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Dear <<First Name>>,

This is the third newsletter of the 18th International HLA and Immunogenetics Workshop with the aim to inform you on various aspects of the workshop, including updates on the organization, project highlights, and component updates of the 18th IHIWS.

Sebastiaan Heidt
Eric Spierings

Newsletter content

  • Organization update
  • ASHI Conference Announcement
  • Official Workshop Partners
  • Project in the Spotlight
  • South American hub: Margareth Afonso Torres

Organization update

The summer season has been all but quiet for the Workshop. Particularly the database and data collection has had our priority. The database structure from the 17th IHIWS served its purpose, but is hard to implement in a cloud-based infrastructure. As such we have decided to rebuild the structure from scratch. These efforts are ongoing and a first release, including user access and project management, has been scheduled for end of September. Data collection will follow soon after that.  With the help of Gottfried Fischer and Loren Gragert, supported by DaSH, we now also have a communication protocol for antibody data. An important achievement for the Bioinformatics Component and crucial for the projects in the Antigenicity & Immunogenicity Component of the present Workshop.
As for the projects, we see quite some subscriptions. Yet, if you haven't done so, make sure you join your projects of interest. Some of the projects will have a project meeting at ASHI. Details are reported in this newsletter. 

ASHI conference announcement

A number of project leaders will have a project meeting during the 45th ASHI Conference in Pittsburgh. Below, you can find a schedule. Note that rooms for these meetings have a limited capacity and priority will be given to participants of the respective projects.

Workshop meetings at the 45th ASHI Conference

 
Date & Time
Project
Chair
Location
25 Sept 5:00-7:00PM IHIWS vendors meeting Sebastiaan Heidt Room 327
Level three

25 Sept 4:00-5:00PM

HLA-DQ immunogenicity:
focus on 2MM1DSA

Anat Tambur

Room 326
Level three
25 Sept 7:00-7:30PM HLA haplotypes in families
NGS on reference cell lines
Definition and immunogenicity of DP epitopes
Tami Vayntrub Room 326
Level three
25 Sept 6:30-7:00PM     Study of haplotypes in families
The allele cataloguing project  
Medhat Asker     Room 326
Level three

 

Official Workshop Partners

This time, we proudly announce the official support of EFI and ASHI for the 18th Workshop. With their contributions, we will be able to keep the registration fees for the Workshop meeting in Amsterdam affordable for all participants. Moreover, they are providing facilites for Workshop meetings at their annual conferences (see above). We therefore are grateful to these two federations for their generous support.

Project in the Spotlight

In this section, we will highlight one of the Workshop projects. This time, it is the project Data Standards Hackathon coordinated by Martin Maiers. 


Detailed project description:

Historically, there have been few standards regarding HLA and KIR genotyping data, and associated meta-data, and very few public tools for the management of these data. Recognizing the tremendous potential of NGS for immunogenomics, and the need for coordinated consolidation of the data for such a broad field, we have organized a series of collaborative software-development events (“hackathons”) focused on the creation of novel tools, standards and services that will maximize the utility of immunogenomic data for clinical and basic research science. These meetings have been supported by the National Marrow Donor Program (NMDP) and several commercial vendors.

During previous Data Standards Hackathon events, participants helped finalize specifications for MIRING, worked on tools implementing it (e.g., HML 1.0, HL7-FHIR), and considered ways how to express novel polymorphisms without human curation (e.g., Gene Feature Enumeration).

 

History:

We have held 6 hackathons before the 17th IHIW, and have held 3 since then. We have also organized smaller, more focused hackathons to address issues specific to donor registries, in collaboration with the World Marrow Donor Association (WMDA), and focused on Electronic Health Records integration with HL7-FHIR (Health Level 7 – Fast Healthcare Interoperability Resources).

HL7-FHIR is emerging as global standard for health IT and we want to collaborate with laboratories and industry partners to roll out its use for HLA. Getting HLA data in/out of the Electronic Medical Record is a dream that is starting to come true. Not only does it reduce manual entry effort and errors, but it allows us to move from “typing” to “sequencing” by accurately and securely transmitting consensus sequence data to better inform research and medical decision making. Recent work has focused on developing secure “apps” using the SMART-on-FHIR specification (OAuth2) that can plug-in to electronic medical records system to allow secure transmission of complex data (like HLA).

 

Accomplishments:

Since the first hackathon in 2014, this project has delivered a number of standards, systems, manuscripts and tools.

 

Challenges/Goals:

There are a number of open problems to be addressed. We have identified a few that are central to the goals of the 17th and 18th IHIWS efforts as they relate to the communication of NGS results.

  •  STRs

    • No PCR-based NGS typing system can resolve STRs in HLA genes. This was widely reported at the 17th IHIWS but we lack data standards for reporting this information.

  •  Re-Analysis of consensus data

    • The 17th IHIWS started collecting data by acquiring FASTQ files but was found to be too vendor-specific and burdensome. The project then transitioned to collecting curated consensus sequence data. In the 17th IHIWS a system was developed for automated annotation of HLA and KIR alleles connected to a Gene Feature Enumeration database that provided unique, computable identifiers via a RESTful web service. This system works well for annotating a single consensus block of a full HLA or KIR gene but many platforms provide either partial-gene sequence and/or multiple consensus blocks per gene. Re-analysis of multi-block consensus (e.g. exon only) remains an open issue. Automated submissions of new variants to standards-based systems like GenBank and ENA has been straightforward with several tools becoming available (TypeLoader, Saddlebags). Automation of submission to IPD-IMGT/HLA or IPD-KIR has been more difficult due to lack of adherence to public standards.

  •  Evaluating compliance with data standards

    • At the 17th IHIWS we determined that data standards can be loosely interpreted in such a way that prevents interoperability. In order to establish compliance, we seek to implement a software service that will provide comprehensive validation of HLA genotyping reports and their compliance with the various standards within (LOINC, WHO).

    • Re-usable and public datasets for research are needed.

  • HL7-FHIR

    • Release 4 (R4) of the HL7-FHIR standard was announced in December 2018. Recognizing the existing efforts to develop an implementation guide for HLA and KIR within the HL7 Clinical Genomics Working Group, we would like to focus on applications (clients and servers) that can implement this standard and connect them.

    • We plan to implement a public conformance server that will perform syntactic and sematic validation of HLA genotyping reports in terms of their compliance with the standards and provide visual feedback. This approach has been shown to be successful in the development of other HL7-FHIR standards (e.g. Argonaut).

 

Suggested topics for this event include

  • Development of tools for translating between proprietary formats and open standards; specifically: HL7-FHIR and semantic validation.

  • Automated annotation and curation of sequence variation. Specifically use the GFE system to annotate the consensus sequence data collected as part of the 18th IHIWS.

  • Validation of population genetics tools. Specifically haplotype frequency estimation (pyPop, Hapl-o-Mat, haplostats, others) and extension to analysis of GFE encoded data

  • Support for incorporation of HLA into smartphone apps

  • Software for analysis of MHC and KIR region genomics

 

Milestones in years:

2019:

  • Data standards Hackathon: WMDA Office, Leiden, Mar 23-24, 2019

  • Data standards Hackathon: Denver, Colorado May 30-31, 2019

  • HLA/HL7-FHIR Data Standards Symposium and Hackathon
    Minneapolis, MN Aug 21-23, 2019

  • HL7-FHIR development at HL7-working group meetings and connectathons.

2020:

  • Data standards hackathons (dates/locations TBD)

2021:

  • Data standards hackathon during IHIWS

Presenting our South American IHIWS hub: 
Margareth Afonso Torres


I am pleased and honored to be the South American hub for the 18th IHIWS. Firstly, I would like to talk about my background. I graduated in Medicine at the Universidade Federal de Juiz de Fora, Brazil, in 1985. After that, I specialized in Nephrology. Afterwards, due to the importance of immunogenetics in transplantation, I improved my knowledge in this area. Then I changed to the Clinical Pathology area. I have been working in the fields of Histocompatibility and Immunogenetics since 1992. I have been ASHI Director of the Histocompatibility and Immunogenetics Laboratory at Hospital Israelita Albert Einstein, São Paulo, Brazil, since 2005. In 2014, we received our first ASHI and FACT Accreditation.
The founders of the Histocompatibility Brazilian Association were the forerunners of immunogenetics in Brazil and had been active in the Association since 7th IHWS. The Histocompatibility Brazilian Association introduced quality program for Histocompatibility laboratories including proficiency testing and accreditation, holding scientific meetings as well as encouraging members in participating of international meetings and workshops. Maria Gerbase de Lima and Maria Elisa Moraes were chairwomen of the 15th IHIWS in Brazil, which was a great opportunity for the participation of Brazilians in scientific projects, incentivating them to carry out immunogenetics research and facilitating the  implementation of new technologies.
The South American population is characterized by a widely genetic diversity, generated by a complex history of migration that took place during centuries, comprising a native population from Asian immigration that occurred nearly 15.000 years ago.  European and African immigrants came between 16th and 17th centuries. Consequently, it became an admixture population which expresses many alleles that are not found in other populations, so the introduction of this genetic diversity in workshop projects, such as the ones that use next generation sequencing (NGS) and the epitopes study, has a relevant importance.
I will do what it takes to encourage our laboratories to participate of Projects like definition of Immunogenic Epitopes and Immunogenetics in 18th IHIWS.

Margareth Afonso Torres
 

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18th International HLA & Immunogenetics Workshop
please visit our website.

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