We built Gencove to bring the power of sequencing to industrial-scale genomics applications. Our approach to this is through low-pass genome sequencing, where thousands of DNA samples can be sequenced in parallel and compared against large haplotype reference panels, resulting in high-quality variant calls across an entire genome for a fraction of the cost of a clinical-grade genome sequence.

In human genomics, one of the key applications that require scale is a genome-wide association study (GWAS) to identify genetic variants that influence risk of disease. For example, GWAS in the UK Biobank of around 500,000 people have successfully identified genetic risk factors for diseases like Alzheimer’s disease and heart disease (and these data are currently being mined to identify risk factors for COVID19). Once genetic risk factors for a disease have been identified, they can be combined into an overall ‘polygenic risk score’ that quantifies the genetic component of an individual’s disease risk; these scores are currently being evaluated in many healthcare contexts. …

Over the past two years, we at Gencove have launched low-pass sequencing products as a superior alternative to genotyping arrays across species, with applications ranging from genome-wide association studies to molecular breeding.

During this time, we’ve seen dramatic decreases in the cost and operational complexity of implementing sequencing workflows— companies like Illumina and BGI continue to drive down the cost to sequence a base of DNA, while library preparation kits are now built with cost-effectiveness and automation in mind (see e.g. offerings from companies like seqWell, Twist, and iGenomX).

With these advances, a small investment in implementing low-pass sequencing can turn any lab into a high-throughput genome center — for example, we run over 1,500 samples at once in a single two-day run of an Illumina NovaSeq machine. To process this volume of low-pass sequencing data, we developed custom imputation tools and optimized software pipelines. …

tl;dr: Gencove now supports analysis of low-pass sequencing data from cattle, chickens, pigs, mice, rats, maize, and soybeans.

We launched Gencove’s low-pass sequencing platform about a year ago with the goal of making genome sequencing technologies accessible and cost-effective for large-scale genomics. Indeed, we’ve been pleased to see low-pass sequencing adopted for human genetics applications ranging from eQTL mapping to pharmacogenetics and polygenic risk score profiling.

Outside of human genetics, we’ve seen increasing interest in sequencing from agricultural companies, who use genomics to guide breeding programs directed at traits as varied as meat quality in cattle, drought resistance in maize, and egg production in chickens. We are now pleased to release low-pass sequencing analysis software and sequencing services for a wide range of agricultural and model organisms, including cattle, chickens, pig, mice, rats, maize, and soybeans. Compared to existing solutions like genotyping arrays, low-pass sequencing provides orders of magnitude more data (many millions of genetic variants called with >99% accuracy) and flexible extension to new species and/or breeds, while providing the throughput and cost-effectiveness needed for large-scale applications. …


Joe Pickrell

Human geneticist. CEO at Gencove.