Complete Linkage Disequilibrium Research Articles

Functional Evaluation of ZNF350 Missense Genetic Variants Associated with Breast Cancer Susceptibility.

ZNF350, a BRCA1-interacting protein, could mediate BRCA1-induced sequence-specific transcriptional repression of several genes, including GADD45α. As a potential breast cancer susceptibility gene, single nucleotide polymorphisms (SNPs), especially missense SNPs, may influence the transcriptional repression of its target tumor suppressor genes and individuals' breast cancer risk. Using the gene-based haplotype-tagging SNPs strategy, we evaluated the association between six ZNF350 polymorphisms and breast cancer risk in a case-control set from a northern Chinese population. The impact of ZNF350 variations on transcriptional repression of GADD45α was also examined. It was found that ZNF350 rs2278420 (L66P) and rs2278415 (S501R) missense genetic variants are in complete linkage disequilibrium and have a significant impact on inter-individual susceptibility to breast cancer. Additionally, ZNF350 GGCGT or GGCGC haplotype is also associated with a significantly increased breast cancer risk compared with the GGCAC haplotype. ZNF350 L66P variant modifies the risk of breast cancer not only by itself but also in a gene-environment interaction manner with age, age at menarche, menopause status, or estrogen receptor status. Interestingly, we observed that ZNF350 L66P and S501R SNPs could weaken the capability of ZNF350-mediated GADD45α transcription repression and it may be an underlying mechanism of the observed epidemiological associations. Our results highlight ZNF350 as an important gene in human mammary oncogenesis and ZNF350 missense genetic polymorphisms confer susceptibility to breast cancer.

Relationship between genetic variation at PPP1R3B and levels of liver glycogen and triglyceride.

These observations are consistent with the notion that the minor allele of rs4841132 promotes a mild form of hepatic glycogenosis that is associated with hepatic injury. (Hepatology 2018;67:2182-2195).

Extent of linkage disequilibrium and effective population size of the Landrace population in Korea.

ObjectiveThe genetic diversity of the Landrace population, a representative maternal pig breed in Korea, is important for genetic improvement. Previously, the effective population size (Ne) has been used to infer the genetic diversity of a population of interest. In this study, we aimed to use single nucleotide polymorphism (SNP) data to characterize linkage disequilibrium (LD) and the Ne of the Korean Landrace population.MethodsWe genotyped 1,128 Landrace individuals from three representative Korean major grand-grand-parent (GGP) farms using the Illumina PorcineSNP60 version2 BeadChip, which covers >61,565 SNPs located across all autosomes and mitochondrial and sex chromosomes. We estimated the expected LD and current Ne, as well as ancestral Ne.ResultsIn the Korean Landrace population, the mean LD (r2) of 3.698 million SNP pairs was 0.135±0.204. The mean r2 decreased slowly with as the distance between SNPs increased, and remained constant beyond 3 Mb. According to the r2 calculations, 8,085 of 3.698 million SNP pairs were in complete LD. The current Ne (±standard deviation) of the Korean Landrace population is approximately 92.27 [79.46; 105.07] individuals. The ancestral Ne exhibited a slow and steady decline from 186.61 to 92.27 over the past 100 generations. Additionally, we observed more a rapid Ne decrease from the past 20 to 10 generations ago, compared with other intervals.ConclusionWe have presented an overview of LD and the current and ancestral Ne values in the Korean Landrace population. The mean LD and current Ne for the Korean Landrace population confirm the genetic diversity and reflect the history of this pig population in Korea.

Polymorphisms in the ICOS/CD28-ICOSL pathway are related to capecitabine-based chemotherapy response in advanced colon cancer patients

Polymorphisms within a gene’s 3′-UTR may modulate posttranscriptional regulation of gene expression, and may explain individual sensitivity of chemotherapy. To investigate the correlation between single nucleotide polymorphisms (SNPs) in 3′-UTRs of B7/CD28 family genes and the response of capecitabine-based chemotherapy in colon cancer, 16 SNPs were identified in 274 advanced colon cancer patients. Statistical analysis indicated that ICOS rs1559931, rs4404254, and rs4675379 were in complete linkage disequilibrium and significantly associated with chemotherapy response. Heterozygous patients with rs1559931 G/A (31.34% vs 48.29%; P = 0.016), rs4404254 T/C (30.43% vs 48.77%; P = 0.011), or rs4675379 G/C (28.13% vs 49.04%; P = 0.004) genotypes showed poorer response to chemotherapy compared to wildtype patients. Moreover, three SNPs, including ICOSL rs15927, ICOSL rs3804033 and CD28 rs3181113, were significantly associated with the occurrence of side effects of chemotherapy. In addition, patients with ICOSL rs15927 G/G (78.26%), ICOSL rs3804033 G/G (76.00%), or CD28 rs3181113 T/T (82.05%) were more prone to enduring adverse events compared to patients bearing other polymorphisms. Taken together, our findings demonstrated that polymorphisms in the 3′-UTRs of genes in the ICOS/CD28-ICOSL pathway may influence the efficacy and occurrence of adverse events of capecitabine-based chemotherapy in advanced colon cancer patients.

Genetic Reduction in Left Ventricular Protein Kinase C-α and Adverse Ventricular Remodeling in Human Subjects

Inhibition of PKC-α (protein kinase C-α) enhances contractility and cardioprotection in animal models, but effects in humans are unknown. Genotypes at rs9912468 strongly associate with PRKCA expression in the left ventricle, enabling genetic approaches to measure effects of reduced PKC-α in human populations. We analyzed the cis expression quantitative trait locus for PRKCA marked by rs9912468 using 313 left ventricular specimens from European Ancestry patients. The forward strand minor allele (G) at rs9912468 is associated with reduced PKC-α transcript abundance (1.7-fold reduction in minor allele homozygotes, P=1×10-41). This association was cardiac specific in expression quantitative trait locus data sets that span 16 human tissues. Cardiac epigenomic data revealed a predicted enhancer in complete (R2=1.0) linkage disequilibrium with rs9912468 within intron 2 of PRKCA. We cloned this region and used reporter constructs to verify cardiac-specific enhancer activity in vitro in cardiac and noncardiac cells and in vivo in zebrafish. The PRKCA enhancer contains 2 common genetic variants and 4 haplotypes; the haplotype correlated with the rs9912468 PKC-α-lowering allele (G) showed lowest activity. In contrast to previous reports in animal models, the PKC-α-lowering allele is associated with adverse left ventricular remodeling (higher mass, larger diastolic dimension), reduced fractional shortening, and higher risk of dilated cardiomyopathy in human populations. These findings support PKC-α as a regulator of the human heart but suggest that PKC-α inhibition may adversely affect the left ventricle depending on timing and duration. Pharmacological studies in human subjects are required to discern potential benefits and harms of PKC-α inhibitors as an approach to treat heart disease.

Lack of association between rheumatoid arthritis and genetic variants rs10889677, rs11209026 and rs2201841 of IL-23R gene

IntroductionRheumatoid arthritis (RA) is an autoimmune diseases, where different genetic variants in cytokine genes may play a pathogenic role. A GWAS in autoimmune diseases highlighted the IL-23R gene as a one of the susceptibility factors. We examined three candidate single nucleotide polymorphisms (SNPs) rs10889677, rs11209026 and rs2201841 of the IL-23R gene, as well as determined their possible association with RA in a Polish population. Patients and methodsThe IL-23R gene polymorphisms were genotyped for 422 RA patients and 348 healthy individuals using TaqMan SNP genotyping assay. ResultsThe genotypes frequency did not deviate from HWE in each examined group. A comparison of the allele as well as genotype frequencies of the IL-23R polymorphisms under codominant, dominant and recessive genetic model revealed no significant differences between RA patients and healthy subjects. We also demonstrated that IL-23R rs2201841 and rs11209026 as well as rs11209026 and rs10889677 were in complete linkage disequilibrium (D′=1.0). Our genotype-phenotype analysis demonstrated that in carriers of rs10889677C and/or rs2201841A allele the RF, extra-articular manifestations and erosion were more frequent present than in patients with rs10889677A and/or rs2201841A allele, although this association was not significant. DiscussionPresent findings indicated that the autoimmune disease-associated genetic variants in IL-23R gene are not associated with RA in the Polish population.

Dual-specificity phosphatase 6 genetic variants associated with risk of lung squamous cell carcinoma in Han Chinese.

Nonsmall cell lung cancer (NSCLC) mainly contains adenocarcinoma (AC) and squamous cell carcinoma (SqCC). This study investigated single nucleotide polymorphism (SNP) of topoisomerase II alpha (TOP2A) and dual-specificity phosphatase 6 (DUSP6) in a hospital-based case and control cohort of individuals for association with risk of different histological subtypes of NSCLC. A total of 454 (237 SqCC and 217 AC) NSCLC patients, and 454 healthy controls were recruited for analysis of TOP2A rs471692 and DUSP6 rs2279574 genotypes using the TaqMan polymerase chain reaction technique. TOP2A rs471692 and DUSP6 rs2279574 SNPs were in complete linkage disequilibrium; however, frequency of DUSP6 rs2279574 genotype was significantly different between the case and control, that is, DUSP6 rs2279574a/A and A/C genotypes might contribute to an increased risk of lung squamous carcinoma compared with the C/C genotype. Moreover, DUSP6 rs2279574 AA genotype was also significantly associated with advanced stages of lung cancer. In contrast, frequency of the TOP2A rs471692 genotype had no association between cases and controls (P = 0.906). Genotype frequency of DUSP6 rs2279574 was 11.9% for C/C, 43.6% for C/A, and 44.5% for A/A in the case versus 16.7% C/C, 43.4% C/A, and 39.9% A/A in the control population (χ2 = 3.136, P= 0.077 by Hardy-Weinberg equilibrium test [HWE]). The genotype frequency of TOP2A rs471692 was 50.0% for C/C, 41.6% for C/T, and 8.4% for T/T in the case versus 50.2% C/C, 43.0% C/T, and 6.8% T/T in the control populations (χ2 = 0.023, P= 0.879 by HWE test). Individuals are carrying DUSP6 rs2279574 AA and AC genotypes associated with an increased risk in developing lung squamous carcinoma in Han Chinese and with advanced NSCLC stages.

Genetic variation in CFH predicts phenytoin-induced maculopapular exanthema in European-descent patients.

ObjectiveTo characterize, among European and Han Chinese populations, the genetic predictors of maculopapular exanthema (MPE), a cutaneous adverse drug reaction common to antiepileptic drugs.MethodsWe conducted a case-control genome-wide association study of autosomal genotypes, including Class I and II human leukocyte antigen (HLA) alleles, in 323 cases and 1,321 drug-tolerant controls from epilepsy cohorts of northern European and Han Chinese descent. Results from each cohort were meta-analyzed.ResultsWe report an association between a rare variant in the complement factor H–related 4 (CFHR4) gene and phenytoin-induced MPE in Europeans (p = 4.5 × 10–11; odds ratio [95% confidence interval] 7 [3.2–16]). This variant is in complete linkage disequilibrium with a missense variant (N1050Y) in the complement factor H (CFH) gene. In addition, our results reinforce the association between HLA-A*31:01 and carbamazepine hypersensitivity. We did not identify significant genetic associations with MPE among Han Chinese patients.ConclusionsThe identification of genetic predictors of MPE in CFHR4 and CFH, members of the complement factor H–related protein family, suggest a new link between regulation of the complement system alternative pathway and phenytoin-induced hypersensitivity in European-ancestral patients.

Sequence analysis of the N-acetyltransferase 2 gene (NAT2) among Jordanian volunteers

ABSTRACTThe present study aimed to identify the NAT2 haplotypes, linkage disequilibrium, and novel NAT2 genetic variants among Jordanian population. We isolated the genomic DNA from 68 healthy, Arab, unrelated Jordanian volunteers to amplify the protein-coding region of NAT2 gene by polymerase chain reaction (PCR). Then, the amplified PCR products were sequenced using Applied Biosystems Model (ABI3730x1). It is found that the allele frequencies of known NAT2 genetic variants 191G>A, 282C>T, 341T>C, 481C>T, 590G>A, and 803A>G were 0.7, 26.5, 48.5, 35.3, 30.9, and 32.4%, respectively. The NAT2 allele frequencies were generally similar to those of white Europeans but different from those of Asian and African populations. The most common NAT2 haplotype was NAT2*5B with a frequency of 29.3%. According to the NAT2 haplotype frequencies, 72% (95% confidence interval 61.4–82.7%) of the volunteers were slow encoding NAT2 haplotype acetylators. The NAT2*5 represented variants 341T>C and 481C>T were in strong but not complete linkage disequilibrium (D′ = 0.8, r2 = 0.63). In addition, this study found a novel nonsynonymous NAT2 436G>A genetic variant with low frequency (0.7%). However, this novel variant was predicted to be tolerated and not harmful to the NAT2 protein, using in silico prediction tools. It is concluded that the frequency of slow encoding NAT2 haplotype was high among Jordanian volunteers, which may have effects on drug responses and susceptibility to some diseases, such as cancers.

The SETDB2 locus: evidence for a genetic link between handedness and atopic disease.

The gene SETDB2, which mediates aspects of laterality in animal model systems, has recently been linked with human handedness as measured continuously on a scale from strong left to strong right. By contrast, it was marginally associated with a left-right dichotomous measure, and it showed no evidence of association with absolute handedness strength independent of direction. We genotyped the SETDB2 handedness-associated single nucleotide polymorphism, rs4942830, in a large healthy population likewise phenotyped for continuous, absolute, and dichotomous handedness variables. Our results demonstrated significant effects of rs4942830 genotype on continuous handedness, and weaker, marginal effects on dichotomous handedness, but no effects on absolute handedness. These results help to establish the locus marked by the SNP rs4942830 as a strong candidate for mediating human handedness. Intriguingly, rs4942830 is also in complete linkage disequilibrium with rs386770867, a polymorphism recently shown to affect human serum levels of IgE production and other atopic phenotypes. These findings implicate this locus in the longstanding links of handedness with asthma and other atopic diseases.

Association between MTHFR microRNA binding site polymorphisms and methotrexate concentrations in Chinese pediatric patients with acute lymphoblastic leukemia.

The pharmacokinetics and therapeutic response to methotrexate (MTX) display large variability in the treatment of acute lymphoblastic leukemia (ALL). The aim of the present study was to investigate the association of two microRNA (miRNA) binding site polymorphisms (rs3737966 G>A and rs35134728 DEL/TTC) in the 3'-untranslated region of MTHFR with serum MTX concentrations, in a Chinese pediatric population with ALL. Genotyping for MTHFR rs3737966 and rs35134728 in 144 children with ALL was performed using the Sequenom MassArray system (Sequenom, San Diego, CA, USA). Serum MTX concentrations were measured by a fluorescence polarization immunoassay 24h (C24h ) and 42h (C42h ) after administration. The effects of the polymorphisms on concentration-to-dose (C/D) ratios of MTX were assessed. Complete linkage disequilibrium between rs3737966 and rs35134728 polymorphisms (r2 =1) was found in the study population. The minor allele frequency observed in the present study (17.4%) was significantly lower than those in European and African samples reported in the 1000 Genomes Project (42.9% and 63.9%, respectively; p<0.01). The C/D ratios of MTX at 24 and 42h for the TTC/TTC-A/A haplotype carriers (11.74 and 0.07μmol/l per g/m2 , respectively) were significantly lower than those in DEL/DEL-G/G or DEL/TTC-G/G haplotype carriers (12.49 and 0.09μmol/l per g/m2 , respectively; p<0.05). Computational predictions suggested that the two polymorphisms overlapped with putative binding sites of several miRNAs. The rs3737966 and rs35134728 polymorphisms in MTHFR were associated with serum MTX concentrations. The findings of the present study indicate that miRNAs might be involved in the post-transcriptional regulation of MTHFR.

A haplotypic variant at the IRGM locus and rs11747270 are related to the susceptibility for chronic periodontitis.

Immunity-regulated GTPase M (IRGM) plays a critical role in the defense against intracellular bacteria by regulating autophagy formation. This direct genetic association study aimed to determine whether variants at the IRGM genetic locus are associated with chronic periodontitis. Using PCR and melting curve analysis 390 periodontitis patients and 770 healthy controls have been genotyped regarding six polymorphisms in the IRGM gene (rs13361189, rs10065172, rs4958847, rs1000113, rs11747270, rs931058). Frequency distribution of alleles and genotypes for the six polymorphisms were not significantly different between the periodontitis and the control group. Also following stratification according to gender and smoking no significant linkage was found for any of the IRGM variants with periodontitis. Analysis of a subsample of patients revealed a significant association for rs11747270 with severe periodontitis (p = 0.003). Pairwise linkage analysis revealed one block composed of rs13361189, rs10065172, rs4958847, rs1000113 and 11747270 with strong or even complete linkage disequilibrium (r 2 > 0.9). Four haplotypes showed a frequency of > 1%, among which the haplotype C-T-A-T-G was significantly associated with chronic periodontitis (p = 0.0051; OR 4.66, 95% CI 1.41-15.42). One rare haplotype of the IRGM locus is significantly associated with chronic periodontitis in a German cohort.

Validating porcine SCD haplotype effects on fatty acid desaturation and fat deposition in different genetic backgrounds

Abstract Fatty acid composition and fat desaturation+ have profound effects on meat quality. One of the major enzymes participating in fatty acid metabolism is the stearoyl-CoA desaturase (SCD), which is the key enzyme involved in the fatty acid desaturation, in particular in the synthesis of C18:1 from C18:0 and C16:1 from C16:0. Previous studies have reported a likely causal SCD haplotype (g.2108C>T, g.2228T>C, g.2281A>G) determining desaturation potential in Duroc-based populations. In the current study we have evaluated the effects of SCD polymorphisms on fatty acid desaturation and SCD gene expression in muscle and subcutaneous fat in three experimental backcrosses and validated these effects in a Chinese-European hybrid pigs. In addition, we have evaluated the joint effects of SCD polymorphisms and major mutations (LEPR c.1987C>T, RYR1c.1843C>T, MC4Rc.1426A>G) previously reported to be involved in porcine fat deposition and fatty acids metabolism, in order to clarify SCD polymorphisms’ actual effects. The obtained results from association and gene expression analyses support the SCD haplotype effects on fatty acid desaturation, and moreover on fat atherogenic and thrombogenic indexes. It also reveals potential effects on intramuscular fat content, not previously reported, likely conditional on breed fatness status. Moreover, a new polymorphism, g.2520G>A, that could impact splicing and SCD translation and which appears in complete linkage disequilibrium with the causal SCD haplotype, has been here identified. In addition, the conducted joint analyses of SCD with LEPR, RYR1 and MC4R genetic variants show complex gene relations that could hamper the discrimination of specific gene effects and the success of selection strategies.

The Identification of SNPs in BCDO2 Gene for Skin Color in Chinese Indigenous Chicken

A complete linkage disequilibrium between the SNP (SNP B) in BCDO2 gene and the yellow skin phenotype in European domestic chicken has been reported. Here, we genotyped the reported SNPs (SNP A, SNP B, and SNP C) of the BCDO2 gene in 183 Chinese Indigenous chickens from 11 breeds/populations, including 57 yellow, 17 white, and 109 black skin chickens. The frequency of all three SNPs were significantly different between yellow and white skin chickens (p<0.01). In black skin chickens, a high frequency of the heterozygous genotype (AG) in SNP A (0.51) and SNP B (0.48) was observed. A total of three haplotypes (AAA, AGA, and GAA) from these three SNPs were obtained. Frequencies of the proposed yellow skin-associated haplotype AGA in yellow skin, white skin, and black skin chickens were 0.81, 0.35, and 0.56, respectively. The results showed that the yellow skin phenotype of the evaluated birds has not been under selection, and that the BCDO2 gene in black skin chickens, evolutionally may undergo a transition phase from yellow to white skin chicken. We concluded that, the SNPs of BCDO2 gene not only can be used to determine whether the chicken was subjected to selection, but may also be used as a marker when selecting for the preferred skin color in chicken breeding programs.

P121 Linkage disequilibrium between specific HLA-DPB1 alleles and a single nucleotide polymorphism RS9277534 in a Southern Chinese population

Aim A single nucleotide polymorphism(SNP), rs9277534, within the 3′untranslated region of HLA-DPB1 has been shown to be involved in the regulation of HLA- DPB1 expression. The risk of graft-versus-host disease(GVHD) associated with HLA-DPB1 mismatching was influenced by the HLA-DPB1 rs9277534 expression marker. We investigate the linkage disequilibrium(LD) between specific HLA-DPB1 alleles and rs9277534 SNP in Chinese Sichuan Han individuals, and provide valuable genetic information for clinical transplantation. Methods We collected 200 blood samples from Sichuan Han population. After DNA extraction, samples were genotyped for HLA-DPB1 and rs9277534 by polymerase chain reaction sequence-based typing. Results The results showed that DPB1∗05:01:01G allele was the most common which the frequency was 0.4125 in Sichuan Han Population. AA, GG and AG of SNP genotype frequencies were 0.165, 0.375 and 0.46. The allele frequencies of A and G were 0.4 and 0.6. There are 35 HLA-DPB1 alleles present in the Sichuan Han population, 10 were found to be in significant LD with the rs9277534 SNP. The DPB1∗04:02:01G, DPB1∗02:01:02G, DPB1∗02:02:01G and DPB1∗17:01:01G were in complete linkage with the rs9277534A allele, while DPB1∗05:01:01G, DPB1∗03:01:01G, DPB1∗13:01:01G, DPB1∗14:01:01G and DPB1∗21:01, were in complete LD with the rs9277534G allele (p 0.05). While not completely, DPB1∗04:01:01G (D′ = 0.95; p 0.01) were found to be in significant LD with the rs9277534A allele. Conclusions These findings provide valuable scientific basis for clinical transplantation for reasonable choice between donor and recipient in a Han Southern Chinese population. If recipients with HLA-DPB1 alleles for DPB1∗05:01:01G, DPB1∗13:01:01G and DPB1∗21:01, and they accept hematopoietic stem cell of donors which HLA-DPB1 alleles for DPB1∗04:01:01G,DPB1∗04:02:01G, DPB1∗02:01:02G and DPB1∗02:02:01G, even if donor-recipient pairs as permissive according to T cell epitope(TCE) algorithm, which may also increase the risk of GVHD. Download : Download high-res image (635KB) Download : Download full-size image

Genotype distributions of CYP2C9 and VKORC1 in southern Thais and their association with warfarin maintenance dose in patients with cardiac surgery

Background: Pharmacodynamics of warfarin are influenced by genetic polymorphisms of its metabolic enzymes. Objectives: To determine CYP2C9 and VKORC1 genotypes in a population in southern Thailand, and their association with warfarin maintenance doses. Methods: We genotyped CYP2C9*2 (rs1799853), CYP2C9*3 (rs1057910), VKORC1 (rs9923231 and rs9934438) from the blood DNA of 210 healthy controls, and determined the association of 2 polymorphic markers (CYP2C9*3 and rs9923231) in 154 patients with aortic valve protheses, with warfarin maintenance dose and coagulopathy. Results: CYP2C9*3 was detected in 17/210 controls; all were heterozygous variants (-*1*3). No CYP2C9*2 polymorphisms were detected. The 2 VKORC1 polymorphisms were in complete linkage disequilibrium. The genotype distribution of VKORC1 (rs9923231) was 118:72:20 for AA:AG:GG. The warfarin maintenance dose in patients with CYP2C9*1*3 (20.7 mg/week) was significantly less than in patients with CYP2C9*1*1 (31.7 mg/ week; P (AA:AG:GG; 23.8:35.3:47.3 mg/week). The incidence of prolonged prothrombin time (INR > 5) was significantly higher in the VKORC1-AA group (45/76) than the AG (22/64) or GG (3/16) groups. The median time to achieve a stable INR was highest for patients with a GG genotype (342 days) compared with 20 days for those with AA, and 160 days for those with AG. Other factors associated with warfarin maintenance dose were body surface area, age (>45 years), and concomitant drug use. Conclusion: Polymorphisms of CYP2C9*3 and VKORC1 are present in southern Thais. We recommend pharmacogenetic studies of these markers as a component of warfarin therapy. Keywords: Pharmacogenetics, Thai patients, warfarin

Missense mutations of NCPAG gene affect calving ease in Piedmontese cattle: preliminary evidences

A previous genome scan on 323 Piedmontese individuals identified a cluster of 13 SNPs significantly associated with direct calving ease and centred on the three genes LAP3, LCORL and NCAPG in chromosome 6. We investigated missense mutations affecting calving ease in Piedmontese cattle in the identified region using sequences from the whole exome in eight Piedmontese individuals chosen from the extremes of the direct calving ease estimated breeding values distribution for this trait. The present study has not found missense variants in LAP3 and LCORL, while two were identified on NCAPG by three different variant calling methods. Other gene candidates in the same region harbour missense mutations, such as PPM1K, PKD2, SPP1 and MEPE, but both SIFT analysis and chi-square test on frequency of alleles make us hypothesise that NCAPG is the single gene responsible for the trait variation. The two SNPs on NCAPG are in complete linkage disequilibrium in our samples; therefore, further investigations are needed in order to discriminate their role.

Characterization of a low expression haplotype in canine glutathione S-transferase (GSTT1) and its prevalence in golden retrievers.

Glutathione S-transferase-theta (GSTT1) is a carcinogen detoxification enzyme, and low activity variants are associated with lymphoma in humans. We recently found a variant in the 3' untranslated region (UTR) of canine GSTT1, *101_102insT, which was predicted to change miRNA binding and was found in 5 of 17 golden retriever (GR) dogs with lymphoma but none of 14 healthy GRs. The aim of this study was to determine whether this variant led to decreased GSTT1 expression and was a discernible risk factor for lymphoma within the GR breed. On resequencing, *101_102insT appeared to be in complete linkage disequilibrium with 3 additional 3'UTR variants, leading to the inferred haplotype *3T>C; *101_102insT; *190C>A; *203T>C. In canine livers that were heterozygous for this variant haplotype, GSTT1 protein expression was significantly lower compared to the reference haplotype (densitometry .40 vs .64, P = .022), and GSTT1 transcript levels by qPCR were also significantly lower (fold difference .52, P = .012), without evidence of substantial allelic expression imbalance. The variant haplotype led to >50% decrease in expression in vitro (.31 ± .07 vs .64 ± .19; P = .019). We found no significant difference in minor allele frequencies between 71 GR dogs with lymphoma (MAF .162) and 33 healthy age-matched controls (MAF .136, P = .69). Our results indicate that the variant GSTT1 3'UTR haplotype containing *101_102insT reduces gene expression, which could lead to impaired carcinogen detoxification, but was not a detectable risk factor for lymphoma in GR dogs.

A GJA9 frameshift variant is associated with polyneuropathy in Leonberger dogs

BackgroundMany inherited polyneuropathies (PN) observed in dogs have clinical similarities to the genetically heterogeneous group of Charcot-Marie-Tooth (CMT) peripheral neuropathies in humans. The canine disorders collectively show a variable expression of progressive clinical signs and ages of onset, and different breed prevalences. Previously in the Leonberger breed, a variant highly associated with a juvenile-onset PN was identified in the canine orthologue of a CMT-associated gene. As this deletion in ARHGEF10 (termed LPN1) does not explain all cases, PN in this breed may encompass variants in several genes with similar clinical and histopathological features.ResultsA genome-wide comparison of 173 k SNP genotypes of 176 cases, excluding dogs homozygous for the ARHGEF10 variant, and 138 controls, was carried out to detect further PN-associated variants. A single suggestive significant association signal on CFA15 was found. The genome of a PN-affected Leonberger homozygous for the associated haplotype was sequenced and variants in the 7.7 Mb sized critical interval were identified. These variants were filtered against a database of variants observed in 202 genomes of various dog breeds and 3 wolves, and 6 private variants in protein-coding genes, all in complete linkage disequilibrium, plus 92 non-coding variants were revealed. Five of the coding variants were predicted to have low or moderate effect on the encoded protein, whereas a 2 bp deletion in GJA9 results in a frameshift of high impact. GJA9 encodes connexin 59, a connexin gap junction family protein, and belongs to a group of CMT-associated genes that have emerged as important components of peripheral myelinated nerve fibers. The association between the GJA9 variant and PN was confirmed in an independent cohort of 296 cases and 312 controls. Population studies showed a dominant mode of inheritance, an average age of onset of approximately 6 years, and incomplete penetrance.ConclusionsThis GJA9 variant represents a highly probable candidate variant for another form of PN in Leonberger dogs, which we have designated LPN2, and a new candidate gene for CMT disease. To date, approximately every third PN-diagnosed Leonberger dog can be explained by the ARHGEF10 or GJA9 variants, and we assume that additional genetic heterogeneity in this condition exists in the breed.

Relationship Between Variants of Detoxification Genes and 3-hydroxybenzo[a]pyrene Concentration in Urine of Coke Plant Workers

ABSTRACTCoke plant workers' exposure to polycyclic aromatic hydrocarbons (PAHs) is monitored with the use of different biomarkers. The variations in genes coding enzymes involved in the first and the second phase of detoxification process can influence PAHs metabolites' production. While 1-hydroxypyrene urinary excretion was extensively examined in relationship to different gene variants, 3-hydroxybenzo[a]pyrene (3-OHBaP) is thought to more closely represent the carcinogenic fraction of PAHs intake. The aim of this study was to examine the relationship between the concentration of 3-OHBaP in the urine of coke plant workers and chosen variants of CYP1A1 (rs1048943 and rs4646903), CYP1B1 (rs1056836), and GST (GSTM1 null and GSTT1 null) genes. Urine samples were analyzed using HPLC method for 3-OHBaP, while polymerase chain reaction (PCR) methods were used for variants detection. 141 men took part in the study. Both CYP1A1 single nucleotide polymorphisms (SNPs) were found to be in complete linkage disequilibrium (rs1048943 is observed only as coexisting with rs4646903). In general, individuals with CYP1A1 variants had the lower concentration of the biomarker in urine, and the rs1048943 SNP was identified as more strongly correlated with this change of biomarker excretion, yielding three times lower concentrations at sampling time for rs1048943 heterozygote than for wild type. CYP1B1 rs1056836 SNP showed weak but statistically significant correlation with the change of biomarker excretion. The biomarker levels were on average 1.8-fold higher for heterozygotes and variant homozygotes at CYP1B1 rs1056836 locus than for wild type. No correlation was found for GSTM1 and GSTT1 null genotypes, smoking status, and air concentrations of benzo[a]pyrene and particulate matter.