Blog

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, below we look back on a few key highlights:

1. Introduction of Gencove Explorer: A Paradigm Shift in Genomic Data Analysis

The launch of Gencove Explorer was a key addition to our suite of genomic tools. Explorer is designed to free scientists from the burdens of managing intricate computational infrastructure and bioinformatics workflows, by serving as the comprehensive data analytics and management cloud. This enables scientists to focus on extracting meaningful biological insights from vast genomic datasets.

Deep Dive into Explorer
In our blog post, we dug into how Explorer stands out in handling and simplifying genomic data analysis. This deep dive provides an understanding of Explorer's user-friendly interface, powerful data processing capabilities, and how it accelerates the journey to actionable genomic insights. We also had our Head of Product, Geoff Benton, feature in a webinar to share how Explorer empowering data science teams and reshaping the landscape of genetic data analytics and management. You can watch it on demand here.

2. Revolutionizing Sequencing in Agriculture

We also saw major advances in the use of sequencing in agricultural genomics, particularly as sequencing becomes more cost-effective and accessible. The throughput and price-sensitivity of agricultural applications of genomics have previously meant that sequencing has not been a viable technology for widespread use, but innovation in sequencing technologies and the applications of those technologies has changed the game in 2023.

Low-pass and Ultra Low-pass Sequencing in Cattle
We shared an analysis that demonstrated that low-pass sequencing, combined with imputation, is highly effective in cattle genotyping. Even at coverage as low as 0.1x, this approach can generate comprehensive genome-wide information with sufficient accuracy for implementing genomic prediction models, marking a significant advancement in livestock genomics.

Low-pass Sequencing Plus Imputation Using Avidity Sequencing as a Cost-Effective Alternative to Traditional SBS
In a joint paper with Element Biosciences, we showcased how Avidity sequencing not only offers a cost-effective alternative to traditional sequencing but also improves data quality. This is particularly beneficial in applications like large-scale agricultural genotyping, where reducing duplication rates and costs is crucial. We also invited the Element team to join us for a webinar to explore the future possibilities of genomic applications in agriculture, you can watch it on demand here.

3. Advancements in Human Reference Panel Performance for Imputation

Our work in enhancing the performance and accuracy of reference panels for genomic imputation has been another focal point this year. As genomics research continues to advance, understanding and addressing reference panel quality and accuracy will be paramount for obtaining accurate and reliable insights from imputed genetic data.

Investigating the Impact of Reference Panel Errors on Imputation Quality and Genotype Accuracy
Gencove’s data science team shared their investigation into how common errors in reference panels impact imputation accuracy and the interplay between the two across a spectrum of sequencing coverages. The research highlights how these errors can impact the quality of imputation and the accuracy of genotypes, providing valuable insights for future improvements in genomic studies. We shared a blog on the key highlights from the research.

The Human Genome Diversity Project plus 1000 Genomes Dataset as the Gold Standard Imputation Reference Panel
Over the past decade, human genomic research has benefited tremendously from the availability of open-access human genome diversity panels like the 1000 Genomes Project (1KG) and the Human Genome Diversity Project (HGDP). We analyzed updates to the combined HGDP1KG panel and concluded that the HGDP1KG panel offers a large set of high-quality genotype calls, and is a comprehensive improvement over the NYCG1KG panel for genotype imputation from low-pass sequences. You can dive into our analysis here or check out our webinar with the team from Dr. Alicia Martin’s lab at the Broad Institute on the harmonization of the dataset.

4. Diverse Applications of the Gencove Platform

Throughout the year, the Gencove platform has been integral to a wide range of groundbreaking projects, across species and populations. Some of the highlights are below:

GWAS and PRS-PheWAS Across Complex Phenotypes in the Human Phenotype Project
Zachary Levine and the team at the Weizmann Institute of Science used low-pass whole genome sequencing in a study from the Human Phenotype Project, analyzing 727 clinical phenotypes and 4,045 molecular features, simplifying traditional Genome-Wide-Association Studies (GWAS).

Cell Type-Specific and Disease-Associated eQTL in the Human Lung
The Translational Genomics Institute, part of City of Hope, researched genes involved in lung diseases such as pulmonary fibrosis by combining single-cell RNA sequencing and low-pass whole genome sequencing on the Gencove platform to link genetic variations to their effects on gene expression in lung cells of patients and healthy individuals.

Unraveling the Genomic Diversity and Evolutionary History of Captive Tigers in the United States
This study analyzes the U.S. captive 'Generic' tiger population, showing they have a genetic mix of all six wild subspecies with similar diversity to wild tigers, and introduces a reference panel effective in identifying individual tigers and their ancestry, aiding future research and global conservation efforts.

Genomic Markers Associated with Antibody Response to Newcastle Disease Virus of Sasso Chickens Raised in Ethiopia
Girma et al.'s study, utilizing the Gencove platform and low-pass whole genome sequencing, discovers genetic markers in Sasso chickens linked to immunity against Newcastle disease, offering valuable information for breeding disease-resistant chickens, crucial for the poultry industry and food security in developing countries.

We expect the advances in new sequencing hardware to continue to propel the adoption of genome sequencing across industries in 2024; we're always looking for new partners who share our vision and would love to hear from you, please reach out!