September 7, 2001
Dear Colleagues,
We hope your respective summers (and winters for those of you in the Southern Hemisphere) have gone well. There has not been much activity beyond data generation to report for the Anthropology Component this summer, so we have not sent out a project update for several months. Now that September has arrived, we want to take this opportunity to remind you of the upcoming project deadlines and let you know about some of the project developments and opportunities that have occurred over the summer.
Changes in personnel
We are sad to announce that Laura Geyer left the Anthropology Component team this April. For the last year, Laura was instrumental in the production and distribution of the Reverse Line Strips used for QC testing and data generation and also evaluated and provided support for the RLS QC typings. We miss Laura's energy and enthusiasm, but are fortunate to already have a new member on our team, ready to assume Laura's responsibilities. Some Anthropology Component participants have already had extensive correspondence with Andrea Jani, and it seems likely that rest of you will in the months to come. Please give Andrea a warm welcome to the IHWG and the Anthropology Component, and do not be surprised if you start getting emails and faxes from her. Andrea can be contacted at andrea.jani@roche.com.
Biostatistics Data Analysis Deadlines
As was mentioned in the March 2001 newsletter, the deadline for complete analysis of data is October 1, 2001. The deadline for partial data analysis is December 31, 2001. Data submitted after this date will be analyzed, but not in time for these analyses to be included as part of the workshop and conference in May, 2002. All data should be submitted via email to the IHWG central database at database@ihwg.org.
Background and Demographic Data forms
Data submission forms for background data and demographic information on populations and samples will soon be available on the IHWG web site. These data must be submitted for both IHWG data (generated using the RLS, SSOP or SBT reagents, or submitted via the SCORE software), as well as for so-called Available data generated previously. Participating laboratories will be notified of the web address for the data submission forms in the near future.
Human Subjects Use Certifications
Please remember that data cannot be accepted to the Central Database if you have not submitted of a Letter of Certification indicating that you have Authorization for Human Subjects Research. A copy of this letter can be downloaded as a PDF document, or as a word document.
Collaborations with other IHWG projects
When possible, the Anthro Component is eager to collaborate in studies of the allele and sequence diversity of genetic markers other than the classical HLA loci (HLA-A, C, B, DR, DQ, and DP). The Null-Alleles Component would like to collaborate with our project to investigate the frequency and distribution of Null-Alleles on a global scale. In order to do this, they need the cooperation of individual laboratories. If routine data generation typing indicates that an allele is a potential Null-Allele (e.g. A*2402/2409N), that laboratory would have to be willing to either carry out a few extra typings using Null-Allele typing reagents or to send samples to a central laboratory for Null-Allele typing. Clearly, it would be advantageous for this collaboration for as many laboratories as possible to participate. However, some laboratories may be restricted in what sorts of researches may be carried out by the specifics of the informed consent which was obtained for their samples, and may not be able to participate. Please let us know if you would like for your laboratory to participate in this collaboration with the Null-Alleles component, or if you have any questions about this collaboration, by sending an email to steve.mack@roche.com.
Sequencing of Ambiguous Alleles
One of the goals of the Anthropology Component is the generation of high-resolution data, but as many Anthro participants are aware, allele-level resolution is often difficult to achieve because of ambiguity at both the allele and genotype level. One strategy we intend to use to increase the resolution of data being generated is to carry out sequencing on samples with ambiguous typing results. In order to do this effectively, samples will be sequenced in collaboration with the IHWG sequencing technology core. In order for this aspect of the project to proceed successfully, individual laboratories will need to send selected ambiguous samples to the central sequencing lab for analysis. Once a dataset has been submitted to the central database a set of representative samples will be selected for sequencing. We will contact the submitting lab to see if any of those samples are available to be sequenced, and hopefully those labs will be able to donate some of each sample for analysis. Please let us know if you anticipate that there will be any difficulties in shipping samples from your laboratory.
Common Haplotypes Component
A new project has been added to the IHWG. The goals of the Genomic Analysis of Common Human MHC Haplotypes Component are to establish an international database of common human MHC haplotypes and a Cell Bank of cell lines expressing common haplotypes representing diverse human populations for participants of the 13th IHWS. Planning and work will continue following the 13th IHWS meeting May 2002 to assure that this important shared resource is sustained and that it continues to accumulate data and selected biological material in support of future research. Specific objectives include:
- Define genomic polymorphisms and linkage disequilibrium for known functional genes and markers.
- Facilitate generation of accurate precise genomic data through establishment of standards and quality control of individual SSO/SSP reagents.
- Assemble and archive raw typing data consisting of primer and hybridisation reactions.
- Achieve high-resolution definition of sequence polymorphisms (microsatellites, SNPs and alleles).
- Support the collection, reporting and storage of data.
- Provide the tools for data interpretation and assignment of genotypes using an updated reference file of known HLA alleles (SCORE software).
- Support the establishment of a comprehensive accessible human MHC database capable of supporting future research in collaboration with NCBI/NIH.
A call for collaborators interested in participating in this project will soon be distributed. If you are interested in participating in this project or have any questions, please relay your remarks to secretary@www.ihwg.org.
IHWG meetings at ASHI 2001
13th IHWG project meetings will be held at the 2001 ASHI on Saturday and Sunday, October 13-14, 2001 at the Hyatt Regency in the Embarcadero, San Francisco, California. The Anthropology Component project meeting will be held on October 14 at 12:45 PM, and the schedule for other project meetings is available on the IHWG website. Questions about the specifics of these meetings should be directed via email to secretary@www.ihwg.org. In addition, Diogo Meyer from the Biostatistics Core and Steve Mack from the Anthropology Component will be leading a workshop on Population Genetic Analyses at 2:30pm on Sunday October 14 wherein the methods which will be used to analyze the IHWG data will be discussed.
We look forward to seeing you in San Francisco this October!
With best regards,
Henry Erlich, Steve Mack, and Andrea Jani
Anthropology / Human Genetic Diversity Component Team
