NICHD-20-082a Bioinformatics Services Support SOW.pdf

Statement of Work (SOW) National Institute on Minority Health and Health Disparities (NIMHD)

Division of Intramural Research (DIR) Bioinformatics Services Support

Purpose of the Requirement The purpose of this acquisition is to acquire bioinformatic services to analyze DNA Methylation Sequencing and Single Nucleus RNA-Sequencing data from racially diverse breast cancer samples.

Background The NIMHD Epidemiology and Genetics research program within the Division of Intramural Research (DIR) requires bioinformatic analyses of DNA Methylation Sequencing and Single Nucleus RNA-sequencing data generated from sequencing of normal/tumor samples from racially and ethnically diverse breast cancer patient samples.

Objective NIMHD DIR Epidemiology and Genetics program seeks a contractor to provide advanced cutting edge and updated bioinformatic services to analyze DNA Methylation Sequencing and Single Nucleus RNA-Sequencing data from normal and breast cancer tumor samples. The contractor shall provide analytic results including quality control analysis, alignment bam files, CpG, CHG and CHH methylation results for DNA methylation for each race. Quality control analysis, dimension reduction and clustering analysis using PCA, t-SNE or UMAP and differential expression analysis for Single Nucleus RNA-Sequencing.

Scope of Work The scope of work is for the contractor to provide advanced bioinformatics services required to analyze DNA Methylation Sequencing and Single Nucleus RNA-Sequencing data from normal and tumor samples from racially and ethnically diverse breast cancer samples.

Tasks to be Performed

The Tasks included the bioinformatics analyses of DNA Methylation Sequencing (Task1 for 100 samples) and Single Nucleus RNA-Sequencing (Task 2 for 20 samples). The total samples are 100 + 20 = 120.

Task 1 – Standard DNA Methylation analyses using Bismark followed by custom bioinformatics analysis.

These analyses shall include:

Standard workflow (100 samples) Quality assessment using FASTQC software

• Sequence alignment BAM file per each sample using Bismark Bisulfite Mapper

• CpG, CHG and CHH methylation results by using bismark_methylation_extractor function

Customized advanced analysis by 6 subgroups, N=100

• There are a total of 100 samples, described above, stratified into the following 6 groups: Hispanic normal (15), Hispanic tumor (15), non- Hispanic Black normal (20), non-Hispanic Black tumor (20), non- Hispanic White normal (15) and non-Hispanic White tumor (15). Further advanced integrative methylation analysis within these 6 groups should be included.

Task 2 – Single Nucleus RNA-Sequencing analysis from 10X Genomics using standard analysis followed by custom bioinformatics analysis for 20 samples.

These analyses shall include:

Standard workflow for 20 samples

• Quality assessment using FASTQC software

• Count table per sample by running Cell Ranger software

• Principal Component Analysis using Seurat

• Clustering analysis using t-SNE and/or UMAP

• Identification of marker genes per cluster

Customized downstream analysis for integrated comparisons between each group among 4 groups (5T AA, 5N AA, 5T EA, 5N EA), N=20

• There are total 20 samples of triple negative breast cancer (TNBC) , stratified into 4 groups: African American tumor (5T AA), African American normal (5N AA), White tumor (5T EA), and White normal (5N EA) samples

• Differential expression analysis in Single Nucleus RNA-Sequencing for racial comparisons in these 5 T/N pair African American and 5 T/N pair European American should be included.

Deliverables NIMHD DIR Epidemiology and Genetics program will deliver pre-processed raw sequencing data for DNA Methylation Sequencing and Single Nucleus RNA-sequencing data generated from sequencing of normal/tumor samples from racially and ethnically diverse breast cancer patient samples in FASTQ via Biowulf/NIH HPC. The raw sequencing file consists of de-identified data of patient sequencing information. No personal identifiers will be transferred to the contractor.

The contractor will return data analysis results via Biowulf/NIH HPC in BAM files, along with the quality assessment report for each sample using FASTQC software. The output shall include MS Excel files and figures as listed above in the task section.

Schedule The contractor shall deliver the final analyzed data with the quality assessment per each sample within two months and the standard analysis should be delivered within one month from the receipt of the raw FASTQ data from the NIMHD DIR Epidemiology and Genetics research program.

Security Requirements All analyses will be transferred in the secure, HIPAA compliant environment using the NIH Biowulf High Performing Computation (HPC) system.

Period of Performance One year from date of award

Summary of Service 100 samples for Standard DNA Methylation analyses using Bismark followed by custom bioinformatic analysis Qty Methylation Analysis – Basic

Advanced Analysis for 6 Groups

20 samples for Single Nucleus RNA-Sequencing analysis from 10X Genomics using standard analysis followed by bioinformatic analysis Qty 10X Single Cell RNA Analysis

Technical Criteria for Contractor Requirements

The contractor shall provide following services:

• Availability of consultations before and after bioinformatics analysis to address specific questions from NIMHD Division of Intramural Research (DIR) staff.

• Free consultation and discussion for questions about analyzed files resulting from single nucleus RNA sequencing bioinformatics analysis and DNA methylation sequencing bioinformatics analysis.

• Secure delivery outcomes after the bioinformatics analysis service to the NIMHD DIR genomics lab at NIH via secure network (i.e.Globus link to NIH) or NIH biowulf HPC.

• Essential performance containing standard and advanced bioinformatics analyses both for DNA methylation sequencing and Single Nucleus RNA sequencing (see Task1 and Task2).