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1.
Isr Med Assoc J ; 22(1): 32-36, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31927803

RESUMO

BACKGROUND: Evaluation of mismatch repair (MMR) deficiency is conducted via immunohistochemistry or by microsatellite instability (MSI) analysis. Heterogeneous immunohistochemistry staining for MMR proteins may show different patterns; however, according to current guidelines, all of those patterns should be interpreted as MMR proficient. This conclusion might lead to false negative results because although most cases of heterogeneity stem from technical factors and biological variability, other types of heterogeneity represent true MMR deficiency. OBJECTIVES: To identify a unique heterogeneity pattern that is associated with true MMR loss. METHODS: We analyzed 145 cases of colorectal carcinoma. Immunohistochemistry staining for MLH1, PMS2, MSH2, and MSH6 were performed. We defined geographic heterogeneity as areas of tumor nuclear staining adjacent to areas of loss of tumor nuclear staining with intact staining in the surrounding stroma. All cases were evaluated for the presence of geographic heterogeneity. In addition, 24 cases were also evaluated by MSI testing. RESULTS: Of the 145 cases, 24 (16.5%) were MMR deficient. Of the 24 cases for which MSI analysis was also available, 10 cases (41.7%) demonstrated biological heterogeneity, 5 (20.8%) demonstrated technical heterogeneity, and 2 (8.3%) demonstrated geographic heterogeneity. Only the two cases with geographic heterogeneity were MSI-high via MSI analysis. In addition, a germline mutation in MSH-6 was identified in one of these cases. CONCLUSIONS: Geographic heterogeneity may raise a suspicion for a MMR-deficient case, which should be further analyzed using additional methodologies such as MSI analysis.


Assuntos
Reparo de Erro de Pareamento de DNA/genética , Proteínas MutS/genética , Adenoma/genética , Adenoma/patologia , Adulto , Neoplasias Colorretais/genética , Neoplasias Colorretais/patologia , Corantes , Heterogeneidade Genética , Humanos , Masculino
2.
J Clin Pathol ; 73(1): 17-22, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31300530

RESUMO

OBJECTIVE: Cutaneous squamous cell carcinoma (cSCC) is the second most common malignancy, most frequently affecting the head and neck. Treatment often requires surgery and can have significant functional morbidity. Research into disease pathogenesis and second line medical management of cSCC is limited. We assess genetic mutations in high-risk, primary head and neck cutaneous squamous cell carcinomas (HNcSCC) that may hinder or be beneficial for use of targeted therapy in disease management. METHODS: Genetic alterations and variant allele frequencies (VAFs) were analysed using a clinically relevant 48 gene panel in 10 primary high-risk non-metastatic treatment-naïve HNcSCC to evaluate applicability of targeted therapeutics. Variants present at all VAFs were evaluated for pathogenicity. Somatic mutation patterns of individual tumours were analysed. RESULTS: High-risk HNcSCC showed a high proportion (82%) of C to T transitions in keeping with ultraviolet-mediated damage. There was significant intratumour genetic heterogeneity in this cohort (MATH scores 20-89) with the two patients <45 years of age showing highest intratumour heterogeneity. TP53 was altered at VAF >22% in all cases, and mutations with highest VAF were observed in tumour suppressor genes in 80%. 70% of cases demonstrated at least one mutation associated with treatment resistance (KIT S821F, KIT T670I, RAS mutations at codons 12 and 13). CONCLUSION: We demonstrate high proportion tumour suppressor loss of function mutations, high intratumour genetic heterogeneity, and presence of well recognised resistance mutations in treatment naïve primary HNcSCC. These factors pose challenges for successful utilisation of targeted therapies.


Assuntos
Biomarcadores Tumorais/genética , Heterogeneidade Genética , Neoplasias de Cabeça e Pescoço/genética , Mutação , Neoplasias Cutâneas/genética , Carcinoma de Células Escamosas de Cabeça e Pescoço/genética , Adulto , Idoso , Idoso de 80 Anos ou mais , Antineoplásicos/uso terapêutico , Tomada de Decisão Clínica , Resistencia a Medicamentos Antineoplásicos/genética , Feminino , Predisposição Genética para Doença , Neoplasias de Cabeça e Pescoço/tratamento farmacológico , Neoplasias de Cabeça e Pescoço/patologia , Humanos , Masculino , Pessoa de Meia-Idade , Terapia de Alvo Molecular , Seleção de Pacientes , Fenótipo , Medicina de Precisão , Neoplasias Cutâneas/tratamento farmacológico , Neoplasias Cutâneas/patologia , Carcinoma de Células Escamosas de Cabeça e Pescoço/tratamento farmacológico , Carcinoma de Células Escamosas de Cabeça e Pescoço/patologia , Transcriptoma
3.
Adv Exp Med Biol ; 1164: 207-224, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31576551

RESUMO

Prostate cancers have a justified reputation as one of the most heterogeneous human tumours. Indeed, there are some who consider that advanced and castration-resistant prostate cancers are incurable, as a direct result of this heterogeneity. However, tumour heterogeneity can be defined in different ways. To a clinician, prostate cancer is a number of different diseases, the treatments for which remain equally heterogeneous and uncertain. To the pathologist, the histopathological appearances of the tumours are notoriously heterogeneous. Indeed, the genius of Donald Gleason in the 1960s was to devise a classification system designed to take into account the heterogeneity of the tumours both individually and in the whole prostate context. To the cell biologist, a prostate tumour consists of multiple epithelial cell types, inter-mingled with various fibroblasts, neuroendocrine cells, endothelial cells, macrophages and lymphocytes, all of which interact to influence treatment responses in a patient-specific manner. Finally, genetic analyses of prostate cancers have been compromised by the variable gene rearrangements and paucity of activating mutations observed, even in large numbers of patient tumours with consistent clinical diagnoses and/or outcomes. Research into familial susceptibility has even generated the least tractable outcome of such studies: the genetic loci are of low penetrance and are of course heterogeneous. By fractionating the tumour (and patient-matched non-malignant tissues) heterogeneity can be resolved, revealing homogeneous markers of patient outcomes.


Assuntos
Células Endoteliais , Neoplasias da Próstata , Células Endoteliais/citologia , Heterogeneidade Genética , Humanos , Masculino , Mutação , Neoplasias da Próstata/diagnóstico , Neoplasias da Próstata/genética , Neoplasias da Próstata/patologia , Neoplasias da Próstata/terapia
4.
Nat Med ; 25(9): 1415-1421, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-31501609

RESUMO

During cancer therapy, tumor heterogeneity can drive the evolution of multiple tumor subclones harboring unique resistance mechanisms in an individual patient1-3. Previous case reports and small case series have suggested that liquid biopsy (specifically, cell-free DNA (cfDNA)) may better capture the heterogeneity of acquired resistance4-8. However, the effectiveness of cfDNA versus standard single-lesion tumor biopsies has not been directly compared in larger-scale prospective cohorts of patients following progression on targeted therapy. Here, in a prospective cohort of 42 patients with molecularly defined gastrointestinal cancers and acquired resistance to targeted therapy, direct comparison of postprogression cfDNA versus tumor biopsy revealed that cfDNA more frequently identified clinically relevant resistance alterations and multiple resistance mechanisms, detecting resistance alterations not found in the matched tumor biopsy in 78% of cases. Whole-exome sequencing of serial cfDNA, tumor biopsies and rapid autopsy specimens elucidated substantial geographic and evolutionary differences across lesions. Our data suggest that acquired resistance is frequently characterized by profound tumor heterogeneity, and that the emergence of multiple resistance alterations in an individual patient may represent the 'rule' rather than the 'exception'. These findings have profound therapeutic implications and highlight the potential advantages of cfDNA over tissue biopsy in the setting of acquired resistance.


Assuntos
Ácidos Nucleicos Livres/sangue , DNA de Neoplasias/sangue , Neoplasias Gastrointestinais/sangue , Biópsia Líquida , Autopsia , Ácidos Nucleicos Livres/genética , Estudos de Coortes , DNA de Neoplasias/genética , Resistencia a Medicamentos Antineoplásicos/genética , Feminino , Neoplasias Gastrointestinais/genética , Neoplasias Gastrointestinais/patologia , Heterogeneidade Genética , Humanos , Masculino , Pessoa de Meia-Idade , Mutação , Proteínas Proto-Oncogênicas B-raf/genética , Sequenciamento Completo do Exoma
5.
Lett Appl Microbiol ; 69(4): 286-293, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31392736

RESUMO

The prevalence of Listeria monocytogenes in the retail fish markets of the Kerala, India was investigated by screening 227 samples comprising of marine finfish (n = 97) shellfish (n = 19), ready-to-cook fish products (n = 47), ready-to-eat fish products (n = 10), dried fish (n = 11) and retail ice (n = 43). The prevalence of L. monocytogenes and L. innocua was 2·7% and 17·2% respectively. Sample category wise, prevalence of L. monocytogenes was higher in marine finfish (1·8%) and retail ice (0·9%). All the L. monocytogenes isolates carried virulent genes namely inlA, inlC, inlJ, hlyA, iap, plcA, prfA genes and majority (82%) belonged to 1/2a, 3a serogroups. L. monocytogenes isolates were multidrug-resistant and showed resistance to ampicillin, penicillin, erythromycin, tetracycline and clindamycin. Enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) delineated 58% genetic heterogeneity among the L. monocytogenes strains. The study reports that genetic similarities of the isolates were interlinked to their serogroup and sample origin. SIGNIFICANCE AND IMPACT OF THE STUDY: Prevalence of Listeria monocytogenes, in the retail fish markets of Kerala, India was low but their relatively higher presence in marine finfish and retail ice and virulent nature of the isolates signifies food safety concerns. Moreover, multidrug-resistant nature of these isolates may potentially lead to spread of antimicrobial resistance. This study identified retail ice as a vehicle for entry of L. monocytogenes in retail fish and hence, there is a need to ensure quality of retail ice used for maintaining the cold-chain.


Assuntos
Antibacterianos/farmacologia , Farmacorresistência Bacteriana Múltipla/genética , Listeria monocytogenes/efeitos dos fármacos , Alimentos Marinhos/microbiologia , Frutos do Mar/microbiologia , Ampicilina/farmacologia , Animais , Clindamicina/farmacologia , Eritromicina/farmacologia , Pesqueiros , Peixes/microbiologia , Microbiologia de Alimentos , Inocuidade dos Alimentos , Heterogeneidade Genética , Gelo/análise , Índia , Listeria monocytogenes/genética , Listeria monocytogenes/isolamento & purificação , Penicilinas/farmacologia , Prevalência , Sorogrupo , Tetraciclina/farmacologia
6.
Medicine (Baltimore) ; 98(34): e16916, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31441872

RESUMO

BACKGROUND: Colorectal Cancer (CRC) is a highly heterogeneous disease. RNA profiles of bulk tumors have enabled transcriptional classification of CRC. However, such ways of sequencing can only target a cell colony and obscure the signatures of distinct cell populations. Alternatively, single-cell RNA sequencing (scRNA-seq), which can provide unbiased analysis of all cell types, opens the possibility to map cellular heterogeneity of CRC unbiasedly. METHODS: In this study, we utilized scRNA-seq to profile cells from cancer tissue of a CRC patient. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to understand the roles of genes within the clusters. RESULTS AND CONCLUSION: The 2824 cells were analyzed and categorized into 5 distinct clusters by scRNA-seq. For every cluster, specific cell markers can be applied, indicating each 1 of them different from another. We discovered that the tumor of CRC displayed a clear sign of heterogenicity, while genes within each cluster serve different functions. GO term analysis also stated that different cluster's relatedness towards the tumor of CRC differs. Three clusters participate in peripheral works in cells, including, energy transport, extracellular matrix generation, etc; Genes in other 2 clusters participate more in immunology processes. Lastly, trajectory plot analysis also supports the viewpoint, in that some clusters present in different states and pseudo-time, while others present in a single state or pseudo time. Our analysis provides more insight into the heterogeneity of CRC, which can provide assistance to further researches on this topic.


Assuntos
Neoplasias Colorretais/genética , Perfilação da Expressão Gênica/métodos , Heterogeneidade Genética , Análise de Sequência de RNA/métodos , Idoso , Biomarcadores Tumorais/genética , Feminino , Humanos
8.
Arq. bras. med. vet. zootec. (Online) ; 71(4): 1277-1285, jul.-ago. 2019. tab, graf, ilus
Artigo em Inglês | LILACS, VETINDEX | ID: biblio-1038601

RESUMO

This study aimed to evaluate the use of some testicular traits to identify boars with low sperm morphological quality. The consistency (scores from 1 to 5), tone with tonometry (mm), parenchyma echogenicity and heterogeneity with ultrasound (pixel) were assessed in 402 mature boars (18.5 months on average). Sperm abnormality thresholds (≤ 25% of total sperm abnormalities, ≤ 5% of heads, acrosome, neck or midpiece defects, ≤ 10% tail defects, and 15% cytoplasmic droplets) were used to classify boars as approved or disapproved. Three classes of testicular traits were formed (extremely low and high values, approximately 15% each, were kept in separated classes). When the traits were individually evaluated, fewer boars were approved if the echogenicity or heterogeneity were high, or if the tone was rigid. When evaluated in combination, the interaction between heterogeneity and tone, and between heterogeneity and echogenicity were significant. The high heterogeneity combined with soft tone or with hypo-echogenicity resulted in lower approval of boars. Tonometry and ultrasonography have a moderate potential to be included in breeding soundness examination of boars. When combined, they provide more reliable information about the impact of testicular parenchymal alterations on morphology of sperm cells.(AU)


O estudo objetivou avaliar o uso de características testiculares para identificar reprodutores com baixa qualidade de morfologia espermática. A consistência (escore de 1 a 5), o tônus por tonometria (mm), a ecogenicidade e a heterogeneidade do parênquima testicular por ultrassonografia (pixel) foram avaliados em 402 machos suínos maduros (18,5 meses, em média). Limiares máximos de anormalidades espermáticas (≤ 25% de defeitos totais, ≤ 5% de defeitos de cabeça, acrossoma, colo e peça intermediária, ≤ 10% de defeitos de cauda e 15% de gota citoplasmática) foram utilizados para classificar os machos como aprovados ou reprovados. Três classes de características testiculares foram formadas (valores extremamente baixos e altos, aproximadamente 15% em cada, foram mantidos em classes separadas). Quando as características testiculares foram avaliadas individualmente, menos machos foram aprovados se a ecogenicidade ou a heterogeneidade foram altas, ou se o tônus era rígido. Quando avaliadas em combinação, a interação entre heterogeneidade e tônus e a interação entre heterogeneidade e ecogenicidade foram significativas. A alta heterogeneidade combinada com testículos flácidos ou com testículos hipoecogênicos resultou em menor aprovação de cachaços. A tonometria e a ultrassonografia possuem potencial moderado para serem incluídas no exame andrológico de cachaços. Quando combinadas, as técnicas fornecem uma informação mais consistente do impacto das alterações do parênquima testicular na morfologia das células espermáticas.(AU)


Assuntos
Animais , Masculino , Suínos/anatomia & histologia , Testículo/anatomia & histologia , Tecido Parenquimatoso/anatomia & histologia , Heterogeneidade Genética , Análise do Sêmen/veterinária , Manometria/veterinária
9.
Genet Epidemiol ; 43(7): 815-830, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31332826

RESUMO

Genotype-stratified variance of a quantitative trait could differ in the presence of gene-gene or gene-environment interactions. Genetic markers associated with phenotypic variance are thus considered promising candidates for follow-up interaction or joint location-scale analyses. However, as in studies of main effects, the X-chromosome is routinely excluded from "whole-genome" scans due to analytical challenges. Specifically, as males carry only one copy of the X-chromosome, the inherent sex-genotype dependency could bias the trait-genotype association, through sexual dimorphism in quantitative traits with sex-specific means or variances. Here we investigate phenotypic variance heterogeneity associated with X-chromosome single nucleotide polymorphisms (SNPs) and propose valid and powerful strategies. Among those, a generalized Levene's test has adequate power and remains robust to sexual dimorphism. An alternative approach is a sex-stratified analysis but at the cost of slightly reduced power and modeling flexibility. We applied both methods to an Estonian study of gene expression quantitative trait loci (eQTL; n = 841), and two complex trait studies of height, hip, and waist circumferences, and body mass index from Multi-Ethnic Study of Atherosclerosis (MESA; n = 2,073) and UK Biobank (UKB; n = 327,393). Consistent with previous eQTL findings on mean, we found some but no conclusive evidence for cis regulators being enriched for variance association. SNP rs2681646 is associated with variance of waist circumference (p = 9.5E-07) at X-chromosome-wide significance in UKB, with a suggestive female-specific effect in MESA (p = 0.048). Collectively, an enrichment analysis using permutated UKB (p < 0.1) and MESA (p < 0.01) datasets, suggests a possible polygenic structure for the variance of human height.


Assuntos
Cromossomos Humanos X/genética , Heterogeneidade Genética , Herança Multifatorial/genética , Locos de Características Quantitativas/genética , Simulação por Computador , Feminino , Interação Gene-Ambiente , Estudo de Associação Genômica Ampla , Genótipo , Humanos , Masculino , Fenótipo , Caracteres Sexuais , Circunferência da Cintura
10.
Nat Biotechnol ; 37(8): 869-876, 2019 08.
Artigo em Inglês | MEDLINE | ID: mdl-31285593

RESUMO

Engineering the synthesis of massive amounts of therapeutics, enzymes or commodity chemicals can select for subpopulations of nonproducer cells, owing to metabolic burden and product toxicity. Deep DNA sequencing can be used to detect undesirable genetic heterogeneity in producer populations and diagnose associated genetic error modes. Hotspots of genetic heterogeneity can pinpoint mechanisms that underlie load problems and product toxicity. Understanding genetic heterogeneity will inform metabolic engineering and synthetic biology strategies to minimize the emergence of nonproducer mutants in scaled-up fermentations and maximize product quality and yield.


Assuntos
Bactérias/genética , Bactérias/metabolismo , Fungos/metabolismo , Heterogeneidade Genética , Sequenciamento de Nucleotídeos em Larga Escala , Engenharia Metabólica/métodos , Animais , Biotecnologia , Linhagem Celular , Indústria Farmacêutica , Fermentação , Fungos/genética , Humanos , Preparações Farmacêuticas , Biologia Sintética
11.
Int J Mol Sci ; 20(12)2019 Jun 18.
Artigo em Inglês | MEDLINE | ID: mdl-31216660

RESUMO

Pulses are the main source of protein and minerals in the vegetarian diet. These are primarily cultivated on marginal lands with few inputs in several resource-poor countries of the world, including several in South Asia. Their cultivation in resource-scarce conditions exposes them to various abiotic and biotic stresses, leading to significant yield losses. Furthermore, climate change due to global warming has increased their vulnerability to emerging new insect pests and abiotic stresses that can become even more serious in the coming years. The changing climate scenario has made it more challenging to breed and develop climate-resilient smart pulses. Although pulses are climate smart, as they simultaneously adapt to and mitigate the effects of climate change, their narrow genetic diversity has always been a major constraint to their improvement for adaptability. However, existing genetic diversity still provides opportunities to exploit novel attributes for developing climate-resilient cultivars. The mining and exploitation of adaptive traits imparting tolerance/resistance to climate-smart pulses can be accelerated further by using cutting-edge approaches of biotechnology such as transgenics, genome editing, and epigenetics. This review discusses various classical and molecular approaches and strategies to exploit adaptive traits for breeding climate-smart pulses.


Assuntos
Adaptação Fisiológica , Mudança Climática , Clima , Característica Quantitativa Herdável , Produtos Agrícolas , Epigenômica , Edição de Genes , Interação Gene-Ambiente , Heterogeneidade Genética , Genômica/métodos , Metabolômica/métodos , Melhoramento Vegetal , Plantas Geneticamente Modificadas , Proteômica/métodos
12.
Nat Genet ; 51(6): 1060-1066, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31152164

RESUMO

Modulation of chromatin structure via histone modification is a major epigenetic mechanism and regulator of gene expression. However, the contribution of chromatin features to tumor heterogeneity and evolution remains unknown. Here we describe a high-throughput droplet microfluidics platform to profile chromatin landscapes of thousands of cells at single-cell resolution. Using patient-derived xenograft models of acquired resistance to chemotherapy and targeted therapy in breast cancer, we found that a subset of cells within untreated drug-sensitive tumors share a common chromatin signature with resistant cells, undetectable using bulk approaches. These cells, and cells from the resistant tumors, have lost chromatin marks-H3K27me3, which is associated with stable transcriptional repression-for genes known to promote resistance to treatment. This single-cell chromatin immunoprecipitation followed by sequencing approach paves the way to study the role of chromatin heterogeneity, not just in cancer but in other diseases and healthy systems, notably during cellular differentiation and development.


Assuntos
Neoplasias da Mama/genética , Imunoprecipitação da Cromatina , Cromatina/genética , Heterogeneidade Genética , Sequenciamento de Nucleotídeos em Larga Escala , Análise de Célula Única , Cromatina/metabolismo , Biologia Computacional/métodos , Epigênese Genética , Feminino , Histonas/metabolismo , Humanos , Técnicas Analíticas Microfluídicas , Análise de Célula Única/métodos , Células Estromais , Fluxo de Trabalho
14.
World J Emerg Surg ; 14: 24, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31164913

RESUMO

Background: Trauma leads to a complex inflammatory cascade that induces both immune activation and a refractory immune state in parallel. Although both components are deemed necessary for recovery, the balance is tight and easily lost. Losing the balance can lead to life-threatening infectious complications as well as long-term immunosuppression with recurrent infections. Neutrophils are known to play a key role in these processes. Therefore, this review focuses on neutrophil characteristics and function after trauma and how these features can be used to identify trauma patients at risk for infectious complications. Results: Distinct neutrophil subtypes exist that play their own role in the recovery and/or development of infectious complications after trauma. Furthermore, the refractory immune state is related to the risk of infectious complications. These findings change the initial concepts of the immune response after trauma and give rise to new biomarkers for monitoring and predicting inflammatory complications in severely injured patients. Conclusion: For early recognition of patients at risk, the immune system should be monitored. Several neutrophil biomarkers show promising results and analysis of these markers has become accessible to such extent that they can be used for point-of-care decision making after trauma.


Assuntos
Doenças Transmissíveis/classificação , Heterogeneidade Genética , Neutrófilos/classificação , Doenças Transmissíveis/fisiopatologia , Humanos , Integrina alfa4beta1/genética , Integrina alfa4beta1/metabolismo , Ferimentos e Lesões/complicações
15.
BMC Cancer ; 19(1): 434, 2019 May 10.
Artigo em Inglês | MEDLINE | ID: mdl-31077166

RESUMO

BACKGROUND: Chromosomal rearrangements are the typical phenomena in cancer genomes causing gene disruptions and fusions, corruption of regulatory elements, damage to chromosome integrity. Among the factors contributing to genomic instability are non-B DNA structures with stem-loops and quadruplexes being the most prevalent. We aimed at investigating the impact of specifically these two classes of non-B DNA structures on cancer breakpoint hotspots using machine learning approach. METHODS: We developed procedure for machine learning model building and evaluation as the considered data are extremely imbalanced and it was required to get a reliable estimate of the prediction power. We built logistic regression models predicting cancer breakpoint hotspots based on the densities of stem-loops and quadruplexes, jointly and separately. We also tested Random Forest models varying different resampling schemes (leave-one-out cross validation, train-test split, 3-fold cross-validation) and class balancing techniques (oversampling, stratification, synthetic minority oversampling). RESULTS: We performed analysis of 487,425 breakpoints from 2234 samples covering 10 cancer types available from the International Cancer Genome Consortium. We showed that distribution of breakpoint hotspots in different types of cancer are not correlated, confirming the heterogeneous nature of cancer. It appeared that stem-loop-based model best explains the blood, brain, liver, and prostate cancer breakpoint hotspot profiles while quadruplex-based model has higher performance for the bone, breast, ovary, pancreatic, and skin cancer. For the overall cancer profile and uterus cancer the joint model shows the highest performance. For particular datasets the constructed models reach high predictive power using just one predictor, and in the majority of the cases, the model built on both predictors does not increase the model performance. CONCLUSION: Despite the heterogeneity in breakpoint hotspots' distribution across different cancer types, our results demonstrate an association between cancer breakpoint hotspots and stem-loops and quadruplexes. Approximately for half of the cancer types stem-loops are the most influential factors while for the others these are quadruplexes. This fact reflects the differences in regulatory potential of stem-loops and quadruplexes at the tissue-specific level, which yet to be discovered at the genome-wide scale. The performed analysis demonstrates that influence of stem-loops and quadruplexes on breakpoint hotspots formation is tissue-specific.


Assuntos
Pontos de Quebra do Cromossomo , DNA/química , Neoplasias/genética , DNA/genética , Feminino , Heterogeneidade Genética , Instabilidade Genômica , Humanos , Modelos Logísticos , Aprendizado de Máquina , Masculino , Conformação de Ácido Nucleico , Especificidade de Órgãos
16.
BMJ Case Rep ; 12(5)2019 May 08.
Artigo em Inglês | MEDLINE | ID: mdl-31068350

RESUMO

Multiple pterygium syndrome of lethal type is a very rare genetic condition affecting the skin, muscles and skeleton. It is characterised by minor facial abnormalities, prenatal growth deficiency, spine defects, joint contractures, and webbing (pterygia) of the neck, elbows, back of the knees, armpits and fingers. We present a case of lethal multiple pterygium syndrome born at our hospital proven by the genetic analysis showing a double homozygous mutation.


Assuntos
Anormalidades Múltiplas/genética , Hipertermia Maligna/diagnóstico , Hipertermia Maligna/genética , Metaloendopeptidases/genética , Mutação , Receptores Nicotínicos/genética , Anormalidades da Pele/diagnóstico , Anormalidades da Pele/genética , Anormalidades Múltiplas/diagnóstico , Anormalidades Múltiplas/fisiopatologia , Consanguinidade , Análise Mutacional de DNA , Suscetibilidade a Doenças , Evolução Fatal , Aconselhamento Genético , Heterogeneidade Genética , Humanos , Recém-Nascido , Masculino , Hipertermia Maligna/fisiopatologia , Linhagem , Anormalidades da Pele/fisiopatologia
17.
Br Poult Sci ; 60(4): 366-372, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31046426

RESUMO

1. In current breeding programmes, uniformity of end products and producing animals that are robust to environmental challenges are desirable. Several studies have provided evidence of the presence of genetic heterogeneity of residual variance and proposed that it could be possible to increase uniformity of livestock productions by selection. The present study aimed to define the micro environmental sensitivity of dual-purpose chickens for body weight at hatch. 2. The data set consisted of 24,321 female and 21,547 male chickens' records of hatch weight from 19 consecutive generations of Mazandaran fowl. The statistical analysis was carried out in a two-step approach: first, an animal model was fitted to the data and then, the impact of additive genetic effects on the residual variance of the studied trait was investigated. 3. The estimate of heritability for body weight at hatch was in the range of 0.23-0.25 for female and 0.14-0.16 for male offspring, respectively. The proportion of maternal environmental variance to phenotypic variance ranged from 0.24 to 0.27 for female and 0.17 to 0.24 for male offspring. Heritabilities in females were higher than males. Estimates of the heritability of residual variance ranged between 0.067 and 0.090. The genetic coefficients of variation were high ranging between 0.83 and 0.86. Genetic correlations between hatch weight and its residual variance estimates from bivariate analysis were -0.39 and -0.44 in females and males, respectively. 4. The results suggest that there is an opportunity to simultaneously improve body weight and the uniformity of body weight by selecting for lower residual variance in native chickens.


Assuntos
Animais Recém-Nascidos/fisiologia , Peso Corporal/genética , Galinhas/fisiologia , Heterogeneidade Genética , Animais , Animais Recém-Nascidos/genética , Galinhas/genética , Feminino , Irã (Geográfico) , Masculino
18.
BMC Cancer ; 19(1): 403, 2019 Apr 29.
Artigo em Inglês | MEDLINE | ID: mdl-31035962

RESUMO

BACKGROUND: Modern cancer treatment strategies aim to target tumour specific genetic (or epigenetic) alterations. Treatment response improves if these alterations are clonal, i.e. present in all cancer cells within tumours. However, the identification of truly clonal alterations is impaired by the tremendous intra-tumour genetic heterogeneity and unavoidable sampling biases. METHODS: Here, we investigate the underlying causes of these spatial sampling biases and how the distribution and sizes of biopsies in sampling protocols can be optimised to minimize such biases. RESULTS: We find that in the ideal case, less than a handful of samples can be enough to infer truly clonal mutations. The frequency of the largest sub-clone at diagnosis is the main factor determining the accuracy of truncal mutation estimation in structured tumours. If the first sub-clone is dominating the tumour, higher spatial dispersion of samples and larger sample size can increase the accuracy of the estimation. In such an improved sampling scheme, fewer samples will enable the detection of truly clonal alterations with the same probability. CONCLUSIONS: Taking spatial tumour structure into account will decrease the probability to misclassify a sub-clonal mutation as clonal and promises better informed treatment decisions.


Assuntos
Heterogeneidade Genética , Mutação , Neoplasias/genética , Algoritmos , Contagem de Células , Células Clonais/metabolismo , Humanos , Modelos Teóricos , Neoplasias/patologia
19.
BMC Med Genet ; 20(1): 80, 2019 05 14.
Artigo em Inglês | MEDLINE | ID: mdl-31088393

RESUMO

BACKGROUND: Intellectual disability/developmental delay is a complex condition with extraordinary heterogeneity. A large proportion of patients lacks a specific diagnosis. Next generation sequencing, enabling identification of genetic variations in multiple genes, has become an efficient strategy for genetic analysis in intellectual disability/developmental delay. METHODS: Clinical data of 112 Chinese families with unexplained intellectual disability/developmental delay was collected. Targeted next generation sequencing of 454 genes related to intellectual disability/developmental delay was performed for all 112 index patients. Patients with promising variants and their other family members underwent Sanger sequencing to validate the authenticity and segregation of the variants. RESULTS: Fourteen promising variants in genes EFNB1, MECP2, ATRX, NAA10, ANKRD11, DHCR7, LAMA1, NFIX, UBE3A, ARID1B and PTPRD were identified in 11 of 112 patients (11/112, 9.82%). Of 14 variants, eight arose de novo, and 13 are novel. Nine patients (9/112, 8.03%) got definite molecular diagnoses. It is the first time to report variants in EFNB1, NAA10, DHCR7, LAMA1 and NFIX in Chinese intellectual disability/developmental delay patients and first report about variants in NAA10 and LAMA1 in affected individuals of Asian ancestry. CONCLUSIONS: Targeted next generation sequencing of 454 genes is an effective test strategy for patients with unexplained intellectual disability/developmental delay. Genetic heterogenicity is significant in this Chinese cohort and de novo variants play an important role in the diagnosis. Findings of this study further delineate the corresponding phenotypes, expand the mutation spectrum and support the involvement of PTPRD in the disease.


Assuntos
Deficiências do Desenvolvimento/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Deficiência Intelectual/genética , Mutação , Adolescente , Criança , Pré-Escolar , China , Cromossomos Humanos X , Feminino , Genes Dominantes , Genes Recessivos , Heterogeneidade Genética , Humanos , Lactente , Masculino , Linhagem , Fenótipo
20.
BMC Med Genet ; 20(1): 90, 2019 05 24.
Artigo em Inglês | MEDLINE | ID: mdl-31126250

RESUMO

BACKGROUND: Hereditary spherocytosis (HS) is a common type of hereditary hemolytic anemia. According to the current diagnostic criteria of HS, patients with a family history of HS, typical clinical features and laboratory investigations could be diagnosed without the requirement of any additional tests, including genetic analysis. However, the clinical heterogeneities incur difficulties in HS diagnosis. We therefore aimed to investigate the application of genetic diagnosis in a family-based cohort. CASE PRESENTATION: In the present Chinese family, two probands sharing similar clinical manifestations, including jaundice, cholelithiasis, splenomegaly and spherocytes, while the clinical features of other family members were inconclusive. Whole-exome sequencing (WES) unexpectedly unveiled two separate disease-causing mutations in the two probands. SPTB R1625X mutation detected in proband D was a de novo mutation; while proband W inherited the SLC4A1 c.G1469A mutation from her mother, which was also inherited by her brother. However, the clinical features of proband W and her mother and brother were discrepant: proband W suffered from significant splenomegaly, jaundice and cholelithiasis, which resulted in cholecystectomy and splenectomy; while her mother and brother's HS were not complicated by cholelithiasis, and their splenomegaly and elevated serum bilirubin were moderate. In addition, additional genomic defects involved with HS-related symptoms have not been detected in this family. CONCLUSIONS: Both genotypes and phenotypes could be heterogeneous in the same HS family. The analysis of pathogenic gene mutations may endeavor to play an indispensable role in the accurate diagnosis and genetic consultation of HS individuals and their family members.


Assuntos
Saúde da Família , Heterogeneidade Genética , Mutação , Esferocitose Hereditária/genética , Adulto , Grupo com Ancestrais do Continente Asiático/genética , China , Feminino , Genótipo , Humanos , Masculino , Pessoa de Meia-Idade , Fenótipo , Esferocitose Hereditária/etnologia , Esferocitose Hereditária/patologia , Sequenciamento Completo do Exoma/métodos
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