High-risk Haplotype Research Articles

1617-P: Association of High-Affinity Autoantibodies with High-Risk HLA Haplotypes

Electrochemiluminescence (ECL) assays are high-affinity autoantibodies (Abs) that are more specific than radiobinding assay (RBA) Abs for the prediction of type 1 diabetes (T1D) in natural history studies screening for risk and progression to T1D. We analyzed 603 subjects from the TrialNet Pathway to Prevention Study who were positive for at least one RBA diabetes related Ab and for whom ECL and HLA data were available. We sought to characterize ECL-GADA and ECL-IAA positivity and levels (z-scores) by HLA genotype and haplotypes. Mean age at initial visit was 19.4 ± 13.7 years; 345 (57.2%) were female and 104 (17.2%) carried the high-risk HLA- DR3/4*0302 genotype. At initial visit 425 (70%) of subjects were positive for either ECL-GADA or ECL-IAA, with 207 (34.3%) ECL-IAA positive subjects and 367 (60.9%) ECL-GADA positive subjects. For subjects with high-risk HLA-DR3/4 genotype (n=104), 80 (76.9%) were positive for ECL-GADA, while 42 (40.4%) were positive for ECL-IAA. ECL and RBA-GADA z-scores were higher in subjects with HLA-DR3 haplotypes, while ECL-IAA (but not RBA-IAA) z-scores were associated with HLA-DR4 haplotypes. Associations of ECL and RIA Abs with high-risk HLA haplotypes are shown in the Table. In conclusion, ECL and RBA-GADA positivity are associated with both HLA-DR3 and DR4 haplotypes, whereas only ECL-IAA (but not RBA-IAA) positivity and levels are associated with HLA-DR4 haplotype. Disclosure T.M. Triolo: None. L. Pyle: None. L. Yu: None. P. Gottlieb: Advisory Panel; Self; Janssen Scientific Affairs, LLC., Tolerion, Inc., Viacyte, Inc. Research Support; Self; Caladrius Biosciences, Inc., Immune Tolerance Network, Janssen Pharmaceuticals, Inc., JDRF, Leona M. and Harry B. Helmsley Charitable Trust, Mercia/Nova Laboratories, National Institute of Diabetes and Digestive and Kidney Diseases, Novo Nordisk Inc. Stock/Shareholder; Self; IM Therapeutics. A. Steck: None. Funding American Diabetes Association (1-14-CD-17 to A.S.); National Institute of Diabetes and Digestive and Kidney Diseases; National Institute of Allergy and Infectious Diseases; Eunice Kennedy Shriver National Institute of Child Health and Human Development; JDRF

Genetic analysis of pseudoexfoliation glaucoma risk in an Irish population

AbstractPurposeGlaucoma is an optic neuropathy and a leading cause of irreversible blindness worldwide. Although there are many factors that may contribute to disease predisposition, severity and progression, pseudoexfoliation (PXF) syndrome represents a significant cause for developing open angle glaucoma. Single nucleotide polymorphisms (SNPs) within the lysyl oxidase like (LOXL) 1 gene have been identified as a major risk factor for PXF syndrome and PXF glaucoma (PXFG), specifically SNPs within the exon 1 and intron 1 regions of the gene. The common haplotype (G‐G) of 2 SNPs within exon 1, rs1048661 and rs3825942, are the strongest associated risk factor for PXF in Caucasian populations. However this risk haplotype is switched in some populations. Herein, a study was undertaken to genotype an Irish population for PXF risk‐associated SNPs within the LOXL1 gene.MethodsPatient cohorts of PXFG, PXF and cataract controls were recruited following informed consent. Patients from each cohort were then genotyped for the 2 high risk associated SNPs within exon 1 (rs1048661 and rs3825942), along with 3 SNPs within intron 1 (rs1550437, rs6495085 and rs6495086) of the LOXL1 gene.ResultsThe high risk haplotype (G‐G) was most prevalent in PXFG patients compared to control patients. The low risk (G‐A) haplotype was only seen in control patients. Additionally, genotypes of several SNPs within intron 1 were also found to be present at higher frequencies within the PXFG/PXF patient cohort compared to control patients.ConclusionCollectively, these results represent the first study to genotype PXF‐associated SNPs within LOXL1 in an Irish population and aids in our understanding of the genetic component of developing PXF and PXFG.

The myopia susceptibility locus vasoactive intestinal peptide receptor 2 (VIPR2) contains variants with opposite effects

Myopia is the commonest eye disorder in the world. High myopes are predisposed to ocular pathologies. The vasoactive intestinal peptide receptor 2 (VIPR2) gene was identified as a myopia susceptibility locus by our group and another group. We continued to fine-map this locus. A case-control study was performed in 4 sequential stages with a total of 941 highly myopic subjects and 846 control subjects, all unrelated Chinese. Stage 1 experimentally genotyped 64.4% of the entire cohort for 152 single-nucleotide polymorphisms (SNPs) and Stage 2 the remaining subjects for 21 SNPs. Stage 3 combined the genotypes for 21 SNPs for the entire cohort, and identified one group of high-risk haplotypes and one group of protective haplotypes significantly associated with high myopia. Stage 4 imputed genotypes for variants in the VIPR2 region and identified two independent groups of variants: one group with high-risk minor alleles and another with protective minor alleles. Variants within each group were generally in strong linkage disequilibrium among themselves while high-risk variants were in linkage equilibrium with protective variants. Therefore, the VIPR2 locus seems to contain variants with opposite effects. This is the first study that has examined the genetic architecture of a myopia susceptibility locus in detail.

Association of NM23 polymorphisms and clinicopathological features and recurrence of invasive pituitary adenomas.

Pituitary adenomas (PAs) are intracranial tumors, deriving from anterior pituitary cells. Previously, expression of non-metastasis-23 (NM23) gene has been shown to correlate with the progression of PAs. In this study, we aim to determine whether there is association between specific NM23 polymorphisms and invasive pituitary adenoma (IPA). Genotypes of rs2302254 and rs16949649 of NM23 were identified in the peripheral venous blood of patients by PCR-RLFP. Next, the correlation between specific genotypes of rs2302254 and rs16949649 and risk of IPA was investigated. Finally, the correlations between NM23 polymorphisms and tumor size, Ki67 LI and recurrence of IPA were analyzed with 3 to 24months follow-up for the enrolled patients. We observed that the TT genotype at rs16949649 correlated closely with a high risk of IPA, while CC and CT genotypes reduced the risk of IPA. CC genotype at rs2302254 increased the risk of IPA, while CT and TT genotypes reduced the risk of IPA. Trs16949649Crs2302254 haplotype of NM23 was found to be a high-risk haplotype for IPA. TT genotype at rs16949649 and CC genotype at rs2302254 were associated with higher rates of tumors larger than 20mm, Ki67 LI and tumor recurrence. Taken together, the present study provides evidence that NM23 polymorphisms are closely associated with the incidence and recurrence of IPA. Specifically, TT genotype at rs16949649 and CC genotype at rs2302254 are risk factors of IPA. NM23 polymorphisms could therefore be used as a reference for clinical diagnosis and prognosis of IPA.

1181 Prevalence of Celiac Disease-Compatible Human Leukocyte Antigen Haplotypes Across Ethnicities and Regions in the United States

INTRODUCTION: The prevalence of celiac disease (CD) is widely variable throughout the United States (US), with a higher prevalence of disease in the Northeast. The reasons for this variability are unknown. In a prior study, we detected ethnic differences within the US, using a name-based algorithm, with prevalence in patients of Jewish ethnicity similar to the overall population, and lower in persons of East Asian ethnicity. CD etiology is dependent on human leukocyte antigen (HLA) haplotype. Typically, either HLA DQ2.5 or DQ8 is required (but not sufficient) for the development of CD, with DQ2.5 being the highest-risk haplotype. To date, no study has characterized regional or ethnic differences in the frequency of CD-compatible HLA haplotypes. Thus, we aimed to measure the frequencies of DQ2.5 and DQ8 across regions and ethnicities in the US. METHODS: We assessed the frequencies of HLA DQ2.5 (DQA1*05:DQB1*02) and DQ8 (DQA1*03:DQB1*03) in an unselected group of genotyped individuals who have used direct-to-consumer genetic testing between 2013 and 2017. Eligible participants were 23andMe customers who consented to participate in research. We assayed two SNPs to classify individuals as DQ2.5 homozygous, DQ2.5 heterozygous, DQ2.5/DQ8, DQ8 homozygous, DQ8 heterozygous, and 0 detected variants. We compared the frequency of each haplotype across four regions of the US. Additionally, we used genome-wide array data to cluster participants into 8 categories that correlate highly with self-reported race and ethnicity, and compared the frequencies of these haplotypes across these ethnic categories (Table 1). RESULTS: Of 1,290,668 individuals studied, at least one CD-compatible haplotype was present in 38.7% of individuals, and this frequency was similar across the four US regions. The frequencies of DQ2.5 homozygotes were also similar across the Northeast, Midwest, South, and West (1.25%, 1.43%, 1.38%, and 1.37%, respectively). In contrast, frequencies differ across ethnic groups: the highest DQ2.5 and DQ8 frequencies were observed in European (12.01%) and Ashkenazi Jewish (16.39%) participants, respectively. CONCLUSION: Previously reported regional variability in CD prevalence in the US may not be due to differences in HLA-based susceptibility; rather, other genetic or environmental factors likely play a role in disease pathogenesis. In addition, these differences carry great significance in view of the development of HLA haplotype-specific non-dietary therapies for CD.

A VNTR Regulates miR-137 Expression Through Novel Alternative Splicing and Contributes to Risk for Schizophrenia

The MIR137HG gene encoding microRNA-137 (miR-137) is genome-wide associated with schizophrenia (SZ), however, the underlying molecular mechanisms remain unknown. Through cloning and sequencing of individual transcripts from fetal and adult human brain tissues we describe novel pri-miR-137 splice variants which exclude the mature miR-137 sequence termed ‘del-miR-137’ that would function to down-regulate miR-137 expression. Sequencing results demonstrate a significant positive association between del-miR-137 transcripts and the length of a proximal variable number tandem repeat (VNTR) element. Additionally, a significantly higher proportion of sequenced transcripts from fetal brain were del-miR-137 transcripts indicating neurodevelopmental splicing regulation. In-silico results predict an independent regulatory function for del-miR-137 transcripts through competitive endogenous RNA function. A case-control haplotype analysis (n = 998) in SZ implicates short VNTR length in risk, with longer lengths imparting a protective effect. Rare high risk haplotypes were also observed indicating multiple risk variants within the region. A second haplotype analysis was performed to evaluate recombination effects excluding the VNTR and results indicate that recombination of the region was found to independently contribute to risk. Evaluation of the evolutionary conservation of the VNTR reveals a human lineage specific expansion. These findings shed further light on the risk architecture of the miR-137 region and provide a novel regulatory mechanism through VNTR length and alternative MIR137HG transcripts which contribute to risk for SZ.

Choroid Plexus Acts as Gatekeeper for TREM2, Abnormal Accumulation of ApoE, and Fibrillary Tau in Alzheimer's Disease and in Down Syndrome Dementia.

Background:Genetic factors that influence Alzheimer’s disease (AD) risk include mutations in TREM2 and allelic variants of Apolipoprotein E, influencing AD pathology in the general population and in Down syndrome (DS). Evidence shows that dysfunction of the choroid plexus may compromise the blood-cerebrospinal fluid (CSF) barrier, altering secretary, transport and immune function that can affect AD pathology.Objective:To investigate the genotype and phenotype of DS individuals in relation to choroid plexus damage and blood-CSF barrier leakage to identify markers that could facilitate early diagnosis of AD in DS.Methods:To assess allele frequency and haplotype associations ApoE, Tau, TREM2, and HLA-DR were analyzed by SNP analysis in DS participants (n = 47) and controls (n = 50). The corresponding plasma protein levels were measured by ELISA. Postmortem brains from DS, AD, and age-matched controls were analyzed by immunohistochemistry.Results:Haplotype analysis showed that individuals with Tau H1/H1 and ApoE ɛ4 genotypes were more prevalent among DS participants with an earlier diagnosis of dementia (17%) compared to H1/H2 haplotypes (6%). Plasma TREM2 levels decreased whereas phospho-tau levels increased with age in DS. In AD and DS brain, insoluble tau and ApoE were found to accumulate in the choroid plexus.Conclusion:Accumulation of tau and ApoE in the choroid plexus may increase the oligomerization rate of Aβ42 and impair tau trafficking, leading to AD pathology. We have identified a high-risk haplotype: ApoE ɛ4, Tau/H1, and TREM2/T, that manifests age-related changes potentially opening a window for treatment many years prior to the manifestation of the AD dementia.

Genetic Variation Within the HLA-DRA1 Gene Modulates Susceptibility to Type 1 Diabetes in HLA-DR3 Homozygotes.

Type 1 diabetes (T1D) involves the interaction of multiple gene variants, environmental factors, and immunoregulatory dysfunction. Major T1D genetic risk loci encode HLA-DR and -DQ. Genetic heterogeneity and linkage disequilibrium in the highly polymorphic HLA region confound attempts to identify additional T1D susceptibility loci. To minimize HLA heterogeneity, T1D patients (N = 365) and control subjects (N = 668) homozygous for the HLA-DR3 high-risk haplotype were selected from multiple large T1D studies and examined to identify new T1D susceptibility loci using molecular inversion probe sequencing technology. We report that risk for T1D in HLA-DR3 homozygotes is increased significantly by a previously unreported haplotype of three single nucleotide polymorphisms (SNPs) within the first intron of HLA-DRA1. The homozygous risk haplotype has an odds ratio of 4.65 relative to the protective homozygous haplotype in our sample. Individually, these SNPs reportedly function as "expression quantitative trait loci," modulating HLA-DR and -DQ expression. From our analysis of available data, we conclude that the tri-SNP haplotype within HLA-DRA1 may modulate class II expression, suggesting that increased T1D risk could be attributable to regulated expression of class II genes. These findings could help clarify the role of HLA in T1D susceptibility and improve diabetes risk assessment, particularly in high-risk HLA-DR3 homozygous individuals.

Pregnancy following exclusion testing for SCA3 on polar bodies in a fresh cycle: a comparison of STR-based targeted haplotyping and genome-wide SNP analysis and meiomapping

Introduction Preimplantation genetic testing of monogenic disease (PGT-M) is allowed in Germany only with approval from the federal ethics committee and autosomal dominant disorders are often rejected. Polar body analysis, however, does not require ethical approval. A 34-year-old asymptomatic patient with a family history of spinocerebellar ataxia type 3 (SCA3) applied for PGT-M on trophectoderm samples but was rejected. The patient's father has a repeat expansion in the ATXN3 gene and is affected with SCA3, a progressive autosomal dominantly inherited neurological disease characterized by ataxia, spasticity and ocular movement abnormalities. As the patient does not want to know her status, we offered exclusion testing based on polar body analysis in a fresh cycle and have compared targeted haplotyping by STR analysis with genome-wide SNP genotyping and meiomap analysis. Material and methods The patient and her father were genotyped for 12 STR markers within 0.44 Mb of the ATXN3 gene on 14q32. 11 STRs were heterozygous (9 fully informative) and used for phasing high and low risk haplotypes. Eggs were collected (Day 0) and the first polar body (PB1) biopsied from mature MII oocytes. ICSI was then performed and PB2 biopsied from three fertilised zygotes on Day 1. After whole genome amplification (WGA) (Repli-g Single Cell Kit; Qiagen, Venlo, Netherlands) multiplex PCR was performed and the products run on a capillary sequencer. Haplotypes were constructed based on the pre-case workup. In addition, genome-wide SNP genotyping of the DNAs from the patient, her father and the WGA products from the polar bodies was carried out (HumanKaryomap-12 SNP array; Illumina, San Diego, USA) for maternal haplotyping and meiomap analysis. Results WGA and multiplex PCR was successful for all of the polar bodies except for the PB2 of Oocyte 1. As all 11 closely linked informative STRs were homozygous for the high-risk haplotype in PB1 from this oocyte, the corresponding PB2 and oocyte was deduced to have the low risk haplotype assuming normal segregation during meiosis. For Oocytes 2 and 3, the PB1 was heterozygous for most STRs and the PB2 of these oocytes were homozygous for the high and low risk haplotypes, respectively. Therefore, the embryos derived from Oocytes 1 and 2 were deduced to have the low risk maternal haplotype while the embryo from Oocyte 3 should have the high-risk haplotype. On Day 5, the blastocysts arising from Oocytes 1 and 2 were transferred, resulting in an ongoing pregnancy (currently week 10). Genome-wide SNP genotyping and meiomap analysis was concordant with STR analysis in all cases. Conclusions We report a pregnancy following targeted STR-based haplotyping and exclusion testing of an autosomal dominant disease by polar body analysis in a fresh cycle. Genome-wide SNP genotyping and meiomap analysis was fully concordant with the STR results but had the advantage that it also demonstrated that segregation of the maternal chromosome 14 was normal and predicted that the embryos from the two oocytes in which both polar bodies were analysed were euploid for all maternal chromosomes.

Correlation between Interleukin-17 gene polymorphism and osteoarthritis susceptibility in Han Chinese population

BackgroundInterleukin-17 (IL-17), a pleiotropic cytokine, plays a significant role in the inflammatory diseases. By a pilot study with small population, IL-17 polymorphisms (IL-17A rs2275913 and IL-17F rs763780) showed a more potential risk factor in knee osteoarthritis (OA) in our recruited subjects. In the current study, the association between IL-17A rs2275913 and IL-17F rs763780and the risk of OA in a Chinese population is studied.MethodsThe IL-17A rs2275913 and IL-17F rs763780 polymorphisms were determined in 594 knee OA cases and 576 healthy controls, using polymerase chain reaction-restriction fragment length polymorphism assay. The relationship between genotype distribution and disease risk, as well as OA severity was analyzed by Chi-square test and multivariate logistic regression.ResultsThe experimental results indicated that the polymorphism in IL-17 gene rs2275913 site were related to knee OA risk after the adjustment of BMI, sex, age, smoking and drinking status (AA vs. GG: odds ratio (OR), 1.411; 95% confidence interval (CI), 1.021–1.950; P = 0.040; A allele vs. G allele: OR, 1.192; P = 0.037; 95% CI, 1.012–1.404;). Similarly, subjects who are bearing the rs763780 variant genotypes (TC and CC) and C allele also had a higher susceptibility to knee OA compared with those who are bearing the TT genotype (TC vs. TT, OR: 1.312; P = 0.039; 95% CI: 1.017–1.692; CC vs. TT, OR: 2.812, P = 0.006, 95% CI: 1.338–5.909; C allele Vs. T allele, OR:1.413, P = 0.002, 95% CI:1.141–1.751). In the meantime, one high-risk haplotypes, AC (OR was 7.22, P < 0.01) was found. Both two polymorphisms do not correlated with OA severity based on Kellgren-Lawrence (K&L) scales. Finally, serum IL-17 levels of knee OA patients were greatly higher than those of controls (P = 0.001).ConclusionsWith the limited size sample, our study shows that IL-17 gene polymorphisms possibly related to the high-risk knee OA occurrence.

Association of VDR and OPG gene polymorphism with osteoporosis risk in Chinese postmenopausal women

Aims: The underlying mechanisms of vitamin D receptor (VDR) and osteoprotegerin (OPG) genetic variation associated with bone mineral density and osteoporosis remain uncertain. This study aimed to investigate the association of VDR and OPG gene polymorphism as well as gene–gene interaction and their haplotype combination with the risk of osteoporosis.Methods: Polymerase chain reaction restriction fragment length polymorphism was carried out for single nucleotide polymorphism (SNP) detection. Generalized multifactor dimension reduction (GMDR) is used to identify the interaction. SHEsis software evaluated the haplotype and logistic regression was performed to assess the association between the SNPs within the VDR and OPG genes and osteoporosis.Results: The risk of osteoporosis in the VDR-rs2228570 polymorphism T-allele carriers was significantly higher than that in CC (CT/TT versus CC) individuals (adjusted odds ratio [OR] [95% confidence interval (CI)] = 1.76 [1.33–2.22]). The risk of osteoporosis was also higher in the G-allele carrier of the OPG-rs3102735 polymorphism than in individuals with the AA genotype (AG/GG vs. AA) (adjusted OR [95% CI] = 1.65 [1.27–2.14]). However, after adjusting for sex, age, and waist circumference covariates, no significant association of VDR-rs17879735 and OPG-rs2073618 with the osteoporosis risk was revealed. The GMDR method identified that gene–gene interactions were significant, but not for gene/AO interaction. Haplotypes were analyzed with SHEsis software. We did not detect a high-risk haplotype combination associated with osteoporosis.Conclusions: Both VDR-rs2228570-T and OPG-rs3102735-G and their interactions are related to the increased risk of osteoporosis.

Common ground: shared risk factors for type 1 diabetes and celiac disease.

Risk factors for most autoimmune diseases are multifactorial genetic variants modified by environmental risk factors. Type 1 diabetes and celiac disease share high-risk HLA haplotypes, and the prevalence of both diseases has increased in many regions during the past half century. Unknown environmental factors are suspected to have increased the disease penetrance. Celiac disease depends on immune responses to dietary gluten, whereas the environmental risk factors for type 1 diabetes are not yet clear. Here, we consider the shared heritable genetic factors and review evidence of the dietary and microbial exposures, particularly in early life, that might influence the pathogenesis of one or both diseases. A deeper mechanistic understanding of the environmental factors responsible for increased risk of these diseases should provide opportunities to manipulate exposure in children carrying defined risk markers and thus prevent and attenuate disease, as well as to identify new therapeutic strategies for patients.

Heterogeneity of Type 1 Diabetes: The Effect of Ethnicity.

Most of the current understanding of type 1 diabetes (T1D) etiology and pathogenesis stemmed from studies conducted in majoritarily Non-Hispanic White (NHW) populations. However, evidence is emerging that unique mechanisms of disease may contribute to the development of T1D in individuals of Hispanic ethnicity. We reviewed the currently available literature on genetic, immunologic, metabolic and clinical characteristics of T1D in Hispanic as compared with NHW individuals. We searched PubMed, Google Scholar, and authors' bibliographies to collect information from relevant articles on the influence of ethnicity on T1D etiology and pathogenesis. There are significant epidemiological variation based on ethnicity, with consistently higher T1D incidence and prevalence rate in NHWs than Hispanics. The frequencies of T1D high-risk HLA haplotypes and genotypes, as well as their susceptibility or protective effects show considerable ethnic differences. There are conflicting data on immunologic factors (e.g. islet autoantibody positivity) and markers of beta-cell function (e.g., C-peptide levels), as well as in some clinical characteristics (e.g. frequencies of diabetic ketoacidosis and severe hypoglycemia), while age of onset is consistently similar between both groups. Higher prevalence of obesity, less intensive diabetes management, and poorer glycemic control were reported in Hispanics. Accordingly, ethnic disparities in clinical outcomes have been demonstrated as well. There are considerable differences in T1D characteristics between NHWs and Hispanics. Better insight into these ethnic differences would not only affect patient care of patients with T1D, but may also inform the design of future prediction and prevention trials.

Polymorphisms of Arsenic (+3 Oxidation State) Methyltransferase and Arsenic Methylation Capacity Affect the Risk of Bladder Cancer.

The mechanisms underlying how arsenic methylation capacity affects bladder cancer (BC) are still unclear. The objective of this study was to explore the effects of polymorphisms of arsenic (+3 oxidation state) methyltransferase (AS3MT) on BC risk. We conducted a hospital-based study and enrolled 216 BC and 648 healthy controls from 2007 to 2011. Urinary arsenic profiles were measured using high-performance liquid chromatography-hydride generation-atomic absorption spectrometry. The gene polymorphisms of AS3MT were identified using the Sequenom MassARRAY platform with iPLEX Gold chemistry. Inefficient arsenic methylation capacity (high monomethylarsonic acid percentage [MMA%] and low dimethylarsinic acid percentage [DMA%]) was associated with increased risk of BC in a dose-response relationship. AS3MT rs11191438 (C > G) G/G genotype, AS3MT rs10748835 (A > G) G/G genotype, and AS3MT rs1046778 (C > T) T/T genotype were found to be related to BC risk, where the odds ratio (OR) (95% CI) was 0.50 (0.31-0.82), 0.49 (0.30-0.79), and 0.54 (0.36-0.80), respectively. The combination of AS3MT haplotype 2 (AS3MT rs11191453, rs11191454, rs10748835, and rs1046778)'s high-risk haplotype (C-G-A-C, T-A-A-C, and T-G-G-T) was significantly associated with increased risk of BC. Among controls, only 3 of the 9 candidate genotypes evaluated, rs1119438 C/C, rs10748835 A/A and rs1046778 C/C, were associated with significantly higher MMA% compared with the other genotypes. No other genotypes or haplotypes were related to arsenic methylation capacity. High MMA%, low DMA% and AS3MT rs1046778 C/C + C/T genotype predicted a significantly higher risk of BC according to stepwise multiple logistic regression analyses. AS3MT gene polymorphisms and arsenic methylation capacity appeared to affect BC risk independently.

CYP2D6 (C2850T, G1846A, C100T) polymorphisms, haplotypes and MDR analysis in predicting coronary artery disease risk in north-west Indian population: A case-control study

AimsThe present study was aimed to evaluate the association of C2850T, G1846A and C100T polymorphisms of the CYP2D6 with coronary artery disease (CAD) in North-West Indian population. MethodsIn this case-control study, 200 patients with CAD and 200 age-, gender- and ethnicity-matched healthy controls were genotyped for C2850T, G1846A and C100T polymorphisms of CYP2D6 using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. ResultsGenotype and allele distributions of C2850T and G1846A polymorphisms of the CYP2D6 were significantly different between cases and controls (p = 0.038, p = 0.021; p = 0.048, p = 0.012, respectively) whereas the distribution of genotype and allele for C100T polymorphism did not differ significantly (p = 0.098, p = 0.117, respectively). The 2850T and1846A variants were significantly associated with the increased risk of developing CAD, as observed from the odds ratios for the 2850 T/T and 1846 G/A genotypes (OR: 2.44, 95% CI: 1.99–4.99, p = 0.015 and OR: 1.62, 95% CI: 1.02–2.56, p = 0.041, respectively). Moreover, the recessive model in C2850T and the dominant model in G1846A are the best fit inheritance models to predict the susceptible gene effects (OR: 2. 07, 95% CI: 1.05–4.08, p = 0.031 and OR: 1.70, 95% CI: 1.10–2.62, p = 0.016, respectively). On gender stratification, these associations were observed only in females in addition to the C/T genotype of C2850T (OR: 2.52, 95% CI: 1.42–4.38, p = 0.001) and C100T (OR: 3.18, 95% CI: 1.52–6.67, p = 0.002). Furthermore, it is also observed that the CAT (OR: 2. 61, 95% CI: 1.07–6.34, p = 0.035) and TAC (OR: 15. 22, 95% CI: 1.97–117.58, p = 0.009) are high-risk haplotypes for CAD in the total group, whereas, the TGC (OR: 1. 64, 95% CI: 1.02–2.62, p = 0.042) and CAT (OR: 4. 21, 95% CI: 1.12–15.59, p = 0.035) haplotypes provide gender-specific risk in females. ConclusionsOur results indicate significant association of C2850T, G1846A and C100T polymorphisms of CYP2D6 with CAD especially in females of North-West Indian population.

A High-risk Haplotype for Premature Menopause in Childhood Cancer Survivors Exposed to Gonadotoxic Therapy.

Childhood cancer survivors are at increased risk of therapy-related premature menopause (PM), with a cumulative incidence of 8.0%, but the contribution of genetic factors is unknown. Genome-wide association analyses were conducted to identify single nucleotide polymorphisms (SNPs) associated with clinically diagnosed PM (menopause < 40 years) among 799 female survivors of childhood cancer participating in the St. Jude Lifetime Cohort Study (SJLIFE). Analyses were adjusted for cyclophosphamide equivalent dose of alkylating agents and ovarian radiotherapy (RT) dose (all P values two-sided). Replication was performed using self-reported PM in 1624 survivors participating in the Childhood Cancer Survivor Study (CCSS). PM was clinically diagnosed in 30 (3.8%) SJLIFE participants. Thirteen SNPs (70 kb region of chromosome 4q32.1) upstream of the Neuropeptide Receptor 2 gene (NPY2R) were associated with PM prevalence (minimum P = 3.3 × 10-7 for rs9999820, all P < 10-5). Being a homozygous carrier of a haplotype formed by four of the 13 SNPs (seen in one in seven in the general population but more than 50% of SJLIFE clinically diagnosed PM) was associated with markedly elevated PM prevalence among survivors exposed to ovarian RT (odds ratio [OR] = 25.89, 95% confidence interval [CI] = 6.18 to 138.31, P = 8.2 × 10-6); this finding was replicated in an independent second cohort of CCSS in spite of its use of self-reported PM (OR = 3.97, 95% CI = 1.67 to 9.41, P = .002). Evidence from bioinformatics data suggests that the haplotype alters the regulation of NPY2R transcription, possibly affecting PM risk through neuroendocrine pathways. The haplotype captures the majority of clinically diagnosed PM cases and, with further validation, may have clinical application in identifying the highest-risk survivors for PM for possible intervention by cryopreservation.

Rare Risk Variants Identification by Identity-by-Descent Mapping and Whole-Exome Sequencing Implicates Neuronal Development Pathways in Schizophrenia and Bipolar Disorder.

Schizophrenia (SCZ) and bipolar disorder (BPD) are highly heritable disorders with an estimated co-heritability of 68%. Hundreds of common alleles have been implicated, but recently a role for rare, high-penetrant variants has been also suggested in both disorders. This study investigated a familial cohort of SCZ and BPD patients from a closed population sample, where the high recurrence of the disorders and the homogenous genetic background indicate a possible enrichment in rare risk alleles. A total of 230 subjects (161 cases, 22 unaffected relatives, and 47 controls) were genetically investigated through an innovative strategy that integrates identity-by-descent (IBD) mapping and whole-exome sequencing (WES). IBD analysis allowed to track high-risk haplotypes (IBDrisk) shared exclusively by multiple patients from different families and possibly carrying the most penetrant alleles. A total of 444 non-synonymous sequence variants, of which 137 disruptive, were identified in IBDrisk haplotypes by WES. Interestingly, gene sets previously implicated in SCZ (i.e., post-synaptic density (PSD) proteins, voltage-gated calcium channels (VGCCs), and fragile X mental retardation protein (FMRP) targets) were found significantly enriched in genes carrying IBDrisk variants. Further, IBDrisk variants were preferentially affecting genes involved in the extracellular matrix (ECM) biology and axon guidance processes which appeared to be functionally connected in the pathway-derived meta-network analysis. Results thus confirm rare risk variants as key factors in SCZ and BPD pathogenesis and highlight a role for the development of neuronal connectivity in the etiology of both disorders.

Preimplantation genetic diagnosis of X-linked Charcot-Marie-Tooth disease by indirect linkage analysis

ObjectiveTo present methodical approach of preimplantation genetic diagnosis (PGD) as an option for an unaffected pregnancy in reproductive-age couples who have a genetic risk of the X-linked dominant peripheral neuropathy Charcot-Marie-Tooth type 1 disease. Patients and methodsWe performed PGD of X-linked Charcot-Marie-Tooth type 1 disease using haplotyping/indirect linkage analysis, when during analysis we reach to exclude embryos that carry a high-risk haplotype linked to the causal mutation p.Leu9Phe in the GJB1 gene. ResultsWithin the PGD cycle, we examined 4 blastomeres biopsied from cleavage-stage embryos and recommended 3 embryos for transfer. Two embryos were implanted into the uterus; however, it resulted in a singleton pregnancy with a male descendant. Three years later, the couple returned again with spontaneous gravidity. A chorionic biopsy examination of this gravidity ascertained the female sex and a pericentric inversion of chromosome 5 in 70% of the cultivated foetal cells. ConclusionUsing indirect linkage analysis, PGD may help to identify genetic X-linked defects within embryos during screening, thereby circumventing the potential problems with abortion.

Gender differences in the association of ENPP1 polymorphisms with type 2 diabetes in a Chinese population

BackgroundEctonucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1) encodes the human plasma-cell membrane differentiation antigen-1, and ENPP1 variants have been shown to be associated with type 2 diabetes (T2D) and insulin resistance. In this study, we investigated the involvement of ENPP1 polymorphisms in T2D. MethodsThe association of the two polymorphisms of ENPP1 (rs7754586 and rs55725924) with T2D and diabetes-related quantitative traits was analyzed in Chinese samples containing 929 T2D patients and 1044 healthy individuals. We also performed the expression quantitative trait loci (eQTL) analysis to study the association of both polymorphisms of ENPP1 with mRNA expression levels using the genotype-tissue expression database. ResultsThe risk allele A of the polymorphism rs7754586 contributed to T2D (odds ratio: 1.252, 95% confidence interval: 1.044–1.615, P=0.018). The polymorphism rs55725924 was associated with the diastolic blood pressure and cholesterol levels. Patients carrying high-risk haplotype A-T of rs7754586 and rs55725924 exhibited a high risk of acquiring T2D. These associations were only observed in males, but not in females. In addition, the eQTL analysis demonstrated that the risk allele of rs7754586 was associated with higher levels of ENPP1 mRNA expression. ConclusionOur findings suggest that the ENPP1 polymorphism rs7754586 may implicate in the pathogenesis of T2D in men, while polymorphism rs55725924 may be involved in diastolic blood pressure and cholesterol of male T2D patients.

Diagnóstico genético preimplantacional de la enfermedad de Charcot-Marie-Tooth ligada al cromosoma X mediante análisis de ligamiento indirecto

ObjectiveTo present methodical approach of preimplantation genetic diagnosis (PGD) as an option for an unaffected pregnancy in reproductive-age couples who have a genetic risk of the X-linked dominant peripheral neuropathy Charcot-Marie-Tooth type 1 disease. Patients and methodsWe performed PGD of X-linked Charcot-Marie-Tooth type 1 disease using haplotyping/indirect linkage analysis, when during analysis we reach to exclude embryos that carry a high-risk haplotype linked to the causal mutation p.Leu9Phe in the GJB1 gene. ResultsWithin the PGD cycle, we examined 4 blastomeres biopsied from cleavage-stage embryos and recommended 3 embryos for transfer. Two embryos were implanted into the uterus; however, it resulted in a singleton pregnancy with a male descendant. Three years later, the couple returned again with spontaneous gravidity. A chorionic biopsy examination of this gravidity ascertained the female sex and a pericentric inversion of chromosome 5 in 70% of the cultivated foetal cells. ConclusionUsing indirect linkage analysis, PGD may help to identify genetic X-linked defects within embryos during screening, thereby circumventing the potential problems with abortion.