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1.
Artigo em Inglês | MEDLINE | ID: mdl-31494266

RESUMO

To unravel the genetic mechanisms of disease and physiological traits, it requires comprehensive sequencing analysis of large sample size in Chinese populations. Here, we report the primary results of the Chinese Academy of Sciences Precision Medicine Initiative (CASPMI) project launched by the Chinese Academy of Sciences, including the de novo assembly of a northern Han reference genome (NH1.0) and whole genome analyses of 597 healthy people coming from most areas in China. Given the two existing reference genomes for Han Chinese (YH and HX1) were both from the south, we constructed NH1.0, a new reference genome from a northern individual, by combining the sequencing strategies of PacBio, 10× Genomics, and Bionano mapping. Using this integrated approach, we obtained an N50 scaffold size of 46.63 Mb for the NH1.0 genome and performed a comparative genome analysis of NH1.0 with YH and HX1. In order to generate a genomic variation map of Chinese populations, we performed the whole-genome sequencing of 597 participants and identified 24.85 million (M) single nucleotide variants (SNVs), 3.85 M small indels, and 106,382 structural variations. In the association analysis with collected phenotypes, we found that the T allele of rs1549293 in KAT8 significantly correlated with the waist circumference in northern Han males. Moreover, significant genetic diversity in MTHFR, TCN2, FADS1, and FADS2, which associate with circulating folate, vitamin B12, or lipid metabolism, was observed between northerners and southerners. Especially, for the homocysteine-increasing allele of rs1801133 (MTHFR 677T), we hypothesize that there exists a "comfort" zone for a high frequency of 677T between latitudes of 35-45 degree North. Taken together, our results provide a high-quality northern Han reference genome and novel population-specific data sets of genetic variants for use in the personalized and precision medicine.

2.
Cell Metab ; 30(4): 784-799.e5, 2019 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-31474566

RESUMO

Fibrosis is the final common pathway leading to end-stage renal failure. By analyzing the kidneys of patients and animal models with fibrosis, we observed a significant mitochondrial defect, including the loss of the mitochondrial transcription factor A (TFAM) in kidney tubule cells. Here, we generated mice with tubule-specific deletion of TFAM (Ksp-Cre/Tfamflox/flox). While these mice developed severe mitochondrial loss and energetic deficit by 6 weeks of age, kidney fibrosis, immune cell infiltration, and progressive azotemia causing death were only observed around 12 weeks of age. In renal cells of TFAM KO (knockout) mice, aberrant packaging of the mitochondrial DNA (mtDNA) resulted in its cytosolic translocation, activation of the cytosolic cGAS-stimulator of interferon genes (STING) DNA sensing pathway, and thus cytokine expression and immune cell recruitment. Ablation of STING ameliorated kidney fibrosis in mouse models of chronic kidney disease, demonstrating how TFAM sequesters mtDNA to limit the inflammation leading to fibrosis.

4.
Blood Adv ; 3(16): 2512-2524, 2019 Aug 27.
Artigo em Inglês | MEDLINE | ID: mdl-31455667

RESUMO

Graft-versus-host disease (GVHD) and infections are the 2 main causes of death without relapse after allogeneic hematopoietic cell transplantation (HCT). Elevated soluble serum simulation-2 (sST2), the product of IL1RL1 in plasma/serum post-HCT, is a validated GVHD biomarker. Hundreds of SNPs at 2q12.1 have been shown to be strongly associated with sST2 concentrations in healthy populations. We therefore hypothesized that the donor genetic variants in IL1RL1 correlate with sST2 protein levels associated with patient survival outcomes after HCT. We used DISCOVeRY-BMT (Determining the Influence of Susceptibility Conveying Variants Related to 1-Year Mortality after Blood and Marrow Transplantation), a genomic study of >3000 donor-recipient pairs, to inform our hypothesis. We first measured pre-HCT plasma/serum sST2 levels in a subset of DISCOVeRY-BMT donors (n = 757) and tested the association of donor sST2 levels with donor single nucleotide polymorphisms (SNPs) in the 2q12.1 region. Donor SNPs associated with sST2 levels were then tested for association with recipient death caused by acute GVHD (aGVHD)-, infection-, and transplant-related mortality in cohorts 1 and 2. Meta-analyses of cohorts 1 and 2 were performed using fixed-effects inverse variance weighting, and P values were corrected for multiple comparisons. Donor risk alleles in rs22441131 (P meta = .00026) and rs2310241 (P meta = .00033) increased the cumulative incidence of aGVHD death up to fourfold and were associated with high sST2 levels. Donor risk alleles at rs4851601 (P meta = 9.7 × 10-7), rs13019803 (P meta = 8.9 × 10-6), and rs13015714 (P meta = 5.3 × 10-4) increased cumulative incidence of infection death to almost sevenfold and were associated with low sST2 levels. These functional variants are biomarkers of infection or aGVHD death and could facilitate donor selection, prophylaxis, and a conditioning regimen to reduce post-HCT mortality.

5.
Int J Cancer ; 2019 Aug 30.
Artigo em Inglês | MEDLINE | ID: mdl-31469419

RESUMO

Women of African ancestry have lower incidence of epithelial ovarian cancer (EOC) yet worse survival compared to women of European ancestry. We conducted a genome-wide association study in African ancestry women with 755 EOC cases, including 537 high-grade serous ovarian carcinomas (HGSOC) and 1,235 controls. We identified four novel loci with suggestive evidence of association with EOC (p < 1 × 10-6 ), including rs4525119 (intronic to AKR1C3), rs7643459 (intronic to LOC101927394), rs4286604 (12 kb 3' of UGT2A2) and rs142091544 (5 kb 5' of WWC1). For HGSOC, we identified six loci with suggestive evidence of association including rs37792 (132 kb 5' of follistatin [FST]), rs57403204 (81 kb 3' of MAGEC1), rs79079890 (LOC105376360 intronic), rs66459581 (5 kb 5' of PRPSAP1), rs116046250 (GABRG3 intronic) and rs192876988 (32 kb 3' of GK2). Among the identified variants, two are near genes known to regulate hormones and diseases of the ovary (AKR1C3 and FST), and two are linked to cancer (AKR1C3 and MAGEC1). In follow-up studies of the 10 identified variants, the GK2 region SNP, rs192876988, showed an inverse association with EOC in European ancestry women (p = 0.002), increased risk of ER positive breast cancer in African ancestry women (p = 0.027) and decreased expression of GK2 in HGSOC tissue from African ancestry women (p = 0.004). A European ancestry-derived polygenic risk score showed positive associations with EOC and HGSOC in women of African ancestry suggesting shared genetic architecture. Our investigation presents evidence of variants for EOC shared among European and African ancestry women and identifies novel EOC risk loci in women of African ancestry.

6.
Environ Sci Pollut Res Int ; 26(25): 25467-25475, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31264152

RESUMO

This paper conducts a convergence analysis on the energy-environmental efficiency to explore the differences between regions that reflect the implementation effect of the policies on energy-saving and emission reduction. Particularly, for the Yangtze River urban agglomeration, additive model (AM model) is applied to calculate the energy-environmental efficiency, and the convergence model is employed to analyze the heterogeneity and spatial evolution of energy-environmental efficiency. From the results, the energy-environmental efficiency for Suzhou is at a good level; the figures for Wuxi, Yangzhou, and Nantong maintain at medium level; for Zhenjiang, qualified level; and for Nanjing, Changzhou, and Taizhou, poor level. The energy-environmental efficiency of the whole Yangtze River urban agglomeration displays a downward trend of fluctuations. While Nantong reveals a divergent energy-environmental efficiency, Zhenjiang, Changzhou, Wuxi, Yangzhou, and Nanjing Cities generally show a trend of convergence. It was also recognized that the energy-environmental efficiency is gradually decreasing from Southeast to North to Southwest regions. In the past decade, the north region of Yangtze River yielded a divergent development trend, while the southeast and southwest regions appear to have a convergent development trend. In the future, the urban agglomeration needs to promote the coordinated development of the economy and the energy environment, impel the optimization and upgrading of the industrial structure, narrow the regional gap, and adjust the energy consumption habits.

7.
Nat Commun ; 10(1): 2461, 2019 06 05.
Artigo em Inglês | MEDLINE | ID: mdl-31165727

RESUMO

Epigenetic changes might provide the biological explanation for the long-lasting impact of metabolic alterations of diabetic kidney disease development. Here we examined cytosine methylation of human kidney tubules using Illumina Infinium 450 K arrays from 91 subjects with and without diabetes and varying degrees of kidney disease using a cross-sectional design. We identify cytosine methylation changes associated with kidney structural damage and build a model for kidney function decline. We find that the methylation levels of 65 probes are associated with the degree of kidney fibrosis at genome wide significance. In total 471 probes improve the model for kidney function decline. Methylation probes associated with kidney damage and functional decline enrich on kidney regulatory regions and associate with gene expression changes, including epidermal growth factor (EGF). Altogether, our work shows that kidney methylation differences can be detected in patients with diabetic kidney disease and improve kidney function decline models indicating that they are potentially functionally important.


Assuntos
Citosina/metabolismo , Metilação de DNA , Nefropatias Diabéticas/genética , Rim/metabolismo , Idoso , Estudos de Casos e Controles , Ilhas de CpG , Estudos Transversais , Nefropatias Diabéticas/metabolismo , Nefropatias Diabéticas/patologia , Progressão da Doença , Epigênese Genética , Feminino , Fibrose , Regulação da Expressão Gênica , Taxa de Filtração Glomerular , Humanos , Rim/patologia , Masculino , Pessoa de Meia-Idade
8.
JCI Insight ; 4(11)2019 06 06.
Artigo em Inglês | MEDLINE | ID: mdl-31167971

RESUMO

In patients with diabetes mellitus, poor metabolic control has a long-lasting impact on kidney disease development. Epigenetic changes, including cytosine methylation, have been proposed as potential mediators of the long-lasting effect of adverse metabolic events. Our understanding of the presence and contribution of methylation changes to disease development is limited because of the lack of comprehensive base-resolution methylome information of human kidney tissue samples and site-specific methylation editing. Base resolution, whole-genome bisulfite sequencing methylome maps of human diabetic kidney disease (DKD) tubule samples, and associated gene expression measured by RNA sequencing highlighted widespread methylation changes in DKD. Pathway analysis highlighted coordinated (methylation and gene expression) changes in immune signaling, including tumor necrosis factor alpha (TNF). Changes in TNF methylation correlated with kidney function decline. dCas9-Tet1-based lowering of the cytosine methylation level of the TNF differentially methylated region resulted in an increase in the TNF transcript level, indicating that methylation of this locus plays an important role in controlling TNF expression. Increasing the TNF level in diabetic mice increased disease severity, such as albuminuria. In summary, our results indicate widespread methylation differences in DKD kidneys and highlights epigenetic changes in the TNF locus and its contribution to the development of nephropathy in patients with diabetes mellitus.

9.
Int J Cancer ; 2019 Jun 21.
Artigo em Inglês | MEDLINE | ID: mdl-31226226

RESUMO

Latinos represent <1% of samples analyzed to date in genome-wide association studies of cancer. The clinical value of genetic information in guiding personalized medicine in populations of non-European ancestry will require additional discovery and risk locus characterization efforts across populations. In the present study, we performed a GWAS of prostate cancer (PrCa) in 2,820 Latino PrCa cases and 5,293 controls to search for novel PrCa risk loci and to examine the generalizability of known PrCa risk loci in Latino men. We also conducted a genetic admixture-mapping scan to identify PrCa risk alleles associated with local ancestry. Genome-wide significant associations were observed with 84 variants all located at the known PrCa risk regions at 8q24 (128.484-128.548) and 10q11.22 (MSMB gene). In admixture mapping, we observed genome-wide significant associations with local African ancestry at 8q24. Of the 162 established PrCa risk variants that are common in Latino men, 135 (83.3%) had effects that were directionally consistent as previously reported, among which 55 (34.0%) were statistically significant with p < 0.05. A polygenic risk model of the known PrCa risk variants showed that, compared to men with average risk (25th-75th percentile of the polygenic risk score distribution), men in the top 10% had a 3.19-fold (95% CI: 2.65, 3.84) increased PrCa risk. In conclusion, we found that the known PrCa risk variants can effectively stratify PrCa risk in Latino men. Larger studies in Latino populations will be required to discover and characterize genetic risk variants for PrCa and improve risk stratification for this population.

10.
Curr Opin Nephrol Hypertens ; 28(3): 219-226, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-30844884

RESUMO

PURPOSE OF REVIEW: Transcriptome analysis of human kidney samples provides an integrated output of genetic, physiological, or environmental inputs. This review summarizes recent findings including gene expression and genetic variation integration, bulk and single cell gene expression analysis, and describes how such studies have improved our understanding of kidney disease development. RECENT FINDINGS: Bulk or whole tissue analysis of patient kidney samples identified a large number of genes, whose levels correlate with kidney function and/or structural damage. These genes were enriched for metabolic and immune functions. Using expression quantitative trait analysis, genetic variations-driven gene expression can be identified. Recent developments in single cell sequencing defined cell-type-specific gene expression changes and highlighted specific cell types for disease development. SUMMARY: Recent advancement in whole tissue transcriptomics, specifically incorporating genotype information and single cell data have been powerful to identify kidney disease-associated genes, pathways, and cell types.

13.
Nat Commun ; 9(1): 4616, 2018 11 05.
Artigo em Inglês | MEDLINE | ID: mdl-30397198

RESUMO

Chromosome 8q24 is a susceptibility locus for multiple cancers, including prostate cancer. Here we combine genetic data across the 8q24 susceptibility region from 71,535 prostate cancer cases and 52,935 controls of European ancestry to define the overall contribution of germline variation at 8q24 to prostate cancer risk. We identify 12 independent risk signals for prostate cancer (p < 4.28 × 10-15), including three risk variants that have yet to be reported. From a polygenic risk score (PRS) model, derived to assess the cumulative effect of risk variants at 8q24, men in the top 1% of the PRS have a 4-fold (95%CI = 3.62-4.40) greater risk compared to the population average. These 12 variants account for ~25% of what can be currently explained of the familial risk of prostate cancer by known genetic risk factors. These findings highlight the overwhelming contribution of germline variation at 8q24 on prostate cancer risk which has implications for population risk stratification.

14.
Biophys Rep ; 4(4): 189-203, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30310856

RESUMO

In plants, photosystem II (PSII) associates with light-harvesting complexes II (LHCII) to form PSII-LHCII supercomplexes. They are multi-subunit supramolecular systems embedded in the thylakoid membrane of chloroplast, functioning as energy-converting and water-splitting machinery powered by light energy. The high-resolution structure of a PSII-LHCII supercomplex, previously solved through cryo-electron microscopy, revealed 34 well-defined lipid molecules per monomer of the homodimeric system. Here we characterize the distribution of lipid-binding sites in plant PSII-LHCII supercomplex and summarize their arrangement pattern within and across the membrane. These lipid molecules have crucial roles in stabilizing the oligomerization interfaces of plant PSII dimer and LHCII trimer. Moreover, they also mediate the interactions among PSII core subunits and contribute to the assembly between peripheral antenna complexes and PSII core. The detailed information of lipid-binding sites within PSII-LHCII supercomplex may serve as a framework for future researches on the functional roles of lipids in plant photosynthesis.

15.
Biomed Pharmacother ; 108: 741-751, 2018 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-30248542

RESUMO

OBJECTIVE: This study aims to explore the role of Epstein-Barr virus (EBV) miR-BART4 in occurrence and progression of nasopharyngeal carcinoma (NPC) and its effect on radiosensitivity. METHOD: The expressions of EBV and miR-BART4 in 108 cases of NPC tissues and 97 cases of chronic nasopharyngeal inflammation tissues were determined by real time quantitative polymerase chain reaction (PCR), and the relationship between the expression of miR-BART4 and the clinicopathological features of NPC was analyzed. Cell lines, HONEl, CNEl, CNE2, C666-1, 6-10B, and NP-69 were used to compare the expression of miR-BART4, in which the CNE2 cells were selected for further experiments. CNE2 cells were grouped into blank group, negative control (NC) group, miR-BART4 inhibitors group and miR-BART4 mimics group. Cells in above groups were under radiation of 6 Gy X ray for 12 h before grouped into control group, 6 Gy group, NC + 6 Gy group, miR-BART4 inhibitors + 6 Gy group and miR-BART4 mimics + 6 Gy group. Cell proliferation, clone formation ability, cell apoptosis, invasion and migration ability were measured by MTT assay, clone formation assay, flow cytometry (FCM), Transwell assay and scratch test, respectively. Western blot analysis was used to detect the expression of apoptosis-related proteins (cleaved caspase-3, Bax and Bcl-2) and epithelial-mesenchymal transition (EMT) marker protein E-cadherin and Vimentin. mRNA and protein expression of PTEN were detected by qRT-PCR and western blot. Bioinformatics software and luciferase activity experiments were used to verify the targeting relationship between miR-BART4 and PTEN. RESULTS: Positive rate of EBV in NPC tissues (93.5%) was remarkably higher than that in chronic nasopharyngeal inflammation tissues (21.6%). miR-BART4 was highly expressed and mRNA and protein expression of PTEN was lowly expressed in EBV positive NPC tissues compared with EBV negative NPC tissues and chronic nasopharyngeal inflammation tissues. The expression of miR-BART4 was related to the clinical stage, lymph node metastasis and differentiation degree of NPC. Expression of miR-BART4 in CNE2, CNEl, HONEl, C666-1, 6-10B, 5-8F cells was higher than that in NP-69 cells. In CNE2 and C666-1 cell experiments, compared with blank group and NC group, miR-BART4 inhibitors group had decreased miR-BART4 expression, increased mRNA and protein expression of PTEN, cell survival rate, invasion and migration ability and increased cell apoptosis rate, which is totally contrary to the observation in miR-BART4 mimics group. The radiosensitive NPC tissues had higher miR-BART4 expression than that in radio-resistance NPC tissues. In comparison to 6 Gy group and NC + 6 Gy group, cell survival rate and clone number was inhibited, but the cell apoptosis rate was increased in miR-BART4 inhibitors +6 G group, in contrary to the observation in miR-BART4 inhibitors + 6 Gy group. Bioinformatics software and luciferase activity experiments confirmed that miR-BART4 could inhibit the expression of PTEN. CONCLUSION: EBV may promote development and progression of NPC by up-regulating miR-BART4 expressions, consequently inhibiting its radiosensitivity, whose effect may be related to the targeting inhibition of PTEN expression.

16.
J Zhejiang Univ Sci B ; 19(8): 581-595, 2018 Aug..
Artigo em Inglês | MEDLINE | ID: mdl-30070082

RESUMO

Under different red (R):blue (B) photon flux ratios, the growth performance of rapeseed (Brassica napus L.) is significantly different. Rapeseed under high R ratios shows shade response, while under high B ratios it shows sun-type morphology. Rapeseed under monochromatic red or blue light is seriously stressed. Transcriptomic and proteomic methods were used to analyze the metabolic pathway change of rapeseed (cv. "Zhongshuang 11") leaves under different R:B photon flux ratios (including 100R:0B%, 75R:25B%, 25R:75B%, and 0R:100B%), based on digital gene expression (DGE) and two-dimensional gel electrophoresis (2-DE). For DGE analysis, 2054 differentially expressed transcripts (|log2(fold change)|≥1, q<0.005) were detected among the treatments. High R ratios (100R:0B% and 75R:25B%) enhanced the expression of cellular structural components, mainly the cell wall and cell membrane. These components participated in plant epidermis development and anatomical structure morphogenesis. This might be related to the shade response induced by red light. High B ratios (25R:75B% and 0R:100B%) promoted the expression of chloroplast-related components, which might be involved in the formation of sun-type chloroplast induced by blue light. For 2-DE analysis, 37 protein spots showed more than a 2-fold difference in expression among the treatments. Monochromatic light (ML; 100R:0B% and 0R:100B%) stimulated accumulation of proteins associated with antioxidation, photosystem II (PSII), DNA and ribosome repairs, while compound light (CL; 75R:25B% and 25R:75B%) accelerated accumulation of proteins associated with carbohydrate, nucleic acid, amino acid, vitamin, and xanthophyll metabolisms. These findings can be useful in understanding the response mechanisms of rapeseed leaves to different R:B photon flux ratios.

17.
Psychogeriatrics ; 2018 Aug 07.
Artigo em Inglês | MEDLINE | ID: mdl-30088311

RESUMO

BACKGROUND: Caregivers of patients with dementia or Alzheimer's disease (AD) face special health challenges due to the progressive nature of the disease. Self-care has crucial importance on individuals' management of life, health, and well-being. However, limited evidence is available on self-care management of dementia and AD caregivers. This study aimed to investigate the influence of caregiving on the self-care management of dementia and AD caregivers based on the caregivers' experience. In addition, the facilitators of caregivers' self-care management were assessed. METHODS: A sample of 45 caregivers of patients with dementia or AD was recruited from a local community in the south-eastern USA. Semi-structured interviews were conducted. Data were transcribed verbatim and analyzed by the method of cross-case thematic analysis of qualitative data. RESULTS: As reported by the caregivers, caregiving negatively influenced their self-care management, including physical self-care and mental and social self-care. Both internal and external facilitators were found that can assist caregivers' self-care. Caregivers differ considerably in their demographic characteristics, caregiving tasks, and self needs. CONCLUSION: Self-care management of dementia and AD caregivers can be largely affected by caregiving. Awareness, motivation, and knowledge of self-care, as well as knowledge of health-care resources, are important prerequisites for caregivers to achieve self-care management. Given the massive differences in caregiving situations, future intervention studies based on the specific needs of individual caregivers are warranted.

18.
Int J Mol Med ; 42(4): 1809-1818, 2018 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-30015823

RESUMO

Fluid shear stress (FSS) may alter ciliary structures and ciliogenesis, and it has been reported that the Wnt signaling pathway may regulate cilia assembly and disassembly. The present study aimed to investigate the effects of FSS on primary cilia, the Wnt/ß­catenin and Wnt/PCP signaling pathways, and the association among them. In the present study, human umbilical vein endothelial cells were subjected to FSS of differing velocities for various periods of time using a shear stress device. Subsequently, immunofluorescence and quantitative polymerase chain reaction were used to detect the expression and localization of the following core proteins: ß­catenin in the Wnt/ß­catenin signaling pathway; and dishevelled segment polarity protein 2 (Dvl2), fuzzy planar cell polarity protein (Fuz) and VANGL planar cell polarity protein 2 (Vangl2) in the Wnt/planar cell polarity (PCP) signaling pathway. Furthermore, the colocalization of Dvl2 with the basal body was analyzed under low FSS and laminar FSS. The results demonstrated that low FSS promoted the expression of Dvl2 and its colocalization with the basal body. Although Fuz expression was decreased with increasing duration of FSS, no visible alterations were detected in its localization, it was ubiquitously localized in the ciliated region. Conversely, the expression of Vangl2 was increased by laminar FSS, and ß­catenin was translocated into the nucleus at the early stage of low FSS. These findings suggested that Dvl2 may participate in low FSS­induced ciliogenesis and ß­catenin may participate at the early stage, whereas Vangl2 may be associated with laminar FSS­induced cilia disassembly.


Assuntos
Regulação da Expressão Gênica , Células Endoteliais da Veia Umbilical Humana/metabolismo , Resistência ao Cisalhamento , Via de Sinalização Wnt , Cílios/genética , Cílios/metabolismo , Células Endoteliais da Veia Umbilical Humana/citologia , Humanos
19.
Nat Genet ; 50(7): 928-936, 2018 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-29892016

RESUMO

Genome-wide association studies (GWAS) and fine-mapping efforts to date have identified more than 100 prostate cancer (PrCa)-susceptibility loci. We meta-analyzed genotype data from a custom high-density array of 46,939 PrCa cases and 27,910 controls of European ancestry with previously genotyped data of 32,255 PrCa cases and 33,202 controls of European ancestry. Our analysis identified 62 novel loci associated (P < 5.0 × 10-8) with PrCa and one locus significantly associated with early-onset PrCa (≤55 years). Our findings include missense variants rs1800057 (odds ratio (OR) = 1.16; P = 8.2 × 10-9; G>C, p.Pro1054Arg) in ATM and rs2066827 (OR = 1.06; P = 2.3 × 10-9; T>G, p.Val109Gly) in CDKN1B. The combination of all loci captured 28.4% of the PrCa familial relative risk, and a polygenic risk score conferred an elevated PrCa risk for men in the ninetieth to ninety-ninth percentiles (relative risk = 2.69; 95% confidence interval (CI): 2.55-2.82) and first percentile (relative risk = 5.71; 95% CI: 5.04-6.48) risk stratum compared with the population average. These findings improve risk prediction, enhance fine-mapping, and provide insight into the underlying biology of PrCa1.

20.
Nat Commun ; 9(1): 2256, 2018 06 11.
Artigo em Inglês | MEDLINE | ID: mdl-29892050

RESUMO

Prostate cancer is a polygenic disease with a large heritable component. A number of common, low-penetrance prostate cancer risk loci have been identified through GWAS. Here we apply the Bayesian multivariate variable selection algorithm JAM to fine-map 84 prostate cancer susceptibility loci, using summary data from a large European ancestry meta-analysis. We observe evidence for multiple independent signals at 12 regions and 99 risk signals overall. Only 15 original GWAS tag SNPs remain among the catalogue of candidate variants identified; the remainder are replaced by more likely candidates. Biological annotation of our credible set of variants indicates significant enrichment within promoter and enhancer elements, and transcription factor-binding sites, including AR, ERG and FOXA1. In 40 regions at least one variant is colocalised with an eQTL in prostate cancer tissue. The refined set of candidate variants substantially increase the proportion of familial relative risk explained by these known susceptibility regions, which highlights the importance of fine-mapping studies and has implications for clinical risk profiling.

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