Joe Pickrell, CEO & Co-founder - Feb 21, 2024
What happens when genome sequencing data is ‘too cheap to meter’?
Effectively we are rapidly approaching a world where sequencing costs per se are irrelevant to companies looking to implement genetic testing at massive scale. The scientific implications of this are fun to consider, but it’s also worth thinking about the overall business implications.
Caitlin M Stewart, Assay Development Scientist & Matthew Gibson, Senior Data Scientist - Feb 05, 2024
A comparison between low-cost library preparation kits for low coverage sequencing
As sequencing costs continue to drop, the upstream (library preparation) and downstream (data analysis & management) pieces of next-generation sequencing are becoming more important. The costs associated with library preparation have remained constant, so finding cost-saving modifications to this step has become increasingly important, especially at Gencove in our mission towards ubiquitous sequencing.
Jesse Hoff, Agrigenomics Product Manager - Jan 30, 2024
A vision for the future of the cattle industry
As we head into 2024’s cattle industry roundup at NCBA, we wanted to take stock of genomics in the cattle industry.
At Gencove, we’ve long talked about Moo-res law, the trend of increasing genotype adoption in the cattle breeding world, with global genotyping in the cattle industry likely to hit 5 million samples annually by mid-decade. The successes of genomic selection are well known, led by the US dairy evaluation’s pioneering efforts over 15 years ago, with adoption following in many cattle breeding programs globally.
Joe Pickrell, CEO & Co-Founder - Dec 21, 2023
2023: Gencove’s Year in Review
As we close the book on 2023, the Gencove team was busier than ever in the pursuit our mission: a healthier and more sustainable civilization through the application of ubiquitous sequencing. Our work with our partners spanned species and populations, today we look back on a few key highlights.
Gencove Team - Dec 06, 2023
Low-pass sequencing plus imputation using avidity sequencing displays comparable imputation accuracy to sequencing by synthesis while reducing duplicates
A recent study from the Gencove and Element Biosciences teams has demonstrated the efficacy of low-pass sequencing plus imputation using avidity sequencing compared to sequencing by synthesis.
Gillian Belbin, Senior Data Scientist - Nov 09, 2023
Gencove platform introduces Human Genome Diversity and 1000 Genome reference panel for build GRCh37
We recently reported on the release of the novel gnomAD_v3.1.2 HGDP1KG human reference panel for build GRCh38. This new panel consists of a total of 4091 individuals, and we have previously discussed its considerable gains in imputation power when compared to other publicly available human reference panels. We have now made the HGDP1KG panel available for build GRCh37.
Lex Flagel, Staff Data Scientist - Oct 04, 2023
Accurate HLA genotyping using low-pass sequence data
The human leukocyte antigen (HLA) locus is a cluster of genes on chromosome 6 of the human genome that play a crucial role in self/non-self recognition in the immune system. Understanding genetic variation at the HLA locus is essential in human genetics; however, accurately genotyping the HLA locus has proven challenging because it is complex and highly polymorphic. Here, we compare these two HLA imputation approaches to learn which path leads to greater accuracy.
Jeremy Li, Director of Data Science - Sep 25, 2023
A deep dive into Explorer analysis cloud
At Gencove, we have repeatedly seen the complexity and insufficiency of existing tools limit research teams from fully unlocking the value of their genetic data. Gencove Explorer analysis cloud represents a full-stack solution that addresses the challenges that exist with currently data solutions, in a single integrated platform and with a minimal learning curve. In doing so, Explorer accelerates the rate at which scientists can answer critical biological questions, and furthers our goal of delivering insights that advance global health and sustainability.
Lex Flagel, Staff Data Scientist - Sep 19, 2023
An updated evaluation of a recent open-access human genome reference panel for low-pass imputation
The Broad recently released an update to the HGDP1KG panel as part of the gnomAD_v3.1.2 release that included several tweaks and changes meant to increase the accuracy of the combined panel. In this blog post we once compare imputation performance of this updated panel to the NYGC1KG panel.
Jeremy Li, Director of Data Science - Sep 08, 2023
Improving biological sample and data management with sample manifests
The new "sample manifests" feature ensures accurate sample identification and reduces errors, streamlining the process from sample collection to solutions delivered by the platform.
Jeremy Li, Director of Data Science - Aug 15, 2023
Investigating the impact of reference panel errors on imputation quality and genotype accuracy
Genotype imputation is an increasingly popular method used in population scale genomic studies that relies on two key elements; the haplotype reference panel (HRP) and the imputation algorithm. A recent preprint from the Gencove data science team dives into how common errors in reference panels impact imputation accuracy and the interplay between the two across a spectrum of sequencing coverages.
Gencove Team - Aug 10, 2023
Low-pass sequencing and imputation for evaluating genetic variation
Low-pass whole genome sequencing is an approach that strikes a balance between the cost-efficiency of microarrays and the broad genomics insights provided by high coverage WGS