Introducing a new manuscript format: Enabling access to immunogenomic population data with short population reports

Abstract

The capacity to replicate the findings of a study is key to the advancement of research, and access to the data on which a study is predicated is required for true replication. Population genetic studies have long been a focus of the immunogenetic research community, but access to the primary genotype data underlying these studies has historically been limited. With the notable exception of the International HLA and Immunogenetics Workshops, it is primarily allele and haplotype frequency data that are made available upon publication for most immunogenetic population studies. However, such frequency data are the products of a prior analysis, and may reflect unreported methodological biases. Access to the primary genotype data allows independent validation and true replication of the study, and knowledge of the ambiguities associated with those genotype data maximizes the utility of population data for replication and meta-analyses. With this issue of Human Immunology, we are introducing a new manuscript format. Structured descriptions of reference populations, populations of anthropological interest and control populations for disease studies, along with genetic data and minimal analyses, can now be submitted as Short Population Reports. Short Population Reports will be peer-reviewed, and will follow a standard format (described below), with the aim of fostering the availability and archiving of the genetic data underlying immunogenetic population studies. Human Immunology is partnering with the Allele Frequencies Net Database (AFND; http://www.allelefrequencies.net) to archive and make primary ambiguous genotype data, allele frequency data and haplotype frequency data for the HLA, KIR, cytokine and MIC genes publically accessible, along with demographic data for each population. Details of the AFND data-submission process can be found at http://www.allelefrequencies.net/submit. While public access to immunogenomic allele and haplotype frequency data has always been part of AFND’s mission, the availability of primary ambiguous genotype data is new. These data will be made available on AFND in one of three ways, as determined by the data submitter in accordance with their data-sharing permissions; the primary data will be (i) publically available for download, or (ii) maintained privately on AFND, and made available for analysis by anyone using software that will be provided by AFND or (iii) maintained privately on AFND and will only be analyzed by AFND for data validation purposes. We encourage all authors to seek data-sharing permissions that allow maximal sharing of their primary data. Genotype, allele and haplotype data deposited in the AFND can be referenced in the corresponding Short Population Report with a unique identifier provided by the AFND. As described below, Short Population Reports should include only three analyses – evaluation of Hardy–Weinberg equilibrium proportions, for validation of the genotyping data, calculation of allele frequencies, and estimation (or calculation) or haplotype frequencies. Population studies that include additional analyses should be submitted as Research Articles. However, authors are encouraged to cite specific Short Population Reports in Research Articles that present more detailed analyses; this approach fosters more in-depth presentation and discussion of methods and analyses in population studies published as Research Articles. An example Short Population Report authored by Williams and Middleton is included in this issue.