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https://www.readbyqxmd.com/read/27910721/care-delivery-considerations-for-widespread-and-equitable-implementation-of-inherited-cancer-predisposition-testing
#1
Deborah Cragun, Anita Y Kinney, Tuya Pal
DNA sequencing advances through next-generation sequencing (NGS) and several practice changing events, have led to shifting paradigms for inherited cancer predisposition testing. These changes necessitated a means by which to maximize health benefits without unnecessarily inflating healthcare costs and exacerbating health disparities. Areas covered: NGS-based tests encompass multi-gene panel tests, whole exome sequencing, and whole genome sequencing, all of which test for multiple genes simultaneously, compared to prior sequencing practices through which testing was performed sequentially for one or two genes...
December 2, 2016: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/27910110/runs-of-homozygosity-current-knowledge-and-applications-in-livestock
#2
REVIEW
E Peripolli, D P Munari, M V G B Silva, A L F Lima, R Irgang, F Baldi
This review presents a broader approach to the implementation and study of runs of homozygosity (ROH) in animal populations, focusing on identifying and characterizing ROH and their practical implications. ROH are continuous homozygous segments that are common in individuals and populations. The ability of these homozygous segments to give insight into a population's genetic events makes them a useful tool that can provide information about the demographic evolution of a population over time. Furthermore, ROH provide useful information about the genetic relatedness among individuals, helping to minimize the inbreeding rate and also helping to expose deleterious variants in the genome...
December 1, 2016: Animal Genetics
https://www.readbyqxmd.com/read/27908280/development-of-a-fast-and-easy-method-for-escherichia-coli-genome-editing-with-crispr-cas9
#3
Dongdong Zhao, Shenli Yuan, Bin Xiong, Hongnian Sun, Lijun Ye, Jing Li, Xueli Zhang, Changhao Bi
BACKGROUND: Microbial genome editing is a powerful tool to modify chromosome in way of deletion, insertion or replacement, which is one of the most important techniques in metabolic engineering research. The emergence of CRISPR/Cas9 technique inspires various genomic editing methods. RESULTS: In this research, the goal of development of a fast and easy method for Escherichia coli genome editing with high efficiency is pursued. For this purpose, we designed modular plasmid assembly strategy, compared effects of different length of homologous arms for recombination, and tested different sets of recombinases...
December 1, 2016: Microbial Cell Factories
https://www.readbyqxmd.com/read/27908228/detection-of-mutations-in-mitochondrial-dna-by-droplet-digital-pcr
#4
J K Sofronova, Y Y Ilinsky, K E Orishchenko, E G Chupakhin, E A Lunev, I O Mazunin
Mutations in mitochondrial DNA (mtDNA) may result in various pathological processes. Detection of mutant mtDNAs is a problem for diagnostic practice that is complicated by heteroplasmy - a phenomenon of the inferring presence of at least two allelic variants of the mitochondrial genome. Also, the level of heteroplasmy largely determines the profile and severity of clinical manifestations. Here we discuss detection of mutations in heteroplasmic mtDNA using up-to-date methods that have not yet been introduced as routine clinical assays...
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27906971/nullomers-and-high-order-nullomers-in-genomic-sequences
#5
Davide Vergni, Daniele Santoni
A nullomer is an oligomer that does not occur as a subsequence in a given DNA sequence, i.e. it is an absent word of that sequence. The importance of nullomers in several applications, from drug discovery to forensic practice, is now debated in the literature. Here, we investigated the nature of nullomers, whether their absence in genomes has just a statistical explanation or it is a peculiar feature of genomic sequences. We introduced an extension of the notion of nullomer, namely high order nullomers, which are nullomers whose mutated sequences are still nullomers...
2016: PloS One
https://www.readbyqxmd.com/read/27906881/stem-cells-and-clinical-practice-new-advances-and-challenges-at-the-time-of-emerging-problems-with-induced-pluripotent-stem-cell-therapies
#6
Mariusz Z Ratajczak, Kamila Bujko, Wojciech Wojakowski
Humans, like other species that reproduce sexually, originate from a fertilized oocyte (zygote), which is a totipotent stem cell giving rise to an adult organism. During the process of embryogenesis, stem cells at different levels of the developmental hierarchy establish all 3 germ layers and give rise to tissue‑committed stem cells, which are responsible for rejuvenation of a given tissue or organ. The robustness of the stem cell compartment is one of the major factors that directly impact life quality as well as lifespan...
November 10, 2016: Polskie Archiwum Medycyny Wewnętrznej
https://www.readbyqxmd.com/read/27904954/the-mathematics-of-xenology-di-cographs-symbolic-ultrametrics-2-structures-and-tree-representable-systems-of-binary-relations
#7
Marc Hellmuth, Peter F Stadler, Nicolas Wieseke
The concepts of orthology, paralogy, and xenology play a key role in molecular evolution. Orthology and paralogy distinguish whether a pair of genes originated by speciation or duplication. The corresponding binary relations on a set of genes form complementary cographs. Allowing more than two types of ancestral event types leads to symmetric symbolic ultrametrics. Horizontal gene transfer, which leads to xenologous gene pairs, however, is inherent asymmetric since one offspring copy "jumps" into another genome, while the other continues to be inherited vertically...
November 30, 2016: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/27904775/disease-evolution-and-heterogeneity-in-bilateral-breast-cancer
#8
Elena Fountzilas, Vassiliki Kotoula, Flora Zagouri, Eleni Giannoulatou, George Kouvatseas, George Pentheroudakis, Triantafyllia Koletsa, Mattheos Bobos, Kyriaki Papadopoulou, Epaminontas Samantas, Efterpi Demiri, Spyros Miliaras, Christos Christodoulou, Sofia Chrisafi, Evangelia Razis, Florentia Fostira, Dimitrios Pectasides, George Zografos, George Fountzilas
Bilateral breast cancers (BBC) are currently treated as independent tumors arising in the same patient. Herein, we investigated whether BBC indeed evolve independently at the genomic level. We examined paired targeted next generation sequencing genotypes from 155 paraffin tumors corresponding to 76 BBC patients (75 women and one man; 52 concurrent and 24 metachronous), for coding mutations (amino acid changing, minor allele frequency <0.1%) and single nucleotide polymorphism (SNP) zygosity. Germline genotypes were available for 29 patients...
2016: American Journal of Cancer Research
https://www.readbyqxmd.com/read/27903821/construction-of-a-minimal-genome-as-a-chassis-for-synthetic-biology
#9
REVIEW
Bong Hyun Sung, Donghui Choe, Sun Chang Kim, Byung-Kwan Cho
Microbial diversity and complexity pose challenges in understanding the voluminous genetic information produced from whole-genome sequences, bioinformatics and high-throughput '-omics' research. These challenges can be overcome by a core blueprint of a genome drawn with a minimal gene set, which is essential for life. Systems biology and large-scale gene inactivation studies have estimated the number of essential genes to be ∼300-500 in many microbial genomes. On the basis of the essential gene set information, minimal-genome strains have been generated using sophisticated genome engineering techniques, such as genome reduction and chemical genome synthesis...
November 30, 2016: Essays in Biochemistry
https://www.readbyqxmd.com/read/27903611/the-genomic-architecture-of-interactions-between-natural-genetic-polymorphisms-and-environments-in-yeast-growth
#10
Xinzhu Wei, Jianzhi Zhang
Gene-environment interaction (G×E) refers to the phenomenon that the same mutation has different phenotypic effects in different environments. Although quantitative trait loci (QTLs) exhibiting G×E have been reported, little is known about the general properties of G×E and those of its underlying QTLs. Here we use the genotypes of 1005 segregants from a cross between two Saccharomyces cerevisiae strains and the growth rates of these segregants in 47 environments to identify growth rate QTLs (gQTLs) in each environment and QTLs that have different growth effects in each pair of environments (g×eQTLs)...
November 30, 2016: Genetics
https://www.readbyqxmd.com/read/27902792/rascaf-improving-genome-assembly-with-rna-sequencing-data
#11
Li Song, Dhruv S Shankar, Liliana Florea
Abundant but short second-generation sequencing reads make assembly difficult, leading to fragmented genomes and gene annotations. Gene structure information from RNA sequences can be used to improve the completeness and contiguity of an assembly, but bioinformatics methods have been lacking. Rascaf is a highly efficient tool leveraging long-range continuity information from intron spanning RNA sequencing (RNA-seq) read pairs to detect new contig connections. It determines a heaviest path in an exon block graph that simultaneously represents a gene and the underlying contig relationships...
November 2016: Plant Genome
https://www.readbyqxmd.com/read/27902790/accuracy-of-genomic-prediction-in-a-commercial-perennial-ryegrass-breeding-program
#12
Dario Fè, Bilal H Ashraf, Morten G Pedersen, Luc Janss, Stephen Byrne, Niels Roulund, Ingo Lenk, Thomas Didion, Torben Asp, Christian S Jensen, Just Jensen
The implementation of genomic selection (GS) in plant breeding, so far, has been mainly evaluated in crops farmed as homogeneous varieties, and the results have been generally positive. Fewer results are available for species, such as forage grasses, that are grown as heterogenous families (developed from multiparent crosses) in which the control of the genetic variation is far more complex. Here we test the potential for implementing GS in the breeding of perennial ryegrass ( L.) using empirical data from a commercial forage breeding program...
November 2016: Plant Genome
https://www.readbyqxmd.com/read/27902417/lantibiotics-produced-by-actinobacteria-and-their-potential-applications-a-review
#13
Karen Gomes, Rafael Silva Duarte, Maria do Carmo de Freire Bastos
The phylum Actinobacteria, which comprises a great variety of Gram-positive bacteria with a high G+C content in their genomes, is known for its large production of bioactive compounds, including those with antimicrobial activity. Among the antimicrobials, bacteriocins, ribosomally-synthesized peptides, represent an important arsenal of potential new drugs to face the increasing prevalence of resistance to antibiotics among microbial pathogens. The actinobacterial bacteriocins form a heterogeneous group of substances that is difficult to adapt to most proposed classification schemes...
November 22, 2016: Microbiology
https://www.readbyqxmd.com/read/27900742/-precision-nursing-individual-based-knowledge-translation
#14
Li-Chi Chiang, Mei-Ling Yeh, Sui-Lung Su
U.S. President Obama announced a new era of precision medicine in the Precision Medicine Initiative (PMI). This initiative aims to accelerate the progress of personalized medicine in light of individual requirements for prevention and treatment in order to improve the state of individual and public health. The recent and dramatic development of large-scale biologic databases (such as the human genome sequence), powerful methods for characterizing patients (such as genomics, microbiome, diverse biomarkers, and even pharmacogenomics), and computational tools for analyzing big data are maximizing the potential benefits of precision medicine...
December 2016: Hu Li za Zhi the Journal of Nursing
https://www.readbyqxmd.com/read/27900684/dna-rna-and-protein-based-stable-isotope-probing-for-high-throughput-biomarker-analysis-of-active-microorganisms
#15
Eleanor Jameson, Martin Taubert, Sara Coyotzi, Yin Chen, Özge Eyice, Hendrik Schäfer, J Colin Murrell, Josh D Neufeld, Marc G Dumont
Stable-isotope probing (SIP) enables researchers to target active populations within complex microbial communities, which is achieved by providing growth substrates enriched in heavy isotopes, usually in the form of (13)C, (18)O, or (15)N. After growth on the substrate and subsequent extraction of microbial biomarkers, typically nucleic acids or proteins, the SIP technique is used for the recovery and analysis of isotope-labeled biomarkers from active microbial populations. In the years following the initial development of DNA- and RNA-based SIP, it was common practice to characterize labeled populations by targeted gene analysis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27900359/homozygous-inactivation-of-chek2-is-linked-to-a-familial-case-of-multiple-primary-lung-cancer-with-accompanying-cancers-in-other-organs
#16
Yoji Kukita, Jiro Okami, Noriko Yoneda-Kato, Ikuko Nakamae, Takeshi Kawabata, Masahiko Higashiyama, Junya Kato, Ken Kodama, Kikuya Kato
In clinical practice, there are a number of cancer patients with clear family histories, but the patients lack mutations in known familial cancer syndrome genes. Recent advances in genomic technologies have enhanced the possibility of identifying causative genes in such cases. Two siblings, an elder sister and a younger brother, were found to have multiple primary lung cancers at the age of 60. The former subsequently developed breast cancer and had a history of uterine myoma. The latter had initially developed prostate cancer at the age of 59 and had a history of colon cancer...
November 2016: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/27899774/-a-review-multigene-assays-for-clinical-utility-in-breast-cancer
#17
Kazuhiro Araki, Yoshinori Ito
Multigene assays that simultaneously measure the expression of various breast cancer genes have been developed to guide the use of adjuvant chemotherapy in early breast cancer. The efficacy of adjuvant therapies depends on the recurrence risk for an individual patient. As a result, accurate prediction of the recurrence risk is vital for precise adjuvant chemotherapy in individual breast cancer patients. The recurrence risk as typically assessed by conventional examination of histological data of immuno-histological biomarkers(ER, PR, HER2, and Ki-67)is not sufficient to select subsets of patients...
November 2016: Gan to Kagaku Ryoho. Cancer & Chemotherapy
https://www.readbyqxmd.com/read/27899662/kegg-new-perspectives-on-genomes-pathways-diseases-and-drugs
#18
Minoru Kanehisa, Miho Furumichi, Mao Tanabe, Yoko Sato, Kanae Morishima
KEGG (http://www.kegg.jp/ or http://www.genome.jp/kegg/) is an encyclopedia of genes and genomes. Assigning functional meanings to genes and genomes both at the molecular and higher levels is the primary objective of the KEGG database project. Molecular-level functions are stored in the KO (KEGG Orthology) database, where each KO is defined as a functional ortholog of genes and proteins. Higher-level functions are represented by networks of molecular interactions, reactions and relations in the forms of KEGG pathway maps, BRITE hierarchies and KEGG modules...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899345/ethics-of-genetic-testing-and-research-in-sport-a-position-statement-from-the-australian-institute-of-sport
#19
Nicole Vlahovich, Peter A Fricker, Matthew A Brown, David Hughes
As Australia's peak high-performance sport agency, the Australian Institute of Sport (AIS) has developed this position statement to address the implications of recent advances in the field of genetics and the ramifications for the health and well-being of athletes. Genetic testing has proven of value in the practice of clinical medicine. There are, however, currently no scientific grounds for the use of genetic testing for athletic performance improvement, sport selection or talent identification. Athletes and coaches should be discouraged from using direct-to-consumer genetic testing because of its lack of validation and replicability and the lack of involvement of a medical practitioner in the process...
November 29, 2016: British Journal of Sports Medicine
https://www.readbyqxmd.com/read/27899195/the-future-of-clinical-cancer-genomics
#20
Kenneth Offit
The current and future applications of genomics to the practice of preventive oncology are being impacted by a number of challenges. These include rapid advances in genomic science and technology that allow massively parallel sequencing of both tumors and the germline, a diminishing of intellectual property restrictions on diagnostic genetic applications, rapid expansion of access to the internet which includes mobile access to both genomic data and tools to communicate and interpret genetic data in a medical context, the expansion of for-profit diagnostic companies seeking to monetize genetic information, and a simultaneous effort to depict medical professionals as barriers to rather than facilitators of understanding one's genome...
October 2016: Seminars in Oncology
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