Publications by authors named "M T Landi"
Motivation: Next-generation sequencing technologies, such as whole genome sequencing (WGS), have become prominent in cancer genomics. However, managing, visualizing, and integratively analyzing WGS results across various bioinformatic pipelines remains challenging, particularly for non-bioinformaticians, hindering the usability of WGS data for biological discovery.
Results: We developed Sherlock-Genome, an R Shiny app for data harmonization, visualization, and integrative analysis of WGS-based cancer genomics studies.
Genome-wide association studies (GWAS) of melanoma risk have identified 68 independent signals at 54 loci. For most loci, specific functional variants and their respective target genes remain to be established. Capture-HiC is an assay that links fine-mapped risk variants to candidate target genes by comprehensively mapping cell-type specific chromatin interactions.
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- Recent genome-wide association studies (GWASs) have discovered various single nucleotide polymorphisms (SNPs) that individually have a minimal impact on melanoma risk, but when combined, they can significantly improve predictions through a polygenic risk score (PRS).
- Researchers genotyped 270 melanoma patients who had negative genetic tests for high/medium-penetrance genes to develop a PRS model based on 57 SNPs, revealing a substantially higher average PRS in melanoma cases compared to controls.
- The study found that the mean PRS was notably higher for patients with multiple primary melanoma compared to those with a single case, indicating that the PRS could help identify high-risk individuals for more intensive monitoring.
Article Synopsis
- * Results showed that a higher PRS was more strongly related to EGFR-positive LUAD cases (OR=8.63) than to EGFR-negative cases (OR=3.50), indicating a significant association based on mutation status.
- * These findings imply that genetic susceptibility to LUAD differs in never-smoking East Asian women depending on whether the cancer has specific mutations, which could affect public health strategies and clinical practices.*