The Future of Genomics and Precision Medicine

By Taryn Engmark

Assistant Editor

Embedded Computing Design

January 26, 2022

Story

The Future of Genomics and Precision Medicine

There are approximately six billion nucleotides in the human diploid genome. At such magnitudes, even a seemingly negligible error rate of 0.01% means 600,000 errors during genome sequencing. But we’ve already sequenced the human genome, so why do it again? According to healthcare officials in multiple countries, widescale human genome sequencing is the key to precision medicine.

 

Precision medicine is another name for personalized healthcare that considers the specifics of an individual patient’s genome, as well as their environment and lifestyle, to deliver targeted treatment across those with both rare and routine genotypes.

The public health implications of this type of care are unprecedented. And as such, the desire to master widespread genomic sequencing has surged in countries across the globe.

The World's Population is Isolated, but Genomics Studies Aren't

Initiated in 2018, Australia’s "Genomics Health Futures Mission" will invest $500 million over the course of a decade to build on existing genomics research to “improve testing and diagnosis for many diseases, help personalise treatment options to better target and improve health outcomes, and reduce unnecessary interventions and health costs.”

The 100,000 Genomes Project" in the UK was established to sequence 100,000 genomes from 85,000 NHS patients who were struggling with cancer or a rare disease. This project was started in 2018, and by December of the same year, they had completed their 100,000th sequence. This project is also responsible for kickstarting a thriving genomics industry in the UK.

The European Union’s "1+ Million Genomes Initiatives" united 22 EU countries alongside the UK and Norway with a goal of having a million sequenced genomes available and accessible in the EU by 2022.

"100,000 Genomes Project'' in China was launched in 2017 and was the largest human genome study in the world up to that point, and was also China’s first largescale plan in human genomics. Its goal was to provide information for clinical diagnoses and disease treatments and was estimated to be completed within four years.

The "All of Us" project in the US was framed around a report released in 2015 by the Precision Medicine Initiative Working Group of the Advisory Committee to the Director. It has invited one million people of diverse backgrounds from across the country to aid in assembling a research database that will inform thousands of health studies on various risk factors related to certain diseases.

Research on human genomes and sequencing has already progressed to the point that the NHS in the United Kingdom and Genomics England plan to offer whole genome sequencing to parents of as many as 200,000 babies via the Newborn Genomes Programme.

But sequencing such a vast number of human genomes comes with its own set of challenges.

Genome Sequencing Made Accessible

Of course, one requirement of sequencing such a large population is the ability to accurately analyze genomic data on premise and at high speed. New technologies are making that possible, such as GeneASIC Technologies’ ultra-fast next-generation sequencing data analysis platform (NGSAAP).

The NGS data analysis solution enables instant, direct access to rare and routine genotypes so that 30X whole genome sequencing (WGS) data secondary analysis from FASTQ (a text-based file format for storing a biological sequence and its corresponding quality scores) to VCF (Variant Call Format — a text file format for storing gene sequence variations) can be completed within 30 minutes.

 

A high coverage ensures the data is reliable and thus clinical grade. While preserving accuracy, GeneASIC Technologies has managed to miniaturize the tedious sequencing analysis pipeline to a compact size.

The smaller footprint also means that GeneASIC NGSAAP workloads consume less power so that, in many cases, it can be performed at the edge directly in research institutes, hospitals, and health check centers. Despite the compression, however, the solution still provides clinical-grade coverage and reliability in an affordable way.

"Presently, the price of GeneASIC NGSAAP costs half the amount of other genome data analysis high-performance computing products," said Alex Lee, Director of Research and Development of GeneASIC Technologies. “This is an opportunity for GeneASIC Technologies to get a foothold in the UK market through NGSAAP and contribute to these efforts.”

The Big Picture

As the world collectively trudges through a time when healthcare is under microscopic-level scrutinization, it’s more important than ever to ensure data like this is available and accessible to formulate the best treatment plans possible for all types of patients.

The databases being compiled already are stepping in a beneficial direction, but in order to continue on this path of research toward customized medical care, accurate, near-real time processing is crucial; and with technology like GeneASIC’s NGSAAP, that becomes possible.