Genomic full-length sequence of the HLA-B*13:64 allele was identified in a Chinese bone marrow donor

Genomic full-length sequence of HLA-B*13:64 was identified in a Chinese individual by sequence-based typing.

Genomic full-length sequence of the HLA-B*44:127 allele was identified in a Chinese bone marrow donor

Genomic full-length sequence of HLA-B*44:127 was identified in a Chinese individual by sequence-based typing.

Genomic full-length sequence of the HLA-A*11:264 allele was identified in a Chinese bone marrow donor

Genomic full-length sequence of HLA-A*11:264 was identified in a Chinese individual by sequence-based typing.

Multiple low-frequency and rare HLA-B allelic variants are associated with reduced risk in 1,105 nasopharyngeal carcinoma patients in Hunan province, southern China

In our study, 1,105 cases of nasopharyngeal carcinoma (NPC) and 1,430 normal controls recruited from Hunan province, southern China were typed for human leukocyte antigen (HLA)-B locus by Sanger sequencing exons 2-4. Besides confirming the NPC association with HLA-B*46:01 allele, HLA-A*02:07-B*46:01 and HLA-A*33:03-B*58:01 haplotypes (all positive), and HLA-B*13 lineage (negative), all of which were relatively common, strong negative associations were observed for five low-frequency and rare alleles or lineages, including HLA-B*07, -B*27:04, -B*39, -B*51:02 and -B*55:02, with odds ratio (OR) ranging from 0.16 to 0.3 (all p_corrected < 0.05). These strong protective associations were independent of linkage disequilibrium (LD) between HLA-A and HLA-B loci. Further analysis indicated a single amino acid change from histidine to tyrosine at residue 171 is probably crucial for the mutant allele, HLA-B*51:02, to mediate resistance to NPC. A subset of NPC cases (n = 821) and normal controls (n = 1,035) were tested for antivirus capsid antigen immunoglobulin A (anti-VCA IgA), which differed drastically between the two groups [67.7% vs. 5.5%, OR (95% confidence interval) = 36 (26.55-48.81), p < 0.0001]. HLA-B allelic variation did not associate with seropositivity for anti-VCA IgA in either group. Results from our study show, more clearly than previously, the existence of a cluster of low-frequency and rare HLA-B variants conferring low, or very low risk to NPC, a phenomenon not observed in other ethnic groups. Our data shed new insights into genetic susceptibility to NPC in southern Chinese populations. Future independent studies are warranted to replicate the findings reported in our study.

Role of Deleterious Rare Alleles for Acute-Onset Diffuse Interstitial Lung Disease in Collagen Diseases

Objective

Acute-onset diffuse interstitial lung disease (AoDILD) includes acute exacerbation of interstitial lung disease (ILD), drug-induced ILD, and Pneumocystis pneumonia in collagen diseases patients. As AoDILD causes a poor prognosis in collagen disease patients, the pathogenesis of AoDILD should be investigated. Exome sequencing studies revealed that rare variants were detected to be causative in some diseases. Recently reported upregulated genes in acute exacerbation of idiopathic pulmonary fibrosis could provide candidate genes for restricted exome analysis of AoDILD in collagen disease. Here, we investigated rare variants in the coding and boundary regions of these candidate genes in AoDILD.

Methods

Deleterious rare variants in the coding and boundary regions of the candidate genes were analyzed by exome sequencing and the deleterious rare allele frequencies in AoDILD were compared with those of controls.

Results

A significant association was detected for deleterious rare alleles in NPL (P = .0044, P _c = .0399, odds ratio [OR] = 10.05, 95% confidence interval [CI] = 3.01-33.55). A deleterious rare allele frequency in the 9 candidate genes (P = .0011, OR = 7.17, 95% CI = 2.80-18.33) was also increased in AoDILD in multigene panel analysis. The Krebs von den Lungen-6 (KL-6) levels in AoDILD patients with deleterious rare alleles were tended to be lower than those without (P = .0168, P _c = .1509).

Conclusions

The deleterious rare alleles in NPL were associated with AoDILD. In addition, the deleterious rare allele frequency in the 9 candidate genes was also increased in AoDILD. The deleterious rare alleles might contribute to the pathogenesis of AoDILD.

Enrichment of rare alleles within epigenetic chromatin marks in the first intron

In previous studies, we demonstrated that some sites in the first intron likely regulate gene expression. In the present work, we sought to further confirm the functional relevance of first intron sites by estimating the quantity of rare alleles in the first intron. A basic hypothesis posited herein is that genomic regions carrying more functionally important sites will have a higher proportion of rare alleles. We estimated the proportions of rare single nucleotide polymorphisms with a minor allele frequency < 0.01 located in several histone marks in the first introns of various genes, and compared them with those in other introns and those in 2-kb upstream regions. As expected, rare alleles were found to be significantly enriched in most of the regulatory sites located in the first introns. Meanwhile, transcription factor binding sites were significantly more enriched in the 2-kb upstream regions (i.e., the regions of putative promoters of genes) than in the first introns. These results strongly support our proposal that the first intron sites of genes may have important regulatory functions in gene expression independent of promoters.

A novel allele of the goldfish chdB gene: Functional evaluation and evolutionary considerations

The twin tail of ornamental goldfish is known to be caused by a nonsense mutation in one chordin paralogue gene. Our previous molecular studies in goldfish revealed that the ancestral chordin gene was duplicated, creating the chdA and chdB genes, and the subsequent introduction of a stop codon allele in the chdA gene ( chdA^E127X) caused the twin‐tail morphology. The chdA^E127X allele was positively selected by breeders, and the allele was genetically fixed in the ornamental twin‐tail goldfish population. However, little is known about the evolutionary history of the chdB paralogue, begging the question: are there the functionally distinct alleles at the chdB locus, and if so, how did they evolve? To address these questions, we conducted molecular sequencing of the chdB gene from five different goldfish strains and discovered two alleles at the chdB gene locus; the two alleles are designated chdB¹ and chdB². The chdB¹ allele is the major allele and was found in all investigated goldfish strains, whereas the chdB² allele is minor, having only been found in one twin‐tail strain. Genetic analyses further suggested that these two alleles are functionally different with regard to survivability ( chdB¹ >  chdB²). These results led us to presume that in contrast to the chdA locus, the chdB locus has tended to be eliminated from the population. We also discuss how the chdB² allele was retained in the goldfish population, despite its disadvantageous function. This study provides empirical evidence of the long‐term retention of a disadvantageous allele under domesticated conditions.

Integrating Rare-Variant Testing, Function Prediction, and Gene Network in Composite Resequencing-Based Genome-Wide Association Studies (CR-GWAS)

High-density array-based genome-wide association studies (GWAS) are complemented by exome sequencing and whole-genome resequencing-based association studies. Here we present a composite resequencing-based genome-wide association study (CR-GWAS) strategy that systematically exploits collective biological information and analytical tools for a robust analysis. We showcased the utility of this strategy by using Arabidopsis (Arabidopsis thaliana) resequencing data. Bioinformatic predictions of biological function alteration at each locus were integrated into the process of association testing of both common and rare variants for complex traits with a suite of statistics. Significant signals were then filtered with a priori candidate loci generated from genome database and gene network models to obtain a posteriori candidate loci. A probabilistic gene network (AraNet) that interrogates network neighborhoods of genes was then used to expand the filtering power to examine the significant testing signals. Using this strategy, we confirmed the known true positives and identified several new promising associations. Promising genes (AP1, FCA, FRI, FLC, FLM, SPL5, FY, and DCL2) were shown to control for flowering time through either common variants or rare variants within a diverse set of Arabidopsis accessions. Although many of these candidate genes were cloned earlier with mutational studies, identifying their allele variation contribution to overall phenotypic variation among diverse natural accessions is critical. Our rare allele testing established a greater number of connections than previous analyses in which this issue was not addressed. More importantly, our results demonstrated the potential of integrating various biological, statistical, and bioinformatic tools into complex trait dissection.