Effects Of Gene Variants Research Articles

Folate metabolism abnormalities in infertile patients with endometriosis.

Background: Homocysteine levels can be impacted by enzymes variations. Aim: To correlate MTHFR, MTR and MTRR variants with homocysteine levels in the blood and follicular fluid and assisted reproduction results. Material & methods:MTHFR (rs2274976, rs1801131, rs1801133), MTR (rs1805087) and MTRR (rs1801394) genotyping was performed by TaqMan assays and compared with homocysteine levels, measured by ELISA, to oocytes retrieved and to the pregnancy status of women with endometriosis and controls. Results: The MTR G allele and GG genotype were more common in patients with endometriosis. They also showed lower levels of homocysteine and more clinical gestations. Epistasis analysis showed a model associated with gestational results, composed of MTHFR+MTR variants (CC+AG). Conclusion: The summation effect of variants in genes participating in folate metabolism was associated with pregnancy status in Brazilian women. MTR variants were more observed in endometriosis patients, as well as lower follicular Hcy levels and increased clinical pregnancy results.

Pharmacogenomics of Fludarabine in Pediatric HCT Recipients: Preliminary Results

Introduction: Total Body Irradiation (TBI) conditioning regimens are considered standard of care for pediatric hematopoietic cell transplant (HCT) recipients. However, TBI has many long-term effects, so avoiding it in young HCT recipients is critical. Fludarabine is frequently used in combination with other chemotherapeutic agents like busulfan and/or thiotepa in non-TBI based conditioning regimens. While multi-drug conditioning aims to avoid TBI-related late-effects, little is known about the effect of variations in genes that metabolize these drugs (pharmacogenomics/PGx) on clinical outcomes including engraftment, relapse, and acute drug-related toxicities. In this study, we investigated the pharmacogenomic effects on HCT outcomes such as event-free outcomes and re-transplantation outcomes, as well as fludarabine's pharmacokinetics (PK).Methods: This ongoing study included pediatric patients from a nationwide multi-center study who received fludarabine in combination with other agents as busulfan and thiotepa. From literature searches and PharmGKB databases, we selected 70 SNPs in 30 candidate pharmacological genes for these drug pathways. SNPs with a minor allele frequency of 10% were further selected for analysis with different endpoints such as: 1) Cumulative incidence with disease relapse with re-transplantation (using Gray's methods, controlling for competing risks); 2) fludarabine PK with cumulative area under the curve (cAUC); 3) 1-month-post-transplant chimerism levels defined as sufficient (CD3 ≥80% and CD14/15 ≥95% chimerism) and insufficient (CD3 <80% and CD14/15 <95% chimerism); and 4) event-free outcomes (comparing patients alive and well vs. others) OR alive re-transplantation outcomes (alive with vs. without re-transplantation). SNPs with an association p-value <0.05 were considered significant using generalized linear models from the SNPassoc R package.Results: Total of 87 patients included in the analysis had a median age of 3.5 (0.2 - 17.9) years, 63% were male, 48% were Caucasian, 85% had received allogenic HCT, and 43% had malignant hematologic disease (Table 1). For SNP rs2277119 in CYP39A1, presence of T allele was associated with greater cumulative incidence of re-transplantation (TC-TT vs. CC genotype: HR=3.64 (95% CI=1.14-11.62), p=0.02, Figure 1A); and SNP rs4715354 in GSTA5, presence of G allele was associated with lower cumulative incidence of re-transplantation (AG-GG vs. AA: HR=0.32 (95% CI=0.11-0.95), p=0.037, Figure 1B). In 79% of patients with available fludarabine cAUC (median of 3.72 mg•hr/L), we evaluated fludarabine pathway gene SNPs for association with cAUC. Within SNPs rs3925058 in CMPK1 and rs11853372 in the uptake transporter SLC28A1, presence of variant allele was associated with higher fludarabine cAUC (rs3925058: GA-AA vs. GG, p=0.049, Figure 2A, and rs11853372 GG-GT vs. TT, p=0.003, Figure 2B); and for a 3'-UTR SNP rs2037067 in TENM3/DCTD, the variant allele was associated with lower fludarabine cAUC levels (CT-CC vs. TT, p=0.005, Figure 2C). In an exploratory analysis with event-free outcomes, patients with variant allele for SNPs rs9937 in RRM1, rs2072671 in CDA, rs324148 in SLC29A1, and rs7533657 in CTPS1 had higher odds of having an event compared to patients with the reference allele; while rs11577910 in CTPS1 had a better outcome with presence of variant allele. With respect to patient's status being alive with re-transplantation outcomes, variants SNPs with rs507964 in SLC29A1, rs4244285 in CYP2C19, rs1021737 in CTH, rs1561876 in STIM1, and rs1130609 in RRM2 have high odds of re-transplantation. At 1-month follow-up, variant SNP rs12144160 in CTPS1 was associated with sufficient chimerism in CD3 and CD14/15.Conclusions: In this study, we have identified a number of SNPs that predict interpatient variability in clinical outcomes and fludarabine levels in pediatric HCT recipients. Results so far showed potential to predict outcomes and develop strategies that will consider pharmacogenomics when determining fludarabine doses in pediatric HCT recipients. Our ongoing study is focused on establishing and validating the pharmacogenetic markers predictive of pharmacokinetics of busulfan, fludarabine and thiotepa and clinical outcomes in pediatric HCT recipients.Acknowledgements: This study was supported by Florida Department of Health - Live Like Bella Discovery Award (9LA04). [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

Sub-genic intolerance, ClinVar, and the epilepsies: A whole-exome sequencing study of 29,165 individuals

Both mild and severe epilepsies are influenced by variants in the same genes, yet an explanation for the resulting phenotypic variation is unknown. As part of the ongoing Epi25 Collaboration, we performed a whole-exome sequencing analysis of 13,487 epilepsy-affected individuals and 15,678 control individuals. While prior Epi25 studies focused on gene-based collapsing analyses, we asked how the pattern of variation within genes differs by epilepsy type. Specifically, we compared the genetic architectures of severe developmental and epileptic encephalopathies (DEEs) and two generally less severe epilepsies, genetic generalized epilepsy and non-acquired focal epilepsy (NAFE). Our gene-based rare variant collapsing analysis used geographic ancestry-based clustering that included broader ancestries than previously possible and revealed novel associations. Using the missense intolerance ratio (MTR), we found that variants in DEE-affected individuals are in significantly more intolerant genic sub-regions than those in NAFE-affected individuals. Only previously reported pathogenic variants absent in available genomic datasets showed a significant burden in epilepsy-affected individuals compared with control individuals, and the ultra-rare pathogenic variants associated with DEE were located in more intolerant genic sub-regions than variants associated with non-DEE epilepsies. MTR filtering improved the yield of ultra-rare pathogenic variants in affected individuals compared with control individuals. Finally, analysis of variants in genes without a disease association revealed a significant burden of loss-of-function variants in the genes most intolerant to such variation, indicating additional epilepsy-risk genes yet to be discovered. Taken together, our study suggests that genic and sub-genic intolerance are critical characteristics for interpreting the effects of variation in genes that influence epilepsy.

Advances in the Immunology and Genetics of Leprosy.

Leprosy, a disease caused by the intracellular parasite Mycobacterium leprae or Mycobacterium lepromatosis, has affected humans for more than 4,000 years and is a stigmatized disease even now. Since clinical manifestations of leprosy patients present as an immune-related spectrum, leprosy is regarded as an ideal model for studying the interaction between host immune response and infection; in fact, the landscape of leprosy immune responses has been extensively investigated. Meanwhile, leprosy is to some extent a genetic disease because the genetic factors of hosts have long been considered major contributors to this disease. Many immune-related genes have been discovered to be associated with leprosy. However, immunological and genetic findings have rarely been studied and discussed together, and as a result, the effects of gene variants on leprosy immune responses and the molecular mechanisms of leprosy pathogenesis are largely unknown. In this context, we summarized advances in both the immunology and genetics of leprosy and discussed the perspective of the combination of immunological and genetic approaches in studying the molecular mechanism of leprosy pathogenesis. In our opinion, the integrating of immunological and genetic approaches in the future may be promising to elucidate the molecular mechanism of leprosy onset and how leprosy develops into different types of leprosy.

P6589Genetic risks for arrhythmia phenotypes in dilated cardiomyopathy

Abstract Background Genotype-phenotype correlations in dilated cardiomyopathy (DCM) and in particular the effects of gene variants on clinical outcomes remain poorly understood. Purpose To investigate the prognostic role of genetic variant carrier status in a large cohort of DCM patients. Methods We analyzed 487 DCM patients by next-generation sequencing and categorized the disease genes into functional gene groups. The following composite outcome measures were assessed: 1) all-cause mortality, heart transplantation or left ventricular assist device (D/HTx/VAD); 2) sudden cardiac death or malignant ventricular arrhythmias (SCD/MVAs); 3) heart failure related death, heart transplantation or left ventricular assist device implantation (DHF/HTx/VAD). Results A total of 187 pathogenic/likely pathogenic variants were found in 180 patients (37%): 55 (11%) TTN; 19 (4%) LMNA; 24 (5%) structural cytoskeleton-Z disk genes; 16 (3%) desmosomal genes; 47 (10%) sarcomeric genes; 8 (2%) ion channels genes; 11 (2%) other genes. The occurrence of D/HTx/VAD was no different between variant carriers and non-carriers (p=0.17). However, carriers of desmosomal and LMNA variants experienced the highest rate of SCD/MVA, which was independent of the left ventricular ejection fraction. Conclusions Desmosomal and LMNA gene variants identify the subset of DCM patients at greatest risk for SCD and life-threatening ventricular arrhythmias, regardless the left ventricular ejection fraction. Acknowledgement/Funding National Institutes of Health grants R01 HL69071, HL116906, and AHA17GRNT33670495

Genetic Risk of Arrhythmic Phenotypes in Patients With Dilated Cardiomyopathy

BackgroundGenotype-phenotype correlations in dilated cardiomyopathy (DCM) and, in particular, the effects of gene variants on clinical outcomes remain poorly understood. ObjectivesThe purpose of this study was to investigate the prognostic role of genetic variant carrier status in a large cohort of DCM patients. MethodsA total of 487 DCM patients were analyzed by next-generation sequencing and categorized the disease genes into functional gene groups. The following composite outcome measures were assessed: 1) all-cause mortality; 2) heart failure–related death, heart transplantation, or destination left ventricular assist device implantation (DHF/HTx/VAD); and 3) sudden cardiac death/sustained ventricular tachycardia/ventricular fibrillation (SCD/VT/VF). ResultsA total of 183 pathogenic/likely pathogenic variants were found in 178 patients (37%): 54 (11%) Titin; 19 (4%) Lamin A/C (LMNA); 24 (5%) structural cytoskeleton-Z disk genes; 16 (3.5%) desmosomal genes; 46 (9.5%) sarcomeric genes; 8 (1.6%) ion channel genes; and 11 (2.5%) other genes. All-cause mortality was no different between variant carriers and noncarriers (p = 0.99). A trend toward worse SCD/VT/VF (p = 0.062) and DHF/HTx/VAD (p = 0.061) was found in carriers. Carriers of desmosomal and LMNA variants experienced the highest rate of SCD/VT/VF, which was independent of the left ventricular ejection fraction. ConclusionsDesmosomal and LMNA gene variants identify the subset of DCM patients who are at greatest risk for SCD and life-threatening ventricular arrhythmias, regardless of the left ventricular ejection fraction.

Pharmacogenetics and Depression: A Critical Perspective.

Depression leads the higher personal and socio-economical burden within psychiatric disorders. Despite the fact that over 40 antidepressants (ADs) are available, suboptimal response still poses a major challenge and is thought to be partially a result of genetic variation. Pharmacogenetics studies the effects of genetic variants on treatment outcomes with the aim of providing tailored treatments, thereby maximizing efficacy and tolerability. After two decades of pharmacogenetic research, variants in genes coding for the cytochromes involved in ADs metabolism (CYP2D6 and CYP2C19) are now considered biomarkers with sufficient scientific support for clinical application, despite the lack of conclusive cost/effectiveness evidence. The effect of variants in genes modulating ADs mechanisms of action (pharmacodynamics) is still controversial, because of the much higher complexity of ADs pharmacodynamics compared to ADs metabolism. Considerable progress has been made since the era of candidate gene studies: the genomic revolution has made possible to assess genetic variance on an unprecedented scale, throughout the whole genome, and to analyze the cumulative effect of different variants. The results have revealed key information on the biological mechanisms mediating ADs effect and identified hypothetical new pharmacological targets. They also paved the way for future availability of polygenic pharmacogenetic panels to predict treatment outcome, which are expected to explain much higher variance in ADs response compared to CYP2D6 and CYP2C19 only. As the demand and availability of AD pharmacogenetic testing is projected to increase, it is important for clinicians to keep abreast of this evolving area to facilitate informed discussions with their patients.

Gene variants of adhesion molecules predispose to MS: A case-control study

ObjectiveTo examine the effect of variants in genes encoding molecules that are implicated in leukocyte trafficking into the CNS on the development of MS.MethodsA total of 389 Greek MS cases and 336 controls were recruited by 3 MS centers in Cyprus and Greece. In total, 147 tagging single nucleotide polymorphisms across 9 genes encoding for P-selectin (SELP), integrins (ITGA4, ITGB1, and ITGB7), adhesion molecules (ICAM1, VCAM1, and MADCAM1), fibronectin 1 (FN1), and osteopontin (SPP1) were genotyped. The clinical end point of the study was diagnosis of MS according to the 2005 revised McDonald criteria. Permutation analysis was used for adjusting for multiple comparisons.ResultsOverall, 21 variants across SELP, ITGA4, ITGB1, ICAM1, VCAM1, MADCAM1, FN1, and SSP1 genes were each associated with MS (pperm < 0.05). The most significant were rs3917779 and rs2076074 (SELP), rs6721763 (ITGA4), and rs1250258 (FN1), all with a permutation p value of less than 1e-004.ConclusionsThe current study provides preliminary evidence that variants across genes encoding adhesion molecules, responsible for lymphocyte adhesion and trafficking within the CNS, are implicated in the risk of developing MS.

Functional consequences of genetic variation in sodium channel modifiers in early onset lone atrial fibrillation.

We investigated the effect of variants in genes encoding sodium channel modifiers SNTA1 and GPD1L found in early onset atrial fibrillation (AF) patients. Genetic screening in patients with early onset lone AF revealed three variants in GPD1L and SNTA1 in three AF patients. Functional analysis was performed by patch-clamp electrophysiology. Co-expression of GPD1L or its p.A326E variant with NaV1.5 did not alter INa density or current kinetics. SNTA1 shifted the peak-current by -5mV. The SNTA1-p.A257G variant significantly increased INa. SNTA1-p.P74L did not produce functional changes. Although genetic variation of sodium channel modifiers may contribute to development of AF at a molecular level, it is unlikely a monogenic cause of the disease.

Effects of gene variants controlling vitamin D metabolism and serum levels on hepatic steatosis

Background/Aims: Common genetic variations in vitamin D metabolism are associated with liver stiffness. Whether these genes are implicated in hepatic steatosis re

Hsp90 regulation affects the treatment of glucocorticoid for pancreatitis-induced lung injury.

Glucocorticoids are commonly used for the treatment of pancreatitis and complicated acute lung injury and help to reduce the mortality rates of both. The effect of gene variants in heat shock protein 90 (Hsp90), a key chaperone molecule of the glucocorticoid receptor (GR), on the therapeutic effect of glucocorticoids is unclear. Our study aims to investigate the different susceptibility to glucocorticoid treatment in BALB/c and C57BL/6 mice carrying different Hsp90 genotypes in an animal model of pancreatitis-induced lung injury. Compared with BALB/c mice, C57BL/6 mice have lower mortality rates, decreased water content in their lungs, and a lower level of IL-1 beta in an animal model of acute pancreatitis. C57BL/6 mice show a greater therapeutic effect and increased GR binding activities with glucocorticoid responsive element compared to BALB/c mice after a 0.4mg/kg dexamethasone (DEX) treatment. Treatment with a higher dose of DEX (4mg/kg) significantly reduced mortality rates and increased GR-GRE binding activity in both strains of mice, and there was no significant difference between the two strains. DEX did not exert a protective role after geldanamycin, a specific inhibitor of Hsp90, was administered in both strains of mice. Our study revealed that Hsp90 gene variants are responsible for the greater therapeutic effect of DEX in C57BL/6 mice compared to BALB/c mice, which implies that combining DEX treatment with Hsp90 regulation would promote the efficiency of DEX and would be an effective way to alleviate the side effects of hormone therapy.

Abstract 2598: Paradigm to ensure curation transparency and consistency of a cancer genomic database - the JAX Clinical Knowledgebase (CKB)

Abstract In the era of personalized medicine, comprehensive cancer genomic databases represent critical tools for interpreting gene variants and their relevant therapies. As the number of cancer genomic databases grow, it is challenging for users to compare and assess the data integrity and validity of such databases. The lack of disclosure of curation processes makes it difficult to cross reference different databases. The JAX Clinical Knowledgebase (CKB) is a comprehensive relational database providing evidence-based information on gene variants, targeted therapies, efficacy evidence, and clinical trials. At the Jackson Laboratory for Genomic Medicine, we have developed a curation paradigm to ensure curation transparency and consistency of the JAX-CKB. First, to ensure standardization of nomenclature, we have integrated standard nomenclature and ontologies, including HGNC approved nomenclatures for genes, HGVS guidelines for variants, and the Disease Ontology for indications/tumor types. Second, we implemented decision matrices to maintain uniformity of our evaluation of scientific and clinical data. For example, evaluation of the effect of gene variants on protein function is solely based on changes in the intrinsic activity of the protein instead of downstream pathway activation or the effects on pathogenesis; the response type of gene variants to therapies are classified based on the evidence of targeting specificity; and the efficacy evidence are further classified as actionable, diagnostic, prognostic, risk factor, emerging, or not active centered on the response type and the strength of the evidence. Third, to provide convenient evaluation of the clinical relevance of efficacy data, we further developed a tier ranking system based on emerging consensus guidelines, which takes response type, evidence type, and approval status into consideration. Finally, all decision matrices are clearly outlined on the JAX-CKB open access website for users’ reference. In summary, we have curated a highly structured and semantically consistent cancer genomic database following a set of specific curation guidelines. As a result, JAX-CKB open access has become a valuable resource for both the clinical and research communities, and is utilized by numerous independent groups for variant interpretation. Citation Format: Taofei Yin, Sara E. Patterson, Cara M. Statz, Anuradha Lakshminarayana, Daniel Durkin, Susan M. Mockus. Paradigm to ensure curation transparency and consistency of a cancer genomic database - the JAX Clinical Knowledgebase (CKB) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2598. doi:10.1158/1538-7445.AM2017-2598

Gene variants of adhesion molecules act as modifiers of disease severity in MS.

Objective:To assess the potential effect of variants in genes encoding molecules that are implicated in leukocyte trafficking into the CNS on the clinical phenotype of multiple sclerosis (MS).Methods:A total of 389 Greek MS cases and 336 controls were recruited in 3 MS centers from Cyprus and Greece. We genotyped 147 tagging single nucleotide polymorphisms (SNPs) in 9 genes encoding for P-selectin (SELP), integrins (ITGA4, ITGB1, and ITGB7), adhesion molecules (ICAM1, VCAM1, and MADCAM1), fibronectin 1 (FN1), and osteopontin (SPP1) involved in lymphocyte adhesion and trafficking into the CNS. Clinical end points of the study were age at MS onset and MS severity as measured by the Multiple Sclerosis Severity Score. Permutation testing was applied to all analyses.Results:SNPs rs6721763 of the ITGA4 and rs6532040 of the SPP1 were found to significantly influence disease severity (permutation p values: 3.00e-06 and 0.009884, respectively). SNP rs1250249 of the FN1 had a dose-dependent effect on age at disease onset (permutation p value: 0.0002).Conclusions:This study provides evidence implicating variants encoding adhesion molecules, responsible for lymphocyte adhesion and trafficking within the CNS, as modifiers of MS disease severity. These genetic biomarkers, which can be available at the time of diagnosis, may be used to assess the biological aggressiveness of the disease and thus guide decisions on treatment.

Genome-wide genetic analyses highlight mitogen-activated protein kinase (MAPK) signaling in the pathogenesis of endometriosis.

STUDY QUESTIONDo genome-wide association study (GWAS) data for endometriosis provide insight into novel biological pathways associated with its pathogenesis?SUMMARY ANSWERGWAS analysis uncovered multiple pathways that are statistically enriched for genetic association signals, analysis of Stage A disease highlighted a novel variant in MAP3K4, while top pathways significantly associated with all endometriosis and Stage A disease included several mitogen-activated protein kinase (MAPK)-related pathways.WHAT IS KNOWN ALREADYEndometriosis is a complex disease with an estimated heritability of 50%. To date, GWAS revealed 10 genomic regions associated with endometriosis, explaining <4% of heritability, while half of the heritability is estimated to be due to common risk variants. Pathway analyses combine the evidence of single variants into gene-based measures, leveraging the aggregate effect of variants in genes and uncovering biological pathways involved in disease pathogenesis.STUDY DESIGN, SIZE, DURATIONPathway analysis was conducted utilizing the International Endogene Consortium GWAS data, comprising 3194 surgically confirmed endometriosis cases and 7060 controls of European ancestry with genotype data imputed up to 1000 Genomes Phase three reference panel. GWAS was performed for all endometriosis cases and for Stage A (revised American Fertility Society (rAFS) I/II, n = 1686) and B (rAFS III/IV, n = 1364) cases separately. The identified significant pathways were compared with pathways previously investigated in the literature through candidate association studies.PARTICIPANTS/MATERIALS, SETTING, METHODSThe most comprehensive biological pathway databases, MSigDB (including BioCarta, KEGG, PID, SA, SIG, ST and GO) and PANTHER were utilized to test for enrichment of genetic variants associated with endometriosis. Statistical enrichment analysis was performed using the MAGENTA (Meta-Analysis Gene-set Enrichment of variaNT Associations) software.MAIN RESULTS AND THE ROLE OF CHANCEThe first genome-wide association analysis for Stage A endometriosis revealed a novel locus, rs144240142 (P = 6.45 × 10−8, OR = 1.71, 95% CI = 1.23–2.37), an intronic single-nucleotide polymorphism (SNP) within MAP3K4. This SNP was not associated with Stage B disease (P = 0.086). MAP3K4 was also shown to be differentially expressed in eutopic endometrium between Stage A endometriosis cases and controls (P = 3.8 × 10−4), but not with Stage B disease (P = 0.26). A total of 14 pathways enriched with genetic endometriosis associations were identified (false discovery rate (FDR)-P < 0.05). The pathways associated with any endometriosis were Grb2-Sos provides linkage to MAPK signaling for integrins pathway (P = 2.8 × 10−5, FDR-P = 3.0 × 10−3), Wnt signaling (P = 0.026, FDR-P = 0.026) and p130Cas linkage to MAPK signaling for integrins pathway (P = 6.0 × 10−4, FDR-P = 0.029); with Stage A endometriosis: extracellular signal-regulated kinase (ERK)1 ERK2 MAPK (P = 5.0 × 10−4, FDR-P = 5.0 × 10−4) and with Stage B endometriosis: two overlapping pathways that related to extracellular matrix biology—Core matrisome (P = 1.4 × 10−3, FDR-P = 0.013) and ECM glycoproteins (P = 1.8 × 10−3, FDR-P = 7.1 × 10−3). Genes arising from endometriosis candidate gene studies performed to date were enriched for Interleukin signaling pathway (P = 2.3 × 10−12), Apoptosis signaling pathway (P = 9.7 × 10−9) and Gonadotropin releasing hormone receptor pathway (P = 1.2 × 10−6); however, these pathways did not feature in the results based on GWAS data.LARGE SCALE DATANot applicable.LIMITATIONS, REASONS FOR CAUTIONThe analysis is restricted to (i) variants in/near genes that can be assigned to pathways, excluding intergenic variants; (ii) the gene-based pathway definition as registered in the databases; (iii) women of European ancestry.WIDER IMPLICATIONS OF THE FINDINGSThe top ranked pathways associated with overall and Stage A endometriosis in particular involve integrin-mediated MAPK activation and intracellular ERK/MAPK acting downstream in the MAPK cascade, both acting in the control of cell division, gene expression, cell movement and survival. Other top enriched pathways in Stage B disease include ECM glycoprotein pathways important for extracellular structure and biochemical support. The results highlight the need for increased efforts to understand the functional role of these pathways in endometriosis pathogenesis, including the investigation of the biological effects of the genetic variants on downstream molecular processes in tissue relevant to endometriosis. Additionally, our results offer further support for the hypothesis of at least partially distinct causal pathophysiology for minimal/mild (rAFS I/II) vs. moderate/severe (rAFS III/IV) endometriosis.STUDY FUNDING/COMPETING INTEREST(S)The genome-wide association data and Wellcome Trust Case Control Consortium (WTCCC) were generated through funding from the Wellcome Trust (WT084766/Z/08/Z, 076113 and 085475) and the National Health and Medical Research Council (NHMRC) of Australia (241944, 339462, 389927, 389875, 389891, 389892, 389938, 443036, 442915, 442981, 496610, 496739, 552485 and 552498). N.R. was funded by a grant from the Medical Research Council UK (MR/K011480/1). A.P.M. is a Wellcome Trust Senior Fellow in Basic Biomedical Science (grant WT098017). All authors declare there are no conflicts of interest.

Pharmacogenetics in obstetric anesthesia.

The 21st century has been billed as the era of "precision/personalized medicine." Genetic investigation of clinical syndromes may guide therapy as well as reveal previously unknown biological or pharmacological pathways that may result in novel drug therapies. Several clinical issues in obstetrics and obstetric anesthesiology have been targets for genetic investigations. These include evaluation of the genetic effects on preterm labor and the progression of labor, spinal anesthesia-induced hypotension and the response to medications used to treat hypotension, and the effect of gene variants on pain and analgesic responses. Most studies have examined specific single nucleotide polymorphisms. Findings have revealed modest effects of genetic variation without tangible impact on current clinical practice. Over the next decade, increased availability of whole exome and genome sequencing, epigenetics, large genetic databases, computational biology and other information technology, and more rapid methods of real-time genotyping may increase the impact of genetics in the clinical arena of obstetrics and obstetric anesthesia.

Transdifferentiation of Human Dermal Fibroblasts to Smooth Muscle-Like Cells to Study the Effect of MYH11 and ACTA2 Mutations in Aortic Aneurysms.

Mutations in genes encoding proteins of the smooth muscle cell (SMC) contractile apparatus contribute to familial aortic aneurysms. To investigate the pathogenicity of these mutations, SMC are required. We demonstrate a novel method to generate SMC-like cells from human dermal fibroblasts by transdifferentiation to study the effect of variants in genes encoding proteins of the SMC contractile apparatus (ACTA2 and MYH11) in patients with aortic aneurysms. Dermal fibroblasts from seven healthy donors and cells from seven patients with MYH11 or ACTA2 variants were transdifferentiated into SMC-like cells within a 2-week duration using 5 ng/ml TGFβ1 on a scaffold containing collagen and elastin. The induced SMC were comparable to primary human aortic SMC in mRNA expression of SMC markers which was confirmed on the protein level by immunofluorescence quantification analysis and Western blotting. In patients with MYH11 or ACTA2 variants, the effect of intronic variants on splicing was demonstrated on the mRNA level in the induced SMC, allowing classification into pathogenic or nonpathogenic variants. In conclusion, direct conversion of human dermal fibroblasts into SMC-like cells is a highly efficient method to investigate the pathogenicity of variants in proteins of the SMC contractile apparatus.

The combined effects of myocardial infarction risk factors: Simulation of the combined effects of gene variants, age, and smoking and an analysis of their interaction

Regression analysis has been used to model the combined influence of adverse factors, namely, specific variants of the CRP (rs1130864), IFNG (rs2430561), TGFB1 (rs1982073), FGB (rs1800788), and PTGS1 (rs3842787) genes; age; and smoking on the risk of myocardial infarction in men, as well as the possible interactions between these factors. The individual effects of each considered genetic factor were comparable in strength to the influence of smoking on the risk of myocardial infarction, and the presence of a combination of two or more genetic variants in nonsmokers resulted in a higher risk of myocardial infarction than in noncarrier smokers. A significant interaction between the presence of the FGB allele rs1800788*T and age was discovered; the protective effect of this allele decreased with age and gradually transformed into a predisposing effect. The study demonstrated that the association of FGB rs1800788*T with the risk of myocardial infarction should be considered only in the context of interaction with age.

Interactions among COX-2, GPIIIa and P2Y1 variants are associated with aspirin responsiveness and adverse events in patients with ischemic stroke.

Background:The effect of gene variants and their interactions on response to aspirin and clinical adverse outcomes after an acute ischemic stroke (IS) is not fully understood. The aim of this study was to investigate the association of aspirin-relevant gene variants and their interactions with clinical adverse outcomes in IS patients taking aspirin.Methods:A total of 14 variants from six genes encoding COX enzymes (COX-1, COX-2), platelet membrane receptors (TXAS1, P2Y1, P2Y12) and glycoprotein receptor (GPIIIa) were examined in 850 acute IS patients. Gene–gene interactions were analyzed using generalized multifactor dimensionality reduction (GMDR) analysis. All patients were followed up for 1 year after admission. Primary outcome was a composite of recurrent ischemic stroke (RIS), myocardial infarction (MI) and death.Results:The primary outcome occurred in 112 (13.5%) patients (81 RIS, 16 MI and 15 deaths). There were no significant differences in the frequencies of the genotypes of the 14 variants between the patients with and without primary outcome using single-locus analytical approach. However, there was significant gene–gene interaction among rs20417, rs1371097 and rs2317676. The high-risk interactive genotypes of rs20417, rs1371097 and rs2317676 were independently associated with primary adverse outcome of RIS, MI, and death after acute IS.Conclusion:The three-loci interactions are associated with sensitivity of IS patients to aspirin and aspirin-induced adverse clinical events. The combinatorial analysis used in this study may be helpful to elucidate complex genetic risk of aspirin resistance (AR).Clinical trial registration:The study described here is registered at http://www.chictr.org/ (unique identifier: ChiCTR-OCH-14004724).

Psychological Consequences of Early Global Deprivation

The English &amp; Romanian Adoptees (ERA) study follows children who spent their first years of life in extremely depriving Romanian institutions before they were adopted by families in the UK. The ERA study constitutes a “natural experiment” that allows the examination of the effects of radical environmental change from a profoundly depriving institutional environment to an adoptive family home. The cohort has been assessed at ages 4, 6, 11, and 15 years, and has provided seminal insights into the effects of early global deprivation. The current paper focuses on the long-term psychological sequelae associated with deprivation experiences. These deprivation-specific problems (DSPs) constitute a striking pattern of behavioral impairments, in its core characterized by deficits in social cognition and behavior, as well as quasi-autistic features, often accompanied by cognitive impairment and symptoms of attention-deficit/hyperactivity disorder (ADHD). Possible moderating influences, including variations in family environment, pre-adoption characteristics, and genetic variation, will be discussed to answer the question why some individuals have prospered while others have struggled. Apart from findings on the moderating effect of variation in genes associated with serotonergic and dopaminergic signaling involving specific phenotypes, heterogeneity in outcome is largely unexplained. The review concludes with an outlook on currently ongoing and future research of the ERA study cohort, which involves the investigation of neurobiological and epigenetic mechanisms as possible mediators of the long-term effects of institutional deprivation.

Obstructive heart defects associated with candidate genes, maternal obesity, and folic acid supplementation.

Right-sided and left-sided obstructive heart defects (OHDs) are subtypes of congenital heart defects, in which the heart valves, arteries, or veins are abnormally narrow or blocked. Previous studies have suggested that the development of OHDs involved a complex interplay between genetic variants and maternal factors. Using the data from 569 OHD case families and 1,644 control families enrolled in the National Birth Defects Prevention Study (NBDPS) between 1997 and 2008, we conducted an analysis to investigate the genetic effects of 877 single nucleotide polymorphisms (SNPs) in 60 candidate genes for association with the risk of OHDs, and their interactions with maternal use of folic acid supplements, and pre-pregnancy obesity. Applying log-linear models based on the hybrid design, we identified a SNP in methylenetetrahydrofolate reductase (MTHFR) gene (C677T polymorphism) with a main genetic effect on the occurrence of OHDs. In addition, multiple SNPs in betaine-homocysteine methyltransferase (BHMT and BHMT2) were also identified to be associated with the occurrence of OHDs through significant main infant genetic effects and interaction effects with maternal use of folic acid supplements. We also identified multiple SNPs in glutamate-cysteine ligase, catalytic subunit (GCLC) and DNA (cytosine-5-)-methyltransferase 3 beta (DNMT3B) that were associated with elevated risk of OHDs among obese women. Our findings suggested that the risk of OHDs was closely related to a combined effect of variations in genes in the folate, homocysteine, or glutathione/transsulfuration pathways, maternal use of folic acid supplements and pre-pregnancy obesity.