SNP Haplotype Research Articles

Affected-embryo-based SNP haplotyping with NGS for the preimplantation genetic testing of Marfan syndrome

ABSTRACT Marfan syndrome (MFS), an autosomal dominant heritable disease of the connective tissue, is characterized by broad clinical manifestations in the musculoskeletal, cardiovascular, pulmonary, and ocular systems. In this study, a male patient with MFS caused by a heterozygous mutation NM_000138.5(FBN1):c.6037 + 2 T > C in the fibrillin 1 gene (FBN1) underwent preimplantation genetic testing (PGT) by using affected-embryo-based single nucleotide polymorphism (SNP) haplotyping. Multiple displacement amplification was used for whole genome amplification of biopsied trophectoderm cells after controlled ovarian stimulation. Sanger sequencing and next-generation sequencing (NGS) were used to detect the state of FBN1 mutation. A total of 14 blastocysts formed after intracytoplasmic sperm injection were biopsied. After NGS, 60 informative polymorphic SNP markers located upstream and downstream of the FBN1 gene and its pathogenic mutation site were linked to individual alleles. Sanger sequencing further confirmed that 8 blastocysts carried the mutation NM_000138.5(FBN1):c.6037 + 2 T > C, while 6 did not. Four of the non-carriers were euploid verified by copy number variation results. A female infant without MFS was born at 37 weeks gestation after a subsequent frozen embryo transfer. In conclusion, the successful case indicates that SNP haplotyping using sibling embryos as a reference is applicable to PGT in monogenetic diseases. Abbreviations MFS: Marfan syndrome; PGT: preimplantation genetic testing; FBN1: fibrillin 1 gene; NGS: next-generation sequencing; SNP: single nucleotide polymorphism.

Genomic Association between SNP Markers and Diseases in the "Curraleiro Pé-Duro" Cattle.

Susceptibility to diseases is inherited and can be transmitted between populations. Single-nucleotide polymorphism (SNPs) in genes related to immune response is associated with diseases in cattle. This study investigated SNPs in the genomic region of cytokines in 702 samples of Curraleiro Pé-Duro cattle and associated them with the occurrence of antibodies in brucellosis, leptospirosis, neosporosis, leukosis, infectious bovine rhinotracheitis (IBR), and bovine viral diarrhea (BVD) tests. DNA samples were evaluated by the kompetitive allele-specific polymerase chain reaction (KASP) method to identify polymorphisms. The gametic phase and SNP haplotypes were determined with the help of PHASE 2.1.1 software. Haplotypes were associated with serological results against Brucella abortus, Leptospira sp., Neospora caninum, leukosis, infectious rhinotracheitis, and BVD using univariate analysis followed by logistic regression. Haplotype 2 of TLR2 was present in 70% of the animals that tested positive for N. caninum infection. Haplotypes of TLR10 and TLR6 and IL10RA were more common in seronegative animals. Haplotypes related to the gene IL10RA were associated with animals negative to all infections. Curraleiro Pé-Duro cattle presented polymorphisms related to resistance to bacterial, viral, and N. caninum infections.

Mapping and characterization QTLs for phenological traits in seven pedigree-connected peach families

BackgroundEnvironmental adaptation and expanding harvest seasons are primary goals of most peach [Prunus persica (L.) Batsch] breeding programs. Breeding perennial crops is a challenging task due to their long breeding cycles and large tree size. Pedigree-based analysis using pedigreed families followed by haplotype construction creates a platform for QTL and marker identification, validation, and the use of marker-assisted selection in breeding programs.ResultsPhenotypic data of seven F1 low to medium chill full-sib families were collected over 2 years at two locations and genotyped using the 9 K SNP Illumina array. Three QTLs were discovered for bloom date (BD) and mapped on linkage group 1 (LG1) (172–182 cM), LG4 (48–54 cM), and LG7 (62–70 cM), explaining 17–54%, 11–55%, and 11–18% of the phenotypic variance, respectively. The QTL for ripening date (RD) and fruit development period (FDP) on LG4 was co-localized at the central part of LG4 (40–46 cM) and explained between 40 and 75% of the phenotypic variance. Haplotype analyses revealed SNP haplotypes and predictive SNP marker(s) associated with desired QTL alleles and the presence of multiple functional alleles with different effects for a single locus for RD and FDP.ConclusionsA multiple pedigree-linked families approach validated major QTLs for the three key phenological traits which were reported in previous studies across diverse materials, geographical distributions, and QTL mapping methods. Haplotype characterization of these genomic regions differentiates this study from the previous QTL studies. Our results will provide the peach breeder with the haplotypes for three BD QTLs and one RD/FDP QTL to create predictive DNA-based molecular marker tests to select parents and/or seedlings that have desired QTL alleles and cull unwanted genotypes in early seedling stages.

Genome wide association mapping for heat tolerance in sub-tropical maize

BackgroundHeat tolerance is becoming increasingly important where maize is grown under spring season in India which coincide with grain filling stage of crop resulting in tassel blast, reduced pollen viability, pollination failure and barren ears that causes devastating yield losses. So, there is need to identify the genomic regions associated with heat tolerance component traits which could be further employed in maize breeding program.ResultsAn association mapping panel, consisting of 662 doubled haploid (DH) lines, was evaluated for yield contributing traits under normal and natural heat stress conditions. Genome wide association studies (GWAS) carried out using 187,000 SNPs and 130 SNPs significantly associated for grain yield (GY), days to 50% anthesis (AD), days to 50% silking (SD), anthesis-silking interval (ASI), plant height (PH), ear height (EH) and ear position (EPO) were identified under normal conditions. A total of 46 SNPs strongly associated with GY, ASI, EH and EPO were detected under heat stress conditions. Fifteen of the SNPs was found to have common association with more than one trait such as two SNPs viz. S10_1,905,273 and S10_1,905,274 showed colocalization with GY, PH and EH whereas S10_7,132,845 SNP associated with GY, AD and SD under normal conditions. No such colocalization of SNP markers with multiple traits was observed under heat stress conditions. Haplotypes trend regression analysis revealed 122 and 85 haplotype blocks, out of which, 20 and 6 haplotype blocks were associated with more than one trait under normal and heat stress conditions, respectively. Based on SNP association and haplotype mapping, nine and seven candidate genes were identified respectively, which belongs to different gene models having different biological functions in stress biology.ConclusionsThe present study identified significant SNPs and haplotype blocks associated with yield contributing traits that help in selection of donor lines with favorable alleles for multiple traits. These results provided insights of genetics of heat stress tolerance. The genomic regions detected in the present study need further validation before being applied in the breeding pipelines.

Association of PTPN22 single nucleotide polymorphisms with chronic spontaneous urticaria.

Chronic spontaneous urticaria (CSU) is thought to be an autoimmune disease in a subpopulation of patients. Protein tyrosine phosphatase-22 (PTPN22) polymorphisms are considered to be one of the strongest contributing factors to autoimmune diseases. In this study, we aimed to investigate the potential association of several PTPN22 single nucleotide polymorphisms (SNPs) with CSU in an Iranian population. A total of 93 CSU patients and 100 healthy individuals were included in this study. Five SNPs within the PTPN22 gene were analyzed using TaqMan genotyping assays. The frequency of alleles, genotypes, and haplotypes of PTPN22 SNPs (rs12760457, rs2476601, rs1310182, rs1217414, and rs33996649) was investigated. A significantly higher prevalence of the rs1310182 T allele was observed among patients compared with controls [OR = 1.75 (95% CI: 1.17-2.63); P = 0.007]. In addition, the rs1310182 CC genotype and TT genotype were 0.47 and 2.06 times more common in patients, respectively (P = 0.03). Moreover, haplotype analysis demonstrated that CGCGC, CGTGC, and TGCGC (P < 0.001) were significantly associated with CSU. No significant differences were observed between the patients and controls in the other analyzed PTPN22 SNPs. Polymorphisms of the PTPN22 gene are associated with an increased susceptibility to CSU in the studied Iranian population.

Single nucleotide polymorphism‐based haplotypes associated with Meloidogyne javanica resistance in Brazilian soybean germplasm

AbstractThe root‐knot nematode (RKN) species Meloidogyne javanica (MJ) causes substantial root damage and yield loss in susceptible soybean [Glycine max (L.) Merr.] cultivars. In this study, a genome wide association study (GWAS) was undertaken to identify genomic regions controlling RKN resistance in a soybean association‐mapping panel, using single nucleotide polymorphism (SNP) markers and haplotype information. This study was carried out with a sample (n = 124) from the Coodetec soybean gene bank, including some commercial Brazilian varieties. For the phenotypic evaluations MJ inoculum was obtained from roots of cultivar CD 206, a highly susceptible soybean used to maintain MJ for studies at Coodetec. The cultivars CD 208 and BRS CONQUISTA were used as resistant checks while CD 206, R7, and Nidera NA 5909 RG were used as susceptible checks and all 124 lines were genotyped with 6,000 SNP markers. MJ resistance determinants in the soybean panel were linked to SNPs with significant effects, with nine SNPs distributed along chromosomes 7, 13, and 20. The observed average MJ resistance in the group of soybean entries with haplotype GCT, ACC, ACT, and GCC in the markers Gm20_44446670_G_A, Gm13_29739984_C_A and Gm07_8166605_T_C, respectively, represents moderately resistant genotypes. Gm13_29739984_C_A and Gm07_8166605_T_C discriminated resistant and susceptible cultivars better than the marker Gm20_44446670_G_A. These results are particularly promising for soybean‐breeding programs, by not only identifying new resistance‐associated haplotypes, but also suggesting new genetic mechanisms in RKN‐resistance sources.

Host genetic control of natural killer cell diversity revealed in the Collaborative Cross

Natural killer (NK) cells are innate effectors armed with cytotoxic and cytokine-secreting capacities whose spontaneous antitumor activity is key to numerous immunotherapeutic strategies. However, current mouse models fail to mirror the extensive immune system variation that exists in the human population which may impact on NK cell-based therapies. We performed a comprehensive profiling of NK cells in the Collaborative Cross (CC), a collection of novel recombinant inbred mouse strains whose genetic diversity matches that of humans, thereby providing a unique and highly diverse small animal model for the study of immune variation. We demonstrate that NK cells from CC strains displayed a breadth of phenotypic and functional variation reminiscent of that reported for humans with regards to cell numbers, key marker expression, and functional capacities. We took advantage of the vast genetic diversity of the CC and identified nine genomic loci through quantitative trait locus mapping driving these phenotypic variations. SNP haplotype patterns and variant effect analyses identified candidate genes associated with lung NK cell numbers, frequencies of CD94+ NK cells, and expression levels of NKp46. Thus, we demonstrate that the CC represents an outstanding resource to study NK cell diversity and its regulation by host genetics.

Successful four-factor preimplantation genetic testing: α- and β-thalassemia, human leukocyte antigen typing, and aneuploidy screening

ABSTRACT Our study established an effective next-generation sequencing (NGS) protocol for four-factor preimplantation genetic testing (PGT) using α- and β-thalassemia, human leukocyte antigen (HLA) typing, and aneuploidy screening. Three couples, in whom both partners were α- and β-double thalassemia carriers, underwent PGT between 2016 and 2018. These individuals sought an opportunity for hematopoietic stem cell transplantation to save their children from β-thalassemia major. A total of 35 biopsied trophectoderm samples underwent multiple displacement amplification (MDA). PGT for α- and β-thalassemia and HLA typing were performed on MDA products using NGS-based single-nucleotide polymorphism (SNP) haplotyping. Although two samples failed MDA, 94.3% (33/35) of samples were successfully amplified, achieving conclusive PGT results. Furthermore, 51.5% (17/33) of the embryos were diagnosed as unaffected non-carriers or carriers. Of the 17 unaffected embryos, nine (52.9%) were tested further and identified as euploid via NGS-based aneuploid screening, in which five had HLA types matching affected children. One family did not achieve any unaffected euploid embryos. The two other families transferred HLA-matched and unaffected euploid embryos, resulting in two healthy ‘savior babies.’ NGS-PGT results were confirmed in prenatal diagnosis. Therefore, NGS-SNP was effective in performing PGT for multipurpose detection within a single PGT cycle.

Association of ISL1 polymorphisms and eosinophilic levels among otitis media patients.

BackgroundOtitis media (OM) is a middle ear inflammatory complex disorder involving genetic and environmental factors. It onsets during childhood and often recurs and perplexes in genetically susceptible patients. Previously, murine models had shown the association of ISL LIM homeobox 1 (ISL1) gene with otitis media with effusion.AimTo investigate the association of ISL1 genetic variants with otitis media.Subjects and methodsA total of 285 cases and 277 controls were recruited for the study. The entire coding region of ISL1 gene was genotyped using Sanger sequencing or single‐strand conformation polymorphism methods. Genotype, haplotype, in silico analysis, and linkage disequilibrium analysis were performed.ResultsThe variants rs2303751 (c.504A>G) and rs121913540 (c.513G>A) were associated with OM, and the OR (95%CI) was 0.74 (0.57–0.95) and 0.43 (0.20–0.91), respectively. Besides, the rs2303751 AA genotype was associated with elevated eosinophil numbers in OM when compared to controls. The 5 SNP haplotype analysis of SNPs c.‐492A>G, c.504A>G, c.513G>A, c.576C>T, and c.*651A>T revealed A‐A‐G‐C‐A to be a risk haplotype in females whereas the 3 SNP haplotype analysis of SNPs c.504A>G, c.513G>A, and c.567C>T suggested G‐A‐C as protective and A‐G‐C to be a risk haplotype for otitis media.ConclusionOurs is the first report which shows a significant association of ISL1 variants (rs2303751 and rs121913540) with hearing‐related disorder like otitis media in humans. These results implicate the possible role of ISL1 gene in the etiopathology of otitis media. The replication of the study in other ethnic populations may strengthen our findings.

Long non-coding RNA ANRIL polymorphisms in papillary thyroid cancer and its severity

ABSTRACT Background: Long non-coding RNAs are likely to have a role in the pathogenesis of many diseases, including cancer. We hypothesised an effect of certain ANRIL single nucleotide polymorphisms (SNPs) in papillary thyroid cancer. Methods: Genomic ANRIL SNPs in rs11333048, rs4977574, rs1333040 and rs10757274 were determined in 134 papillary thyroid cancer patients and 155 age- and sex-matched controls. Results: None of the ANRIL SNPs were individually linked to papillary thyroid cancer. However, the AAAC haplotype (A from rs11333048, A from rs4977574, A from rs1333040 and C from rs10757274, respectively) showed a protective effect from papillary thyroid cancer whilst the CAAC and CAGT haplotypes were associated with cancer. The rs1333048 CC variant was more frequent in patients with larger tumour size (≥1 cm) in a recessive model (OR 3.4 [95%CI, 1.1–11], P = 0.035). The rs4977574 AC variant was associated with smaller tumour size in an over-dominant model (OR 0.4 [95%CI, 0.2–1.0], P = 0.041). SNPs in rs10757274 (AA: p = 0.045) and rs1333040 (CC: p = 0.019) are linked to a lower likelihood of III–IV cancer stages in dominant or codominant models. Conclusions: Certain haplotypes of ANRIL SNPs are associated with papillary thyroid cancer. ANRIL rs1333048 and rs4977574 variants were associated with larger and smaller tumour sizes, respectively. rs10757274 and rs1333040 variants might lead to lower III–IV cancer stages. These SNPs may be important in the diagnosis of this form of thyroid cancer.

Regulation of the Acute Sickness Response by the P2RX7 Receptor.

The acute sickness response to infection is a stereotyped set of illness manifestations initiated by proinflammatory signals in the periphery but mediated centrally. P2RX7 is a highly polymorphic gene encoding an ATP-gated cationic pore, widely expressed on immune cells and the brain, and regulating the NLRP3 inflammasome, as well as diverse neural functions. Associations between P2RX7 genotype, pore activity, and illness manifestations were examined in a cohort with acute viral and bacterial infections (n = 484). Genotyping of 12 P2RX7 function-modifying single-nucleotide polymorphisms (SNPs) was used to identify haplotypes and diplotypes. Leucocyte pore activity was measured by uptake of the fluorescent dye, YO-PRO-1, and by ATP-induced interleukin-1β (IL-1β) release. Associations were sought with scores describing the symptom domains, or endophenotypes, derived from principal components analysis. Among the 12 SNPs, a 4-SNP haplotype block with 5 variants was found in 99.5% of the subjects. These haplotypes and diplotypes were closely associated with variations in pore activity and IL-1β production. Homozygous diplotypes were associated with overall illness severity as well as fatigue, pain, and mood disturbances. P2RX7 signaling plays a significant role in the acute sickness response to infection, likely acting in both the immune system and the brain.

Accuracy of Imputation of Microsatellite Markers from a 50K SNP Chip in Spanish Assaf Sheep.

Simple SummaryParentage misassignments directly affect genetic gain in traditional breeding programs. The use of genetic markers facilitates parentage verification. In sheep, microsatellite markers and single nucleotide polymorphism (SNP) markers have been proposed by the International Society of Animal Sciences (ISAG) for parentage testing. Since the implementation of genomic selection, the microsatellite information used for parental testing in previous generations is gradually being replaced by SNPs. However, parentage verifications should all be performed using the same technology. A strategy for transitioning from microsatellites to SNP markers, while avoiding extra genotyping costs, is the imputation of microsatellite alleles from SNP haplotypes. This study aims to identify the optimum approach, using a minimum number of SNPs to accurately impute microsatellite markers and developing a low-density SNP chip for parentage verification in the Assaf sheep breed. The imputation approach described here reached high accuracies using a low number of SNP markers, which supports the development of a low-density SNP chip that could avoid the problems of genotyping with both technologies, being a cost-effective method for parentage testing. This study will help sheep breeders to perform parentage verification when different genotyping platforms have been used across generations.Transitioning from traditional to new genotyping technologies requires the development of bridging methodologies to avoid extra genotyping costs. This study aims to identify the optimum number of single nucleotide polymorphisms (SNPs) necessary to accurately impute microsatellite markers to develop a low-density SNP chip for parentage verification in the Assaf sheep breed. The accuracy of microsatellite marker imputation was assessed with three metrics: genotype concordance (C), genotype dosage (length r2), and allelic dosage (allelic r2), for all imputation scenarios tested (0.5–10 Mb microsatellite flanking SNP windows). The imputation accuracy for the three metrics analyzed for all haplotype lengths tested was higher than 0.90 (C), 0.80 (length r2), and 0.75 (allelic r2), indicating strong genotype concordance. The window with 2 Mb length provides the best accuracy for the imputation procedure and the design of an affordable low-density SNP chip for parentage testing. We additionally evaluated imputation performance under two null models, naive (imputing the most common allele) and random (imputing by randomly selecting the allele), which in comparison showed weak genotype concordances (0.41 and 0.15, respectively). Therefore, we describe a precise methodology in the present article to impute multiallelic microsatellite genotypes from a low-density SNP chip in sheep and solve the problem of parentage verification when different genotyping platforms have been used across generations.

Use of SNPs from Illumina BovineSNP50K BeadChip v3 for imputation of microsatellite alleles for parentage verification and QTL reporting

The present study aimed to test the possibility of avoiding expensive retesting of the whole parental generation for single nucleotide polymorphisms (SNPs), to provide additional analysis of microsatellites in offspring in the transitional period and to analyse the likelihood of imputation of the International Society for Animal Genetics-recommended microsatellite markers from selected SNPs. The imputation and pedigree verification of 9 520 animals (representing 84 dairy bulls, 285 dairy cows, 3 202 beef bulls and 5 949 beef cows) were analysed by the method using 9 410 SNP haplotypes (incorporating an average of 73 SNPs per haplotype). The imputation method was confirmed to allow the parentage verification of up to 87% of the analysed animals without the need for retesting. The most problematic locus was TGLA53, with only 78% successful imputation. Seven loci (BM2113, ETH225, TGLA227, BM1824, SPS115, TGLA122 and TGLA126) had more than 90% imputing accuracy and success of imputation. The success of imputation also depends on the breed and the call rate of the test results. The highest imputation accuracy was found for the Holstein breed; the other six breeds had over 90% successful imputation rates, four breeds had imputation rates between 85.0 and 89.9%, and ten breeds (rarely bred in the Czech Republic) had imputation rates below 85.0%. A call rate of SNP tests lower than 90% indicates problems with haplotype construction and thus deterioration in the success of imputation. The analysis of a possibility of using all possible information from Illumina BovineSNP50K BeadChip v3 showed 109 SNPs encoding 51 quantitative trait loci markers. Haplotypes were designed for interpretation of the most important markers for diseases, exterior and performance. The most important markers for Holstein breeders were chosen as kappa- (variants A, B and E) and beta-casein (variants A1, A2), Holstein haplotypes affecting fertility (HH1, HH3, and HH4) and loci causing genetic defects, bovine leukocyte adhesion deficiency and deficiency of uridine monophosphate synthetase. The results estimated from bovine bead chips corresponded to the expected distribution of the incidence of these traits in the population and were verified by PCR-RFLP tests.

The association between SLC16A11 haplotype and lipid metabolism in Japanese patients with type 2 diabetes

Solute carrier (SLC) 16A11 has been reported as a risk gene for type 2 diabetes (T2D). However, the physiological function of SLC16A11 has not yet been clarified, and the relationship between SLC16A11 and T2D condition remains unclear. Therefore, we performed an association analysis between the SLC16A11 genotype and T2D pathology. The SLC16A11 genotype was determined by direct sequencing in 85 Japanese patients with T2D. The genotypes were analyzed by Mann–Whitney’s U test and Chi-square test. Six single nucleotide polymorphisms (SNPs) were detected in the SLC16A11 gene, and five of them formed a haplotype (5SNP haplotype). The 5SNP haplotype carriers had significantly higher fasting plasma glucose (FPG), total cholesterol (T-CHO), and low-density lipoprotein cholesterol (LDL-C) than the noncarriers. The SLC16A11 genotype affected the values of laboratory parameters for T2D, particularly of blood lipids. The function of SLC16A11 may be related to lipid metabolism.

Intracellular hyaluronic acid-binding protein 4 (HABP4): a candidate tumor suppressor in colorectal cancer.

Hyaluronic Acid-binding protein 4 (HABP4) is a regulatory protein of 57 kDa that is functionally involved in transcription regulation and RNA metabolism and shows several characteristics common to oncoproteins or tumor suppressors, including altered expression in cancer tissues, nucleus/cytoplasm shuttling, intrinsic lack of protein structure, complex interactomes and post translational modifications. Its gene has been found in a region on chromosome 9q22.3-31, which contains SNP haplotypes occurring in individuals with a high risk for familial colon cancer. To test a possible role of HABP4 in tumorigenesis we generated knockout mice by the CRISPR/Cas9 method and treated the animals with azoxymethane (AOM)/dextran sodium sulfate (DSS) for induction of colon tumors. HABP4–/– mice, compared to wild type mice, had more and larger tumors, and expressed more of the proliferation marker proteins Cyclin-D1, CDK4 and PCNA. Furthermore, the cells of the bottom of the colon crypts in the HABP4–/– mice divided more rapidly. Next, we generated also HABP4–/– HCT 116 cells, in cell culture and found again an increased proliferation in clonogenic assays in comparison to wild-type cells. Our study of the protein expression levels of HABP4 in human colon cancer samples, through immunohistochemistry assays, showed, that 30% of the tumors analyzed had low expression of HABP4. Our data suggest that HABP4 is involved in proliferation regulation of colon cells in vitro and in vivo and that it is a promising new candidate for a tumor suppressor protein that can be explored both in the diagnosis and possibly therapy of colon cancer.

Tracing the mutated HTT and haplotype of the African ancestor who spread Huntington disease into the Middle East

PurposeWe aimed to determine the origin and genetic characteristics of Huntington disease (HD) in the Middle East. MethodsWe performed genetic and genealogical analyses to establish the ancestral origin of the HTT pathgenic variant from a large kindred from Oman (hereafter called the OM-HD-01 pedigree) by single-nucleotide polymorphism and dense haplotype analysis genotyping. ResultsWe traced the oldest ancestry of the largest, eight-generation, OM-HD-01 pedigree (n=302 subjects, with 54 showing manifest HD) back to sub-Saharan Africa and identified a unique HD haplotype carried by all pedigree members, which consisted of portions of the C6 and C9 haplotypes and was carried by all affected members. Such a unique HD haplotype was of African origin and appeared to be associated with large CAG repeat expansions on average and high frequency of juvenile-onset HD. Three other families from the same area were also identified and found carrying a Caucasian HD haplotype A, also shared by most families of Arab ancestry. ConclusionMutated HTT spread into Middle East with a unique haplotype of African origin, appeared to be associated with juvenile-onset, a HD condition frequently occurring in Black Africans, and may have a significant impact on further development of novel targeted genetic therapies.

CMIP SNPs and their haplotypes are associated with dyslipidaemia and clinicopathologic features of IgA nephropathy.

The relationship between serum lipid profiles and related clinicopathologic features of IgA nephropathy (IgAN) and c-Maf-inducing protein (CMIP) gene polymorphisms is unclear. The present study was designed to examine the effect of CMIP single-nucleotide polymorphisms (SNPs) on dyslipidaemia and clinicopathologic features of IgAN. Clinical and pathological data from patients with IgAN diagnosed at the First Affiliated Hospital of Guangxi Medical University were collected. DNA was extracted from blood samples. CMIP rs2925979 and CMIP rs16955379 genotypes were determined by PCR and direct sequencing. Among 543 patients, 281 had dyslipidaemia (51.7%). Compared with the non-dyslipidaemia group, the dyslipidaemia group exhibited higher blood pressure, blood urea nitrogen, uric acid, and body mass index; higher prevalence of oedema, haematuria, tubular atrophy, and interstitial fibrosis; and lower albumin and estimated glomerular filtration rate. In the dyslipidaemia group, the frequency of C allele carriers was higher than that of non-C allele carriers for rs16955379. Multivariate linear regression analysis showed that total cholesterol, low-density lipoprotein and high-density lipoprotein were associated with rs16955379C allele carriers. Apolipoprotein B was associated with A allele carriers of rs2925979. Linkage disequilibrium was observed between rs16955379 and rs2925979, and rs2925979G-rs16955379T was the most common haplotype. The frequencies of the four CMIP SNP haplotypes differed between dyslipidaemia and non-dyslipidaemia groups in IgAN (P<0.05, for all above). Dyslipidaemia is a common complication in IgAN patients, and those with dyslipidaemia present poor clinicopathologic features. CMIP SNPs and their haplotypes are closely correlated with the occurrence of dyslipidaemia and clinicopathologic damage in IgAN patients.

Association of ERAP2 polymorphisms in Colombian HLA-B27+ or HLA-B15+ patients with SpA and its relationship with clinical presentation: axial or peripheral predominance

ObjectiveTo determine the association between endoplasmic reticulum aminopeptidase (ERAP)1 and ERAP2 single-nucleotide polymorphisms (SNPs) and human leukocyte antigens (HLA)-B27+ or HLA-B15+ patients with spondyloarthritis (SpA).Methods104 patients with SpA according to...

Genetic diversity of MHC-B in 12 chicken populations in Korea revealed by single-nucleotide polymorphisms.

This study used a single-nucleotide polymorphism (SNP) panel to characterise the diversity in the major histocompatibility complex B region (MHC-B) in 12 chicken populations in Korea. Samples were genotyped for 96 MHC-B SNPs using an Illumina GoldenGate genotyping assay. The MHC-B SNP haplotypes were predicted using 58 informative SNPs and a coalescence-based Bayesian algorithm implemented by the PHASE program and a manual curation process. In total, 117 haplotypes, including 24 shared and 93 unique haplotypes, were identified. The unique haplotype numbers ranged from 0 in Rhode Island Red to 32 in the Korean native commercial chicken population 2 ("Hanhyup-3ho"). Population and haplotype principal component analysis (PCA) indicated no clear population structure based on the MHC haplotypes. Three haplotype clusters (A, B, C) segregated in these populations highlighted the relationship between the haplotypes in each cluster. The sequences from two clusters (B and C) overlapped, whereas the sequences from the third cluster (A) were very different. Overall, native breeds had high genetic diversity in the MHC-B region compared with the commercial breeds. This highlights their immune capabilities and genetic potential for resistance to many different pathogens.

A minor allele of the haplotype located in the 19q13 loci is associated with a decreased risk of hyper-LDL-cholesterolemia, and a balanced diet and high protein intake can reduce the risk

BackgroundAlthough the human chromosome 19q13 loci are reported to be associated with hyper-LDL-cholesterolemia, the haplotype of single nucleotide polymorphism (SNP) has not been studied. Therefore, the association of the haplotype in 19q13 loci with hyper-LDL-cholesterolemia was determined and their interactions with lifestyles and nutrient intakes were evaluated in 28,445 Koreans aged > 40 years.MethodsSNPs were selected from 19q13 loci that had an association with hyper-LDL-cholesterolemia with the adjustment of confounders (age, gender, area of residence, and body mass index). Haplotype was constructed from the selected SNPs. An adjusted odds ratio of the haplotype for hyper-LDL-cholesterolemia and the interaction between haplotype and lifestyles was analyzed after adjusting for covariates.ResultsHyper-LDL-cholesterolemia had an association with apolipoprotein E (APOE)_ rs7259620, translocase of outer mitochondrial membrane 40(TOMM40)_rs157581, poliovirus receptor-related 2(PVRL2)_rs403155, exocyst complex component 3-like 2(EXOC3L2)_ rs10406604 and CD3e molecule-associated protein (CD3EAP)_rs3212986 in 19q13. The haplotype of these SNPs had a negative association with hyper-total-cholesterolemia and hyper-LDL-cholesterolemia by 0.669 and 0.684 times, respectively, after adjusting for covariates. The incidence of cardiovascular diseases, especially myocardial infarction, had a negative association with the minor alleles. The balanced diet pattern (BD) and protein intake had a significant interaction with the haplotype: the major-allele of the haplotype exhibited a positive association with hyper-LDL-cholesterolemia, compared to the minor allele, only when combined with a high intake of BD. The participants with the minor allele exhibited a lower hyper-LDL-cholesterolemia risk compared to those with the major allele only with high protein intake.ConclusionThe minor allele of haplotype located in 19q13 loci protected against hyper-LDL-cholesterolemia, especially with BD and high protein intake. The minor allele also had a negative association with myocardial infarction events.