Annotation of Loci

This is side repository to assign a gene name to each locus lead variant and to assess presence of epitope effect within the pQTL meta-analysis using annotations from Michele F.

Gene Name Annotation Process

This process was designed to determine the gene names for 7,870 variants mapped to different genetic regions associated with various protein sequence IDs and was done in several steps:

• A filename was generated for each variant using seqid, locus, and SNPID columns.
• These filenames were compared against 12,095 annotated files provided by Michele F.
• The grep_gene_lb() algorithm was applied to extract the correct gene names where a match was found.
• Using this approach, 7,815 out of 7,870 variants were successfully annotated.

Identification of Epitope Effect

Multiple steps were implemented to define epitpe-related information:

• Read the LB file which has path to each annotated TXT file.
• Loop through each row, read the corresponding annotated TXT file, and filter relevant rows.
• Check if the consequence column contains mid- or high-impact consequences.
• If there’s a match, store TRUE and the corresponding SNPID; otherwise, store FALSE and NA.

Finally, we reported below variables along with annotated LB results:

• epitope_effect_cojo: Yes/No/NA, Yes (only for cis) if all COJO variants (or proxies by r² > 0.8) have VEP-derived moderate or high impact consequence (as defined by Gene symbol) on the gene encoding the measured protein. No if this was not the case. NA for trans-pQTLs.
• cis_epitope_effect: Yes/No/NA, Yes (only for cis) if any COJO variants (or proxies by r² > 0.8) have VEP-derived moderate or high impact consequence (as defined by Gene symbol) on the gene encoding the measured protein. No if this was not the case. NA for trans-pQTLs.
• epitope_causing_snp: List of variants causing epitope effect for a locus.
• affected_genes_from_vep: List of all unique gene symbols for which an epitope effect was observed.
• impact_variant_vep: Yes/No, Yes if all COJO variants (or proxies by r² > 0.8) have VEP-derived moderate or high IMPACT consequence on any protein-coding gene. No otherwise.