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Medical genomics

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https://www.readbyqxmd.com/read/29792177/investigation-of-the-thermophilic-mechanism-in-the-genus-porphyrobacter-by-comparative-genomic-analysis
#1
Lin Xu, Yue-Hong Wu, Peng Zhou, Hong Cheng, Qian Liu, Xue-Wei Xu
BACKGROUND: Type strains of the genus Porphyrobacter belonging to the family Erythrobacteraceae and the class Alphaproteobacteria have been isolated from various environments, such as swimming pools, lake water and hot springs. P. cryptus DSM 12079T and P. tepidarius DSM 10594T out of all Erythrobacteraceae type strains, are two type strains that have been isolated from geothermal environments. Next-generation sequencing (NGS) technology offers a convenient approach for detecting situational types based on protein sequence differences between thermophiles and mesophiles; amino acid substitutions can lead to protein structural changes, improving the thermal stabilities of proteins...
May 23, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29790928/using-meshes-for-mesh-term-enrichment-and-semantic-analyses
#2
Guangchuang Yu
Summary: Medical Subject Headings (MeSH) is the NLM controlled vocabulary used to manually index articles for MEDLINE/PubMed. MeSH provides unique and comprehensive annotations for life science. The meshes package implements measurement of the semantic similarity of MeSH terms and gene products to help using MeSH vocabulary in knowledge mining. Enrichment analysis to extract the biological meanings from gene list, expression profile and genomic regions is also provided using MeSH annotation...
May 22, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29790872/genomic-sequencing-identifies-secondary-findings-in-a-cohort-of-parent-study-participants
#3
Michelle L Thompson, Candice R Finnila, Kevin M Bowling, Kyle B Brothers, Matthew B Neu, Michelle D Amaral, Susan M Hiatt, Kelly M East, David E Gray, James M J Lawlor, Whitley V Kelley, Edward J Lose, Carla A Rich, Shirley Simmons, Shawn E Levy, Richard M Myers, Gregory S Barsh, E Martina Bebin, Gregory M Cooper
PurposeClinically relevant secondary variants were identified in parents enrolled with a child with developmental delay and intellectual disability.MethodsExome/genome sequencing and analysis of 789 "unaffected" parents was performed.ResultsPathogenic/likely pathogenic variants were identified in 21 genes within 25 individuals (3.2%), with 11 (1.4%) participants harboring variation in a gene defined as clinically actionable by the American College of Medical Genetics and Genomics. These 25 individuals self-reported either relevant clinical diagnoses (5); relevant family history or symptoms (13); or no relevant family history, symptoms, or clinical diagnoses (7)...
April 12, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29789557/measuring-coverage-and-accuracy-of-whole-exome-sequencing-in-clinical-context
#4
Sek Won Kong, In-Hee Lee, Xuanshi Liu, Joel N Hirschhorn, Kenneth D Mandl
PurposeTo evaluate the coverage and accuracy of whole-exome sequencing (WES) across vendors.MethodsBlood samples from three trios underwent WES at three vendors. Relative performance of the three WES services was measured for breadth and depth of coverage. The false-negative rates (FNRs) were estimated using the segregation pattern within each trio.ResultsMean depth of coverage for all genes was 189.0, 124.9, and 38.3 for the three vendor services. Fifty-five of the American College of Medical Genetics and Genomics 56 genes, but only 56 of 63 pharmacogenes, were 100% covered at 10 × in at least one of the nine individuals for all vendors; however, there was substantial interindividual variability...
April 12, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29788166/combined-pathologic-genomic-algorithm-for-early-stage-breast-cancer-improves-cost-effective-use-of-the-21-gene-recurrence-score-assay
#5
M M Gage, W C Mylander, M Rosman, T Fujii, F Le Du, A Raghavendra, A K Sinha, J R Espinosa Fernandez, A James, N T Ueno, L Tafra, R S Jackson
Background: The 21-gene recurrence score (RS) (Oncotype DX®; Genomic Health, Redwood City, CA) partitions hormone receptor positive, node negative breast cancers into three risk groups for recurrence. The Anne Arundel Medical Center (AAMC) model has previously been shown to accurately predict RS risk categories using standard pathology data. A pathologic-genomic (P-G) algorithm then is presented using the AAMC model and reserving the RS assay only for AAMC intermediate-risk patients...
May 1, 2018: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29779145/comprehensive-genetic-testing-for-female-and-male-infertility-using-next-generation-sequencing
#6
Bonny Patel, Sasha Parets, Matthew Akana, Gregory Kellogg, Michael Jansen, Chihyu Chang, Ying Cai, Rebecca Fox, Mohammad Niknazar, Roman Shraga, Colby Hunter, Andrew Pollock, Robert Wisotzkey, Malgorzata Jaremko, Alex Bisignano, Oscar Puig
PURPOSE: To develop a comprehensive genetic test for female and male infertility in support of medical decisions during assisted reproductive technology (ART) protocols. METHODS: We developed a next-generation sequencing (NGS) gene panel consisting of 87 genes including promoters, 5' and 3' untranslated regions, exons, and selected introns. In addition, sex chromosome aneuploidies and Y chromosome microdeletions were analyzed concomitantly using the same panel. RESULTS: The NGS panel was analytically validated by retrospective analysis of 118 genomic DNA samples with known variants in loci representative of female and male infertility...
May 19, 2018: Journal of Assisted Reproduction and Genetics
https://www.readbyqxmd.com/read/29769160/cross-border-outbreak-of-extensively-drug-resistant-tuberculosis-linked-to-a-university-in-romania
#7
O Popovici, Ph Monk, D Chemtob, D Chiotan, P J Freidlin, R Groenheit, M Haanperä, D Homorodean, M Mansjö, E Robinson, E Rorman, G Smith, H Soini, M J Van Der Werf
Extensively drug-resistant (XDR) tuberculosis (TB) poses a threat to public health due to its complicated, expensive and often unsuccessful treatment. A cluster of three XDR TB cases was detected among foreign medical students of a Romanian university. The contact investigations included tuberculin skin testing or interferon gamma release assay, chest X-ray, sputum smear microscopy, culture, drug susceptibility testing, genotyping and whole-genome sequencing (WGS), and were addressed to students, personnel of the university, family members or other close contacts of the cases...
May 2018: Epidemiology and Infection
https://www.readbyqxmd.com/read/29767702/long-reads-their-purpose-and-place
#8
Martin O Pollard, Deepti Gurdasani, Alexander J Mentzer, Tarryn Porter, Manjinder S Sandhu
In recent years long read technologies have moved from being a niche and specialist field to a point of relative maturity likely to feature frequently in the genomic landscape. Analogous to next generation sequencing (NGS), the cost of sequencing using long read technologies has materially dropped whilst the instrument throughput continues to increase. Together these changes present the prospect of sequencing large numbers of individuals with the aim of fully characterising genomes at high resolution. In this article, we will endeavour to present an introduction to long read technologies showing: what long reads are; how they are distinct from short reads; why long reads are useful; and how they are being used...
May 14, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29767669/identification-of-mutations-in-patients-with-acquired-pure-red-cell-aplasia
#9
Xinchao Zhang, Yi Shi, Lingjun Song, Chang Shen, Qi Cai, Zhou Zhang, Jun Wu, Guohui Fu, Weiwei Shen
Idiopathic acquired pure red cell aplasia (PRCA) is a rare, autoimmune-related disease. This study aimed to describe the previously unidentified DNA alterations associated with PRCA. Here, next generation sequencing using a panel containing 295 critical genes was applied to detect potentially pathogenic mutations in four patients with PRCA. A total of 529 mutations were identified and further classified into three categories, namely, uncertain (n = 25), likely benign (n = 20) and benign (n = 484) mutations, based on the American College of Medical Genetics and Genomics (ACMG) 2015 guidelines and ClinVar database...
May 15, 2018: Acta Biochimica et Biophysica Sinica
https://www.readbyqxmd.com/read/29767375/strategies-to-guide-the-return-of-genomic-research-findings-an-australian-perspective
#10
Lisa Eckstein, Margaret Otlowski
In Australia, along with many other countries, limited guidance or other support strategies are currently available to researchers, institutional research ethics committees, and others responsible for making decisions about whether to return genomic findings with potential value to participants or their blood relatives. This lack of guidance results in onerous decision-making burdens-traversing technical, interpretative, and ethical dimensions-as well as uncertainty and inconsistencies for research participants...
May 16, 2018: Journal of Bioethical Inquiry
https://www.readbyqxmd.com/read/29767355/overview-of-gene-expression-analysis-transcriptomics
#11
Nalini Raghavachari, Natàlia Garcia-Reyero
Currently, the study of the transcriptome is widely used to interpret the functional elements of the genome and molecular constituents of cells and tissues in an effort to unravel biological pathways associated with development and disease. The advent of technologies is now enabling the study of such comprehensive transcriptional characterization of mRNA, miRNA, lncRNA, and small RNA in a robust and successful manner. Transcriptomic strategies are gaining momentum across diverse areas of biological, plant sciences, medical, clinical, and pharmaceutical research for biomarker discovery, and disease diagnosis and prognosis...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29765029/the-crispr-tool-kit-for-genome-editing-and-beyond
#12
REVIEW
Mazhar Adli
CRISPR is becoming an indispensable tool in biological research. Once known as the bacterial immune system against invading viruses, the programmable capacity of the Cas9 enzyme is now revolutionizing diverse fields of medical research, biotechnology, and agriculture. CRISPR-Cas9 is no longer just a gene-editing tool; the application areas of catalytically impaired inactive Cas9, including gene regulation, epigenetic editing, chromatin engineering, and imaging, now exceed the gene-editing functionality of WT Cas9...
May 15, 2018: Nature Communications
https://www.readbyqxmd.com/read/29764369/vareporter-variant-reporter-for-cancer-research-of-massive-parallel-sequencing
#13
Po-Jung Huang, Chi-Ching Lee, Ling-Ya Chiu, Kuo-Yang Huang, Yuan-Ming Yeh, Chia-Yu Yang, Cheng-Hsun Chiu, Petrus Tang
BACKGROUND: High throughput sequencing technologies have been an increasingly critical aspect of precision medicine owing to a better identification of disease targets, which contributes to improved health care cost and clinical outcomes. In particular, disease-oriented targeted enrichment sequencing is becoming a widely-accepted application for diagnostic purposes, which can interrogate known diagnostic variants as well as identify novel biomarkers from panels of entire human coding exome or disease-associated genes...
May 9, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29763720/bap1-loss-is-unusual-in-well-differentiated-papillary-mesothelioma-and-may-predict-development-of-malignant-mesothelioma
#14
Hee Eun Lee, Julian R Molina, William R Sukov, Anja C Roden, Eunhee S Yi
Literature on BRCA1-associated protein 1 (BAP1) expression status in well-differentiated papillary mesothelioma (WDPM) is limited. In the present study, we examined the prevalence of BAP1 loss in WDPM by immunohistochemistry with clinical correlation, along with CDKN2A deletion status by fluorescence in situ hybridization (FISH). Eight patients diagnosed as WDPM were identified from the surgical pathology file. Adenomatoid tumors (n=8) and malignant mesothelioma (MM) (n=39) were included for comparison. BAP1 immunohistochemistry was performed on representative block(s) from each case...
May 12, 2018: Human Pathology
https://www.readbyqxmd.com/read/29762787/litvar-a-semantic-search-engine-for-linking-genomic-variant-data-in-pubmed-and-pmc
#15
Alexis Allot, Yifan Peng, Chih-Hsuan Wei, Kyubum Lee, Lon Phan, Zhiyong Lu
The identification and interpretation of genomic variants play a key role in the diagnosis of genetic diseases and related research. These tasks increasingly rely on accessing relevant manually curated information from domain databases (e.g. SwissProt or ClinVar). However, due to the sheer volume of medical literature and high cost of expert curation, curated variant information in existing databases are often incomplete and out-of-date. In addition, the same genetic variant can be mentioned in publications with various names (e...
May 14, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29762087/genomics-and-epigenomics-of-congenital-heart-defects-expert-review-and-lessons-learned-in-africa
#16
Nicholas Ekow Thomford, Kevin Dzobo, Nana Akyaa Yao, Emile Chimusa, Jonathan Evans, Emmanuel Okai, Paul Kruszka, Maximilian Muenke, Gordon Awandare, Ambroise Wonkam, Collet Dandara
Congenital heart defects (CHD) are structural malformations found at birth with a prevalence of 1%. The clinical trajectory of CHD is highly variable and thus in need of robust diagnostics and therapeutics. Major surgical interventions are often required for most CHDs. In Africa, despite advances in life sciences infrastructure and improving education of medical scholars, the limited clinical data suggest that CHD detection and correction are still not at par with the rest of the world. But the toll and genetics of CHDs in Africa has seldom been systematically investigated...
May 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29761785/discovery-and-characterization-of-a-prevalent-human-gut-bacterial-enzyme-sufficient-for-the-inactivation-of-a-family-of-plant-toxins
#17
Nitzan Koppel, Jordan E Bisanz, Maria-Eirini Pandelia, Peter J Turnbaugh, Emily P Balskus
Although the human gut microbiome plays a prominent role in xenobiotic transformation, most of the genes and enzymes responsible for this metabolism are unknown. Recently, we linked the two-gene 'cardiac glycoside reductase' ( cgr ) operon encoded by the gut Actinobacterium Eggerthella lenta to inactivation of the cardiac medication and plant natural product digoxin. Here, we compared the genomes of 25 E. lenta strains and close relatives, revealing an expanded 8-gene cgr -associated gene cluster present in all digoxin metabolizers and absent in non-metabolizers...
May 15, 2018: ELife
https://www.readbyqxmd.com/read/29761117/genomic-analysis-identifies-masqueraders-of-full-term-cerebral-palsy
#18
Yusuke Takezawa, Atsuo Kikuchi, Kazuhiro Haginoya, Tetsuya Niihori, Yurika Numata-Uematsu, Takehiko Inui, Saeko Yamamura-Suzuki, Takuya Miyabayashi, Mai Anzai, Sato Suzuki-Muromoto, Yukimune Okubo, Wakaba Endo, Noriko Togashi, Yasuko Kobayashi, Akira Onuma, Ryo Funayama, Matsuyuki Shirota, Keiko Nakayama, Yoko Aoki, Shigeo Kure
Objective: Cerebral palsy is a common, heterogeneous neurodevelopmental disorder that causes movement and postural disabilities. Recent studies have suggested genetic diseases can be misdiagnosed as cerebral palsy. We hypothesized that two simple criteria, that is, full-term births and nonspecific brain MRI findings, are keys to extracting masqueraders among cerebral palsy cases due to the following: (1) preterm infants are susceptible to multiple environmental factors and therefore demonstrate an increased risk of cerebral palsy and (2) brain MRI assessment is essential for excluding environmental causes and other particular disorders...
May 2018: Annals of Clinical and Translational Neurology
https://www.readbyqxmd.com/read/29760616/high-frequency-of-primary-hereditary-ichthyoses-in-the-north-east-region-of-cairo-egypt
#19
Nermine El-Sayed, Neveen S Seifeldin, Christine K T Gobrial
Introduction: Inherited ichthyoses are caused by mutations in various genes important for keratinocyte differentiation and epidermal barrier function. Although ichthyoses are rare disorders, they require costly long-term medical management, and thus there is a need for efficient preventive and therapeutic strategies. Aim: We performed a retrospective study to determine the frequency, types, clinical presentation and associated genomic errors of primary hereditary ichthyoses in Egyptian patients and their relatives consulting the Genetics Clinic, Pediatric Hospital, Ain Shams University...
April 2018: Postȩpy Dermatologii i Alergologii
https://www.readbyqxmd.com/read/29759551/genomics-and-pharmacogenomics-of-pediatric-acute-lymphoblastic-leukemia
#20
REVIEW
Chuan Wu, Wei Li
Acute lymphoblastic leukaemia (ALL) is a prevalent form of pediatric cancer that accounts for 70-80% of all leukemias. Genome-based analysis, exome sequencing, transcriptomics and proteomics have provided insight into genetic classification of ALL and helped identify novel subtypes of the disease. B and T cell-based ALL are two well-characterized genomic subtypes, significantly marked by bone marrow disorders, along with mutations in trisomy 21 and T53. The other ALLs include Early T-cell precursor ALL, Philadelphia chromosome-like ALL, Down syndrome-associated ALL and Relapsed ALL...
June 2018: Critical Reviews in Oncology/hematology
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