keyword
MENU ▼
Read by QxMD icon Read
search

snps

keyword
https://www.readbyqxmd.com/read/28945025/-dna-marker-assisted-selection-of-medicinal-plants-%C3%A2-breeding-research-of-disease-resistant-cultivars-of-panax-notoginseng
#1
Lin-Lin Dong, Zhong-Jian Chen, Yong Wang, Fu-Gang Wei, Lian-Juan Zhang, Jiang Xu, Guang-Fei Wei, Rui Wang, Juan Yang, Wei-Lin Liu, Xi-Wen Li, Yu-Qi Yu, Shi-Lin Chen
DNA marker-assisted selection of medicinal plants is based on the DNA polymorphism, selects the DNA sequences related to the phenotypes such as high yields, superior quality, stress-resistance and so on according to the technologies of molecular hybridization, polymerase chain reaction and high-throughput sequencing, and assists the breeding of new cultivars. This study bred the first disease-resistant cultivar of notoginseng "Miaoxiang Kangqi 1" using the technology of DNA marker-assisted selection of medicinal plants and systematic breeding...
January 2017: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28944299/geographic-genetic-analysis-of-plasmodium-falciparum-parasite-populations-from-surveys-of-primary-school-children-in-western-kenya
#2
Irene Omedo, Polycarp Mogeni, Kirk Rockett, Alice Kamau, Christina Hubbart, Anna Jeffreys, Lynette Isabella Ochola-Oyier, Etienne P de Villiers, Caroline W Gitonga, Abdisalan M Noor, Robert W Snow, Dominic Kwiatkowski, Philip Bejon
Background. Malaria control, and finally malaria elimination, requires the identification and targeting of residual foci or hotspots of transmission. However, the level of parasite mixing within and between geographical locations is likely to impact the effectiveness and durability of control interventions and thus should be taken into consideration when developing control programs. Methods. In order to determine the geographic-genetic patterns of Plasmodium falciparum parasite populations at a sub-national level in Kenya, we used the Sequenom platform to genotype 111 genome-wide distributed single nucleotide polymorphic (SNP) positions in 2486 isolates collected from children in 95 primary schools in western Kenya...
2017: Wellcome Open Research
https://www.readbyqxmd.com/read/28944015/signatures-of-selection-in-mammalian-clock-genes-with-coding-trinucleotide-repeats-implications-for-studying-the-genomics-of-high-pace-adaptation
#3
Melanie B Prentice, Jeff Bowman, Jillian L Lalor, Michelle M McKay, Lindsay A Thomson, Cristen M Watt, Andrew G McAdam, Dennis L Murray, Paul J Wilson
Climate change is predicted to affect the reproductive ecology of wildlife; however, we have yet to understand if and how species can adapt to the rapid pace of change. Clock genes are functional genes likely critical for adaptation to shifting seasonal conditions through shifts in timing cues. Many of these genes contain coding trinucleotide repeats, which offer the potential for higher rates of change than single nucleotide polymorphisms (SNPs) at coding sites, and, thus, may translate to faster rates of adaptation in changing environments...
September 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28943953/six-low-penetrance-snps-for-the-estimation-of-breast-cancer-heritability-a-family-based-study-in-caucasian-italian-patients
#4
Simona De Summa, Francesca Graziano, Brunella Pilato, Rosamaria Pinto, Katia Danza, Rosanna Lacalamita, Simona Serratì, Domenico Sambiasi, Mario Grassi, Stefania Tommasi
Breast cancer is a malignancy with a strong heritable component. Genetic counseling has been principally focused on families carrying high-penetrance breast cancer 1/2, early onset genes. Current modeling suggests that the majority of the unexplained fraction of familial risk is likely to be explained by a polygenic model. The aim of the present study was to estimate the heritability (h(2)) of breast cancer susceptibility through the analysis of 6 single nucleotide polymorphisms (SNPs), nuclear mitotic apparatus protein 1, cyclin D1, cytochrome C oxidase copper chaperone, fibroblast growth factor receptor 2, TOX high mobility group box family member 3 and solute carrier family 4 member 7...
October 2017: Oncology Letters
https://www.readbyqxmd.com/read/28943727/a-genomic-signature-for-genotyping-mycobacterium-tuberculosis
#5
David Tarazona, Luis Jaramillo, Victor Borda, Kelly Levano, Marco Galarza, Heinner Guio
Mycobacterium tuberculosis (MTB), the causative agent of tuberculosis (TB), has a vast diversity of genotypes including Beijing, CAS, EAI, Haarlem, LAM, X, Ural, T, AFRI1 and AFRI2. However, genotyping can be expensive, time consuming and in some cases, results may vary depending on methodology used. Here, we proposed a new set of 10 SNPs using a total of 249 MTB genomes, and selected by first the inclusion/ exclusion (IE) criteria using spoligotyping and phylogenies, followed by the selection of the nonsynonymous SNPs present in the most conserved cluster of orthologous groups (COG) of each genotype of MTB...
2017: Bioinformation
https://www.readbyqxmd.com/read/28943632/differences-in-abca1-r219k-polymorphisms-and-serum-indexes-in-alzheimer-and-parkinson-diseases-in-northern-china
#6
Lagai Ya, Zuneng Lu
BACKGROUND ABCA1 R219K single-nucleotide polymorphisms (SNPs) was related to Alzheimer disease (AD) but not Parkinson disease (PD). Here, we analyzed the associations among ABCA1 R219K distribution, serum biomarkers, AD, and PD in a population in northern China. MATERIAL AND METHODS We used the Mini-Mental State Examination (MMSE) and the Hoehn and Yahr scale (H-Y) to evaluate AD and PD progression, separately. ABCA1 R219K was analyzed by matrix-assisted laser desorption ionization time of flight time mass spectrometry (MALDI-TOF-MS)...
September 25, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/28943493/the-european-collaborative-project-on-inflammation-and-vascular-wall-remodeling-in-atherosclerosis-intravascular-ultrasound-atheroremo-ivus-study
#7
Sanneke P M de Boer, Yael Baran, Hector M Garcia-Garcia, Itamar Eskin, Mattie Lenzen, Marcus E Kleber, Evelyn Regar, Peter J de Jaegere, Jurgen M Ligthart, Robert Jan van Geuns, Tehro Lehtimäki, Reijo Laaksonen, Eric Boersma, Winfried März, Erin Halperin, Patrick W Serruys, Wolfgang Koenig
AIMS: The European Collaborative Project on Inflammation and Vascular Wall Remodelling in Atherosclerosis - Intravascular Ultrasound (ATHEROREMO-IVUS) study has been designed as an exploratory clinical study to investigate the associations between genetic variation, coronary atherosclerosis phenotypes, and plaque vulnerability as determined by IVUS. METHODS AND RESULTS: The ATHEROREMO-IVUS study is a prospective, observational study of 581 patients with stable angina pectoris or acute coronary syndrome (ACS) who were referred for coronary angiography to the Thoraxcenter, Rotterdam, enriched with 265 IBIS-2 participants (total population, n=846)...
September 26, 2017: EuroIntervention
https://www.readbyqxmd.com/read/28943389/single-step-genome-wide-association-studies-based-on-genotyping-by-sequence-data-reveals-novel-loci-for-the-litter-traits-of-domestic-pigs
#8
Pingxian Wu, Qiang Yang, Kai Wang, Jie Zhou, Jideng Ma, Qianzhi Tang, Long Jin, Weihang Xiao, Anan Jiang, Yanzhi Jiang, Li Zhu, Xuewei Li, Guoqing Tang
In this study, data genotyping by sequence (GBS) was used to perform single step GWAS (ssGWAS) to identify SNPs associated with the litter traits in domestic pigs and search for candidate genes in the region of significant SNPs. After quality control, 167,355 high-quality SNPs from 532 pigs were obtained. Phenotypic traits on 2112 gilt litters from 532 pigs were recorded including total number born (TNB), number born alive (NBA), and litter weight born alive (LWB). A single-step genomic BLUP approach (ssGBLUP) was used to implement the genome-wide association analysis at a 5% genome-wide significance level...
September 21, 2017: Genomics
https://www.readbyqxmd.com/read/28943344/polymorphisms-of-the-folate-metabolizing-enzymes-association-with-sle-susceptibility-and-in-silico-analysis
#9
Saeedeh Salimi, Farshid Keshavarzi, Abbas Mohammadpour-Gharehbagh, Mahdieh Moodi, Mahdieh Mousavi, Mohammad Karimian, Mahnaz Sandoughi
Systemic lupus erythematosus (SLE) is a typical autoimmune disorder with multiple organ involvement and unknown etiology. It has been shown that polymorphic variants of the genes encoding key enzymes of folate and methionine metabolism may influence DNA methylation. Genomic DNA was extracted from blood samples of 150 SLE patients and 160 controls, matching age, sex, and ethnicity. MTHFR rs1801133C>T and MTR rs1805087A>G polymorphisms were genotyped by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method...
September 21, 2017: Gene
https://www.readbyqxmd.com/read/28943335/single-nucleotide-polymorphism-relevance-learning-with-random-forests-for-type-2-diabetes-risk-prediction
#10
Beatriz López, Ferran Torrent-Fontbona, Ramón Viñas, José Manuel Fernández-Real
OBJECTIVE: The use of artificial intelligence techniques to find out which Single Nucleotide Polymorphisms (SNPs) promote the development of a disease is one of the features of medical research, as such techniques may potentially aid early diagnosis and help in the prescription of preventive measures. In particular, the aim is to help physicians to identify the relevant SNPs related to Type 2 diabetes, and to build a decision-support tool for risk prediction. METHODS: We use the Random Forest (RF) technique in order to search for the most important attributes (SNPs) related to diabetes, giving a weight (degree of importance), ranging between 0 and 1, to each attribute...
September 21, 2017: Artificial Intelligence in Medicine
https://www.readbyqxmd.com/read/28942459/novel-and-major-qtl-for-branch-angle-detected-by-using-dh-population-from-an-exotic-introgression-in-rapeseed-brassica-napus-l
#11
Yusen Shen, Yi Yang, Ensheng Xu, Xianhong Ge, Yang Xiang, Zaiyun Li
A high-density SNP map was constructed and several novel QTL for branch angle across six environments in Brassica napus were identified. Branch angle is a major determinant for the ideotype of a plant, while the mechanisms underlying this trait in Brassica napus remain elusive. Herein, we developed one doubled haploid population from a cross involving one Capsella bursa-pastoris derived B. napus intertribal introgression line with the compressed branches and wooden stems, and constructed a high-density SNP map covering the genetic distance of 2242...
September 23, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28942153/the-absence-of-an-association-between-interleukin-1%C3%AE-gene-polymorphisms-and-recurrent-aphthous-stomatitis-ras
#12
Zuzanna Ślebioda, Anna Kowalska, Marta Rozmiarek, Ewa Krawiecka, Elżbieta Szponar, Barbara Dorocka-Bobkowska
OBJECTIVES: Recurrent aphthous stomatitis (RAS) is a chronic, ulcerative disease with a probable polygenic mode of inheritance and complex etiology with a strong immunological background. The aim of the present study was to determine the possible association between two single nucleotide polymorphisms (SNPs) of the IL-1β gene: IL-1β-511 T>C (rs16944) and IL-1β+3954C>T (rs1143634) and RAS susceptibility in a moderately large group of patients. DESIGN: One hundred and four patients with minor, major and herpetiform RAS and 75 healthy volunteers were genotyped at IL-1β-511 T>C (rs16944) and IL-1β+3954C>T (rs1143634) using the PCR-RFLP approach...
September 19, 2017: Archives of Oral Biology
https://www.readbyqxmd.com/read/28942111/open-source-software-euroformix-can-be-used-to-analyse-complex-snp-mixtures
#13
Øyvind Bleka, Mayra Eduardoff, Carla Santos, Chris Phillips, Walther Parson, Peter Gill
A series of two- and three-person mixtures of varying dilutions were prepared and analysed with Life Technologies' HID-Ion AmpliSeq™ Identity Panel v2.2 using the Ion PGM™ massively parallel sequencing (MPS) system. From this panel we used 134 autosomal SNPs. Using the reference samples of three donors, we evaluated the strength of evidence with likelihood ratio (LR) calculations using the open-source quantitative EuroForMix program and compared the results with a previous study using a qualitative software (LRmix)...
August 18, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28941036/association-of-donor-sumo4-rs237025-genetic-variant-with-tacrolimus-elimination-in-the-early-period-after-liver-transplantation
#14
Tao Zhang, Yuan Liu, Rong Zeng, Qi Ling, Peihao Wen, Junwei Fan, Zhihai Peng
BACKGROUNDS & AIMS: Individualized tacrolimus treatment can improve drug safety and efficacy. In this study, we aimed to investigate the association of donor and recipient small ubiquitin-like modifier 4 (SUMO4) rs237025 polymorphisms with tacrolimus elimination and the potential mechanism. METHODS: A total of 297 liver transplant patients were enrolled in the study. CYP3A5 rs776746 and SUMO4 rs237025 were genotyped using TaqMan SNPs assays. The activity of nuclear factor-kB (NF-kB) was evaluated by luciferase assay...
September 21, 2017: Liver International: Official Journal of the International Association for the Study of the Liver
https://www.readbyqxmd.com/read/28940904/genotyping-of-the-abcg2-gene-using-matrix-associated-laser-desorption-ionisation-time-of-flight-mass-spectrometry
#15
M Tanaka, I Kamada, J Takahashi, T Kimura, Y Tani
OBJECTIVES: The aim of this study was to evaluate the applicability of genotyping of the ABCG2 gene using MALDI-TOF MS and to estimate the allele frequency in the Japanese population. BACKGROUND: Jr (a-) phenotype has a prevalence of approximately 0·05% among Japanese blood donors; DNA-based genotyping was conducted to investigate the molecular basis of the Jr (a-) phenotype along with serological typing. To detect all SNPs of the ABCG2 gene, a high-throughput SNP genotyping platform is needed...
September 21, 2017: Transfusion Medicine
https://www.readbyqxmd.com/read/28940847/genetic-mapping-using-1-4m-snp-array-refined-loci-for-fatty-acid-composition-traits-in-chinese-erhualian-and-bamaxiang-pigs
#16
J Zhang, Y Zhang, H Gong, L Cui, T Huang, H Ai, J Ren, L Huang, B Yang
Chinese indigenous pigs display marked genetic and phenotypic differences compared with western commercial pigs. In this study, we tested the association between 660K SNPs and longissimus muscle fatty acid composition traits in Chinese Erhualian (n = 331) and Bamaxiang (n = 315) pigs based on a customized 1.4 million SNP array. We identified a total of 64 significant associations for 20 fatty acid composition traits at the p-value threshold of 1 × 10(-6) among which 42 associations in low linkage disequilibrium (r(2 ) < ...
September 20, 2017: Journal of Animal Breeding and Genetics, Zeitschrift Für Tierzüchtung und Züchtungsbiologie
https://www.readbyqxmd.com/read/28940489/polymorphisms-in-homologous-recombination-repair-genes-and-the-risk-and-survival-of-breast-cancer
#17
Yu-Huang Liao, Jun-Ting Ren, Wei Zhang, Zheng-Zheng Zhang, Ying Lin, Feng-Xi Su, Wei-Hua Jia, Lu-Ying Tang, Ze-Fang Ren
BACKGROUND: IgA antibody of Epstein-Barr virus (EBV) was found to associate with breast cancer, while the IgA positivity was related to a series of genetic markers in the genes of homologous recombination repair system (HRRs). We then assessed the associations of the polymorphisms in HRR genes with the risk and survival of breast cancer. MATERIALS AND METHODS: A case-control study was conducted with 1551 BC cases and 1605 age-matched healthy controls between October 2008 and March 2012 in the Guangzhou Breast Cancer Study (GZBCS), China, and the case population were followed up until January 31 2016...
September 23, 2017: Journal of Gene Medicine
https://www.readbyqxmd.com/read/28940218/genetic-and-clinical-factors-are-associated-with-statin-related-myotoxicity-of-moderate-severity-a-case-control-study
#18
Nur Salwani Bakar, Dermot Neely, Peter Avery, Colin Brown, Ann K Daly, Farhad Kamali
We evaluated the contribution of patient specific clinical and genetic factors to statin-related muscle toxicity (SRM) without significant creatine kinase elevation (125 cases related to simvastatin or atorvastatin and 481 controls). The association between 12 SNPs in nine candidate genes and clinical factors with SRM was evaluated. Of the 12 SNPs genotyped, only rs4149056 in SLCO1B1 was associated with SRM in univariate analysis (with any statin, OR=1.73, 95% CI= 1.14-2.62, P = 0.010) and this association was influenced by sex (P= 0...
September 22, 2017: Clinical Pharmacology and Therapeutics
https://www.readbyqxmd.com/read/28939865/a-replication-study-of-genetic-risk-loci-for-ischemic-stroke-in-a-dutch-population-a-case-control-study
#19
Allard J Hauer, Sara L Pulit, Leonard H van den Berg, Paul I W de Bakker, Jan H Veldink, Ynte M Ruigrok
We aimed to replicate reported associations of 10 SNPs at eight distinct loci with overall ischemic stroke (IS) and its subtypes in an independent cohort of Dutch IS patients. We included 1,375 IS patients enrolled in a prospective multicenter hospital-based cohort in the Netherlands, and 1,533 population-level controls of Dutch descent. We tested these SNPs for association with overall IS and its subtypes (large artery atherosclerosis, small vessel disease and cardioembolic stroke (CE), as classified by TOAST) using an additive multivariable logistic regression model, adjusting for age and sex...
September 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28939587/expression-and-genetic-variation-in-neuroendocrine-signaling-pathways-in-lethal-and-nonlethal-prostate-cancer-among-men-diagnosed-with-localized-disease
#20
Donghao Lu, Jessica Carlsson, Kathryn L Penney, Sabina Davidsson, Swen-Olof Andersson, Lorelei A Mucci, Unnur Valdimarsdóttir, Ove Andrén, Fang Fang, Katja Fall
BACKGROUND: Recent data suggest that neuroendocrine signaling pathways may play a role in the progression of prostate cancer, particularly for early-stage disease. We aimed to explore whether expression of selected genes in the adrenergic, serotoninergic, glucocorticoid, and dopaminergic pathways differs in prostate tumor tissue from men with lethal disease compared to men with nonlethal disease. METHODS: Based on the Swedish Watchful Waiting Cohort, we included 511 men diagnosed with incidental prostate cancer through TURP during 1977-1998 with follow-up up to 30 years...
September 22, 2017: Cancer Epidemiology, Biomarkers & Prevention
keyword
keyword
84203
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"