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genomic in practice

M Ariel Geer Wallace, Tzipporah M Kormos, Joachim D Pleil
Environmental health science aims to link environmental pollution sources to adverse health outcomes to develop effective exposure intervention strategies that reduce long-term disease risks. Over the past few decades, the public health community recognized that health risk is driven by interaction between the human genome and external environment. Now that the human genetic code has been sequenced, establishing this "G × E" (gene-environment) interaction requires a similar effort to decode the human exposome, which is the accumulation of an individual's environmental exposures and metabolic responses throughout the person's lifetime...
October 19, 2016: Journal of Toxicology and Environmental Health. Part B, Critical Reviews
Daniel Nava Rodrigues, Gunther Boysen, Semini Sumanasuriya, George Seed, Angelo M De Marzo, Johann de Bono
Prostate cancer (PCa) is a clinically heterogeneous disease and current treatment strategies are based largely on anatomical and pathological parameters. In the recent past, several DNA sequencing studies of primary and advanced PCa have revealed recurrent patterns of genomic aberrations that expose mechanisms of resistance to available therapies and potential new drug targets. Suppression of androgen receptor (AR) signalling is the cornerstone of advanced prostate cancer treatment. Genomic aberrations of the androgen receptor or alternative splicing of its mRNA are increasingly recognized as biomarkers of resistance to AR-targeted therapy such as abiraterone or enzalutamide...
October 18, 2016: Journal of Pathology
Stephen Burgess, Jack Bowden, Tove Fall, Erik Ingelsson, Simon G Thompson
Mendelian randomization investigations are becoming more powerful and simpler to perform, due to the increasing size and coverage of genome-wide association studies and the increasing availability of summarized data on genetic associations with risk factors and disease outcomes. However, when using multiple genetic variants from different gene regions in a Mendelian randomization analysis, it is highly implausible that all the genetic variants satisfy the instrumental variable assumptions. This means that a simple instrumental variable analysis alone should not be relied on to give a causal conclusion...
September 26, 2016: Epidemiology
Zachery R Reichert, Maha Hussain
The development of metastatic castration-resistant prostate cancer (mCRPC) signals the terminal disease phase. The preceding hormone-dependent disease setting is effectively managed with androgen deprivation therapy. This foundation of treatment has a high rate of biochemical and clinical response and meaningful clinical benefit but is finite in duration as most cancers will progress to castration resistance. Historically, treatment for mCRPC entailed androgen receptor (AR) inhibitors (nilutamide, flutamide, bicalutamide), nonspecific steroidal biosynthesis inhibitors (ketoconazole, itraconazole), steroids (prednisone, diethylstilbesterol, dexamethasone), or palliative chemotherapy (mitoxantrone, estramustine), but none of these strategies impacted survival...
September 2016: Cancer Journal
Zhijiao Song, Miaomiao Zhang, Fagen Li, Qijie Weng, Chanpin Zhou, Mei Li, Jie Li, Huanhua Huang, Xiaoyong Mo, Siming Gan
Identification of loci or genes under natural selection is important for both understanding the genetic basis of local adaptation and practical applications, and genome scans provide a powerful means for such identification purposes. In this study, genome-wide simple sequence repeats markers (SSRs) were used to scan for molecular footprints of divergent selection in Eucalyptus grandis, a hardwood species occurring widely in costal areas from 32° S to 16° S in Australia. High population diversity levels and weak population structure were detected with putatively neutral genomic SSRs...
October 17, 2016: Scientific Reports
Michael P Heaton, Timothy P L Smith, Jacky K Carnahan, Veronica Basnayake, Jiansheng Qiu, Barry Simpson, Theodore S Kalbfleisch
The availability of whole genome sequence (WGS) data has made it possible to discover protein variants in silico. However, existing bovine WGS databases do not show data in a form conducive to protein variant analysis, and tend to under represent the breadth of genetic diversity in U.S. beef cattle. Thus, our first aim was to use 96 beef sires, sharing minimal pedigree relationships, to create a searchable and publicly viewable set of mapped genomes relevant for 19 popular breeds of U.S. cattle. Our second aim was to identify protein variants encoded by the bovine endothelial PAS domain-containing protein 1 gene ( EPAS1), a gene associated with high-altitude pulmonary hypertension in Angus cattle...
2016: F1000Research
Michael S Leapman, Peter R Carroll
INTRODUCTION: Selective treatment approaches for prostate cancer (PCa) are warranted given the highly varied nature of the disease and the consequences associated with definitive therapy. MATERIALS AND METHODS: We present a stepwise overview of strategies to not treat PCa, ranging from improved early detection practices that seek to improve the yield at initial diagnosis, as well as refinements to risk prediction and the performance of active surveillance. RESULTS: Adherence to screening guidelines is non-uniform...
October 13, 2016: Urologic Oncology
Julio Delgado, Neus Villamor, Armando López-Guillermo, Elías Campo
Next-generation sequencing provides a comprehensive understanding of the genomic, epigenomic and transcriptomic underpinnings of chronic lymphocytic leukaemia. Recent studies have uncovered new drivers, including mutations in non-coding regions, and signalling pathways whose role in cancer was previously unknown or poorly understood. Moreover, massive scale epigenomics and transcriptomics have supplied the foundations for the cellular origin of the disease. Some drivers could be targeted pharmacologically, and the ability to detect mutations present in minority subclones might even allow treatment before clonal selection occurs, thus preventing disease refractoriness...
March 2016: Best Practice & Research. Clinical Haematology
Priyakshi Kalita-de Croft, Fares Al-Ejeh, Amy E McCart Reed, Jodi M Saunus, Sunil R Lakhani
Our understanding of the natural history of breast cancer has evolved alongside technologies to study its genomic, transcriptomic, proteomic, and metabolomics landscapes. These technologies have helped decipher multiple molecular pathways dysregulated in breast cancer. First-generation 'omics analyses considered each of these dimensions individually, but it is becoming increasingly clear that more holistic, integrative approaches are required to fully understand complex biological systems. The 'omics represent an exciting era of discovery in breast cancer research, although important issues need to be addressed to realize the clinical utility of these data through precision cancer care...
November 2016: Advances in Anatomic Pathology
Tom Hartmann, An-Chiang Chu, Martin Middendorf, Matthias Bernt
The tandem duplication random loss operation (TDRL) is an important genome rearrangement operation in metazoan mitochondrial genomes. A TDRL consists of a duplication of a contiguous set of genes in tandem followed by a random loss of one copy of each duplicated gene. This paper presents an analysis of the combinatorics of TDRLs on circular genomes, e.g., the mitochondrial genome. In particular, results on TDRLs for circular genomes and their linear representatives are established. Moreover, the distance between gene orders with respect to linear TDRLs and circular TDRLs is studied...
September 26, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
June C Carroll, Tutsirai Makuwaza, Donna P Manca, Nicolette Sopcak, Joanne A Permaul, Mary Ann O'Brien, Ruth Heisey, Elizabeth A Eisenhauer, Julie Easley, Monika K Krzyzanowska, Baukje Miedema, Sandhya Pruthi, Carol Sawka, Nancy Schneider, Jonathan Sussman, Robin Urquhart, Catarina Versaevel, Eva Grunfeld
OBJECTIVE: To assess primary care providers' (PCPs') experiences with, perceptions of, and desired role in personalized medicine, with a focus on cancer. DESIGN: Qualitative study involving focus groups. SETTING: Urban and rural interprofessional primary care team practices in Alberta and Ontario. PARTICIPANTS: Fifty-one PCPs. METHODS: Semistructured focus groups were conducted and audiorecorded...
October 2016: Canadian Family Physician Médecin de Famille Canadien
Xingyun Su, Weibin Wang, Guodong Ruan, Min Liang, Jing Zheng, Ye Chen, Huiling Wu, Thomas J Fahey, Minxin Guan, Lisong Teng
Nuclear genetic alterations have been widely investigated in papillary thyroid cancer (PTC), however, the characteristics of the mitochondrial genome remain uncertain. We sequenced the entire mitochondrial genome of 66 PTCs, 16 normal thyroid tissues and 376 blood samples of healthy individuals. There were 2508 variations (543 sites) detected in PTCs, among which 33 variations were novel. Nearly half of the PTCs (31/66) had heteroplasmic variations. Among the 31 PTCs, 28 specimens harbored a total of 52 somatic mutations distributed in 44 sites...
October 10, 2016: International Journal of Molecular Sciences
Zhang Ke, Feng Guangde, Zhang Baoyun, Xiang Wei, Chen Long, Yang Fang, Chu Mingxing, Wang Pingqing
Livestock phenotypes are determined by the interaction of a variety of factors, including the genome, the epigenome and the environment. Epigenetics refers to gene expression changes without DNA sequence alterations. Epigenetic markers mainly include DNA methylation, histone modifications, non-coding RNAs, and imprinting genes. More and more researches show that epigenetic markers play an important role in the traits of pigs by modulating phenotype changes via gene expression. However, the role of epigenetic markers has caught little attention in swine breeding...
July 20, 2016: Yi Chuan, Hereditas
Haixu Tang, Xiaoqian Jiang, Xiaofeng Wang, Shuang Wang, Heidi Sofia, Dov Fox, Kristin Lauter, Bradley Malin, Amalio Telenti, Li Xiong, Lucila Ohno-Machado
The outsourcing of genomic data into public cloud computing settings raises concerns over privacy and security. Significant advancements in secure computation methods have emerged over the past several years, but such techniques need to be rigorously evaluated for their ability to support the analysis of human genomic data in an efficient and cost-effective manner. With respect to public cloud environments, there are concerns about the inadvertent exposure of human genomic data to unauthorized users. In analyses involving multiple institutions, there is additional concern about data being used beyond agreed research scope and being prcoessed in untrused computational environments, which may not satisfy institutional policies...
October 13, 2016: BMC Medical Genomics
Thabiso E Motaung, Toi J Tsilo, Hiromasa Saitoh
Plant pathogenic fungi cause diseases to all major crop plants world-wide and threaten global food security. Underpinning fungal diseases are virulence genes facilitating plant host colonization that often marks pathogenesis and crop failures, as well a rise in staple food prices. Fungal molecular genetics is therefore the cornerstone to sustainable prevention of disease outbreaks. Pathogenicity studies using mutant collections provide immense function-based information regarding virulence genes of economically relevant fungi...
October 12, 2016: Molecular Plant Pathology
Hongliang Chu, Chunxiao Li, Xiaoxia Guo, Hengduan Zhang, Peng Luo, Zhonghua Wu, Gang Wang, Tongyan Zhao
The known mosquito mitogenomes, containing a total of 34 species, which belong to five genera, were collected from GenBank, and the practicality and effectiveness of the variation in the complete mitochondrial DNA genome and portions of mitochondrial COI gene were assessed to reconstruct the phylogeny of mosquitoes. Phylogenetic trees were reconstructed on the basis of parsimony, maximum likelihood, and Bayesian (BI) methods. It is concluded that: (1) Both mitogenomes and COI gene support the monophly of following taxa: Subgenus Nyssorhynchus, Subgenus Cellia, Anopheles albitarsis complex, Anopheles gambiae complex, and Anopheles punctulatus group; (2) Genus Aedes is not monophyletic relative to Ochlerotatus vigilax; (3) The mitogenome results indicate a close relationship between Anopheles epiroticus and Anopheles gambiae complex, Anopheles dirus complex and Anopheles punctulatus group, respectively; (4) The Bayesian posterior probability (BPP) within phylogenetic tree reconstructed by mitogenomes is higher than COI tree...
October 12, 2016: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
W P Martins, C O Nastri, L Rienzi, S Z van der Poel, C Gracia, C Racowsky
OBJECTIVES: Blastocyst transfer could be advantageous because it allows a more physiologic timing of exposure of the embryo to the uterine environment and permit embryo self-selection after activation of the embryonic genome on day 3. Conversely, the in vitro environment is probably inferior to that provided in vivo and in vitro culture beyond embryonic genomic activation could potentially harm embryos. Our objective was to identify, appraise and summarize the available evidence comparing the effectiveness of blastocyst and cleavage stage embryo transfer...
October 12, 2016: Ultrasound in Obstetrics & Gynecology
R Liang, B Meiser, S Smith, N A Kasparian, C R Lewis, M Chin, G V Long, R Ward, A M Menzies, J N Harris-Wai, R Kaur
Somatic mutations in key oncogenes in non-small cell lung cancer (NSCLC) and melanoma are important determinants of tumour sensitivity to targeted therapies. Molecular screening for these predictive biomarkers is routinely used to inform treatment decisions; however, little is known about how best to communicate testing and results to patients. This qualitative study aimed to explore advanced cancer patients' attitudes and experiences regarding somatic tumour screening to identify their information and support needs...
October 11, 2016: European Journal of Cancer Care
Frederick L Baehner
In vitro diagnostic multivariate index assays are highly complex molecular assays that can provide clinically actionable information regarding the underlying tumour biology and facilitate personalised treatment. These assays are only useful in clinical practice if all of the following are established: analytical validation (i.e., how accurately/reliably the assay measures the molecular characteristics), clinical validation (i.e., how consistently/accurately the test detects/predicts the outcomes of interest), and clinical utility (i...
2016: Ecancermedicalscience
Jacob B Hall, William S Bush
Most analyses of genome-wide association data consider each variant independently without considering or adjusting for the genetic background present in the rest of the genome. New approaches to genome analysis use representations of genomic sharing to better account for confounding factors like population stratification or to directly approximate heritability through the estimated sharing of individuals in a dataset. These approaches use mixed linear models, which relate genotypic sharing to phenotypic sharing, and rely on the efficient computation of genetic sharing among individuals in a dataset...
October 11, 2016: Current Protocols in Human Genetics
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