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1.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 41(4): 456-460, 2024 Apr 10.
Artigo em Chinês | MEDLINE | ID: mdl-38565512

RESUMO

OBJECTIVE: To explore the genetic basis for a patient with autosomal dominant retinitis pigmentosa (RP). METHODS: A male patient with RP treated at Gansu Provincial Maternal and Child Health Care Hospital in September 2019 was selected as the study subject. Clinical data was collected. Peripheral blood samples of the patient and his parents were subjected to whole exome sequencing (WES). Candidate variant was validated by Sanger sequencing and bioinformatic analysis. RESULTS: The patient, a 29-year-old male, developed night blindness, amblyopia, visual field defects and optic disc abnormalities since childhood. Gene sequencing revealed that he has harbored a heterozygous c.942G>C (p.Lys314Asn) variant of the IMPDH1 gene, which was inherited from his mother, whilst his father was of the wild type. Based on the guidelines from the American College of Medical Genetics and Genomics, the c.942G>C variant was predicted as likely pathogenic (PM1+PM2_Supporting+PP3+PP1). CONCLUSION: The c.942G>C (p.Lys314Asn) variant in the IMPDH1 gene probably underlay the RP in this patient.


Assuntos
Retinite Pigmentosa , Adulto , Feminino , Humanos , Masculino , Biologia Computacional , Genômica , Heterozigoto , IMP Desidrogenase , Mães , Mutação , Retinite Pigmentosa/genética
2.
Nat Commun ; 15(1): 2964, 2024 Apr 05.
Artigo em Inglês | MEDLINE | ID: mdl-38580638

RESUMO

The high sequencing error rate has impeded the application of long noisy reads for diploid genome assembly. Most existing assemblers failed to generate high-quality phased assemblies using long noisy reads. Here, we present PECAT, a Phased Error Correction and Assembly Tool, for reconstructing diploid genomes from long noisy reads. We design a haplotype-aware error correction method that can retain heterozygote alleles while correcting sequencing errors. We combine a corrected read SNP caller and a raw read SNP caller to further improve the identification of inconsistent overlaps in the string graph. We use a grouping method to assign reads to different haplotype groups. PECAT efficiently assembles diploid genomes using Nanopore R9, PacBio CLR or Nanopore R10 reads only. PECAT generates more contiguous haplotype-specific contigs compared to other assemblers. Especially, PECAT achieves nearly haplotype-resolved assembly on B. taurus (Bison×Simmental) using Nanopore R9 reads and phase block NG50 with 59.4/58.0 Mb for HG002 using Nanopore R10 reads.


Assuntos
Diploide , Nanoporos , Alelos , Haplótipos , Heterozigoto , Análise de Sequência de DNA/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos
3.
Sci Rep ; 14(1): 8088, 2024 04 06.
Artigo em Inglês | MEDLINE | ID: mdl-38582794

RESUMO

The Amur tiger is currently confronted with challenges of anthropogenic development, leading to its population becoming fragmented into two geographically isolated groups: smaller and larger ones. Small and isolated populations frequently face a greater extinction risk, yet the small tiger population's genetic status and survival potential have not been assessed. Here, a total of 210 samples of suspected Amur tiger feces were collected from this small population, and the genetic background and population survival potentials were assessed by using 14 microsatellite loci. Our results demonstrated that the mean number of alleles in all loci was 3.7 and expected heterozygosity was 0.6, indicating a comparatively lower level of population genetic diversity compared to previously reported studies on other subspecies. The genetic estimates of effective population size (Ne) and the Ne/N ratio were merely 7.6 and 0.152, respectively, representing lower values in comparison to the Amur tiger population in Sikhote-Alin (the larger group). However, multiple methods have indicated the possibility of genetic divergence within our isolated population under study. Meanwhile, the maximum kinship recorded was 0.441, and the mean inbreeding coefficient stood at 0.0868, both of which are higher than those observed in other endangered species, such as the African lion and the grey wolf. Additionally, we have identified a significant risk of future extinction if the lethal equivalents were to reach 6.26, which is higher than that of other large carnivores. Further, our simulation results indicated that an increase in the number of breeding females would enhance the prospects of this population. In summary, our findings provide a critical theoretical basis for further bailout strategies concerning Amur tigers.


Assuntos
Leões , Tigres , Animais , Feminino , Tigres/genética , Espécies em Perigo de Extinção , Heterozigoto , Densidade Demográfica , Repetições de Microssatélites/genética , Leões/genética , Conservação dos Recursos Naturais , Variação Genética
4.
BMC Pediatr ; 24(1): 232, 2024 Apr 02.
Artigo em Inglês | MEDLINE | ID: mdl-38566089

RESUMO

BACKGROUND: Zhu-Tokita-Takenouchi-Kim syndrome (ZTTK syndrome) is a severe multi-systemic developmental disorder, caused by variants in the SON gene. A patient diagnosed with ZTTK syndrome who carried a de novo SON mutation and exhibited recurrent myocardial injury was described in this case. CASE PRESENTATION: A 7-year-old girl was admitted to the Cardiology Department of Beijing Children's Hospital in November 2019 due to myocardial injury following respiratory infection. She displayed elevated myocardial enzymes and severe T-wave changes on electrocardiogram. Over the past three years, she had experienced myocardial injury on three occasions. Additionally, she exhibited intellectual disability, congenital amblyopia, and dysmorphic facial features. Genetic analysis revealed a de novo heterozygous mutation c.3852_3856delGGTAT in the SON gene, which was confirmed by Sanger sequencing of her parents. She received anti-infection treatment and was administered metoprolol orally. Her condition was stable at the time of discharge. Over a 42-month follow-up period at the outpatient clinic, she complained intermittent fatigue and palpitation. CONCLUSIONS: The identified SON mutation, which plays a crucial role in heart development and mitochondrial function, may be associated with an increased susceptibility to myocardial injury or cardiomyopathy. This case report contributes novel insights into this rare condition and suggests the expansion of the ZTTK syndrome phenotype.


Assuntos
Anormalidades do Olho , Deficiência Intelectual , Criança , Feminino , Humanos , Deficiência Intelectual/genética , Mutação , Heterozigoto , Fenótipo , Arritmias Cardíacas
5.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 41(4): 393-398, 2024 Apr 10.
Artigo em Chinês | MEDLINE | ID: mdl-38565502

RESUMO

OBJECTIVE: To analyze the types of genetic variants and clinical characteristics of three Chinese pedigrees affected with Hereditary coagulation factor Ⅶ (FⅦ) deficiency. METHODS: Three pedigrees who had visited the First Affiliated Hospital of Wenzhou Medical University between December 2021 and October 2022 were selected as the study subjects. Prothrombin time (PT), activated partial thromboplastin time (APTT) and FⅦ activity (FⅦ:C) were measured in the three probands and their pedigree members. All exons and their flanking sequences were analyzed by direct sequencing, and candidate variants were verified by reverse sequencing. The corresponding variant loci in the family members were also analyzed. ClustalX-2.1-win was used to analyze the conservation of the variant loci. Varcards and Spcards online software was used to predict the pathogenicity of the variants. Pymol software was used to analyze the changes in protein structure and molecular forces. RESULTS: Three cases of hereditary FⅦ deficiency were found to have decreased FⅦ:C, prolonged PT and normal APTT. Genetic analysis identified a total of four genetic variants, and all three probands had harbored compound heterozygous variants of the F7 gene, including p.Cys389Gly and p.His408Gln in proband 1, p.Cys389Gly and IVS6+1G>T in proband 2, and IVS6+1G>T and IVS1a+5G>A in proband 3. Conservation analysis showed that both the p.Cys389 and p.His408 loci are highly conserved among orthologous species. Analysis with Varcards and Spcards software showed that these variants were pathogenic. Protein modeling analysis showed that the p.Cys389Gly and p.His408Gln variants may result in altered protein structures and changes in hydrogen bonds. CONCLUSION: The clinical manifestations of the three FⅦ-deficient probands may be attributed to the compound heterozygous variants of p.Cys389Gly/p.His408Gln, p.Cys389Gly/IVS6+1G>T and IVS6+1G>T/IVS1a+5G>A of the F7 gene. The combination of the three compound heterozygous variants was unreported previously.


Assuntos
Deficiência do Fator VII , Humanos , Linhagem , Heterozigoto , Deficiência do Fator VII/genética , Mutação , Fator VII/genética , China
8.
PeerJ ; 12: e16934, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38529304

RESUMO

Background: Ischemic stroke (IS) is the main cause of death and adult disability. However, the pathogenesis of this complicated disease is unknown. The present study aimed to assess the relationship between ITLN1 single nucleotide polymorphisms (SNPs) and the susceptibility to IS in Xi'an population, Shaanxi province. Methods: In this study, we designed polymerase chain reaction (PCR) primers located at -3,308 bp upstream of the transcription initiation site within promoter region of the ITLN1 gene. The target fragment was amplified by PCR and identified by agarose gel electrophoresis. Sanger sequencing was then performed in the samples extracted from a cohort comprising 1,272 participants (636 controls and 636 cases), and the obtained sequences were compared with the reference sequences available on the National Center for Biotechnology Information (NCBI) website to detect SNPs in the ITLN1 gene promoter region. Logistic regression analysis was employed to assess the relationship between ITLN1 polymorphisms and IS risk, with adjustments for age and gender. Significant positive results were tested by false-positive report probability (FPRP) and false discovery rate (FDR). The interaction among noteworthy SNPs and their predictive relationship with IS risk were explored using the Multi-Factor Dimensionality Reduction (MDR) software. Results: The results of Sanger sequencing were compared with the reference sequences on the NCBI website, and we found 14 SNPs in ITLN1 gene promoter satisfied Hardy-Weinberg equilibrium (HWE). Logistic regression analysis showed that ITLN1 was associated with a decreased risk of IS (rs6427553: Homozygous C/C: adjusted OR: 0.69, 95% CI [0.48-0.97]; Log-additive: adjusted OR: 0.83, 95% CI [0.70-0.98]; rs7411035: Homozygous G/G: adjusted OR: 0.66, 95% CI [0.47-0.94]; Dominant G/T-G/G: adjusted OR: 0.78, 95% CI [0.62-0.98]; Log-additive: adjusted OR: 0.81, 95% CI [0.69-0.96]; rs4656958: Heterozygous G/A: adjusted OR: 0.74, 95% CI [0.59-0.94]; Homozygous A/A: adjusted OR: 0.51, 95% CI [0.31-0.84]; Dominant G/A-A/A: adjusted OR: 0.71, 95% CI [0.57-0.89]; Recessive A/A: adjusted OR: 0.59, 95% CI [0.36-0.96]; Log-additive: adjusted OR: 0.73, 95% CI [0.61-0.88]), especially in people aged less than 60 years and males. Conclusions: In short, our study revealed a correlation between ITLN1 variants (rs6427553, rs7411035 and rs4656958) and IS risk in Xi'an population, Shaanxi province, laying a foundation for ITLN1 gene as a potential biomarker for predicting susceptibility to IS.


Assuntos
AVC Isquêmico , Polimorfismo de Nucleotídeo Único , Adulto , Humanos , Biomarcadores , Predisposição Genética para Doença/genética , Heterozigoto , AVC Isquêmico/genética , Polimorfismo de Nucleotídeo Único/genética , Citocinas/genética , Lectinas/genética , Proteínas Ligadas por GPI/genética
9.
Intern Med ; 63(5): 687-692, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38432894

RESUMO

17q12 deletion syndrome is a rare chromosomal anomaly with variable phenotypes, caused by the heterozygous deletion of chromosome 17q12. We herein report a 35-year-old Japanese patient with chromosomal 17q12 deletion syndrome identified by de novo deletion of the 1.46 Mb segment at the 17q12 band by genetic analyses. He exhibited a wide range of phenotypes, such as maturity-onset diabetes of the young (MODY) type 5, structural or functional abnormalities of the kidney, liver, and pancreas; facial dysmorphic features, electrolyte disorders; keratoconus, and acquired perforating dermatosis. This case report provides valuable resources concerning the clinical spectrum of rare 17q12 deletion syndrome.


Assuntos
Doenças do Sistema Nervoso Central , Esmalte Dentário/anormalidades , Diabetes Mellitus Tipo 2 , Doenças Renais Císticas , Masculino , Humanos , Adulto , Japão , Face , Heterozigoto
10.
Mol Ecol Resour ; 24(4): e13947, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38433491

RESUMO

Genetic diversity is frequently described using heterozygosity, particularly in a conservation context. Often, it is estimated using single nucleotide polymorphisms (SNPs); however, it has been shown that heterozygosity values calculated from SNPs can be biased by both study design and filtering parameters. Though solutions have been proposed to address these issues, our own work has found them to be inadequate in some circumstances. Here, we aimed to improve the reliability and comparability of heterozygosity estimates, specifically by investigating how sample size and missing data thresholds influenced the calculation of autosomal heterozygosity (heterozygosity calculated from across the genome, i.e. fixed and variable sites). We also explored how the standard practice of tri- and tetra-allelic site exclusion could bias heterozygosity estimates and influence eventual conclusions relating to genetic diversity. Across three distinct taxa (a frog, Litoria rubella; a tree, Eucalyptus microcarpa; and a grasshopper, Keyacris scurra), we found heterozygosity estimates to be meaningfully affected by sample size and missing data thresholds, partly due to the exclusion of tri- and tetra-allelic sites. These biases were inconsistent both between species and populations, with more diverse populations tending to have their estimates more severely affected, thus having potential to dramatically alter interpretations of genetic diversity. We propose a modified framework for calculating heterozygosity that reduces bias and improves the utility of heterozygosity as a measure of genetic diversity, whilst also highlighting the need for existing population genetic pipelines to be adjusted such that tri- and tetra-allelic sites be included in calculations.


Assuntos
Genética Populacional , Polimorfismo de Nucleotídeo Único , Reprodutibilidade dos Testes , Heterozigoto , Alelos
11.
Sci Rep ; 14(1): 6876, 2024 03 22.
Artigo em Inglês | MEDLINE | ID: mdl-38519579

RESUMO

Hydatidiform moles are abnormal conceptuses. Many hydatidiform moles are diploid androgenetic, and of these, most are homozygous in all loci. Additionally, most hydatidiform moles are euploid. Using Single Nucleotide Polymorphism (SNP) array analysis, in two studies a higher frequency of aneuploidy was observed in diploid androgenetic heterozygous conceptuses, than in their homozygous counterparts. In the Danish Mole Project, we analyze conceptuses suspected to be hydatidiform moles due to the clinical presentation, using karyotyping and Short Tandem Repeat (STR) analysis. Among 278 diploid androgenetic conceptuses, 226 were homozygous in all loci and 52 (18.7%) were heterozygous in several loci. Among 142 triploid diandric conceptuses, 141 were heterozygous for paternally inherited alleles in several loci. Here we show that the frequencies of aneuploidy in diploid androgenetic heterozygous and triploid diandric heterozygous conceptuses were significantly higher than the frequency of aneuploidy in diploid androgenetic homozygous conceptuses. In diploid androgenetic and triploid diandric conceptuses that are heterozygous for paternally inherited alleles, the two paternally inherited sets of genomes originate in two spermatozoa. Each spermatozoon provides one pair of centrioles to the zygote. The presence of two pairs of centrioles may cause an increased risk of aneuploidy.


Assuntos
Mola Hidatiforme , Neoplasias Uterinas , Masculino , Gravidez , Feminino , Humanos , Diploide , Triploidia , Mola Hidatiforme/genética , Heterozigoto , Aneuploidia
12.
Stem Cell Res ; 76: 103368, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38430736

RESUMO

Type 1 familial glucocorticoid deficiency (FGD) is a rare autosomal recessive disorder due to variation of the melanocortin-2-receptor (MC2R) gene. Induced pluripotent stem cell (iPSC) line SDQLCHi029-A was successfully generated from peripheral blood mononuclear cells obtained from a 5-day-old girl with MC2R mutations (c.428C > T and c.409C > T). The iPSC line showed genetically stable and matched the donor's PBMCs. displayed a normal karyotype, expressed high pluripotent markers, and exhibited differentiation potential of three germ layers in vitro. The iPSC line could be a good model to study the pathogenesis of FGD type 1 and screen new drugs for the disease.


Assuntos
Células-Tronco Pluripotentes Induzidas , Feminino , Humanos , Células-Tronco Pluripotentes Induzidas/metabolismo , Glucocorticoides , Heterozigoto , Receptor Tipo 2 de Melanocortina/genética , Receptor Tipo 2 de Melanocortina/metabolismo , Leucócitos Mononucleares/metabolismo , Mutação/genética
13.
Stem Cell Res ; 76: 103374, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38458031

RESUMO

The NR2F2 gene encodes the transcription factor COUP-TFII, which is upregulated in embryonic mesoderm. Heterozygous variants in NR2F2 cause a spectrum of congenital anomalies including cardiac and gonadal phenotypes. We generated heterozygous (MCRIi030-A-1) and homozygous (MCRIi030-A-2) NR2F2-knockout induced pluripotent stem cell (iPSC) lines from human fibroblasts using a one-step protocol for CRISPR/Cas9 gene-editing and episomal-based reprogramming. Both iPSC lines exhibited a normal karyotype, typical pluripotent cell morphology, pluripotency marker expression, and the capacity to differentiate into the three embryonic germ layers. These lines will allow us to explore the role of NR2F2 during development and disease.


Assuntos
Células-Tronco Pluripotentes Induzidas , Humanos , Células-Tronco Pluripotentes Induzidas/metabolismo , Coração , Heterozigoto , Homozigoto , Fenótipo , Sistemas CRISPR-Cas/genética , Fator II de Transcrição COUP/genética , Fator II de Transcrição COUP/metabolismo
14.
Stem Cell Res ; 76: 103367, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38479087

RESUMO

Many developmental and epileptic encephalopathies (DEEs) result from variants in cation channel genes. Using mRNA transfection, we generated and characterised an induced pluripotent stem cell (iPSC) line from the fibroblasts of a male late-onset DEE patient carrying a heterozygous missense variant (E1211K) in Nav1.2(SCN2A) protein. The iPSC line displays features characteristic of the human iPSCs, colony morphology and expression of pluripotency-associated marker genes, ability to produce derivatives of all three embryonic germ layers, and normal karyotype without SNP array-detectable abnormalities. We anticipate that this iPSC line will aid in the modelling and development of precision therapies for this debilitating condition.


Assuntos
Encefalopatias , Células-Tronco Pluripotentes Induzidas , Humanos , Masculino , Células-Tronco Pluripotentes Induzidas/metabolismo , Mutação de Sentido Incorreto , Heterozigoto , Mutação , Canal de Sódio Disparado por Voltagem NAV1.2/genética
15.
Proc Biol Sci ; 291(2019): 20232519, 2024 Mar 27.
Artigo em Inglês | MEDLINE | ID: mdl-38503331

RESUMO

Despite decades of research, surprisingly little is known about the mechanism(s) by which an individual's genotype is encoded in odour. Many studies have focused on the role of the major histocompatibility complex (MHC) owing to its importance for survival and mate choice. However, the salience of MHC-mediated odours compared to chemicals influenced by the rest of the genome remains unclear, especially in wild populations where it is challenging to quantify and control for the effects of the genomic background. We addressed this issue in Antarctic fur seals by analysing skin swabs together with full-length MHC DQB II exon 2 sequences and data from 41 genome-wide distributed microsatellites. We did not find any effects of MHC relatedness on chemical similarity and there was also no relationship between MHC heterozygosity and chemical diversity. However, multilocus heterozygosity showed a significant positive association with chemical diversity, even after controlling for MHC heterozygosity. Our results appear to rule out a dominant role of the MHC in the chemical encoding of genetic information in a wild vertebrate population and highlight the need for genome-wide approaches to elucidate the mechanism(s) and specific genes underlying genotype-odour associations.


Assuntos
Otárias , Animais , Otárias/genética , Genótipo , Heterozigoto , Complexo Principal de Histocompatibilidade/genética , Odorantes , Regiões Antárticas
16.
Medicine (Baltimore) ; 103(10): e37446, 2024 Mar 08.
Artigo em Inglês | MEDLINE | ID: mdl-38457547

RESUMO

RATIONALE: Compound heterozygotes for deletional ß-thalassemia can be difficult to diagnose due to its diverse clinical presentations and no routine screenings. This can lead to disease progression and delay in treatment. PATIENT CONCERNS: We reported pedigree analysis and genetic research in a family with rare ß-thalassemia. DIAGNOSIS: Pedigree analysis and genetic research demonstrated that the patient was a compound heterozygote for ß-thalassemia CD17/Southeast Asian hereditary persistence of fetal hemoglobin deletion, inherited from the parents. Magnetic resonance imaging T2* examination revealed severe iron deposition in the liver. Echocardiography revealed endocardial cushion defect. INTERVENTIONS: The patient was treated with Deferasirox after receiving the final molecular genetic diagnosis. The initial once-daily dose of Deferasirox was 20 mg/kg/d. OUTCOMES: The patient discontinued the medication three months after the first visit. Two years later, the patient visited the Department of Hepatobiliary and Pancreatic Diseases. He was recommended to undergo splenectomy after surgical repair of the congenital heart disease. However, the patient refused surgical treatment because of the economic burden. LESSONS: We report that fetal hemoglobin is a sensitive indicator for screening large deletions of the ß-globin gene, which can be effectively confirmed by the multiplex ligation-dependent probe amplification assay. In non-transfusion-dependent thalassemia patients, iron status assessment should be regularly performed, and iron chelation treatment should be initiated early. This case will provide insights for the diagnosis of rare genotypes of ß-thalassemia and has important implications for genetic counseling.


Assuntos
Talassemia beta , Masculino , Humanos , Talassemia beta/genética , Talassemia beta/diagnóstico , Hemoglobina Fetal/genética , Linhagem , Deferasirox , População do Sudeste Asiático , Pesquisa em Genética , China , Ferro , Heterozigoto
17.
Medicine (Baltimore) ; 103(9): e37361, 2024 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-38428858

RESUMO

BACKGROUND: Benign prostatic hyperplasia (BPH) is one of the global public health challenges due to the complexity of its mechanisms of occurrence. Many studies have suggested that vitamin D receptor gene polymorphisms are associated with BPH susceptibility. Still, their conflicting findings need to be analyzed in aggregate to gain a better understanding. METHODS: We identified 10 trials involving 1539 BPH cases and 1915 controls through a systematic search of Embase using, data obtained from the Web of Science, PubMed, and China Knowledge Network databases as of December 31, 2021. A meta-analysis was performed to investigate the association between 4 constant polymorphisms of this associated vitamin D receptor gene (Fok-1, Bsm-1, Taq-1, and Apa-1) and BPH risk. RESULTS: In the overall population analysis, a significant positive association with BPH risk was found only in the Taq-1 variant (P < .001). Of these, the pure-hybrid model (95% confidence interval [CI] = 1.384-3.196), the heterozygous model (95% CI = 1.207-2.021), the dominant model (95% CI = 1.312-2.133) and the allelic inheritance model (95% CI = 1.205-1.730) showed low heterogeneity. In subtype analyses, Bsm-1 variants showed a significant association with BPH risk for both the recessive (95% CI = 0.100-0.943, P = .039) and over-dominant (95% CI = 1.553-3.100, P = 0) models in the Caucasian population, and for the recessive (95% CI = 1.242-3.283, P = .039) and over-dominant (95% CI = 0.281-0.680, P = 0) models in the Asian population. In addition, a high degree of heterogeneity was found in the subgroup analysis of the association between Fok-1 variants and BPH risk. CONCLUSION: Overall, there is an association between vitamin D receptor polymorphisms and BPH risk. Identification of BPH susceptibility by vitamin D receptor gene polymorphisms has potential.


Assuntos
Hiperplasia Prostática , Receptores de Calcitriol , Humanos , Masculino , Predisposição Genética para Doença , Heterozigoto , Polimorfismo Genético , Polimorfismo de Nucleotídeo Único , Hiperplasia Prostática/genética , Receptores de Calcitriol/genética
18.
Parasit Vectors ; 17(1): 106, 2024 Mar 04.
Artigo em Inglês | MEDLINE | ID: mdl-38439081

RESUMO

BACKGROUND: Although whole-genome sequencing (WGS) is the preferred genotyping method for most genomic analyses, limitations are often experienced when studying genomes characterized by a high percentage of repetitive elements, high linkage, and recombination deserts. The Asian tiger mosquito (Aedes albopictus), for example, has a genome comprising up to 72% repetitive elements, and therefore we set out to develop a single-nucleotide polymorphism (SNP) chip to be more cost-effective. Aedes albopictus is an invasive species originating from Southeast Asia that has recently spread around the world and is a vector for many human diseases. Developing an accessible genotyping platform is essential in advancing biological control methods and understanding the population dynamics of this pest species, with significant implications for public health. METHODS: We designed a SNP chip for Ae. albopictus (Aealbo chip) based on approximately 2.7 million SNPs identified using WGS data from 819 worldwide samples. We validated the chip using laboratory single-pair crosses, comparing technical replicates, and comparing genotypes of samples genotyped by WGS and the SNP chip. We then used the chip for a population genomic analysis of 237 samples from 28 sites in the native range to evaluate its usefulness in describing patterns of genomic variation and tracing the origins of invasions. RESULTS: Probes on the Aealbo chip targeted 175,396 SNPs in coding and non-coding regions across all three chromosomes, with a density of 102 SNPs per 1 Mb window, and at least one SNP in each of the 17,461 protein-coding genes. Overall, 70% of the probes captured the genetic variation. Segregation analysis found that 98% of the SNPs followed expectations of single-copy Mendelian genes. Comparisons with WGS indicated that sites with genotype disagreements were mostly heterozygotes at loci with WGS read depth < 20, while there was near complete agreement with WGS read depths > 20, indicating that the chip more accurately detects heterozygotes than low-coverage WGS. Sample sizes did not affect the accuracy of the SNP chip genotype calls. Ancestry analyses identified four to five genetic clusters in the native range with various levels of admixture. CONCLUSIONS: The Aealbo chip is highly accurate, is concordant with genotypes from WGS with high sequence coverage, and may be more accurate than low-coverage WGS.


Assuntos
Aedes , Mosquitos Vetores , Humanos , Animais , Genótipo , Mosquitos Vetores/genética , Heterozigoto , Aedes/genética
19.
J Cardiovasc Med (Hagerstown) ; 25(5): 370-378, 2024 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-38526957

RESUMO

AIMS: Three physical signs, namely tendon xanthomas, corneal arcus and xanthelasma, have been associated with heterozygous familial hypercholesterolemia (heFH). The prevalence and clinical significance of these signs are not well established among contemporary heFH individuals. This study explored the frequency as well as the association of these physical signs with prevalent atherosclerotic cardiovascular disease (ASCVD) in heFH individuals. METHODS: Data from the Hellenic Familial Hypercholesterolemia Registry were applied for this analysis. The diagnosis of heFH was based on the Dutch Lipid Clinic Network Score. Multivariate logistic regression analysis was conducted to examine the association of heFH-related physical signs with prevalent ASCVD. RESULTS: Adult patients ( n  = 2156, mean age 50 ±â€Š15 years, 47.7% women) were included in this analysis. Among them, 14.5% had at least one heFH-related physical sign present. The prevalence of corneal arcus before the age of 45 years was 6.6%, tendon xanthomas 5.3%, and xanthelasmas 5.8%. Among physical signs, only the presence of corneal arcus before the age of 45 years was independently associated with the presence of premature coronary artery disease (CAD). No association of any physical sign with total CAD, stroke or peripheral artery disease was found. Patients with physical signs were more likely to receive higher intensity statin therapy and dual lipid-lowering therapy, but only a minority reached optimal lipid targets. CONCLUSION: The prevalence of physical signs is relatively low in contemporary heFH patients. The presence of corneal arcus before the age of 45 years is independently associated with premature CAD.


Assuntos
Arco Senil , Aterosclerose , Doenças Cardiovasculares , Doença da Artéria Coronariana , Hipercolesterolemia , Hiperlipoproteinemia Tipo II , Xantomatose , Adulto , Humanos , Feminino , Pessoa de Meia-Idade , Idoso , Masculino , Doenças Cardiovasculares/epidemiologia , Arco Senil/diagnóstico , Arco Senil/epidemiologia , Arco Senil/etiologia , Heterozigoto , Hiperlipoproteinemia Tipo II/complicações , Hiperlipoproteinemia Tipo II/diagnóstico , Hiperlipoproteinemia Tipo II/tratamento farmacológico , Aterosclerose/epidemiologia , Hipercolesterolemia/complicações , Doença da Artéria Coronariana/etiologia , Doença da Artéria Coronariana/complicações , Lipídeos , Sistema de Registros , Xantomatose/etiologia , Xantomatose/complicações
20.
Trends Genet ; 40(4): 364-378, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38453542

RESUMO

Dominance is usually considered a constant value that describes the relative difference in fitness or phenotype between heterozygotes and the average of homozygotes at a focal polymorphic locus. However, the observed dominance can vary with the genetic background of the focal locus. Here, alleles at other loci modify the observed phenotype through position effects or dominance modifiers that are sometimes associated with pathogen resistance, lineage, sex, or mating type. Theoretical models have illustrated how variable dominance appears in the context of multi-locus interaction (epistasis). Here, we review empirical evidence for variable dominance and how the observed patterns may be captured by proposed epistatic models. We highlight how integrating epistasis and dominance is crucial for comprehensively understanding adaptation and speciation.


Assuntos
Epistasia Genética , Modelos Genéticos , Heterozigoto , Fenótipo , Homozigoto , Alelos
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