Introduction

Autozygosity mapping is a powerful technique for the identification of rare, autosomal recessive, disease-causing genes. The ease with which this category of disease gene can be identified has greatly increased through the availability of genome-wide SNP genotyping microarrays and subsequently of exome sequencing. Although these methods have simplified the generation of experimental data, its analysis, particularly when disparate data types must be integrated, remains time consuming. Moreover, the huge volume of sequence variant data generated from next generation sequencing experiments opens up the possibility of using these data instead of microarray genotype data to identify disease loci. To allow these two types of data to be used in an integrated fashion, we have developed AgileVCFMapper, a program that performs both the mapping of disease loci by SNP genotyping and the analysis of potentially deleterious variants using exome sequence variant data, in a single step. This method does not require microarray SNP genotype data, although analysis with a combination of microarray and exome genotype data enables more precise delineation of disease loci, due to superior marker density and distribution.

Publications

  1. Rapid Detection of Rare Deleterious Variants by Next Generation Sequencing with Optional Microarray SNP Genotype Data.
    Cite this
    Watson CM, Crinnion LA, Gurgel-Gianetti J, Harrison SM, Daly C, Antanavicuite A, Lascelles C, Markham AF, Pena SD, Bonthron DT, Carr IM, 2015-09-01 - Human mutation

Credits

  1. Christopher M Watson
    Developer

    Yorkshire Regional Genetics Service, St James's University Hospital, United Kingdom of Great Britain and Northern Ireland

  2. Laura A Crinnion
    Developer

    Yorkshire Regional Genetics Service, St James's University Hospital, United Kingdom of Great Britain and Northern Ireland

  3. Juliana Gurgel-Gianetti
    Developer

    Department of Pediatrics, Faculty of Medicine, Brazil

  4. Sally M Harrison
    Developer

    School of Medicine, University of Leeds, United Kingdom of Great Britain and Northern Ireland

  5. Catherine Daly
    Developer

    School of Medicine, University of Leeds, United Kingdom of Great Britain and Northern Ireland

  6. Agne Antanavicuite
    Developer

    School of Medicine, University of Leeds, United Kingdom of Great Britain and Northern Ireland

  7. Carolina Lascelles
    Developer

    School of Medicine, University of Leeds, United Kingdom of Great Britain and Northern Ireland

  8. Alexander F Markham
    Developer

    School of Medicine, University of Leeds, United Kingdom of Great Britain and Northern Ireland

  9. Sergio D J Pena
    Developer

    GENE-Nucleo de Genetica Medica de Minas Gerais, Belo Horizonte, Brazil

  10. David T Bonthron
    Developer

    Yorkshire Regional Genetics Service, St James's University Hospital, United Kingdom of Great Britain and Northern Ireland

  11. Ian M Carr
    Investigator

    School of Medicine, University of Leeds, United Kingdom of Great Britain and Northern Ireland

Community Ratings

UsabilityEfficiencyReliabilityRated By
0 user
Sign in to rate
Summary
AccessionBT004030
Tool TypeApplication
Category
PlatformsWindows
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited Kingdom of Great Britain and Northern Ireland
Submitted ByIan M Carr