Year: 2018
Type: article
Abstract: A significant portion of genes in vertebrate genomes belongs to multigene families, with each family containing several gene copies whose presence/absence, as well as isoform structure, can be highly variable across individuals. Existing de novo techniques for assaying the sequences of such highly-similar gene families fall short of reconstructing end-to-end transcripts with nucleotide-level precision or assigning alternatively spliced transcripts to their respective gene copies. We present IsoCon, a high-precision method using long PacBio Iso-Seq reads to tackle this challenge. We apply IsoCon to nine Y chromosome ampliconic gene families and show that it outperforms existing methods on both experimental and simulated data. IsoCon has allowed us to detect an unprecedented number of novel isoforms and has opened the door for unraveling the structure of many multigene families and gaining a deeper understanding of genome evolution and human diseases.
Source: Nature Communications
Institution: Pennsylvania State University
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $6,990
Funders: National Science Foundation, U.S. Department of Health and Human Services, Pennsylvania Department of Health, Yale University, University of Pennsylvania, Pennsylvania State University, National Institutes of Health, National Center for Research Resources, Division of Computing and Communication Foundations, Division of Information and Intelligent Systems, Division of Biological Infrastructure, National Center for Advancing Translational Sciences
Awards: G1357753120, G1635679356, Penn State Clinical and Translational Science Institute, ABI Innovation: A Novel Framework for Detecting Genomic Structural Variation, G3158255397, G3209732092, III: Small: Reconstructing viral population without using a reference genome, G3903935367, XPS: FULL: DSD: End-to-end Acceleration of Genomic Workflows on Emerging Heterogeneous Supercomputers, CAREER: De Novo Assembly of Large Genomic Data, Computational Tools and Statistical Analysis of Co-Varying Rates of Different Mutation Types, G8185672151, G8587584207, Penn State Clinical and Translational Science Institute
OpenAlex ID: W2899345312