Next generation HLA sequencing

Dianne De Santis, Richard Allcock

While we envisage this component of the 16th International HLA and Immunogenetics Workshop may only be of interest to a minority group within the HLA community at this time, we felt that it was important to begin work in this area and see this as an evolving area for future workshops.

We see that the ‘Next Generation HLA Sequencing’ component will be addressed in a number of phases, the first being addressed in this Workshop.

PHASE 1 of the Next Generation component for 16th IHIW:

Aim:
The aim of this phase would be to:

1. Compare the different “Next Generation” approaches (small and large amplicon approaches and the capture approach) utilised throughout the world for HLA typing.
2. To compare the “Next Generation” technologies to current Sanger HLA Sequence based typing methods or alternative methods.
3. To identify the “pros and cons” of utilising the technologies for HLA typing.

Participants will be asked to complete a questionnaire prior to the workshop and then given the opportunity to present and discuss their own experiences with HLA genotyping and Next Generation Sequencing at the workshop. Discussion points would include the following;

1. HLA Null alleles,
2. Novel alleles
3. Cis/trans ambiguity resolution
4. Polymorphisms within the 5’UTR regions
5. Tandem repeats within a region
6. Promoter regions of genes
7. Intronic data
8. Allelic dropout.
9. Bioinformatics
10. Cost
11. Turnaround times/Workflow

Time Frame:

• 2011 Oct: Close registration
• 2011 Nov: Send out the questionnaire for completion by participants
• 2012 Jan: Submit questionnaire to DCI
• 2012-16th IHIW: Participants to discuss laboratory experiences.

Costs: Nil

Contacts:

Please let us know if you would like to participate in the workshop. We will provide you with further information as the project proceeds.

Dr Dianne De Santis
Department of Clinical Immunology
Royal Perth Hospital, PathWest
Level 2, North Block,
Wellington St, Perth 6000
Western Australia
E-mail: dianne [dot] desantis [at] health [dot] wa [dot] gov [dot] au

Richard Allcock
School of Pathology and Laboratory
Medicine, University of Western
Australia
Royal Perth Hospital, PathWest
Level 2, North Block,
Wellington St, Perth 6000

E-mail: richard [dot] allcock [at] uwa [dot] edu [dot] au
Tel: 61-8-92241175
Fax: 61-8-92242920

Download a PDF of the ASHI 2011 Presentation - download PDF file.

Nov 10, 2011 Posted by Admin