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1.
Breast Cancer Res Treat ; 189(2): 533-539, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34196900

RESUMO

PURPOSE: Mutations in hereditary breast cancer genes play an important role in the risk for cancer. METHODS: Cancer susceptibility genes were sequenced in 664 unselected breast cancer cases from Guatemala. Variants were annotated with ClinVar and VarSome. RESULTS: A total of 73 out of 664 subjects (11%) had a pathogenic variant in a high or moderate penetrance gene. The most frequently mutated genes were BRCA1 (37/664, 5.6%) followed by BRCA2 (15/664, 2.3%), PALB2 (5/664, 0.8%), and TP53 (5/664, 0.8%). Pathogenic variants were also detected in the moderate penetrance genes ATM, BARD1, CHEK2, and MSH6. The high ratio of BRCA1/BRCA2 mutations is due to two potential founder mutations: BRCA1 c.212 + 1G > A splice mutation (15 cases) and BRCA1 c.799delT (9 cases). Cases with pathogenic mutations had a significantly earlier age at diagnosis (45 vs 51 years, P < 0.001), are more likely to have had diagnosis before menopause, and a higher percentage had a relative with any cancer (51% vs 37%, P = 0.038) or breast cancer (33% vs 15%, P < 0.001). CONCLUSIONS: Hereditary breast cancer mutations were observed among Guatemalan women, and these women are more likely to have early age at diagnosis and family history of cancer. These data suggest the use of genetic testing in breast cancer patients and those at high risk as part of a strategy to reduce breast cancer mortality in Guatemala.


Assuntos
Neoplasias da Mama , Predisposição Genética para Doença , Mutação em Linhagem Germinativa , Proteína BRCA1/genética , Proteína BRCA2/genética , Neoplasias da Mama/diagnóstico , Neoplasias da Mama/epidemiologia , Neoplasias da Mama/genética , Feminino , Genes BRCA2 , Células Germinativas , Guatemala , Humanos
2.
Sci Rep ; 10(1): 12898, 2020 07 30.
Artigo em Inglês | MEDLINE | ID: mdl-32732891

RESUMO

It is challenging to identify somatic variants from high-throughput sequence reads due to tumor heterogeneity, sub-clonality, and sequencing artifacts. In this study, we evaluated the performance of eight primary somatic variant callers and multiple ensemble methods using both real and synthetic whole-genome sequencing, whole-exome sequencing, and deep targeted sequencing datasets with the NA12878 cell line. The test results showed that a simple consensus approach can significantly improve performance even with a limited number of callers and is more robust and stable than machine learning based ensemble approaches. To fully exploit the multi-callers, we also developed a software package, SomaticCombiner, that can combine multiple callers and integrates a new variant allelic frequency (VAF) adaptive majority voting approach, which can maintain sensitive detection for variants with low VAFs.


Assuntos
Algoritmos , Bases de Dados de Ácidos Nucleicos , Exoma , Neoplasias/genética , Polimorfismo de Nucleotídeo Único , Software , Biologia Computacional , Sequenciamento de Nucleotídeos em Larga Escala , Humanos
3.
Health Sci Rep ; 3(2): e155, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32382660

RESUMO

Background and aims: Guatemala has the highest incidence of hepatocellular carcinoma (HCC) in the Western hemisphere. The major risk factors in Guatemala are not well characterized, but the prevalence of hepatitis B virus (HBV) and hepatitis C virus (HCV) appears to be low, while the prevalence of aflatoxin (AFB1) exposure appears to be high. To examine whether AFB1 may contribute to the elevated incidence of HCC in Guatemala, this study examined the frequency of the AFB1-signature mutation in the TP53 gene (R249S) as well as other somatic mutations. In addition, we assessed whether the frequency of the TP53 mutation differed by sex. Methods: Formalin-fixed, paraffin-embedded (FFPE) HCC tissues were obtained from three hospitals in Guatemala City between 2016 and 2017. In addition, tumor tissues preserved in RNAlater were also obtained. Sociodemographic and clinical information including HBV and HCV status were collected. Targeted sequencing of TP53 was performed in the FFPE samples, and a panel of 253 cancer-related genes was sequenced in the RNAlater samples. Results: Ninety-one FFPE tissues were examined, from 52 men and 39 women. Median (IQR) age at diagnosis was 62 (51-70). Among those with known HBV and HCV status, two were HBV+ and three were HCV+. Overall, 47% of the HCCs had a TP53 mutation. The AFB1-signature R249S mutation was present in 24%. No overlap between the R249S mutation and HBV+ was observed in this cohort. Among 18 RNAlater samples examined, 44% had any TP53 mutation and 33% had the R249S mutation. Other somatic mutations were identified in known HCC driver genes. Conclusions: The presence of the TP53 R249S mutation in the samples studied suggests that AFB1 may contribute to the high incidence of HCC in Guatemala. The proportion of HBV+ tumors was low, suggesting that AFB1 may be associated with HCC in the absence of concomitant HBV infection. Further investigation of AFB1 and other risk factors for HCC in Guatemala is warranted.

4.
Opt Express ; 27(21): 30009-30019, 2019 Oct 14.
Artigo em Inglês | MEDLINE | ID: mdl-31684255

RESUMO

Simultaneously controlling the spatial distribution of multiple parameters of a light field in a three-dimensional (3D) space is highly desirable because of its prominent applications in the areas of optical imaging, microscopy, and manipulation. Phase-only encoding techniques that use a phase-only computer-generated hologram (CGH) to reshape and efficiently reconstruct target fields have fostered substantial interests. In this paper, we propose a convenient encoding method to construct vector fields with spatially structured multiple parameters in a 3D space by integrating the Fourier phase-only encoding technique into a modified Sagnac polarization conversion system. Without spatial filtering, various vector fields are constructed instantly at the image plane. Furthermore, utilizing a macro-pixel encoding approach, we demonstrate the possibility of a simultaneous and an independent construction of multiple vector fields in a 3D space. This method can also benefit the design of a metasurface to implement a polarization hologram.

5.
Opt Express ; 25(5): 5821-5831, 2017 Mar 06.
Artigo em Inglês | MEDLINE | ID: mdl-28380840

RESUMO

We propose a generalized model for the creation of vector Bessel-Gauss (BG) beams having state of polarization (SoP) varying along the propagation direction. By engineering longitudinally varying Pancharatnam-Berry (PB) phases of two constituent components with orthogonal polarizations, we create zeroth- and higher-order vector BG beams having (i) uniform polarizations in the transverse plane that change along z following either the equator or meridian of the Poincaré sphere and (ii) inhomogeneous polarizations in the transverse plane that rotate during propagation along z. Moreover, we evaluate the self-healing capability of these vector BG beams after two disparate obstacles. The self-healing capability of spatial SoP information may enrich the application of BG beams in light-matter interaction, polarization metrology and microscopy.

6.
Int J Clin Exp Med ; 8(10): 17362-76, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26770328

RESUMO

PURPOSE: A meta-analysis was undertaken to examine the correlation between ankylosing spondylitis (AS) progression and serum levels of pro-inflammatory cytokines, Interleukin-6 (IL-6) and Interleukin-17 (IL-17) in AS patients. METHODS: PubMed, EBSCO, Cochrane Library database, Ovid, Springer link, WANFANG, China national knowledge infrastructure (CNKI) and VIP databases(last updated search in October, 2014) were exhaustively searched for published case-control studies using keywords related to IL-6, IL-17 and AS. The search results were screened using stringent inclusion and exclusion criteria, and the data from selected high-quality studies was analyzed with Comprehensive Meta-analysis 2.0 software. RESULTS: Thirteen case-control studies were selected for this meta-analysis and contained a pooled total of 514 AS patients and 358 healthy controls. Our main result revealed strikingly higher serum levels of IL-6 and IL-17 in AS patients, compared to healthy controls (IL-6: SMD = 2.51, 95% CI = 1.33~3.70, P = 0.01; IL-17: SMD = 3.05, 95% CI = 2.09~4.02, P < 0.001). Ethnicity-based subgroup analysis showed a statistically correlation of high IL-6 and IL-17 serum levels with AS both in Asian (IL-6: SMD = 3.15, 95% CI = 0.75~5.55, P < 0.001; IL-17: SMD = 3.30, 95% CI = 1.93~4.66, P < 0.001) and Caucasian populations (IL-6: SMD = 1.34, 95% CI = 0.33~2.35, P = 0.009; IL-17: SMD = 2.52, 95% CI = 1.06~3.98, P = 0.001). CONCLUSION: Meta-analysis of pooled data from thirteen high-quality studies revealed a strong correlation between elevated IL-6 and IL-17 serum levels and the development of AS. Therefore, IL-6 and IL-17 could be used as markers for diagnosis and assessment of treatment outcomes in AS patients.

7.
Artigo em Inglês | MEDLINE | ID: mdl-17282242

RESUMO

As an official rule for healthcare privacy and security, Health Insurance Portability and Accountability Act (HIPAA) requires security services supporting implementation features: Access control; Audit controls; Authorization control; Data authentication; and Entity authentication. Audit controls proposed by HIPPA Security Standards are audit trails, which audit activities, to assess compliance with a secure domain's policies, to detect instances of non-compliant behavior, and to facilitate detection of improper creation, access, modification and deletion of Protected Health Information (PHI). Although current medical imaging systems generate activity logs, there is a lack of regular description to integrate these large volumes of log data into generating HIPPA compliant auditing trails. The paper outlines the design of a HIPAA's compliant auditing system for medical imaging system such as PACS and RIS and discusses the development of this security monitoring system based on the Supplement 95 of the DICOM standard: Audit Trail Messages.

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