Rodolphe Jantzen, Sophie Camilleri-Broët, Nicole Ezer, Philippe Broët
INTRODUCTION: 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, remains controversial. One of the hypotheses concerns the genetic contribution of the sex chromosomes. However, while genomewide association studies identified many lung cancer susceptibility loci, these analyses have excluded X-linked loci...
June 14, 2024: Human Heredity
Lulu Zhang, Yi Zhang, Chunru Han, Juean Jiang, Jianhua Jiang, Xiuying Cai, Liqiang Yu, Huan Qi, Qi Fang, Dongxue Ding
Introduction 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. Methods We performed targeted next-generation sequencing of all exons of the CAPN3 gene in four patients with sporadic LGMD and further analyzed the effects of the novel identified variant using various software tools. Results We found 5 variants in CAPN3 gene in four patients, c...
June 3, 2024: Human Heredity
Vincent Pascat, Liudmila Zudina, Anna Ulrich, Jared G Maina, Marika Kaakinen, Igor Pupko, Amélie Bonnefond, Ayşe Demirkan, Zhanna Balkhiyarova, Philippe Froguel, Inga Prokopenko
Introduction Polygenic Score (PGS) is a valuable method for assessing the estimated genetic liability to a given outcome or genetic variability contributing to a quantitative trait. While PRSs are widely used for complex traits, their application in uncovering shared genetic predisposition between phenotypes, i.e. when genetic variants influence more than one phenotype, remains limited. Methods We developed an R package, comorbidPGS, which facilitates a systematic evaluation of shared genetic effects among (cor)related phenotypes using PGSs...
May 13, 2024: Human Heredity
Yue Zhai, Claire Bardel, Maxime Vallée, Jean Iwaz, Pascal Roy
INTRODUCTION: Ideally, evaluating NGS performance requires a gold standard; in its absence, concordance between replicates is often used as substitute standard. However, the appropriateness of the concordance-discordance criterion has been rarely evaluated. This study analyzes the relationship between the probability of discordance and the probability of error under different conditions. METHODS: This study used a conditional probability approach under conditional dependence then conditional independence between two sequencing results and compares the probabilities of discordance and error in different theoretical conditions of sensitivity, specificity, and correlation between replicates, then on real results of sequencing genome NA12878...
March 16, 2024: Human Heredity
Stefan Wellek, Martina Mueller-Nurasyid, Konstantin Strauch
INTRODUCTION: The standard way of using tests for compatibility of genetic markers with the Hardy-Weinberg equilibrium (HWE) assumptionvas a means of quality control in genetic association studies (GAS) is to vcarry out this step of preliminary data analysis with the sample of non-diseased vindividuals only. We show that this strategy has no rational basis whenever the genotype--phenotype relation for avmarker under consideration satisfies the assumption of co-dominance. METHODS/RESULTS: The justification of this statement is the fact rigorously shown here that under co-dominance, the genotype distribution of a diallelic marker is in HWE among the controls if and only if the same holds true for the cases...
March 2, 2024: Human Heredity
David Curtis
Introduction 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. Methods 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...
February 10, 2024: Human Heredity
Markus Brugger, Manuel Lutz, Martina Müller-Nurasyid, Peter Lichtner, Emily P Slater, Elvira Matthäi, Detlef K Bartsch, Konstantin Strauch
INTRODUCTION: 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. METHODS: 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...
January 10, 2024: Human Heredity
Senmao Chai, Deyang Liu, Yajing Liu, Ming Sang
INTRODUCTION: Spinocerebellar ataxia (SCA) is an autosomal dominant genetic disease characterized by cerebellar neurological deficits. Specifically, its primary clinical manifestation is ataxia accompanied by peripheral nerve damage. A total of 48 causative genes of SCA have been identified. This study aimed to identify causative genes of autosomal dominant SCA in a four-generation Chinese kindred comprised of eight affected individuals. METHODS: Genomic DNA samples were extracted from the pedigree members, and genomic whole-exome sequencing (WES) was performed, followed by bidirectional Sanger sequencing, and minigene assays to identify mutation sites...
October 27, 2023: Human Heredity
Stephen Burgess
INTRODUCTION: 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...
August 31, 2023: Human Heredity
Wenjing Zhang, Xinmiao Nie, Lei Shi, Fengmin Shao, Lihua Cao
Introduction Porokeratosis is a rare chronic progressive hypokeratotic skin disease, possibly related to the mevalonate pathway. Variations in four enzymes, including phosphomevalonate kinase (PMVK) may alter this pathway, ultimately leading to porokeratosis. Methods In this study, Sanger sequencing was used to identify the gene variant causative of porokeratosis; its population frequency was investigated by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) in four patients and three normal individuals as well as in 100 normal unrelated controls; finally, the pathogenicity of the mutation and the associated structural changes were predicted...
June 14, 2023: Human Heredity
Tianhao Wu, Yanlong Zhang, Aqin Peng, Xirui Wu
INTRODUCTION: Rheumatoid arthritis (RA), a chronic autoimmune disorder, is currently a severe health threat. Previous studies have documented the altered expression of various miRNAs in RA patients. This study determined the expression of miR-124a in RA patients and estimated its diagnostic value for RA. METHODS: Total 80 RA patients were enrolled as the study subjects and 36 patients with osteoarthritis were included, with another 36 healthy people as the controls...
June 14, 2023: Human Heredity
Alexandre Bureau, Yuang Tian, Patrick Levallois, Yves Giguère, Jinbo Chen, Hong Zhang
INTRODUCTION: 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. METHODS: 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)...
April 26, 2023: Human Heredity
Hongqiang Ren, Yijun Liu, Zhen Tan, Guiquan Luo, Mei Zhang, Shuang Li, Tingwei Tang, Zhao Li
Introduction The role of ARRB2 in cardiovascular disease has recently gained increasing attention. However, the association between ARRB2 polymorphisms and heart failure (HF) has not yet been investigated. Methods A total of 2386 hospitalized patients with chronic heart failure were enrolled as the first cohort and followed up for a mean period of 20.2 months. Meanwhile, ethnically and geographically matched 3000 individuals without evidence of HF were included as healthy controls. We genotyped the common variant in ARRB2 gene to identify the association between variant and HF...
April 26, 2023: Human Heredity
Fang Wang, Yan-Hong Gu, Jin Guo, YiHua Bao, ZhiYong Qiu, Ping Zheng, Masaru Ushijima, Masaaki Matsuura, Ting Zhang
INTRODUCTION: We have reported that high total homocysteine (tHCY), 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 regulate 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. METHODS: We performed a case-control study from 2007 to 2009 that included pregnant women from Lüliang, Shanxi Province, China...
March 21, 2023: Human Heredity
Zhitao Li, Xinyu Sun, Jia He, Dongyan Kong, Jinyi Wang, Lili Wang
INTRODUCTION: 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...
March 13, 2023: Human Heredity
Mahmoud Ghanei, Seyedeh Helia Sadat Fatemi, Tayebeh Hamzehlouei
BACKGROUND: Hyperphenylalaninemia (HPA) is an autosomal recessive disorder that results from a deficiency in the phenylalanine hydroxylase enzyme (PAH) or from a flaw in the genes that are responsible for the biosynthesis or regeneration of the cofactor tetrahydrobiopterin (BH4), including GCH1, SR, QDPR, PTS, and PCD. Identification of disease-causing variants in these genes can help physicians and clinical geneticists in differential diagnosis, appropriate prescription drugs, and saving time and cost...
January 16, 2023: Human Heredity
Inga Prokopenko, Ayşe Demirkan, Marika Kaakinen
2023: Human Heredity
Shiguo Chen, Jian Gao, Qunyan Wu, Xi Li, Sheng Lin, Jindi Su, Kaifeng Zheng, Zhaopeng Guo, Jilong Yao, Shan Duan
OBJECTIVE: Glucose-6-phosphate dehydrogenase (G6PD) deficiency is an X-linked genetic disorder that results in impaired enzyme activity. The G6PD/6PGD ratio assay was routinely used for G6PD deficiency screening in China, but there is an apparent defect of missed diagnosis in heterozygous females. The study aims to explore the means to improve its accuracy. METHODS: A total of 4161 Chinese females of childbearing age were collected in this retrospective study. All samples were first subjected to G6PD/6PGD ratio assay and then screened by amplification refractory mutation system PCR (ARMS-PCR) for six hotspot mutants in Chinese population (c...
October 31, 2022: Human Heredity
Ngoc T Nguyen, Linh T Nguyen, Xuan T Nguyen
Purpose Polycythemia vera is a hematological malignancy characterized by the overproduction of red blood cells in the bone marrow. Pathogenesis of Polycythemia vera was thought to be caused by genetic mutations of the Janus kinase 2 (JAK2) gene, especially the JAK2 V617F and exon 12 mutations since those mutations were found frequently in the patients. The prevalence of JAK2 exon 12 mutations among Polycythemia Vera patients in Vietnam has not been studied yet. Objectives The overall study objective is to investigate the frequency of JAK2 exon 12 mutations among V617F-negative Polycythemia Vera patients in Vietnam...
August 3, 2022: Human Heredity
Baohua Zhou, Xuelian Chu, Caijuan Zhang, Xiufeng Liang
OBJECTIVES: Impairment of mitochondrial function caused by pathogenic mitochondrial DNA (mtDNA) mutations has been found to be associated with pre-eclampsia (PE). However, the underlying mechanism of PE remains poorly undetermined. The aim of this study is to evaluate the relationship between mitochondrial tRNAs (mt-tRNAs) variants and PE. MATERIAL AND METHODS: The mt-tRNAs variants in a cohort of 100 pregnant women with PE and 100 healthy subjects were examined by PCR-Sager sequencing...
July 18, 2022: Human Heredity
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