2008-04-14: HapMap Rel #23a available in HapMart

Genotypes, frequency and assay data for SNPs for release #23a (NCBI build 36, dbSNP b126) are now available for analysis through the HapMart utility. New platform and genotyping center implemented.

2008-04-01: HapMap Public Release #23a available

Genotypes and frequency data for this release are now available for bulk download and browsing. Positional errors identified in previous release #23 have now been corrected. Please refer to the release notes for additional information.

2008-03-25: Genetic map for CEU and YRI available

Genome-wide recombination rates for CEU and YRI are now available for bulk download. A new genetic map including JPT+CHB data is expected to be released later in the year.

2008-03-06: Phased haplotypes for JPT+CHB under scrutiny

Phased haplotypes for JPT+CHB have been removed from public view. An announcement will be made when this has been sorted out.

2008-02-21: Incorrect position for merged SNPs in rel #23

The position of ~24,500 SNPs was inadvertently entered incorrectly in HapMap release #23 bulk files (genotypes and frequencies). A complete list of affected SNPs can be found here. Errors are being corrected and new genotypes and frequency files will be made available shortly under HapMap release #23a.

2008-02-06: HapMap inferred genotypes (rel#22)

Genotypes were inferred for 73 CEPH children using the method of Burdick et al. (Nat Genet 38:1002-4) and based on the genotypes of 60 CEPH individuals in the same families. Data and list of CEPH samples are available here.

2008-01-31: HapMap Public Release #23

Genotypes and frequency data for this release are now available for bulk download. These datasets include SNPs in the Affymetrix 6.0 array, as well as SNPs excluded from release #22 which have now been merged into new rs# identifiers in dbSNP 126 (NCBI b36). Lists of merged SNPs may be found here. Please refer to the release notes for additional information.

2007-12-20: Official release of HapMap Phased Haplotypes in NCBI b36 coordinates

2007-12-12: Genotype imputation using MACH1 software now available on HapMap Genome Browser

Impute genotypes for all HapMap SNPs in a given region by providing a subset of genotypes on HapMap SNPs. Browse a region of interest, upload your own data (Impute Data plugin), and modify the visualization of user-provided and imputed SNPs. MACH1 imputation available for release #21 (NCBI build 35).

2007-12-12: Assembly errors in rel#22 phased files

2007-10-17: HapMap Phase II article published

2007-08-13: Phased haplotypes in NCBI b36 coordinates

2007-07-17: HapMap Tutorial: Working with the HapMap Website
ASHG Annual Meeting, San Diego, California, USA
October 25th, 2007 at 18:30 PST

San Diego Marriott Hotel and Marina, Rancho Las Palmas, 4th Level, South Tower

The HapMap Data Coordination Center is pleased to present a one-hour tutorial during the 2007 ASHG Annual Meeting.The tutorial will provide an overview of the International HapMap Project, a comprehensive tour of the HapMap website, a live demo of new tools and resources, and Q&A session.

2007-06-04: Predicted OMIM associations available in GBrowse

The OMIM associations track presents data from the MutaGeneSys database, which links genotype data from HapMap and whole genome association studies with the known disease variants reported by the OMIM database. Example of a region with multiple OMIM associations: Chr1:194923128..194933127

2007-05-29: Newly phased haplotypes available for non-par segment of ChrX

Genotyping data for phase I+II (rel #21) was rephased for the non-pseudoautosomal (non-par) region of chromosome X. Data is currently available for bulk download.

2006-06-14: Wellcome Trust Course: Working with the HapMap
Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
November 16-19th, 2007

The Wellcome Trust Course: Working with the HapMap will be held on November 16-19th, 2007 at the Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. The deadline for application is 10th August 2007. Further information can be found at: http://www.wellcome.ac.uk/doc_WTX038039.html with details of how to apply.

2007-04-20: HapMap Rel #22 available in GBrowse and HapMart

Genotypes, frequency and assay data for SNPs remapped to NCBI build 36 (dbSNP b126) coordinates are now available for graphic display and through the HapMart utility.

Note: Phased genotypes for HapMap data in NCBI build 36 coordinates are being generated and will be made available at a future date.

2007-04-12: Perlegen amplicon mapping data available

Perlegen amplicon mapping data is available for bulk download.

2007-03-02: HapMap Public Release #22

Genotypes and frequency data for SNPs remapped to NCBI build 36 (dbSNP b126) coordinates are now available for bulk download. These datasets will subsequently be made available in the HapMap genome browser and HapMart utility.

As detailed in the release notes, a number of SNPs were excluded from this release due to mapping inconsistencies in Build 35 relative to Build 36. Lists of excluded SNPs according to various criteria may be found here. Please refer to the README file for exclusion criteria and additional information.

2007-02-11: Discrepancies found in phased haplotypes for non-par segment of ChrX

Substantial discrepancies between genotyping data and phased haplotypes were identified for the non-pseudoautosomal (non-par) region of chromosome X. These inconsistencies appear to largely involve hemizygous males of all population panels. Caution is advised when using phased data for the region between SNPs rs5939319 and rs557132 until further notice.

2007-01-17: Reactome links updated

Links to the Reactome pathway database from the HapMap genome browser have been updated and improved. Click here for an example.

2007-01-11: HapMap Public Release #21a

Genotype frequencies and assays for phase I and phase II of the HapMap project are now available for bulk download and browsing.

This release contains all processed data from the HapMap project, and includes all data from phases I+II of the project. This release also contains genotypes from the Illumina Infinium 100k and 300k genotyping arrays, Affymetrix nsSNPs, and SNPs typed for a high-resolution map (De Bakker et al. 2006) of the extended MHC locus.

New features in this release include Segmental Duplications and Copy Number Variation (CNV). Segmental Duplications correspond to High-Depth Celera Reads (She et al. 2004; Bailey et al. 2001 & 2002). Structural Variation datasets include:

CNV regions determined in HapMap samples (Redon et al. 2006)

CNV datasets (Iafrate et al. 2004, Sebat et al. 2004, Sharp et al. 2005, Tuzun et al. 2005)

Deletions (Hinds et al. 2006, Conrad et al. 2006; McCarroll et al. 2006)

2006-11-30: Wellcome Trust Course: Working with the HapMap
Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
April 2nd - April 5th, 2007

The Wellcome Trust Course: Working with the HapMap will be held on April 2nd - April 5th, 2007 at the Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. The deadline for application is 10th January 2007. Further information can be found at: http://www.wellcome.ac.uk/doc_WTX030611.html with details of how to apply.

This 4-day residential course will provide a comprehensive overview of the International HapMap Project, and will include practical experience of working with the HapMap data to map phenotypic traits to locations in the human genome. Theoretical lectures will be combined with hands-on practical sessions and introduction to relevant databases and tools.

Topics include: Introduction to the HapMap, Introduction to Association Studies, Data collection and repositories, Genetic variation and selection, Tools and resources, Association analysis, and Case studies.

Course instructors and speakers include: Paul de Bakker (MIT), Manolis Dermitzakis (Sanger Institute), Mike Feolo (NIH/NCBI), Jonathan Marchini (Oxford University), Gil McVean (Oxford University), Steve Sherry (NIH/NCBI)), Albert Vernon Smith (CSHL), Barbara Stranger (Sanger Institute), Eleftheria Zeggini (Wellcome Trust Center for Human Genetics), Lon Cardon (Wellcome Trust Center for Human Genetics), Panos Deloukas (Sanger Institute), John Todd (Cambridge University).

2006-11-14: Phased haplotypes now available in HapMart
Phased haplotypes output now available for the CEU, YRI and the combined Asian panel (JPT+CHB) datasets.

2006-10-09:New Features and Datasets Available
The website of the International Haplotype Map Project has a number of new features and datasets which are being released today.

New Features at hapmap.org:
• When browsing data from release 21, there is now a new "region" view. This is intermediate between the detailed view, and the chromosomal overview. The region view displays 200kb, giving a broader overview of the chromosomal region, while greater details can still be seen concurrently in the detailed view.
• There are new tracks in the browser which display expected LD values (r^2) within windows along the chromosome
• Recombination rates and hotspots data are now available for release 21.
• There is a new plugin which downloads phased genotypes for the region being browsed. Under the configuration options, one can chose the panel to download, as well as additional options for filtering the SNPs. To download, select "Download Phased Haplotype Data" under "Reports & Analysis".

New datasets:

• The raw data (CEL files) from the Affymetrix GeneChip 500k Mapping Arrays on the HapMap samples are available for download.
• Genotypes inferred using the method of Burdick et al. (Nat Genet 38:1002-4). Starting with the genotype of 60 CEPH individuals, the methodology infers the genotypes for 78 CEPH children in the same families.

2006-07-20: HapMap Public Release #21
Genotypes, frequencies and assays for phase I and phase II of the HapMap project are now available for bulk download. The files contain all phase I and II data combined.

In addition to expressing the genotypes relative to the dbSNP rs sequence, this release contains a set of files expressing genotypes relative to the forward strand of NCBI build 35. The genotypes are identical, and are complement for SNPs where the rs sequence maps to the reverse strand of the genome build.

The phased genotypes are expressed relative to the forward strand of build 35, so the displayed alleles will read as a haplotype across a single strand along the chromosome.

2006-03-30: Wellcome Trust Course: Working with the HapMap
Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Jul 31st - Aug 2nd, 2006

The Wellcome Trust Course: Working with the HapMap will be held on July 31st - August 2nd, 2006 at the Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. The deadline for application is 14th April 2006. Further information can be found at: http://www.wellcome.ac.uk/doc_wtx030611.html and details of how to apply.

This 3-day residential course will provide a comprehensive overview of the International HapMap Project, and will include practical experience of working with the HapMap data to map phenotypic traits to locations in ethe human genome. Theoretical lectures will be combined with hands-on practical sessions and introduction to relevant databases and tools.

Course instructors: Goncalo Abecasis (University of Michigan), Paul de Bakker (MIT), Andy Clark (Cornell University), Panos Deloukas (Sanger Institute), Jonathan Marchini (Oxford University), Albert Vernon Smith (CSHL), Ellen Wright Clayton (Vanderbilt University), Gil McVean (Oxford University), Steve Sherry (NIH/NCBI)), Mike Feolo (NIH/NCBI).

2006-01-24: HapMap Public Release #20
The HapMap project is happy to make a new release of the dataset. This release contains a remapping of the previous release (#19) on NCBI Build 35 coordinates. As detailed in the release notes, 30,828 SNPs were excluded from this release due to mapping inconsistencies in Build 34 relative to mappings in Build 35.
The data are available for bulk download and for graphical browsing. At the moment, the release does not include phased haplotypes, as that data still needs to be calculated.

2006-02-24: Beyond HapMap 3rd Annual International HapMap Project Community Analysis Meeting
The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
May 8-10, 2006

The deadline for submitting an abstract is Friday, March 31, 2006.
The deadline for registration is Friday, April 14, 2006.

Lecture seating is limited; therefore, early registration is encouraged. Capacity may be met prior to the April 14 deadline. Complete instructions for abstract submission and registration, and further details of the conference, can be found at conference web site.

2005-10-24: HapMap Public Release #19
Genotypes, frequencies and assays for phase I and phase II of the HapMap project are now available for bulk download. The files contain all phase I and II data combined.

2005-09-28: Recombination rates and hotspots for HapMap PhaseI dataset released
Recombination rates and hotspot data is now available for bulk download.

2005-09-28: HapMap Public Release #18
Genotypes, frequency and assays for the chromosomes 2,6,11,14,15 and 21 is now available for bulk download only. Please note that this represents complete phase II data on these chromosomes for CEU and YRI samples. This is a dump with all phase I and II data combined. Genotype summary for SNPs in this release is as follows:

2005-09-21: HapMap Tutorial Session- ASHG 2005 Annual Meeting

Salt Palace Convention Center, Ballroom ABCD, Thursday, October 27, 6:30 pm - 8:30 pm

The Wellcome Trust and the NIH/NHGRI offer a 2-hour tutorial on effective HapMap usage. This tutorial will include a HapMap introduction by Dr. Aravinda Chakravarti (Johns Hopkins University), use of t\ he HapMap for association studies, tag SNP selection, and improving analyses using chips with pre-selected SNPs, by Dr. Mark Daly (Broad Institute), and a guide to the HapMap web pages by Dr. Lincoln Stein (CSHL). Other speakers include Dr. Toshihiro Tanaka (RIKEN), Dr. Michael Boehnke (University of Michigan), and Dr. Augustine Kong (deCODE), who will each give a short presentation on HapMap applications.

Registration is limited to the first 1,000 people. You must register for this tutorial by October 14th, 2005, in order to participate. There is no additional fee, but participants must first be registered for the ASHG Meeting.

For further details,and to register, visit http://www.capconcorp.com/hapmaptutorial.

2005-09-19: HapMap User's Survey
Please take a moment to take the HapMap User's Survey which will help us to improve the site to meet your needs.

2005-08-17: HapMap public release
The first release of data from HapMap Phase II is now available. This release contains data from the initial pilot work in Phase II covering chromosome 2p. This data complements the previous Phase I release (16c.1), and full data is available by combining the files. In total, 600,180 new genotype sets are available in this release, which cover 54,016,200 genotypes. Summary of genotyped SNPs by population:

2005-06-21: HapMap public release #16c.1
This is the final Phase I data freeze as used in analyses for the upcoming primary HapMap publication (see Data freezes for more info). Also, note that with this release the abbreviation for the Han Chinese in Beijing population is changed to CHB. (See Guidelines for Referring to HapMap Populations for more info)
Summary of genotyped SNPs:

2005-05-27: Upcoming HapMap data release.

The HapMap data is constantly scrutinized to identify experimental and data processing errors that may lead to inacccuracies in a small subset of the data. During a recent review, we identified a number of such issues. A new release that corrects all known issues, Release 16c, will be available by June 03. In the meanwhile a description of the issues and affected SNPs can be found here.

2005-03-01: HapMap public release #16.
ATTN: This the so-called Phase I data freeze which marks a major milestone of the project: a genotyped common SNP every 5Kb in all populations under study. Data available for bulk download and graphical browsing. Summary of genotyped SNPs:

2005-02-18: Scheduled Network Outage -Japanese Mirror Site
Due to schedule network maintenance at Japan Science and Technology Agency, HapMap (and the related production sites) will be unavailable between 6.00PM(JST) on Feb 18th until approximately 11.00AM (JST) on Feb 21st. We apologize for the disruption. However, the main site will be available as usual.

2005-02-18: HapMap public release #15.
Additional information about the samples/individuals for the Han Chinese, Japanese and Yoruba population is available here. Please note, the genotypes are available for bulk download only. A release update will follow as early as next week, providing the full GBrowse graphical component. Summary of genotyped SNPs:

2005-02-08: HapMap News Volume 1, 2004
This is the first in a series of newsletters to be published by the Coriell Institute for Medical Research to inform communities how their samples are being used. Each issue of the newsletter will be available in the primary languages of all the participating communities.

2005-02-07:International HapMap Consortium Expands Mapping Effort
The International HapMap Consortium, boosted by an additional 3.3 million in public-private support, announces plans to create an even more powerful map of human genetic variation than originally envisioned. The map will accelerate the discovery of genes related to common diseases, such as asthma, cancer, diabetes and heart disease.

2005-01-24: Scheduled Network Outage
Due to schedule network maintenance at Cold Spring Harbor Laboratories, HapMap (and the related production sites) will be unavailable between 5.30PM to 10.30PM (EST) on Jan 25th. We apologize for the disruption. However, the Japanese mirror site will be available as usual.

2004-12-10: It is no longer necessary to sign a clickwrap agreement in order to access HapMap genotype data.
Users are asked to respect the terms of the data usage guidelines, which ensures free and unencumbered access to the data. A copy of the old agreement is available for reference.

2004-12-10:Conference Announcement: Genomic Studies and the HapMap, University of Oxford, UK: March 15-18, 2005

We invite participation and registration for this meeting and encourage the submission of abstracts for posters or short presentations.
The deadline for submitting an abstract is January 28, 2005.
The deadline for registration/lodging reservations is February 25, 2005.
Complete instructions for abstract submission and registration, and further details of the conference, can be found at the conference Web site, http:/www.hapmap.org/oxford_conference/default.html

2004-12-10: HapMap public release #14.
Additional information about the samples/individuals for the Han Chinese, Japanese and Yoruba population is available here. The genotypes are available for bulk download. Summary of genotyped SNPs:

2004-11-17: HapMap public release #13 now has data for all the HapMap populations.
Additional information about the samples/individuals for the Han Chinese, Japanese and Yoruba population is available here. The genotypes are available for bulk download. Summary of genotyped SNPs:

2004-10-12: New Generic Genome Browser Feature
LD, Heterozygosity and SNP coverage tracks are now available for viewing. Three LD properties LOD score, D' and r² visualized. Overview tracks on the browser can now be turned on/off. New representation of the allele frequency information on the Genotype SNP track.

2004-10-12: Protocols used in the Project now available
New Protocols page has information on assay design, genotyping, and data submission processing used in the project.

2004-10-12 : Public data release #12
Genotypes, frequencies and assays for 752,208 SNPs (67,698,720 genotypes) released for bulk download and graphical browsing.

2004-08-26: Additional information about the HapMap Project released
What is HapMap?,Origins of Haplotypes, Human Health Benefits, Populations Sampled, Ethical Issues, and Data Release Policy is now available.

2004-09-02 : Public data release #11
Genotypes, frequencies and assays for 693,255 SNPs (62,393,760 genotypes) released for bulk download and graphical browsing.

2004-09-28: Scheduled Network Outage
Due to schedule network maintenance at Cold Spring Harbor Laboratories, HapMap (and the related production sites) will be unavailable between 11PM (EDT) on Oct 2nd until approximately 6AM(EDT) on Oct 3rd. We apologize for the disruption. However, the Japanese mirror site will be available as usual.

2004-08-16:Public data release#10
Genotypes, frequencies and assays for 661,094 SNPs (59,498,460 genotypes) released for bulk download and graphical browsing. Included in this release are the SNPs genotyped in the HapMap ENCODE Project, available here. See HapMap ENCODE Page for summary numbers.

2004-07-20 : Public data release #9
Genotypes, frequencies and assays for 639,110 SNPs (57,519,900 genotypes) released for bulk download and graphical browsing.

2004-06-15 : Public data release #8
Genotypes, frequencies and assays for 614,030 SNPs (55,262,700 genotypes) released for bulk download and graphical browsing.

2004-05-27: 'Integrating ethics and science in the International HapMap Project'
Paper published in the Nature Reviews Genetics 2004 Jun;5(6):467-75 .

2004-05-26: HapMap Mirror Site now Available
The HapMap website is now mirrored in Japan at http://hapmap.jst.go.jp. Maintained by the Japan Science and Technology Agency's group, this mirror will provide faster services to users in Asia and Pacifica.

2004-05-04 : Public data release #7
Genotypes, frequencies and assays for 557,083 SNPs (50,137,470 genotypes) released for bulk download and graphical browsing.

2004-04-09 : Public data release #6
Genotypes, frequencies and assays for 462,670 SNPs (41,640,300 genotypes) released for bulk download and graphical browsing.

This meeting will discuss data analysis and methodological issues relevant to the International Haplotype Map Project. This will include approaches to describing linkage disequilibrium, properties of linkage disequilibrium, inference of haplotypes and haplotype frequencies, and methods for utilizing the haplotype map in association and other disease studies. The meeting will provide an important opportunity for a diverse community of investigators (both those involved directly in the project, and those in the broader community) to come together to define and debate a range of issues in the creation of the Haplotype Map resource.

The meeting is scheduled to begin with presentations and a reception from 6pm on April 18, and will conclude no later than 3pm on April 20. It is being hosted by the McKusick-Nathans Institute of Genetic Medicine/Johns Hopkins University and the National Human Genome Research Institute. For further details, to register, and/or to submit an abstract visit International HapMap Community Analysis Meeting website.

Investigators wishing to apply methods to the current data should use the March freeze of the HapMap data and of a denser data set, from the ENCODE project, available at www.hapmap.org/genotypes/ENCODE/.

2004-03-05 : Public data release #5
Genotypes, frequencies and assays for 369,784 SNPs (33,280,560 genotypes) released for bulk download and graphical browsing.

2004-02-06 : Public data release #4
Genotypes, frequencies and assays for 324,613 SNPs (29,215,170 genotypes) released for bulk download and graphical browsing.

2004-01-07 : Public data release #3
Genotypes, frequencies and assays for 274,571 SNPs (24 000,000 genotypes) released for bulk download and graphical browsing.

2003-12-16: Public data release #2!
Genotypes, frequencies and assays for 218,497 SNPs released for download and graphical browsing. ATTN please note change in file formats, see README's for details (new genotype format requires HaploView v2.03)

2003-11-01: First major public data release!
Over 13 million genotypes from 145,554 SNPs, as well as associated frequency and assay data have been released for public download. See Data section for bulk downloads and GBrowse for graphical browsing of chromosome regions.

2003-10-01: Data submitted for over 12 million genotypes from 137,964 SNPs.

2003-09-01: Data submitted for over 11 million genotypes.

2003-08-01: Data submitted for over 10 million genotypes and 117,000 SNPs.

2003-07-01: Quality control SNPs
1500 QC SNPs submitted for analysis.

2003-07-01: Submission progress
7.7 million genotypes have been submitted for analysis to the HapMap Project as well as over 77,000 assays.

2003-06-25: Allele frequencies submitted to dbSNP

2003-06-01: Submission progress
We now have over 6 million genotype submissions and 65,000 assays.

May 27-28, 2003: International HapMap Meeting at CSHL
Two day meeting at Cold Spring Harbor Laboratory with representatives from all participanting groups.

2003-05-01: Submission progress
3.8 million genotypes have been submitted to date and 40,000 assays.

2003-01-21: Conceptual Web Site up