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BMC Medical Genomics

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https://www.readbyqxmd.com/read/28427387/serum-microrna-profile-in-patients-with-colon-adenomas-or-cancer
#1
Yajie Zhang, Min Li, Yijiang Ding, Zhimin Fan, Jinchun Zhang, Hongying Zhang, Bin Jiang, Yong Zhu
BACKGROUND: Colon cancer, one of the most common causes of cancer-related deaths, arises from adenomatous polyps. In these years, circulating microRNAs (miRNAs) have attracted increasing attention as novel biomarkers for colon cancers. The dysregulated circulating miRNAs in patients with colon adenomas has not been well-understood. METHODS: Here, we aimed to identify miRNA profile in the serum of patients with colon adenomas or colon cancer by using microarray. Then we validated eight differentially expressed miRNAs (DEMs) by qRT-PCR and predicted their targets...
April 20, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28416017/patient-complexity-and-genotype-phenotype-correlations-in-biliary-atresia-a-cross-sectional-analysis
#2
Guo Cheng, Patrick Ho-Yu Chung, Edwin Kin-Wai Chan, Man-Ting So, Pak-Chung Sham, Stacey S Cherny, Paul Kwong-Hang Tam, Maria-Mercè Garcia-Barceló
BACKGROUND: Biliary Atresia (BA) is rare and genetically complex, and the pathogenesis is elusive. The disease course is variable and can represent heterogeneity, which hinders effective disease management. Deciphering the BA phenotypic variance is a priority in clinics and can be achieved by the integrative analysis of genotype and phenotype. We aim to explore the BA phenotypic features and to delineate the source of its variance. METHODS: The study is a cross-sectional observational study collating with case/control association analysis...
April 17, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28390424/grmd-cardiac-and-skeletal-muscle-metabolism-gene-profiles-are-distinct
#3
Larry W Markham, Candice L Brinkmeyer-Langford, Jonathan H Soslow, Manisha Gupte, Douglas B Sawyer, Joe N Kornegay, Cristi L Galindo
BACKGROUND: Duchenne muscular dystrophy (DMD) is caused by mutations in the DMD gene, which codes for the dystrophin protein. While progress has been made in defining the molecular basis and pathogenesis of DMD, major gaps remain in understanding mechanisms that contribute to the marked delay in cardiac compared to skeletal muscle dysfunction. METHODS: To address this question, we analyzed cardiac and skeletal muscle tissue microarrays from golden retriever muscular dystrophy (GRMD) dogs, a genetically and clinically homologous model for DMD...
April 8, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28359308/revealing-cancer-subtypes-with-higher-order-correlations-applied-to-imaging-and-omics-data
#4
Kiley Graim, Tiffany Ting Liu, Achal S Achrol, Evan O Paull, Yulia Newton, Steven D Chang, Griffith R Harsh, Sergio P Cordero, Daniel L Rubin, Joshua M Stuart
BACKGROUND: Patient stratification to identify subtypes with different disease manifestations, severity, and expected survival time is a critical task in cancer diagnosis and treatment. While stratification approaches using various biomarkers (including high-throughput gene expression measurements) for patient-to-patient comparisons have been successful in elucidating previously unseen subtypes, there remains an untapped potential of incorporating various genotypic and phenotypic data to discover novel or improved groupings...
March 31, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28351365/basal-like-breast-cancer-molecular-profiles-clinical-features-and-survival-outcomes
#5
Heloisa H Milioli, Inna Tishchenko, Carlos Riveros, Regina Berretta, Pablo Moscato
BACKGROUND: Basal-like constitutes an important molecular subtype of breast cancer characterised by an aggressive behaviour and a limited therapy response. The outcome of patients within this subtype is, however, divergent. Some individuals show an increased risk of dying in the first five years, and others a long-term survival of over ten years after the diagnosis. In this study, we aim at identifying markers associated with basal-like patients' survival and characterising subgroups with distinct disease outcome...
March 28, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28340577/gene-and-protein-analysis-reveals-that-p53-pathway-is-functionally-inactivated-in-cytogenetically-normal-acute-myeloid-leukemia-and-acute-promyelocytic-leukemia
#6
Julia Abramowitz, Tzahi Neuman, Riki Perlman, Dina Ben-Yehuda
BACKGROUND: Mechanisms that inactivate the p53 pathway in Acute Myeloid Leukemia (AML), other than rare mutations, are still not well understood. METHODS: We performed a bioinformatics study of the p53 pathway function at the gene expression level on our collection of 1153 p53-pathway related genes. Publically available Affymetrix data of 607 de-novo AML patients at diagnosis were analyzed according to the patients cytogenetic, FAB and molecular mutations subtypes...
March 24, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28315634/comparing-mutation-calls-in-fixed-tumour-samples-between-the-affymetrix-oncoscan%C3%A2-array-and-pcr-based-next-generation-sequencing
#7
Henry M Wood, Joseph M Foster, Morag Taylor, Emma Tinkler-Hundal, Fiona S Togneri, Paula Wojtowicz, Assa Oumie, Karen G Spink, Fiona Brew, Philip Quirke
BACKGROUND: The importance of accurate and affordable mutation calling in fixed pathology samples is becoming increasingly important as we move into the era of personalised medicine. The Affymetrix OncoScan® Array platform is designed to produce actionable mutation calls in archival material. METHODS: We compared calls made using the OncoScan platform with calls made using a custom designed PCR panel followed by next-generation sequencing (NGS), in order to benchmark the sensitivity and specificity of the OncoScan calls in a large cohort of fixed tumour samples...
March 18, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28298217/large-scale-gene-network-analysis-reveals-the-significance-of-extracellular-matrix-pathway-and-homeobox-genes-in-acute-myeloid-leukemia-an-introduction-to-the-pigengene-package-and-its-applications
#8
Amir Foroushani, Rupesh Agrahari, Roderick Docking, Linda Chang, Gerben Duns, Monika Hudoba, Aly Karsan, Habil Zare
BACKGROUND: The distinct types of hematological malignancies have different biological mechanisms and prognoses. For instance, myelodysplastic syndrome (MDS) is generally indolent and low risk; however, it may transform into acute myeloid leukemia (AML), which is much more aggressive. METHODS: We develop a novel network analysis approach that uses expression of eigengenes to delineate the biological differences between these two diseases. RESULTS: We find that specific genes in the extracellular matrix pathway are underexpressed in AML...
March 16, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28298214/climat-het-detecting-subclonal-copy-number-alterations-and-loss-of-heterozygosity-in-heterogeneous-tumor-samples-from-whole-genome-sequencing-data
#9
Zhenhua Yu, Ao Li, Minghui Wang
BACKGROUND: Copy number alterations (CNA) and loss of heterozygosity (LOH) represent a large proportion of genetic structural variations of cancer genomes. These aberrations are continuously accumulated during the procedure of clonal evolution and patterned by phylogenetic branching. This invariably results in the emergence of multiple cell populations with distinct complement of mutational landscapes in tumor sample. With the advent of next-generation sequencing technology, inference of subclonal populations has become one of the focused interests in cancer-associated studies, and is usually based on the assessment of combinations of somatic single-nucleotide variations (SNV), CNA and LOH...
March 15, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28292312/comprehensive-discovery-of-subsample-gene-expression-components-by-information-explanation-therapeutic-implications-in-cancer
#10
Shirley Pepke, Greg Ver Steeg
BACKGROUND: De novo inference of clinically relevant gene function relationships from tumor RNA-seq remains a challenging task. Current methods typically either partition patient samples into a few subtypes or rely upon analysis of pairwise gene correlations that will miss some groups in noisy data. Leveraging higher dimensional information can be expected to increase the power to discern targetable pathways, but this is commonly thought to be an intractable computational problem. METHODS: In this work we adapt a recently developed machine learning algorithm for sensitive detection of complex gene relationships...
March 15, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28279210/computational-analysis-of-the-mesenchymal-signature-landscape-in-gliomas
#11
Orieta Celiku, Anita Tandle, Joon-Yong Chung, Stephen M Hewitt, Kevin Camphausen, Uma Shankavaram
BACKGROUND: Epithelial to mesenchymal transition, and mimicking processes, contribute to cancer invasion and metastasis, and are known to be responsible for resistance to various therapeutic agents in many cancers. While a number of studies have proposed molecular signatures that characterize the spectrum of such transition, more work is needed to understand how the mesenchymal signature (MS) is regulated in non-epithelial cancers like gliomas, to identify markers with the most prognostic significance, and potential for therapeutic targeting...
March 9, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28279176/palb2-mutations-in-brca1-2-mutation-negative-breast-and-ovarian-cancer-patients-from-poland
#12
Anna Kluska, Aneta Balabas, Magdalena Piatkowska, Katarzyna Czarny, Katarzyna Paczkowska, Dorota Nowakowska, Michal Mikula, Jerzy Ostrowski
BACKGROUND: The PALB2 gene encodes a protein that plays a crucial role in maintaining genomic integrity. Germline inactivating mutations in PALB2 are associated with an increased risk of breast and ovarian cancer. The prevalence and spectrum of recurrent PALB2 germline mutations in breast and ovarian cancer patients from Poland is not clearly defined. METHODS: PALB2 exons were amplified from 460 BRCA1/2-mutation negative women with familial breast and/or ovarian cancer and early-onset breast cancer using AmpliSeq technology and sequenced on an Ion Torrent PGM sequencer...
March 9, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28231836/epigenetic-modifications-and-glucocorticoid-sensitivity-in-myalgic-encephalomyelitis-chronic-fatigue-syndrome-me-cfs
#13
Wilfred C de Vega, Santiago Herrera, Suzanne D Vernon, Patrick O McGowan
BACKGROUND: Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a debilitating idiopathic disease characterized by unexplained fatigue that fails to resolve with sufficient rest. Diagnosis is based on a list of symptoms and exclusion of other fatigue-related health conditions. Despite a heterogeneous patient population, immune and hypothalamic-pituitary-adrenal (HPA) axis function differences, such as enhanced negative feedback to glucocorticoids, are recurring findings in ME/CFS studies...
February 23, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28228131/whole-genome-sequencing-of-one-complex-pedigree-illustrates-challenges-with-genomic-medicine
#14
Han Fang, Yiyang Wu, Hui Yang, Margaret Yoon, Laura T Jiménez-Barrón, David Mittelman, Reid Robison, Kai Wang, Gholson J Lyon
BACKGROUND: Human Phenotype Ontology (HPO) has risen as a useful tool for precision medicine by providing a standardized vocabulary of phenotypic abnormalities to describe presentations of human pathologies; however, there have been relatively few reports combining whole genome sequencing (WGS) and HPO, especially in the context of structural variants. METHODS: We illustrate an integrative analysis of WGS and HPO using an extended pedigree, which involves Prader-Willi Syndrome (PWS), hereditary hemochromatosis (HH), and dysautonomia-like symptoms...
February 23, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28222731/genomic-newborn-screening-public-health-policy-considerations-and-recommendations
#15
Jan M Friedman, Martina C Cornel, Aaron J Goldenberg, Karla J Lister, Karine Sénécal, Danya F Vears
BACKGROUND: The use of genome-wide (whole genome or exome) sequencing for population-based newborn screening presents an opportunity to detect and treat or prevent many more serious early-onset health conditions than is possible today. METHODS: The Paediatric Task Team of the Global Alliance for Genomics and Health's Regulatory and Ethics Working Group reviewed current understanding and concerns regarding the use of genomic technologies for population-based newborn screening and developed, by consensus, eight recommendations for clinicians, clinical laboratory scientists, and policy makers...
February 21, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28202063/next-generation-sequencing-in-familial-breast-cancer-patients-from-lebanon
#16
Nadine Jalkh, Eliane Chouery, Zahraa Haidar, Christina Khater, David Atallah, Hamad Ali, Makia J Marafie, Mohamed R Al-Mulla, Fahd Al-Mulla, Andre Megarbane
BACKGROUND: Familial breast cancer (BC) represents 5 to 10% of all BC cases. Mutations in two high susceptibility BRCA1 and BRCA2 genes explain 16-40% of familial BC, while other high, moderate and low susceptibility genes explain up to 20% more of BC families. The Lebanese reported prevalence of BRCA1 and BRCA2 deleterious mutations (5.6% and 12.5%) were lower than those reported in the literature. METHODS: In the presented study, 45 Lebanese patients with a reported family history of BC were tested using Whole Exome Sequencing (WES) technique followed by Sanger sequencing validation...
February 15, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28143555/investigation-of-coordination-and-order-in-transcription-regulation-of-innate-and-adaptive-immunity-genes-in-type-1-diabetes
#17
Shouguo Gao, Nathaniel Wolanyk, Ye Chen, Shuang Jia, Martin J Hessner, Xujing Wang
BACKGROUND: Type 1 diabetes (T1D) is an autoimmune disease and extensive evidence has indicated a critical role of both the innate and the adaptive arms of immune system in disease development. To date most clinical trials of immunomodulation therapies failed to show efficacy. A number of gene expression studies of T1D have been carried out. However, a systems analysis of the expression variations of the innate and adaptive immunity gene sets, or their co-expression network structures in cohorts at different disease states or of different disease risks, is not available till now...
January 31, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28137248/multidisciplinary-insight-into-clonal-expansion-of-htlv-1-infected-cells-in-adult-t-cell-leukemia-via-modeling-by-deterministic-finite-automata-coupled-with-high-throughput-sequencing
#18
Amir Farmanbar, Sanaz Firouzi, Sung-Joon Park, Kenta Nakai, Kaoru Uchimaru, Toshiki Watanabe
BACKGROUND: Clonal expansion of leukemic cells leads to onset of adult T-cell leukemia (ATL), an aggressive lymphoid malignancy with a very poor prognosis. Infection with human T-cell leukemia virus type-1 (HTLV-1) is the direct cause of ATL onset, and integration of HTLV-1 into the human genome is essential for clonal expansion of leukemic cells. Therefore, monitoring clonal expansion of HTLV-1-infected cells via isolation of integration sites assists in analyzing infected individuals from early infection to the final stage of ATL development...
January 31, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28081699/erratum-to-experiences-and-attitudes-of-residents-regarding-a-community-based-genome-cohort-study-in-japan-a-population-based-cross-sectional-study
#19
Keiko Miyamoto, Miho Iwakuma, Takeo Nakayama
No abstract text is available yet for this article.
January 12, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28077143/pregnant-women-carrying-microcephaly-foetuses-and-zika-virus-contain-potentially-pathogenic-microbes-and-parasites-in-their-amniotic-fluid
#20
Diogo Antonio Tschoeke, Louisi Souza de Oliveira, Luciana Leomil, Amilcar Tanuri, Fabiano Lopes Thompson
BACKGROUND: Microcephaly has become a major public health problem in Brazil. The total number of newborns with microcephaly was reported to be >4000 in June 2016. Studies suggest that Zika Virus is a major cause of new microcephaly cases in Brazil. Inside the uterus, the foetus is surrounded by the Amniotic Fluid, a proximal fluid that contains foetal and maternal cells as well as microorganisms and where Zika Virus was already found. CASE PRESENTATION: A previous study reported the presence of the Zika Virus in the amniotic fluid (collected in the 28th gestational week) of two pregnant women carrying microcephaly foetuses in Brazil...
January 11, 2017: BMC Medical Genomics
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