keyword
MENU ▼
Read by QxMD icon Read
search

Medical genomics

keyword
https://www.readbyqxmd.com/read/28108552/predicted-residual-error-sum-of-squares-of-mixed-models-an-application-to-genomic-prediction
#1
Shizhong Xu
Genomic prediction is a statistical method to predict phenotypes of polygenic traits using high throughput genomic data. Most diseases and behaviors in human and animals are polygenic traits. The majority of agronomic traits in crops are also polygenic. Accurate prediction of these traits can help medical professionals diagnose acute diseases and breeders to increase food products, and therefore, significantly contribute to human health and global food security. The best linear unbiased prediction (BLUP) is an important tool to analyze high throughput genomic data for prediction...
January 20, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28107396/mixfit-methodology-for-computing-ancestry-related-genetic-scores-at-the-individual-level-and-its-application-to-the-estonian-and-finnish-population-studies
#2
Toomas Haller, Liis Leitsalu, Krista Fischer, Marja-Liisa Nuotio, Tõnu Esko, Dorothea Irene Boomsma, Kirsten Ohm Kyvik, Tim D Spector, Markus Perola, Andres Metspalu
Ancestry information at the individual level can be a valuable resource for personalized medicine, medical, demographical and history research, as well as for tracing back personal history. We report a new method for quantitatively determining personal genetic ancestry based on genome-wide data. Numerical ancestry component scores are assigned to individuals based on comparisons with reference populations. These comparisons are conducted with an existing analytical pipeline making use of genotype phasing, similarity matrix computation and our addition-multidimensional best fitting by MixFit...
2017: PloS One
https://www.readbyqxmd.com/read/28106839/the-importance-of-the-nucleus-during-flavivirus-replication
#3
REVIEW
Adam J Lopez-Denman, Jason M Mackenzie
Flaviviruses are a large group of arboviruses of significant medical concern worldwide. With outbreaks a common occurrence, the need for efficient viral control is required more than ever. It is well understood that flaviviruses modulate the composition and structure of membranes in the cytoplasm that are crucial for efficient replication and evading immune detection. As the flavivirus genome consists of positive sense RNA, replication can occur wholly within the cytoplasm. What is becoming more evident is that some viral proteins also have the ability to translocate to the nucleus, with potential roles in replication and immune system perturbation...
January 19, 2017: Viruses
https://www.readbyqxmd.com/read/28106529/a-joint-cross-border-investigation-of-a-cluster-of-multidrug-resistant-tuberculosis-in-austria-romania-and-germany-in-2014-using-classic-genotyping-and-whole-genome-sequencing-methods-lessons-learnt
#4
Lena Fiebig, Thomas A Kohl, Odette Popovici, Margarita Mühlenfeld, Alexander Indra, Daniela Homorodean, Domnica Chiotan, Elvira Richter, Sabine Rüsch-Gerdes, Beatrix Schmidgruber, Patrick Beckert, Barbara Hauer, Stefan Niemann, Franz Allerberger, Walter Haas
Molecular surveillance of multidrug-resistant tuberculosis (MDR-TB) using 24-loci MIRU-VNTR in the European Union suggests the occurrence of international transmission. In early 2014, Austria detected a molecular MDR-TB cluster of five isolates. Links to Romania and Germany prompted the three countries to investigate possible cross-border MDR-TB transmission jointly. We searched genotyping databases, genotyped additional isolates from Romania, used whole genome sequencing (WGS) to infer putative transmission links, and investigated pairwise epidemiological links and patient mobility...
January 12, 2017: Euro Surveillance: Bulletin Européen sur les Maladies Transmissibles, European Communicable Disease Bulletin
https://www.readbyqxmd.com/read/28106333/translating-precision
#5
EDITORIAL
Michael A Pacanowski
Precision medicine is based on a simple precept that deep information about an individual patient can be used to guide his or her health care. In the not-too-distant future, clinicians may have point-of-care access to an individual's entire genome, dense data captured from wearable devices, and informatics tools that aggregate data from clinical experience to allow for real-time decision support. The innovative technologies being developed in pursuit of precision medicine afford researchers and clinicians the opportunity to generate and consume information at an unprecedented scale...
January 20, 2017: Clinical and Translational Science
https://www.readbyqxmd.com/read/28105927/candidate-snp-markers-of-aggressiveness-related-complications-and-comorbidities-of-genetic-diseases-are-predicted-by-a-significant-change-in-the-affinity-of-tata-binding-protein-for-human-gene-promoters
#6
Irina V Chadaeva, Mikhail P Ponomarenko, Dmitry A Rasskazov, Ekaterina B Sharypova, Elena V Kashina, Marina Yu Matveeva, Tatjana V Arshinova, Petr M Ponomarenko, Olga V Arkova, Natalia P Bondar, Ludmila K Savinkova, Nikolay A Kolchanov
BACKGROUND: Aggressiveness in humans is a hereditary behavioral trait that mobilizes all systems of the body-first of all, the nervous and endocrine systems, and then the respiratory, vascular, muscular, and others-e.g., for the defense of oneself, children, family, shelter, territory, and other possessions as well as personal interests. The level of aggressiveness of a person determines many other characteristics of quality of life and lifespan, acting as a stress factor. Aggressive behavior depends on many parameters such as age, gender, diseases and treatment, diet, and environmental conditions...
December 28, 2016: BMC Genomics
https://www.readbyqxmd.com/read/28104200/crispr-genome-editing-a-medical-revolution
#7
EDITORIAL
James R Butler, A Joseph Tector
No abstract text is available yet for this article.
February 2017: Journal of Thoracic and Cardiovascular Surgery
https://www.readbyqxmd.com/read/28102863/a-taxonomy-of-medical-uncertainties-in-clinical-genome-sequencing
#8
Paul K J Han, Kendall L Umstead, Barbara A Bernhardt, Robert C Green, Steven Joffe, Barbara Koenig, Ian Krantz, Leo B Waterston, Leslie G Biesecker, Barbara B Biesecker
PURPOSE: Clinical next-generation sequencing (CNGS) is introducing new opportunities and challenges into the practice of medicine. Simultaneously, these technologies are generating uncertainties of an unprecedented scale that laboratories, clinicians, and patients are required to address and manage. We describe in this report the conceptual design of a new taxonomy of uncertainties around the use of CNGS in health care. METHODS: Interviews to delineate the dimensions of uncertainty in CNGS were conducted with genomics experts and themes were extracted in order to expand on a previously published three-dimensional taxonomy of medical uncertainty...
January 19, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28102331/investigating-causality-in-associations-between-smoking-initiation-and-schizophrenia-using-mendelian-randomization
#9
Suzanne H Gage, Hannah J Jones, Amy E Taylor, Stephen Burgess, Stanley Zammit, Marcus R Munafò
Smoking is strongly associated with schizophrenia. Although it has been widely assumed that this reflects self-medication, recent studies suggest that smoking may be a risk factor for schizophrenia. We performed two-sample bi-directional Mendelian randomization using summary level genomewide association data from the Tobacco And Genetics Consortium and Psychiatric Genomics Consortium. Variants associated with smoking initiation and schizophrenia were combined using an inverse-variance weighted fixed-effects approach...
January 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28102032/nonpromoter-methylation-of-the-cdkn2a-gene-with-active-transcription-is-associated-with-improved-locoregional-control-in-laryngeal-squamous-cell-carcinoma
#10
Miriam M Ben-Dayan, Thomas J Ow, Thomas J Belbin, Joshua Wetzler, Richard V Smith, Geoffrey Childs, Brenda Diergaarde, D Neil Hayes, Jennifer R Grandis, Michael B Prystowsky, Nicolas F Schlecht
We previously reported a novel association between CDKN2A nonpromoter methylation and transcription (ARF/INK4a) in human papillomavirus associated oropharyngeal tumors. In this study we assessed whether nonpromoter CDKN2A methylation in laryngeal squamous cell carcinomas (LXSCC) conferred a similar association with transcription that predicted patient outcome. We compared DNA methylation and ARF/INK4a RNA expression levels for the CDKN2A locus using the Illumina HumanMethylation27 beadchip and RT-PCR in 43 LXSCC tumor samples collected from a prospective study of head and neck cancer patients treated at Montefiore Medical Center (MMC)...
January 19, 2017: Cancer Medicine
https://www.readbyqxmd.com/read/28101821/prevalence-and-characteristics-of-patients-with-suspected-inherited-renal-cell-cancer-application-of-the-acmg-nsgc-genetic-referral-guidelines-to-patient-cohorts
#11
Hong Truong, Sarah E Hegarty, Leonard G Gomella, William K Kelly, Edouard J Trabulsi, Costas D Lallas, Veda N Giri
Patients with suspected hereditary renal cell cancer (RCC) are under-referred for genetic evaluation. Characterizing the prevalence and characteristics of suspected inherited RCC is a crucial step toward advancing personalized, genetically-based cancer risk management for patients and their families. To evaluate the prevalence and characteristics of suspected inherited RCC syndromes based on consensus criteria, we performed a cross-sectional analysis of patients with a diagnosis of RCC in SEER (2001-2011, n = 105,754) and in our institutional cancer registry (2004-2013, n = 998)...
January 19, 2017: Journal of Genetic Counseling
https://www.readbyqxmd.com/read/28101462/identification-and-molecular-characterization-of-genes-coding-pharmaceutically-important-enzymes-from-halo-thermo-tolerant-bacillus
#12
Azam Safary, Rezvan Moniri, Maryam Hamzeh-Mivehroud, Siavoush Dastmalchi
Purpose: Robust pharmaceutical and industrial enzymes from extremophile microorganisms are main source of enzymes with tremendous stability under harsh conditions which make them potential tools for commercial and biotechnological applications. Methods: The genome of a Gram-positive halo-thermotolerant Bacillus sp. SL1, new isolate from Saline Lake, was investigated for the presence of genes coding for potentially pharmaceutical enzymes. We determined gene sequences for the enzymes laccase (CotA), l-asparaginase (ansA3, ansA1), glutamate-specific endopeptidase (blaSE), l-arabinose isomerase (araA2), endo-1,4-β mannosidase (gmuG), glutaminase (glsA), pectate lyase (pelA), cellulase (bglC1), aldehyde dehydrogenase (ycbD) and allantoinases (pucH) in the genome of Bacillus sp...
December 2016: Advanced Pharmaceutical Bulletin
https://www.readbyqxmd.com/read/28100623/temperature-sensitive-lesion-in-the-n-terminal-domain-of-the-rotavirus-polymerase-affects-its-intracellular-localization-and-enzymatic-activity
#13
Allison O McKell, Leslie E W LaConte, Sarah M McDonald
: Temperature-sensitive (ts) mutants of simian rotavirus (RV) strain SA11 have been previously created to investigate the functions of viral proteins during replication. One mutant, SA11-tsC, maps to the gene encoding the VP1 polymerase and shows diminished growth and RNA synthesis at 39°C as compared to 31°C. In the current study, we sequenced all 11 genes of SA11-tsC, confirming the presence of an L138P mutation in the VP1 N-terminal domain and identifying 52 additional mutations in four other viral proteins (VP7, VP4, NSP2, and NSP1)...
January 18, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28099825/transmission-of-extensively-drug-resistant-tuberculosis-in-south-africa
#14
N Sarita Shah, Sara C Auld, James C M Brust, Barun Mathema, Nazir Ismail, Pravi Moodley, Koleka Mlisana, Salim Allana, Angela Campbell, Thuli Mthiyane, Natashia Morris, Primrose Mpangase, Hermina van der Meulen, Shaheed V Omar, Tyler S Brown, Apurva Narechania, Elena Shaskina, Thandi Kapwata, Barry Kreiswirth, Neel R Gandhi
Background Drug-resistant tuberculosis threatens recent gains in the treatment of tuberculosis and human immunodeficiency virus (HIV) infection worldwide. A widespread epidemic of extensively drug-resistant (XDR) tuberculosis is occurring in South Africa, where cases have increased substantially since 2002. The factors driving this rapid increase have not been fully elucidated, but such knowledge is needed to guide public health interventions. Methods We conducted a prospective study involving 404 participants in KwaZulu-Natal Province, South Africa, with a diagnosis of XDR tuberculosis between 2011 and 2014...
19, 2017: New England Journal of Medicine
https://www.readbyqxmd.com/read/28096882/design-and-methods-of-the-mood-disorder-cohort-research-consortium-mdcrc-study
#15
Chul-Hyun Cho, Yong-Min Ahn, Se Joo Kim, Tae Hyun Ha, Hong Jin Jeon, Boseok Cha, Eunsoo Moon, Dong Yeon Park, Ji Hyun Baek, Hee-Ju Kang, Vin Ryu, Hyonggin An, Heon-Jeong Lee
The Mood Disorder Cohort Research Consortium (MDCRC) study is designed as a naturalistic observational prospective cohort study for early-onset mood disorders (major depressive disorders, bipolar disorders type 1 and 2) in South Korea. The study subjects consist of two populations: 1) patients with mood disorders under 25 years old and 2) patients with mood disorders within 2 years of treatment under 35 years old. After successful screening, the subjects are evaluated using baseline assessments and serial follow-up assessments at 3-month intervals...
January 2017: Psychiatry Investigation
https://www.readbyqxmd.com/read/28095174/medical-oncologists-experiences-in-using-genomic-testing-for-lung-and-colorectal-cancer-care
#16
Stacy W Gray, Benjamin Kim, Lynette Sholl, Angel Cronin, Aparna R Parikh, Carrie N Klabunde, Katherine L Kahn, David A Haggstrom, Nancy L Keating
PURPOSE: Genomic testing improves outcomes for many at-risk individuals and patients with cancer; however, little is known about how genomic testing for non-small-cell lung cancer (NSCLC) and colorectal cancer (CRC) is used in clinical practice. PATIENTS AND METHODS: In 2012 to 2013, we surveyed medical oncologists who care for patients in diverse practice and health care settings across the United States about their use of guideline- and non-guideline-endorsed genetic tests...
January 17, 2017: Journal of Oncology Practice
https://www.readbyqxmd.com/read/28094792/identification-of-a-nuclear-respiratory-factor-1-recognition-motif-in-the-apolipoprotein-e-variant-apoe4-linked-to-alzheimer-s-disease
#17
Anne Urfer-Buchwalder, Roman Urfer
Alzheimer's disease affects tens of millions of people worldwide and its prevalence continues to rise. It is caused by a combination of a subject's heredity, environment, lifestyle, and medical condition. The most significant genetic risk factor for late onset Alzheimer's disease is a variant of the apolipoprotein E gene, APOE4. Here we show that the single nucleotide polymorphism rs429358 that defines APOE4 is located in a short sequence motif repeated several times within exon 4 of apolipoprotein E, reminiscent of the structure of transcriptional enhancers...
January 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28090653/genome-wide-study-links-pnpla3-variant-with-elevated-hepatic-transaminase-after-acute-lymphoblastic-leukemia-therapy
#18
Yiwei Liu, Christian A Fernandez, Colton Smith, Wenjian Yang, Cheng Cheng, John C Panetta, Nancy Kornegay, Chengcheng Liu, Laura B Ramsey, Seth E Karol, Laura J Janke, Eric C Larsen, Naomi Winick, William L Carroll, Mignon L Loh, Elizabeth A Raetz, Stephen P Hunger, Meenakshi Devidas, Jun J Yang, Charles G Mullighan, Jinghui Zhang, William E Evans, Sima Jeha, Ching-Hon Pui, Mary V Relling
Remission induction therapy for acute lymphoblastic leukemia (ALL) includes medications that may cause hepatotoxicity, including asparaginase. We used a genome-wide association study (GWAS) to identify loci associated with elevated alanine transaminase (ALT) levels after induction therapy in children with ALL enrolled on St. Jude Children's Research Hospital (SJCRH) protocols. Germline DNA was genotyped using arrays and exome sequencing. Adjusting for age, body mass index, ancestry, asparaginase preparation and dosage, the PNPLA3 rs738409 (C>G) I148M variant, previously associated with fatty liver disease risk, had the strongest genetic association with ALT (P = 2...
January 16, 2017: Clinical Pharmacology and Therapeutics
https://www.readbyqxmd.com/read/28088185/igc-an-integrated-analysis-package-of-gene-expression-and-copy-number-alteration
#19
Yi-Pin Lai, Liang-Bo Wang, Wei-An Wang, Liang-Chuan Lai, Mong-Hsun Tsai, Tzu-Pin Lu, Eric Y Chuang
BACKGROUND: With the advancement in high-throughput technologies, researchers can simultaneously investigate gene expression and copy number alteration (CNA) data from individual patients at a lower cost. Traditional analysis methods analyze each type of data individually and integrate their results using Venn diagrams. Challenges arise, however, when the results are irreproducible and inconsistent across multiple platforms. To address these issues, one possible approach is to concurrently analyze both gene expression profiling and CNAs in the same individual...
January 14, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28087772/possible-roles-of-new-mutations-shared-by-asian-and-american-zika-viruses
#20
Shozo Yokoyama, William T Starmer
Originating in Africa, the Zika virus (ZIKV) has spread to Asia, Pacific Islands and now to the Americas and beyond. Since the first isolation in 1947, ZIKV strains have been sampled at various times in the last 69 years, but this history has not been reflected in studying the patterns of mutation accumulation in their genomes. Implementing the viral history, we show that the ZIKV ancestor appeared sometime in 1930-1945 and, at that point, its mutation rate was probably less than 0.2 x 10(-3)/nucleotide site/year and subsequently increased significantly in most of its descendants...
January 12, 2017: Molecular Biology and Evolution
keyword
keyword
41849
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"