What is it about?
We have developed a system to sequence the whole gene from 5’-UTR to 3’-UTR for the HLA loci A, B, C, DQB1 and DPB1 for submission to the European Molecular Biology Laboratory - European Nucleotide Archive (EMBL-ENA) and the IPD-IMGT/HLA Database. Our workflow is based on a dual redundant sequencing strategy. Using shotgun sequencing on an Illumina MiSeq instrument and Single Molecule Real-Time (SMRT) sequencing on a PacBio® RS II instrument, we are able to achieve highly accurate HLA full-length consensus sequences.
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Why is it important?
Given the increasing application of next generation sequencing (NGS) for full gene characterisation in clinical practice, extending the HLA database concomitantly is highly desirable. Therefore, we propose this dual redundant sequencing strategy as a workflow for submission of novel full-length alleles and characterisation of sequences that are as yet incomplete. This would help to mitigate the predominance of partially known alleles in the database.
Perspectives
I am very proud to present the reader an opportunity to expand the IPD-IMGT/HLA Database repository comprehensively using the Illumina and PacBio platforms in standard sequencing workflows. With that we sequenced and submitted more than 1000 HLA alleles so far and could increase the number of fully characterised alleles in the IPD-IMGT/HLA Database massively. I would love to see other people getting inspired by this paper and encourage you to do the same by starting to provide the IPD-IMGT/HLA Database full-length sequences in high quality.
Viviane Albrecht
Read the Original
This page is a summary of: Dual redundant sequencing strategy: Full-length gene characterisation of 1056 novel and confirmatory HLA alleles, HLA, May 2017, Wiley,
DOI: 10.1111/tan.13057.
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