Clinical Analysis of Genomic Sequencing Data

Project

On August 16, the National Agency for Research and Innovation (ANII) approved financing the project "Tools for clinical analysis of genomic sequencing data” presented at the implementation of innovation window, by ICT4V, Genlives and Quanam.

This project is the result of brainstorming sessions on bioinformatics, organized by ICT4V, in December 2015. A wide range of organizations and professionals who are involved in this topic in Uruguay, took part in these discussions.

Genlives is a company that seeks to bring genomic medicine closer to doctors and the general public. This is the way it works. A physician requests a genomic test of their patients on an on-line platform. The services offered with this innovation include sequencing the entire genome, full exoma or panels with genes and selected regions, subsequent bioinformatic and biomedical analysis of these data, as well as giving the physician advice on genomics during, the entire process. Genlives is a business start-up incubated at Institut Pasteur in Montevideo, as part of BIOESPINN program (ANII incubation program implemented at the Institute). 

Quanam, a structural partner of ICT4V, has a work group specialised in Big Data, which was formed out of the vision of the current massive growth of information, its variety and speed of release. On the one hand, this phenomenon certainly poses companies significant critical challenges, but on the other hand, it is a crucial asset for businesses to bucket the trend before anyone else. 

Information volume, speed, and sources increase every second. Big Data carries valuable knowledge, capable of transforming organizations and businesses. The most common difficulties linked to handling this enormous amount of data is centered in collection, storage, retrieval, breaking-down, analysis and visualization. Processing genome sequencing results is an excellent vertical application of Big Data, given the enormous mass of information involved. The human genome is the DNA sequence, contained in 23 pairs of chromosomes in the nucleus of each human cell, which has a total length of approximately 3,200 million pairs of DNA base, which contain about 25,000 genes approx. This implies processing massive amounts of information to identify patterns or reach conclusions to elaborate more accurate diagnosis and/or individualized treatments.

Goals of the project

Progress in DNA sequencing technologies both in terms of processing time, and cost reduction – will lead, in the near future, to complete exonomic/genomic sequencing services for costs lower than U$S 1,000. Eventually,  new services involving genomic information analysis will be offered. This technology is particularly useful in the case of preventive health care, diagnosis, treatment of genetic diseases and genetic predisposition to major diseases. 

Processing genomic information with this objective is based on the identification and valuation of variants which are relevant to the reference genome, using public databases and tested algorithms. This process reduces the load of information on patients’ genome and doctors’ tremendous effort involved in manually reviewing all of it, which would otherwise be unmanageable (around 5,000 to 1 in the case of exoma and 50,000 to 1 for complete genome). In addition to this phenomenal volume of information, there is an increasing number of research results in medical and academic publications which double every year.

The goal of the project is to build genomic data-processing services featuring: 

- results targeted to a genetist doctor user profile
- task automation to release efforts of highly qualified human resources,
- efficient management of sources dynamism,
- effective management of massive volumes of information,
- adequate handling of sensitive private information,
- traceability of conclusions,
- alignment with standards and best practices of the sector
- incorporation of local genomic specific characteristics