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Clinical Genetics Jun 2023Exome sequencing of genes associated with heritable thoracic aortic disease (HTAD) failed to identify a pathogenic variant in a large family with Marfan syndrome (MFS)....
Exome sequencing of genes associated with heritable thoracic aortic disease (HTAD) failed to identify a pathogenic variant in a large family with Marfan syndrome (MFS). A genome-wide linkage analysis for thoracic aortic disease identified a peak at 15q21.1, and genome sequencing identified a novel deep intronic FBN1 variant that segregated with thoracic aortic disease in the family (LOD score 2.7) and was predicted to alter splicing. RT-PCR and bulk RNA sequencing of RNA harvested from fibroblasts explanted from the affected proband revealed an insertion of a pseudoexon between exons 13 and 14 of the FBN1 transcript, predicted to lead to nonsense mediated decay (NMD). Treating the fibroblasts with an NMD inhibitor, cycloheximide, greatly improved the detection of the pseudoexon-containing transcript. Family members with the FBN1 variant had later onset aortic events and fewer MFS systemic features than typical for individuals with haploinsufficiency of FBN1. Variable penetrance of the phenotype and negative genetic testing in MFS families should raise the possibility of deep intronic FBN1 variants and the need for additional molecular studies.
Topics: Humans; Marfan Syndrome; Fibrillin-1; Mutation; Phenotype; Aortic Diseases
PubMed: 36861389
DOI: 10.1111/cge.14322 -
Archives of Sexual Behavior Nov 2021Male sexual orientation is a scientifically and socially important trait shown by family and twin studies to be influenced by environmental and complex genetic factors.... (Meta-Analysis)
Meta-Analysis
Male sexual orientation is a scientifically and socially important trait shown by family and twin studies to be influenced by environmental and complex genetic factors. Individual genome-wide linkage studies (GWLS) have been conducted, but not jointly analyzed. Two main datasets account for > 90% of the published GWLS concordant sibling pairs on the trait and are jointly analyzed here: MGSOSO (Molecular Genetic Study of Sexual Orientation; 409 concordant sibling pairs in 384 families, Sanders et al. (2015)) and Hamer (155 concordant sibling pairs in 145 families, Mustanski et al. (2005)). We conducted multipoint linkage analyses with Merlin on the datasets separately since they were genotyped differently, integrated genetic marker positions, and combined the resultant LOD (logarithm of the odds) scores at each 1 cM grid position. We continue to find the strongest linkage support at pericentromeric chromosome 8 and chromosome Xq28. We also incorporated the remaining published GWLS dataset (on 55 families) by using meta-analytic approaches on published summary statistics. The meta-analysis has maximized the positional information from GWLS of currently available family resources and can help prioritize findings from genome-wide association studies (GWAS) and other approaches. Although increasing evidence highlights genetic contributions to male sexual orientation, our current understanding of contributory loci is still limited, consistent with the complexity of the trait. Further increasing genetic knowledge about male sexual orientation, especially via large GWAS, should help advance our understanding of the biology of this important trait.
Topics: Female; Genetic Linkage; Genome, Human; Genome-Wide Association Study; Humans; Lod Score; Male; Sexual Behavior
PubMed: 34080073
DOI: 10.1007/s10508-021-02035-3 -
Genome Medicine Aug 2021Obesity predisposes individuals to multiple cardiometabolic disorders, including type 2 diabetes (T2D). As body mass index (BMI) cannot reliably differentiate fat from...
BACKGROUND
Obesity predisposes individuals to multiple cardiometabolic disorders, including type 2 diabetes (T2D). As body mass index (BMI) cannot reliably differentiate fat from lean mass, the metabolically detrimental abdominal obesity has been estimated using waist-hip ratio (WHR). Waist-hip ratio adjusted for body mass index (WHRadjBMI) in turn is a well-established sex-specific marker for abdominal fat and adiposity, and a predictor of adverse metabolic outcomes, such as T2D. However, the underlying genes and regulatory mechanisms orchestrating the sex differences in obesity and body fat distribution in humans are not well understood.
METHODS
We searched for genetic master regulators of WHRadjBMI by employing integrative genomics approaches on human subcutaneous adipose RNA sequencing (RNA-seq) data (n ~ 1400) and WHRadjBMI GWAS data (n ~ 700,000) from the WHRadjBMI GWAS cohorts and the UK Biobank (UKB), using co-expression network, transcriptome-wide association study (TWAS), and polygenic risk score (PRS) approaches. Finally, we functionally verified our genomic results using gene knockdown experiments in a human primary cell type that is critical for adipose tissue function.
RESULTS
Here, we identified an adipose gene co-expression network that contains 35 obesity GWAS genes and explains a significant amount of polygenic risk for abdominal obesity and T2D in the UKB (n = 392,551) in a sex-dependent way. We showed that this network is preserved in the adipose tissue data from the Finnish Kuopio Obesity Study and Mexican Obesity Study. The network is controlled by a novel adipose master transcription factor (TF), TBX15, a WHRadjBMI GWAS gene that regulates the network in trans. Knockdown of TBX15 in human primary preadipocytes resulted in changes in expression of 130 network genes, including the key adipose TFs, PPARG and KLF15, which were significantly impacted (FDR < 0.05), thus functionally verifying the trans regulatory effect of TBX15 on the WHRadjBMI co-expression network.
CONCLUSIONS
Our study discovers a novel key function for the TBX15 TF in trans regulating an adipose co-expression network of 347 adipose, mitochondrial, and metabolically important genes, including PPARG, KLF15, PPARA, ADIPOQ, and 35 obesity GWAS genes. Thus, based on our converging genomic, transcriptional, and functional evidence, we interpret the role of TBX15 to be a main transcriptional regulator in the adipose tissue and discover its importance in human abdominal obesity.
Topics: Adipocytes; Adipose Tissue; Adiposity; Aged; Algorithms; Biomarkers; Body Mass Index; Cells, Cultured; Computational Biology; Diabetes Mellitus, Type 2; Disease Susceptibility; Gene Expression Profiling; Gene Expression Regulation; Gene Knockdown Techniques; Gene Regulatory Networks; Genome-Wide Association Study; High-Throughput Nucleotide Sequencing; Humans; Lod Score; Male; Middle Aged; Obesity, Abdominal; T-Box Domain Proteins; Trans-Activators; Waist-Hip Ratio
PubMed: 34340684
DOI: 10.1186/s13073-021-00939-2 -
The Science of the Total Environment Aug 2022Enantiomeric profiling can supplement wastewater-based epidemiology (WBE) by providing additional information on drug origin (licit or illicit), improving consumption...
Enantiomeric profiling can supplement wastewater-based epidemiology (WBE) by providing additional information on drug origin (licit or illicit), improving consumption estimates, i.e., differentiating between disposal and consumption, and offering an insight into the potency of drugs available on the illicit drug market. We report on the enantiomeric profiling of amphetamines in wastewater using R(-)-α-methoxy-α-(trifluoromethyl) phenylacetyl chloride (R-MTPCl), a chiral derivatising agent and GC-MS/MS. The method performed well when evaluated against the SANTE/12682/2019 guidelines in terms of recovery (81-99%), accuracy (99-111%), repeatability (1-8%RSD) and linearity (LOQ-1000 ng/mL). The LOD and LOQ were 120 ng/L and 400 ng/L, respectively. The method was applied to samples of raw wastewater from two Slovene municipalities with unusual levels of amphetamines: Ljubljana (LJ1) and Velenje (VE1). LJ1 had an anomalously high mass load of MDMA (3,4-methylenedioxymethamphetamine) identified during SCORE 2020, and VE1 is a representative sample of the consistently high mass load of amphetamine. A second Ljubljana sample (LJ2) was chosen as a representative sample. The presence of racemic MDMA (EF = 0.511) in LJ1 indicated the disposal of the unused drug into the sewer, while the enrichment of R-MDMA (EF = 0.666) in the combined extract sample from Ljubljana (LJ2) indicated consumption. In the case of Velenje and Ljubljana, it is impossible to distinguish between the direct disposal and consumption of amphetamine and methamphetamine. Also, since amphetamine/methamphetamine-based prescription medications are unavailable in Slovenia, racemic amphetamine in VE1 (EF = 0.514) and LJ2 (EF = 0.459) indicate racemic and the more potent S-amphetamine are sold on the illicit drug market. Only S-methamphetamine was detected in wastewater (LJ2: EF = 0), indicating the presence of only the more potent S-methamphetamine on the illicit drug market. Overall, enantiomeric profiling provided useful information on amphetamine residues. In addition, chiral derivatisation can be a cost-effective alternative to using chiral chromatographic columns for the enantiomeric profiling of amphetamines in wastewater.
Topics: Amphetamine; Amphetamines; Gas Chromatography-Mass Spectrometry; Illicit Drugs; Methamphetamine; N-Methyl-3,4-methylenedioxyamphetamine; Substance Abuse Detection; Tandem Mass Spectrometry; Wastewater; Water Pollutants, Chemical
PubMed: 35490814
DOI: 10.1016/j.scitotenv.2022.155594 -
PloS One 2020Primary focal hyperhidrosis (PFH, OMIM %144110) is a genetically influenced condition characterised by excessive sweating. Prevalence varies between 1.0-6.1% in the...
Primary focal hyperhidrosis (PFH, OMIM %144110) is a genetically influenced condition characterised by excessive sweating. Prevalence varies between 1.0-6.1% in the general population, dependent on ethnicity. The aetiology of PFH remains unclear but an autosomal dominant mode of inheritance, incomplete penetrance and variable phenotypes have been reported. In our study, nine pedigrees (50 affected, 53 non-affected individuals) were included. Clinical characterisation was performed at the German Hyperhidrosis Centre, Munich, by using physiological and psychological questionnaires. Genome-wide parametric linkage analysis with GeneHunter was performed based on the Illumina genome-wide SNP arrays. Haplotypes were constructed using easyLINKAGE and visualised via HaploPainter. Whole-exome sequencing (WES) with 100x coverage in 31 selected members (24 affected, 7 non-affected) from our pedigrees was achieved by next generation sequencing. We identified four genome-wide significant loci, 1q41-1q42.3, 2p14-2p13.3, 2q21.2-2q23.3 and 15q26.3-15q26.3 for PFH. Three pedigrees map to a shared locus at 2q21.2-2q23.3, with a genome-wide significant LOD score of 3.45. The chromosomal region identified here overlaps with a locus at chromosome 2q22.1-2q31.1 reported previously. Three families support 1q41-1q42.3 (LOD = 3.69), two families share a region identical by descent at 2p14-2p13.3 (LOD = 3.15) and another two families at 15q26.3 (LOD = 3.01). Thus, our results point to considerable genetic heterogeneity. WES did not reveal any causative variants, suggesting that variants or mutations located outside the coding regions might be involved in the molecular pathogenesis of PFH. We suggest a strategy based on whole-genome or targeted next generation sequencing to identify causative genes or variants for PFH.
Topics: Chromosome Mapping; Female; Genetic Linkage; Genetic Predisposition to Disease; Genome-Wide Association Study; Germany; Haplotypes; High-Throughput Nucleotide Sequencing; Humans; Hyperhidrosis; Male; Pedigree; Polymorphism, Single Nucleotide; Exome Sequencing
PubMed: 33378362
DOI: 10.1371/journal.pone.0244565 -
Atherosclerosis Jan 2020Oxidative stress is associated with cardiometabolic traits in observational studies, yet the underlying causal relationship remains unclear. Apolipoprotein E-deficient...
BACKGROUND AND AIMS
Oxidative stress is associated with cardiometabolic traits in observational studies, yet the underlying causal relationship remains unclear. Apolipoprotein E-deficient (Apoe) mice develop significant hyperlipidemia and hyperglycemia on a Western diet. Here we conducted linkage analysis to investigate genetic connections between cardiometabolic traits and oxidative stress.
METHODS
266 female F2 mice were generated from an intercross between C57BL/6 (B6) and BALB/c (BALB) Apoe mice and fed 12 weeks of Western diet. Plasma levels of HDL, LDL cholesterol, triglycerides, glucose and malondialdehyde (MDA) and atherosclerosis in aortic root and left carotid artery were measured. 127 microsatellite markers across the genome were genotyped.
RESULTS
One significant locus at 78.3 cM on chromosome (Chr) 1 (LOD score: 3.85), named Mda1, and two suggestive loci near 60.3 cM on Chr1 (LOD score: 2.32, named Mda2 due to replication in a separate cross) and 19.6 cM on Chr4 (LOD score: 2.34) were identified for MDA levels. Mda1 coincided precisely with loci for LDL, triglyceride, glucose, and body weight and overlapped with a locus for atherosclerosis in the aortic root. Plasma LDL, triglyceride, and glucose explained 25.5, 19.2, and 24.2% of the variation in MDA levels of F2 mice, respectively. After correction for triglyceride or LDL, QTLs for MDA on Chr1 and Chr4 disappeared. QTLs on Chr1 disappeared, remained on Chr4, and additional QTLs on Chr12 and Chr13 were detected after correction for glucose. The QTL on Chr12, named Mda3, had a significant LOD score of 8.034 and peaked 62.22 at cM.
CONCLUSIONS
We demonstrated a causative role for cardiometabolic traits in oxidative stress and identified hyperlipidemia and hyperglycemia as a major driver of oxidative stress.
Topics: Animals; Apolipoproteins E; Cholesterol, LDL; Crosses, Genetic; Disease Models, Animal; Female; Genetic Linkage; Genotype; Hyperlipidemias; Mice; Mice, Inbred BALB C; Mice, Inbred C57BL; Mice, Knockout; Oxidative Stress; Triglycerides
PubMed: 31821957
DOI: 10.1016/j.atherosclerosis.2019.11.034 -
Journal of Medical Genetics Sep 2022Auriculocondylar syndrome (ARCND) is a rare genetic disease that affects structures derived from the first and second pharyngeal arches, mainly resulting in micrognathia...
BACKGROUND
Auriculocondylar syndrome (ARCND) is a rare genetic disease that affects structures derived from the first and second pharyngeal arches, mainly resulting in micrognathia and auricular malformations. To date, pathogenic variants have been identified in three genes involved in the EDN1-DLX5/6 pathway (, and ) and some cases remain unsolved. Here we studied a large unsolved four-generation family.
METHODS
We performed linkage analysis, resequencing and Capture-C to investigate the causative variant of this family. To test the pathogenicity of the CNV found, we modelled the disease in patient craniofacial progenitor cells, including induced pluripotent cell (iPSC)-derived neural crest and mesenchymal cells.
RESULTS
This study highlights a fourth locus causative of ARCND, represented by a tandem duplication of 430 kb in a candidate region on chromosome 7 defined by linkage analysis. This duplication segregates with the disease in the family (LOD score=2.88) and includes , which is located over 200 kb telomeric to the top candidate gene . Notably, Capture-C analysis revealed multiple cis interactions between the promoter and possible regulatory elements within the duplicated region. Modelling of the disease revealed an increased expression of and its neighbouring gene, , in neural crest cells. We also identified decreased migration of iPSC-derived neural crest cells together with dysregulation of osteogenic differentiation in iPSC-affected mesenchymal stem cells.
CONCLUSION
Our findings support the hypothesis that the 430 kb duplication is causative of the ARCND phenotype in this family and that deregulation of expression during craniofacial development can contribute to the phenotype.
Topics: Ear; Ear Diseases; Humans; Nuclear Proteins; Osteogenesis; Regulatory Sequences, Nucleic Acid; Twist-Related Protein 1
PubMed: 34750192
DOI: 10.1136/jmedgenet-2021-107825 -
International Journal of Molecular... Nov 2023Rice plant height is an agricultural trait closely related to biomass, lodging tolerance, and yield. Identifying quantitative trait loci (QTL) regions related to plant...
Rice plant height is an agricultural trait closely related to biomass, lodging tolerance, and yield. Identifying quantitative trait loci (QTL) regions related to plant height regulation and developing strategies to screen potential candidate genes can improve agricultural traits in rice. In this study, a double haploid population (CNDH), derived by crossing 'Cheongcheong' and 'Nagdong' individuals, was used, and a genetic map was constructed with 222 single-sequence repeat markers. In the RM3482-RM212 region on chromosome 1, , , , , and were identified for five consecutive years. The phenotypic variance explained ranged from 9.3% to 13.1%, and the LOD score ranged between 3.6 and 17.6. , a candidate gene related to plant height regulation, was screened in RM3482-RM212. is an ortholog of gibberellin 20 oxidase 2, and its haplotype was distinguished by nine SNPs. Plants were divided into two groups based on their height, and tall and short plants were distinguished and clustered according to the expression level of . QTLs and candidate genes related to plant height regulation, and thus, biomass regulation, were screened and identified in this study, but the molecular mechanism of the regulation remains poorly known. The information obtained in this study will help develop molecular markers for marker-assisted selection and breeding through rice plant height control.
Topics: Humans; Quantitative Trait Loci; Chromosome Mapping; Oryza; Plant Breeding; Phenotype
PubMed: 38069217
DOI: 10.3390/ijms242316895 -
Sensitivity and performance of three novel quantitative assays of SARS-CoV-2 nucleoprotein in blood.Scientific Reports Feb 2023To assess if SARS-CoV-2 (COVID-19) systemic disease can be determined by available nucleoprotein assays, we compared the performance of three commercial SARS-CoV-2...
To assess if SARS-CoV-2 (COVID-19) systemic disease can be determined by available nucleoprotein assays, we compared the performance of three commercial SARS-CoV-2 nucleoprotein (N) assays in plasma. A total of 272 plasma samples collected in the period November-December 2021 were analyzed by the methods Simoa SARS CoV-2 N Protein Advantage Kit [Quanterix Simoa], Solsten SARS-CoV-2 Antigen enzyme immunosorbent assay (ELISA) [Solsten ELISA], and Elecsys SARS-CoV-2 Antigen electrochemiluminescence immunoassay [Elecsys ECLIA]. Additionally, a dilution series of inactivated virus culture was analyzed by the three assays. The SARS CoV-2 PCR-status was not known for the patients. Linear correlation in the pairwise correlation between assays as well as linearity of dilution series of inactivated virus culture was estimated by Spearman score. Sensitivity and specificity were estimated by pairwise comparison. The three assays showed poor agreement on patient samples with regards to concentration. Performance on virus culture was excellent but with different level of detection (LOD). Positive vs negative results show comparable sensitivity and specificity of Quanterix Simoa and Solsten ELISA, with a higher LOD in Elecsys ECLIA and thus lower sensitivity and high specificity. N by all tested assays can be used as a marker for systemic COVID-19 disease.
Topics: Humans; SARS-CoV-2; COVID-19; Plasma; Biological Assay; Immunosorbents; Nucleoproteins
PubMed: 36806155
DOI: 10.1038/s41598-023-29973-3 -
Chemicke Zvesti 2023In this study an efficient and environment friendly electrochemical sensor has been designed for the analysis of acetaminophen (APAP) drug. Electrochemical impedance...
UNLABELLED
In this study an efficient and environment friendly electrochemical sensor has been designed for the analysis of acetaminophen (APAP) drug. Electrochemical impedance spectroscopy, differential pulse voltammetry and cyclic voltammetric techniques were used to demonstrate the fabricated erGO/GCE sensor performance. Voltammetric assessment of acetaminophen drug was done using bare GC electrode, drop-casted GO/GC electrode and erGO/GCE electrochemical sensor. Proposed sensor was precisely validated for APAP detection by differential pulse voltammetric technique. Subsequently LOD, LOQ, sensitivity and linearity were determined and found to be 7.23 nM, 21.909 nM, 20.14 μA nM cm and 0.0219-2.30 μM, respectively. The diffusion coefficient of APAP was determined by chronoamperometry, and it was found to be 2.24 × 10 cm.s. The synthetic and analytical steps were assessed as per the Green Chemistry's 12 Principles giving a 66 score (acceptable) and 93 score (excellent) for the said steps, respectively.
SUPPLEMENTARY INFORMATION
The online version contains supplementary material available at 10.1007/s11696-022-02628-9.
PubMed: 36589858
DOI: 10.1007/s11696-022-02628-9