W81XWH17T0135_0002.pdf

AMENDMENT OF SOLICITATION/MODIFICATION OF CONTRACT

Except as provided herein, all terms and conditions of the document referenced in Item 9A or 10A, as heretofore changed, remains unchanged and in full force and effect.

15A. NAME AND TITLE OF SIGNER (Type or print)

30-105-04EXCEPTION TO SF 30

APPROVED BY OIRM 11-84

STANDARD FORM 30 (Rev. 10-83) Prescribed by GSA

FAR (48 CFR) 53.243

The Purpose of this Amendment is to:

1. Incorporate a Revised PWS.

2. Incorporate by Reference the Government Response to Questions; the Response w ill be Posted to FBO.Gov See Summary of Changes

1. CONTRACT ID CODE PAGE OF PAGES

J 1 8

16A. NAME AND TITLE OF CONTRACTING OFFICER (Type or print)

16C. DATE SIGNED

BY 15-Mar-2017

16B. UNITED STATES OF AMERICA15C. DATE SIGNED15B. CONTRACTOR/OFFEROR

(Signature of Contracting Officer)(Signature of person authorized to sign)

8. NAME AND ADDRESS OF CONTRACTOR (No., Street, County, State and Zip Code) X W81XWH-17-T-0135

X 9B. DATED (SEE ITEM 11)

16-Feb-2017

10B. DATED (SEE ITEM 13)

9A. AMENDMENT OF SOLICITATION NO.

11. THIS ITEM ONLY APPLIES TO AMENDMENTS OF SOLICITATIONS

X The above numbered solicitation is amended as set forth in Item 14. The hour and date specified for receipt of Offer is extended, X is not extended.

Offer must acknowledge receipt of this amendment prior to the hour and date specified in the solicitation or as amended by one of the following methods:

(a) By completing Items 8 and 15, and returning 1 copies of the amendment; (b) By acknowledging receipt of this amendment on each copy of the offer submitted;

or (c) By separate letter or telegram which includes a reference to the solicitation and amendment numbers. FAILURE OF YOUR ACKNOWLEDGMENT TO BE RECEIVED AT THE PLACE DESIGNATED FOR THE RECEIPT OF OFFERS PRIOR TO THE HOUR AND DATE SPECIFIED MAY RESULT IN REJECTION OF YOUR OFFER. If by virtue of this amendment you desire to change an offer already submitted, such change may be made by telegram or letter, provided each telegram or letter makes reference to the solicitation and this amendment, and is received prior to the opening hour and date specified.

12. ACCOUNTING AND APPROPRIATION DATA (If required)

13. THIS ITEM APPLIES ONLY TO MODIFICATIONS OF CONTRACTS/ORDERS.

IT MODIFIES THE CONTRACT/ORDER NO. AS DESCRIBED IN ITEM 14.

A. THIS CHANGE ORDER IS ISSUED PURSUANT TO: (Specify authority) THE CHANGES SET FORTH IN ITEM 14 ARE MADE IN THE

CONTRACT ORDER NO. IN ITEM 10A.

B. THE ABOVE NUMBERED CONTRACT/ORDER IS MODIFIED TO REFLECT THE ADMINISTRATIVE CHANGES (such as changes in paying office, appropriation date, etc.) SET FORTH IN ITEM 14, PURSUANT TO THE AUTHORITY OF FAR 43.103(B).

C. THIS SUPPLEMENTAL AGREEMENT IS ENTERED INTO PURSUANT TO AUTHORITY OF:

D. OTHER (Specify type of modification and authority)

E. IMPORTANT: Contractor is not, is required to sign this document and return copies to the issuing office.

14. DESCRIPTION OF AMENDMENT/MODIFICATION (Organized by UCF section headings, including solicitation/contract subject matter where feasible.)

10A. MOD. OF CONTRACT/ORDER NO.

2. AMENDMENT/MODIFICATION NO. 5. PROJECT NO.(If applicable)

6. ISSUED BY

3. EFFECTIVE DATE

15-Mar-2017

CODE

USA MED RESEARCH ACQ ACTIVITY

820 CHANDLER ST

FORT DETRICK MD 21702-5014

W81XWH 7. ADMINISTERED BY (If other than item 6)

4. REQUISITION/PURCHASE REQ. NO.

CODE

See Item 6

FACILITY CODECODE

EMAIL:TEL:

W81XWH-17-T-0135

SECTION SF 30 BLOCK 14 CONTINUATION PAGE

SUMMARY OF CHANGES

SECTION SF 1449 - CONTINUATION SHEET

The following have been modified:

PWS

PERFORMANCE WORK STATEMENT (PWS)

REVISED 03/15/17

EFFECTIVE 03/15/17

VERSION 2.0

Chronic wound metagenomics and metatranscriptomics studies

Vision Statement (United States Army Institute of Surgical Research) (USAISR) The USAISR Dental and Craniofacial Trauma Research and Tissue Regeneration Directorate mission is to provide militarily relevant research and solutions for the prevention and rehabilitation of craniofacial trauma and infections dental diseases.

1.0. Introduction

The U.S. Army Institute of Surgical Research (USAISR) Dental and Craniofacial Trauma Research and Tissue Regeneration Directorate. The goal of this study is to apply a high-resolution metagenomics strategy in conjunction with metatranscriptomics approach towards tissue specimens from chronic human wound debridement to understand the microbial ecosystem (virulence profile) present in healing-impaired wounds at the genomic and transcriptomic level. Next, the microbial profile of these chronic wound specimens, which are classified as ulcer pressure, diabetic foot ulcer, and venous leg ulcer, will be computationally correlated with the wound etiology and other clinically relevant metadata (e.g., comorbidity). Better defining the microbial composition and genotypic profile of chronic wound residents including bacteria, fungi, and viruses (microbial metagenome) via high-throughput deep sequencing will aid in defining the molecular crosstalk and interplay between different chronic wound inhabitants that result in changes in survival, fitness, or virulence; thus providing the foundation for understanding the homeostatic state and mechanisms contributing to development of chronic wounds. Moreover, identifying the genotypic features of a diverse collection of chronic wounds can ultimately lead to novel therapeutic strategies (e.g., probiotics). Metatranscriptomics profiling of the microbiota that reside in different types of chronic wounds will provide the mechanistic insight to better understand the functional characteristics of the human wound microbiome and its susceptibility to treatment.

1.2. Background

The U.S. Army Institute of Surgical Research (USAISR) Dental and Craniofacial Trauma Research and Tissue Regeneration Directorate has a need for Next Generation Sequencing (NGS) services using latest deep-sequencing, high-throughput, HiSeq NGS technology for whole-genome shotgun sequencing (metagenome) and RNA-sequencing (metatranscriptome) of viral, fungal and bacterial communities residing in the microbiome of major classes of chronic wounds. Prior expertise and proficiency is required to utilize the proper library prep and NGS sequencing chemistry (e.g., low-input versus high-input) for each task to generate high-quality sequenced reads with sufficient sequenced read length and coverage for statistically sound downstream computational analysis. A proficient bioinformatics group that provides expertise in assembly, annotation, and analysis of fungal, viral, and bacterial sequences is needed for the timely completion of downstream computational analyses for the different tasks described below.

1.3. Scope of Work

1.3.1. This PWS contains no services that are inherently governmental functions, as defined in FAR Part 2.1. The Government shall neither supervise contractor employees nor control the method by which the contractor performs the required tasks. Under no circumstances shall the Government assign tasks to, or prepare work schedules for, individual contractor employees. It shall be the responsibility of the contractor to manage its employees and to guard against any actions that are of the nature of personal services, or give the perception of personal services. If the contractor believes that any actions constitute, or are perceived to constitute personal services, it shall be the contractor's responsibility to notify the Contracting Officer (KO) immediately.

2.0 Performance Requirements.

First Year of the Wound Microbiome Project

2.1 Metagenomics Study. Use the latest deep-sequencing high-throughput NGS technology, conduct whole-genome shotgun sequencing (WGS) of 45 samples (one-time collection) in the form of purified genomic DNA extract, to capture and characterize microbial residents of chronic wounds including fungi, bacteria, and viruses (ssDNA and dsDNA). The details of the capabilities and approaches for library preparation and NGS sequencing will be provided by the vender and discussed with ISR investigators. Due to the nature of the study, the samples (DNA/RNA extracts) will not be provided as a single big batch. Instead, samples will be provided in batches.

Number of samples in each batch may vary. The purified genomic DNA extracts are eluted in ultra-pure water and shipped and subjected to whole-genome sequencing prior to shipment of total RNA extracts. The microbial isolation method involves enzymatic/chemical lysis and genomic DNA is eluted in PCR-grade water.

2.2 DNA Library Preparation

2.2.1 Offer capability and skills to utilize the appropriate strategy based on microbial DNA concentration and findings from our microbial survey data (previous study):

2.2.2 Capture DNA sequences of both ssDNA and dsDNA present in the wound metagenome; which is necessary for detection of the wound’s viral community, the virome, using technology such as the Accel-NGS 1S DNA system.

2.2.3 If DNA concentration of a sample is too low for the steps described in 2.2.2, one can capture microbial DNA present at very low concentrations, as low as10pg, using systems such as Accel-NGS 2S to detect rare and low abundant wound microbial residents.

2.3 Whole-metagenome sequencing

2.3.1 Use Ultra-High-throughput and deep sequencing technologies to include but not limited to the HiSeq 3000 or HiSeq 4000 sequencing systems for paired-end (PE) sequencing at 150bp length of chronic wound samples that provides us with sequenced reads of at least 300 million reads with a possible read coverage of 50 to 100X from a single sequencing run.

2.3.2 Any modifications or adjustments to the parameters of sequencing run will be in accordance to the microbial biodiversity and species richness of each specimen.

2.4 DNA Bioinformatics Analysis

2.4.1 Pre-process sequenced reads to trim and filter sequenced read files followed by reference-based and de novo assembly. For reference-based analysis, in order to capture the complete metagenome, we expect that the computational team uses custom-made specific reference databases for each kingdom (fungi, bacteria, archaea, viruses) encompassing reference sequences available from trusted and well-established databases.

2.4.2 Remove any human DNA carryover.

2.4.3 Conduct gene prediction and annotation of assembled contigs for fungi, bacteria, and viruses.

2.4.4 Conduct comparative genomics of the fungal, viral, and bacterial sequences within and across the wound samples.

2.4.5 Conduct genotypic profiling and pathogenome characterization of the sequenced data for the presence of known genotypes or genetic features that are associated with factors including virulence, survival, and host-immune evasion.

2.4.6 Perform metagenomic-related analyses including the well-established features of Biobakery and CloVR-metagenome.

2.5.6 In addition to providing raw and filtered sequence files (e.g., FASTA and FASTQ), the vendor will provide investigators with the results and analysis data in the appropriate publication-ready format (e.g., charts, spreadsheets, and graphs) accompanied with a corresponding summary of computational analysis workflow/parameters and findings.

Second Year of the Microbiome Project

2.5 Metatranscriptomics Study. Capture transcripts produced by bacteria and fungi from 45 chronic wound samples (one-time collection) while also detecting the presence of RNA viruses (ssRNA and dsRNA). Use purified RNA extract (provided by investigator) with RNA-Seq technology to generate a total transcriptome profile (metatranscriptome) of wound specimens to investigate dynamics of gene expression, overall pathway landscape, and the metabolome profile of the wound’s microbial community. The details of the capabilities and approaches offered for library preparation and RNA-sequencing will be detailed and provided by the vender and discussed with ISR investigator. The microbiome RNA extraction approach and methodology is currently being optimized;

however, the RNA eluent will be provided in ultra-pure water.

2.6 cDNA Library Preparation

2.6.1 Develop cDNA libraries from human wound specimens that is based on factors including metagenomics findings as well as concentration of each RNA sample.

2.6.2 Deplete rRNA using yeast- and bacterial- specific kits (RiboZero rRNA Removal kit for yeast and bacteria).

2.6.3 If early RNA sequencing runs reveals significant loss of microbial RNA during mammalian RNA depletion steps, alternative library prep and sequencing approach is required to increase microbial sequencing coverage and improve downstream bioinformatics analysis.

2.6.4 SMARTer Low Input RNA system is needed for low RNA concentrations (200pg to 10ng) to capture presence of fungi, bacteria, and viral RNA transcripts from wound specimens.

2.7 RNA-Sequencing of microbiome metatranscriptome

2.7.1 Capture the total transcriptome profile of fungi, bacteria, and RNA viruses present in each of the 45 purified total RNA wound extracts from the same chronic wound specimens used in 2.1, at ultra-high-throughput and deep sequencing coverage using Paired-end library at 100bp length with the capacity of at least 300 million reads per sequencing run to facilitate accurate and robust downstream sequence analysis. Such ultra-high-throughput sequencing technology may include but is not limited to the HiSeq 3000 or the HiSeq 4000 sequencing systems. Due to the nature of cellular transcription, the read coverage will vary within and across wound specimens depending on differential gene expression profiles. The purified total RNA extracts are eluted in ultra-pure water and shipped after the shipment of purified microbial genomic DNA extracts.

2.8 RNA Bioinformatics Analysis

2.8.1 The human RNA reads are removed using human reference genome and the remaining reads are normalized (e.g., RPKM for microbial and VPMM for viral) and assembled using the metagenomics findings for referenced assembly.

2.8.2 For RNA-based virome studies, viral reads need to undergo De novo and reference-based assembly, as applicable, followed by normalization of reads (e.g.,VPMM, viral reads per million per unique mapped reads).

2.8.3 Create a separate comprehensive gene expression profile for fungal and bacterial wound residents.

2.8.4 Characterize the metabolome and describe the pathway landscape using metabolic flux analysis (MFA), in dynamic and/or static mode, as applicable.

2.8.5 In addition to providing raw and filtered sequenced read files (e.g., FASTA and FASTQ), the vendor will provide the investigators with the analysis data and findings in the appropriate publication-ready format (e.g., charts, spreadsheets, and graphs) accompanied with a corresponding summary of computational analysis workflow/parameters and findings.

Deliverables. Deliverables must meet accepted industry standards and meet the requirements set forth in contractual documentation. The contractor will be responsible for delivering/accomplishing all end items specified.

Number Deliverable Title Due Date

Provide output sequenced reads (fasta, fastq, BAM) of metagenomic sequencing data in raw and processed/assembled format. Sequenced read files stored and delivered on Hard drive.

Within first year of contract

Conduct assembly, annotation, and computational analysis of metagenomics sequenced read files using tools appropriate for each sample microbial population. Figures, Stats, and results depicting the progress of sequence analysis can be shared via email.

Within first year of contract

Provide ISR investigators with finalized, polished, publication ready results and figures. The figures will present data pertaining to comparative metagenomics, genetic profiling, and microbiome characterization in appropriate formats (e.g., PDF, SVG, CSV). The analysis result files and figures will be stored and delivered on a hard drive.

Within first year of contract

Provide output of transcript reads of RNA-sequencing (fasta, fastq, BAM) in the raw and processed format that is stored and delivered on a hard drive.

Within second year of contract

Conduct assembly, annotation, and computational analysis of the metatranscriptome sequenced read files using tools appropriate for each sample microbial population makeup.

Figures, Stats, and results depicting the progress of transcriptomic sequence analysis can be shared via email.

Within second year of contract

Provide ISR investigators with finalized, polished, publication ready results and figures. The figures will present data pertaining to comparative metatranscriptomics, metabolomics profiling, and microbiome gene expression characterization in appropriate formats (e.g., PDF, SVG, CSV). The analysis

Within second year of contract result files and figures will be stored and delivered on a hard drive.

3.0 The Government shall neither supervise contractor employees nor control the method by which the Contractor performs the required tasks. Under no circumstances shall the Government assign tasks to, or prepare work schedules for, individual Contractor employees. It shall be the responsibility of the Contractor to manage its employees and to guard against any actions that are of the nature of personal services, or give the perception of personal services. If the Contractor believes that any actions constitute, or are perceived to constitute personal services, it shall be the Contractor's responsibility to notify the Contracting Officer (KO) immediately.

4.0. Government Data. The Contractor shall manage all data created for Government use or legally controlled by the Government, in support of the functional activity or required by AF publication, IAW with the records management procedures in Air Force Instruction (AFI) 33 - 322, Records Management Program, Air Force Manual (AFMAN) 33-363, Management of Records, and the Air Force Records Disposition Schedule (AF RDS) located at https://www.my.af.mil/gcss-af61a/afrims/afrims/rims.cfm.

4.1.. Reporting Requirements. The Contractor shall comply with AFI 71-101, Volume 1, Criminal Investigations and Volume-2, Protective Service Matters and AFI 31-401 (Chapter 8). Contractor shall report to Security Forces any information or circumstances which may pose a threat to DoD or Contractor personnel, resources, or DoD information.

4.2. All data received, processed, evaluated, loaded, and created as a result of this contract shall remain the sole property of the Government and shall be returned to the Government at the conclusion of the contract unless the KO grants specific exception.

4.3. All products including files, software, and other information, which are created, produced or developed during the period of performance is the property of the Government and shall be returned unless the Government grants the contractor permission to retain the materials and products for continued development or publication.

4.4.The Contractor shall sign one copy of the non-disclosure statement on behalf of their company and shall also ensure that all staff including all employees, subcontractors and consultants assigned to or performing on that order execute, sign, and adhere to the terms of the following non-disclosure statement. Assignment of staff who has not executed this statement or failure to adhere to this statement shall constitute default on the part of the Contractor.

4.5. Organizational Conflicts of Interest (OIC). The USAMRMC has categorized all service procurements into one of the following three, mutually exclusive categories, regardless of the contract vehicle used to procure the services:

Category 1 - Program and/or Administrative Support. Services which, by their very nature, give the Contractor access to non-public procurement sensitive data about the contract requirements, other contractors’ proprietary information, or put the contractor in a position to influence the award decision on a contract in which they are participating. Services would be characterized as having access to Command Wide procurement sensitive information, or work that could likely have an influence over follow-on awards or contracts within subordinate directorates/Commands.

Category 2 - Program and/or Administrative Support. Services which assist in planning and managing an organization’s activities and programs. These include, for example: requirements analysis, acquisition support, budget planning and management, business, process reengineering, program planning and execution support, and independent technical management support. Services would be characterized as having access to only Directorate or Subordinate Command level procurement sensitive information or work that would have little influence on follow-on requirements or requirements of other directorates/Subordinate Commands.

Category 3 - Product Support. Services or end items required to meet the mission requirements of the organization’s activities and programs. These include, for example: concept exploration and development, system design, system development and integration, COTS Procurement and integration, internal development testing, deployment, installation, operations, and maintenance. Services can be characterized as having little or no access to procurement sensitive information other than the immediate requirement and little chances of follow-on work that can be influenced by the immediate requirement. This requirement specifically excludes – Category 1 – Program and/or Administrative Support and Category 3 Product Support.

4.6. For Information Assurance (IA)/Information Technology (IT) certification. Per DoD 8570.01-M , DFARS

252.239.7001 and AR 25-2, the contractor employees supporting IA/IT functions shall be appropriately certified upon contract award. The baseline certification as stipulated in DoD 8570.01-M must be completed upon contract award.

4.6.1. The Contractor shall protect all data in the strictest confidence; prevent the unauthorized duplication, use and disclosure of information that is subject to the Privacy Act of 1974, Health Insurance Portability and Accountability Act (HIPAA) IAW applicable statutory, regulations, local policies and procedures.

4.6.2. All technical data created as a result of this CONTRACT shall be handled in accordance with DFARS

252.227-7013, DFARS 252.227-7015.

4.6.3. The Contractor is prohibited from appropriation, disclosure, or unauthorized use of proprietary information that is acquired in the execution of this CONTRACT.

4.6.4. All products including files, software, and other information, which are created, produced or developed during the period of performance is the property of the Government and shall be returned unless the Government grants the Contractor permission to retain the materials and products for continued development or publication.

4.6.5. Information Assurance

5.1. General Security Requirements. The Contractor shall establish appropriate administrative, technical, and physical safeguards to protect any and all Government data, to ensure the confidentiality, integrity, and availability of Government data. At a minimum, this shall include provisions for personnel security, electronic security and physical security as listed in the sections that follow:

5.2. Health Insurance Portability And Accountability Act (HIPAA). The Contractor shall comply with the Health Insurance Portability and Accountability Act of 1996 (HIPAA) (P.L. 104-191) requirements, specifically the administrative simplification provisions of the law and the associated rules and regulations published by the Secretary, Health and Human Services (HHS). This includes the Standards for Electronic Transactions and the Standards for Privacy of Individually Identifiable Health Information. It is expected that the Contractor shall comply with all HIPAA-related rules and regulations as they are published and as HCE requirements are defined (including security standards, identifiers for providers, employers, health plans, and individuals, and standards for claims attachment transactions).

5.2.6. Personnel Security and Information Assurance

5.2.6.1. The Contractor shall comply with DoD Directive 8500.1, Information Assurance, DoD Instruction 8500.2, Privacy Act Program Requirements (DoD 5400.11), DoD Health Information Privacy Regulation (DoD 6025.18-R) and Personnel Security Program Requirements (5200.2-R).

5.2.6.2. Contractor responsibilities for ensuring personnel security include, but are not limited to, meeting the following requirements:

a. Immediately report to the appointed COR if any Contractor employee filling a sensitive position receives an unfavorable National Agency Check (NAC) adjudication, or if information that would result in an unfavorable NAC becomes available. Notify the USAMRAA Contracting Office within five (5) working days if, at any time, a Contractor employee has privileges revoked to a DoD data or system data because of security concerns.

b. Immediately deny access to any automated information system (AIS) or network, to the Contractor employee if, at any time, the individual receives an unfavorable NAC adjudication, or if directed to do so by the appropriate government representative for security reasons.

c. Ensure that all Contractor personnel receive information assurance (AI) training before being granted access to DoD AISs or networks.

6.2.7. Electronic Security. Department of Defense Information Assurance Certification and Accreditation Process (DIACAP). The Contractor shall acquire, develop and maintain the DIACAP documentation to ensure both initial and continued DIACAP for all Contractor systems and networks with a physical or logical connection to a DIACAP certified network. The Contractor shall also put in place processes that provide and ensure an acceptable level of security protection for any Contractor Owned, Contractor Operated – includes outsourced IT services networks that process DoD-owned Sensitive Informations (ISs) and DoD-controlled ISs. These requirements are further defined in DoD Instruction (DoDI) 8510.01, DIACAP dated 28 November 2007 (http://www.dtic.mil/whs/directives/corres/pdf/851001p.pdf).

6.2.8. Public Key Infrastructure and Encryption. The Contractor shall follow the DoD standards, policies, and procedures for the use of Public Key Infrastructure (PKI) certificates and biometrics for positive authentication.

Where interoperable PKI is required for the exchange of unclassified information between DoD and its vendors and Contractors, industry partners shall obtain all necessary certificates. The Contractor must turn over to the Government all encryption keys for deployed systems, backdoor algorithms, and procedures for their use in remote support. The Contractor must provide a written report detailing all of the above, prior to TASK ORDER expiration, regardless of modifications or extensions.

6.2.9. Information Systems (IS)/Networks Physical Security. The Contractor shall employ physical security safeguards for IS/Networks involved in processing or storage of Government Data to prevent the unauthorized access, disclosure, modification, destruction, use, etc., and to otherwise protect the confidentiality and ensure use conforms with DoD regulations.

7.0 Contractor Manpower Reporting

"The contractor shall report ALL contractor labor hours (including subcontractor labor hours) required for performance of services provided under this contract for the US Army Institute of Surgical Research via a secure data collection site. The contractor is required to completely fill in all required data fields using the following web address: http://www.ecmra.mil/ Reporting inputs will be for the labor executed during the period of performance during each Government fiscal year (FY), which runs October 1 through September 30. While inputs may be reported any time during the FY, all data shall be reported no later than October 31 of each calendar year, beginning with 2016. Contractors may direct questions to the Help Desk at at http://www.ecmra.mil.

(End of Summary of Changes)