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Two Novel Variants of the CAPN3 Gene in Chinese Patients with Limb-Girdle Muscular Dystrophy Recessive 1. 中国肢腰肌营养不良症隐性1型患者的两种CAPN3基因新变异。
IF 1.1 4区 生物学
Human Heredity Pub Date : 2024-01-01 Epub Date: 2024-06-05 DOI: 10.1159/000539521
Lulu Zhang, Yi Zhang, Chunru Han, Juean Jiang, Jianhua Jiang, Xiuying Cai, Liqiang Yu, Huan Qi, Qi Fang, Dongxue Ding
{"title":"Two Novel Variants of the CAPN3 Gene in Chinese Patients with Limb-Girdle Muscular Dystrophy Recessive 1.","authors":"Lulu Zhang, Yi Zhang, Chunru Han, Juean Jiang, Jianhua Jiang, Xiuying Cai, Liqiang Yu, Huan Qi, Qi Fang, Dongxue Ding","doi":"10.1159/000539521","DOIUrl":"10.1159/000539521","url":null,"abstract":"<p><strong>Introduction: </strong>Recessive mutations in the CAPN3 gene can lead to limb-girdle muscular dystrophy recessive 1 (LGMD R1). Targeted next-generation sequencing facilitates the discovery of new mutations linked with disease, owing to its ability to selectively enrich specific genomic regions.</p><p><strong>Methods: </strong>We performed targeted next-generation sequencing of all exons of the CAPN3 gene in 4 patients with sporadic limb-girdle muscular dystrophy (LGMD) and further analyzed the effects of the novel identified variant using various software tools.</p><p><strong>Results: </strong>We found 5 variants in CAPN3 gene in 4 patients, c.82_83insC (insertion mutation) and c.1115+2T&gt;C (splicing mutation) are reported for the first time in CAPN3 (NM_000070.2). The bioinformatics analysis indicated that these two novel variants affected CAPN3 transcription as well as translation.</p><p><strong>Discussion: </strong>Our findings reveal previously unreported splicing mutation and insertion mutation in CAPN3 gene, further expanding the pathogenic gene profile of LGMD.</p>","PeriodicalId":13226,"journal":{"name":"Human Heredity","volume":" ","pages":"52-59"},"PeriodicalIF":1.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141237836","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Screening for Mitochondrial tRNA Variants in 200 Patients with Systemic Lupus Erythematosus. 筛查 200 名系统性红斑狼疮患者的线粒体 tRNA 变异。
IF 1.1 4区 生物学
Human Heredity Pub Date : 2024-01-01 Epub Date: 2024-11-13 DOI: 10.1159/000542357
Dan Xuan, Fuyong Qiang, Hui Xu, Li Wang, Yonghui Xia
{"title":"Screening for Mitochondrial tRNA Variants in 200 Patients with Systemic Lupus Erythematosus.","authors":"Dan Xuan, Fuyong Qiang, Hui Xu, Li Wang, Yonghui Xia","doi":"10.1159/000542357","DOIUrl":"10.1159/000542357","url":null,"abstract":"<p><strong>Introduction: </strong>Systemic lupus erythematosus (SLE) is a common autoimmune disease with unknown etiology. Recently, a growing number of evidence suggested that mitochondrial dysfunctions played active roles in the pathogenesis of SLE, but its detailed mechanism remains largely undetermined. The aim of this study was to analyze the frequencies of mitochondrial tRNA (mt-tRNA) variants in Chinese individuals with SLE.</p><p><strong>Methods: </strong>We carried out a mutational screening of mt-tRNA variants in a cohort of 200 patients with SLE and 200 control subjects by PCR-Sanger sequencing. The potential pathogenicity of mt-tRNA variants was evaluated by phylogenetic conservation and haplogroup analyses. In addition, trans-mitochondrial cybrid cell lines were established, and mitochondrial functions including ATP, reactive oxygen species (ROS), mitochondrial DNA (mtDNA) copy number, mitochondrial membrane potential (MMP), superoxide dismutase (SOD), and mt-RNA transcription were analyzed in cybrids with and without these putative pathogenic mt-tRNA variants.</p><p><strong>Results: </strong>We identified five possible pathogenic variants: tRNAVal G1606A, tRNALeu(UUR) A3243G, tRNAIle A4295G, tRNAGly T9997C, and tRNAThr A15924G that only found in SLE patients but were absent in controls. Interestingly, these variants were located at extremely conserved nucleotides of the corresponding tRNAs and may alter tRNAs' structure and function. Furthermore, cells carrying these tRNA variants had much lower levels of ATP, mtDNA copy number, MMP, and SOD than controls; by contrast, the levels of ROS increased significantly (p < 0.05 for all). Furthermore, a significant reduction in mt-ND1, ND2, ND3, ND5, and A6 mRNA expression was observed in cells with these mt-tRNA variants, while compared with controls. Thus, failures in tRNA metabolism caused by these variants would impair mitochondrial translation and subsequently lead to mitochondrial dysfunction that was involved in the progression and pathogenesis of SLE.</p><p><strong>Conclusions: </strong>Our study suggested that mt-tRNA variants were important causes for SLE, and screening for mt-tRNA pathogenic variants was recommended for early detection and prevention for this disorder.</p>","PeriodicalId":13226,"journal":{"name":"Human Heredity","volume":" ","pages":"84-97"},"PeriodicalIF":1.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11844679/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142619350","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Joint Linkage and Association Analysis Using GENEHUNTER-MODSCORE with an Application to Familial Pancreatic Cancer. 利用 GENEHUNTER-MODSCORE 对家族性胰腺癌进行联合联系和关联分析。
IF 1.1 4区 生物学
Human Heredity Pub Date : 2024-01-01 Epub Date: 2024-01-10 DOI: 10.1159/000535840
Markus Brugger, Manuel Lutz, Martina Müller-Nurasyid, Peter Lichtner, Emily P Slater, Elvira Matthäi, Detlef K Bartsch, Konstantin Strauch
{"title":"Joint Linkage and Association Analysis Using GENEHUNTER-MODSCORE with an Application to Familial Pancreatic Cancer.","authors":"Markus Brugger, Manuel Lutz, Martina Müller-Nurasyid, Peter Lichtner, Emily P Slater, Elvira Matthäi, Detlef K Bartsch, Konstantin Strauch","doi":"10.1159/000535840","DOIUrl":"10.1159/000535840","url":null,"abstract":"<p><strong>Introduction: </strong>Joint linkage and association (JLA) analysis combines two disease gene mapping strategies: linkage information contained in families and association information contained in populations. Such a JLA analysis can increase mapping power, especially when the evidence for both linkage and association is low to moderate. Similarly, an association analysis based on haplotypes instead of single markers can increase mapping power when the association pattern is complex.</p><p><strong>Methods: </strong>In this paper, we present an extension to the GENEHUNTER-MODSCORE software package that enables a JLA analysis based on haplotypes and uses information from arbitrary pedigree types and unrelated individuals. Our new JLA method is an extension of the MOD score approach for linkage analysis, which allows the estimation of trait-model and linkage disequilibrium (LD) parameters, i.e., penetrance, disease-allele frequency, and haplotype frequencies. LD is modeled between alleles at a single diallelic disease locus and up to three diallelic test markers. Linkage information is contributed by additional multi-allelic flanking markers. We investigated the statistical properties of our JLA implementation using extensive simulations, and we compared our approach to another commonly used single-marker JLA test. To demonstrate the applicability of our new method in practice, we analyzed pedigree data from the German National Case Collection for Familial Pancreatic Cancer (FaPaCa).</p><p><strong>Results: </strong>Based on the simulated data, we demonstrated the validity of our JLA-MOD score analysis implementation and identified scenarios in which haplotype-based tests outperformed the single-marker test. The estimated trait-model and LD parameters were in good accordance with the simulated values. Our method outperformed another commonly used JLA single-marker test when the LD pattern was complex. The exploratory analysis of the FaPaCa families led to the identification of a promising genetic region on chromosome 22q13.33, which can serve as a starting point for future mutation analysis and molecular research in pancreatic cancer.</p><p><strong>Conclusion: </strong>Our newly proposed JLA-MOD score method proves to be a valuable gene mapping and characterization tool, especially when either linkage or association information alone provide insufficient power to identify the disease-causing genetic variants.</p>","PeriodicalId":13226,"journal":{"name":"Human Heredity","volume":" ","pages":"8-31"},"PeriodicalIF":1.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139416888","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Investigation of Recessive Effects of Coding Variants on Common Clinical Phenotypes in Exome-Sequenced UK Biobank Participants. 在外显子组测序的英国生物库参与者中调查编码变异对常见临床表型的隐性影响。
IF 1.1 4区 生物学
Human Heredity Pub Date : 2024-01-01 Epub Date: 2024-02-10 DOI: 10.1159/000537771
David Curtis
{"title":"Investigation of Recessive Effects of Coding Variants on Common Clinical Phenotypes in Exome-Sequenced UK Biobank Participants.","authors":"David Curtis","doi":"10.1159/000537771","DOIUrl":"10.1159/000537771","url":null,"abstract":"<p><strong>Introduction: </strong>Previous studies have demonstrated effects of rare coding variants on common, clinically relevant phenotypes although the additive burden of these variants makes only a small contribution to overall trait variance. Although recessive effects of individual homozygous variants have been studied, little work has been done to elucidate the impact of rare coding variants occurring together as compound heterozygotes.</p><p><strong>Methods: </strong>In this study, attempts were made to identify pairs of variants likely to be occurring as compound heterozygotes using 200,000 exome-sequenced subjects from the UK Biobank. Pairs of variants, which were seen together in the same subject more often than would be expected by chance, were excluded as it was assumed that these might be present in the same haplotype. Attention was restricted to variants with minor allele frequency ≤0.05 and to those predicted to alter amino acid sequence or prevent normal gene expression. For each gene, compound heterozygotes were assigned scores based on the rarity and predicted functional consequences of the constituent variants and the scores were used in a logistic regression analysis to test for association with hypertension, hyperlipidaemia, and type 2 diabetes.</p><p><strong>Results: </strong>No statistically significant associations were observed and the results conformed to the distribution, which would be expected under the null hypothesis. The average number of apparently compound heterozygous subjects for each gene was only 282.2.</p><p><strong>Conclusion: </strong>It seems difficult to detect an effect of compound heterozygotes on the risk of these phenotypes. Even if recessive effects from compound heterozygotes do occur, they would only affect a small number of people and overall would not make a substantial contribution to phenotypic variance. This research has been conducted using the UK Biobank Resource.</p>","PeriodicalId":13226,"journal":{"name":"Human Heredity","volume":" ","pages":"1-7"},"PeriodicalIF":1.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139717489","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A Statistical Testing Strategy Accounting for Random and Nonrandom (Skewed) X-Chromosome Inactivation Identifies Lung Cancer Susceptibility Loci among Smokers. 考虑到随机和非随机(偏斜)X 染色体失活的统计检测策略确定了吸烟者的肺癌易感基因位点。
IF 1.1 4区 生物学
Human Heredity Pub Date : 2024-01-01 Epub Date: 2024-06-14 DOI: 10.1159/000539520
Rodolphe Jantzen, Sophie Camilleri-Broët, Nicole Ezer, Philippe Broët
{"title":"A Statistical Testing Strategy Accounting for Random and Nonrandom (Skewed) X-Chromosome Inactivation Identifies Lung Cancer Susceptibility Loci among Smokers.","authors":"Rodolphe Jantzen, Sophie Camilleri-Broët, Nicole Ezer, Philippe Broët","doi":"10.1159/000539520","DOIUrl":"10.1159/000539520","url":null,"abstract":"<p><strong>Introduction: </strong>Lung cancer is the most common cancer worldwide in mortality and the second in incidence. Epidemiological studies found a higher lung cancer risk for smoking women in comparison to men, but these sex differences, irrespective of smoking habits, remain controversial. One of the hypotheses concerns the genetic contribution of the sex chromosomes. However, while genome-wide association studies identified many lung cancer susceptibility loci, these analyses have excluded X-linked loci.</p><p><strong>Methods: </strong>To account for nongenetic factors, we first presented an association test based on an additive-multiplicative hazard model accounting for random/nonrandom X-inactivation process. A simulation study was performed to investigate the properties of the proposed test as compared with the Wald test from a Cox model with random X-inactivation process and the partial likelihood ratio test proposed by Xu et al. accounting for nonrandom X-inactivation process. Then, we performed an X chromosome-wide association study on 9,261 individuals from the population-based cohort CARTaGENE to identify susceptibility loci for lung cancer among current and past smokers. We adjusted for the PLCOm2012 lung cancer risk score used in screening programs.</p><p><strong>Results: </strong>Simulation results show the good behavior of the proposed test in terms of power and type I error probability as compared to the Xu et al. and the Wald test. Using the proposed test statistic and adjusting for the PLCOm2012 score, the X chromosome-wide statistical analysis identified two SNPs in low-linkage disequilibrium located in the IL1RAPL1 (IL-1 R accessory protein-like) gene: rs12558491 (p = 2.75×10-9) and rs12835699 (p = 1.26×10-6). For both SNPs, the minor allele was associated with lower lung cancer risk. Adjusting for multiple testing, no signal was detected using the Wald or the Xu et al. likelihood ratio tests.</p><p><strong>Conclusion: </strong>By taking into account smoking behavior and the X-inactivation process, the investigation of the X chromosome has shed a new light on the association between X-linked loci and lung cancer. We identified two loci associated with lung cancer located in the IL1RAPL1 gene. This finding would have been overlooked by examining only results from other test statistics.</p>","PeriodicalId":13226,"journal":{"name":"Human Heredity","volume":" ","pages":"71-83"},"PeriodicalIF":1.1,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141330785","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Identification of a Hypoxia-Related Signature as Candidate Detector for Schizophrenia Based on Genome-Wide Gene Expression. 基于全基因组基因表达的精神分裂症候选检测基因缺氧相关特征的鉴定
IF 1.1 4区 生物学
Human Heredity Pub Date : 2023-01-01 Epub Date: 2023-03-13 DOI: 10.1159/000529902
Zhitao Li, Xinyu Sun, Jia He, Dongyan Kong, Jinyi Wang, Lili Wang
{"title":"Identification of a Hypoxia-Related Signature as Candidate Detector for Schizophrenia Based on Genome-Wide Gene Expression.","authors":"Zhitao Li, Xinyu Sun, Jia He, Dongyan Kong, Jinyi Wang, Lili Wang","doi":"10.1159/000529902","DOIUrl":"10.1159/000529902","url":null,"abstract":"<p><strong>Introduction: </strong>Schizophrenia (SCZ), a severe neuropsychiatric disorder with high genetic susceptibility, has high rates of misdiagnosis due to the unavoidably subjective factors and heterogeneous clinical presentations. Hypoxia has been identified as an importantly risk factor that participates in the development of SCZ. Therefore, development of a hypoxia-related biomarker for SCZ diagnosis is promising. Therefore, we dedicated to develop a biomarker that could contribute to distinguishing healthy controls and SCZ patients.</p><p><strong>Methods: </strong>GSE17612, GSE21935, and GSE53987 datasets, consisting of 97 control samples and 99 SCZ samples, were involved in our study. The hypoxia score was calculated based on the single-sample gene-set enrichment analysis using the hypoxia-related differentially expressed genes to quantify the expression levels of these genes for each SCZ patient. Patients in high-score groups were defined if their hypoxia score was in the upper half of all hypoxia scores and patients in low-score groups if their hypoxia score was in the lower half. GSEA was applied to detect the functional pathway of these differently expressed genes. CIBERSORT algorithm was utilized to evaluate the tumor-infiltrating immune cells of SCZ patients.</p><p><strong>Results: </strong>In this study, we developed and validated a biomarker consisting of 12 hypoxia-related genes that could distinguish healthy controls and SCZ patients robustly. We found that the metabolism reprogramming might be activated in the patient with high hypoxia score. Finally, CIBERSORT analysis illustrated that lower composition of naive B cells and higher composition of memory B cells might be observed in low-score groups of SCZ patients.</p><p><strong>Conclusion: </strong>These findings revealed that the hypoxia-related signature was acceptable as a detector for SCZ, providing further insight into effective diagnosis and treatment strategies for SCZ.</p>","PeriodicalId":13226,"journal":{"name":"Human Heredity","volume":" ","pages":"18-28"},"PeriodicalIF":1.1,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10124753/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9352414","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Polymorphisms of Placental Iodothyronine Deiodinase Genes in a Rural Area of Northern China with High Prevalence of Neural Tube Defects. 神经管畸形高发的中国北方农村地区胎盘碘甲腺原氨酸脱碘酶基因的多态性
IF 1.1 4区 生物学
Human Heredity Pub Date : 2023-01-01 Epub Date: 2023-03-21 DOI: 10.1159/000530112
Fang Wang, Yan-Hong Gu, Jin Guo, YiHua Bao, ZhiYong Qiu, Ping Zheng, Masaru Ushijima, Masaaki Matsuura, Ting Zhang
{"title":"Polymorphisms of Placental Iodothyronine Deiodinase Genes in a Rural Area of Northern China with High Prevalence of Neural Tube Defects.","authors":"Fang Wang, Yan-Hong Gu, Jin Guo, YiHua Bao, ZhiYong Qiu, Ping Zheng, Masaru Ushijima, Masaaki Matsuura, Ting Zhang","doi":"10.1159/000530112","DOIUrl":"10.1159/000530112","url":null,"abstract":"<p><strong>Introduction: </strong>We have reported that high total homocysteine and the coexistence of inadequate thyroid hormones in maternal serum increase the risk of fetal neural tube defects (NTDs). Placental iodothyronine deiodinases (DIOs: DIO1, DIO2, and DIO3) play a role in regulating the conversions between different forms of maternal thyroid hormones. This study hypothesized that single nucleotide polymorphisms (SNPs) in placental DIOs genes could be related to NTDs.</p><p><strong>Methods: </strong>We performed a case-control study from 2007 to 2009 that included pregnant women from Lüliang, Shanxi Province, China. Nine distinct SNPs in DIOs genes were analyzed, and placental samples were obtained from 83 pregnant women with NTD fetuses and 90 pregnant women with normal fetuses. The nine SNPs were analyzed using the Cochran-Armitage test and the Fisher's exact test.</p><p><strong>Results: </strong>There were no statistically significant differences between case and control in the nine SNPs of DIOs (p &gt; 0.05).</p><p><strong>Conclusions: </strong>The results of this study suggested that SNPs of DIO genes in the placenta among pregnant women have no statistically significant difference between the two groups, suggesting that other factors might be involved in metabolism of maternal thyroid hormone provided to fetuses, such as epigenetic modification of methylation and homocysteinylation and genomic imprinting in the placenta. Further functional studies on placenta samples are necessary.</p>","PeriodicalId":13226,"journal":{"name":"Human Heredity","volume":" ","pages":"29-37"},"PeriodicalIF":1.1,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9164096","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Violation of the Constant Genetic Effect Assumption Can Result in Biased Estimates for Non-Linear Mendelian Randomization. 违反恒定遗传效应假设可能导致对非线性孟德尔随机化的有偏估计。
IF 1.1 4区 生物学
Human Heredity Pub Date : 2023-01-01 Epub Date: 2023-08-31 DOI: 10.1159/000531659
Stephen Burgess
{"title":"Violation of the Constant Genetic Effect Assumption Can Result in Biased Estimates for Non-Linear Mendelian Randomization.","authors":"Stephen Burgess","doi":"10.1159/000531659","DOIUrl":"10.1159/000531659","url":null,"abstract":"<p><strong>Introduction: </strong>Non-linear Mendelian randomization is an extension of conventional Mendelian randomization that performs separate instrumental variable analyses in strata of the study population with different average levels of the exposure. The approach estimates a localized average causal effect function, representing the average causal effect of the exposure on the outcome at different levels of the exposure. The commonly used residual method for dividing the population into strata works under the assumption that the effect of the genetic instrument on the exposure is linear and constant in the study population. However, this assumption may not hold in practice.</p><p><strong>Methods: </strong>We use the recently developed doubly ranked method to re-analyse various datasets previously analysed using the residual method. In particular, we consider a genetic score for 25-hydroxyvitamin D (25[OH]D) used in a recent non-linear Mendelian randomization analysis to assess the potential effect of vitamin D supplementation on all-cause mortality.</p><p><strong>Results: </strong>The effect of the genetic score on 25(OH)D concentrations varies strongly, with a five-fold difference in the estimated genetic association with the exposure in the lowest and highest decile groups. Evidence for a protective causal effect of vitamin D supplementation on all-cause mortality in low vitamin D individuals is evident for the residual method but not for the doubly ranked method. We show that the constant genetic effect assumption is more reasonable for some exposures and less reasonable for others. If the doubly ranked method indicates that this assumption is violated, then estimates from both the residual and doubly ranked methods can be biased, although bias was smaller on average in the doubly ranked method.</p><p><strong>Conclusion: </strong>Analysts wanting to perform non-linear Mendelian randomization should compare results from both the residual and doubly ranked methods, as well as consider transforming the exposure for the residual method to reduce heterogeneity in the genetic effect on the exposure.</p>","PeriodicalId":13226,"journal":{"name":"Human Heredity","volume":" ","pages":"79-90"},"PeriodicalIF":1.1,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10614256/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10129348","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Methods and Software to Analyze Gene-Environment Interactions under a Case-Mother-Control-Mother Design with Partially Missing Child Genotype. 分析具有部分缺失儿童基因型的病例-母亲-对照-母亲设计下基因-环境相互作用的方法和软件。
IF 1.1 4区 生物学
Human Heredity Pub Date : 2023-01-01 Epub Date: 2023-04-26 DOI: 10.1159/000529559
Alexandre Bureau, Yuang Tian, Patrick Levallois, Yves Giguère, Jinbo Chen, Hong Zhang
{"title":"Methods and Software to Analyze Gene-Environment Interactions under a Case-Mother-Control-Mother Design with Partially Missing Child Genotype.","authors":"Alexandre Bureau, Yuang Tian, Patrick Levallois, Yves Giguère, Jinbo Chen, Hong Zhang","doi":"10.1159/000529559","DOIUrl":"10.1159/000529559","url":null,"abstract":"<p><strong>Introduction: </strong>The case-mother-control-mother design allows to study fetal and maternal genetic factors together with environmental exposures on early life outcomes. Mendelian constraints and conditional independence between child genotype and environmental factors enabled semiparametric likelihood methods to estimate logistic models with greater efficiency than standard logistic regression. Difficulties in child genotype collection require methods handling missing child genotype.</p><p><strong>Methods: </strong>We review a stratified retrospective likelihood and two semiparametric likelihood approaches: a prospective one and a modified retrospective one, the latter either modeling the maternal genotype as a function of covariates or leaving their joint distribution unspecified (robust version). We also review software implementing these modeling alternatives, compare their statistical properties in a simulation study, and illustrate their application, focusing on gene-environment interactions and partially missing child genotype.</p><p><strong>Results: </strong>The robust retrospective likelihood provides generally unbiased estimates, with standard errors only slightly larger than when modeling maternal genotype based on exposure. The prospective likelihood encounters maximization problems. In the application to the association of small-for-gestational-age babies with CYP2E1 and drinking water disinfection by-products, the retrospective likelihood allowed a full array of covariates, while the prospective likelihood was limited to few covariates.</p><p><strong>Conclusion: </strong>We recommend the robust version of the modified retrospective likelihood.</p>","PeriodicalId":13226,"journal":{"name":"Human Heredity","volume":" ","pages":"38-49"},"PeriodicalIF":1.1,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10308538/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9725507","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
51st European Mathematical Genetics Meeting (EMGM) 2023. 第 51 届欧洲数学遗传学会议(EMGM)2023。
IF 1.8 4区 生物学
Human Heredity Pub Date : 2023-01-01 Epub Date: 2023-12-12 DOI: 10.1159/000535389
Inga Prokopenko, Ayşe Demirkan, Marika Kaakinen
{"title":"51st European Mathematical Genetics Meeting (EMGM) 2023.","authors":"Inga Prokopenko, Ayşe Demirkan, Marika Kaakinen","doi":"10.1159/000535389","DOIUrl":"https://doi.org/10.1159/000535389","url":null,"abstract":"<p><p>NA.</p>","PeriodicalId":13226,"journal":{"name":"Human Heredity","volume":"88 Suppl 1 ","pages":"1-72"},"PeriodicalIF":1.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138801680","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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