NIEHS2015020_-_NextGen_Solicitation.pdf

NIH/National Institute of Environmental Health Sciences (NIEHS)

Solicitation No: NIEHS2015020 Date Issued: February 27, 2015

Due Date: TUESDAY, MARCH 17, 2015 by 1:00 pm et

Issued by: Deitra C. Lunney, Contract Specialist Email: lunney@niehs.nih.gov Telephone: 919-541-0387

Courier/Overnight Delivery USPS Mail Delivery NIH/NIEHS/Office of Acquisitions NIH/NIEHS Attn: Deitra Lunney Attn: Deitra Lunney Keystone Office Bldg., Rm. 1045 Office of Acquisitions 530 Davis Drive P.O. Box 12874, MD K1-04 Morrisville, NC 27560 Research Triangle Park, NC 27709

Goods/Services to be purchased: NextGen Sequencing Project

The NIEHS intends to acquire NextGen Sequencing Services to commence on April 1, 2015 through March 31, 2020 for an ordering period of five (5) years.

Award will be a firm-fixed price Indefinite-Delivery – Requirements contract.

NOTICES:

1. This is a Combined Synopsis/Solicitation.

2. Solicitation is issued as Full and Open Competition.

The NAICS Code is 541380 with a Size Standard of $14.0 Million.

3. Any questions regarding this announcement must be submitted in writing no later than Friday, March 6, 2015, 3:00 pm edt to Deitra Lunney via email at lunney@niehs.nih.gov.

mailto:lunney@niehs.nih.gov

I. Combined Synopsis Solicitation.

This is a combined synopsis/solicitation for commercial services prepared in accordance with the format in Subpart 12.6, as supplemented with additional information included in this notice. This announcement constitutes the only solicitation; proposals are being requested and a written solicitation will not be issued. This solicitation is issued as a Request for Quotations (RFQ) under NIEHS2015020. This solicitation document incorporates all mandatory commercial item provisions and clauses that are in effect through Federal Acquisition Circular (FAC) 2005-78 dated December 26, 2014.

FULL AND OPEN COMPETITION - NAICS Code/Size: 541380/$14.0 Million

II. Instructions:

For any questions regarding this announcement or requests for additional information must be submitted in writing to Deitra Lunney via email at lunney@niehs.nih.gov. Notification of any changes shall be made only via the FedBizOpps solicitation posting site. Quotations submitted in response to this notice shall include the solicitation number, DUNS and Tax ID/Employer Identification Numbers, payment terms, and be signed, dated and submitted to an address shown on page 1 of this RFQ. Vendors not registered in the Central Contractor Registration (CCR) database at the time the requirement is to be awarded will not be considered. Vendors may register with CCR by calling 1-888-227-2423 or (269) 961-5757, or by accessing www.ccr.gov.

FAR 52.212-3, Offeror Representations and Certifications-Commercial Items (Dec 2014) is included by reference (full text is available electronically at http://www.acquisition.gov/far. A completed copy of this provision must be included with response. Offeror shall complete only paragraph (j) of this provision if the offeror has completed the annual representations and certifications electronically at http://orca.bpn.gov. If an offeror has not completed the annual representations and certifications electronically at the ORCA website, the offeror shall complete only paragraphs (b) through (i) of this provision.

III. Basis for Award:

Offeror should be aware that the Government shall perform a “best value analysis” and the selection for award shall be made to the Offeror whose proposal is most advantageous to the Government, taking into consideration the technical factors listed in the solicitation and the total proposed price across the contract ordering period.

http://www.acquisition.gov/far

IV. Supplies, Services, and Prices

This will be awarded as an Indefinite-Delivery Requirements Contract. Prices quoted will be binding on the contract for the estimated ordering periods as listed below. Task orders will be placed on an as-needed basis with the totals for each item not exceeded the quantity listed.

Furnish and deliver, as required by the National Institute of Environmental Health Sciences, at the following fixed price(s):

Provide NextGen Sequencing Services as per the Statement of Work (pages 7 - 11).

Unit Extended

Items Quantity Unit Price Price

CLIN 1: Description of Services – Est. Ordering Period – 4/01/2015-3/31/2016

Illumina HiSeq DNA Sequencing Samples:

Lane of RNA-Seq or DNA-Seq 50 ea ___________ ____________

Sequence Data Analysis:

Analysis per lane, RNA-Seq or DNA-Seq 50 ea ___________ ____________

Unit of Transcript Confirmation Sequencing 8 ea ___________ ____________

Metabolomic Samples 60 ea ___________ ____________

Proteomic Samples 40 ea ____________ ____________

TOTAL CLIN 1: $ _______________________

CLIN 2: Description of Services – Est. Ordering Period – 4/01/2016-3/31/2017

Sequence Data Analysis:

Analysis per lane, RNA-Seq or DNA-Seq 50 ea ___________ ____________

Unit of Transcript Confirmation Sequencing 8 ea ___________ ____________

TOTAL CLIN 2: $ _______________________

CLIN 3: Description of Services – Est. Ordering Period – 4/01/2017-3/31/2018

Sequence Data Analysis:

Analysis per lane, RNA-Seq or DNA-Seq 50 ea ___________ ____________

Unit of Transcript Confirmation Sequencing 8 ea ___________ ____________

TOTAL CLIN 3: $ _______________________

CLIN 4: Description of Services – Est. Ordering Period – 4/01/2018-3/31/2019

Sequence Data Analysis:

Analysis per lane, RNA-Seq or DNA-Seq 50 ea ___________ ____________

Unit of Transcript Confirmation Sequencing 8 ea ___________ ____________

TOTAL CLIN 4: $ _______________________

CLIN 5: Description of Services – Est. Ordering Period – 4/01/2019-3/31/2020

Sequence Data Analysis:

Analysis per lane, RNA-Seq or DNA-Seq 50 ea ___________ ____________

Unit of Transcript Confirmation Sequencing 8 ea ___________ ____________

TOTAL CLIN 5: $ _______________________

CLIN 6: Description of Services – Est. Ordering Period – 4/01/2020-9/30/2020

Lane of RNA-Seq or DNA-Seq 25 ea ___________ ____________

Sequence Data Analysis:

Analysis per lane, RNA-Seq or DNA-Seq 25 ea ___________ ____________

Unit of Transcript Confirmation Sequencing 4 ea ___________ ____________

Metabolomic Samples 30 ea ___________ ____________

Proteomic Samples 20 ea ____________ ____________

TOTAL CLIN 6: $ _______________________

Total CLIN 1: $ _________________

Total CLIN 2: $ _________________

Total CLIN 3: $ _________________

Total CLIN 4: $ _________________

Total CLIN 5: $ _________________

Total CLIN 6: $ _________________

TOTAL ALL CLINS: $ _______________________

Statement of Work

NextGen Sequencing and Omics Services for the National Toxicology Program (NTP)

1. Background. The National Toxicology Program (NTP) is an interagency program whose mission is to evaluate agents of public health concern by developing and applying tools of modern toxicology and molecular biology. The program maintains an objective, science-based approach in dealing with critical issues in toxicology and is committed to using the best science available to prioritize, design, conduct, and interpret its studies. To that end, NTP is continually evolving to remain at the cutting edge of scientific research and to develop and apply new technologies.

The NTP has a service requirement for NextGen sequencing technologies combined with metabolomics and proteomics platforms to study the effects of chemically-induced toxicity in support of the high throughput screening and toxicity testing programs. A major premise of this project is that gene, protein, and metabolite expression changes underlie organ toxicity and development of chemically-induced pathology and tumors. Activation of critical genes and other regulatory pathways reflected in protein and metabolite expression enhance or repress pathways leading to toxicity or cancer susceptibility. Changes in gene, protein, and metabolite expression can be interpreted as molecular biomarkers which can precede or inform histopathology and other measures of toxicity.

The contractor selected for this requirement shall provide the knowledge and expertise in NextGen genomic sequencing, proteomics and metabolomics by proposed technology platforms. The purpose of conducting Omics studies, that include metabolomics and proteomics, shall be to complement the results from DNA or RNA NextGen sequencing.

2. References. No reference material is needed by the contractor.

3. Scope. The NextGen Sequencing and Omics contract shall provide for a) NextGen Sequencing that includes: DNA or RNA extraction and methylated DNA enrichment; sequence library construction; and NextGen DNA or RNA sequencing services and accompanying bioinformatics support; and transcript confirmation sequencing b) proteomics services including sample preparation, and protein analysis and informatics; and c) metabolomics including sample preparation, and metabolite analysis and informatics. The scope of sample analysis is anticipated to be wide-ranging and may involve cells, tissues, or biofluids (e.g. serum or urine).

4. Technical Requirements.

4.1. NextGen Sequencing – Samples shall be processed and prepared for DNA or RNA sequencing on an

Illumina HiSeq series sequencing instrument (e.g., HiSeq2000 or HiSeq2500) to deliver one .fastq sequence file per ‘sequencing lane’. NIEHS may order one sequencing lane or several sequencing lanes at the start of a specific project. The following set of general procedures for sample preparation and sequencing shall occur with appropriate direction from NIEHS. NIEHS anticipates that, during the five (5) year ordering period, up to a maximum of 50 sequencing lanes may be needed per year for NextGen sequence analysis.

4.1.1. RNA or DNA extraction: The NIEHS shall ship and provide biological samples to the contractor.

The contractor shall provide supplies to extract RNA or DNA from biological samples. Prior to the time of shipment (e.g. 1 week), NIEHS shall provide direction to the contractor on sample preparation (e.g. poly-A enrichment, methylated DNA enrichment) for each sequencing lane.

4.1.2. DNA library construction: Sample DNA or RNA shall be bar-coded as necessary for library construction. NIEHS shall specify prior to analysis (e.g. 1 week), the size of read length (e.g.

Read length are the base pairs (bp) standard at time of analysis; currently 100bp) and shall specify if reads shall be single end or paired end (e.g. paired end is standard).

4.1.3. Sequence analysis: One lane of RNA-Seq or DNA-Seq analysis shall be performed on samples from an Illumina HiSeq instrument that provides at least 200 million reads per lane.

4.2. NextGen Sequence Bioinformatic Data Analysis – A sequence alignment file for samples on each sequencing lane shall be generated, analyzed and delivered to NIEHS. NIEHS may order data analysis for each sequencing lane or analyses on several sequencing lanes at the start of a specific project. NIEHS anticipates that, during the potential five (5) year ordering period, NextGen data analysis may be needed for up to a maximum of 50 lanes per year.

4.2.1. Data output file: Metrics of quality and sequencing statistics shall be captured by the contractor in accordance with commercial standards for Illumina HiSeq2000 series instruments.

4.2.2. Mapping sequence data file: The bioinformatics analysis on DNA or RNA sequence data shall be to map raw .fastq data to the appropriate reference genome to create a mapped file (e.g. .bam file format).

4.3. Transcript confirmation sequencing – NIEHS shall select a group of transcripts (1 group = sequences for 10 transcripts) that are derived from NextGen sequencing data for sequence confirmation and cloning by the contractor. Methods such as Rapid Amplification of cDNA Ends (RACE) using high fidelity Taq polymerase are recommended procedures for determining 5’prime and 3’prime ends of a cDNA product derived from transcripts of interest. NIEHS anticipates at least a 50 percent success rate for confirmation of submitted sequences. A 50 percent success rate shall equal a deliverable of 5 sequence files and 5 bacterial clones. Sequenced cDNA products from RACE methods shall be inserted into an appropriate bacterial clone (e.g. In-Fusion cloning vector; or TOPO TA cloning vector). NIEHS may order one group or several groups of transcripts for confirmation sequencing and cloning at the start of a specific project. NIEHS anticipates that, during the potential five (5) year ordering period, up to a maximum of 8 groups of transcripts may be submitted per year for sequence confirmation and cloning.

4.3.1. Determination of 5’prime start sites – NIEHS shall provide RNA sequences to the contractor for a group of ten transcripts for which 5’prime start sites shall be determined.

4.3.2. Transcript sequencing – A cDNA product shall be produced for each transcript and each sequence shall be confirmed by Sanger sequencing instrument (e.g. Applied Biosystems 3730 DNA analyzer) or 454 DNA sequencing instrument (e.g. Roche 454 GS-FLX)

4.3.3. Clone cDNA product – A cDNA product for each transcript shall be produced using an appropriate cloning vector (e.g. In-Fusion cloning vector; or TOPO TA cloning vector) to preserve the cDNA.

4.4. Metabolomics - Metabolomics analysis (e.g. global analysis of small-molecule metabolites) shall be applied to samples consisting of cells, tissues, and biofluids (e.g. serum, urine). Samples shall be shipped by NIEHS to the contractor so that they may prepare samples for metabolomic analysis by LC-MS and/or GC-MS (Liquid Chromatography and Mass Spectrometry; Gas Chromatography and Mass Spectrometry). NIEHS may order metabolomic analysis on one sample or several samples at the start of a specific project. NIEHS anticipates that, during the potential five (5) year ordering period, up to a maximum of 60 samples per year may be submitted for metabolomic analysis.

4.4.1. Sample preparation: The contractor shall prepare samples in a manner appropriate for metabolomics analysis using LC-MS and/or GC-MS instrument platforms.

4.4.2. Metabolomic analysis: The contractor shall perform metabolomics analysis for metabolite profiling using LC-MS and/or GC-MS platforms, equipped with a compound library containing known metabolites.

4.4.3. Data analysis: The contractor shall perform statistical analysis and graphical representation of metabolomics data among various treatment groups. Differential metabolite profile shall be generated in a spreadsheet format (MS Excel or equivalent) among comparator groups as specified by NIEHS.

4.5. Proteomics - Proteomics analysis (e.g. global analysis of proteins) shall be applied to cells, tissues cells and biofluids (e.g. serum, urine) using a separation system connected to a tandem mass spectrometer (LC-MS/MS). Samples shall be shipped by NIEHS to the contractor so that they may prepare samples and apply proteomic analysis by LC-MS/MS (Liquid Chromatography and Mass Spectrometry/ Mass Spectrometry) to separate and identify proteins. NIEHS anticipates that, during the potential five (5) year ordering period, up to a maximum of 40 samples per year may be submitted for proteomic analysis. NIEHS may order proteomic analysis on one sample or several samples at the start of a specific project.

4.5.1. Sample preparation: The contractor shall prepare samples by enzymatic digestion of proteins into peptides to ready them for proteomic analysis using an LC-MS/MS instrument platform.

4.5.2. Proteomic analysis: The contractor shall perform proteomics analysis for protein profiling such that protein identification is performed by automated database searches of peptide tandem mass spectrometry data.

4.5.3. Data analysis: After protein identification and relative estimates of protein amounts, differential protein profiles shall be generated among comparator groups as specified by NIEHS. Protein identities and amounts accompanied by appropriate statistical analysis shall be generated into spreadsheets (MS Excel or equivalent).

5. Key Personnel. Certain skilled experienced technical personnel are essential for accomplishing the work to be performed. At a minimum, the following personnel have been defined as key for this contract:

• Principal Investigator (PI) - The PI shall oversee the conduct of NextGen sequencing using Illumina HighSeq2000 series including production of NextGen data, data analysis, packaging and transmission, and coordination of personnel that staff the genomics facility. The PI shall oversee supplemental studies involving metabolomics and proteomics. The PI shall have an MS., Ph.D., M.D., or equivalent in the biological sciences, chemistry, and/or medical sciences.

• Genomic Facility Leader - The Genomics Leader shall manage and conduct the day-to-day operations of a NextGen sequencing facility. This person shall have experience constructing RNA and DNA sequencing libraries, QA/QC procedures in production of NextGen data, data packaging and transmission, and coordination of genomics facility staff. The leader shall coordinate with bioinformatic staff for alignment, sequencing statistics and appropriate analysis of NextGen data.

The Genomics leader shall be capable of molecular skills for sequence validation and cloning of transcripts derived from NextGen data. The Genomics Facility Leader shall have demonstrated skills in molecular biology, biochemistry, and accompanying instrumentation. The Genomics leader shall have a Ph.D., M.D., or equivalent in the biological sciences, chemistry, and/or medical sciences.

5.1. If any change to key personnel becomes necessary (substitutions or additions), the Contractor shall immediately notify the Contracting Officer in writing, accompanied by the resume of the proposed replacement personnel who shall be of equal ability and qualifications as the individuals currently approved for that position. The Contracting Officer shall approve all changes in key personnel.

5.2. No substitution or replacement of key personnel shall be approved within the first ninety (90) days after contract award, unless unavailability of the key personnel is due to serious illness of the key personnel, death of the key personnel, or resignation of the key personnel from the contractor’s firm.

6. Data Rights. The government maintains sole ownership of the data produced under this contract and any anticipated or unanticipated copyrights or patents.

7. Place of Performance. The opportunities for sample degradation and compromising the quality of data are greater with the continued movement of samples to various sites for analysis, therefore; analysis shall take place in a single facility or facilities within close proximity (i.e. university campus) located within the contiguous United States (CONUS).

8. Contractor Facilities/Equipment. The contractor shall provide a list of equipment to be provided and a layout of the work areas for conducting DNA sequencing as well as for metabolomics and proteomics to the

COR.

9. Health and Safety. All work shall conform to the applicable local, state, and Federal statutes related to occupational safety and health and environmental protection for the subject facilities. Controlled substances, if required, shall be handled in accordance with applicable regulations.

10. Meetings/Teleconferences. Telephonic tasking updates, between the contractor and contracting officer representative (COR), shall be conducted at a minimum bimonthly. An annual report shall be filed by the contractor summarizing individual projects and completion dates over the preceding year.

11. Government Furnished Equipment/Materials.

11.1. NIEHS shall furnish biological samples for analysis. NIEHS shall notify the contractor, via email, approximately 15 days prior to furnishing biological samples for analysis.

11.2. NIEHS shall furnish external hard drives for data transfer of files due to size limitations.

12. Shipping and Packaging. NIEHS shall ship biological materials to the contractor via a commercial carrier on dry ice in a suitable and protective container. The contractor shall notify NIEHS the same day as receipt. The cost of shipping an external hard drive to the contractor and back to NIEHS shall be paid for by

NIEHS.

13. Deliverables.

13.1. In accordance with (IAW) section 4.1 of the SOW, the contractor shall deliver an Illumina .fastq file electronically, via FTP site, to the COR. For files too large for FTP site submission, a NIEHS hard drive shall be provided with return shipping costs at NIEHS expense. File submissions shall be submitted no later than 30 days after task completion.

13.2. In accordance with (IAW) section 4.2 of the SOW, all deliverables from one sequencing lane, including sequence alignment data files (.bam files), spreadsheet (MS Excel or equivalent) of differential expression, normalized reads, appropriate statistical data and instrument sequencing quality data shall be delivered to the COR electronically via FTP site. For files too large for FTP site submission, an NIEHS hard drive shall be provided with return shipping costs at NIEHS expense. All deliverables shall be submitted no later than 30 days after task completion.

13.3. IAW section 4.3 of the SOW, for one validation group of 10 transcripts, at least 5 sequence files shall be sent electronically, via FTP site, to the COR. For files too large for FTP site submission, an NIEHS hard drive shall be provided with return shipping costs at NIEHS expense. For one validation group of 10 transcripts, the contractor shall produce and ship to NIEHS at least 5 bacterial clones which are frozen on dry ice. The bacterial clones shall be submitted no later than 30 days after task completion.

13.4. IAW section 4.4 of the SOW, metabolomic data files for each sample shall be submitted electronically, via FTP site, to the COR. For files too large for FTP site submission, an NIEHS hard

13.5. IAW section 4.5 of the SOW, proteomic data analysis files for each sample shall be submitted electronically, via FTP site, to the COR. For files too large for FTP site submission, an NIEHS hard

13.6. IAW section 8 of the SOW, the contractor shall submit to the COR a list of equipment to be provided and a layout of the work areas within 15 days after contract award.

13.7. An annual report shall be filed by the contractor summarizing individual projects and completion dates over the preceding year.

V. Contract Clauses, Terms, Conditions and Instructions

1. Period of Performance

a. The period of performance of this contract shall be from April 1, 2015 through March, 31, 2020

b. If the Government exercises its options pursuant to Contract Clauses and Provisions, FAR 52.217-8 Option to Extend Services, the period of performance will be increased for an additional 6 months as listed below:

Option Option Period

Option Period 1 April 1, 2020 through September 30, 2020

2. FAR 52.252-2 Clauses Incorporated by Reference (FEB 1998)

This contract incorporates one or more clauses by reference, with the same force and effect as if they were given in full text. Upon request, the Contracting Officer will make their full text available. Also, the full text of a clause may be accessed electronically at this address:

http://www.acquisition.gov/far.

3. The following clauses are included by reference:

FAR 52.203-17 Contractor Employee Whistleblower Rights and Requirements to Inform Employees of Whistleblower Rights (Apr 2014) FAR 52.204-4 Printed or Copied Double-Sided on Recycled Paper (May 2011) FAR 52.212-4 Contract Terms & Conditions-Commercial Items (Dec 2014) FAR 52.232-39 Unenforceability of Unauthorized Obligations (June 2013) FAR 52.246-2 Inspection of Supplies – Fixed-Price (Aug 1996)

Addendum to FAR 52.212-4:

1. Stop Work Order, FAR Clause 52.242-15 (August 1989)

(a) The Contracting Officer may, at any time, by written order to the Contractor, require the Contractor to stop all, or any part, of the work called for by this contract for a period of 90 days after the order is delivered to the Contractor, and for any further period to which the parties may agree. The order shall be specifically identified as a stop-work order issued under this clause. Upon receipt of the order, the Contractor shall immediately comply with its terms and take all reasonable steps to minimize the incurrence of costs allocable to the work covered by the order during the period of work stoppage. Within a period of 90 days after a stop-work is delivered to the Contractor, or within any extension of that period to which the parties shall have agreed, the Contracting Officer shall either—

(1) Cancel the stop-work order; or

(2) Terminate the work covered by the order as provided in the Default, or the Termination for Convenience of the Government, clause of this contract.

(b) If a stop-work order issued under this clause is canceled or the period of the order or any extension thereof expires, the Contractor shall resume work. The Contracting Officer shall make an equitable adjustment in the delivery schedule or contract price, or both, and the contract shall be modified, in writing, accordingly, if—

(1) The stop-work order results in an increase in the time required for, or in the Contractor’s cost properly allocable to, the performance of any part of this contract; and

(2) The Contractor asserts its right to the adjustment within 30 days after the end of the period of work stoppage; provided, that, if the Contracting Officer decides the facts justify the action, the Contracting Officer may receive and act upon the claim submitted at any time before final payment under this contract.

(c) If a stop-work order is not canceled and the work covered by the order is terminated for the convenience of the Government, the Contracting Officer shall allow reasonable costs resulting from the stop-work order in arriving at the termination settlement.

(d) If a stop-work order is not canceled and the work covered by the order is terminated for default, the Contracting Officer shall allow, by equitable adjustment or otherwise, reasonable costs resulting from the stop-work order.

(End of clause)

4. The following HHSAR clauses are incorporated by reference:

352.223-70 Safety and Health (JAN 2006)

5. FAR 52.212-5 Contract Terms and Conditions Required to Implement Statutes or Executive Orders—Commercial Items. (Dec 2015)

(a) The Contractor shall comply with the following Federal Acquisition Regulation (FAR) clauses, which are incorporated in this contract by reference, to implement provisions of law or Executive orders applicable to acquisitions of commercial items:

(1) 52.209-10, Prohibition on Contracting with Inverted Domestic Corporations (Dec 2014)

(2) 52.222-50, Combating Trafficking in Persons (Feb 2009) (22 U.S.C. 7104(g)).

Alternate I (Aug 2007) of 52.222-50 (22 U.S.C. 7104(g)).

(3) 52.233-3, Protest After Award (AUG 1996) (31 U.S.C. 3553).

(4) 52.233-4, Applicable Law for Breach of Contract Claim (OCT 2004)"(Public Laws 108-77 and 108-78

(19 U.S.C. 3805 note)).

(b) The Contractor shall comply with the FAR clauses in this paragraph (b) that the Contracting Officer has indicated as being incorporated in this contract by reference to implement provisions of law or Executive orders applicable to acquisitions of commercial items:

52.203-6, Restrictions on Subcontractor Sales to the Government (Sept 2006), with Alternate I (Oct 1995) (41 U.S.C. 4704 and 10 U.S.C. 2402).

52.204-10, Reporting Executive Compensation and First-Tier Subcontract Awards (Jul 2013) (Pub. L.

109-282) (31 U.S.C. 6101 note).

52.204-15, Service Contract Reporting Requirements for Indefinite-Delivery Contracts (Jan 2014) (Pub.

L. 111-117, section 743 of Div. C).

52.209-6, Protecting the Government’s Interest When Subcontracting with Contractors Debarred, Suspended, or Proposed for Debarment. (Aug 2013) (31 U.S.C. 6101 note).

52.209-9, Updates of Publicly Available Information Regarding Responsibility Matters (Jul 2013) (41 U.S.C. 2313).

52.219-8, Utilization of Small Business Concerns (Oct 2014) (15 U.S.C. 637(d)(2) and (3)).

52.219-9, Small Business Subcontracting Plan (Oct 2014) (15 U.S.C. 637(d)(4)).

(iii) Alternate II (Oct 2001) of 52.219-9.

52.219-16, Liquidated Damages—Subcon-tracting Plan (Jan 1999) (15 U.S.C. 637(d)(4)(F)(i)).

52.219-28, Post Award Small Business Program Rerepresentation (Jul 2013) (15 U.S.C. 632(a)(2)).

52.222-3, Convict Labor (June 2003) (E.O. 11755).

52.222-19, Child Labor—Cooperation with Authorities and Remedies (Jan 2014) (E.O. 13126).

52.222-21, Prohibition of Segregated Facilities (Feb 1999).

52.222-26, Equal Opportunity (Mar 2007) (E.O. 11246).

52.222-35, Equal Opportunity for Veterans (Jul 2014)(38 U.S.C. 4212).

52.222-36, Equal Opportunity for Workers with Disabilities (Jul 2014) (29 U.S.C. 793).

52.222-37, Employment Reports on Veterans (JUL 2014) (38 U.S.C. 4212).

52.222-40, Notification of Employee Rights Under the National Labor Relations Act (Dec 2010) 52.223-18, Encouraging Contractor Policies to Ban Text Messaging While Driving (AUG 2011) 52.225-13, Restrictions on Certain Foreign Purchases (June 2008) (E.O.’s, proclamations, and statutes administered by the Office of Foreign Assets Control of the Department of the Treasury).

52.232-33, Payment by Electronic Funds Transfer—System for Award Management (Jul 2013) https://acquisition.gov/far/current/html/52_207_211.html#wp1146366 https://acquisition.gov/far/current/html/52_222.html#wp1151848 http://uscode.house.gov/ https://acquisition.gov/far/current/html/52_222.html#wp1151848 http://uscode.house.gov/ https://acquisition.gov/far/current/html/52_233_240.html#wp1113329 http://uscode.house.gov/uscode-cgi/fastweb.exe?getdoc+uscview+t29t32+1665+30++%2831%29%20%20AND%20%28%2831%29%20ADJ%20USC%29%3ACITE%20%20%20%20%20%20%20%20%20 https://acquisition.gov/far/current/html/52_233_240.html#wp1113344 http://uscode.house.gov/ https://acquisition.gov/far/current/html/52_200_206.html#wp1137622 http://uscode.house.gov/ http://uscode.house.gov/ https://acquisition.gov/far/current/html/52_200_206.html#wp1141649 http://uscode.house.gov/ https://acquisition.gov/far/current/html/52_200_206.html#wp1151299 https://acquisition.gov/far/current/html/52_207_211.html#wp1140926 https://acquisition.gov/far/current/html/52_207_211.html#wp1145644 https://acquisition.gov/far/current/html/52_217_221.html#wp1136032 http://uscode.house.gov/uscode-cgi/fastweb.exe?getdoc+uscview+t13t16+492+90++%2815%29%20%20AND%20%28%2815%29%20ADJ%20USC%29%3ACITE%20%20%20%20%20%20%20%20%20 https://acquisition.gov/far/current/html/52_217_221.html#wp1136058 http://uscode.house.gov/uscode-cgi/fastweb.exe?getdoc+uscview+t13t16+492+90++%2815%29%20%20AND%20%28%2815%29%20ADJ%20USC%29%3ACITE%20%20%20%20%20%20%20%20%20 https://acquisition.gov/far/current/html/52_217_221.html#wp1136058 https://acquisition.gov/far/current/html/52_217_221.html#wp1136186 http://uscode.house.gov/uscode-cgi/fastweb.exe?getdoc+uscview+t13t16+492+90++%2815%29%20%20AND%20%28%2815%29%20ADJ%20USC%29%3ACITE%20%20%20%20%20%20%20%20%20 https://acquisition.gov/far/current/html/52_217_221.html#wp1139913 http://uscode.house.gov/uscode-cgi/fastweb.exe?getdoc+uscview+t13t16+492+90++%2815%29%20%20AND%20%28%2815%29%20ADJ%20USC%29%3ACITE%20%20%20%20%20%20%20%20%20 https://acquisition.gov/far/current/html/52_222.html#wp1147479 https://acquisition.gov/far/current/html/52_222.html#wp1147630 https://acquisition.gov/far/current/html/52_222.html#wp1147656 https://acquisition.gov/far/current/html/52_222.html#wp1147711 https://acquisition.gov/far/current/html/52_222.html#wp1158632 http://uscode.house.gov/uscode-cgi/fastweb.exe?getdoc+uscview+t37t40+200+2++%2838%29%20%20AND%20%28%2838%29%20ADJ%20USC%29%3ACITE%20%20%20%20%20%20%20%20%20 https://acquisition.gov/far/current/html/52_222.html#wp1162802 http://uscode.house.gov/uscode-cgi/fastweb.exe?getdoc+uscview+t29t32+2+78++%2829%29%20%20AND%20%28%2829%29%20ADJ%20USC%29%3ACITE%20%20%20%20%20%20%20%20%20 https://acquisition.gov/far/current/html/52_222.html#wp1148123 https://acquisition.gov/far/current/html/52_222.html#wp1160019 https://acquisition.gov/far/current/html/52_223_226.html#wp1188603 https://acquisition.gov/far/current/html/52_223_226.html#wp1169608 https://acquisition.gov/far/current/html/52_232.html#wp1153351

6. FAR 52.216-18 Ordering (Oct 1995)

(a) Any supplies and services to be furnished under this contract shall be ordered by issuance of delivery orders or task orders by the individuals or activities designated in the Schedule. Such orders may be issued from _April 1, 2015__ through _March 31, 2020___ .

(b) All delivery orders or task orders are subject to the terms and conditions of this contract. In the event of conflict between a delivery order or task order and this contract, the contract shall control.

(c) If mailed, a delivery order or task order is considered “issued” when the Government deposits the order in the mail. Orders may be issued orally, by facsimile, or by electronic commerce methods only if authorized in the Schedule.

7. FAR 52.216-19 Order Limitations (Oct 1995)

(a) Minimum order. When the Government requires supplies or services covered by this contract in an amount of less than 25 each of Lane of RNA-Seq or DNA-Seq; 25 each Analysis per lane; 4 each Unit of Transcript Confirmation; 30 each Metabolomic samples and 20 each Proteomic Samples, the Government is not obligated to purchase, nor is the Contractor obligated to furnish, those supplies or services under the contract.

(b) Maximum order. The Contractor is not obligated to honor—

(1) Any order for a single item in excess of the quantities reflected for each line item during the ordering period;

(2) Any order for a combination of items in excess of the quantities reflected for each line during the ordering period; or

(3) A series of orders from the same ordering office within 30 days that together call for quantities exceeding the limitation in paragraph (b)(1) or (2) of this section.

(c) If this is a requirements contract (i.e., includes the Requirements clause at subsection 52.216-21 of the

Federal Acquisition Regulation (FAR)), the Government is not required to order a part of any one requirement from the Contractor if that requirement exceeds the maximum-order limitations in paragraph (b) of this section.

(d) Notwithstanding paragraphs (b) and (c) of this section, the Contractor shall honor any order exceeding the maximum order limitations in paragraph (b), unless that order (or orders) is returned to the ordering office within __2___ days after issuance, with written notice stating the Contractor’s intent not to ship the item (or items) called for and the reasons. Upon receiving this notice, the Government may acquire the supplies or services from another source.

https://acquisition.gov/far/current/html/52_216.html#wp1115057

8. FAR 52.216-21 Requirements (Oct 1995)

(a) This is a requirements contract for the supplies or services specified, and effective for the period stated, in the Schedule. The quantities of supplies or services specified in the Schedule are estimates only and are not purchased by this contract. Except as this contract may otherwise provide, if the Government’s requirements do not result in orders in the quantities described as “estimated” or “maximum” in the Schedule, that fact shall not constitute the basis for an equitable price adjustment.

(b) Delivery or performance shall be made only as authorized by orders issued in accordance with the Ordering clause. Subject to any limitations in the Order Limitations clause or elsewhere in this contract, the Contractor shall furnish to the Government all supplies or services specified in the Schedule and called for by orders issued in accordance with the Ordering clause. The Government may issue orders requiring delivery to multiple destinations or performance at multiple locations.

(c) Except as this contract otherwise provides, the Government shall order from the Contractor all the supplies or services specified in the Schedule that are required to be purchased by the Government activity or activities specified in the Schedule.

(d) The Government is not required to purchase from the Contractor requirements in excess of any limit on total orders under this contract.

(e) If the Government urgently requires delivery of any quantity of an item before the earliest date that delivery may be specified under this contract, and if the Contractor will not accept an order providing for the accelerated delivery, the Government may acquire the urgently required goods or services from another source.

(f) Any order issued during the effective period of this contract and not completed within that period shall be completed by the Contractor within the time specified in the order. The contract shall govern the Contractor’s and Government’s rights and obligations with respect to that order to the same extent as if the order were completed during the contract’s effective period; provided, that the Contractor shall not be required to make any deliveries under this contract after __October 30, 2020____ .

9. FAR 52.217-8 Option to Extend Services (Nov 1999)

The Government may require continued performance of any services within the limits and at the rates specified in the contract. These rates may be adjusted only as a result of revisions to prevailing labor rates provided by the Secretary of Labor. The option provision may be exercised more than once, but the total extension of performance hereunder shall not exceed 6 months. The Contracting Officer may exercise the option by written notice to the Contractor within the performance period.

10. Responsible Officials

1. Contracting Officer Authority for Changes

The Contracting Officer is designated on the contract face page. Only the Contracting Officer has the authority to approve any deviations from the specifications and terms of this contract. Undertakings and/or agreements relative to this contract must be taken up in writing with the Contracting Officer, and Matters handled otherwise will not be recognized as binding upon the government. The contractor shall accept no instructions which deviate from the contract if issued by any person other than the Contracting Officer.

2. Contracting Officer’s Representative (COR)

a) (To be completed at time of award) is hereby designated as the COR for this contract.

b) Alternate COR: The name of the COR's alternate is (To be completed at time of award). The Alternate COR has the same authority as the COR, and may exercise that authority at the discretion of the Government, to the extent described below. All references to the COR throughout this contract shall be construed as applying equally to the Alternate.

c) The Government may unilaterally change its COR and/or Alternate designations.

d) The COR will be responsible for coordinating with the contractor in administering the technical aspects of the contract. The project officer is not authorized to make any changes which affect the contract amount, terms, or conditions. Such changes shall be only by action of the Contracting Officer. Services performed under this contract shall be subject to inspection and approval by the COR at any time.

e) The COR is specifically responsible for:

1) Monitoring the contractor's technical progress, including the surveillance and assessment of performance;

2) Recommending to the Contracting Officer changes in requirements;

3) Advising the Contracting Officer of technical interpretations;

4) Performing technical evaluations as needed;

5) Performing technical inspections and acceptances required by this contract;

6) Consulting with the contractor relative to the resolution of technical problems encountered during performance;

7) Providing technical information to the contractor (at the option of the Government) which assists in the interpretation of drawings, specifications, or technical portions of the work description;

8) Reviewing and approving or disapproving technical reports, drawings, specifications, technical information, etc. when the contract provides that such items will be delivered by the contractor to the Government under the contract.

f) The COR cannot authorize or direct any work or actions outside the express terms and conditions of the contract. For guidance to the contractor to be valid, it must:

1) Be consistent with the description of work set forth in this contract;

2) Not constitute new assignments of work;

3) Not constitute any change to the expressed terms, conditions, or specifications incorporated into this contract;

4) Not constitute a basis for an extension to the period of performance or contract delivery schedule;

5) Not constitute a change as defined in the contract clause entitled "Changes";

6) Not constitute a basis for any increase or decrease in the contract price, or any extension or other change to the contract delivery schedules or performance periods.

g) Contractor's Responsibility with Regard to Interaction with the COR, Alternate, or other individuals:

Note: The following procedures shall be applicable to directions provided during the term of this contract with the exception of directions provided by Government personnel in emergency situations. Emergency situations to include only those unanticipated emergency conditions which impose a threat to the safety of individuals or have the potential for significant damage to Government property if not immediately corrected. In other words, this clause shall be applied to instructions which could be temporarily postponed and do not require immediate reaction by the contractor to insure the protection of life and/or property from extensive harm.

If, in the opinion of the contractor, any instructions, interpretations, directions, or other actions of the COR, or Alternate, or any other individual create a condition or conditions described in item f) 1) through 6) above, or will create situations during the term of the contract which will fall within one of the categories defined in item f)1) through 6) above, the contractor shall not proceed. The contractor shall immediately notify the Contracting Officer verbally, if possible, of its concerns in this regard. The verbal notification shall be followed by a written notification to the Contracting Officer documenting the information or actions taken by the COR, Alternate, or other individual, and the basis for the contractor's opinion that those actions, instructions, directions, or interpretations will impact on the contract terms and conditions. The written notice shall be due within five (5) working days after the receipt of the COR's actions which stimulated the concern. The Contracting Officer will gather available information, and will determine whether or not the input actually constitutes a change or other condition prohibited by Section f)1) through 6) above. If it is determined that a change or other prohibited condition will occur, the Contracting Officer will so notify the contractor, and either negotiate and award a formal supplemental agreement, issue a change order, or cancel the directions. If the action by the COR is not determined by the Contracting Officer to be a "change" to the existing contract's terms and conditions, the Contracting Officer will so notify the contractor of this decision and the reasons therefore, and the contractor would be expected to immediately comply. The contractor would retain the rights provided under the "Changes" clause of this contract in the event that proper actions, as described above, are taken to notify the Contracting Officer and obtain Contracting Officer approval before proceeding with directions from any individual that are deemed to be questionable under Section f)1) through 6) above.

11. HHSAR 352.242-70 Key Personnel.

The key personnel specified in this contract are considered to be essential to work performance. At least 30 days prior to diverting any of the specified individuals to other programs or contracts (or as soon as possible, if an individual must be replaced, for example, as a result of leaving the employ of the Contractor), the Contractor shall notify the Contracting Officer and shall submit comprehensive justification for the diversion or replacement request (including proposed substitutions for key personnel) to permit evaluation by the Government of the impact on performance under this contract. The Contractor shall not divert or otherwise replace any key personnel without the written consent of the Contracting Officer. The Government may modify the contract to add or delete key personnel at the request of the contractor or Government.

The following applies to Key Personnel assigned to this contract:

Name Title

(To be completed at time of award) Principle Investigator

(To be completed at time of award) Genomic Facility Leader

When Key Personnel have been identified in this contract, it has been determined that such named personnel are necessary for the successful performance of this contract. The contractor agrees to assign such persons to the performance of the work under this contract, and shall not assign or remove any of them without the consent of the Contracting Officer.

During the first ninety (90) days of performance, the contractor shall make no substitutions of Key Personnel unless the substitution is necessitated by illness, death, or termination of employment. The contractor shall notify the Contracting Officer immediately after the occurrence of any of these events and provide the information required by the paragraph below. After the initial ninety (90) day period, the contractor shall submit the information required by the following paragraph to the Contracting Officer at least 30 calendar days prior to making any permanent substitution.

The contractor shall provide a detailed explanation of the circumstances necessitating the proposed substitutions, complete resumes for the proposed substitutes, and any additional information requested by the Contracting Officer. Proposed substitutes shall have substantially equal abilities and qualifications to those of the persons being replaced. The Contracting Officer will notify the contractor within 15 calendar days after receipt of all required information of the decision or substitutions. This article will be modified to reflect any approved change of Key Personnel.

12. Post Award Evaluation and Contractor Performance

1) Interim and final evaluations of Contractor performance will be prepared on this contract in accordance with FAR 42.15. The final performance evaluation will be prepared at the time of completion of work. In addition to the final evaluation, interim evaluation(s) shall be submitted annually based on ending date of each option period.

2) Interim and final evaluations will be provided to the Contractor as soon as practicable after completion of the evaluation. The Contractor will be permitted thirty days to review the document and to submit additional information or a rebutting statement. If agreement cannot be reached between the parties, the matter will be referred to an individual one level above the Contracting Officer, whose decision will be final.

3) Copies of the evaluations, Contractor responses, and review comments, if any, will be retained as part of the contract file, and may be used to support future award decisions.

VI. Supplemental Purchase Order Terms and Conditions For Supplies and Services

1. NEW EQUIPMENT

New equipment and/or supplies shall be furnished by the Contractor. No used, surplus, gray market or reconditioned equipment or supplies shall be furnished.

2. NEEDLE EXCHANGE

The Contractor shall not use contract funds to carry out any program of distributing sterile needles or syringes for the hypodermic injection of any illegal drug.

3. PRESS RELEASES

The Contractor shall clearly state, when issuing statements, press releases, requests for proposals, bid solicitations and other documents describing projects or programs funded in whole or in part with Federal money: (1) the percentage of the total costs of the program or project which will be financed with Federal money; (2) the dollar amount of Federal funds for the project or program; and (3) the percentage and dollar amount of the total costs of the project or program that will be financed by nongovernmental sources.

4. REPORTING MATTERS INVOLVING FRAUD, WASTE AND ABUSE

Anyone who becomes aware of the existence or apparent existence of fraud, waste and abuse in NIH funded programs is encouraged to report such matters to the HHS Inspector General's Office in writing or on the Inspector General's Hotline. The toll free number is 1-800-HHS-TIPS (1-800-447-8477). All telephone calls will be handled confidentially. The e-mail address is Htips@os.dhhs.gov and the mailing address is:

Office of Inspector General Department of Health and Human Services

TIPS HOTLINE

P.O. Box 23489 Washington, D.C. 20026

5. RESTRICTION ON EMPLOYMENT OF UNAUTHORIZED ALIEN WORKERS

The Contractor shall not use contract funds to employ workers described in section 274A(h)(3) of the Immigration and Nationality Act, which reads as follows:

“(3) Definition of unauthorized alien.-As used in this section, the term ‘unauthorized alien’ means, with respect to the employment of an alien at a particular time, that the alien is not at that time either (A) an alien lawfully admitted for permanent residence, or (B) authorized to be so employed by this Act or by the Attorney General.”

mailto:Htips@os.dhhs.gov

6. RESTRICTION ON DISCLOSURE AND USE OF DATA

Offerors that include in their proposal data that they do not want disclosed to the public for any purpose, or used by the Government except for evaluation purposes, shall-

a. Mark the title page with the following legend: "This proposal includes data that shall not be disclosed outside the Government and shall not be duplicated, used, or disclosed- in whole or in part- for any purpose other than to evaluate this proposal. If, however, a contract is award to this offeror as a result of-or in connection with- the submission of this data, the Government shall have the right to duplicate, use, or disclose the data to the extent provided in the resulting contract.