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Table 2 Predicted HLA types of the CEU trio samples with HLA-VBSeq.

From: HLA-VBSeq: accurate HLA typing at full resolution from whole-genome sequencing data

Sample

Predicted HLA types

NA12878 (child)

A*01:01:01:01

A*11:01:01

 

B*08:01:01

B*56:01:01

 

C*01:02:01

C*07:01:01:01

 

DQA1*01:01:02

DQA1*05:01:01:02

 

DQB1*02:01:01

DQB1*05:01:01:02

 

DRB1*03:01:01:01

DRB1*01:01:01

NA12891 (father)

A*01:01:01:01

A*24:02:01:01

 

B*07:02:01

B*08:01:01

 

C*07:01:01:01

C*07:02:01:03

 

DQA1*01:02:01:01

DQA1*05:01:01:02

 

DQB1*02:01:01

DQB1*06:02:01

 

DRB1*03:01:01:01

DRB1*15:01:01:02

NA12892 (mother)

A*02:01:01:01

A*11:01:01

 

B*15:01:01:01

B*56:01:01

 

C*01:02:01

C*04:01:01:01

 

DQA1*01:01:02

DQA1*01:01:02

 

DQB1*05:01:01:02

DQB1*05:01:01:01

 

DRB1*01:01:01

DRB1*01:01:01

  1. Predicted HLA types of HLA-A, -B, and -C loci with HLA-VBSeq were experimentally validated at 4-digit resolution in [10], which is shown in bold text. Predicted HLA types of HLA-DQA1, -DQB1 and -DRB1 loci with HLA-VBSeq were coincided with those with PHLAT at 6-digit resolution except DQA1*01:01:02 (one allele in NA12878 and two alleles in NA12892). PHLAT instead predicted them as DQA1*01:01:01, whose genomic sequence was missing in the IMGT database release 3.15.0., and hence HLA-VBSeq could not predict the HLA allele in our experimental condition.
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BMC Genomics

ISSN: 1471-2164

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