Genome-wide detection of intervals of genetic heterogeneity associated with complex traits

Motivation: Genetic heterogeneity, the fact that several sequence variants give rise to the same phenotype, is a phenomenon that is of the utmost interest in the analysis of complex phenotypes. Current approaches for finding regions in the genome that exhibit genetic heterogeneity suffer from at least one of two shortcomings: (i) they require the definition of an exact interval in the genome that is to be tested for genetic heterogeneity, potentially missing intervals of high relevance, or (ii) they suffer from an enormous multiple hypothesis testing problem due to the large number of potential candidate intervals being tested, which results in either many false positives or a lack of power to detect true intervals. Results: Here, we present an approach that overcomes both problems: it allows one to automatically find all contiguous sequences of single nucleotide polymorphisms in the genome that are jointly associated with the phenotype. It also solves both the inherent computational efficiency problem and the statistical problem of multiple hypothesis testing, which are both caused by the huge number of candidate intervals. We demonstrate on Arabidopsis thaliana genome-wide association study data that our approach can discover regions that exhibit genetic heterogeneity and would be missed by single-locus mapping. Conclusions: Our novel approach can contribute to the genome-wide discovery of intervals that are involved in the genetic heterogeneity underlying complex phenotypes. Availability and implementation: The code can be obtained at: http://www.bsse.ethz.ch/mlcb/research/bioinformatics-and-computational-biology/sis.html. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics onlin

The International Virus Bioinformatics Meeting 2023

The 2023 International Virus Bioinformatics Meeting was held in Valencia, Spain, from 24–26 May 2023, attracting approximately 180 participants worldwide. The primary objective of the conference was to establish a dynamic scientific environment conducive to discussion, collaboration, and the generation of novel research ideas. As the first in-person event following the SARS-CoV-2 pandemic, the meeting facilitated highly interactive exchanges among attendees. It served as a pivotal gathering for gaining insights into the current status of virus bioinformatics research and engaging with leading researchers and emerging scientists. The event comprised eight invited talks, 19 contributed talks, and 74 poster presentations across eleven sessions spanning three days. Topics covered included machine learning, bacteriophages, virus discovery, virus classification, virus visualization, viral infection, viromics, molecular epidemiology, phylodynamic analysis, RNA viruses, viral sequence analysis, viral surveillance, and metagenomics. This report provides rewritten abstracts of the presentations, a summary of the key research findings, and highlights shared during the meeting

The Evaluation of Tools Used to Predict the Impact of Missense Variants Is Hindered by Two Types of Circularity

International audienc

The International Virus Bioinformatics Meeting 2023

Peer reviewed: TrueAcknowledgements: The conference organizers thank all speakers, poster presenters, chairs and participants for creating a highly interactive scientific environment and making the meeting a success. The conference organisers acknowledge sponsorship from Promega Biotech Ibérica SL. We thank Milena Žarković, Ruben Rose, Christina Martínez Christophersen, Lea Paltzow, Mohsen M. Hegab, Anna Wansorra, Akash Srivastava, Andi Krumbholz, Pablo A. Gutiérrez, João M.F. Silva, Juan C. Muñoz-Sánchez, Maria J. Olmo-Uceda, José A. Oteo and Carlos P. Garay, Yanhua Xu, Dominik Wojtczak, Matthew Baylis, Joaquin Mould-Quevedo, Markus Braun, Gibran Rubio Quintanares, Pauline Santos, Erica Margiotta, Janice Brückmann, Csaba Miskey, Johannes Blümel, Renate König, Liam Childs, Frank O. Aylward, Alexander Lukashev, Artem Orlov, Celia Jakob, Hardin Bolte, Christian Höner zu Siederdissen, Martin Schwemmle.Funder: VirBio 01KI2106Funder: The Pandemic Institute & CSL Seqirus Influenza Research Partnership (LB)Funder: LPIThe 2023 International Virus Bioinformatics Meeting was held in Valencia, Spain, from 24–26 May 2023, attracting approximately 180 participants worldwide. The primary objective of the conference was to establish a dynamic scientific environment conducive to discussion, collaboration, and the generation of novel research ideas. As the first in-person event following the SARS-CoV-2 pandemic, the meeting facilitated highly interactive exchanges among attendees. It served as a pivotal gathering for gaining insights into the current status of virus bioinformatics research and engaging with leading researchers and emerging scientists. The event comprised eight invited talks, 19 contributed talks, and 74 poster presentations across eleven sessions spanning three days. Topics covered included machine learning, bacteriophages, virus discovery, virus classification, virus visualization, viral infection, viromics, molecular epidemiology, phylodynamic analysis, RNA viruses, viral sequence analysis, viral surveillance, and metagenomics. This report provides rewritten abstracts of the presentations, a summary of the key research findings, and highlights shared during the meeting