IMMUNOGENOMIC NEXT GENERATION SEQUENCING DATA CONSORTIUM
The consortium achieved the following objectives in 2012 and 2013:
- Gained agreement that a single data reporting standard is needed for NGS immunogenomic data
- Assessed current status of standards development and existing challenges
- Developed proposals for establishing a standard and addressing challenges
- Gained commitment from suppliers for sponsorship of a consortium website
- Presented a preliminary information-standard for reporting immunogenomic genotype data generated via NGS methodology
- Discussed strategies for testing and validating the standard prior to its implementation.
On September 26th and 27th of 2014, the draft Minimum Information for Reporting Immunogenomic NGS Genotyping (MIRING) guidelines were vetted and updated as part of the first Data Standards Hackathon for NGS based typing of HLA & KIR (DaSH for NGS) held in conjunction with the FDA Workshop on NGS Standards.
The goal of the hackathon was to develop a toolset that was integrated with the various NGS systems and analysis software packages currently in use, the specific aims of achieving interoperability for the histocompatibility and immunogenetics community, vetting HML 1.0 and vetting MIRING.
Hackathon attendees provided feedback on:
- how well the tools work together,
- how they work with extant NGS software and standards,
- elements that need fixing (and fix them), and
- additional elements required for MIRING.
MIRING version 2 was developed as part of these DaSH for NGS efforts.
This new version of MIRING defines 8 elements of a message that capture the minimum information necessary to report a NGS HLA or KIR genotype.
On September 24, 2014, the draft MIRING reporting guidelines were presented at the Food and Drug Administration's Public Workshop on Next Generation Sequencing Data Standards in Bethesda, MD by Dr. Steven J. Mack.
- Minimum Information for Reporting Immunogenomic NGS Genotyping (MIRING): Reporting Guidelines for HLA and KIR Genotyping via Next Generation Sequencing.
Steven J. Mack, Robert P. Milius, Benjamin D. Gifford, James Robinson, Cherie Holcomb, Erik H. Rozemuller, Maarten T. Penning, Marc L. Salit, Carlheinz Müller, Tim Hague, Gottfried Fischer, Marcelo Fernandez-Viña, Jill A. Hollenbach, Paul J. Norman, Martin Maiers.
On June 26, 2014, the draft MIRING data reporting guidelines were presented at the European Federation for Immunogenetics meetin in Stockholm, Sweden by Benjamin D. Gifford in Abstract session 2: Bioinformatics.
MIRING (MINIMUM INFORMATION FOR REPORTING IMMUNOGENOMIC NGS GENOTYPING): REPORTING GUIDELINES FOR HLA GENOTYPING VIA NEXT GENERATION SEQUENCING.
BD Gifford, RP Milius, J Robinson, CL Holcomb, EH Rozemuller, M Penning, ML Salit, C Mueller, T Hague, GF Fischer, M Maiers, PJ Norman, MA Fernandez-Vina, JA Hollenbach, SJ Mack.
Read the Minimum Information for Reporting Immunogenomic NGS Genotyping (MIRING) minimum information reporting guidelines, and appendices.
Chicago, Illinois, USA
Presentation/Discussion of the Data Standard Implementation
The participants of the consortium agreed to submit
the final version of the letter of comment on the Draft NIH GDS Policy on behalf of the Immunogenomic NGS Data Consortium.
Validation and Testing of the Standard
- Steven J. Mack (CHORI): A MIBBI Standard for NGS Genotyping
- Benjamin Gifford (Life Technologies): Genomic Formats and the HLA Data Standard
- Robert P. Milius (NMDP): HML as an Implementation of the "standard"
- Marc Salit (NIST, Stanford ABMS):Validate the Data Standard: Interlab Study of NGS HLA Typing
Maastricht, The Netherlands
Data standards for the field as a whole
- NMDP: Martin Maiers
San Juan, Puerto Rico, USA