SPECIAL NOTICE
Q -- Long Non-coding RNA and Small RNA Sequencing for Identification of RNA Biomarkers for Radiation Biodosimetry
- Notice Date
- 4/21/2020 12:44:15 PM
- Notice Type
- Special Notice
- NAICS
- 541380
— Testing Laboratories
- Contracting Office
- NIH National Cancer Institute Rockville MD 20850 USA
- ZIP Code
- 20850
- Solicitation Number
- 75N91020Q00053
- Response Due
- 4/29/2020 8:00:00 AM
- Archive Date
- 05/14/2020
- Point of Contact
- Adam Hernandez, Phone: 2402765633
- 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), Center for Cancer Research (CCR), Radiation Oncology Branch (ROB), Experimental Therapeutics Section (ETS) intends to procure, on a sole source basis, services for long non-coding RNA and small RNA sequencing for identification of RNA biomarkers for radiation biodosimetry from Novogene Corporation Inc, 823 Anchorage Place, Suite 105, Chula Vista, CA, 91914-4534, 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. 1.0 BACKGROUND Radiological attacks and nuclear detonations can cause mass casualties. Victims may have received substantial radiation doses and may not immediately exhibit visible symptoms of radiation sickness. Victims, with whole body or substantial partial body exposure >2 Gray (Gy) will require immediate treatment, within 24 hours, to mitigate radiation injury while others will require both intermediate and long-term management for possible injury to the marrow, gastrointestinal tract, lung and other organs. Early prediction of possible acute, intermediate and delayed effects will enable timely therapeutic interventions, which will not only reduce death, but also improve quality of life for the victims. To that end the NCI has designed this study to explore both long non-coding and small RNAs which change in response to radiation using high throughput NGS sequencing platforms. 1.1 OBJECTIVE The U.S. Department of Health and Human Services (DHHS), National Institutes of Health (NIH), National Cancer Institute (NCI), Center for Cancer Research (CCR), Radiation Oncology Branch (ROB), Experimental Therapeutics Section (ETS) requires microRNA (miRNA) expression information through small RNA Sequencing (Small RNA-Seq) and long non-coding RNA (lncRNA) and mRNA expression information through lncRNA Sequencing (lncRNA-Seq) to identify biomarker signatures of general radiation exposure and organ-specific radiation injury. 2.0 SCOPE This project involves mRNA- and lncRNA-Seq (216 samples) and Small RNA-Seq (96 samples) of 312 total samples. It is a multi-step process with each step dependent on successful completion of the former. The project workflow shall consist of the following: Preparation of cDNA libraries for both mRNA-/lncRNA-Seq and small RNA-Seq RNA quality control for all samples before and after library preparation Performance of� RNA-Seq workflows mRNA-/lncRNA-Seq for 216 samples using an Illumina platform Small RNA-Seq for 96 samples, including clustering prior to sequencing, using an Illumina platform Quality control of all reads Alignment of reads to reference genome Data analysis for identification of differentially expressed coding and non-coding RNAs 3.0 �������� CONTRACT REQUIREMENTS/ AND PERSONNEL QUALIFICATIONS The contractor shall perform the following tasks: 3.1�mRNA and lncRNA sequencing of 216 samples 3.1.1 Total RNA sample quality control: 3.1.1.1 Assessment of RNA sample purity by measuring absorbance at wavelengths of 230nm, 260nm, and 280nm using a NanoDrop spectrophotometer. The samples must meet the following criteria: 3.1.1.1.1 260/280 ratio ? 2.0 3.1.1.1.2 260/230 ratio ? 1.8 3.1.1.2 Agarose Gel Electrophoresis on 1% gels to ensure no RNA degradation and no contamination 3.1.1.3 Assessment of RNA integrity using an Agilent 2100 Bioanalyzer. The sample must meet the following criteria: 3.1.1.3.1 RNA Integrity Number (RIN) ? 8 3.1.2 Library Construction: 3.1.2.1 Purification with oligo-dT beads and fragmentation of mRNA and lncRNA from total RNA to prepare samples for complementary DNA (cDNA) synthesis 3.1.2.2 cDNA synthesis 3.1.2.2.1 Reverse transcription of RNA fragments into first strand cDNA using reverse transcriptase enzymes and random primers 3.1.2.2.2 Removal of RNA template and synthesis of a second cDNA strand using a custom Illumina second-strand synthesis buffer, dNTPsm RNase H, and Escheria coli polymerase I, resulting in double-stranded cDNA 3.1.2.2.3 Purification and terminal repair to remove overhanging nucleotides and ensure each strand of cDNA contains 5� phosphate and 3� hydroxyl groups 3.1.2.2.4 Addition of an �A� nucleotide to the 3� end of fragments (A-tailing) to prevent fragments from ligating to one another during ligation (4.1.2.2.5) 3.1.2.2.5 Ligation of sequencing adaptors to enable specific amplification 3.1.2.2.6 Size selection of fragments ~150-200 base pairs (bp) and polymerase chain reaction (PCR) enrichment to amplify sequences with adapters 3.1.3 Library Quality Control: 3.1.3.1 Quantification of cDNA using a Qubit 2.0 fluorometer to ensure library meets the following criteria: 3.1.3.1.1 Concentration ?20 ng/�L 3.1.3.1.2 Total ?100ng 3.1.3.2 Dilution of sample to 1 ng/�L followed by assessment of purity using an Agilent 2100 Bioanalyzer to ensure the following criteria: 3.1.3.2.1 Fragments between 400 bp and 5000bp 3.1.3.2.2 Main peak at approximately 2000bp 3.1.3.3 Quantitative PCR to quantify samples to greater accuracy and ensure the following criteria: 3.1.3.3.2 Library activity > 2nM 3.1.4 Sequencing using Illumina platforms and the following parameters: 3.1.4.1 Read length: 125-150bp paired-end reads 3.1.4.2 Sequencing depth: ? 15-20G raw reads per sample 3.1.4.3 Data quality: ? 80% of bases with Q30 (percentage of bases with correct base recognition rates greater than 99.9% in total bases) 3.1.5�Data Analysis: 3.1.5.1 Quality control to obtain clean data by filtering data as follows: 3.1.5.1.1 Discard reads with adapter contamination 3.1.5.1.2 Discard reads comprised of > 10% uncertain nucleotides 3.1.5.1.3 Discard reads in which > 50% is comprised of nucleotides with a base quality 10% uncertain nucleotides 3.2.5.1.3 Discard reads in which > 50% is comprised of nucleotides with a base quality < 20� 3.2.5.2 Map reads to reference genomes 4.0 �������� TYPE OF ORDER This is a firm-fixed-price purchase order. 4.1��������� NON-SEVERABLE SERVICES This is a non-severable firm fixed price purchase order. 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 one (1) 12-month base period. 6.0�� ����� PLACE OF PERFORMANCE All work shall be performed at the Contractor�s facility. 7.0��������� REPORTS AND DELIVERABLES All written drafts and final deliverable products shall be submitted as an electronic copy in the form of PDF files, Excel workbooks or text files for review and comment by the Government�s technical point of contact (TPOC) for a review period not to exceed thirty (30) days. Final copies of approved drafts shall be delivered to the TPOC within ten (10) business days after receipt of the Government�s comments. Deliverable #1 � Task 3.1; lncRNA and mRNA sequencing data for 216 samples shall be due within 6 months after award Deliverable #2 � Task 3.2; miRNA sequencing data for 96 samples shall be due within 6 months after award 8.0��������� UNIQUE QUALIFICATIONS OF THE CONTRACTOR In Fiscal Year 2019, NCI/CCR/ROB/ETS conducted pilot studies using mRNA and miRNA sequencing services with Novogene Corporation Inc under purchase order 75N91019P00752 which had a period of performance of 09/19/2019 through 12/18/2019. The sequencing data under the previous purchase order award has been unparalleled with respect to quality control, accuracy, and reproducibility. ETS has validated the results from the preliminary services and have found 100% accuracy of the data provided. To expand and complete the ongoing research, the miRNA/mRNA sequencing analysis for the current requirement must be compatible with previous findings provided by Novogene. Due to variability and limited size of samples, the ability to generate consistent results from difficult sample conditions is required for the requested services. Changing variables at this time would be detrimental to current gene expression studies performed at the NCI and therefore, 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 11:00 A.M. EST Wednesday, April 29, 2020 (04/29/2020). 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: 75N91020Q00053 on all correspondence.
- Web Link
-
SAM.gov Permalink
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- Record
- SN05630443-F 20200423/200422060348 (samdaily.us)
- Source
-
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