20-042 Synopsis1.pdf

This is a combined synopsis/solicitation for commercial items prepared in accordance with the format in FAR 12.6 as supplemented with additional information included in this notice. This announcement constitutes the only solicitation and a separate written solicitation will not be issued. This solicitation number is NIH-NICHD-20-042 and is issued as a Request for Quotation (RFQ). The solicitation/contract will include all applicable provisions and clauses in effect through Federal Acquisition Circular 2020-04. The North American Industry Classification (NAICS) Code is 541380 and the business size standard is $16.5M. However, this solicitation is not set aside for small business.

It is the intent of The National Institutes of Health (NIH), National Institute on Minority Health and Health Disparities (NIMHD) to purchase Whole Exome Sequencing (WES), RNA sequencing and DNA Methylation Sequencing services on samples from racially/ethnically diverse breast cancer patients from Psomagen, Inc., 1330 Piccard Drive, Rockville, MD 20850 pursuant to 41 U.S.C. 253(c)(1)—Only one responsible source and no other supplies or services will satisfy agency requirements.

The proposed contractor, Psomagen is the only contractor that has the experience using the advanced kits we need for the sequencing services. The proposed contractor utilizes a cutting-edge kit, SureSelect V6+ UTR for whole exome sequencing, which offers the advantage of recruiting a more targeted region of 89 Mb, including untranslated regions (UTR) that are responsible for regulatory gene pathways. They also use dual index rather than single index runs, which has additional read capacity while sequencing and generates more accurate data than using single index. For RNA sequencing, the Library TruSeq Stranded Total RNA kit will be used. For DNA Methylation Sequencing, the contractor will use SureselectXT Methyl- Seq with 60M read pairs for library preparation so that it generates more than 18 Gb data even at lower amounts of DNA input. Furthermore, the contractor utilizes NovaSeq6000 S4 150bp paired end as the sequencing platform. We need to stay with the same gene sequencing services to be able to consistently describe in scientific manuscripts the quality control, collection and sequencing protocol used and to be able to make valid comparisons across batches of samples. This approach enhances scientific reproducibility and helps ensure successful peer-review of scientific manuscripts.

Scope of Work

The scope of work is for the contractor to conduct Whole Exome Sequencing (WES), RNA Sequencing, and DNA Methylation Sequencing on purified DNA/RNA samples to be provided by the NIMHD DIR genomics program at NIH. Sequencing will include library preparation, quality control, and sequencing the library products. The samples consist of 192 tumor DNA samples and 192 normal DNA samples (total 384 DNA samples) for WES sequencing; 149 tumor RNA samples for RNA sequencing; and 100 DNA samples for DNA Methylation Sequencing. WES and RNA Sequencing will identify genomic mutations with high frequency at coding and non-coding regions and novel transcript discovery, fusion detection, mRNA, and noncoding RNA. DNA Methylation Sequencing will determine the signature of cell type specific gene function in breast cancer samples.

This is a Firm Fixed Price contract

Sequencing Facility Contractor Requirements

The sequencing facility will use an advanced and cutting-edge kit, such as Agilent SureSelect V6+ UTR, for Whole Exome Sequencing which offers the advantage of recruiting a more targeted region of 89 Mb including untranslated regions (UTR) responsible for important regulatory gene pathways. The sequencing facility will use dual index that has additional read capacity while sequencing so that it generates more accurate data than using single index. The sequencing facility will deliver the raw data for 100X for normal and 200X for tumor raw depth with NovaSeq 150PE running more than 9 Gb per sample. The sequencing facility will use Library TruSeq Stranded Total RNA kits for RNA Sequencing that will provide the raw data with 100M total reads per RNA-Sequencing sample. For DNA Methylation Sequencing, the sequencing facility will use SureselectXT Methyl-Seq with 60M read pairs for library preparation so that it generates more than 18 Gb data, even at lower amounts of DNA input, and utilize NovaSeq6000 S4 150bp paired end as the sequencing platform. The contractor will provide us the data via secure designated cloud server or FTP downloadable protocols.

DESCRIPTION OF TASK Number of Samples

PRICE/

COST

384 DNA SAMPLES FOR WHOLTE EXOME SEQUENCING

Whole Exome Sequencing of Normal DNA: Library preparation & QC

& Sequencing WES using 89 Mb Agilent SureSelect V6+UTR 100x

Whole Exome Sequencing of Tumor DNA: Library preparation & QC & Sequencing WES using 89 Mb Agilent SureSelect V6+UTR 200x

149 RNA SAMPLES FOR RNA SEQUENCING

Tumor RNA: Library Preparation, Illumina, TruSeq Stranded Total RNA Library Preparation Illumina, TruSeq RNA Access Kit Sequencing, NovaSeq 6000, 100PE Sequencing S2

100 DNA METHYLATION SEQUENCING

Library Preparation, SureSelectXT Methyl-Seq with Sequencing platform of NovaSeq6000 S4 150 bp paired end generating 60M read pair with

18Gb

Other Direct Costs (ODCs)

TOTAL 633

Harris, Dana (NIH/NICHD) [E] Since I didn’t review any cost information do you already have an estimate per sample – only asking because since you include price as the most important factor in Evaluation Factors Section you are gonna need to be prepared to state that the government estimated a per sample price of $XXX.

The sequencing facility will offer free pick up and return of samples to and from the NIMHD DIR genomics lab at NIH and provide us with a no-cost consultation for all sequenced files to answer questions on the sequencing data they generate, e.g., Fastq and .bam files after sequencing. The data will be deleted from the Contractor's server after 3 months of turning over the data to NIMHD. No personal identifiers will be used throughout.

Government Responsibilities

NIMHD DIR genomics program will provide the sequencing facility with purified DNA and RNA samples for their Whole Exome Sequencing, RNA Sequencing and DNA Methylation Sequencing services when the contract is approved.

Milestones and Deliverables

Deliverables

Due Date from date of contract award

1. Pre-sequencing consultation 1 week

2. Pick up DNA, RNA samples 1 week

3. Delivery of sequencing data for WES, RNA-Seq, DNA Methylation 1 month

4. Post-sequencing consultations Ongoing through duration of contract period

EVALUATION FACTORS FOR AWARD

I. GENERAL

The Selection of an offeror for contract award will be based on an evaluation of proposals against three factors and corresponding subfactors. The factors in order of importance are: technical, cost and past performance. The technical factors and corresponding subfactors are listed in order of importance. All evaluation factors other than cost or price, when combined, are significantly more important than cost. The Government intends to make an award(s) to that vendor/offeror whose quote/proposal provides the best overall value to the Government. The Government will use an adjectival rating scale on all quotes/proposals.

The evaluation will be based on the demonstrated capabilities of the prospective Contractors in relation to the needs of the project as set forth in the RFQ. The merits of each quote/proposal will be evaluated carefully. Each

Harris, Dana (NIH/NICHD) [E] For any/all deliverables are there any additional instructions needed; if so should insert below.

Harris, Dana (NIH/NICHD) [E] When you say order of importance you have cost-price as first is that really the order of importance or is Technical first?

proposal must document the feasibility of successful implementation of the requirements of the RFQ. Vendors/Offerors must submit information sufficient to evaluate their quotes/proposals based on the detailed factors listed below.

Although technical factors are of paramount consideration in the award of the contract, past performance, and cost/price are also important to the overall contract award decision. As proposals become more equal in terms of technical merit and past performance, the cost or price becomes more important.

The Government intends to make an award to that vendor/offeror whose quote/proposal provides the best overall value to the Government.

1. TECHNICAL EVALUATION RATINGS

The Government shall evaluate proposals in accordance with the factors and criteria established in the Solicitation. The rating definitions provided below will be used for the evaluation of each technical evaluation factor and subfactor and to assign each proposal with an overall rating. Quotes/Proposals shall be evaluated using adjectival rating system – definitions of the ratings are shown below:

Outstanding (O):

Significantly exceeds most or all solicitation requirements for this factor or subfactor or overall. Response exceeds a “Good” rating. The risk of unsuccessful contract performance is extremely low.

Good (G):

Fully meets all solicitation minimum requirements and exceeds many of the solicitation requirements for this factor or subfactor or overall; OR exceeds a small number of the minimum requirements but to a significant degree or in a valuable way for this factor or subfactor or overall. Response exceeds an “Acceptable” rating. The risk of unsuccessful contract performance is very low.

Acceptable (A):

Fully meets all solicitation minimum requirements for this factor or subfactor or overall. Areas where the proposal exceeds the minimum solicitation requirements, if any, are of little or no value to the Government. The risk of unsuccessful contract performance is low.

Marginal (M):

Less than “Acceptable.” Does not meet all solicitation minimum requirements for this factor or subfactor or overall. The proposal indicates a superficial or vague understanding of the program goals and the methods, resources, schedules and/or other aspects essential to contract performance. The risk of unsuccessful contract performance is moderate.

Unacceptable (U):

Technical proposal has many or significant deficiencies and/or substantial omissions for a factor or subfactor or overall AND/OR the proposal demonstrates a lack of understanding of the program goals, methods, resources, schedules and/or other aspects essential to contract performance.

The risk of unsuccessful contract performance is high.

2. TECHNICAL EVALUATION FACTORS

The technical evaluation criteria for the review of each quote/proposal are specified below; listed in order of importance.

a. Technical Approach

The Offeror shall demonstrate in their proposal an understanding of the technical tasks and subtasks for this technical category identified in the Statement of Work (SOW). The Offeror shall provide evidence of experience and expertise in the following:

• Use of a cutting-edge kit, SureSelect V6+ UTR which offers the advantage of covering a more targeted region of 89 Mb including untranslated regions (UTR) responsible for important regulatory gene pathways.

• The sequencing facility should deliver the raw data for 100X for normal and 200X for tumor raw depth with NovaSeq 150PE running more than 9 Gb per sample. The sequencing facility should use the Library TruSeq Stranded Total RNA kit for RNA Sequencing that will provide us with the raw data with 100 M total reads per RNA-Sequencing sample.

• The Government prefers the sequencing facility to use Library TruSeq Stranded Total RNA kits for RNA Sequencing that will provide the raw data with 100M total reads per RNA- Sequencing sample

• Use of dual index that has additional reads capacity while sequencing so that it generates more accurate data than using single index.

• Delivering raw data for 100X for normal and 200X for tumor raw depth for whole exome sequencing sample.

• Providing raw data with 100M total reads per RNA-Sequencing sample.

Haun, Patricia (NIH/NICHD) [E] I know this was used before, I am not comfortable having Agilent as an example. Can you describe what the cutting-edge kit does?

b. Service, Training, Consultation

The Government prefers the availability of the following services:

• Availability of consultations before sequencing to address specific questions NIMHD Division of Intramural Research (DIR) staff may have regarding the sequencing.

• Free sample pickup and delivery service to and from the National Institutes of Health.

• Free training sessions for demonstration of library preparation techniques to our NIMHD DIR genomics staff.

• Free consultation and discussion for questions about sequenced files (e.g., .fastq, .bam) resulting from whole exome sequencing and RNA sequencing.

3. COST/PRICE EVALUATION

Vendor/Offeror(s) cost/price quote/proposal will be evaluated for reasonableness; the cost/price analysis based on the level of experience and expertise being proposed under a labor category may deem a price to be unreasonable to perform the requirement(s).

4. PAST PERFORMANCE

The Government will evaluate the quality of the offeror's past performance based on information obtained from references provided by the offeror, as well as other relevant past performance information obtained from other sources known to the Government.

Evaluation of past performance will be a subjective assessment based on consideration of all relevant facts and circumstances. It will not be based on absolute standards of acceptable performance. The Government is seeking to determine whether the offeror has consistently demonstrated a commitment to customer satisfaction and timely delivery of services at fair and reasonable prices. The assessment of the offeror's past performance will be used as a means of evaluating the capability of the offeror. Thus, an offeror with an exceptional record of past performance may receive a more favorable evaluation than one with an acceptable record.

Past performance will not be scored, but the Government's conclusions about overall quality of the offeror's past performance will be influential in determining the merits of the offeror's proposal and in selecting the offeror whose proposal is considered most advantageous to the Government.

By past performance, the Government means the offeror's record of conforming to specifications and to standards of good workmanship; the offeror's record of forecasting and controlling costs; the offeror's adherence to contract schedules, including the administrative aspects of performance; the offeror's reputation for reasonable and cooperative behavior and commitment to customer satisfaction; and generally, the offeror's business-like concern for the interest of the customer.

The Government will consider the number or severity of an offeror's problems, the effectiveness of corrective actions taken, the offeror's overall work record, and the age and relevance of past performance information. The lack of a performance record may result in an unknown performance risk assessment, which will not be used to the advantage or disadvantage of the offeror.

The offeror must include a completed copy of the provision of FAR Clause 52.212-3, Offeror Representations and Certifications – Commercial Items with its offer. The provisions of FAR Clause 52.212-1 Instructions to Offerors – Commercial Items; FAR Clause 52.212-2, Evaluation – Commercial Items; FAR Clause 52.212-4, Contract Terms and Conditions – Commercial Items; and FAR 52.212-5, Contract Terms and Conditions Required to Implement Statutes or Executive Orders – Commercial Items – Deviation for Simplified Acquisitions applies to this acquisition. FAR Clause 52.204-24, Representation Regarding Certain Telecommunication and Video Surveillance Services or Equipment; FAR Clause 52.204-25, Prohibition on Contracting for Certain Telecommunications and Video Surveillance Services or Equipment; FAR Clause 52.213-4 to reflect the changes in FAC 2019-05 and FAR Clause 52.244-6 to reflect the changes in FAC 2019-05. The offeror must include their Dun & Bradstreet Number (DUNS), the Taxpayer Identification Number (TIN), and the certification of business size. The clauses are available in full text at http://www.arnet.gov/far. Interested vendors capable of providing the Government with the equipment specified in this synopsis should submit their quotation to the below address. Quotations will be due ten (15) calendar days from the publication date of this synopsis or February 20, 2020 at 12:00 PM. The quotation must reference “Solicitation number” NIH-NICHD-20-042. All responsible sources may submit a quotation, which if timely received, shall be considered by the agency. Quotations must be submitted by email to Patricia Haun at haunp@mail.nih.gov. Faxed copies will not be accepted

PLEASE NOTE: In order to receive an award, contractor must be registered and have valid certification in System for Award Management (SAM) at www.sam.gov/SAM http://www.arnet.gov/far