About AlloPipe

The allogenomics.com webserver is based on AlloPipe, which is a computational tool designed for large- scale genomic comparisons between two human samples. The AlloPipe tool has been developed in the context of transplantation - whether Solid Organ Transplantation (SOT) or Haematopoietic Cell Transplantation (HCT). From high throughput sequencing data - such as Whole Exome Sequencing (WES) or Whole Genome Sequencing (WGS) - AlloPipe first returns the directional amino acid missmatches potentially triggering indirect alloreactivity :

• after solid organ transplantation: directional amino acid missmatches of interest are the ones present by the donor but absent by the recipient, i.e. triggerring the recipient's immune system
• after allogeneic haematopoietic cell transplantation: directional amino acid missmatches of interest are the ones present by the recipient but absent by the donor, i.e. triggerring the donor's immune system

Those directional amino acid missmatches are returned as a quantitative output that is the Allogenomic Mismatch Score (AMS) and as a qualitative output that is the mismatches table countaining relevant information such as the genomic position involved in amino acid, the rsID, the impact on the protein, the gene ID, the transcript ID, ..., allowing broad analysis on these data and/or data filtering if needed.

The webserver interface allows to perform simple filtering such as on :

• the genomic position
• the rsIDs
• the genes/transcripts of interest

Finally, it outputs the list of peptides reconstructed around the directional amino acid missmatches that are the minor histocompatibility (mHAgs) candidates within a fasta file. This fasta file can be separately proceed to get the affinity towards the HLA molecules using dedicated webservers such as NetMHCpan or MixMHCpred. the HLA molecules.