GeniePool 2.0: advancing variant analysis through CHM13-T2T, AlphaMissense, gnomAD V4 integration, and variant co-occurrence queries

Abstract

Originally developed to meet the challenges of genomic data deluge, GeniePool emerged as a pioneering platform, enabling efficient storage, accessibility, and analysis of vast genomic datasets, enabled due to its data lake architecture. Building on this foundation, GeniePool 2.0 advances genomic analysis through the integration of cutting-edge variant databases, such as CHM13-T2T, AlphaMissense, and gnomAD V4, coupled with the capability for variant co-occurrence queries. This evolution offers an unprecedented level of granularity and scope in genomic analyses, from enhancing our understanding of variant pathogenicity and phenotypic associations to facilitating research collaborations. The introduction of CHM13-T2T provides a more accurate reference for human genetic variation, AlphaMissense enriches the platform with protein-level impact predictions of missense mutations, and gnomAD V4 offers a comprehensive view of human genetic diversity. Additionally, the innovative feature for variant co-occurrence analysis is pivotal for exploring the combined effects of genetic variations, advancing our comprehension of compound heterozygosity, epistasis, and polygenic risk factors in disease pathogenesis. GeniePool 2.0 is a comprehensive and scalable platform, which aims to enhance genomic data analysis and contribute to genomic research, potentially supporting new discoveries and clinical innovations. Database URL: https://GeniePool.link.

Figure 1.

GeniePool 2.0 user interface. Genomic coordinates for either a single variant or co-occurrence of two variants are searched within NGS samples from SRA. Resulting variants can be filtered by sample attributes. Selected variants will provide information about each variant and its study.