Attachment 1 Purchase Description.pdf

Version 11-30-2016-1 FAR Part 11—Describing Agency Needs

PURCHASE DESCRIPTION

1. Statement of Need and Purpose:

The Talmage lab (NIMH) requires analysis services for Next Generation Sequencing (NGS) data currently for bulk RNA-Seq experiments and for single-cell sequencing experiments.

2. Background Information and Objective:

The Talmage lab is studying the effect of a psychosis-associated mutation in Nrg1 on brain development and function. The lab has previously identified this mutation to reduce nuclear signaling by Nrg1, which has been hypothesized to regulate gene expression. To further elucidate the consequences of this mutation on gene expression in developing brain circuits, the lab is performing RNA-sequencing analysis to identify potential genes that are dysregulated and then identify the functional consequences of those impacted genes. This approach will help identify the biological mechanisms that might underlie disorders with complex etiologies such as schizophrenia.

3. Generic requirement:

Next Generation Sequencing (NGS) Analysis.

4. Project Requirements:

The vendor shall provide NGS data analytics services with the following specifications.

Services shall allow for:

1. Pre-processing RNA-Seq data by performing quality control (QC),

2. Perform alignment to a reference genome using industry standard methods,

3. Quantify and normalize gene/transcript counts,

4. Perform differential gene expression analysis using DESeq2 or other industry standard methods,

5. Perform differential splicing analysis,

6. Perform weighted gene co-expression network analysis (WGCNA),

7. Provide visualizations for all analyses.

8. Capability to download analysis data in excel files and graphical reports.

Other Specifications:

1. The vendor shall provide NGS analysis pipeline automation, integration with Illumina Basespace (where all raw data is uploaded), without the need for advanced bioinformatics capabilities.

2. Allow for direct importing of collected NGS data from Illumina Basespace to the analysis pipeline eliminating need for downloading and uploading large amounts of data (>60GB).

3. Capability for analysis to be started immediately eliminating any turnaround time dependent upon an external bioinformatician.

Version 11-30-2016-1 FAR Part 11—Describing Agency Needs

4. The Graphical User Interface (GUI) shall offer transparency if any inspection and modification of any feature of the analysis is needed.

5. Shall provide the ability to customize and add new analysis pipelines as they become available with new publications allowing to keep up with the latest techniques.

6. Once uploaded, each sample can be analyzed using any pipeline offered and can be reanalyzed without additional costs.

Government Resposibilities

No Government furnished property shall be provided. Project related data will be provided to the Contractor for performance of work efforts. All data provided to the Contractor must be treated as confidential and not be disclosed to any third party. Project data will be collected and stored by NINDS. NINDS will provide data as needed to the consultant each time it requests service. The consultant may store data up to 12 months after initially receiving it, after that time the consultant should either delete the data files and sanitize the computer using NIST SP 800-88 (current revision) or if information is still needed contact the COR for permission to store data longer.

Confidentiality of Information:

The Government will not provide to the Contractor any information or data of a personal nature about individual(s) or proprietary information or data pertaining to an institution or organization which is confidential. The Contractor is not expected to generate information or data which is confidential.

Data Rights:

The National Institute of Neurological Disorders and Stroke shall have unlimited rights to and ownership of all deliverables provided under this procurement including reports, analyses, recommendations and all other deliverables. In addition, it includes any additional deliverables required by contract change. The definition of “unlimited rights” is contained in Federal Acquisition Regulation (FAR) 27.401, “Definitions.” FAR clause 52.227-14, “Rights in Data-General,” shall be incorporated into any resulting award by reference.

Section 508—Electronic and Information Technology Standards:

The Contractor shall comply with Section 508 of the Rehabilitation Act (29 U.S.C. § 794d), as amended by the Workforce Investment Act of 1998 (P.L. 105-220), August 7, 1998.

5. Quantity:

Analysis for 270 samples.

6. Delivery:

Electronic delivery on or before 30 days after award.

7. Period of Performance:

Base Period: 12 Months

8. Optional Quantities:

Vendor shall allow for a optional quantiy for analysis of up to 50 samples.

PURCHASE DESCRIPTION