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Report of the Anthropology / Human Genetic Diversity Component December 2, 2003 Dear Colleagues, It has been more than a year since our last project update. We appreciate the commitment and dedication that you have shown over the last several years, and hope that you are looking forward to participating in this next round of project activity. Many of you have been waiting for news about the publication of HLA 2002, the availability of RLS reagents, and the 14th Workshop. We hope to address your questions here, and outline some plans for the 14th Workshop. Finally, we encourage you to contribute your thoughts for this next round of the project. HLA 2002 For the last year we have been collecting and editing the short population reports for the population datasets that were analyzed as part of the 13th Workshop, as well as preparing the reports of the analyses of these data for publication in HLA 2002: Immunobiology of the Human MHC. All of these reports will be collected as chapters in the Anthropology / Human Genetic Diversity Component’s Joint Report in HLA 2002. We are still in the process of finalizing this Joint Report, and intend to be done by the end of this year. Once our completed Joint Report has been submitted to the publisher, galley proofs (in the form of PDF files) will be distributed to the contributing authors of the short population reports. In addition, the IHWG requires that we obtain copyright releases from each author on each paper included in the Joint Report. The contributing authors will be contacted regarding these copyright releases. Because the publication of HLA 2002 has taken longer than expected, we have worked closely with the NCBI to make the 13th Workshop data available as part of the dbMHC database (see below). In addition, HLA 2002: Immunobiology of the Human MHC can be advance ordered from the IHWG at www.ihwc.org/book.htm. Workshop Data available on dbMHC The 13th Workshop data and analyses will soon be available to the public. The datasets that were analyzed as part of the 13th Workshop are now available as part of the NCBI’s MHC database (dbMHC) in the form of genotypes as well as allele and haplotype frequencies (see www.ncbi.nlm.nih.gov/mhc/ihwg.cgi?ID=9&cmd=PRJOV). Analyses will follow early next year. Because HLA 2002 is still in press, the data for each population have been linked to citations referring to the short population reports that will appear in HLA 2002. In addition, the data from the 12th International Workshop will be made available through dbMHC next year as well. The tools for viewing and manipulating the Anthropology data available in the dbMHC are still basic. If you have suggestions or ideas for ways that these interface tools can be improved, or if you have ideas for new tools, please contact Steve Mack (steve.mack@roche.com) and we will work to incorporate these tools into the dbMHC. Continuing IHWG projects and cores There have been some changes to the projects supported by the IHWG. The Anthropology, HLA and Disease, NK/KIR, HLA-E, F, and G, SNPs, HCT, MHC Haplotypes and Peptides projects continue as part of the IHWG, as do the Administrative, Biostatistics, Cell and Gene Bank, Database, and Technology cores. 14th Workshop The 14th International HLA and Immunogenetics Workshop will be held in Melbourne, Australia from November 29th to December 3rd, 2005. Information about the 14th Workshop can be found at http://www.microbiol.unimelb.edu.au/14ihiws. Plans for the coming year We are currently in the process of determining the organizational structure and plans for the next round of project activity, culminating in the 14th Workshop in 2005. We plan to support continued high-resolution genotyping at the class I loci using the RLS typing reagents and intend to offer class II RLS genotyping reagents for use early next year (see below). In offering class II reagents, we hope to be able to more completely genotype population samples that were genotyped at class I loci as part of the 13th Workshop. In addition, we hope that populations genotyped at intermediate resolution or for a limited number of loci as part of the 12th Workshop will be genotyped at higher resolution for both class I and class II loci in this round of the project. With these goals in mind, we will be contacting those of you who submitted Anthropology data to the12th and 13th Workshops to identify those population samples for which additional genotyping will be feasible. Our priority for the 14th Workshop is to obtain high-resolution genotypes at all HLA loci for populations that have been included in previous Workshops. In addition, we are eager to include new population samples in the Anthropology project, with a focus on geographic regions that were poorly represented in the 13th Workshop (e.g., sub-Saharan African, Southwest, central, and Southeast Asia, and the Pacific, among others). If you have access to new population samples, or know of investigators with new population samples who might be interested in joining the Anthropology project, please contact either Steve Mack or Alicia Sanchez-Mazas. Some datasets were submitted for analysis in the 13th Workshop reporting serological –level polymorphism or reporting high-resolution data in non-standard formats, and it was not possible to include these datasets in the 13th Workshop analyses. For example, we were unable to analyze several Indian population samples for this reason. The inclusion and analysis of these datasets for the 14th Workshop will be a high priority in the next six months, along with serological-level analyses of all datasets. One of the obstacles to rapid and efficient data review and analysis has been the requirement to handle data transactions manually via email. We are pleased to announce that the IHWG will be implementing a web-based interface early next year, which will permit web-based data submission and on-demand data review by submitting laboratories. We hope that this new interface will make the Anthropology project (and other IHWG projects) more accessible to all participants. Finally, we are actively seeking to recruit new project participants. In particular, we are hoping to increase participation from Africa, East Asia, Australia and South America. If you have any colleagues who are interested in participating in the IHWG Anthropology project as part of the 14th workshop, or have suggestions for investigators that we should recruit, please contact Steve Mack or Alicia Sanchez-Mazas. Those collaborators who recently joined the IHWG Anthropology component project will be receiving additional information about participation later this month. Availability of PyPop Software The Python for Population Genetics (PyPop) software package was developed by the IHWG Biostatistical core for the purpose of carrying out population genetic analyses (Hardy-Weinberg equilibrium tests, Ewens-Watterson homozygosity tests, Linkage-Disequilibrium and Haplotype estimates) on large, polymorphic datasets (e.g., HLA datasets), and was used for the Anthropology component data analyses in the 13th Workshop. In addition to HLA analyses, PyPop can be used to analyze genotypes and allele frequencies from other loci, along with microsatellites, SNPs, and nucleotide and amino acid sequences. PyPop will be available for general distribution from the IHWG Biostatistics Core by the end of this year. Personnel Changes We are sad to announce that Andrea Jani has left the Anthropology project to pursue her graduate degree. However, Andrea has been replaced by Heather Dron, who some of you had the pleasure of meeting last October at the ASHI meeting in Miami Beach. Heather will be communicating with you regarding orders for RLS reagents and QC evaluations. You can contact Heather by email at the following address: heather.dron@roche.com. RLS 2003 reagents New lots of Reverse Line Strip (RLS) class I (HLA-A, C, and B) reagents are now available for distribution. We know that many of you have been waiting some time for these reagents, and we appreciate your patience. These reagents are produced in a high-density 84-probe format (the previous lot of RLS reagents had a maximum of 57 probes), which means that all of the HLA-B probes are now on a single strip. The RLS protocol has been updated to reflect this change (HLA-B typing requires fewer reagents), and the RLS genotyping software has been updated to include a new single-strip interface for HLA-B. This software has also been updated to meet March 2003 WHO Nomenclature Committee standards for allele names and nomenclature. In order to distinguish these high-density format reagents and updated genotyping software from the previous lots of strips and the previous version of the software, we care calling this system the RLS 2003 typing system. These reagents are being offered at the same price as the previous lots of RLS reagents (i.e., $1750 for 50 A, C and B tests). Orders for RLS 2003 reagents can now be placed by faxing the order form (available at www.ihwg.org/forms/reagentforms.htm) to Steve Mack or Heather Dron at 510-883-7910. Class II RLS reagents We plan to begin distributing typing reagents for the class II (DRB1, DQA1, DQB1, DPA1, and DPB1 loci) next year. These reagents will follow the same protocols and procedures as the RLS 2003 typing reagents for the class I (HLA-A, C and B) loci. The higher density of probes on these strips (84 probes maximum instead of 57 probes) means that the probes for the DQA1 and DQB1 loci and the probes for the DPA1 and DPB1 loci can be put on single strips, so that these class II RLS typing reagents will consist of a DRB1general typing strip, a DRB1 subtyping strip, a DQ strip and a DP strip. Details on these reagents will be made available early next year. Quality Control evaluations for new RLS reagents As was the case for laboratories that wished to use the RLS reagents as part of the 13th Workshop, laboratories wanting to use the new RLS class II reagents and laboratories that wish to use RLS 2003 reagents at loci for which they did not pass the original RLS quality control (QC) evaluation will be required pass a QC evaluation for each locus with 92% accuracy. For now, labs that passed the RLS QC evaluations at a given locus will not have to pass a second round of evaluations at that locus. This new round of QC evaluations will begin early next year, and more information will be made available at that time. Please feel free to contact us if you have any questions about or suggestions for the ongoing IHWG Anthropology project. We are looking forward to working with you with renewed commitment. With best regards, Henry Erlich, Steve Mack, Alicia Sanchez-Mazas and Heather Dron Anthropology / Human Genetic Diversity Component |