November 9, 2001
Dear Colleagues,
It was very nice to meet some of you and discuss project status and goals at ASHI this October past. We want to take this time to update the rest of you about our project meeting, and to let all of you know about some of the developments which have occurred since the meeting. In particular, please note the changes to our contact information, below. For those of you who are new additions to this project, welcome! We try to send out updates like this one on a regular basis, and we encourage you to review the old updates available on the IHWG web site at http://www.ihwg.org/components/diversr.htm.
New Contact Information
The Anthropology Component team has moved to new offices in Berkeley, California, and as a result, we have new contact information. Our email addresses remain the same, but should you wish to contact us by any other means, all communication for the Anthropology Component (to Henry Erlich, Steve Mack, or Andrea Jani) should now be sent to:
Department of Human Genetics
Roche Molecular Systems
2929 7th Street
Suite 100 / Carel 212
Berkeley, CA 94720
Fax : 510 883-0636 (may only be temporary)
Phones :
Steve : 510 883-7926
Andrea : 510 883-7906
Faxes and mail sent to the old numbers and address will eventually get to us, but it could take some time. Because all of the kinks are still being worked out of our new office systems, our current fax machine is physically very distant from our offices. We have some small concern that faxes may get lost in the shuffle, so we would appreciate it if you could send us a brief email letting us know that you sent a fax. It seems likely that we will change our fax number sometime in the near future, but in the meantime we appreciate the extra effort.
Data Submission and Data Analysis Status
We passed the first deadline for data submission on October 1, 2001, and we are pleased to announce that we had a very strong response from participants. By the time we met at ASHI last month, we had received typing data for approximately thirty populations from more than twenty participating laboratories out of a total of seventy active laboratories. Our next goal in collaboration with the Biostatistics Core is to send these data back to the submitting laboratories (along with the results of the Phase One and Phase Two analyses) for review in mid-December 2001. While we do not anticipate major errors, we would appreciate it if each lab could review the data to confirm that the data being analyzed are the same as the data that were submitted. In addition, it would be helpful for each lab to review and offer any comments on the results of the Phase One and Phase Two analyses, and to send these comments back to the Biostatistics Core along with the confirmation of the validity of the raw data by mid-January. With these confirmations and comments in hand, the Biostatistics Core will be able to proceed with the Phase Three and Phase Four analyses. A discussion of the timetable and analyses to be carried out in each of the phases can be found in the March 2002 Anthropology Component Newsletter, available on the IHWG web site (http://www.ihwg.org/components/diversupdate6.htm). The next deadline for data submission is December 31, 2001.
Workshop and Congress in 2002
The preliminary program and call for abstracts for the 13th International Histocompatibility Workshop and the International Congress of Histocompatibility and Immunogenetics (IHWC) is now available on the web at www.ihwc.org. Please note that this page is different from the IHWG web page. The scheduled events include the Workshop Meeting held from May 12-16, 2002 in Victoria, British Columbia, Canada, the Educational Workshop held from May 17-18, 2002 in Seattle, Washington and the International Congress held from May 19 - 22, 2002 also in Seattle. Registration is now open, and the submission deadline for Abstracts is Jan 11, 2002. The preliminary program and call for abstracts will be mailed in the week of November 22, 2001.
In addition, we would like to get an idea of the number of Anthropology participants and collaborators who intend to attend the Workshop and Conference. We would appreciate it if you could let us know (informally) if you plan on coming. Please send any such emails to steve.mack@roche.com.
Data Submission via SCORE Software
The Virtual DNA Analysis (VDA) Component's SCORE Software has successfully been used to submit SSOP and SBT data to the central database (database@ihwg.org). If you have SSOP or SBT data (either QC data or typing data), please contact the VDA component (http://www.ihwg.org/components/vda/vda.htm) to obtain the SCORE program. In addition, so-called Available Data (SSP data and pre-IHWG SSOP/Line Blot Data) can also be submitted to the central database using the SCORE program. Reverse Line Strip (RLS) users do not have to use SCORE, and can simply email the unedited output of the RLS typing software to database@ihwg.org.
Anthropology Demographic and Background data forms
In March 2001, we described the Demographic and Background data form, and these are finally complete. This form and the associated documentation should be available on the Database section of the IHWG web site (http://www.ihwg.org/shared/database.htm#Anthropology) this month. This form can be downloaded as an Excel file that includes all of the necessary lookup tables and documentation fields. Entered data is divided into two sections, one for population-specific data, and a second section for sample/subject-specific data. If family data is available for a population, demographic and background data for family members for whom samples were not collected can still be entered in the subject-specific section of the form. Population-specific data for a given population need only be entered once. This form will also be available for use by participants in the Cytokine Polymorphisms Component (chaired by Drs. Joannis Mytilineos and Ken Welsh), for this component's own Anthropology studies.
Collaboration with RSCA Component
In the September 2001 newsletter, we discussed collaborations with the Null Alleles Component as well as the Anthropology Component's plan for sequencing ambiguous alleles and genotypes. After discussions at ASHI, we now also intend to collaborate with the IHWG Reference Strand Conformation Analysis (RSCA) Component (http://www.ihwg.org/components/rsca.htm) to use RSCA typing to resolve ambiguity and identify potential new alleles. As with the other collaborations, we will contact participating laboratories with samples of interest to determine the availability of DNA for testing, but please contact us and let us know if you are interested in participating in this collaboration, or have samples of particular interest.
Reverse Line Strip Software Upgrade
In November of 2000, we revised the probe reactivity pattern for the HLA-A*6603 allele for the Reverse Line Strip system. Because this revision required that RLS users upgrade their pattern interpretation software, we made an upgrade for the RLS software available on the IHWG web site (http://www.ihwg.org/components/anthro/RLSupdate.htm). Over the course of the last year, about half of the Anthro Component participants using the RLS system have upgraded to the corrected hit-table. We urge all remaining RLS users to upgrade their software as soon as possible to avoid delays in data analysis which will be introduced if we have to re-analyze HLA-A data generated using the old HLA-A hit table. Please contact us if you have concerns or questions about this required software upgrade.
Human Subjects Use Certification
Finally, we want to remind participants who have not submitted a Letter of Certification of Authorization for Human Subjects Research to submit this form as soon as possible. If we do not have a copy of this certification on file, we will be unable to store your data in the central database, analyze your data, or include your data in the Workshop. A copy of this letter can be downloaded as a PDF document (http://www.ihwg.org/components/IRBLetter.pdf) or as a word document (http://www.ihwg.org/components/IRBLetter.doc) from the IHWG web site.
Please do not hesitate to contact us if you have any questions or need any assistance with the Anthropology Component.
With Best Regards,
Henry Erlich, Steve Mack, and Andrea Jani
Anthropology / Human Genetic Diversity Component
Henry A. Erlich, Ph.D., Chair and Steven J. Mack, Ph.D.
ROCHE MOLECULAR SYSTEMS
CHILDREN'S HOSPITAL OAKLAND RESEARCH INSTITUTE
