Family genome browser: visualizing genomes with pedigree information

Bioinformatics
Liran JuanYadong Wang

Abstract

Families with inherited diseases are widely used in Mendelian/complex disease studies. Owing to the advances in high-throughput sequencing technologies, family genome sequencing becomes more and more prevalent. Visualizing family genomes can greatly facilitate human genetics studies and personalized medicine. However, due to the complex genetic relationships and high similarities among genomes of consanguineous family members, family genomes are difficult to be visualized in traditional genome visualization framework. How to visualize the family genome variants and their functions with integrated pedigree information remains a critical challenge. We developed the Family Genome Browser (FGB) to provide comprehensive analysis and visualization for family genomes. The FGB can visualize family genomes in both individual level and variant level effectively, through integrating genome data with pedigree information. Family genome analysis, including determination of parental origin of the variants, detection of de novo mutations, identification of potential recombination events and identical-by-decent segments, etc., can be performed flexibly. Diverse annotations for the family genome variants, such as dbSNP memberships, linkage dise...Continue Reading

References

Jan 11, 2000·Nucleic Acids Research·S T SherryK Sirotkin
Jun 5, 2002·Genome Research·W James KentDavid Haussler
Oct 9, 2002·Genome Research·Lincoln D SteinSuzanna Lewis
Sep 21, 2004·Bioinformatics·Holger Thiele, Peter Nürnberg
Dec 21, 2004·Nucleic Acids Research·Ada HamoshVictor A McKusick
Mar 14, 2007·Genome Biology·Michael C SchatzSteven L Salzberg
Nov 28, 2008·Nucleic Acids Research·Nelson AxelrodSamuel Levy
Jan 24, 2009·Nature Genetics·Augustine KongKari Stefansson
Jan 12, 2011·Nature Biotechnology·James T RobinsonJill P Mesirov
Jun 10, 2011·Bioinformatics·Petr DanecekUNKNOWN 1000 Genomes Project Analysis Group
Dec 1, 2011·Nature Methods·Xin ZhouTing Wang
Mar 9, 2012·Methods in Molecular Biology·Adam Auton, Gil McVean
May 29, 2012·Nucleic Acids Research·Marc FiumeMichael Brudno
Oct 23, 2012·The Journal of Heredity·Roeland E VoorripsW Eric van de Weg
Oct 25, 2012·Bioinformatics·Androniki Menelaou, Jonathan Marchini
Nov 7, 2012·Nature·UNKNOWN 1000 Genomes Project ConsortiumGil A McVean
Nov 20, 2012·Nucleic Acids Research·Kristian A GrayElspeth A Bruford
Nov 30, 2012·Nucleic Acids Research·UNKNOWN NCBI Resource Coordinators
Feb 22, 2013·Proceedings of the National Academy of Sciences of the United States of America·Gang PengWenyi Wang
Jun 12, 2013·Bioinformatics·Masahiko KumagaiTakeshi Itoh
Jul 23, 2013·PLoS Computational Biology·Umadevi PailaAaron R Quinlan
Nov 26, 2013·Nucleic Acids Research·Donna KarolchikW James Kent
Dec 3, 2013·Nature Chemical Biology·Luc G Berthiaume
Dec 10, 2013·Nucleic Acids Research·Paul FlicekStephen M J Searle
Feb 25, 2014·American Journal of Human Genetics·Daniel C KoboldtStephen P Daiger
May 7, 2014·Nucleic Acids Research·Liran JuanYadong Wang
Jul 31, 2014·Bioinformatics·Sungkyoung ChoiSungho Won

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