In Attendance:
Present: Marin Maiers, Jill Hollenbach, Steve Marsh, Glenys Thomson, Pierre-Antoine Gourraud, Steve Mack, Henry Erlich
Phone in: Marcelo Fernandez-Vina
Skype in: Alex Lancaster, Rich Single, Hazael Maldonado-Torres, Uma Kanga
Guest: Jeff Rice, NIH
Agenda items:
1 - KIR data-management and analysis issues
Jill led a discussion of some issues of KIR data management and analysis in light of the KIR Polymorphism Meeting that was starting later in the day. We discussed how to deal with KIR "loci" that are recognized as separate genes, but which segregate as alleles at a single locus (e.g., 2DL2 and 2DL3, or 3DL1 and 3DS1), primarily in terms of accurately recording data, as well as in terms of how best to analyze data for these loci. Nomenclature options for describing these loci were discussed (e.g., 2DL2OR3 or 2DL6, and 3DLS1), but we achieved no consensus. We also discussed how to deal with data management and analysis of KIR locus copy number variants in the context of the great variation of KIR haplotypes, and this discussion also developed into a nomenclature discussion, with a similar lack of consensus.
2 - Prospect of developing an IDAWG STREGA-type statement
Pierre-Antoine presented an overview of the STrengthening the REporting of OBservational studies on Epidemiology (STROBE) set of publication guidelines and its extension to the STrengthening the REporting of Genetic Association studies (STREGA) guideline statement. These guidelines are intended to promote transparency and consistency in epidemiology and GWAS publications, by outlining the key areas of research that should be presented and discussed in the literature (e.g., in the case of STREGA, genotyping errors, population stratification, haplotype variation, Hardy-Weinberg deviations, and the replication of results). Pierre-Antoine proposed that the IDAWG work to develop a set of publication guidelines that would extend STREGA to immunogenomic studies (STengthening the REporting of Immunogenomic StudieS (STREISS). There was consensus among those present that such publication standards would be useful additions to the field, and that the group should work toward developing some sort of statement along the lines of STREGA, with a goal of presenting it at the 16th Workshop.
To read the STREGA statement (Little et al. (2009) Strengthening the reporting of genetic association studies (STREGA): an extension of the STROBE Statement. Human Genetics 125(2) 1432-1203.), visit http://www.annals.org/cgi/content/full/150/3/206
3 - Tissue Antigens Commentary
Rich described an exchange he had had with Jim McCluskey at Tissue Antigens regarding the need for standards for immunogenomic data analyses and the reporting of those analyses, and Jim suggested that this group could author a Commentary for Tissue Antigens describing that need. Pierre-Antoine pointed out how two papers had recently been published in Tissue Antigens describing the same SNP, but which used different names for that same polymorphism. Steve Marsh suggested that Pierre-Antoine write a letter to Tissue Antigens regarding the problem, and therein reference this group and the more comprehensive Commentary being written by the group. There was general consensus that such a Commentary could lay out the issues that would eventually be dealt with in an STREISS-type statement. We agreed to send around an outline of the Commentary, and that members of the group could decide what sections of the outline they would like to contribute to.
4 - Present and Demo the ANTT and UNCL
Steve Mack and Jill presented the Allele Name Translation Tool, and Update NomenCLature, two software tools designed to automatically translate current-nomenclature allele names to the new, colon-delimited allele names and new nomenclature rules that will be adopted early in 2010. Jill demoed UNCL, and the group provided useful feedback as to how UNCL could be further developed.
5 - Truncation Rules for HLA alleles
Steve Mack led a discussion about the current rules for the truncation of HLA allele names, as laid out in the 1995 and 1996 Nomenclature reports, in the context of the impending nomenclature change, and the automation of allele name translation. We concluded that truncated allele-names should not be extended to include two trailing zeros (e.g. *0200), and that they should instead be extended to include two trailing X's (e.g., 02XX), as the "XX" suffix is a valid NMDP allele code, and that other non-standard forms of truncation (e.g., truncation to odd numbers of digits) were not acceptable.
6 - Aardvark - possible benefit to Immunogenetics community
Pierre-Antoine presented Aardvark, an experimental social-networking tool that he proposed might be of use to the immunogenetic community for rapidly finding expert answers to difficult imunogenetics-related questions. Use of Aardvark would involve a large section of the Immunogenetics community agreeing to participate in the experiment. Jeff Rice suggested that EPERNICUS, which he described as a "science facebook" might be a more rigorous alternative.
7 - Grant support update
Steve Mack, Jill and Alex briefly presented an overview of their recently submitted NIH R01 application, "Solutions for Immunogenomic Data Management and Analysis", which aims to develop methods and tools for the standardized management and analysis of HLA and KIR data (as well as data for other highly-polymorphic loci), and to integrate these tools into a single analytical framework built around a database. Alex described the framework and database in detail.
At this point, the meeting adjourned.
Items not discussed:
ASHI SCAC meeting and status of the group as an ASHI Ad Hoc committee
Pre-SCAC meeting IDAWG meeting at ASHI
ASEATTA IDAWG meeting