Research articles
Gencove Team - Mar 12, 2024
Short Reads, Deep Insights: Imputing Structural Variants From Short-Read Sequencing Data
Detecting structural variants in the human genome remains a substantial challenge for most sequencing projects. Most DNA sequencing projects use short-read NGS platforms, making it challenging to accurately resolve long, complex structural mutations. While long-read sequencing platforms are both available and well-suited for structural variant detection, the significant cost of using these platforms has prevented their widespread use.
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.
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.
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.
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 - 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.