Mellowes Center for Genomic Sciences and Precision Medicine Mini-Grants

Mellowes Center Mini-Grants NGS-Based Pilot Projects – Sequencing, Bioinformatics, and Analysis 

Request for Applications 

Purpose and Overview 

To advance the cellular and molecular understanding of individualized and population health, undiagnosed diseases, adverse events, and more, the partnership between CTSI and the Mellowes Center for Genomic Sciences and Precision Medicine (MC), is seeking proposals for small-scale research projects that utilize any combination of the genomic, transcriptomic, or epigenomic technologies and bioinformatics platforms available in the MC. Responsive proposals will describe projects that improve our understanding of disease initiation, progression, or therapeutic resistance that will, in the future, strengthen and extend clinical care models. 

Eligibility and Pre-application 

• Faculty meeting MCW PI eligibility, or PI eligibility at another CTSI partner, that have an imminently implementable project involving NGS-based methodologies (see MC Technology & Bioinformatics Platforms below).
  • Sequencing data should meet minimum QC metrics appropriate for the NGS technology. 
  • Projects need the requisite data available within three months of acceptance of the award. 
• Agree to abide by NIH data management sharing policy.1 
• Completion of a 30-minute consultation with the MC ‘Omics technology and bioinformatics team to ensure appropriate allocation of resources and clear communication of project design.

1NIH 2023 Data Management Sharing Policy

Sample and Data Ready Requirement

To be eligible for funding, applicants must indicate the ability to transfer NGS ‘Omics data (prefer fastq or BAM files) for bioinformatic analysis.

Number of Awards and Budget

CTSI Leadership expects to fund up to 10 eligible projects annually.

• Projects will receive up to 18 hours of MC bioinformatics analytics services.
• Each project is eligible for 1 MC mini-grant. Renewals are not allowed.

Grant Application Instructions

Link to application will be sent to PI upon completion of the 30-minute MC consultation

Application Format: Use standard 11-point font, single space, and half-inch margins throughout the application. Consecutively number all pages. Limit 2 pages.

• Scientific Abstract: Provide a summary of the project. (250-word limit).
• Research plan: Provide the aim(s) of the study, background, significance and rationale for the use of existing NGS data for analysis. Describe availability of data set(s) to be analyzed (e.g., doi, SRA identifier, or clear file format description) and expected impact of proposed study.
• Future Plans: Provide clear information on how the award will lead to external grant funding, high-impact manuscripts, etc.
• References. List references cited (not counted in page limit).
• Biographical sketches. Provide a NIH-format biosketch for each PI and co-investigator (not counted in page limit).

Evaluation Criteria and Reporting

Applications will be reviewed by CTSI and Mellowes Center Leadership, and decisions for funding made within one month of submission. Proposals showing promise to support high-impact manuscripts or extramural grant funding will be prioritized.

Awardees will be required to respond to routine post-award surveys.

Mellowes Center Bioinformatics Platforms with Examples of Projects and Analysis

• DNA-Based testing
  • Tumor and/or somatic variant calling and analysis
  • Germline variant calling and analysis for cancer patients to investigate etiology or predisposition
  • Differences in variant (SNV, MNV, INDEL, CNV) frequencies between cases and controls
  • Analysis of specific inheritance patterns among duos, trios, or quads
• RNA-Seq differential expression analysis
  • Differential expression by pairwise conditions or among groups of conditions/phenotypes
  • Results summary via PCA (dimensionality reduction), volcano plot, heatmaps, and pathway analysis
  • Example: Compile RNAseq data from multiple investigators that investigated different subtypes of a disease; consider if increasing sample number clarifies genes and pathways important to the subtypes of disease
  • Example: Consider the correlation of clinical phenotypes (extent of phenotype, machine outputs, etc.) with transcriptional data from diseased tissue
  • Example: Deconvolute and predict immune cells types present in a bulk RNAseq profile from a heterogenous sample type
• DNA accessibility profiles via ATAC-Seq
  • Report on genome-wide patterns of peak position and intensity differences
  • Summary on genes and their proximal regulatory regions
• DNA CpG Methylation via RRBS or EPIC methylation arrays
  • Global profile summaries, CpG calling and quantification, region-based quantification (tiling or DMRs), annotation with TFs and/or marks
  • Differential CpG and DMR calling among conditions
  • Summary of genes and their proximal regulatory regions with altered methylation
  • Example: Compile methylation data from multiple investigators that sequenced different subtypes of a disease
• Histone-based ChIP-Seq and/or cut-and-run
  • Report on genome-wide patterns of peak position and intensity differences
  • Summary on genes and their proximal regulatory regions
• Integrate multiple NGS methodologies
  • Example: Consider overlap of genes expressed in an RNAseq data set with the alteration of DNA accessibility evidenced at promoters of the same genes

Click the link below to view a downloadable version of the RFA: