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1.
Commun Biol ; 4(1): 266, 2021 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-33649486

RESUMO

Keratoconus is characterised by reduced rigidity of the cornea with distortion and focal thinning that causes blurred vision, however, the pathogenetic mechanisms are unknown. It can lead to severe visual morbidity in children and young adults and is a common indication for corneal transplantation worldwide. Here we report the first large scale genome-wide association study of keratoconus including 4,669 cases and 116,547 controls. We have identified significant association with 36 genomic loci that, for the first time, implicate both dysregulation of corneal collagen matrix integrity and cell differentiation pathways as primary disease-causing mechanisms. The results also suggest pleiotropy, with some disease mechanisms shared with other corneal diseases, such as Fuchs endothelial corneal dystrophy. The common variants associated with keratoconus explain 12.5% of the genetic variance, which shows potential for the future development of a diagnostic test to detect susceptibility to disease.

2.
Haematologica ; 2021 Feb 11.
Artigo em Inglês | MEDLINE | ID: mdl-33567813

RESUMO

Symptomatic methotrexate-related central neurotoxicity, 'MTX neurotoxicity', is a severe toxicity experienced during acute lymphoblastic leukemia (ALL) therapy with potential long-term neurologic complications. Risk factors and long-term outcomes require further study. We conducted a systematic, retrospective review of 1251 consecutive Australian children enrolled on BFM or COG-based protocols between 1998-2013. Clinical risk predictors for MTX neurotoxicity were analyzed using regression. A genome-wide association study (GWAS) was performed on 48 cases and 537 controls. The incidence of MTX neurotoxicity was 7.6% (n=95/1251), at a median of 4 months from ALL diagnosis and 8 days after intravenous or intrathecal MTX. Grade 3 elevation of serum aspartate aminotransferase (P=0.005, OR 2.31 (1.28-4.16)) in induction/consolidation was associated with MTX neurotoxicity, after accounting for the only established risk factor, age a10 years. Cumulative incidence of CNS relapse was increased in children where intrathecal MTX was omitted following symptomatic MTX neurotoxicity (n=48) compared to where intrathecal MTX was continued throughout therapy (n=1174) (P=0.047). Five-year CNS relapsefree survival was 89.2%±4.6% when intrathecal MTX was ceased compared to 95.4%±0.6% when intrathecal MTX was continued. Recurrence of MTX neurotoxicity was low (12.9%) for patients whose intrathecal MTX was continued after their first episode. The GWAS identified SNPs associated with MTX neurotoxicity near genes regulating neuronal growth, neuronal differentiation and cytoskeletal organization (P>1E-06). In conclusion, increased serum aspartate aminotransferase and age a10 years at diagnosis were independent risk factors for MTX neurotoxicity. Our data do not support cessation of intrathecal MTX after a first MTX neurotoxicity event.

3.
Hum Mol Genet ; 29(21): 3578-3587, 2021 Jan 06.
Artigo em Inglês | MEDLINE | ID: mdl-33410475

RESUMO

Germline genetic variants have been identified, which predispose individuals and families to develop melanoma. Tumor thickness is the strongest predictor of outcome for clinically localized primary melanoma patients. We sought to determine whether there is a heritable genetic contribution to variation in tumor thickness. If confirmed, this will justify the search for specific genetic variants influencing tumor thickness. To address this, we estimated the proportion of variation in tumor thickness attributable to genome-wide genetic variation (variant-based heritability) using unrelated patients with measured primary cutaneous melanoma thickness. As a secondary analysis, we conducted a genome-wide association study (GWAS) of tumor thickness. The analyses utilized 10 604 individuals with primary cutaneous melanoma drawn from nine GWAS datasets from eight cohorts recruited from the general population, primary care and melanoma treatment centers. Following quality control and filtering to unrelated individuals with study phenotypes, 8125 patients were used in the primary analysis to test whether tumor thickness is heritable. An expanded set of 8505 individuals (47.6% female) were analyzed for the secondary GWAS meta-analysis. Analyses were adjusted for participant age, sex, cohort and ancestry. We found that 26.6% (SE 11.9%, P = 0.0128) of variation in tumor thickness is attributable to genome-wide genetic variation. While requiring replication, a chromosome 11 locus was associated (P < 5 × 10-8) with tumor thickness. Our work indicates that sufficiently large datasets will enable the discovery of genetic variants associated with greater tumor thickness, and this will lead to the identification of host biological processes influencing melanoma growth and invasion.

4.
Nat Commun ; 12(1): 246, 2021 01 11.
Artigo em Inglês | MEDLINE | ID: mdl-33431812

RESUMO

Previous Mendelian randomization (MR) studies on 25-hydroxyvitamin D (25(OH)D) and cancer have typically adopted a handful of variants and found no relationship between 25(OH)D and cancer; however, issues of horizontal pleiotropy cannot be reliably addressed. Using a larger set of variants associated with 25(OH)D (74 SNPs, up from 6 previously), we perform a unified MR analysis to re-evaluate the relationship between 25(OH)D and ten cancers. Our findings are broadly consistent with previous MR studies indicating no relationship, apart from ovarian cancers (OR 0.89; 95% C.I: 0.82 to 0.96 per 1 SD change in 25(OH)D concentration) and basal cell carcinoma (OR 1.16; 95% C.I.: 1.04 to 1.28). However, after adjustment for pigmentation related variables in a multivariable MR framework, the BCC findings were attenuated. Here we report that lower 25(OH)D is unlikely to be a causal risk factor for most cancers, with our study providing more precise confidence intervals than previously possible.


Assuntos
Predisposição Genética para Doença , Análise da Randomização Mendeliana , Neoplasias/genética , Vitamina D/metabolismo , Estudos de Casos e Controles , Criança , Humanos , Análise Multivariada , Pigmentação/genética , Fatores de Risco , Queimadura Solar/genética
5.
PLoS One ; 16(1): e0236904, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33465101

RESUMO

BACKGROUND: Observational studies have reported either null or weak protective associations for coffee consumption and risk of breast cancer. METHODS: We conducted a two-sample Mendelian randomization (MR) analysis to evaluate the relationship between coffee consumption and breast cancer risk using 33 single-nucleotide polymorphisms (SNPs) associated with coffee consumption from a genome-wide association (GWA) study on 212,119 female UK Biobank participants of White British ancestry. Risk estimates for breast cancer were retrieved from publicly available GWA summary statistics from the Breast Cancer Association Consortium (BCAC) on 122,977 cases (of which 69,501 were estrogen receptor (ER)-positive, 21,468 ER-negative) and 105,974 controls of European ancestry. Random-effects inverse variance weighted (IVW) MR analyses were performed along with several sensitivity analyses to assess the impact of potential MR assumption violations. RESULTS: One cup per day increase in genetically predicted coffee consumption in women was not associated with risk of total (IVW random-effects; odds ratio (OR): 0.91, 95% confidence intervals (CI): 0.80-1.02, P: 0.12, P for instrument heterogeneity: 7.17e-13), ER-positive (OR = 0.90, 95% CI: 0.79-1.02, P: 0.09) and ER-negative breast cancer (OR: 0.88, 95% CI: 0.75-1.03, P: 0.12). Null associations were also found in the sensitivity analyses using MR-Egger (total breast cancer; OR: 1.00, 95% CI: 0.80-1.25), weighted median (OR: 0.97, 95% CI: 0.89-1.05) and weighted mode (OR: 1.00, CI: 0.93-1.07). CONCLUSIONS: The results of this large MR study do not support an association of genetically predicted coffee consumption on breast cancer risk, but we cannot rule out existence of a weak association.

6.
JAMA Ophthalmol ; 139(2): 224-231, 2021 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-33331888

RESUMO

Importance: Glaucoma is the world's leading cause of irreversible blindness. Primary open-angle glaucoma (POAG) is typically asymptomatic early in the disease process, and unfortunately, many are diagnosed too late to prevent vision loss. Observations: Genome-wide association studies, which evaluate the association between genetic variants and phenotype across the genome, have mapped many genes for POAG. As well as uncovering new biology, genetic information can be combined into a polygenic risk score (PRS), which aggregates an individual's disease risk over many genetic variants. In this nonsystematic review, performed from June 21, 2019, to October 1, 2020, we address a series of questions to explain the challenges and opportunities in translating genetic discoveries in POAG. We summarize what is known about POAG genetics and how its endophenotypes, such as intraocular pressure or cup-disc ratio, can help with prediction. We discuss the sample sizes available and how increases in the future may have an effect on the utility of prediction approaches. We explore particular scenarios, such as the use of PRS in risk stratification, and applications for individuals who are particularly high risk for POAG as a result of them carrying both a high penetrance mutation and an unfavorable PRS. Finally, we discuss the issue of equity in applying these tests and the prospects for prediction for people from various ancestry groups. The cost-effectiveness evaluation of glaucoma PRS in direct-to-consumer genetic testing and across different ancestry groups is warranted in future research. Conclusions and Relevance: Advances in glaucoma genetics have opened the door for risk stratification based on genetic risk predictions. The PRS approach has shown good promise in predicting who will be at highest risk of POAG, which could improve outcomes if these predictions can be acted on to result in improved clinical outcomes.

7.
Ophthalmol Glaucoma ; 2020 Dec 11.
Artigo em Inglês | MEDLINE | ID: mdl-33316431

RESUMO

PURPOSE: Intraocular pressure (IOP) elevations may occur in early morning or outside office hours and can be missed during routine in-clinic IOP measurements. Such fluctuations or peaks likely contribute to glaucoma progression. We sought to investigate the relationship between an IOP polygenic risk score (PRS) and short-term IOP profile. DESIGN: Cross-sectional study. PARTICIPANTS: Four hundred seventy-three eyes from 239 participants with suspected or established primary open-angle glaucoma sampled from 4 outpatient clinics in Australia between August 2016 and December 2019. METHODS: Participants underwent Icare HOME (Icare Oy, Vanda, Finland) tonometer measurements to record IOP 4 times daily for 5 days. Unreliable measurements were excluded. A minimum of 2 days with at least 3 reliable measurements were required. We used a validated IOP PRS derived from 146 IOP-associated variants in a linear regression model adjusted for central corneal thickness and age. MAIN OUTCOME MEASURES: Highest recorded early morning IOP and mean IOP within and outside office hours. Early morning IOP spikes were defined by a higher early morning IOP than the maximum in-office hours IOP. RESULTS: Reliable measurements were obtained from 334 eyes of 176 participants (mean age, 64 ± 9 years). Eyes in the highest IOP PRS quintile showed an early morning IOP increase of 4.3 mmHg (95% confidence interval [CI], 1.4-7.3; P = 0.005) and mean increase in IOP outside office hours of 2.7 mmHg (95% CI, 0.61-4.7; P = 0.013) than the lowest quintile, which were significant independently after accounting for a recent in-clinic IOP measured by Goldmann applanation tonometry. Eyes in the highest PRS quintile were 5.4-fold more likely to show early morning IOP spikes than the lowest quintile (odds ratio 95% CI, 1.3-23.6; P = 0.023). CONCLUSIONS: A validated IOP PRS was associated with higher early morning IOP and mean IOP outside office hours. These findings support a role for genetic risk prediction of susceptibility to elevated IOP that may not be apparent during in-clinic hours, requiring more detailed clinical phenotyping using home tonometry, the results of which may guide additional interventions to improve IOP control.

8.
Int J Epidemiol ; 2020 Dec 28.
Artigo em Inglês | MEDLINE | ID: mdl-33370439

RESUMO

BACKGROUND: Epidemiological studies have consistently documented an increased risk of developing primary non-cutaneous malignancies among people with a history of keratinocyte carcinoma (KC). However, the mechanisms underlying this association remain unclear. We conducted two separate analyses to test whether genetically predicted KC is related to the risk of developing cancers at other sites. METHODS: In the first approach (one-sample), we calculated the polygenic risk scores (PRS) for KC using individual-level data in the UK Biobank (n = 394 306) and QSkin cohort (n = 16 896). The association between the KC PRS and each cancer site was assessed using logistic regression. In the secondary (two-sample) approach, we used genome-wide association study (GWAS) summary statistics identified from the most recent GWAS meta-analysis of KC and obtained GWAS data for each cancer site from the UK-Biobank participants only. We used inverse-variance-weighted methods to estimate risks across all genetic variants. RESULTS: Using the one-sample approach, we found that the risks of cancer at other sites increased monotonically with KC PRS quartiles, with an odds ratio (OR) of 1.16, 95% confidence interval (CI): 1.13-1.19 for those in KC PRS quartile 4 compared with those in quartile 1. In the two-sample approach, the pooled risk of developing other cancers was statistically significantly elevated, with an OR of 1.05, 95% CI: 1.03-1.07 per doubling in the odds of KC. We observed similar trends of increasing cancer risk with increasing KC PRS in the QSkin cohort. CONCLUSION: Two different genetic approaches provide compelling evidence that an instrumental variable for KC constructed from genetic variants predicts the risk of cancers at other sites.

9.
Int J Epidemiol ; 2020 Nov 19.
Artigo em Inglês | MEDLINE | ID: mdl-33211829

RESUMO

BACKGROUND: Age-related macular degeneration (AMD) is a leading cause of vision loss. Whereas lipids have been studied extensively to understand their effects on cardiovascular diseases, their relationship with AMD remains unclear. METHODS: Two-sample Mendelian randomization (MR) analyses were performed to systematically evaluate the causal relationships between eight serum lipid biomarkers, consisting of apolipoprotein A1 (ApoA1), apolipoprotein B (ApoB), total cholesterol (CHOL), high-density lipoprotein cholesterol (HDL-C), direct low-density lipoprotein cholesterol (LDL-C), lipoprotein A [Lp(a)], triglycerides (TG) and non-HDL cholesterol (non-HDL-C), and the risk of different AMD stages and subtypes. We derived 64-407 genetic instruments for eight serum lipid biomarkers in 419 649 participants of European descent from the UK Biobank cohort. We conducted genome-wide association studies (GWAS) for 12 711 advanced AMD cases [8544 choroidal neovascularization (CNV) and 2656 geographic atrophy (GA) specific AMD subtypes] and 5336 intermediate AMD cases with 14 590 controls of European descent from the International AMD Genomics Consortium. RESULTS: Higher genetically predicted HDL-C and ApoA1 levels increased the risk of all AMD subtypes. LDL-C, ApoB, CHOL and non-HDL-C levels were associated with decreased risk of intermediate and GA AMD but not with CNV. Genetically predicted TG levels were associated with decreased risk of different AMD subtypes. Sensitivity analyses revealed no evidence for directional pleiotropy effects. In our multivariable MR analyses, adjusting for the effects of correlated lipid biomarkers yielded similar results. CONCLUSION: These results suggest the role of lipid metabolism in drusen formation and particularly in AMD development at the early and intermediate stages. Mechanistic studies are warranted to investigate the utility of lipid pathways for therapeutic treatment in preventing AMD.

10.
J Am Chem Soc ; 142(43): 18330-18335, 2020 Oct 28.
Artigo em Inglês | MEDLINE | ID: mdl-33052653

RESUMO

We report on the synthesis of an alkane-soluble Zintl cluster, [η4-Ge9(Hyp)3]Rh(COD), that can catalytically hydrogenate cyclic alkenes such as 1,5-cyclooctadiene and cis-cyclooctene. This is the first example of a well-defined Zintl-cluster-based homogeneous catalyst.

11.
Inorg Chem ; 59(21): 15606-15619, 2020 Nov 02.
Artigo em Inglês | MEDLINE | ID: mdl-33074685

RESUMO

The preparation and reactivity with H2 of two Ru complexes of the novel ZnPhos ligand (ZnPhos = Zn(o-C6H4PPh2)2) are described. Ru(ZnPhos)(CO)3 (2) and Ru(ZnPhos)(IMe4)2 (4; IMe4 = 1,3,4,5-tetramethylimidazol-2-ylidene) are formed directly from the reaction of Ru(PPh3)(C6H4PPh2)2(ZnMe)2 (1) or Ru(PPh3)3HCl/LiCH2TMS/ZnMe2 with CO and IMe4, respectively. Structural and electronic structure analyses characterize both 2 and 4 as Ru(0) species in which Ru donates to the Z-type Zn center of the ZnPhos ligand; in 2, Ru adopts an octahedral coordination, while 4 displays square-pyramidal coordination with Zn in the axial position. Under photolytic conditions, 2 loses CO to give Ru(ZnPhos)(CO)2 that then adds H2 over the Ru-Zn bond to form Ru(ZnPhos)(CO)2(µ-H)2 (3). In contrast, 4 reacts directly with H2 to set up an equilibrium with Ru(ZnPhos)(IMe4)2H2 (5), the product of oxidative addition at the Ru center. DFT calculations rationalize these different outcomes in terms of the energies of the square-pyramidal Ru(ZnPhos)L2 intermediates in which Zn sits in a basal site: for L = CO, this is readily accessed and allows H2 to add across the Ru-Zn bond, but for L = IMe4, this species is kinetically inaccessible and reaction can only occur at the Ru center. This difference is related to the strong π-acceptor ability of CO compared to IMe4. Steric effects associated with the larger IMe4 ligands are not significant. Species 4 can be considered as a Ru(0)L4 species that is stabilized by the Ru→Zn interaction. As such, it is a rare example of a stable Ru(0)L4 species devoid of strong π-acceptor ligands.

12.
Chemistry ; 2020 Oct 28.
Artigo em Inglês | MEDLINE | ID: mdl-33112000

RESUMO

By using single-crystal to single-crystal solid-state molecular organometallic (SMOM) techniques, the  σ -alkane complex [Rh( t Bu 2 PCH 2 CH 2 CH 2 P t Bu 2 )( η 2 , η 2 -C 7 H 12 )][BAr F 4 ] (Ar F  = 3,5-(CF 3 ) 2 C 6 H 3 ) is synthesized and structurally characterized, in which the alkane (norbornane) binds through two  exo -C-H···Rh interactions. In contrast, the bis-cyclohexyl phosphine analogue shows  endo -alkane binding. Comparison of the two systems, supported by periodic DFT calculations, NCI plots and Hirshfeld surface analyses, trace this different regioselectivity to subtle changes in the local microenvironment surrounding the alkane ligand. A tertiary periodic structure supporting a secondary microenvironment that controls binding at the metal site has parallels with enzymes. The new  σ -alkane complex is also a catalyst for solid/gas 1-butene isomerization, and catalyst resting states are identified for this.

13.
Int J Cancer ; 2020 Sep 25.
Artigo em Inglês | MEDLINE | ID: mdl-32976626

RESUMO

Alcohol consumption is correlated positively with risk for breast cancer in observational studies, but observational studies are subject to reverse causation and confounding. The association with epithelial ovarian cancer (EOC) is unclear. We performed both observational Cox regression and two-sample Mendelian randomization (MR) analyses using data from various European cohort studies (observational) and publicly available cancer consortia (MR). These estimates were compared to World Cancer Research Fund (WCRF) findings. In our observational analyses, the multivariable-adjusted hazard ratios (HR) for a one standard drink/day increase was 1.06 (95% confidence interval [CI]; 1.04, 1.08) for breast cancer and 1.00 (0.92, 1.08) for EOC, both of which were consistent with previous WCRF findings. MR ORs per genetically predicted one standard drink/day increase estimated via 34 SNPs using MR-PRESSO were 1.00 (0.93, 1.08) for breast cancer and 0.95 (0.85, 1.06) for EOC. Stratification by EOC subtype or estrogen receptor status in breast cancers made no meaningful difference to the results. For breast cancer, the CIs for the genetically derived estimates include the point-estimate from observational studies so are not inconsistent with a small increase in risk. Our data provide additional evidence that alcohol intake is unlikely to have anything other than a very small effect on risk of EOC.

14.
Hum Mol Genet ; 29(17): 2976-2985, 2020 Oct 10.
Artigo em Inglês | MEDLINE | ID: mdl-32716505

RESUMO

Cancers, including cutaneous melanoma, can cluster in families. In addition to environmental etiological factors such as ultraviolet radiation, cutaneous melanoma has a strong genetic component. Genetic risks for cutaneous melanoma range from rare, high-penetrance mutations to common, low-penetrance variants. Known high-penetrance mutations account for only about half of all densely affected cutaneous melanoma families, and the causes of familial clustering in the remainder are unknown. We hypothesize that some clustering is due to the cumulative effect of a large number of variants of individually small effect. Common, low-penetrance genetic risk variants can be combined into polygenic risk scores. We used a polygenic risk score for cutaneous melanoma to compare families without known high-penetrance mutations with unrelated melanoma cases and melanoma-free controls. Family members had significantly higher mean polygenic load for cutaneous melanoma than unrelated cases or melanoma-free healthy controls (Bonferroni-corrected t-test P = 1.5 × 10-5 and 6.3 × 10-45, respectively). Whole genome sequencing of germline DNA from 51 members of 21 families with low polygenic risk for melanoma identified a CDKN2A p.G101W mutation in a single family but no other candidate high-penetrance melanoma susceptibility genes. This work provides further evidence that melanoma, like many other common complex disorders, can arise from the joint action of multiple predisposing factors, including rare high-penetrance mutations, as well as via a combination of large numbers of alleles of small effect.

15.
Ophthalmology ; 2020 Jul 28.
Artigo em Inglês | MEDLINE | ID: mdl-32730956

RESUMO

PURPOSE: To investigate the association between cardiovascular disease and baseline structural defects and disease progression in glaucoma. DESIGN: Prospective, longitudinal study of preperimetric and perimetric glaucoma. PARTICIPANTS: Two thousand six hundred twenty-eight eyes from 1314 participants recruited to the Progression Risk of Glaucoma: Relevant SNPs with Significant Association (PROGRESSA) study were evaluated for baseline and longitudinal structural thinning using spectral-domain OCT and for visual field progression on Humphrey visual field (HVF) assessment. METHODS: Patients were classified as either predominantly macula ganglion cell-inner plexiform layer (mGCIPL), predominantly peripapillary retinal nerve fiber layer (pRNFL), or both mGCIPL and pRNFL structural change at enrollment, and then evaluated for longitudinal OCT or HVF progression. Cardiovascular disease and medication characteristics of the participants were compared with a reference group of stable patients. MAIN OUTCOME MEASURES: OCT and HVF baseline status and longitudinal progression. RESULTS: After accounting for age and cardiovascular characteristics, patients with predominantly mGCIPL thinning at baseline showed a higher prevalence of hypertension (odds ratio [OR], 2.70; 95% confidence interval [CI], 1.66-4.41; P < 0.001), antihypertensive use (OR, 2.03; 95% CI, 1.20-3.46; P = 0.008), and statin use (OR, 1.98; 95% CI, 1.07-3.66; P = 0.029) than reference patients. Patients with predominantly pRNFL thinning exhibited a comparable prevalence of cardiovascular disease or medication with reference patients. Review of longitudinal OCT and HVF data (mean follow-up, 5.34 ± 1.29 years) showed that hypertension was associated with an increased risk of both OCT (OR, 1.79; 95% CI, 1.17-2.75; P = 0.006) and HVF progression (OR, 1.92; 95% CI, 1.18-3.15; P = 0.013). A 1-standard deviation (approximately 21 mmHg) increase in systolic blood pressure at baseline was associated with a greater risk of OCT progression (OR, 1.27; 95% CI, 1.01-1.63; P = 0.041) and HVF progression (OR, 1.32; 95% CI, 1.01-1.73; P = 0.043). The association between systolic blood pressure and structural progression was comparable to that observed between intraocular pressure and structural progression (OR, 1.30; 95% CI, 1.01-1.67; P = 0.039). CONCLUSIONS: Cardiovascular disease is an important risk factor for glaucoma progression.

16.
Twin Res Hum Genet ; 23(2): 90-93, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-32638676

RESUMO

One of Nick's key early achievements at QIMR was to establish a twin study on melanoma risk factors. The Brisbane Twin Nevus Study (BTNS) had an initial focus on nevus (mole) count in adolescents but, reflecting Nick's broad interests, expanded in scope enormously over the decades. In the skin cancer arena, BTNS was essential to genetic discoveries in melanoma, eye color and pigmentation. Later studies amassed data on thousands of phenotypes, ranging from molecular phenotypes such as gene expression to studies where gene mapping findings in adolescents turned out to have translational potential in late-onset diseases. Nick's twin data have formed the basis for an enormous range of discoveries, with Nick and his colleagues continuing to capitalize on these data.

17.
J Invest Dermatol ; 2020 Jun 29.
Artigo em Inglês | MEDLINE | ID: mdl-32615124

RESUMO

Organ-transplant recipients have an elevated risk of keratinocyte cancers: basal cell carcinoma (BCC) and squamous cell carcinoma. We assessed whether polygenic risk scores (PRSs) generated in nontransplantees from the UK Biobank and 23andMe (13,981 squamous cell carcinoma, 33,736 BCC, and >560,000 controls) can predict keratinocyte cancer risk in an independent organ-transplant recipient cohort. After adjusting for traditional risk factors, compared with the bottom 20%, organ-transplant recipients in the top 20% PRS had an increased risk of BCC (OR = 3.25, 95% confidence interval = 1.44-7.31, P = 4.4 × 10-3) and squamous cell carcinoma (OR = 2.11, 95% confidence interval = 0.98-4.53, P = 0.055). For BCC, the top 20% PRS individuals had an absolute risk of 23%, whereas the risk in the bottom 20% was similar to that in the general nontransplantee population. Adding PRS to a model containing traditional skin cancer risk factors yielded a 3% increase in the area under the curve for receiver operating characteristic curve for BCC (0.73 vs. 0.70); adding the PRS did not significantly increase the area under the curve for receiver operating characteristic curve for squamous cell carcinoma. Organ-transplant recipients in the highest genetic risk quintile could benefit from more intense keratinocyte cancer screening and preventive strategies compared with their counterparts. The BCC PRS improves prediction over and above the traditional skin cancer risk factors by 3%.

18.
Nat Commun ; 11(1): 3353, 2020 07 03.
Artigo em Inglês | MEDLINE | ID: mdl-32620889

RESUMO

Genome-wide association studies (GWAS) have led to the identification of hundreds of susceptibility loci across cancers, but the impact of further studies remains uncertain. Here we analyse summary-level data from GWAS of European ancestry across fourteen cancer sites to estimate the number of common susceptibility variants (polygenicity) and underlying effect-size distribution. All cancers show a high degree of polygenicity, involving at a minimum of thousands of loci. We project that sample sizes required to explain 80% of GWAS heritability vary from 60,000 cases for testicular to over 1,000,000 cases for lung cancer. The maximum relative risk achievable for subjects at the 99th risk percentile of underlying polygenic risk scores (PRS), compared to average risk, ranges from 12 for testicular to 2.5 for ovarian cancer. We show that PRS have potential for risk stratification for cancers of breast, colon and prostate, but less so for others because of modest heritability and lower incidence.


Assuntos
Predisposição Genética para Doença , Modelos Genéticos , Herança Multifatorial , Neoplasias/epidemiologia , Animais , Feminino , Estudo de Associação Genômica Ampla , Humanos , Incidência , Masculino , Neoplasias/genética , Polimorfismo de Nucleotídeo Único , Medição de Risco/métodos , Fatores de Risco
19.
Methods Mol Biol ; 2160: 13-28, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32529426

RESUMO

In hermaphroditic flowering plants, the female pistil serves as the main gatekeeper of mate acceptance as several mechanisms are present to prevent fertilization by unsuitable pollen. The characteristic Brassicaceae dry stigma at the top of pistil represents the first layer that requires pollen recognition to elicit appropriate physiological responses from the pistil. Successful pollen-stigma interactions then lead to pollen hydration, pollen germination, and pollen tube entry into the stigmatic surface. To assess these early stages in detail, our lab has used three experimental procedures to quantitatively and qualitatively characterize the outcome of compatible pollen-stigma interactions that would ultimately lead to the successful fertilization. These assays are also useful for assessing self-incompatible pollinations and mutations that affect these pathways. The model organism, Arabidopsis thaliana, offers an excellent platform for these investigations as loss-of-function or gain-of-function mutants can be easily generated using CRISPR/Cas9 technology, existing T-DNA insertion mutant collections, and heterologous expression constructs, respectively. Here, we provide a detailed description of the methods for these inexpensive assays that can be reliably used to assess pollen-stigma interactions and used to identify new players regulating these processes.

20.
Dalton Trans ; 49(19): 6478-6487, 2020 May 19.
Artigo em Inglês | MEDLINE | ID: mdl-32363358

RESUMO

Co(iii) complexes are increasingly prevalent in homogeneous catalysis. Catalytic cycles involve multiple intermediates, many of which will feature unsaturated metal centres. This raises the possibility of multi-state character along reaction pathways and so requires an accurate approach to calculating spin-state energetics. Here we report an assessment of the performance of DLPNO-CCSD(T) (domain-based local pair natural orbital approximation to coupled cluster theory) against experimental 1Co to 3Co spin splitting energies for a series of pseudo-octahedral Co(iii) complexes. The alternative NEVPT2 (strongly-contracted n-electron valence perturbation theory) and a range of density functionals are also assessed. DLPNO-CCSD(T) is identified as a highly promising method, with mean absolute deviations (MADs) as small as 1.3 kcal mol-1 when Kohn-Sham reference orbitals are used. DLPNO-CCSD(T) out-performs NEVPT2 for which a MAD of 3.5 kcal mol-1 can be achieved when a (10,12) active space is employed. Of the nine DFT methods investigated TPSS is the leading functional, with a MAD of 1.9 kcal mol-1. Our results show how DLPNO-CCSD(T) can provide accurate spin state energetics for Co(iii) species in particular and first row transition metal systems in general. DLPNO-CCSD(T) is therefore a promising method for applications in the burgeoning field of homogeneous catalysis based on Co(iii) species.

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