dashboard; 4) strain coverage tables or operational taxonomic unit tables via alignment to a curated reference database with species and genus assignments where available; 5) functional profiling by direct observation or predicted via marker genes and PICRUSt software, reported as KEGG orthology groups, modules, and pathways where available; and 6) best-practice diversity analysis and data visualization. 3.6 Return residual DNA to the NCI on dry ice using overnight shipping as identified in section 7.0 below. 4.0 TYPE OF ORDER This is a Firm-Fixed-Price purchase order for non-severable services. The services specified in each contract line item (CLIN) have been determined to be non-severable services - a specific undertaking or entire job with a defined end product of value to the Government. 5.0 PERIOD OF PERFORMANCE The anticipated period of performance shall be for twelve (12) months from date of award. 6.0 PLACE OF PERFORMANCE All work shall be performed at the Contractor�s facility. 7.0 REPORTS AND DELIVERABLES On completion of the lab measurements, the Contractor shall submit a report as an electronic copy in the form of FASTQ files, FASTA files, online dashboard, Excel workbooks or text files of the measurements for review, comment, and approval by the NCI Technical Point of Contact (TPC). Final copies of the approved draft(s) shall be delivered to the TPC within five (5) business days after receipt of the Government�s comments. All written draft and final deliverable products shall be submitted in electronic copy for review and comment.� TPC: TBD at Award Deliverable #1 � Due six (6) months after date of award: Sequencing results from 16S rRNA gene sequencing, ITS2 gene sequencing, and shotgun metagenomics in accordance with section 3.0 above in the form of FASTQ files, FASTA files, online dashboard, .txt files, .csv files, and/or .xlsx files as appropriate. Deliverable #2 Within two (2) weeks of the approved final report, the Contractor shall coordinate with the TPC to send the residual samples and extracted DNA to the NCI repository (address below) on dry ice using overnight shipping. Return shipping/handling shall be included in the quote. NCI at Frederick Central Repository American Type Culture Collection (ATCC) 4600 Wedgewood Blvd, Suite H & K Frederick, MD� 21703 8.0��������� UNIQUE QUALIFICATIONS OF THE CONTRACTOR Variability between laboratories for microbiome sequencing is a serious issue which has been extensively studied by investigators within MEB (see, for example: https://pubmed.ncbi.nlm.nih.gov/28967885/). To ensure scientific integrity, MEB must use a laboratory who previously extracted quality control samples (including bacterial artificial communities and artificial gut samples) to have appropriate reference data. In Fiscal Year 2019, CoreBiome, Inc. (now Diversigen, Inc.) sequenced quality control samples under purchase order number 75N91019P00640 and MEB will include these quality control samples in each batch under the subsequent award to monitor performance and facilitate pooling of data. A change in vendor would provide results that are not scientifically comparable to previous findings and would disrupt the overall body of research. This notice is not a request for competitive quotations. However, if any interested party, especially a small business, believes it can meet the above requirement, it may submit a proposal or quote for the Government to consider. The response and any other information furnished must be in writing and must contain material in enough detail to allow NCI to determine if the party can perform the requirement. All responses and questions must be submitted via email to Adam Hernandez, Contract Specialist at adam.hernandez@nih.gov. Responses are due no later than 1:00 P.M. EST Friday, July 24, 2020 (07/24/2020). 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 determining whether to conduct a competitive procurement. To receive an award, Contractors must be registered and have valid certification in the System for Award Management (SAM) through SAM.gov, and have Representations and Certifications filled out. Reference: 75N91020Q00090 on all correspondence.
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- Record
- SN05724535-F 20200719/200717230135 (samdaily.us)
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