Research Tools

Genomics

At Karkinos foundation we have state-of-the art sequencing machines including Illumina’s Novaseq, NextSeq and Thermo’s Genexus and S5 prime. We study cancer genomes using various genomic techniques including whole genome sequencing (WGS), whole exome sequencing (WES), targeted panel sequencing.

Transcriptomics

The RNA repertoire of the cancer cells is studied at Karkinos foundation by studying both the bulk RNAs and single cell RNAs from the individual cells. Several in-house pipelines are actively being developed for analysis of transcriptomic and genomics datasets including easy visualizations of the results for the clinicians and non-programmers.

Proteomics

We use qualitative and quantitative proteomics approaches to identify biomarkers in various cancers. Quantitative methods including TMT labeling, iTRAQ, and targeted proteomics are routinely used to study cancer proteomes. We also employ phosphoproteomics approaches include serine/threonine and phospho-tyrosine assays to understand the signaling mechanisms in solid cancers.

Proteogenomics

We at Karkinos foundation aim to have a comprehensive understanding of the complex biological systems in cancer, which would require different omics layers to be integrated. Proteogeomics in one such tool which leverages the power of genomics and proteomics to discover novel biological insights. We are using proteogenomics approaches to integrate genomics, transcriptomics and proteomics data from different cancers to identify novel epitopes, novel genes, and RNA editing candidates to name a few.