Imputation of class <scp>I</scp> and <scp>II HLA</scp> loci using high‐density <scp>SNP</scp>s from <scp>I</scp>mmuno<scp>C</scp>hip and their associations with <scp>K</scp>awasaki disease in family‐based study

Shrestha, Sadeep; Wiener, Howard W.; Aissani, Brahim; Shendre, Aditi; Tang, Jianming; Portman, Michael A.

doi:10.1111/iji.12190

Cited by 15 publications

(9 citation statements)

References 42 publications

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“…Viral-like inclusion bodies were found in the lungs of this patient similar to findings in other patients with KD and supporting an underlying viral etiology [7]. Increasing evidence suggests that an individual's immune response to the inciting event or pathogen, as determined by their genetic background, exerts a significant influence on the severity of presentation and responsiveness of the illness to IVIG [8,9]. As the era of personalized medicine gains support, inflammatory diseases such as KD may benefit from the development of tools to precisely define the risk for severe/refractory disease, and allow practitioners to tailor treatment regimens with better precision.…”

Section: Discussionsupporting

confidence: 77%

Systemic arterial aneurysms in a 5 month old male with severe refractory Kawasaki’s disease

Hsu¹,

Soriano²,

Salamet³

et al. 2016

Pediatr Dimensions

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This is the presentation of a 5 month old infant male initially diagnosed with atypical Kawasaki's disease who developed disseminated coronary artery dilation and multiple aneurysms in mid-size systemic arteries. He suffered an acute bleeding event and later died. This case underscores the possibility of systemic arterial involvement in severe cases of Kawasaki's disease and raises the issue whether wider screening for extracardiac vascular abnormalities might be indicated.

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Section: Discussionsupporting

confidence: 77%

Systemic arterial aneurysms in a 5 month old male with severe refractory Kawasaki’s disease

Hsu¹,

Soriano²,

Salamet³

et al. 2016

Pediatr Dimensions

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“…We find that SNP2HLA generated high confidence imputation at one- and two-field resolution which was validated by SSP-based direct HLA typing for 5 loci. Imputation of HLA alleles and amino acid polymorphisms using SNP2HLA has been successfully implemented for genetic studies of associations in a range of traits [44], [45], [46], [47], [48].…”

Section: Discussionmentioning

confidence: 99%

High resolution HLA haplotyping by imputation for a British population bioresource

et al. 2017

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This study aimed to establish the occurrence and frequency of HLA alleles and haplotypes for a healthy British Caucasian population bioresource from Oxfordshire. We present the results of imputation from HLA SNP genotyping data using SNP2HLA for 5553 individuals from Oxford Biobank, defining one- and two-field alleles together with amino acid polymorphisms. We show that this achieves a high level of accuracy with validation using sequence-specific primer amplification PCR. We define six- and eight-locus HLA haplotypes for this population by Bayesian methods implemented using PHASE. We determine patterns of linkage disequilibrium and recombination for these individuals involving classical HLA loci and show how analysis within a haplotype block structure may be more tractable for imputed data. Our findings contribute to knowledge of HLA diversity in healthy populations and further validate future large-scale use of HLA imputation as an informative approach in population bioresources.

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“…In addition, our findings revealed a novel pathogenic effect of HLA-C molecules, which can be exerted by leucine at amino-acid position 116 in the middle of the epitope-binding site. This residue was correlated with one of the HLA-C*15 alleles that have been suggested to be associated with Kawasaki disease, Behçet’s disease, and leprosy [ 15 – 17 ]. However, because this study had no replication cohort and previous European studies have not reported the association for HLA-C amino-acid position 116, this association needs to be validated in an independent cohort in the future.…”

Section: Discussionmentioning

confidence: 99%

An HLA-C amino-acid variant in addition to HLA-B*27 confers risk for ankylosing spondylitis in the Korean population

et al. 2015

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IntroductionThe presence of the HLA-B*27 allele is a major risk factor for the development of ankylosing spondylitis (AS), which causes chronic inflammation of the spine and other sites. We investigated residual effects outside HLA-B within the major histocompatibility complex (MHC) region in the Korean population.MethodsUsing the Korean HLA reference panel, we inferred the classic HLA alleles and amino-acid residues of the six HLA genes (HLA-A, -B, -C,-DPB1, -DQB1, and -DRB1) and MHC single-nucleotide polymorphisms in 3820 Korean subjects, including 654 Korean cases of AS and 3166 controls, who were genotyped by using Immunochip. Logistic regression and log-likelihood ratio tests were used in AS association tests for imputed markers.ResultsThe most significant associations were identified at amino-acid positions in the epitope-binding site of HLA-B (P = 1.71 × 10−481 at position 70, P = 7.20 × 10−479 at position 97, and P = 2.54 × 10−484 at positions 114), highlighting the risk effect of the HLA-B*27 allele and the protective effects of other classic alleles. A secondary effect was located at the leucine at amino-acid position 116 in the epitope-binding site of HLA-C (P = 1.69 × 10−14), completely tagging the HLA-C*15:02 allele. This residue had a large effect in HLA-B*27-negative patients (odds ratio = 6.6, 95 % confidence interval = 3.8 to 11.4).ConclusionsThe four amino-acid positions of HLA-B and -C account for most of the associations between AS and MHC in the Korean population. This finding updates the list of AS susceptibility loci and provides new insight into AS pathogenesis mediated by MHC class I molecules.Electronic supplementary materialThe online version of this article (doi:10.1186/s13075-015-0855-3) contains supplementary material, which is available to authorized users.

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Imputation of class I and II HLA loci using high‐density SNPs from ImmunoChip and their associations with Kawasaki disease in family‐based study

Cited by 15 publications

References 42 publications

Systemic arterial aneurysms in a 5 month old male with severe refractory Kawasaki’s disease

Systemic arterial aneurysms in a 5 month old male with severe refractory Kawasaki’s disease

High resolution HLA haplotyping by imputation for a British population bioresource

An HLA-C amino-acid variant in addition to HLA-B*27 confers risk for ankylosing spondylitis in the Korean population

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