KEY TAKEAWAYS
- The study aimed to explore genetic associations between cancer types using GWAS data and bioinformatics.
- The findings highlighted key haplotype structures and miRNA interactions, potentially useful for genetic panels.
Genome-wide association studies (GWAS) have revealed numerous genetic variants linked to cancer risk. These data are crucial for cancer prevention and understanding cancer mechanisms.
Morteza Gholami and the team aimed to explore genetic links between various cancers using GWAS data and bioinformatics methods.
The study identified significant GWAS variants linked to multiple cancer types. Common linkage disequilibrium (LD) variants between different cancers were found using 1000 Genomes phase 3 LD data. Haplotype blocks were determined through analysis of 1000 Genomes phase 3 genotyping data in GWAS populations.
Subsequent analyses included functional SNP analyses and TCGA gene expression data. Significant GWAS variants (P<5E-8) revealed the following haplotype associations in the European population: GT rs4808075-rs8170 haplotype on BABAM1 with breast and ovarian cancers, GC rs16857609-rs11693806 haplotype on DIRC3 with breast and thyroid cancers, GCG rs380286-rs401681-rs31487 haplotype on CLPTM1L with skin and lung cancers, GGG rs4430796-rs11651052-rs11263763 haplotype on HNF1B with prostate and endometrial cancers, and GT rs10505477-rs6983267 haplotype on CASC8 with colorectal and prostate cancers.
All these genes showed significantly different expressions in tumor tissues (P<1E-3). Additionally, the rs11693806 variant is located in the hsa-miR-873-5p binding site and enhances the hsa-miR-873-5p interaction.
The study’s novel haplotype structures and miRNA interactions are crucial for understanding common genetic links between cancers. These findings could be applied to genetic panels.
No funding information was available.
Source: https://pubmed.ncbi.nlm.nih.gov/39031745/
Gholami M. (2024) “Common and novel haplotype structures between different types of cancer.” Cancer Rep (Hoboken). 2024 Jun;7(6):e2107. doi: 10.1002/cnr2.2107. PMID: 39031745; PMCID: PMC11190585.
