A cloud-based precision oncology framework for whole genome sequence analysis

Abstract

Cancer is one of the wide-ranging diseases which have a high mortality rate impacting globally. This scenario can be switched by early detection and correct precision treatment, a major concern for cancer patients. Clinicians can figure out the best-suited treatments for cancer patients by analyzing the patient's genome, which will treat the patient well and minimize the chances of side effects as well. Therefore, we have developed a fast, robust, and efficient solution as our precision oncology framework based on the whole genome sequencing of the individual's DNA. This platform can perform the entire genomic analysis, starting from the quality assessment of the input file to the variant annotation and functional prediction, followed by a certain level of interpretation. This analysis helps in the molecular profiling of the tumors for the identification of the targetable alterations. It takes in FASTQ or BAM file as an input and provides us with two output reports: a primary report, which consists of the patients' details, a summary of the analysis, and a secondary report, which is an elaborated report comprised of numerous results obtained from the analysis such as base changes, codon changes, amino acid changes, TMB analysis, MSI analysis, the variant frequency with its effects and impacts, affected biomarkers, etc. This framework can be effectively utilized for cancer treatment guidance, identification and validation of novel biomarkers, oncology research & development, genomic analysis, and gene manipulation.