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https://www.readbyqxmd.com/read/29160420/next-generation-sequencing-based-genomic-profiling-fostering-innovation-in-cancer-care
#1
Gustavo S Fernandes, Daniel F Marques, Daniel M Girardi, Maria Ignez F Braghiroli, Renata A Coudry, Sibele I Meireles, Artur Katz, Paulo M Hoff
OBJECTIVES: With the development of next-generation sequencing (NGS) technologies, DNA sequencing has been increasingly utilized in clinical practice. Our goal was to investigate the impact of genomic evaluation on treatment decisions for heavily pretreated patients with metastatic cancer. METHODS: We analyzed metastatic cancer patients from a single institution whose cancers had progressed after all available standard-of-care therapies and whose tumors underwent next-generation sequencing analysis...
October 2017: Clinics
https://www.readbyqxmd.com/read/29159886/radiomics-in-lung-cancer-its-time-is-here
#2
Mannudeep Kalra, Ge Wang, Colin G Orton
Of the 8.8 million deaths from cancer in 2015, per the World Health Organization, lung cancer was the most common cause of death (1.69 million). With the introduction of low-dose CT for lung cancer screening and emergence of precision medicine for often-fatal lung cancer, there is a need for deep access to critical information, i.e. radiomics, not possible with conventional subjective interpretation of CT images. Quantitative image analyses for radiomics have been applied in lung cancers to determine their spatial complexity, genomic composition, viability or aggressiveness, and responses to targeted therapies...
November 21, 2017: Medical Physics
https://www.readbyqxmd.com/read/29159748/molecular-genomic-testing-for-breast-cancer-utility-for-surgeons
#3
REVIEW
Oluwadamilola M Fayanju, Ko Un Park, Anthony Lucci
Molecular genomic testing provides clinicians with both prognostic and (sometimes) predictive information that can help individualize treatment and decrease the risk of over- or under-treatment. We review the genomic tests that are currently available for clinical use in management of breast cancer, discuss ongoing research related to validating and expanding their utility in different patient populations, and explain why it is important for surgeons to know how to incorporate these tools into their clinical practice in order to individualize patient treatment, reduce unnecessary morbidity, and, accordingly, improve outcomes...
November 20, 2017: Annals of Surgical Oncology
https://www.readbyqxmd.com/read/29159425/novel-biosynthetic-pathway-for-sulfur-amino-acids-in-cryptococcus-neoformans
#4
Akio Toh-E, Misako Ohkusu, Kiminori Shimizu, Naruhiko Ishiwada, Akira Watanabe, Katsuhiko Kamei
We elucidated a unique feature of sulfur metabolism in Cryptococcus neoformans. C. neoformans produces cysteine solely by the O-acetylserine pathway that consists of serine-O-acetyl transferase and cysteine synthase. We designated the gene encoding the former enzyme CYS2 (locus tag CNE02740) and the latter enzyme CYS1 (locus tag CNL05880). The cys1Δmutant strain was found to be avirulent in a murine infection model. Methionine practically does not support growth of the cys1Δ strain, and cysteine does not serve as a methionine source, indicating that the transsulfuration pathway does not contribute to sulfur amino acid synthesis in C...
November 20, 2017: Current Genetics
https://www.readbyqxmd.com/read/29158988/a-16-gene-signature-predicting-prognosis-of-patients-with-oral-tongue-squamous-cell-carcinoma
#5
Zeting Qiu, Wei Sun, Shaowei Gao, Huaqiang Zhou, Wulin Tan, Minghui Cao, Wenqi Huang
Background: Oral tongue squamous cell carcinoma (OTSCC) is the most common subtype of oral cancer. A predictive gene signature is necessary for prognosis of OTSCC. Methods: Five microarray data sets of OTSCC from the Gene Expression Omnibus (GEO) and one data set from The Cancer Genome Atlas (TCGA) were obtained. Differentially expressed genes (DEGs) of GEO data sets were identified by integrated analysis. The DEGs associated with prognosis were screened in the TCGA data set by univariate survival analysis to obtain a gene signature...
2017: PeerJ
https://www.readbyqxmd.com/read/29158769/physicians-duty-to-recontact-and-update-genetic-advice
#6
Yvonne A Stevens, Grant D Senner, Gary E Marchant
This perspective addresses whether physicians have a duty to recontact former or current patients to update clinical advice based on newly discovered genomic information. Genetic information is unique compared with other medical data in that the underlying data do not appreciably change during the patients' lifetime, but the clinical significance of that information will continue to evolve. Based on relevant case law and guidelines, there is no general, established legal duty for physicians to affirmatively recontact former or current patients to update clinical advice based on newly discovered genetic information...
2017: Personalized Medicine
https://www.readbyqxmd.com/read/29158581/improved-ethical-guidance-for-the-return-of-results-from-psychiatric-genomics-research
#7
G Lázaro-Muñoz, M S Farrell, J J Crowley, D M Filmyer, R A Shaughnessy, R C Josiassen, P F Sullivan
There is an emerging consensus that genomic researchers should, at a minimum, offer to return to individual participants clinically valid, medically important and medically actionable genomic findings (for example, pathogenic variants in BRCA1) identified in the course of research. However, this is not a common practice in psychiatric genetics research. Furthermore, psychiatry researchers often generate findings that do not meet all of these criteria, yet there may be ethically compelling arguments to offer selected results...
November 21, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/29156198/the-evolving-role-of-genomic-testing-in-assessing-prognosis-of-patients-with-myelodysplastic-syndromes
#8
REVIEW
David P Steensma
The introduction into routine hematology-oncology clinical practice of molecular genetic testing assays based on next-generation sequencing platforms is prompting reassessment of the importance of molecular assay results in comparison to existing disease-specific risk stratification tools based on clinical assessment and light microscopy. For patients with myelodysplastic syndromes (MDS), the most commonly used tools for prognostication currently include the International Prognostic Scoring System (IPSS) and the Revised IPSS (IPSS-R), which are based on marrow blast proportion, number and degree of cytopenias, and the metaphase karyotype...
December 2017: Best Practice & Research. Clinical Haematology
https://www.readbyqxmd.com/read/29155419/catching-hidden-variation-systematic-correction-of-reference-minor-allele-annotation-in-clinical-variant-calling
#9
Yury A Barbitoff, Igor V Bezdvornykh, Dmitrii E Polev, Elena A Serebryakova, Andrey S Glotov, Oleg S Glotov, Alexander V Predeus
PurposeWe comprehensively assessed the influence of reference minor alleles (RMAs), one of the inherent problems of the human reference genome sequence.MethodsThe variant call format (VCF) files provided by the 1000 Genomes and Exome Aggregation Consortium (ExAC) consortia were used to identify RMA sites. All coding RMA sites were checked for concordance with UniProt and the presence of same codon variants. RMA-corrected predictions of functional effect were obtained with SIFT, PolyPhen-2, and PROVEAN standalone tools and compared with dbNSFP v2...
October 26, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29154853/standards-and-guidelines-for-validating-next-generation-sequencing-bioinformatics-pipelines-a-joint-recommendation-of-the-association-for-molecular-pathology-and-the-college-of-american-pathologists
#10
REVIEW
Somak Roy, Christopher Coldren, Arivarasan Karunamurthy, Nefize S Kip, Eric W Klee, Stephen E Lincoln, Annette Leon, Mrudula Pullambhatla, Robyn L Temple-Smolkin, Karl V Voelkerding, Chen Wang, Alexis B Carter
Bioinformatics pipelines are an integral component of next-generation sequencing (NGS). Processing raw sequence data to detect genomic alterations has significant impact on disease management and patient care. Because of the lack of published guidance, there is currently a high degree of variability in how members of the global molecular genetics and pathology community establish and validate bioinformatics pipelines. Improperly developed, validated, and/or monitored pipelines may generate inaccurate results that may have negative consequences for patient care...
November 17, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29154141/novel-genes-associated-with-amyotrophic-lateral-sclerosis-diagnostic-and-clinical-implications
#11
REVIEW
Ruth Chia, Adriano Chiò, Bryan J Traynor
BACKGROUND: The disease course of amyotrophic lateral sclerosis (ALS) is rapid and, because its pathophysiology is unclear, few effective treatments are available. Genetic research aims to understand the underlying mechanisms of ALS and identify potential therapeutic targets. The first gene associated with ALS was SOD1, identified in 1993 and, by early 2014, more than 20 genes had been identified as causative of, or highly associated with, ALS. These genetic discoveries have identified key disease pathways that are therapeutically testable and could potentially lead to the development of better treatments for people with ALS...
November 16, 2017: Lancet Neurology
https://www.readbyqxmd.com/read/29153404/fungal-phylogeny-in-the-age-of-genomics-insights-into-phylogenetic-inference-from-genome-scale-datasets
#12
László G Nagy, Gergely Szöllősi
The genomic era has been transformative for many fields, including our understanding of the phylogenetic relationships between organisms. The wide availability of whole-genome sequences practically eliminated data availability as a limiting factor for inferring phylogenetic trees, providing hundreds to thousands of loci for analyses, leading to molecular phylogenetics gradually being replaced by phylogenomics. The new era has also brought new challenges: systematic errors (resulting from, e.g., model violation) can be more pronounced in phylogenomic datasets and can lead to strongly supported incorrect relationships, creating significant incongruence among studies...
2017: Advances in Genetics
https://www.readbyqxmd.com/read/29153166/a-100-year-review-practical-female-reproductive-management
#13
J S Stevenson, J H Britt
Basic knowledge of mechanisms controlling reproductive processes in mammals was limited in the early 20th century. Discoveries of physiologic processes and mechanisms made early in the last century laid the foundation to develop technologies and programs used today to manage and control reproduction in dairy cattle. Beyond advances made in understanding of gonadotropic support and control of ovarian and uterine functions in basic reproductive biology, advancements made in artificial insemination (AI) and genetics facilitated rapid genetic progress of economically important traits in dairy cattle...
December 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/29153163/a-100-year-review-methods-and-impact-of-genetic-selection-in-dairy-cattle-from-daughter-dam-comparisons-to-deep-learning-algorithms
#14
K A Weigel, P M VanRaden, H D Norman, H Grosu
In the early 1900s, breed society herdbooks had been established and milk-recording programs were in their infancy. Farmers wanted to improve the productivity of their cattle, but the foundations of population genetics, quantitative genetics, and animal breeding had not been laid. Early animal breeders struggled to identify genetically superior families using performance records that were influenced by local environmental conditions and herd-specific management practices. Daughter-dam comparisons were used for more than 30 yr and, although genetic progress was minimal, the attention given to performance recording, genetic theory, and statistical methods paid off in future years...
December 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/29152587/a-synthetic-community-system-for-probing-microbial-interactions-driven-by-exometabolites
#15
John L Chodkowski, Ashley Shade
Though most microorganisms live within a community, we have modest knowledge about microbial interactions and their implications for community properties and ecosystem functions. To advance understanding of microbial interactions, we describe a straightforward synthetic community system that can be used to interrogate exometabolite interactions among microorganisms. The filter plate system (also known as the Transwell system) physically separates microbial populations, but allows for chemical interactions via a shared medium reservoir...
November 2017: MSystems
https://www.readbyqxmd.com/read/29149131/genetics-and-genomics-an-oncology-nurse-s-journey-in-practice
#16
Suzanne M Mahon
BACKGROUND: Cancer genetics and genomics are now an integral component of oncology care. Genetics and genomics guide recommendations not only for cancer prevention and early detection, but also for cancer treatment. 
. OBJECTIVES: This article documents the personal experiences of an oncology nurse who has worked in cancer prevention and early detection since the 1990s and describes the many changes that have occurred in cancer-related genetic and genomic care during that time...
December 1, 2017: Clinical Journal of Oncology Nursing
https://www.readbyqxmd.com/read/29149120/genomics-education-knowledge-of-nurses-across-the-profession-and-integration-into-practice
#17
Lisa B Aiello
BACKGROUND: Since the completion of the Human Genome Project in 2003, the implications of genetics and genomics for health and illness have become clearer. All nurses, at all levels and across all specialties, must have a basic understanding of genetics and genomics to provide appropriate care. 
. OBJECTIVES: This article provides an overview of the integration of genetics and genomics into nursing education, as well as continued barriers to nursing knowledge of genetics and genomics...
December 1, 2017: Clinical Journal of Oncology Nursing
https://www.readbyqxmd.com/read/29147432/the-era-of-multigene-panels-comes-the-clinical-utility-of-oncotype-dx-and-mammaprint
#18
REVIEW
Ling Xin, Yin-Hua Liu, Tracey A Martin, Wen G Jiang
The AJCC Cancer Staging Manual, eighth edition published in late 2016, will become the new global guideline for cancer diagnosis and treatment from January 1, 2018. The new edition for the tumor staging system has numerous updates, including building up the prognostic stage group of tumors for the first time and adding a large number of non-anatomical factors into the prognostic evaluation. Oncotype DX and MammaPrint are two of the genomic predictors that will be part of routine clinical practice in the future...
April 2017: World Journal of Oncology
https://www.readbyqxmd.com/read/29145425/statistical-analysis-of-co-occurrence-patterns-in-microbial-presence-absence-datasets
#19
Kumar P Mainali, Sharon Bewick, Peter Thielen, Thomas Mehoke, Florian P Breitwieser, Shishir Paudel, Arjun Adhikari, Joshua Wolfe, Eric V Slud, David Karig, William F Fagan
Drawing on a long history in macroecology, correlation analysis of microbiome datasets is becoming a common practice for identifying relationships or shared ecological niches among bacterial taxa. However, many of the statistical issues that plague such analyses in macroscale communities remain unresolved for microbial communities. Here, we discuss problems in the analysis of microbial species correlations based on presence-absence data. We focus on presence-absence data because this information is more readily obtainable from sequencing studies, especially for whole-genome sequencing, where abundance estimation is still in its infancy...
2017: PloS One
https://www.readbyqxmd.com/read/29144792/effect-of-blood-collection-tube-type-and-time-to-processing-on-the-enumeration-and-high-content-characterization-of-circulating-tumor-cells-using-the-high-definition-single-cell-assay
#20
Mariam Rodríguez-Lee, Anand Kolatkar, Madelyn McCormick, Angel D Dago, Jude Kendall, Nils Anders Carlsson, Kelly Bethel, Emily J Greenspan, Shelley E Hwang, Kathryn R Waitman, Jorge J Nieva, James Hicks, Peter Kuhn
CONTEXT: - As circulating tumor cell (CTC) assays gain clinical relevance, it is essential to address preanalytic variability and to develop standard operating procedures for sample handling in order to successfully implement genomically informed, precision health care. OBJECTIVE: - To evaluate the effects of blood collection tube (BCT) type and time-to-assay (TTA) on the enumeration and high-content characterization of CTCs by using the high-definition single-cell assay (HD-SCA)...
November 16, 2017: Archives of Pathology & Laboratory Medicine
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