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Figure 2 | BMC Genomics

Figure 2

From: Inference of high resolution HLA types using genome-wide RNA or DNA sequencing reads

Figure 2

Analysis of frequently mistyped alleles. (A) The histograms illustrate the type (x-axis) and the number (y-axis) of the misidentified alleles at the HLA-DQA1 (left panel) and HLA-DQB1 (right panel) loci, summarized over the HapMap RNAseq, the 1000 Genome WXS and the HapMap WXS datasets. (B) Visualization of the mapped reads in one representative sample (subject NA12156, Additional file 1: Table S1) where the HLA-DQA1*03:01 allele is mistyped as the HLA-DQA1*03:03 allele. The mapped reads are shown around the single SNP position (chr6: 32609965, highlighted in between two vertical dashed lines) that distinguishes the two alleles. The hg19 reference sequence of the HLA-DQA1 gene is shown at the bottom of the panel. The nucleotide bases A, C, G, T are colored in green, red, blue grey and blue, respectively. The bases in the reads, if different from the reference sequence at the aligned positions, are visualized in the same color code. The pileup counts of the A, C, G, T bases at the highlighted SNP are 141, 117, 0 and 0, respectively. (C) The alignment of a 135-nucleotide segment from the HLA-DQA1*03:03 allele, noted as the query, with the HLA-DQA2 reference sequence in human genome hg19. The query sequence is simplified as a horizontal bar with only the mismatches indicated. The existing dbSNP record at the mismatch is labeled with a red vertical marker and the associated identification numbers (e.g. rs62619945) followed by a parenthesis indicating the major and the alternative base sequences. The alignment of the SNP that differ the DQA1*03:01 and DQA1*03:03 alleles is boxed.

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