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‣ Absence of PRKAR1A loss of heterozygosity in laser-captured microdissected pigmented nodular adrenocortical tissue from a patient with Carney complex caused by the novel nonsense mutation p.Y21X; Ausência da perda de heterozigose do PRKAR1A em células capturadas por microdissecção a laser de tecido de nódulo pigmentoso adrenocortical de um paciente com complexo de Carney causado por uma nova mutação nonsense

ALMEIDA, Madson Q.; BRITO, Luciana Pinto; DOMENICE, Sorahia; COSTA, Marcia Helena Soares; PINTO, Emilia Modolo; OSÓRIO, Cynthia A. Toledo; LATRONICO, Ana Claudia; MENDONCA, Berenice B.; FRAGOSO, Maria Candida B. V.
Fonte: Sociedade Brasileira de Endocrinologia e Metabologia Publicador: Sociedade Brasileira de Endocrinologia e Metabologia
Tipo: Artigo de Revista Científica
Português
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OBJECTIVE: Primary pigmented nodular adrenocortical disease (PPNAD) is the main endocrine manifestation of Carney complex, a multiple neoplasia syndrome caused by PRKAR1A gene mutations. The presence of PRKAR1A loss of heterozygosity (LOH) in adrenocortical tumorigenesis remains controversial. The aim of the present study is to investigate the presence of PRKAR1A LOH in adrenocortical cells in a patient with Carney complex. METHODS: The LOH was investigated using a PRKAR1A informative intragenic marker by GeneScan software analysis in DNA obtained from laser-captured microdissected cells of several adrenal nodules. Patients: A young adult male patient with Carney complex and his family were studied. RESULTS: A novel heterozygous mutation (p. Y21X) was identified at PRKAR1A in blood DNA of the male proband and his relatives. No PRKAR1A LOH was evidenced in the laser-captured microdissected cells from PPNAD tissue by different methodologies. CONCLUSION: We identified a new PRKAR1A nonsense mutation and in addition we did not evidence PRKAR1A LOH in laser-captured nodules cells, suggesting that adrenocortical tumorigenesis in PPNAD may occurs apart from the second hit.; OBJETIVO: A doença adrenocortical nodular pigmentosa primária (PPNAD) é uma das manifestações do complexo de Carney...

‣ Absence of PRKAR1A loss of heterozygosity in laser-captured microdissected pigmented nodular adrenocortical tissue from a patient with Carney complex caused by the novel nonsense mutation p.Y21X

Almeida,Madson Q.; Brito,Luciana Pinto; Domenice,Sorahia; Costa,Marcia Helena Soares; Pinto,Emilia Modolo; Osório,Cynthia A. Toledo; Latronico,Ana Claudia; Mendonca,Berenice B.; Fragoso,Maria Candida B. V.
Fonte: Sociedade Brasileira de Endocrinologia e Metabologia Publicador: Sociedade Brasileira de Endocrinologia e Metabologia
Tipo: Artigo de Revista Científica Formato: text/html
Publicado em 01/11/2008 Português
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OBJECTIVE: Primary pigmented nodular adrenocortical disease (PPNAD) is the main endocrine manifestation of Carney complex, a multiple neoplasia syndrome caused by PRKAR1A gene mutations. The presence of PRKAR1A loss of heterozygosity (LOH) in adrenocortical tumorigenesis remains controversial. The aim of the present study is to investigate the presence of PRKAR1A LOH in adrenocortical cells in a patient with Carney complex. METHODS: The LOH was investigated using a PRKAR1A informative intragenic marker by GeneScan software analysis in DNA obtained from laser-captured microdissected cells of several adrenal nodules. Patients: A young adult male patient with Carney complex and his family were studied. RESULTS: A novel heterozygous mutation (p. Y21X) was identified at PRKAR1A in blood DNA of the male proband and his relatives. No PRKAR1A LOH was evidenced in the laser-captured microdissected cells from PPNAD tissue by different methodologies. CONCLUSION: We identified a new PRKAR1A nonsense mutation and in addition we did not evidence PRKAR1A LOH in laser-captured nodules cells, suggesting that adrenocortical tumorigenesis in PPNAD may occurs apart from the second hit.

‣ Patterns of allelic loss (LOH) in vulvar squamous carcinomas and adjacent noninvasive epithelia.

Lin, M. C.; Mutter, G. L.; Trivijisilp, P.; Boynton, K. A.; Sun, D.; Crum, C. P.
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em /05/1998 Português
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The pathogenesis of carcinoma of the vulva is diverse and includes both human papilloma virus (HPV)-positive and HPV-negative pathways. The objective of this study was to correlate the morphology with patterns of loss of heterozygosity (LOH) within four vulvar carcinomas and in adjacent vulvar epithelia. Tumors were categorized as HPV positive or negative by polymerase chain reaction (PCR) analysis. Forty-one different sites of normal squamous mucosa, hyperplasia, vulvar intraepithelial neoplasia (VIN), and carcinoma were microdissected in duplicate, and each extracted DNA was analyzed in duplicate for LOH at 10 chromosomal loci by PCR and polyacrylamide gel electrophoresis. Patterns of LOH were compared within different sites of tumors and between the tumor and the noninvasive epithelia. Of three tumors with multiple invasive foci analyzed, divergent patterns of LOH were identified in two, correlating in one with differences in tumor grade. In one HPV-16-positive case, multiple sites of VIN displayed heterogeneity for LOH consistent with divergent clonal or subclonal populations, some of which were not shared by the tumor. In one HPV-negative case, LOH was found in foci of hyperplasia and differentiated VIN (atypical hyperplasia)...

‣ An increased NM23H1 copy number may be a poor prognostic factor independent of LOH on 1p in neuroblastomas.

Takeda, O.; Handa, M.; Uehara, T.; Maseki, N.; Sakashita, A.; Sakurai, M.; Kanda, N.; Arai, Y.; Kaneko, Y.
Fonte: Nature Publishing Group Publicador: Nature Publishing Group
Tipo: Artigo de Revista Científica
Publicado em /11/1996 Português
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In a study of 154 neuroblastomas, loss of heterozygosity (LOH) was observed on 1p (13%, 19/143), 11q (19%, 11/59), 14q (15%, 15/97), 17p (5%, 5/105) and 17q (17%, 9/52). We also found an increase in NM23H1 copy number in 14% (13/95) of neuroblastomas. All except one tumour with an increased copy number stained positive with anti-NM23H1 monoclonal antibody. Event-free survival (EFS) was significantly shorter in 19 patients with LOH on 1p than in 128 without (41% vs 77% 4 year EFS, P=0.0093), and in 13 patients with increased NM23H1 copy numbers than in 82 with normal copy numbers of the gene (61% vs 84% 4 year EFS, P=0.0103). LOH on 11q, 14q or 17q did not affect EFS. Most tumours with LOH on 1p, increased NM23H1 copy numbers or MYCN amplification occurred in patients aged 12 months or more, those with advanced stage disease, and those who showed near diploidy or pseudodiploidy. However, LOH on 1p was found in only 1 of the 13 tumours with increased NM23H1 copy numbers, and MYCN amplification of four copies occurred in only one other such tumour. These findings suggest that the increased NM23H1 copy number may be a predictor for poor prognosis, independent of LOH on 1p, and probably also of MYCN amplification.

‣ Direct Inference of SNP Heterozygosity Rates and Resolution of LOH Detection

Li, Xiaohong; Self, Steven G; Galipeau, Patricia C; Paulson, Thomas G; Reid, Brian J
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
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Single nucleotide polymorphisms (SNPs) have been increasingly utilized to investigate somatic genetic abnormalities in premalignancy and cancer. LOH is a common alteration observed during cancer development, and SNP assays have been used to identify LOH at specific chromosomal regions. The design of such studies requires consideration of the resolution for detecting LOH throughout the genome and identification of the number and location of SNPs required to detect genetic alterations in specific genomic regions. Our study evaluated SNP distribution patterns and used probability models, Monte Carlo simulation, and real human subject genotype data to investigate the relationships between the number of SNPs, SNP HET rates, and the sensitivity (resolution) for detecting LOH. We report that variances of SNP heterozygosity rate in dbSNP are high for a large proportion of SNPs. Two statistical methods proposed for directly inferring SNP heterozygosity rates require much smaller sample sizes (intermediate sizes) and are feasible for practical use in SNP selection or verification. Using HapMap data, we showed that a region of LOH greater than 200 kb can be reliably detected, with losses smaller than 50 kb having a substantially lower detection probability when using all SNPs currently in the HapMap database. Higher densities of SNPs may exist in certain local chromosomal regions that provide some opportunities for reliably detecting LOH of segment sizes smaller than 50 kb. These results suggest that the interpretation of the results from genome-wide scans for LOH using commercial arrays need to consider the relationships among inter-SNP distance...

‣ European multicenter study on LOH of APOC3 at 11q23 in 766 breast cancer patients: relation to clinical variables

Launonen, V; Laake, K; Huusko, P; Niederacher, D; Beckmann, M W; Barkardottir, R B; Geirsdottir, E K; Gudmundsson, J; Rio, P; Bignon, Y-J; Seitz, S; Scherneck, S; Bièche, I; Champème, M-H; Birnbaum, D; White, G; Varley, J; Sztán, M; Olah, E; Osorio, A;
Fonte: Nature Publishing Group Publicador: Nature Publishing Group
Tipo: Artigo de Revista Científica
Publicado em /05/1999 Português
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High frequencies of loss of heterozygosity (LOH) in chromosome 11q22-qter have been observed in various malignancies, including breast cancer. Previous studies on breast carcinomas by Winqvist et al (Cancer Res 55: 2660–2664) have indicated that a survival factor gene is located in band 11q23, and that the highly informative microsatellite polymorphism at the APOC3 locus would be a suitable tool to perform more extensive LOH studies. In this European multicentre study, we have examined the occurrence of APOC3 LOH and evaluated the effect of LOH of this chromosomal subregion on the clinical behaviour of the disease in a cohort of 766 breast cancer patients in more detail. LOH for APOC3 was found in 42% of the studied tumours, but it was not found to be significantly associated with any of the studied clinical variables, including cancer-specific survival time or survival time after recurrent/metastatic disease. According to the present findings, the putative survival factor gene on 11q23 is not located close enough to the APOC3 gene, but apparently at a more proximal location. © 1999 Cancer Research Campaign

‣ Loss of heterozygosity (LOH), malignancy grade and clonality in microdissected prostate cancer

Hügel, A; Wernert, N
Fonte: Nature Publishing Group Publicador: Nature Publishing Group
Tipo: Artigo de Revista Científica
Publicado em /02/1999 Português
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The aim of the present study was to find out whether increasing malignancy of prostate carcinoma correlates with an overall increase of loss of heterozygosity (LOH), and whether LOH typing of microdissected tumour areas can help to distinguish between multifocal or clonal tumour development. In 47 carcinomas analysed at 25 chromosomal loci, the overall LOH rate was found to be significantly lower in grade 1 areas (2.2%) compared with grade 2 (9.4%) and grade 3 areas (8.3%, P = 0.007). A similar tendency was found for the mean fractional allele loss (FAL, 0.043 for grade 1, 0.2 for grade 2 and 0.23 for grade 3, P = 0.0004). Of 20 tumours (65%) with LOH in several microdissected areas, 13 had identical losses at 1–4 loci within two or three areas, suggesting clonal development of these areas. Markers near RB, DCC, BBC1, TP53 and at D13S325 (13q21–22) showed higher loss rates in grades 2 and 3 (between 25% and 44.4%) compared with grade 1 (0–6.6%). Tumour-suppressor genes (TSGs) near these loci might, thus, be important for tumour progression. TP53 mutations were detected in 27%, but BBC1 mutations in only 7%, of samples with LOH. Evaluation of all 25 loci in every tumour made evident that each prostate cancer has its own pattern of allelic losses. © 1999 Cancer Research Campaign

‣ Dissecting Loss of Heterozygosity (LOH) in Neurofibromatosis Type 1-Associated Neurofibromas: Importance of Copy Neutral LOH

Garcia-Linares, Carles; Fernández-Rodríguez, Juana; Terribas, Ernest; Mercadé, Jaume; Pros, Eva; Benito, Llúcia; Benavente, Yolanda; Capellà, Gabriel; Ravella, Anna; Blanco, Ignacio; Kehrer-Sawatzki, Hildegard; Lázaro, Conxi; Serra, Eduard
Fonte: Wiley Subscription Services, Inc., A Wiley Company Publicador: Wiley Subscription Services, Inc., A Wiley Company
Tipo: Artigo de Revista Científica
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Dermal neurofibromas (dNFs) are benign tumors of the peripheral nervous system typically associated with Neurofibromatosis type 1 (NF1) patients. Genes controlling the integrity of the DNA are likely to influence the number of neurofibromas developed because dNFs are caused by somatic mutational inactivation of the NF1 gene, frequently evidenced by loss of heterozygosity (LOH). We performed a comprehensive analysis of the prevalence and mechanisms of LOH in dNFs. Our study included 518 dNFs from 113 patients. LOH was detected in 25% of the dNFs (N = 129). The most frequent mechanism causing LOH was mitotic recombination, which was observed in 62% of LOH-tumors (N = 80), and which does not reduce the number of NF1 gene copies. All events were generated by a single crossover located between the centromere and the NF1 gene, resulting in isodisomy of 17q. LOH due to the loss of the NF1 gene accounted for a 38% of dNFs with LOH (N = 49), with deletions ranging in size from ∼80 kb to ∼8 Mb within 17q. In one tumor we identified the first example of a neurofibroma-associated second-hit type-2 NF1 deletion. Analysis of the prevalence of mechanisms causing LOH in dNFs in individual patients (possibly under genetic control) will elucidate whether there exist interindividual variation. Hum Mutat 32:78–90...

‣ High-Resolution Genome-Wide Analysis of Irradiated (UV and γ-Rays) Diploid Yeast Cells Reveals a High Frequency of Genomic Loss of Heterozygosity (LOH) Events

St. Charles, Jordan; Hazkani-Covo, Einat; Yin, Yi; Andersen, Sabrina L.; Dietrich, Fred S.; Greenwell, Patricia W.; Malc, Ewa; Mieczkowski, Piotr; Petes, Thomas D.
Fonte: Genetics Society of America Publicador: Genetics Society of America
Tipo: Artigo de Revista Científica
Publicado em /04/2012 Português
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In diploid eukaryotes, repair of double-stranded DNA breaks by homologous recombination often leads to loss of heterozygosity (LOH). Most previous studies of mitotic recombination in Saccharomyces cerevisiae have focused on a single chromosome or a single region of one chromosome at which LOH events can be selected. In this study, we used two techniques (single-nucleotide polymorphism microarrays and high-throughput DNA sequencing) to examine genome-wide LOH in a diploid yeast strain at a resolution averaging 1 kb. We examined both selected LOH events on chromosome V and unselected events throughout the genome in untreated cells and in cells treated with either γ-radiation or ultraviolet (UV) radiation. Our analysis shows the following: (1) spontaneous and damage-induced mitotic gene conversion tracts are more than three times larger than meiotic conversion tracts, and conversion tracts associated with crossovers are usually longer and more complex than those unassociated with crossovers; (2) most of the crossovers and conversions reflect the repair of two sister chromatids broken at the same position; and (3) both UV and γ-radiation efficiently induce LOH at doses of radiation that cause no significant loss of viability. Using high-throughput DNA sequencing...

‣ Single Nucleotide Polymorphism (SNP)-Based Loss of Heterozygosity (LOH) Testing by Real Time PCR in Patients Suspect of Myeloproliferative Disease

Huijsmans, Cornelis J. J.; Poodt, Jeroen; Damen, Jan; van der Linden, Johannes C.; Savelkoul, Paul H. M.; Pruijt, Johannes F. M.; Hilbink, Mirrian; Hermans, Mirjam H. A.
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Publicado em 02/07/2012 Português
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During tumor development, loss of heterozygosity (LOH) often occurs. When LOH is preceded by an oncogene activating mutation, the mutant allele may be further potentiated if the wild-type allele is lost or inactivated. In myeloproliferative neoplasms (MPN) somatic acquisition of JAK2V617F may be followed by LOH resulting in loss of the wild type allele. The occurrence of LOH in MPN and other proliferative diseases may lead to a further potentiating the mutant allele and thereby increasing morbidity. A real time PCR based SNP profiling assay was developed and validated for LOH detection of the JAK2 region (JAK2LOH). Blood of a cohort of 12 JAK2V617F-positive patients (n = 6 25–50% and n = 6>50% JAK2V617F) and a cohort of 81 patients suspected of MPN was stored with EDTA and subsequently used for validation. To generate germ-line profiles, non-neoplastic formalin-fixed paraffin-embedded tissue from each patient was analyzed. Results of the SNP assay were compared to those of an established Short Tandem Repeat (STR) assay. Both assays revealed JAK2LOH in 1/6 patients with 25–50% JAK2V617F. In patients with >50% JAK2V617F, JAK2LOH was detected in 6/6 by the SNP assay and 5/6 patients by the STR assay. Of the 81 patients suspected of MPN...

‣ Hsp27 (HSPB1): a possible surrogate molecular marker for loss of heterozygosity (LOH) of chromosome 1p in oligodendrogliomas but not in astrocytomas

Castro, Gisela N.; Cayado-Gutiérrez, Niubys; Moncalero, Vera L.; Lima, Patricia; De Angelis, Rodolfo Lucero; Chávez, Victor; Cuello-Carrión, F. Darío; Ciocca, Daniel R.
Fonte: Springer Netherlands Publicador: Springer Netherlands
Tipo: Artigo de Revista Científica
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In oligodendrogliomas, 1p loss of heterozygosity (LOH) is a predictor of good prognosis and treatment response. In contrast, in uveal melanomas, LOH of chromosome 3 has been linked to poor prognosis and downregulation of Hsp27. In the present study, we have analyzed the expression of heat-shock proteins (Hsps) to characterize subtypes of gliomas and their histopathologic features and to correlate with other molecular markers including LOH of 1p. Biopsies from patients with primary gliomas (n = 65) were analyzed by immunohistochemistry, chromogenic in situ hybridization and fluorescent in situ hybridization and methylation-specific PCR (MSP). Elevated Hsp27 and total Hsp70 expression levels were associated with high-grade astrocytomas (p = 0.0001 and p = 0.01, respectively). In grade III oligodendrogliomas, the Hsp27 levels were significantly higher (p = 0.03). Low O6-methylguanine-DNA methyltransferase (MGMT) expression was associated with grade II astrocytomas. Elevated β-catenin expression was associated with grade III/IV astrocytomas (p = 0.003); p53 (+) tumors were more frequently found in grade III/IV astrocytomas (p = 0,001). LOH on 1p was associated with oligodendroglial tumours. In addition, a higher Hsp27 expression correlated with LOH of 1p (p = 0.017); this was also tested in two glioma cell lines. MSP was successful in only six samples. No significant correlations were found for the other markers. In conclusion...

‣ Contribution of retinoblastoma LOH and the p53 Arg/Pro polymorphism to cervical cancer

ELTAHIR, HUDA A.; ELHASSAN, AHMED M.; IBRAHIM, MUNTASER E.
Fonte: D.A. Spandidos Publicador: D.A. Spandidos
Tipo: Artigo de Revista Científica
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Epidemiological studies indicate that infections by certain types of human papillomaviruses (HPVs) are causally linked to the development of cervical cancer. It is also known that HPV infections alone do not cause progression to cervical cancer, as additional genetic changes such as loss of distinct chromosomal regions, inactivation of tumor-suppressor genes and activation of oncogenes must also occur in order for malignant transformation to take place. In the present study, 78 patients diagnosed with cervical cancer and 36 cervical cancer-free cases (control) were analyzed for high-risk HPV genotypes (16 and 18) by polymerase chain reaction (PCR). Loss of heterozygosity (LOH) of the retinoblastoma gene (Rb) at two polymorphic intronic sites (intron 1 and 17) and the p53 polymorphism in codon 72 were detected by RFLP and allele-specific PCR, respectively. HPV 16 and 18 were found at frequencies of 93.6 and 8.3% in the cervical cancer and control samples, respectively. LOH was detected in 63% of patients in intron 1 and/or intron 17. p53 allele frequency for Arg/Arg was 43.6% (34/78), for Arg/Pro 37.2% (29/78) and for Pro/Pro 19.2% (15/78). The relative risk (RR) of LOH and Arg/Arg alone was 1.7 and 1.1, respectively, while the combined RR for Rb LOH and p53 Arg/Arg was 2.5. The present study showed a significant association of the chromosomal allelic loss of Rb in Sudanese cervical cancer patients...

‣ Loss of Heterozygosity (LOH) Profiles – Validated Risk Predictors for Progression to Oral Cancer

Zhang, Lewei; Poh, Catherine F.; Williams, Michele; Laronde, Denise M.; Berean, Ken; Gardner, Pamela J.; Jiang, Huijun; Wu, Lang; Lee, J. Jack; Rosin, Miriam P.
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
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A major barrier to oral cancer prevention has been the lack of validated risk predictors for oral premalignant lesions (OPLs). In 2000, we proposed a loss of heterozygosity (LOH) risk model in a retrospective study. This paper validated the previously reported LOH profiles as risk predictors and developed refined models via the largest longitudinal study to date of low-grade OPLs from a population-based patient group. Analysis involved a prospective cohort of 296 patients with primary mild/moderate oral dysplasia enrolled in the Oral Cancer Prediction Longitudinal Study. LOH status was determined in these OPLs. Patients were classified into high-risk or low-risk profiles to validate the 2000 model. Risk models were refined using recursive partitioning and Cox regression analyses. The prospective cohort validated that the high-risk lesions (3p &/or 9p LOH) had a 22·6 - fold increase in risk (P = 0·002) compared to low-risk lesions (3p & 9p retention). Addition of another two markers (loci on 4q/17p) further improved the risk prediction, with five-year progression rates of 3·1%, 16·3%, and 63·1% for the low-, intermediate-, and high-risk lesions, respectively. Compared to the low-risk group, intermediate- and high-risk groups had 11·6-fold and 52·1-fold increase in risk (P < 0·001). LOH profiles as risk predictors in the refined model were validated in the retrospective cohort. Multi-covariate analysis with clinical features showed LOH models to be the most significant predictors of progression. LOH profiles can reliably differentiate progression risk for OPLs. Potential uses include increasing surveillance for patients with elevated risk...

‣ Identifying Human Genome-Wide CNV, LOH and UPD by Targeted Sequencing of Selected Regions

Wang, Yu; Li, Wei; Xia, Yingying; Wang, Chongzhi; Tang, Y. Tom; Guo, Wenying; Li, Jinliang; Zhao, Xia; Sun, Yepeng; Hu, Juan; Zhen, Hefu; Zhang, Xiandong; Chen, Chao; Shi, Yujian; Li, Lin; Cao, Hongzhi; Du, Hongli; Li, Jian
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Publicado em 28/04/2015 Português
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Copy-number variations (CNV), loss of heterozygosity (LOH), and uniparental disomy (UPD) are large genomic aberrations leading to many common inherited diseases, cancers, and other complex diseases. An integrated tool to identify these aberrations is essential in understanding diseases and in designing clinical interventions. Previous discovery methods based on whole-genome sequencing (WGS) require very high depth of coverage on the whole genome scale, and are cost-wise inefficient. Another approach, whole exome genome sequencing (WEGS), is limited to discovering variations within exons. Thus, we are lacking efficient methods to detect genomic aberrations on the whole genome scale using next-generation sequencing technology. Here we present a method to identify genome-wide CNV, LOH and UPD for the human genome via selectively sequencing a small portion of genome termed Selected Target Regions (SeTRs). In our experiments, the SeTRs are covered by 99.73%~99.95% with sufficient depth. Our developed bioinformatics pipeline calls genome-wide CNVs with high confidence, revealing 8 credible events of LOH and 3 UPD events larger than 5M from 15 individual samples. We demonstrate that genome-wide CNV, LOH and UPD can be detected using a cost-effective SeTRs sequencing approach...

‣ Avaliação Genético-Molecular do Carcinoma das Células Escamosas da Laringe; Assessing the Molecular and Genetic Aspects of Squamous Cell Carcinoma of the Larynx

SILVA, Cláudio Carlos da
Fonte: Universidade Federal de Goiás; BR; UFG; Doutorado em Biologia; Ciencias Biologicas Publicador: Universidade Federal de Goiás; BR; UFG; Doutorado em Biologia; Ciencias Biologicas
Tipo: Tese de Doutorado Formato: application/pdf
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The larynx is a structure of the upper aerodigestive tract responsible for the production of sounds as well as protecting the lower airways and helping during the normal act of swallowing. Any pathology which affects the larynx can impose several challenges that disrupt its normal physiological function, and consequently and directly resulting in reduction of the patient s quality of life. Among the different diseases that affect the larynx, cancer is one of the most serious. The squamous cell carcinoma (SCC) of the larynx is a multifactorial disease, influenced by environmental factors and individual behavioral, habits, and susceptibility. The current study describes the molecular and genetic assessment of 20 patients with the squamous cell carcinoma of the larynx. In summary, the study strategy included the analyses of the genetic polymorphism of codon 72 of the TP53, the detection and genotyping of HPV genome, assessing genomic instability (MIS and LOH) and random chromosomal imbalances using PCR and CGH approaches. Regarding to the polymorphism of the TP53 gene, arginine homozygous genotypes (p53AA) and arginine-proline heterozygous genotypes (p53PA) were found in 65% (13/20) and 35% (7 / 20) of cases, respectively. HPV genome was found in association with tumor cells in 20% of SCC cases. HPV 16...

‣ An integrated Bayesian analysis of LOH and copy number data

Rancoita, Paola M. V.; Hutter, Marcus; Bertoni, Francesco; Kwee, Ivo
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Artigo de Revista Científica
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BACKGROUND Cancer and other disorders are due to genomic lesions. SNP-microarrays are able to measure simultaneously both genotype and copy number (CN) at several Single Nucleotide Polymorphisms (SNPs) along the genome. CN is defined as the number of DNA copies, and the normal is two, since we have two copies of each chromosome. The genotype of a SNP is the status given by the nucleotides (alleles) which are present on the two copies of DNA. It is defined homozygous or heterozygous if the two alleles are the same or if they differ, respectively. Loss of heterozygosity (LOH) is the loss of the heterozygous status due to genomic events. Combining CN and LOH data, it is possible to better identify different types of genomic aberrations. For example, a long sequence of homozygous SNPs might be caused by either the physical loss of one copy or a uniparental disomy event (UPD), i.e. each SNP has two identical nucleotides both derived from only one parent. In this situation, the knowledge of the CN can help in distinguishing between these two events. RESULTS To better identify genomic aberrations, we propose a method (called gBPCR) which infers the type of aberration occurred, taking into account all the possible influence in the microarray detection of the homozygosity status of the SNPs...

‣ Identifizierung und Charakterisierung von Tumor-Progressions-Genen in einem Melanoma Modellsystem; Identification and characterizsation of tumor progression genes in a melanoma model system

Hildebrandt, Tobias
Fonte: Universität Tübingen Publicador: Universität Tübingen
Tipo: Dissertation; info:eu-repo/semantics/doctoralThesis
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Mit Hilfe der Methode des Differential Displays wurde das Expressionsprofil zweier Melanoma-Zellinien miteinander verglichen. Durch die Analyse der Expressionsmuster dieser beiden Zellinien sollten bekannte und/oder neue differentiell exprimierte Gene identifiziert werden, die in den Prozess der Metastasierung involviert sind. Es konnten fünf differentiell exprimierte Gene identifiziert und zum Teil näher charakterisiert werden. Es handelte sich dabei um die Beta-Ketten von zwei verschiedenen HLA Klasse II Genen (HLA-DR und HLA-SB), sowie um eine Stearoyl-CoA Desaturase. Ferner konnten zwei, bis dahin völlig unbekannte Gene (URIM und THW) identifiziert werden. Eine Überexpression des bis dahin unbekannten Gens URIM wurde in der metastasierenden Zellinie NMCL-1, gegenüber der Zellinie 530 gefunden. URIM war ebenfalls in einem Panel von metastasierenden Mammakarzinom-Zellinien gegenüber Zellinien aus Primär-Tumoren überexprimiert. Mit Hilfe der RACE-PCR konnte die 750 bp lange cDNA isoliert werden. Die Nukleotidsequenz kodiert im ORF für ein aus 206 Aminosäuren bestehendes Protein. Die genomische Lokalisation von URIM konnte auf dem Chromosom 22q11, in der sogenannten 'DiGeorge Critical Region' lokalisiert werden. Das zweite neu identifizierte Gen (THW) ist als ca. 2 kb Transkript in der nicht-metastasierenden Zellinie 530...

‣ Identification of novel prognostic markers in cervical intraepithelial neoplasia using LDMAS (LOH Data Management and Analysis Software)

Hamoudi, Rifat A.; El-Hamidi, Amina; Du, Ming-Qing
Fonte: Universidade de Cambridge Publicador: Universidade de Cambridge
Tipo: Article; Published Version
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RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.; Abstract Background Detection of Loss of Heterozygosity (LOH) is one of the most common molecular applications in the study of human diseases, in particular cancer. The technique is commonly used to examine whether a known tumour suppressor gene is inactivated or to map unknown tumour suppressor gene(s). However, with the increasing number of samples analysed using different software, no tool is currently available to integrate and facilitate the extensive and efficient data retrieval and analyses, such as correlation of LOH data with various clinical data sets. Results An algorithm to identify prognostic disease markers is devised and implemented as novel software called LDMAS. LDMAS is a software suite designed for data retrieval, management and integrated analysis of the clinico-pathological data and molecular results from independent databases. LDMAS is used in stratification of disease stages according to clinical stage or histological features and correlation of various clinico-pathological features with molecular findings to obtain relevant prognostic markers such as those used in predicting the outcome of cervical intraepithelial neoplasia (CIN). This approach lead to the identification of novel prognostic cervical cancer markers and extraction of useful clinical information such as correlation of Human Papilloma Virus (HPV) status with CIN lesions. Conclusions A novel software called LDMAS is implemented and used to extract and identify prognostic disease markers. The software is used to successfully identify 4 novel prognostic markers that can be used to predict the outcome of CIN. LDMAS provides an essential platform for the extraction of useful information from large amount of data generated by LOH studies. LDMAS provides three unique and novel features for LOH analysis : (1) automatic extraction of relevant data from patient records and reports (2) correlation of LOH data with clinico-pathological data and (3) storage of complex data in flexible format. The first feature automates the creation of database of clinically relevant information from huge amount of data...

‣ Caracterización biomolecular del cáncer de laringe: relación entre ploidia, actividad proliferativa y LOH en la región 9p21

Zanna,I.; Sanz-Casla,M.T.; Maestro,M.L.; Bazan,V.; Corsale,S.; Quintana,P.L.; Gebbia,N.; Bernáldez,R.; Campillo,J.A.; S-Rueda,D.; Valor,S.; Russo,A.
Fonte: Revista de Diagnóstico Biológico Publicador: Revista de Diagnóstico Biológico
Tipo: info:eu-repo/semantics/article; journal article; info:eu-repo/semantics/publishedVersion Formato: text/html; application/pdf
Publicado em 01/09/2001 Português
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El carcinoma escamoso de laringe o LSCC (Laryngeal Squamous Cell Carcinoma) representa más del 95% de las neoplasias de laringe. Representa cerca del 2% de todos los cánceres humanos en el mundo Occidental y es una importante causa de muerte entre los tumores de cabeza y cuello. A pesar de los avances en el estudio de LSCC los indicadores pronóstico "clasicos" no permiten identificar los pacientes con elevado riesgo de recaída o muerte. En los últimos años se intentan identificar nuevos factores biológicos para predecir la evolución del tumor. El objetivo de este trabajo es el estudio de los factores biológicos implicados en el carcinoma escamoso de laringe: actividad proliferativa (SPF), contenido celular de DNA y la determinación de posibles alteraciones genéticas en el gen supresor p16, pérdida de heterocigosidad (LOH) y mutaciones puntuales. Este estudio se realizó en 56 pacientes intervenidos quirúrgicamente de cáncer de laringe. Se realizó la evaluación de la ploidía y de la SPF mediante citometría de flujo. Para la valoración de la LOH en el gen p16 se realizó extracción de DNA, electroferesis en un gel de poliacrilamida al 8% y coloración con nitrato de plata. Las mutaciones en el gen p16 fueron detectadas mediante análisis SSCP después de la amplificación mediante PCR del exón 1. Se detectó aneuploidía en el 63% de los pacientes y de ellos el 9% presentaban multiclonalidad. En nuestra serie de pacientes...

‣ Análisis de microsatélites en células exfoliadas del sedimento urinario: Su utilidad para la detección del cáncer vesical. Estudio comparativo con citología urinaria

Molina Burgos,R.; Millán Salvador,J.M.; Oltra Soler,J.S.; Jiménez Cruz,J.F.
Fonte: Actas Urológicas Españolas Publicador: Actas Urológicas Españolas
Tipo: info:eu-repo/semantics/article; journal article; info:eu-repo/semantics/publishedVersion Formato: text/html; application/pdf
Publicado em 01/09/2003 Português
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INTRODUCCIÓN: Teniendo en cuenta la precocidad de las alteraciones genéticas en la carcinogénesis de los tumores de vejiga, la valoración de estos cambios a nivel de 9p 21-22 por medio de marcadores microsatélites podrían ser útiles para el diagnóstico y seguimiento. OBJETIVO: Evaluar el uso de marcadores microsatélites y la utilidad de pérdida de heterocigosidad (LOH) e inestabilidad de microsatélites (MSI) en células exfoliadas del sedimento urinario para él diagnostico de tumores vesicales. MATERIAL Y MÉTODO: Amplificamos con PCR el DNA de muestras de orina y sangre de 160 pacientes con tumor vesical. Con 4 marcadores microsatélites de 9p 21-22 (D9S747-D9S171-D9S162-IFNA) y 1 de cromosoma 4 (D4S243) se analizó LOH/MSI en células del sedimento urinario. Utilizamos la citología urinaria como método comparativo y el análisis histológico del tejido obtenido por R.T.U, como diagnóstico de referencia. Calculamos la sensibilidad y especificidad del método y si existía alguna correlación con estadio y grado tumoral. RESULTADOS: Se pudo utilizar correctamente 150 muestras. En 111 encontramos LOH/MSI (sensibilidad del 74%). La citología pudo descubrir solamente 60 pacientes (sensibilidad 40%). Encontramos mayor número de alteraciones microsatélites (AM) en tumores superficiales (sensibilidad 77...