Sources Sought NICHD-20-082 Psomagen Specs.docx

Objective 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.