Summary
This project focuses on identifying causative genes and mutations within quantitative trait locus (QTL) regions in P. falciparum using genetic mapping, deep sequencing, bioinformatics, and CRISPR/Cas9 gene editing.
Peaks to genes: Fine mapping of QTLs and functional analysis
US · IL
NIH
grant
awarded
#nih-5P01AI127338-07
What they want
Core B will interface with RP01-03 for QTL location, candidate gene prioritization, and candidate validation. This involves sequencing and analyzing Bulk Segregant Approaches (BSA) experiments, generating long-read (nanopore) reference sequences for parental parasites, and developing bioinformatic and experimental approaches to prioritize candidate genes. Prioritization will utilize genomic analyses, SNP functionality predictions, mutagenesis libraries, knockout studies, and expression QTL (eQTL) analyses. Validation will involve systematic CRISPR/Cas9 gene editing, including SNP editing, conditional knockouts, or conditional protein mislocalization strategies, to determine the loci and specific mutations underlying parasite phenotypes.
Deliverables
- efficient computational and experimental approaches for rapid identification of genes and causative mutations
- gene edited parasite lines
- sequence data
- bioinformatic tools
Technical requirements
- Bulk Segregant Approaches (BSA)
- deep sequencing of F2 progeny populations
- long-read (nanopore) reference sequences
- bioinformatic and experimental approaches for candidate gene prioritization
- genomic analyses of P. falciparum populations
- computation predictions of SNP functionality
- P. falciparum piggyBac mutagenesis libraries
- rodent malaria (P. berghei) knockout studies
- expression QTL (eQTL) analyses
- CRISPR/Cas9 gene editing
