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1.
Lancet Oncol ; 24(6): 646-657, 2023 06.
Artigo em Inglês | MEDLINE | ID: mdl-37182538

RESUMO

BACKGROUND: Adding CDK4/6 inhibitor dalpiciclib to fulvestrant significantly prolonged progression-free survival in patients with hormone receptor-positive, HER2-negative advanced breast cancer progressing after endocrine therapy. We aimed to assess the efficacy and safety of dalpiciclib plus letrozole or anastrozole in patients with hormone receptor-positive, HER2-negative advanced breast cancer who had no previous systemic therapy in the advanced setting. METHODS: DAWNA-2 is a randomised, double-blind, placebo-controlled, phase 3 trial done at 42 hospitals in China. Eligible patients were aged 18-75 years, of any menopausal status, had an ECOG performance status of 0-1, and had pathologically confirmed hormone receptor-positive, HER2-negative untreated advanced breast cancer. Patients were randomly assigned (2:1) to receive oral dalpiciclib (150 mg per day for 3 weeks, followed by 1 week off) or matching placebo. Both groups also received endocrine therapy: either 2·5 mg letrozole or 1 mg anastrozole orally once daily continuously. Randomisation was using an interactive web response system (block size of six) and stratified according to visceral metastasis, previous endocrine therapy in the adjuvant or neoadjuvant setting, and endocrine therapy partner. All investigators, patients, and the funders of the study were masked to group allocation. We present the results of the preplanned interim analyses for the primary endpoint of investigator-assessed progression-free survival, which was assessed in all randomly assigned patients who met the eligibility criteria by intention-to treat. Safety was analysed in all randomly assigned patients who received at least one dose of study treatment. The superiority boundary was calculated as a one-sided p value of 0·0076 or less. This trial is registered with ClinicalTrials.gov, NCT03966898, and is ongoing but closed to recruitment. FINDINGS: Between July 19, 2019, and Dec 25, 2020, 580 patients were screened and 456 were eligible and randomly assigned to the dalpiciclib group (n=303) or placebo group (n=153). At data cutoff (June 1, 2022), median follow-up was 21·6 months (IQR 18·3-25·9), and 103 (34%) of 303 patients in the dalpiciclib group and 83 (54%) of 153 patients in the placebo group had disease progression or died. Median progression-free survival was significantly longer in the dalpiciclib group than in the placebo group (30·6 months [95% CI 30·6-not reached] vs 18·2 months [16·5-22·5]; stratified hazard ratio 0·51 [95% CI 0·38-0·69]; one-sided log-rank p<0·0001). Adverse events of grade 3 or 4 were reported in 271 (90%) of 302 patients in the dalpiciclib group and 18 (12%) of 153 patients in the placebo group. The most common adverse events of grade 3 or 4 were neutropenia (259 [86%] in the dalpiciclib group vs none in the placebo group) and leukopenia (201 [67%] vs none). Serious adverse events were reported for 36 (12%) patients in the dalpiciclib group and ten (7%) patients in the placebo group. Two treatment-related deaths occurred, both in the dalpiciclib group (deaths from unknown causes). INTERPRETATION: Our findings suggest that dalpiciclib plus letrozole or anastrozole could be a novel standard first-line treatment for patients with hormone receptor-positive, HER2-negative advanced breast cancer, and is an alternative option to the current treatment landscape. FUNDING: Jiangsu Hengrui Pharmaceuticals and Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences. TRANSLATION: For the Chinese translation of the abstract see Supplementary Materials section.


Assuntos
Neoplasias da Mama , Humanos , Feminino , Neoplasias da Mama/patologia , Letrozol , Anastrozol , Resultado do Tratamento , Intervalo Livre de Doença , Receptor ErbB-2 , Protocolos de Quimioterapia Combinada Antineoplásica/efeitos adversos , Método Duplo-Cego
2.
Am J Hum Genet ; 102(6): 1115-1125, 2018 06 07.
Artigo em Inglês | MEDLINE | ID: mdl-29805041

RESUMO

Spondylocarpotarsal synostosis syndrome (SCTS) is characterized by intervertebral fusions and fusion of the carpal and tarsal bones. Biallelic mutations in FLNB cause this condition in some families, whereas monoallelic variants in MYH3, encoding embryonic heavy chain myosin 3, have been implicated in dominantly inherited forms of the disorder. Here, five individuals without FLNB mutations from three families were hypothesized to be affected by recessive SCTS on account of sibling recurrence of the phenotype. Initial whole-exome sequencing (WES) showed that all five were heterozygous for one of two independent splice-site variants in MYH3. Despite evidence indicating that three of the five individuals shared two allelic haplotypes encompassing MYH3, no second variant could be located in the WES datasets. Subsequent genome sequencing of these three individuals demonstrated a variant altering a 5' UTR splice donor site (rs557849165 in MYH3) not represented by exome-capture platforms. When the cohort was expanded to 16 SCTS-affected individuals without FLNB mutations, nine had truncating mutations transmitted by unaffected parents, and six inherited the rs557849165 variant in trans, an observation at odds with the population allele frequency for this variant. The rs557849165 variant disrupts splicing in the 5' UTR but is still permissive of MYH3 translational initiation, albeit with reduced efficiency. Although some MYH3 variants cause dominant SCTS, these data indicate that others (notably truncating variants) do not, except in the context of compound heterozygosity for a second hypomorphic allele. These observations make genetic diagnosis challenging in the context of simplex presentations of the disorder.


Assuntos
Anormalidades Múltiplas/genética , Genes Recessivos , Vértebras Lombares/anormalidades , Doenças Musculoesqueléticas/genética , Mutação/genética , Cadeias Pesadas de Miosina/genética , Escoliose/congênito , Sinostose/genética , Vértebras Torácicas/anormalidades , Alelos , Mapeamento Cromossômico , Feminino , Filaminas/genética , Haplótipos/genética , Heterozigoto , Humanos , Masculino , Linhagem , Fenótipo , Splicing de RNA/genética , Escoliose/genética , Síndrome , Sequenciamento do Exoma
3.
J Hum Genet ; 66(2): 161-169, 2021 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-32778763

RESUMO

Gout is a complex inflammatory arthritis affecting ~20% of people with an elevated serum urate level (hyperuricemia). Gout and hyperuricemia are essentially specific to humans and other higher primates, with varied prevalence across ancestral groups. SLC2A9 and ABCG2 are major loci associated with both urate and gout in multiple ancestral groups. However, fine mapping has been challenging due to extensive linkage disequilibrium underlying the associated regions. We used trans-ancestral fine mapping integrated with primate-specific genomic information to address this challenge. Trans-ancestral meta-analyses of GWAS cohorts of either European (EUR) or East Asian (EAS) ancestry resulted in single-variant resolution mappings for SLC2A9 (rs3775948 for urate and rs4697701 for gout) and ABCG2 (rs2622621 for gout). Tests of colocalization of variants in both urate and gout suggested existence of a shared candidate causal variant for SLC2A9 only in EUR and for ABCG2 only in EAS. The fine-mapped gout variant rs4697701 was within an ancient enhancer, whereas rs2622621 was within a primate-specific transposable element, both supported by functional evidence from the Roadmap Epigenomics project in human primary tissues relevant to urate and gout. Additional primate-specific elements were found near both loci and those adjacent to SLC2A9 overlapped with known statistical epistatic interactions associated with urate as well as multiple super-enhancers identified in urate-relevant tissues. We conclude that by leveraging ancestral differences trans-ancestral fine mapping has identified ancestral and functional variants for SLC2A9 or ABCG2 with primate-specific regulatory effects on urate and gout.


Assuntos
Membro 2 da Subfamília G de Transportadores de Cassetes de Ligação de ATP/genética , Proteínas Facilitadoras de Transporte de Glucose/genética , Gota/genética , Hiperuricemia/genética , Proteínas de Neoplasias/genética , Locos de Características Quantitativas , Característica Quantitativa Herdável , Sequências Reguladoras de Ácido Nucleico , Animais , Evolução Molecular , Predisposição Genética para Doença , Estudo de Associação Genômica Ampla , Gota/patologia , Humanos , Hiperuricemia/patologia , Masculino , Polimorfismo de Nucleotídeo Único , Primatas , Especificidade da Espécie , Ácido Úrico/sangue
4.
Nat Rev Genet ; 15(11): 722-33, 2014 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-25200660

RESUMO

Genome-wide association studies (GWASs) have become the focus of the statistical analysis of complex traits in humans, successfully shedding light on several aspects of genetic architecture and biological aetiology. Single-nucleotide polymorphisms (SNPs) are usually modelled as having additive, cumulative and independent effects on the phenotype. Although evidently a useful approach, it is often argued that this is not a realistic biological model and that epistasis (that is, the statistical interaction between SNPs) should be included. The purpose of this Review is to summarize recent directions in methodology for detecting epistasis and to discuss evidence of the role of epistasis in human complex trait variation. We also discuss the relevance of epistasis in the context of GWASs and potential hazards in the interpretation of statistical interaction terms.


Assuntos
Epistasia Genética/genética , Genoma Humano/genética , Estudo de Associação Genômica Ampla/métodos , Polimorfismo de Nucleotídeo Único/genética , Algoritmos , Estudo de Associação Genômica Ampla/estatística & dados numéricos , Genótipo , Humanos , Desequilíbrio de Ligação , Modelos Biológicos , Fenótipo
5.
J Hum Genet ; 64(8): 831, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31123311

RESUMO

This article was originally published under a CC BY-NC-SA License, but has now been made available under a CC BY 4.0 License.

6.
Circ Res ; 120(2): 341-353, 2017 Jan 20.
Artigo em Inglês | MEDLINE | ID: mdl-27899403

RESUMO

RATIONALE: Abdominal aortic aneurysm (AAA) is a complex disease with both genetic and environmental risk factors. Together, 6 previously identified risk loci only explain a small proportion of the heritability of AAA. OBJECTIVE: To identify additional AAA risk loci using data from all available genome-wide association studies. METHODS AND RESULTS: Through a meta-analysis of 6 genome-wide association study data sets and a validation study totaling 10 204 cases and 107 766 controls, we identified 4 new AAA risk loci: 1q32.3 (SMYD2), 13q12.11 (LINC00540), 20q13.12 (near PCIF1/MMP9/ZNF335), and 21q22.2 (ERG). In various database searches, we observed no new associations between the lead AAA single nucleotide polymorphisms and coronary artery disease, blood pressure, lipids, or diabetes mellitus. Network analyses identified ERG, IL6R, and LDLR as modifiers of MMP9, with a direct interaction between ERG and MMP9. CONCLUSIONS: The 4 new risk loci for AAA seem to be specific for AAA compared with other cardiovascular diseases and related traits suggesting that traditional cardiovascular risk factor management may only have limited value in preventing the progression of aneurysmal disease.


Assuntos
Aneurisma da Aorta Abdominal/diagnóstico , Aneurisma da Aorta Abdominal/genética , Loci Gênicos/genética , Predisposição Genética para Doença/genética , Estudo de Associação Genômica Ampla/métodos , Aneurisma da Aorta Abdominal/epidemiologia , Predisposição Genética para Doença/epidemiologia , Variação Genética/genética , Estudo de Associação Genômica Ampla/tendências , Humanos
7.
Am J Med Genet B Neuropsychiatr Genet ; 180(7): 488-495, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31264768

RESUMO

Genome-wide association studies (GWAS) of developmental dyslexia (DD) often used European samples and identified only a handful associations with moderate or weak effects. This study aims to identify DD functional variants by integrating the GWAS associations with tissue-specific functional data and test the variants in a Chinese DD study cohort named READ. We colocalized associations from nine DD related GWAS with expression quantitative trait loci (eQTL) derived from brain tissues and identified two eSNPs rs349045 and rs201605. Both eSNPs had supportive evidence of chromatin interactions observed in human hippocampus tissues and their respective target genes ZNF45 and DNAH9 both had lower expression in brain tissues in schizophrenia patients than controls. In contrast, an eSNP rs4234898 previously identified based on eQTL from the lymphoblastic cell lines of dyslexic children had no chromatin interaction with its target gene SLC2A3 in hippocampus tissues and SLC2A3 expressed higher in the schizophrenia patients than controls. We genotyped the three eSNPs in the READ cohort of 372 cases and 354 controls and discovered only weak associations in rs201605 and rs4234898 with three DD symptoms (p < .05). The lack of associations could be due to low power in READ but could also implicate different etiology of DD in Chinese.


Assuntos
Povo Asiático/genética , Dislexia/genética , Dineínas do Axonema/genética , Criança , Estudos de Coortes , Dislexia/metabolismo , Feminino , Predisposição Genética para Doença , Estudo de Associação Genômica Ampla , Genótipo , Humanos , Fatores de Transcrição Kruppel-Like/genética , Masculino , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas/genética , Proteínas Repressoras/genética , População Branca/genética
8.
Hum Mutat ; 39(1): 103-113, 2018 01.
Artigo em Inglês | MEDLINE | ID: mdl-29024177

RESUMO

Loss-of-function mutations in the X-linked gene FLNA can lead to abnormal neuronal migration, vascular and cardiac defects, and congenital intestinal pseudo-obstruction (CIPO), the latter characterized by anomalous intestinal smooth muscle layering. Survival in male hemizygotes for such mutations is dependent on retention of residual FLNA function but it is unclear why a subgroup of males with mutations in the 5' end of the gene can present with CIPO alone. Here, we demonstrate evidence for the presence of two FLNA isoforms differing by 28 residues at the N-terminus initiated at ATG+1 and ATG+82 . A male with CIPO (c.18_19del) exclusively expressed FLNA ATG+82 , implicating the longer protein isoform (ATG+1 ) in smooth muscle development. In contrast, mutations leading to reduction of both isoforms are associated with compound phenotypes affecting the brain, heart, and intestine. RNA-seq data revealed three distinct transcription start sites, two of which produce a protein isoform utilizing ATG+1 while the third utilizes ATG+82 . Transcripts sponsoring translational initiation at ATG+1 predominate in intestinal smooth muscle, and are more abundant compared with the level measured in fibroblasts. Together these observations describe a new mechanism of tissue-specific regulation of FLNA that could reflect the differing mechanical requirements of these cell types during development.


Assuntos
Filaminas/genética , Estudos de Associação Genética , Heterogeneidade Genética , Mutação com Perda de Função , Fenótipo , Transcrição Gênica , Adolescente , Encéfalo/anormalidades , Encéfalo/diagnóstico por imagem , Criança , Sequência Conservada , Análise Mutacional de DNA , Feminino , Filaminas/química , Filaminas/metabolismo , Trato Gastrointestinal/metabolismo , Expressão Gênica , Humanos , Imageamento por Ressonância Magnética , Masculino , Músculo Liso/metabolismo , Isoformas de Proteínas , Adulto Jovem
9.
J Hum Genet ; 63(3): 289-296, 2018 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-29259305

RESUMO

Genome-wide association studies (GWASs) have identified a number of loci for psoriasis but largely ignored non-additive effects. We report a genotypic variability-based GWAS (vGWAS) that can prioritize non-additive loci without requiring prior knowledge of interaction types or interacting factors in two steps, using a mixed model to partition dichotomous phenotypes into an additive component and non-additive environmental residuals on the liability scale and then the Levene's (Brown-Forsythe) test to assess equality of the residual variances across genotype groups genome widely. The vGWAS identified two genome-wide significant (P < 5.0e-08) non-additive loci HLA-C and IL12B that were also genome-wide significant in an accompanying GWAS in the discovery cohort. Both loci were statistically replicated in vGWAS of an independent cohort with a small sample size. HLA-C and IL12B were reported in moderate gene-gene and/or gene-environment interactions in several occasions. We found a moderate interaction with age-of-onset of psoriasis, which was replicated indirectly. The vGWAS also revealed five suggestive loci (P < 6.76e-05) including FUT2 that was associated with psoriasis with environmental aspects triggered by virus infection and/or metabolic factors. Replication and functional investigation are needed to validate the suggestive vGWAS loci.


Assuntos
Predisposição Genética para Doença , Variação Genética , Genótipo , Antígenos HLA-C/genética , Subunidade p40 da Interleucina-12/genética , Psoríase/genética , Locos de Características Quantitativas , Algoritmos , Estudos de Coortes , Estudo de Associação Genômica Ampla , Humanos , Modelos Genéticos , Fenótipo , Polimorfismo de Nucleotídeo Único
11.
Hum Mol Genet ; 23(19): 5061-8, 2014 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-24821702

RESUMO

Human serum uric acid concentration (SUA) is a complex trait. A recent meta-analysis of multiple genome-wide association studies (GWAS) identified 28 loci associated with SUA jointly explaining only 7.7% of the SUA variance, with 3.4% explained by two major loci (SLC2A9 and ABCG2). Here we examined whether gene-gene interactions had any roles in regulating SUA using two large GWAS cohorts included in the meta-analysis [the Atherosclerosis Risk in Communities study cohort (ARIC) and the Framingham Heart Study cohort (FHS)]. We found abundant genome-wide significant local interactions in ARIC in the 4p16.1 region located mostly in an intergenic area near SLC2A9 that were not driven by linkage disequilibrium and were replicated in FHS. Taking the forward selection approach, we constructed a model of five SNPs with marginal effects and three epistatic SNP pairs in ARIC-three marginal SNPs were located within SLC2A9 and the remaining SNPs were all located in the nearby intergenic area. The full model explained 1.5% more SUA variance than that explained by the lead SNP alone, but only 0.3% was contributed by the marginal and epistatic effects of the SNPs in the intergenic area. Functional analysis revealed strong evidence that the epistatically interacting SNPs in the intergenic area were unusually enriched at enhancers active in ENCODE hepatic (HepG2, P = 4.7E-05) and precursor red blood (K562, P = 5.0E-06) cells, putatively regulating transcription of WDR1 and SLC2A9. These results suggest that exploring epistatic interactions is valuable in uncovering the complex functional mechanisms underlying the 4p16.1 region.


Assuntos
Cromossomos Humanos Par 4 , Epistasia Genética , Proteínas Facilitadoras de Transporte de Glucose/genética , Característica Quantitativa Herdável , Ácido Úrico/sangue , Linhagem Celular , Biologia Computacional , Elementos Facilitadores Genéticos , Feminino , Estudo de Associação Genômica Ampla , Genômica , Proteínas Facilitadoras de Transporte de Glucose/metabolismo , Humanos , Masculino , Modelos Genéticos , Modelos Estatísticos , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas
13.
Chem Pharm Bull (Tokyo) ; 63(10): 780-91, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26423034

RESUMO

Estrogen receptor α (ERα) and estrogen receptor ß (ERß) regulate different sets of gene expression, and have different ligand responses, which make the estrogen tissue-specific. Thus, the estrogen receptor (ER) subtype-selective ligands can improve the target-site selectivity and decrease the off-target effect. In order to discover the selective ER subtype ligands with novel scaffolds, in this work three-dimensional (3D) pharmacophore models of the ERα ligands (Hypo 1) and the ERß ligands (Hypo 2) were established (correlation coefficients were 0.959 and 0.966) and validated (R=0.936 and 0.879; enrichment factors (EFs) at 2% were 16.2 and 8.4; areas under the concentration-time curve (AUC) of the receiver operating curve (ROC) were 0.88 and 0.91) using the Discovery Studio 4.0 software package. Hypo 1 and Hypo 2 were then employed for virtual screening and ten hits were found as potential candidate leads. Based on their ERα/ERß binding affinity results by fluorescence polarization technology, two of these leads, AH-262/34334025 (AH) and AG-670/08803023 (AG) with novel scaffolds were identified as selective ERα ligands. A molecular docking study was also performed, which provided the explanation for the ER subtype preferences for AH and AG.


Assuntos
Descoberta de Drogas , Receptor alfa de Estrogênio/metabolismo , Receptor beta de Estrogênio/metabolismo , Bibliotecas de Moléculas Pequenas/química , Bibliotecas de Moléculas Pequenas/farmacologia , Bases de Dados de Produtos Farmacêuticos , Humanos , Ligantes , Modelos Moleculares , Ligação Proteica
14.
Nucleic Acids Res ; 40(Web Server issue): W628-32, 2012 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-22689639

RESUMO

Genome-wide association studies (GWAS) have discovered many loci associated with common disease and quantitative traits. However, most GWAS have not studied the gene-gene interactions (epistasis) that could be important in complex trait genetics. A major challenge in analysing epistasis in GWAS is the enormous computational demands of analysing billions of SNP combinations. Several methods have been developed recently to address this, some using computers equipped with particular graphical processing units, most restricted to binary disease traits and all poorly suited to general usage on the most widely used operating systems. We have developed the BiForce Toolbox to address the demand for high-throughput analysis of pairwise epistasis in GWAS of quantitative and disease traits across all commonly used computer systems. BiForce Toolbox is a stand-alone Java program that integrates bitwise computing with multithreaded parallelization and thus allows rapid full pairwise genome scans via a graphical user interface or the command line. Furthermore, BiForce Toolbox incorporates additional tests of interactions involving SNPs with significant marginal effects, potentially increasing the power of detection of epistasis. BiForce Toolbox is easy to use and has been applied in multiple studies of epistasis in large GWAS data sets, identifying interesting interaction signals and pathways.


Assuntos
Epistasia Genética , Estudo de Associação Genômica Ampla , Software , Genômica/métodos , Internet , Polimorfismo de Nucleotídeo Único
15.
Transfus Clin Biol ; 2024 Jun 12.
Artigo em Inglês | MEDLINE | ID: mdl-38871075

RESUMO

OBJECTIVES: This study aims to demonstrate that utilizing a personalized approach to apheresis stem cell collection, can safely optimize the collection outcomes, especially in the context of poor mobilizers and high cell targets. BACKGROUND: The optimal mobilization and harvesting of peripheral blood stem cells is critical to the success of the stem cell transplant. The ideal strategy that promotes better cell yields, with sustainable use of resources and assuring patient safety, should be pursued. METHODS: PBSC collections for autologous stem cell transplant data according to a fixed-processed volume strategy (One Size Fits All) or individualized to patients CD34+ peripheral blood content and target approach (Custom-Tailored or CT) were retrospectively compared. RESULTS: A total of 263 collections from 142 patients were assessed. The majority of patients were male, had multiple myeloma and were mobilized with isolated G-CSF. The CT strategy promoted a significantly higher CD34+ cell yield when the pre-collection CD34 was lower than 20/µl (1.02 ± 0.16 versus 1.36 ± 0.23, p < 0.001) and also a decrease in the proportion of mobilization cycles that needed 3 apheresis (31% versus 14%, p = 0.02). There was no difference in apheresis-related adverse events between the groups. CONCLUSION: Tailoring the apheresis procedures to the patient-specific characteristics and objectives, can effectively promote better patient outcome.

16.
Genes Brain Behav ; 23(3): e12899, 2024 06.
Artigo em Inglês | MEDLINE | ID: mdl-38752599

RESUMO

Reading disorders (RD) are human-specific neuropsychological conditions associated with decoding printed words and/or reading comprehension. So far only a handful of candidate genes segregated in families and 42 loci from genome-wide association study (GWAS) have been identified that jointly provided little clues of pathophysiology. Leveraging human-specific genomic information, we critically assessed the RD candidates for the first time and found substantial human-specific features within. The GWAS candidates (i.e., population signals) were distinct from the familial counterparts and were more likely pleiotropic in neuropsychiatric traits and to harbor human-specific regulatory elements (HSREs). Candidate genes associated with human cortical morphology indeed showed human-specific expression in adult brain cortices, particularly in neuroglia likely regulated by HSREs. Expression levels of candidate genes across human brain developmental stages showed a clear pattern of uplifted expression in early brain development crucial to RD development. Following the new insights and loci pleiotropic in cognitive traits, we identified four novel genes from the GWAS sub-significant associations (i.e., FOXO3, MAPT, KMT2E and HTT) and the Semaphorin gene family with functional priors (i.e., SEMA3A, SEMA3E and SEMA5B). These novel genes were related to neuronal plasticity and disorders, mostly conserved the pattern of uplifted expression in early brain development and had evident expression in cortical neuroglial cells. Our findings jointly illuminated the association of RD with neuroglia regulation-an emerging hotspot in studying neurodevelopmental disorders, and highlighted the need of improving RD phenotyping to avoid jeopardizing future genetic studies of RD.


Assuntos
Dislexia , Estudo de Associação Genômica Ampla , Neuroglia , Humanos , Dislexia/genética , Neuroglia/metabolismo
17.
Front Microbiol ; 15: 1392090, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38808273

RESUMO

Introduction: Through the combined use of two nitrification inhibitors, Dicyandiamide (DCD) and chlorate with nitrogen amendment, this study aimed to investigate the contribution of comammox Nitrospira clade B, ammonia oxidizing bacteria (AOB) and archaea (AOA) to nitrification in a high fertility grassland soil, in a 90-day incubation study. Methods: The soil was treated with nitrogen (N) at three levels: 0 mg-N kg-1 soil, 50 mg-N kg-1 soil, and 700 mg-N kg-1 soil, with or without the two nitrification inhibitors. The abundance of comammox Nitrospira, AOA, AOB, and nitrite oxidising bacteria (NOB) was measured using qPCR. The comammox Nitrospira community structure was assessed using Illumina sequencing. Results and Discussion: The results showed that the application of chlorate inhibited the oxidation of both NH4+ and NO2- in all three nitrogen treatments. The application of chlorate significantly reduced the abundance of comammox Nitrospira amoA and nxrB genes across the 90-day experimental period. Chlorate also had a significant effect on the beta diversity (Bray-Curtis dissimilarity) of the comammox Nitrospira clade B community. Whilst AOB grew in response to the N substrate additions and were inhibited by both inhibitors, AOA showed litle or no response to either the N substrate or inhibitor treatments. In contrast, comammox Nitrospira clade B were inhibited by the high ammonium concentrations released from the urine substrates. These results demonstrate the differential and niche responses of the three ammonia oxidising communities to N substrate additions and nitrification inhibitor treatments. Further research is needed to investigate the specificity of the two inhibitors on the different ammonia oxidising communities.

18.
Bioinformatics ; 28(15): 1957-64, 2012 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-22618535

RESUMO

MOTIVATION: Gene-gene interactions (epistasis) are thought to be important in shaping complex traits, but they have been under-explored in genome-wide association studies (GWAS) due to the computational challenge of enumerating billions of single nucleotide polymorphism (SNP) combinations. Fast screening tools are needed to make epistasis analysis routinely available in GWAS. RESULTS: We present BiForce to support high-throughput analysis of epistasis in GWAS for either quantitative or binary disease (case-control) traits. BiForce achieves great computational efficiency by using memory efficient data structures, Boolean bitwise operations and multithreaded parallelization. It performs a full pair-wise genome scan to detect interactions involving SNPs with or without significant marginal effects using appropriate Bonferroni-corrected significance thresholds. We show that BiForce is more powerful and significantly faster than published tools for both binary and quantitative traits in a series of performance tests on simulated and real datasets. We demonstrate BiForce in analysing eight metabolic traits in a GWAS cohort (323 697 SNPs, >4500 individuals) and two disease traits in another (>340 000 SNPs, >1750 cases and 1500 controls) on a 32-node computing cluster. BiForce completed analyses of the eight metabolic traits within 1 day, identified nine epistatic pairs of SNPs in five metabolic traits and 18 SNP pairs in two disease traits. BiForce can make the analysis of epistasis a routine exercise in GWAS and thus improve our understanding of the role of epistasis in the genetic regulation of complex traits. AVAILABILITY AND IMPLEMENTATION: The software is free and can be downloaded from http://bioinfo.utu.fi/BiForce/. CONTACT: wenhua.wei@igmm.ed.ac.uk SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Assuntos
Biologia Computacional/métodos , Epistasia Genética , Estudo de Associação Genômica Ampla , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Software , Algoritmos , Simulação por Computador , Humanos , Modelos Genéticos , Polimorfismo de Nucleotídeo Único
19.
Front Bioinform ; 3: 1161167, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37056664

RESUMO

Genomic changes specific to higher primates are regarded as primate-specific genomic information (PSI). Using PSI to inform genetic studies is highly desirable but hampered by three factors: heterogeneity among PSI studies, lack of integrated profiles of the identified PSI elements and dearth of relevant functional information. We report a database of 19,767 PSI elements collated from nine types of brain-related studies, which form 19,473 non-overlapping PSI regions that distribute unevenly but jointly cover only 0.81% of the genome. About 2.5% of the PSI regions colocalized with variants identified in genome-wide association studies, with disease loci more likely colocalized than quantitative trait loci (p = 1.6 × 10-5), particularly in regions without obvious regulatory roles. We further showed an LRP4 exemplar region with PSI elements orchestrated with common and rare disease variants and other functional elements. Our results render PSI elements as a valuable source to inform genetic studies of complex diseases.

20.
Blood Transfus ; 21(5): 428-436, 2023 09.
Artigo em Inglês | MEDLINE | ID: mdl-36580030

RESUMO

BACKGROUND: Children have different clinical and physiological drivers for transfusion from adult recipients. However, adverse transfusion reactions (ATRs) in pediatric patients are usually reported using the same criteria as for adults. Broad assessments of pediatric ATRs neglect substantial variation in different developmental stages. MATERIALS AND METHODS: This retrospective study included 342,950 patients, ~2.43 million transfusions, and 5,540 ATR reports collated from New Zealand hospitals between 2005 and 2021. Using 16 years as the upper age limit, 138,856 pediatric transfusions and 402 pediatric ATR reports were identified and dissected at three levels: pediatric as a whole, pediatric developmental stage (i.e., neonate, infant, preschool, and school), and chronological age to identify patients at high risk of ATRs. Multivariate logistic regression analysis was followed to quantify risk factors. RESULTS: Pediatric recipients had a higher ATR risk than adults (p=6.9-07) but the high risk was associated mainly with children older than 2 years. Neonates and infants accounted for 75.0% of pediatric recipients but had much lower ATR rates than adults. Pediatric transfusion recipients showed a clear male bias prior to age 11 years and then a female bias. However, gender difference in experiencing ATRs was significant only after age 13 years (p=2.3-04). Analyses focusing on the high-risk group revealed allergic reactions being the cause of the elevated risk and identified the main risk factors of number of transfusions (p=4.5-10) and multiple types of components transfused (p=2.0-13). DISCUSSION: The identified ATR risk factors signal linkage with the biological drivers for transfusion. Low ATR rates in infancy could also be attributed to use of neonatal components, low transfusions per patient, and less developed immunity. The relative increase in female recipients from age 11 may be associated with increased red blood cell demand following puberty.


Assuntos
Hipersensibilidade , Reação Transfusional , Recém-Nascido , Lactente , Adulto , Humanos , Criança , Masculino , Pré-Escolar , Feminino , Adolescente , Estudos Retrospectivos , Nova Zelândia/epidemiologia , Transfusão de Sangue , Reação Transfusional/epidemiologia , Reação Transfusional/etiologia , Hipersensibilidade/etiologia
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