Attachment_1_-_SOW _NIHES2015052_RNA_Sequencing_IDIQ.pdf

STATEMENT OF WORK FOR

NEXTGEN RIBONUCLEIC ACID SEQUENCING SERVICES

EPIGENOMICS CORE LABORATORY

NATIONAL INSTITUTES OF ENVIRONMENTAL HEALTH SCIENCES

1.0. BACKGROUND: The National Institute of Environmental Health Science (NIEHS) located in Research

Triangle Park, North Carolina, is one (1) of 27 research institutes and centers that comprise the National Institutes of

Health (NIH), U.S. Department of Health and Human Services (DHHS). The mission of the NIEHS is to discover how the environment affects people in order to promote healthier lives. Some branches and laboratories at NIEHS fall under the Intramural Research Division (IRD). In-house, or intramural research, is performed by scientists in laboratories at the NIEHS who collaborate extensively with partners in other institutes, agencies, and academia to conduct research with the following branches and laboratories: Biostatistics and Computational Biology; Clinical

Research; Comparative Medicine; Epidemiology; Epigenetics and Stem Cell Biology; Genome Integrity and

Structural Biology; Immunity, Inflammation, and Disease; Neurobiology; Reproductive and Developmental Biology;

and Signal Transduction.

The NIEHS has a requirement in support of the IRD to contract for NextGen sequencing services for Ribonucleic acid

(RNA). Investigators at the NIEHS utilize many model systems to explore environmental impacts on human health and disease. The objective is to establish a reliable, rapid and cost-effective NextGen DNA/RNA sequencing services vehicle to support ongoing research projects led by NIEHS investigators within the IRD. NextGen sequencing data provides vital information to ongoing investigations regarding environmental disease mechanisms and the genetic, genomic, and epigenomic components of susceptibility, outcomes and progression of environmental diseases. In order to maintain the integrity of current research projects and research data continuity it is imperative that additional

NextGen sequencing be provided using the same technology currently in use. The data from this project must be provided to the NIEHS via ftp and the data files must be provided in both the. fastq and .cel format.

2.0. OBJECTIVES: The purpose of this acquisition is to provide continued support of NextGen sequencing service’s in progress that support DIR research objective’s and to further explore how human health and human disease are caused by the interactions of the environment.

3.0. SCOPE: The Contractor is required to provide NextGen Sequencing services that include: high quality NextGen library construction with proper QC confirmation, NextGen DNA or RNA sequencing runs/lanes of high quality constructed libraries with accompanying bioinformatics support. The continuity of sequencing information will provide vital information to on-going investigations regarding environmental disease mechanisms and the genetic component involved in causes, outcomes and progression of environmental diseases. The Contractor is also required to perform the following tasks:

NextGen Sequencing;

RNA or DNA extraction;

DNA library construction;

Sequence analysis;

NextGen Sequence Bioinformatics Data Analysis;

Data output file; and

Mapping sequence data file

More specifically, the Contractor shall provide the following:

Sequencing services to IRD using the same technology and novel form of analysis (Illumina MiSeq and

NextSeq 500 technologies) as currently being used;

Produce high dimensionality of sequencing data;

Identify differences in sequencing data using methods that not yield significant false positives;

Use a DNA sequencing analysis data method that can mitigate the multiple testing issues by calculating a false discovery rate from a reference data distribution generated from our experimental data;

Provide sequencing support that will provide the data in both fastq and in cel file format. The .cel format data is required to allow IRD to compare the RNA-seq results to previously obtained microarray results;

Provide reliable sequence data necessary with low error within the sequencing data;

Provide NextGen data to produce enough sequencing reads to meet the needs of DIR researchers;

Provide a combination of Illumina Bio-analyzer and the novel bio-informatic analysis;

Ensure method used mitigates the multiple testing issues by calculating a false discovery rate from a reference data distribution generated from our experimental data; and

Allow researchers to accurately determine error rate and provide the best data possible

The following on-going projects will be the focus of the services:

On-going project within the Systems Biology Group requires further NextGen Sequencing Analysis of samples to continue to define mechanisms of gene regulation at various regulated stages of gene expression. In particular, the group is interested in understanding and identifying how transcription regulators and epigenetic modifications regulate gene expression programs during cellular development and differentiation. The group uses a combination of systems, molecular, and functional genomic approaches to map and characterize regulatory elements and epigenomes in human and mouse embryonic/hematopoietic stem cells, T cells, and cancer cells;

On-going project within the Chromatin and Gene Expression Group requires further NextGen

Sequencing Analysis of samples to continue to define: evaluating how chromatin remodeling complexes and transcription factors function in transcription from chromatin, analyzing the ubiquitin proteasome system interface with chromatin remodeling, epigenetics and hormone signaling and to understand how chromatin and epigenetics contribute to human ES cell pluripotency;

On-going project within the Transcriptional Responses to the Environment Group requires further

NextGen Sequencing Analysis of samples to continue to define the dynamic interplay between signals from the environment and transcription by RNA polymerase II (Pol II). The ability to rapidly integrate multiple extra- and intra-cellular cues to produce specific patterns of gene expression is essential for the growth, development, and survival of all organisms; however, the molecular mechanisms leading from these signals to the coordinated activation of gene networks are not well understood and could be identified by NextGen Sequencing;

On-going project within the Post-Transcriptional Gene Expression Group requires further NextGen

Sequencing Analysis of samples to continue to define: the roles of a small family of CCCH tandem zinc finger proteins, exemplified by tristetraprolin or TTP, in the physiological regulation of mRNA turnover and translation. Members of this family of proteins exist in essentially all eukaryotes, from plants to humans, and are important in species-specific control of mRNA turnover, in some cases in response to environmental cues; and

On-going project within the Reproductive Medicine Group requires further NextGen Sequencing

Analysis of samples to continue to define reproductive biology of early mammalian embryogenesis including gametes, fertilization, preimplantation embryo development, and implantation. The basic bench science is focused on specific questions that have direct relevance to human reproduction, and how the environment influences these aspects of reproduction. Previous experiments involving mouse preimplantation embryos, which showed that THO proteins are needed for proper embryo development to the blastocyst stage, when the embryo is beginning to generate pluripotent stem cells. Characterizing the network or pathway is a key objective.

4.0. TASKS: The Contractor shall perform the following tasks:

4.1. Task 1 - NextGen Sequencing: The Contractor shall process and prepare approximately 450 sequencing samples for DNA or RNA sequencing on an Illumina HiSeq series sequencing instrument (HiSeq2000, HiSeq2500, or equivalent). The Contractor shall utilize the following set of general procedures for sample preparation and sequencing shall occur with appropriate direction from NIEHS.

4.1.1. 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 to the contractor and it shall be delivered to the

NIEHS Epigenomics Core Lab at no cost to NIEHS. File submissions shall be submitted no later than five (5) days after task completion. The contractor shall maintain a local copy of all data for at least 30 days to allow NIEHS staff sufficient time to verify data transfer integrity.

4.2. Task 2 - RNA or DNA extraction: The contractor shall provide supplies to extract RNA or DNA from biological samples the NIEHS ships and provides to the Contractor. Some samples may not need extraction prior to library construction for which the NIEHS will provide pre-extracted high quality DNA or RNA. Prior to the time of shipment (e.g. 3 days), NIEHS shall provide direction to the contractor on sample preparation (e.g. poly-A enrichment, methylated DNA enrichment, etc.) for each sequencing sample.

4.2.1. The Contractor shall deliver results from each sequencing sample, 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 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 one (1) day after task completion.

4.3. Task 3 - Sequence Analysis: The Contractor shall perform one lane of RNA-Seq or DNA-Seq analysis on multiple samples from an Illumina HiSeq instrument that provides at least 25 Million reads per sample.

4.4. Task 4 - DNA Library Construction: Sample DNA or RNA shall be bar-coded (indexed) as necessary for library construction. NIEHS shall specify prior to analysis (e.g. 1 week), the size of read length and shall specify if reads shall be single end or paired end (paired end is standard). Some samples shall arrive to the contractor in which the library construction was performed by NIEHS and are ready to be run immediately upon arrival.

4.5. Task 5 - Data Output File: The Contractor shall capture metrics of quality and sequencing statistics in accordance with standards for Illumina HiSeq2000 series instruments. These data shall be provided to the COR within 1 day of completion of the task.

4.6. Task 6 - Mapping Sequence Data File: The Contractor shall perform a bioinformatics analysis on DNA or RNA sequence data and shall map quality filtered .fastq data to the appropriate reference genome to create a mapped file

(e.g. .bam file format).

5.0. DATA RIGHTS: The Government has unlimited rights to all documents/material produced under this contract to the extent permitted by the data rights clauses. The parties mutually acknowledge their understanding that this is the government’s intent. All documents and materials, to include the source codes of any software, produced under this task order shall be government owned and are the property of the government with all rights and privileges of ownership/copyright belonging exclusively to the government. These documents and materials may not be used or sold by the contractor without written permission from the contracting officer. All materials supplied to the

Government will be the sole property of the government and may not be used for any other purpose. This right does not abrogate any other government rights.

6.0. 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 located within the contiguous United States (CONUS).

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

7.0. SAFETY AND HEALTH: The Contractor shall comply with all Federal, North Carolina State, Occupational

Safety and Health Administration (OSHA) standards and local laws and regulations concerning the environmental, occupational safety and health, and hazardous material. The contractor shall ensure employees have all required training and certifications related to OSHA requirements. The documentation shall be readily available for the

Contracting Officer to review at any time during the life of the contract.

8.0. GOVERNMENT FURNISHED EQUIPMENT/MATERIALS/SERVICES:

8.1. Materials: NIEHS will furnish biological samples for analysis. NIEHS will notify the contractor, via email or telephone, approximately one (1) day prior to furnishing biological samples for analysis.

8.2. Equipment: NIEHS will furnish external hard drives for data transfer of files necessary due to size limitations.

8.3. Services: NIEHS will either ship biological materials to the contractor via a commercial carrier or hand deliver biological materials on dry ice in a suitable 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.

9.0. DELIVERABLE SCHEDULE:

SOW Ref Deliverable Media Deliver To

4.1.1

Provide an Illumina .fastq file no later than five (5) days after task completion. Local copy of all data shall be maintained for 30 days.

Electronically via FTP site. Large files use NIEHS hard drive.

COR & CO

4.2.1

Provide results from each sequencing sample, 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 no later than one (1) day after task completion.

Electronically via FTP site. Large files use NIEHS hard drive.

COR & CO