At Gencove, our mission is to make genome sequencing accessible and interpretable. Over the past several weeks, it has become clear that a key missing piece of the response to the coronavirus crisis in the United States involves sequencing to monitor virus strains as they arise and spread. This was driven home by the identification of an apparently more contagious virus lineage in the UK and a potentially similar report from South Africa.

It seems certain that virus lineages with worrying properties (e.g. increased transmission or vaccine escape) are arising elsewhere in the world; these variants were only identified in…

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…

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…

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…

tl;dr: Gencove has opened up a platform for low-pass sequencing, available at gencove.com

About ten months ago, I discussed the arguments for using low-pass sequencing as a replacement for genotyping arrays. The key argument is that sequencing-based technologies (when combined with advances in imputation algorithms) allow one to collect more data at a lower cost than genotyping technologies.

Since I wrote that blog post, sequencing costs have continued to decline, our molecular biology processes have become more efficient, and our imputation algorithms have continued to improve. Indeed, we have been offering low-pass sequencing as a service to leading academic, biotech…

We are making some important changes at Gencove.

In the last year, we’ve seen increasing demand for our low-pass sequencing technology from researchers looking for accessible and effective sequencing, and we have been working hard to launch exciting new capabilities for this technology. You can read more about what we are doing here.

But this also means that we have decided to fully focus on our sequencing platform and that we will need to gradually discontinue our direct-to-consumer products. What does this mean for you?

To start, we will discontinue DNA data uploads and kit orders for individual customers as…

This is a modified version of a blog post I initially wrote two years ago. With the increasing interest in genetic ancestry testing over these two years, the question “What is ancestry?” is worth keeping in mind.

Anyone who has used commercial genetic testing products like those offered by 23andMe, AncestryDNA, or Gencove is familiar with the idea of “genetic ancestry”. After mailing in a saliva kit, we return a report that tells you the percentage of your DNA that is most similar to different populations around the world.

At a superficial level, it seems like getting this estimate should…

tl;dr: for discovery of genetic variants associated with traits, sequencing outperforms genotyping arrays and costs less.

Over the last ten years, the field of human genomics has made unbelievable progress in identifying genetic variants that influence disease susceptibility and other traits (see, e.g. this review). The technological advance that drove this progress was the development of genotyping microarrays: a technology for the measurement of hundreds of thousands to millions of genetic variants in a single person.

The benefits and limitations of genetic studies using this technology (often confusingly called genome-wide association studies [1]) have been debated since before anyone even…