VDA Component

Virtual DNA Analysis (VDA)

Download SCORE software

Get your update patch! JAN/2002

SBT patch! AUG/2002

F.A.Q.

SCORE
hardware requirements:
PC; Windows 95/98/00/NT;
CD-ROM drive or Internet Access;
specification of typing kits used in your laboratory.
SCORE is not available for the MAC

Register

form or
MS Word file

VDA Component- Building the Human MHC Database

Project Description

The goals of the VDA project are to:

	Generate a comprehensive, permanent and accessible database of typing reagents (SSO/SSP) based on the sequence polymorphisms detected by each method.
	Storage raw typing data consisting of primer and hybridization reactions.
	Facilitate data collection, storage and transfer.
	Provide the tools for data interpretation and assignment of genotypes using an updated reference file of known HLA alleles.
	Quality control of individual SSO/SSP reagents.

Your contribution

Participants will be supplied with software (SCORE) for virtual DNA analysis of HLA data generated with SSO/SSP typing reagents. The software will be used for data collection, storage, interpretation and exchange. You will be asked to type the IHWG VDA Reference Cell Panel using your routine typing methods and to enter raw typing results into the software program. All HLA loci should be typed, but data for selected loci will be accepted as well. The program will create an export file that can be mailed (email or floppy disk) to the IHWG Database in Seattle. Following data entry, the program allows you to interpret any combination of your raw typing data with an updated allele database. The allele database will be updated in the future as the sequences for new alleles are published.

System Requirements

PC; Windows 95/98/00/NT; CD-ROM drive or Internet Access; specification of typing kits used in your laboratory.
Sorry, but SCORE is not available for the MAC.

Costs

Shipping costs for the cell panel and software, along with actual typing expenses must be covered by each participating laboratory. The cell panel and the software themselves are free.

Background

DNA-based HLA typing results are generally stored as interpreted allele assignments. There are major drawbacks, however, to storing assigned allele data instead of the original raw typing data. The allele assignment itself is strictly dependent on the allele database used. Thus, a given typing result will, over time, show a varying degree of ambiguity depending on the number of new alleles taken into account. Once interpreted, typing results without raw data cannot be updated as additional alleles are discovered. These drawbacks can be avoided if the data are stored in raw (uninterpreted) form. The raw typing data must be linked to critical sequence information about the SSO probes and SSP primers used to generate the data. Based on the overall reactivity pattern of the individual sequences, a retrospective "virtual DNA analysis" can be constructed.

To Register:
If you would like to participate in this project, please complete the

registration form. Questions may be directed to Wolfgang Helmbert (helmberg@ncbi.nlm.nih.gov) or phone 301-402-2781.

VDA COMPONENT PLAN:

Establishment of a Central SSO/SSP Database

The shared resources developed for the IHWG and the 13th International Histocompatibility Workshop provide an ideal platform for establishing a common accessible sequence polymorphism database. Before this can be achieved, it is necessary to establish a centralised probe/primer database. This database should contain the sequence motifs detected by the primers and probes used in each individual typing system or typing kit. This resource will be essential for the establishment of a sequence database, and it will also serve to assist individual typing labs meet the accreditation guidelines of ASHI and EFI.

All individual labs, institutions or companies actively involved in the production of typing reagents are encouraged to submit data describing the essential characteristics of their reagents (i.e. primer and probe sequences) to this database. Laboratories using home-made reagents will be provided detailed instructions on how to submit this information.

Long-term goals for establishment of a permanent human MHC database.

This database is currently under construction at the National Center for Biotechnology Information (NCBI) and will be made a public resource following conclusion of the 13th IHWS.

Quality control typing data

To validate the probe data, participating laboratories are asked to type the IHWG SSOP/SSP Reference Cell Panel using their routine typing method. All participating laboratories will be provided a VDA software package (SCORE) with which to enter and analyse their raw typing data. Raw typing data will then be collected and evaluated. Evaluation will focus on:

	quality of individual SSO/SSP probes/primers
	robustness of the same reagents when comparing results from independent testing performed in different laboratories
	evaluation of SSO versus SSP typing techniques

All typing data will be made available to IHWG participants. The identity of individual participating laboratories will be coded and remain confidential.

Time line

February, 2001 Registration of participating laboratories

March, 2001 Distribution of IHWG-SCORE software & distribution of DNA from the IHWG SSO/SSP Reference Cell Panel

December 1, 2001 Data submission and analysis

Organising Committee:
Chairman: Wolfgang Helmberg (Bethesda, MD) Committee members: E Albert (Munich), C Hurley (Washington DC), M Maiers (Minneapolis), SGE Marsh (London), C Mueller (Ulm), E Petersdorf (Seattle), E Rozemuller (Utrecht), M Tilanus (Utrecht).