Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 128
Filtrar
1.
PLoS One ; 16(5): e0250700, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33945570

RESUMO

Myopia is the most common refractive error. Surgical correction with laser is possible. LASIK and SMILE are the techniques currently most used. Aim of the study was to compare changes in corneal volume and thickness after the respective laser treatment. 104 eyes of 52 patients were matched based on refractive error into two equally sized groups, either treated with LASIK or SMILE. Measurements were obtained from the Scheimpflug camera (Pentacam) preoperatively and at 3 and 12 months postoperatively. 3 months postoperatively, the flapless SMILE procedure resulted in a significant overall greater loss of corneal volume (P < 0.01) and corneal thickness (P < 0.01) compared to LASIK. No significant difference was found when comparing the 3 to 12-months values in each group. Within the currently used ranges of refractive error correction, loss in central corneal thickness and corneal volume with SMILE is higher in comparison to LASIK. As greater loss in corneal volume and thickness might contribute to higher level of corneal instability maximum ranges of refractive error correction with SMILE should not supersede those set currently for LASIK until more long-term results on corneal ectasia are available for SMILE.

2.
Gastroenterology ; 2021 Apr 26.
Artigo em Inglês | MEDLINE | ID: mdl-33915173

RESUMO

BACKGROUND AND AIMS: Pancreatic ductal adenocarcinoma (PDAC) is characterised by advanced disease stage at presentation, aggressive disease biology and resistance to therapy resulting in extremely poor five-year survival <10%. PDAC is classified into transcriptional subtypes with distinct survival characteristics, although how these arise is not known. Epigenetic deregulation, rather than genetics, has been proposed to underpin progression but exactly why is unclear and hindered by technical limitations of analysing clinical samples. METHODS: Genome-wide epigenetic mapping of DNA modifications 5-methylcytosine (5mc) and 5-hydroxymethylcytosine (5hmc) using oxidative bisulphite sequencing (oxBS) from formalin embedded sections. Bioinformatics using iCluster and mutational profiling to identify overlap with transcriptional signatures in FFPE from resected patients and confirmation in vivo. RESULTS: We find that aggressive squamous-like PDAC subtypes result from epigenetic inactivation of loci including GATA6 that promote differentiated classical-pancreatic subtypes. We show that squamous-like PDAC transcriptional subtypes are associated with greater loss of 5hmc due to reduced expression of the 5mc-hydroxylase TET2. Furthermore, we find that SMAD4 directly supports TET2 levels in classical-pancreatic tumors and loss of SMAD4 expression is associated reduced 5hmc, GATA6 and squamous-like tumors. Importantly, enhancing TET2 stability using Metformin and VitaminC/ascorbic acid (AA) restores 5hmc and GATA6 levels, reverting squamous-like tumor phenotypes and WNT-dependence in vitro and in vivo. CONCLUSIONS: We identify epigenetic deregulation of pancreatic differentiation as an underpinning event behind the emergence of transcriptomic subtypes in PDAC. Our data shows that restoring epigenetic control increases biomarkers of classical-pancreatic tumors which are associated with improved therapeutic responses and survival.

3.
Sci Rep ; 11(1): 6408, 2021 Mar 19.
Artigo em Inglês | MEDLINE | ID: mdl-33742045

RESUMO

Recent advances in throughput and accuracy mean that the Oxford Nanopore Technologies PromethION platform is a now a viable solution for genome sequencing. Much of the validation of bioinformatic tools for this long-read data has focussed on calling germline variants (including structural variants). Somatic variants are outnumbered many-fold by germline variants and their detection is further complicated by the effects of tumour purity/subclonality. Here, we evaluate the extent to which Nanopore sequencing enables detection and analysis of somatic variation. We do this through sequencing tumour and germline genomes for a patient with diffuse B-cell lymphoma and comparing results with 150 bp short-read sequencing of the same samples. Calling germline single nucleotide variants (SNVs) from specific chromosomes of the long-read data achieved good specificity and sensitivity. However, results of somatic SNV calling highlight the need for the development of specialised joint calling algorithms. We find the comparative genome-wide performance of different tools varies significantly between structural variant types, and suggest long reads are especially advantageous for calling large somatic deletions and duplications. Finally, we highlight the utility of long reads for phasing clinically relevant variants, confirming that a somatic 1.6 Mb deletion and a p.(Arg249Met) mutation involving TP53 are oriented in trans.

4.
Blood Adv ; 5(5): 1403-1411, 2021 Mar 09.
Artigo em Inglês | MEDLINE | ID: mdl-33666650

RESUMO

Imatinib is the mainstay of treatment of patients with chronic myeloid leukemia (CML) in Tanzania. Monitoring molecular response to therapy by real-time polymerase chain reaction at defined milestones is necessary for early detection of treatment failure. However, this assay is not routinely performed in Tanzania; therefore, the depth of molecular response among patients with CML is not known. A total of 158 patients with previously diagnosed CML who received imatinib treatment were recruited from January 2019 and followed up through October 2020 at Ocean Road Cancer Institute. Information was obtained at the time of diagnosis and follow-up. Blood samples were collected in EDTA tubes to measure the BCR/ABL ratio on the Gene Xpert system for molecular response determination. The median age of the 158 adult patients was 45 years (range, 18-86). By reference to established treatment milestones, only 37 (23.4%) achieved optimal molecular response. Signs of advanced-stage disease, in particular the need for red cell transfusions before diagnosis (adjusted odds ratio [AOR], 3.4; 95% CI, 1.32-9.17) and cytopenias (AOR, 2.26; 95% CI, 1.03-4.96) necessitating drug interruptions were statistically validated predictors of treatment failure on multivariate, multinomial logistic regression. Patient survival at the 22-month follow-up was lowest, with 78.6% (95% CI, 69.4-85.4) in the failure-to-respond category and highest in patients achieving optimal response 97.0% (95% CI, 80.9-99.6). In summary, the majority of patients with CML treated with imatinib in Tanzania do not obtain deep molecular response. This outcome can be attributed to late diagnosis, the development of cytopenias requiring multiple drug interruptions, and poor adherence to treatment.

5.
Artigo em Inglês | MEDLINE | ID: mdl-33540463

RESUMO

PURPOSE: To evaluate the effect of IPL (intense pulsed light) treatment in patients with meibomian gland dysfunction (MGD). METHODS: Clinical data of 25 patients with MGD who underwent IPL treatment at the department of ophthalmology of Ludwig-Maximilians-University between 2016 and 2018 were analyzed. Demographics, clinical history, examination findings (eyelid vascularization, meibomian gland findings, conjunctival redness, tear film break-up time [TFBUT], corneal staining (Oxford grading scale [OGS]), and subjective patients' findings (including ocular surface disease index [OSDI]) were collected from each visit (D1, D15, D45, D75). RESULTS: All included patients underwent three sessions of IPL treatment in both eyes (D1, D15, D45). There was a significant improvement after IPL treatment (D75) in TFBUT (p < 0.001), corneal staining (OGS) (p < 0.001), conjunctival redness (p < 0.001), lid margin edema (p < 0.001) and redness (p < 0.001), meibum quality (p < 0.001), lid margin telangiectasia (p = 0.005), meibomian gland obstruction (p = 0.001), and OSDI score (p = 0.004). Even after the first IPL session, significant improvements in TFBUT (p < 0.001), corneal staining (OGS p < 0.001), conjunctival redness (p < 0.022), lid margin edema (p < 0.001) and redness (p < 0.016), meibum quality (p = 0.014), and OSDI score (p < 0.013) were noted. There were no relevant negative side effects. Subgroup analysis for age, sex, duration or severity of disease, and associated diagnosis of rosacea showed no significant difference in effectiveness. CONCLUSION: IPL is an effective and safe treatment for patients with MGD, which can be used as a supportive therapeutic option.

6.
Nat Commun ; 12(1): 665, 2021 01 28.
Artigo em Inglês | MEDLINE | ID: mdl-33510140

RESUMO

Prognostication in patients with chronic lymphocytic leukemia (CLL) is challenging due to heterogeneity in clinical course. We hypothesize that constitutional genetic variation affects disease progression and could aid prognostication. Pooling data from seven studies incorporating 842 cases identifies two genomic locations associated with time from diagnosis to treatment, including 10q26.13 (rs736456, hazard ratio (HR) = 1.78, 95% confidence interval (CI) = 1.47-2.15; P = 2.71 × 10-9) and 6p (rs3778076, HR = 1.99, 95% CI = 1.55-2.55; P = 5.08 × 10-8), which are particularly powerful prognostic markers in patients with early stage CLL otherwise characterized by low-risk features. Expression quantitative trait loci analysis identifies putative functional genes implicated in modulating B-cell receptor or innate immune responses, key pathways in CLL pathogenesis. In this work we identify rs736456 and rs3778076 as prognostic in CLL, demonstrating that disease progression is determined by constitutional genetic variation as well as known somatic drivers.


Assuntos
Predisposição Genética para Doença/genética , Estudo de Associação Genômica Ampla/métodos , Leucemia Linfocítica Crônica de Células B/genética , Polimorfismo de Nucleotídeo Único , Idoso , Progressão da Doença , Feminino , Humanos , Estimativa de Kaplan-Meier , Leucemia Linfocítica Crônica de Células B/patologia , Masculino , Pessoa de Meia-Idade , Análise Multivariada , Prognóstico , Locos de Características Quantitativas/genética
7.
Am J Ophthalmol ; 224: 150-157, 2021 04.
Artigo em Inglês | MEDLINE | ID: mdl-33309811

RESUMO

PURPOSE: The study was performed to evaluate the refractive and visual outcome of patients with misaligned toric intraocular lenses (IOLs) after operative realignment, with and without back-calculation of the toric axis after implantation of the IOL. DESIGN: Institutional, retrospective case-control study. METHODS: This is a retrospective case series of 39 patients who underwent a second operation to realign a misaligned toric IOL from August 2013 to December 2019 at the Department of Ophthalmology, Goethe University, Frankfurt, Germany. Ideal toric axis was calculated using the back-calculator astigmatismfix.com. RESULTS: The study consists of 39 treated eyes (20 [51%] right eyes). The toric IOLs showed a postoperative misalignment of 25.69 ± 26.06°. Postrotational, uncorrected distance visual acuity (UDVA) improved from 0.39 ± 0.29 logMAR to 0.27 ± 0.18 logMAR. Refractive outcome showed a reduction of residual sphere and cylinder. The postoperative UDVA when performing alignment to the preoperative calculated axis (51%) was 0.24 ± 0.16 logMAR with a cylinder of 0.90 ± 0.90 diopter (D). In the group with alignment to a back-calculated axis (49%), the UDVA was 0.32 ± 0.20 logMAR with a cylinder of 0.76 ± 0.72 D. High cylinder power IOLs (≥2 D) showed a higher decrease in residual cylinder when back-calculation was performed than low cylinder power IOLs (<2 D) (27% vs 9%). The mean spherical equivalent prediction error of the back-calculator was 0.54 ± 0.55 D. CONCLUSION: Realignment of misaligned toric IOLs improves visual acuity and reduces residual refractive errors. Especially for high cylinder power IOLs, better refractive outcome can be seen when performing a back-calculation before realignment.

8.
Hemoglobin ; : 1-7, 2020 Nov 29.
Artigo em Inglês | MEDLINE | ID: mdl-33249879

RESUMO

Hb Manitoba [α102(G9)Ser→Arg] is a rare α chain variant with diverse ethnic origins. It is mildly unstable with an expression of around 10.0-14.2% in the heterozygous state in most literature. In this study, 12 cases of Hb Manitoba [11 cases carried Hb Manitoba II (HBA1: c.309C>A) and one case carried Hb Manitoba IV (HBA1: c.307A>C)] were detected during a wide-spectrum study of α chain variants in the UK. Fluctuation in variant expression from 6.9 to 15.2% of total Hb on high performance liquid chromatography (HPLC) would pose a diagnostic dilemma in routine laboratories. Focusing on the variant expression, the median of Hb Manitoba was around 11.5% of total Hb in three cases, apparently with normal hemoglobin (Hb), and normal red blood cell (RBC) indices. Two cases showed a higher expression (13.9 and 15.2%) and five cases showed a lower expression (6.9-9.9%). The common α-thalassemia (α-thal) -α3.7 (rightward) deletion coexisted with one case of increased Hb Manitoba expression. Iron (or other nutrient) deficiency was likely the cause of decreased Hb Manitoba percentage in this study. The α73(EF2)Val→Val (α2) (HBA2: c.222G>T) polymorphism is published for the first time and coexisted with two cases. The Cap +14 (C>G) (HBA2: c.-24C>G) polymorphism coexisted with another case in a heterozygous state. In conclusion, the fluctuation in variant expression can cause a diagnostic dilemma, especially in routine laboratories. Screening for the common -α3.7 deletion and iron deficiency is recommended when an α chain variant is suspected.

9.
Sci Rep ; 10(1): 19308, 2020 11 09.
Artigo em Inglês | MEDLINE | ID: mdl-33168836

RESUMO

Keratoconus is a progressive ectatic corneal disorder, which can result in severe visual impairment. The new ABCD keratoconus classification system allows differentiated description of the disease. Aim of the study was to evaluate the components of this novel staging system (ARC, PRC, thinnest pachymetry) as well as topometric indices, deviation of normality indices, and other parameters in terms of repeatability and reliability. 317 eyes with keratoconus were examined twice with a Scheimpflug device (Pentacam, Oculus). Bland Altman analysis and intraclass correlations were carried out to evaluate the parameters repeatability and reliability. Apart from IHA (ICC = 0.730), all parameters showed excellent reliability (ICC > 0.900). ARC, PRC, thinnest pachymetry, Kmax, CKI, KI, Rmin, and Progression Avg were the best repeatable parameters with relative repeatability values < 2.5%. Other parameters performing well in terms of repeatability were IHD, ISV, IVA, and final D (RR < 13%). Regression analysis revealed consistently high repeatability along all stages of keratoconus for PRC, thinnest pachymetry, and CKI. All parameters of the ABCD staging system showed excellent reliability and repeatability, PRC and thinnest pachymetry even at all stages of keratoconus and can consequently be reliably used in the determination of keratoconus progression.

10.
Blood ; 2020 Nov 18.
Artigo em Inglês | MEDLINE | ID: mdl-33206936

RESUMO

The transformation of chronic lymphocytic leukemia (CLL) to high-grade B-cell lymphoma is known as Richter's Syndrome (RS) and it is a rare event with dismal prognosis. In this study, we conducted whole genome sequencing (WGS) of paired circulating CLL (PB-CLL) and RS biopsies (tissue-RS) from 17 clinical trial (CHOP-O) patients. We found that tissue-RS was enriched for mutations in poor-risk CLL drivers and genes in the DNA damage response (DDR) pathway. In addition, we identified genomic aberrations not previously implicated in RS, including the protein tyrosine phosphatase receptor (PTPRD) and tumour necrosis factor receptor associated factor three (TRAF3). In the non-coding genome, we discovered AID-related and unrelated kataegis in tissue-RS affecting regulatory regions of key immune regulatory genes. These include BTG2, CXCR4, NFATC1, PAX5, NOTCH-1, SLC44A5, FCRL3, SELL, TNIP2 andTRIM13. Furthermore, differences between the global mutation signatures of pairs of PB-CLL and tissue-RS samples implicate DDR as the dominant mechanism driving transformation. Pathway-based clonal de-convolution analysis showed that genes in the MAPK and DDR pathways demonstrate high clonal expansion probability. Direct comparison of nodal-CLL and tissue-RS pairs from an independent cohort confirmed differential expression of the same pathways by RNA expression profiling. Our integrated analysis of WGS and RNA expression data significantly extends previous targeted approaches, which were limited by the lack of germline samples, and it facilitates the identification of novel genomic correlates implicated in RS transformation, which could be targeted therapeutically. Our results inform the future selection of investigative agents for a UK clinical platform study (NCT03899337).

11.
Hemoglobin ; : 1-4, 2020 Sep 14.
Artigo em Inglês | MEDLINE | ID: mdl-32924661

RESUMO

Hb J-Meerut [HBA2: c.362C>A (or HBA1)] is a rare, stable, nonpathogenic α-globin gene variant that peaks in the area between the P3 and A0 windows on high performance liquid chromatography (HPLC). Few cases from different ethnic origins have been published but the majority were Asian Indians. Coinheritance with other hemoglobin (Hb) variants are rarer and can change the Hb J-Meerut phenotype making a diagnostic dilemma. In this study, we have reported 15 cases of Hb J-Meerut, discovered during a wide spectrum study of α-globin chain variants in the UK. The diagnosis was confirmed by forward and reverse DNA sequencing of the α1- and α2-globin genes. The average of the Hb J-Meerut expression was 20.9% of total Hb and characterized by a retention time (RT) of 1.9 min. (on average) on HPLC. The median of isoelectric focusing (IEF) was 5.6 mm above Hb A. Among the 15 cases studied, one case coinherited the Hb E (HBB: c.79G>A) mutation in heterozygosity and another case was associated with the Cap +14 (C>G) [HBA1: c.-24C>G (or HBA2)] variant. We noticed that the coinheritance of the Hb E mutation reduced the Hb J-Meerut expression with the formation of a hybrid peak missed on the HPLC chromatograph. We also noticed an increased expression of Hb J-Meerut in the case showing the coinheritance of the HBA2: c.-24C>G (or HBA1) variant.

12.
Bioinformatics ; 2020 Jul 28.
Artigo em Inglês | MEDLINE | ID: mdl-32722772

RESUMO

MOTIVATION: Tumours are composed of distinct cancer cell populations (clones), which continuously adapt to their local micro-environment. Standard methods for clonal deconvolution seek to identify groups of mutations and estimate the prevalence of each group in the tumour, while taking into account its purity and copy number profile. These methods have been applied on cross-sectional data and on longitudinal data after discarding information on the timing of sample collection. Two key questions are how can we incorporate such information in our analyses and is there any benefit in doing so? RESULTS: We developed a clonal deconvolution method, which incorporates explicitly the temporal spacing of longitudinally sampled tumours. By merging a Dirichlet Process Mixture Model with Gaussian Process priors and using as input a sequence of several sparsely collected samples, our method can reconstruct the temporal profile of the abundance of any mutation cluster supported by the data as a continuous function of time. We benchmarked our method on whole genome, whole exome and targeted sequencing data from patients with chronic lymphocytic leukaemia, on liquid biopsy data from a patient with melanoma and on synthetic data and we found that incorporating information on the timing of tissue collection improves model performance, as long as data of sufficient volume and complexity are available for estimating free model parameters. Thus, our approach is particularly useful when collecting a relatively long sequence of tumour samples is feasible, as in liquid cancers (e.g. leukaemia) and liquid biopsies. AVAILABILITY: The statistical methodology presented in this paper is freely available at github.com/dvav/clonosGP. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

13.
BMC Med Genomics ; 13(1): 94, 2020 07 06.
Artigo em Inglês | MEDLINE | ID: mdl-32631411

RESUMO

BACKGROUND: Research grade Fresh Frozen (FF) DNA material is not yet routinely collected in clinical practice. Many hospitals, however, collect and store Formalin Fixed Paraffin Embedded (FFPE) tumor samples. Consequently, the sample size of whole genome cancer cohort studies could be increased tremendously by including FFPE samples, although the presence of artefacts might obfuscate the variant calling. To assess whether FFPE material can be used for cohort studies, we performed an in-depth comparison of somatic SNVs called on matching FF and FFPE Whole Genome Sequence (WGS) samples extracted from the same tumor. METHODS: Four variant callers (i.e. Strelka2, Mutect2, VarScan2 and Shimmer) were used to call somatic variants on matching FF and FFPE WGS samples from a metastatic prostate tumor. Using the variants identified by these callers, we developed a heuristic to maximize the overlap between the FF and its FFPE counterpart in terms of sensitivity and precision. The proposed variant calling approach was then validated on nine matched primary samples. Finally, we assessed what fraction of the discrepancy could be attributed to intra-tumor heterogeneity (ITH), by comparing the overlap in clonal and subclonal somatic variants. RESULTS: We first compared variants between an FF and an FFPE sample from a metastatic prostate tumor, showing that on average 50% of the calls in the FF are recovered in the FFPE sample, with notable differences between callers. Combining the variants of the different callers using a simple heuristic, increases both the precision and the sensitivity of the variant calling. Validating the heuristic on nine additional matched FF-FFPE samples, resulted in an average F1-score of 0.58 and an outperformance of any of the individual callers. In addition, we could show that part of the discrepancy between the FF and the FFPE samples can be attributed to ITH. CONCLUSION: This study illustrates that when using the correct variant calling strategy, the majority of clonal SNVs can be recovered in an FFPE sample with high precision and sensitivity. These results suggest that somatic variants derived from WGS of FFPE material can be used in cohort studies.

15.
Hemoglobin ; 44(3): 195-200, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-32597250

RESUMO

Over many years, cases of suspected α-globin chain variants were collected from different parts of the UK. The suspicion was based on the clinical picture, high performance liquid chromatography (HPLC) variant percentage, retention time (RT) and isoelectric focusing (IEF). DNA sequencing and the restriction enzyme EaeI were used for definitive diagnosis. One hundred and forty-eight variants were confirmed on one or both of the two α-globin genes (HBA2, HBA1). These cases were identified as 46 different α-globin chain variants. The most common variants were Hb J-Meerut [HBA2: c.362C>A (or HBA1)] (10.1%) and Hb Q-India (HBA1: c.193G>C) (8.1%), followed by Hb J-Paris-I [HBA2: c.38C>A (or HBA1)] and Hb Manitoba II (HBA1: c.309C>A) (7.4% for each). Other α variants were detected at lower frequencies. Two novel alleles were also detected: Hb Walsgrave [α116(GH4)Glu→Val (HBA2: c.350A>T)] and Hb Coombe Park [α127(H10)Lys→Glu (HBA2: c.382A>G)]. The majority of the ethnic origin was Indian. The positive predictive value for α variant identification by HPLC-RT analysis was 65.9%, 41.9% by IEF, and using both RT and IEF, the value was 72.1%. The number of variants was higher in HBA1 than in HBA2 genes and in exons 1 and 2 than in exon 3. There was no clustering of mutations in consecutive codons. This study, the characterization of a wide spectrum of α-globin chain variants, can facilitate the presumptive diagnosis of these variants prior to screening by a panel of amplification refractory mutation system-polymerase chain reaction (ARMS-PCR), and a definitive diagnosis by DNA sequencing.

16.
Cell Rep ; 31(6): 107640, 2020 05 12.
Artigo em Inglês | MEDLINE | ID: mdl-32402273

RESUMO

The anti-leukemia agent forodesine causes cytotoxic overload of intracellular deoxyguanosine triphosphate (dGTP) but is efficacious only in a subset of patients. We report that SAMHD1, a phosphohydrolase degrading deoxyribonucleoside triphosphate (dNTP), protects cells against the effects of dNTP imbalances. SAMHD1-deficient cells induce intrinsic apoptosis upon provision of deoxyribonucleosides, particularly deoxyguanosine (dG). Moreover, dG and forodesine act synergistically to kill cells lacking SAMHD1. Using mass cytometry, we find that these compounds kill SAMHD1-deficient malignant cells in patients with chronic lymphocytic leukemia (CLL). Normal cells and CLL cells from patients without SAMHD1 mutation are unaffected. We therefore propose to use forodesine as a precision medicine for leukemia, stratifying patients by SAMHD1 genotype or expression.

17.
Br J Haematol ; 190(5): 736-740, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32236950

RESUMO

The Complement 1 trial investigated the efficacy and safety of ofatumumab + chlorambucil with chlorambucil monotherapy in patients with previously untreated chronic lymphocytic leukaemia (CLL). On long-term follow-up in the chemoimmunotherapy arm vs. the chemotherapy arm there was an estimated 12% (not significant) and 39% risk reduction in overall survival and progression-free survival, respectively. A high rate (61%) of treatment with next-line therapies in both the treatment arms may dilute any potential OS difference and confound the interpretation of the OS results. Addition of ofatumumab to chlorambucil demonstrated clinical benefit and tolerability as a frontline treatment option in patients unfit for fludarabine-containing therapy, with no new safety concerns.

SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA
...