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Making Immunogenomic Data more Accessible
CHORI Scientists Lead Charge for Creating Community Standards in Immunogenomic Data Reporting and Analysis

CHORI scientists, Steven Mack, PhD and Jill Hollenbach, PhD, MPH, and their colleagues from the Immunogenomics Data Analysis Working Group, or IDAWG, have published an invited commentary in the November 2011 issue of Tissue Antigens outlining the urgent need to develop a common standard for reporting the results of immunogenomic studies.

“Many immunogenomic studies are funded with federal dollars and deposited into the public forum with a few publications, and that is where it ends. There is currently no clear way to make use of the wealth of data generated in these studies,” explains Dr. Mack. “We’d like to change that by developing a reporting standard that every researcher can use.”
“We'd like to develop a reporting standard for immuno-
genomic studies that every research can use.”

The advent of next generation sequencing has made it possible to get large quantities of high quality data in a very short amount of time. This results in the broader question of how to deal with all these data in a meaningful way that will allow researchers to understand and replicate each other’s results, and to use data from different studies for different purposes.

The scientific community has already made strides in trying to create uniform standards for handling this new wealth of genetic information, by establishing the the ‘STrengthening the Reporting of OBservational studies in Epidemiology’ (STROBE) and ‘STrengthening the Reporting of Genetic Association studies’ (STREGA) statements, which provide guidelines for genetic epidemiology studies, and single nucleotide polymorphism (SNP) based genome-wide association studies (GWAS). These statements only have limited application to immunogenomic and histocompatbility data, however.

“There are two sides to the immune system, the adaptive immune system and the innate immune system,” explains Dr. Mack. “The active immune system is moderated by those genes which code for the human leukocyte antigen (HLA), while the innate immune system is moderated by those genes which code for killer-cell immunoglobulin-like receptor (KIR).”

Unlike SNP-GWA studies, which generally involve markers with limited variation, HLA and KIR genes are highly polymorphic. For the nine HLA loci that are commonly typed for, there are approximately seven thousand alleles that have been seen worldwide. In any given population, a single HLA gene might have 40 different variants.

Currently, HLA and KIR data are generated in a very heterogeneous fashion, in part because methodologies vary from country to country and because different international registries have different requirements. In addition, the clinical and basic research applications of these data can differ significantly, so that it can often be unclear what was done to the data over the course of a study.

“When you generate immunogenomic data, there can potentially be many possibilities in terms of how to interpret them, and different groups rely on their own experiences in terms of those interpretations, but they don’t necessarily make that clear when they publish their findings.”

The Tissue Antigens commentary serves as an announcement that IDAWG is working to extend the STROBE and STREGA statements with a STrengthening the REporting of Immunogenomic Studies (STREIS) statement that applies more directly to immunogenomic data. In addition, Drs. Mack and Hollenbach and their colleagues provide an overall discussion as to why such an extension is necessary, and a call to arms to get as many people from the immunogenomic community involved in the process of developing that statement.

“What we are hoping to achieve with our statement is to make it easier to understand what different researchers are doing to the data in their studies to both increase the ability to replicate and verify results, and to develop a standard language for data-management. This will increase the utility of data across different groups and different studies, and make published data resources useful across time.”

The IDAWG group plans to unveil a working draft of the STREIS statement at the 16th International HLA and Immunogenetics Workshop in Liverpool, England this spring, which they hope to finalize with the input of the entire immunogenomic community.


Thursday, January 12, 2012 12:31 PM

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