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Background
This operating plan is established to provide a mechanism for the acquisition, verification, reporting and dissemination of newly defined HLA alleles that are submitted to the WHO Nomenclature Committee and the IMGT/HLA Sequence Database. Currently, there is no organized method for verifying that newly defined alleles actually have the reported sequence, nor is there a mechanism for providing cells or DNA representative of these alleles to interested investigators worldwide. This plan proposes a method for linking the activities of the "discovering" laboratory, the WHO Nomenclature Committee, the IMGT/HLA Sequence Database maintained at the Anthony Nolan Research Institute (ANRI), and the 13th International Histocompatibility Working Group (IHWG). The overall goal of this project is to establish an ongoing mechanism for verifying the sequence of newly reported alleles, for collecting cells expressing these alleles in a central repository, and for making them available to investigators worldwide in a coordinated and effective manner. The overall plan is illustrated below.
A. Previously reported alleles
HLA alleles reported to the WHO Nomenclature Committee since 1989 have been assigned official HLA designations, but their sequences have not necessarily been confirmed by a second independent laboratory. To insure that all submitted allele sequences have been confirmed, the following procedure, facilitated through the 13th International Histocompatibility Working Group (IHWG), is proposed:
1. The IHWG will obtain a list of all HLA alleles submitted to the HLA Nomenclature Committee since 1989 from Dr. Steven Marsh, Anthony Nolan Research Institute, London. The master list will be sent to Dr. Ekkehard Albert, chair of the WHO Nomenclature Committee and project leader of the New Allele Project sponsored by the 13th IHWG. A copy of the list will also be sent to the project leader of the Core Cell and Gene Bank of the 13th IHWG. The list will identify the allele as well as the allele sequence and will contain contact information for the submitting laboratory.
2. The chair of the WHO Nomenclature Committee will contact each laboratory having submitted an unconfirmed allele to ask that a sample from the allele donor be submitted to the 13th IHWG Core Cell and Gene Bank (Seattle). Optimally, the sample will consist of a transformed B-lymphoblastoid cell line (B-LCL). Alternatively, peripheral blood mononuclear cells (PBMC) or DNA may be submitted if a B-LCL is not available. The 13th IHWG New Allele Project will insure, as far as possible, that a complete inventory of all newly defined alleles is established and maintained.
3. If only PBMC are available:
a. The submitting laboratory will be asked to transform the PBMC into a cell line and send the transformed cell line to the 13th IHWG Core Cell and Gene Bank.
b. If the submitting laboratory cannot perform the transformation, they will be asked to send cells to a regional laboratory in their area. A nearby laboratory is recommended to avoid delays and complications resulting from shipping viable PBMC over long distances.
c. The regional reference laboratory will perform the transformation and send the transformed cell line to Seattle.
4. Appropriate reference laboratories will be identified to perform confirmatory testing of newly defined alleles if this has not been previously done. Each reference laboratory will be sent an appropriate sample as requested: B-LCL (if available); pelleted PBMC or pelleted B-LCL (if available) or DNA.
5. The reference laboratory will perform the confirmatory sequencing of the specified allele. The reference laboratory may also be requested to sequence additional exons, introns and/or adjacent loci as appropriate.
6. The reference laboratory will report the confirmed sequence to the 13th IHWG New Allele Project (Dr. Albert, Project Leader) for submission to the WHO Nomenclature Committee and listing in the EMBL, GenBank or DDBJ libraries. The confirmed sequence will also be reported to the IMGT/HLA Sequence Database (Dr. Marsh, Liaison) and to the 13th IHWG Core Cell and Gene Bank for listing in the 13th IHWG database.
7. In the event that the originally reported sequence is not confirmed by the reference laboratory, a second sample will be requested from the submitting laboratory for re-sequencing at a second reference laboratory.
B. Newly reported alleles
1. Laboratories submitting newly reported alleles to the WHO Nomenclature Committee will be asked to submit PBMC, B-LCL and/or DNA from the allele donor to the central repository in Seattle.
2. As each new allele is submitted to the WHO Nomenclature Committee for registration and official assignment of nomenclature, Dr. Marsh of the Anthony Nolan Research Institute will notify the project leader of the 13th IHWG New Allele Project and the IHWG Cell and Gene Bank.
3. An appropriate sample - B-LCL, PBMC or DNA - will be sent to the Seattle laboratory for placing in inventory and sending to an appropriate reference laboratory for confirmatory sequencing, as in (A) above.
4. If only PBMC are available:
a. The submitting laboratory will be asked to transform the PBMC into a cell line and send the transformed cell line to Seattle.
b. If the submitting laboratory cannot perform the transformation, they will be asked to send cells to a regional laboratory in their area. A nearby laboratory is recommended to avoid delays and complications resulting from shipping viable PBMC over long distances.
c. The regional reference laboratory will perform the transformation and send the transformed cell line to Seattle.
5. The remainder of the confirmatory activity is identical to steps 4 through 7 in (A) above. | |
New Allele Registry
