Complex disease trait mapping, genome mapping, linkage analysis

Introduction Software Database Genetic Maps Physical Maps Radiation Hybrid Maps Education Newsgroup Companies, Institute and Lab Literatures Books Glossaries

Can't find the complex disease trait mapping, genome mapping or linkage analysis information you want in my site?  Try a Google search!

Introduction

• An Introduction to genetic association and linkage analysis - a good review on the basics of linkage anlaysis.
• A quick glimpse of linkage analysis
• bionet.molbio.gene-linkage FAQ - a FAQ of bionet.molbio.gene-linkage
• Genome Mapping @ NCBI - A simple and yet comprehensive introduction to the topic.
  

Software

Download

• An Alphabetic List of Genetic Analysis Software - The most comprehensive alphabetic list of genetic analysis software maintained by WenTian Li. You can find virtually all of the software in this world for genetic analysis here!
• FTP server of EBI - Good repositories of many linkage analysis softwares. It also mirrors many other linkage software ftp servers including Joseph Terwilliger site for linkage programs at Columbia U, Prof. Jurg Ott FTP site for linkage software, whitehead institute in MIT, Linkage programs at the Wellcome Trust Centre for Human Genetics University of Oxford and genetic analysis programs from University College London.
• Statgen software - Software from the Division of Statistical Genetics, Department of Human Genetics, University of Pittsburgh. Include: SIMWALK2, HAPLO, VITESSE, PEDCHECK

Commonly used software

Softwares

Database

• dbSNP
• Entrez Genome
  
• GenLink - A multimedia database resource for human genetics research
• GDB (The Genome DataBase) - Official central repository for genomic mapping data resulting from theHuman Genome Initiative.
• GeneMapDB - The goal of this project is to create a resource of mapped bacterial artificial chromosome (BAC) clones that span the human genome at 1-Mb intervals. GenMapDB is a database that contains information on the mapped BAC clones.
  
• Genetic Association Database - an archive of human genetic association studies of complex diseases and disorders. The goal of this database is to allow the user to rapidly identify medically relevant polymorphism from the large volume of polymorphism and mutational data, in the context of standardized nomenclature.
• Human Chromosome 21 cSNP Database and MAP - A joint project between the Division of Medical Genetics of the University of Geneva Medical School and the Swiss Institute of Bioinformatics
• Human SNP Database
• OMIM Home Page -- Online Mendelian Inheritance in Man

Genetic Maps

• CHLC Genetic Maps
• Généthon Map
• HuGeMap
• Marshfield Map

Physical Maps

• CEPH-Généthon integrated map
• HuGeMap
• Human Chromosome 21 cSNP Database and MAP - A joint project between the Division of Medical Genetics of the University of Geneva Medical School and the Swiss Institute of Bioinformatics
• Whitehead Map

Radiation Hybrid Maps

• GeneMap'99
• RH map
• RHdb

Education

• An Introduction to genetic association and linkage analysis - a good review on the basics of linkage anlaysis.
• Mathematical Sciences Research Institute (MSRI) - provides a number of online video seminars on mathematical analysis on genomics, microarray, bioinformatics, proteomics, linkage analysis and genome mapping
• Nonlinear Estimation and Classification, March 19 - 29, 2001
• Nonlinear estimation and classification: Challenges from genomics - by Terry Speed [video]
• MSRI/PMMB Short Course: Mathematical and Computational Challenges in Molecular and  Cell Biology, June 12-23, 2000
• Chromosome maps - by Terry Speed [video]
• Linkage Analysis of Complex Human Traits Using Identity by Descent Data - by Sandrine Dudoit [video]
• 1. Monte Carlo Likelihood for genetic analyses and 2. Coalescents, phylogenies, and disequilibrium mapping - by Elizabeth Thompson [video]
• Mathematics and Computational Biology of Genome Analysis, June 12-23, 2000
• Genetic Variation in the NIDDM1 Region - by Nancy J. Cox [video]
• LINKAGE ANALYSIS; past, present and future - by Elizabeth A. Thompson [video]
• Understanding the Genome: Technological and Mathematical Challenges, May 21-23, 1998
• Gene Hunting Without Genomic Sequencing: the Twenty Questions Game with Genes - by Pavel Pevzner [video]
• Statistical aspects of gene mapping - by David Siegmund [video]
• Statistical and Computational Contributions to Gene Mapping: History and Current Developments -  by Ellen Wijsman [video]
• Statistics 606 Statistical Computing - The online course notes by Shedden K from University of Michigan. Related topics included Markov Chain Monte Carlo.
• Statistics in Genetics - Dr. Terry Speed's statistics course note on genetics, covering HMMs, MCMCs, sequence alignment, motif finding, gene finding and microarray analysis.

Conference

• Linking Phenotype to Genotype. April 23-25, 2003  Hilton Munich Park Munich, Germany; organized by Cambridge Healthtech Institute.

Newsgroup

• bionet.molbio.gene-linkage - a USENET newsgroup dedicated to genetic linkage
• International communication forum in human molecular genetics

Companies, Institute and Lab

• Churchill's Statistical Genetics group - Dr. Churchill's group focused in genetic mapping of loci associated with complex and quantitative traits. There are a few very interesting papers on statistical microarray data analysis in his homepage
• Jurg Ott Group - Prof. Ott group is focused on developing, implementing and applying statistical analysis methods for human genetic data
• UK human genome mapping project resource centre - provided computing tools, resources and training courses for linkage study.
• Wentian Li's Statistical Genetics page - This site maintained by Dr. WentianLi in Rockefeller University contains a very comprehensive collection of papers on linkage analysis and softwares links

Literatures

Books

Glossaries

• Genomics Glossary - A comprehensive genomic glossary draft covering many aspects, maintained by Mary Chitty of Cambridge Healthtech Institute