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https://www.readbyqxmd.com/read/28930911/an-enrichment-strategy-yields-seven-novel-single-nucleotide-polymorphisms-associated-with-mortality-and-altered-th17-responses-following-blunt-trauma
#1
Lukas Schimunek, Rami A Namas, Jinling Yin, Dongmei Liu, Derek Barclay, Fayten El-Dehaibi, Andrew Abboud, Haley Lindberg, Ruben Zamora, R Billiar Timothy, Yoram Vodovotz
Trauma is the leading cause of death worldwide for individuals under the age of 55. Interpatient genomic differences, in the form of candidate single nucleotide polymorphisms (SNPs), have been associated previously with adverse outcomes after trauma. However, the utility of these SNPs to predict outcomes based on a meaningful endpoint such as survival is as yet undefined. We hypothesized that specific SNP haplotypes could segregate trauma survivors from non-survivors. Genomic DNA samples were obtained from 453 blunt trauma patients, for whom complete daily clinical and biomarker data were available for 397...
September 19, 2017: Shock
https://www.readbyqxmd.com/read/28928973/prospective-replication-study-implicates-the-catechol-o-methyltransferase-val-158-met-polymorphism-as-a-biomarker-for-the-response-to-morphine-in-patients-with-cancer
#2
Hiromichi Matsuoka, Chihiro Makimura, Atsuko Koyama, Yoshihiko Fujita, Junji Tsurutani, Kiyohiro Sakai, Ryo Sakamoto, Kazuto Nishio, Kazuhiko Nakagawa
Genetic differences in humans cause clinical difficulties in opioid treatment. Previous studies indicate that a single nucleotide polymorphism in the catechol-O-methyltransferase (COMT) gene (rs4680; p.Val(158)Met) may present as a predictive biomarker for the response to morphine treatment. In our previous pilot exploratory study, patients with a G/G genotype were demonstrated to require a higher dose of morphine, compared with patients with A/A and A/G genotypes. In the present study, the aim was to replicate the findings in an independent cohort of opioid-treatment-naïve patients exhibiting various types of cancer...
October 2017: Biomedical Reports
https://www.readbyqxmd.com/read/28928763/comparative-mapping-and-candidate-gene-analysis-of-ssiia-associated-with-grain-amylopectin-content-in-barley-hordeum-vulgare-l
#3
Xiangyun Fan, Juan Zhu, Wenbin Dong, Yuandong Sun, Chao Lv, Baojian Guo, Rugen Xu
Amylopectin concentration in barley endosperm has important effects on grain quality and end-use. In this study, quantitative trait locus (QTL) analysis together with genome-wide association studies (GWAS) were performed to identify markers linked to grain amylopectin content respectively using a doubled haploid (DH) population of 178 lines and a collection of 185 diverse barley germplasms both genotyped by genotyping-by-sequencing (GBS). A stable QTL on chromosome 7H and 11 associated single nucleotide polymorphisms (SNPs) were detected...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28928742/a-streamlined-approach-to-antibody-novel-germline-allele-prediction-and-validation
#4
Ben S Wendel, Chenfeng He, Peter D Crompton, Susan K Pierce, Ning Jiang
Advancements in high-throughput sequencing and molecular identifier-based error correction have opened the door to antibody repertoire sequencing with single mutation precision, increasing both the breadth and depth of immune response characterization. However, improvements in sequencing technology cannot resolve one key aspect of antibody repertoire sequencing accuracy: the possibility of undocumented novel germline alleles. Somatic hypermutation (SHM) calling requires a reference germline sequence, and the antibody variable region gene alleles collected by the IMGT database, although large in number, are not comprehensive...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28928439/polymorphisms-in-mica-but-not-in-depdc5-hcp5-or-pnpla3-are-associated-with-chronic-hepatitis-c-related-hepatocellular-carcinoma
#5
Hoang Hai, Akihiro Tamori, Le Thi Thanh Thuy, Kanako Yoshida, Atsushi Hagihara, Etsushi Kawamura, Sawako Uchida-Kobayashi, Hiroyasu Morikawa, Masaru Enomoto, Yoshiki Murakami, Norifumi Kawada
Recently, the MICA rs2596542 and DEPDC5 rs1012068 variants in Japanese individuals as well as the HCP5 rs2244546 and PNPLA3 rs738409 variants in European individuals have been found associated with hepatocellular carcinoma (HCC). The present study determined which single nucleotide polymorphism (SNP) is the most predictive for developing hepatitis C virus (HCV)-related HCC in a Japanese cohort. Of the 4 SNPs analysed, only the MICA genotypes were significantly associated with development of HCC (p = 0.0185)...
September 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28927471/a-vascular-endothelial-growth-factor-a-genetic-variant-is-associated-with-improved-ventricular-function-and-transplant-free-survival-after-surgery-for-non-syndromic-chd
#6
Constantine D Mavroudis, Daniel Seung Kim, Nancy Burnham, Alexandra H Morss, Jerry H Kim, Amber A Burt, David R Crosslin, Donna M McDonald-McGinn, Elaine H Zackai, Meryl S Cohen, Susan C Nicolson, Thomas L Spray, Ian B Stanaway, Deborah A Nickerson, Mark W Russell, Hakon Hakonarson, Gail P Jarvik, J William Gaynor
BACKGROUND: We have previously shown that the minor alleles of vascular endothelial growth factor A (VEGFA) single-nucleotide polymorphism rs833069 and superoxide dismutase 2 (SOD2) single-nucleotide polymorphism rs2758331 are both associated with improved transplant-free survival after surgery for CHD in infants, but the underlying mechanisms are unknown. We hypothesised that one or both of these minor alleles are associated with better systemic ventricular function, resulting in improved survival...
September 20, 2017: Cardiology in the Young
https://www.readbyqxmd.com/read/28926576/receptor-for-advanced-glycation-end-products-and-world-trade-center-particulate-induced-lung-function-loss-a-case-cohort-study-and-murine-model-of-acute-particulate-exposure
#7
Erin J Caraher, Sophia Kwon, Syed H Haider, George Crowley, Audrey Lee, Minah Ebrahim, Liqun Zhang, Lung-Chi Chen, Terry Gordon, Mengling Liu, David J Prezant, Ann Marie Schmidt, Anna Nolan
World Trade Center-particulate matter(WTC-PM) exposure and metabolic-risk are associated with WTC-Lung Injury(WTC-LI). The receptor for advanced glycation end-products (RAGE) is most highly expressed in the lung, mediates metabolic risk, and single-nucleotide polymorphisms at the AGER-locus predict forced expiratory volume(FEV). Our objectives were to test the hypotheses that RAGE is a biomarker of WTC-LI in the FDNY-cohort and that loss of RAGE in a murine model would protect against acute PM-induced lung disease...
2017: PloS One
https://www.readbyqxmd.com/read/28926565/a-snp-panel-and-online-tool-for-checking-genotype-concordance-through-comparing-qr-codes
#8
Yonghong Du, Joshua S Martin, John McGee, Yuchen Yang, Eric Yi Liu, Yingrui Sun, Matthias Geihs, Xuejun Kong, Eric Lingfeng Zhou, Yun Li, Jie Huang
In the current precision medicine era, more and more samples get genotyped and sequenced. Both researchers and commercial companies expend significant time and resources to reduce the error rate. However, it has been reported that there is a sample mix-up rate of between 0.1% and 1%, not to mention the possibly higher mix-up rate during the down-stream genetic reporting processes. Even on the low end of this estimate, this translates to a significant number of mislabeled samples, especially over the projected one billion people that will be sequenced within the next decade...
2017: PloS One
https://www.readbyqxmd.com/read/28926398/association-of-a-3-untranslated-region-polymorphism-in-pcsk9-with-hiv-viral-load-and-cd4-levels-in-hiv-hepatitis-c-virus-co-infected-women
#9
Mark H Kuniholm, Hua Liang, Kathryn Anastos, Deborah Gustafson, Seble Kassaye, Marek Nowicki, Beverly E Sha, Emilia J Pawlowski, Stephen J Gange, Bradley E Aouizerat, Tatiana Pushkarsky, Michael I Bukrinsky, Vinayaka R Prasad
OBJECTIVE: To assess variation in genes that regulate cholesterol metabolism in relation to the natural history of HIV infection. DESIGN: Cross-sectional and longitudinal analysis of the Women's Interagency HIV Study (WIHS). METHODS: We examined 2,050 single nucleotide polymorphisms (SNPs) in 19 genes known to regulate cholesterol metabolism in relation to HIV viral load and CD4 T cell levels in a multiracial cohort of 1,066 antiretroviral therapy (ART) naïve women...
September 18, 2017: AIDS
https://www.readbyqxmd.com/read/28921602/human-leukocyte-antigen-variants-and-risk-of-hepatocellular-carcinoma-modified-by-hcv-genotypes-a-genome-wide-association-study
#10
Mei-Hsuan Lee, Yu-Han Huang, Hsuan-Yu Chen, Charles Seik-Soon Khor, Ya-Hsuan Chang, Yu-Ju Lin, Chin-Lan Jen, Sheng-Nan Lu, Hwai-I Yang, Nao Nishida, Masaya Sugiyama, Masashi Mizokami, Yong Yuan, Gibert L'Italien, Katsushi Tokunaga, Chien-Jen Chen
BACKGROUND & AIMS: We conducted a genome-wide association study (GWAS) to discover genetic variants associated with hepatitis C virus (HCV)-related hepatocellular carcinoma (HCC). METHODS: We genotyped 502 HCC cases and 749 non-HCC controls by using the Axiom(TM) -CHB genome-wide array. After identifying single nucleotide polymorphism (SNP) cluster located in the human leukocyte antigen region which were potentially associated with HCC, HLA-DQB1 genotyping was performed to analyze 994 anti-HCV seropositives collected in the period of 1991-2013 in a community-based cohort for evaluating long-term predictability of HLA variants for identifying the risk of HCC...
September 16, 2017: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/28920408/characterization-of-gene-expression-and-genetic-variation-of-horse-errfi1-in-thoroughbreds
#11
Jae-Young Choi, Hyun-Jun Jang, Jeong-Woong Park, Jae-Don Oh, Donghyun Shin, Nam Young Kim, Jin Hyeog Oh, Ki-Duk Song, Byung-Wook Cho
Objective: This study aimed to test the expression patterns of ERBB receptor feedback inhibitor 1 (ERRFI1) before and after exercise and the association of non-synonymous single-nucleotide polymorphisms (nsSNPs) of horse ERRFI1 with racing traits in Thoroughbreds. Methods: We performed bioinformatics and gene expression analyses for horse ERRFI1. Transcription factor (TF) binding sites in the 5'-regulatory region of this gene were identified through PROMO. A general linear model (GLM) was used to detect the association between the nsSNP (LOC42830758 A to G) and race performance...
September 18, 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28918577/microarray-based-snp-genotyping-to-identify-genetic-risk-factors-of-triple-negative-breast-cancer-tnbc-in-south-indian-population
#12
M Aravind Kumar, Vineeta Singh, Shaik Mohammad Naushad, Uday Shanker, M Lakshmi Narasu
In the view of aggressive nature of Triple-Negative Breast cancer (TNBC) due to the lack of receptors (ER, PR, HER2) and high incidence of drug resistance associated with it, a case-control association study was conducted to identify the contributing genetic risk factors for Triple-negative breast cancer (TNBC). A total of 30 TNBC patients and 50 age and gender-matched controls of Indian origin were screened for 9,00,000 SNP markers using microarray-based SNP genotyping approach. The initial PLINK association analysis (p < 0...
September 16, 2017: Molecular and Cellular Biochemistry
https://www.readbyqxmd.com/read/28916649/genomic-prediction-within-and-across-biparental-families-means-and-variances-of-prediction-accuracy-and-usefulness-of-deterministic-equations
#13
Pascal Schopp, Dominik Müller, Yvonne C J Wientjes, Albrecht E Melchinger
A major application of genomic prediction (GP) in plant breeding is the identification of superior inbred lines within families derived from biparental crosses. When models for various traits were trained within related or unrelated biparental families (BPFs), experimental studies found substantial variation in prediction accuracy (PA), but little is known about the underlying factors. We used SNP marker genotypes of inbred lines from either elite germplasm or landraces of maize (Zea mays L.) as parents to generate in silico 300 BPFs of doubled-haploid lines...
September 15, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28913866/conversion-of-array-based-single-nucleotide-polymorphic-markers-for-use-in-targeted-genotyping-by-sequencing-in-hexaploid-wheat-triticum-aestivum
#14
Amanda J Burridge, Paul A Wilkinson, Mark O Winfield, Gary L A Barker, Alexandra M Allen, Jane A Coghill, Christy Waterfall, Keith J Edwards
Wheat breeders and academics alike use Single Nucleotide Polymorphisms (SNPs) as molecular markers to characterise regions of interest within the hexaploid wheat genome. A number of SNP-based genotyping platforms are available and their utility depends upon factors such as the available technologies, number of data points required, budgets and the technical expertise required. Unfortunately, markers can rarely be exchanged between existing and newly developed platforms, meaning that previously generated data cannot be compared, or combined, with more recently generated datasets...
September 15, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28911016/quantifying-rooting-at-depth-in-a-wheat-doubled-haploid-population-with-introgression-from-wild-emmer
#15
Christina K Clarke, Peter J Gregory, Martin Lukac, Amanda J Burridge, Alexandra M Allen, Keith J Edwards, Mike J Gooding
Background and Aims: The genetic basis of increased rooting below the plough layer, post-anthesis in the field, of an elite wheat line (Triticum aestivum 'Shamrock') with recent introgression from wild emmer (T. dicoccoides), is investigated. Shamrock has a non-glaucous canopy phenotype mapped to the short arm of chromosome 2B (2BS), derived from the wild emmer. A secondary aim was to determine whether genetic effects found in the field could have been predicted by other assessment methods...
September 1, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28906356/shared-polymorphisms-and-modifiable-behavior-factors-for-myocardial-infarction-and-high-cholesterol-in-a-retrospective-population-study
#16
Yulan Liang, Arpad Kelemen
Genetic and environmental (behavior, clinical, and demographic) factors are associated with increased risks of both myocardial infarction (MI) and high cholesterol (HC). It is known that HC is major risk factor that may cause MI. However, whether there are common single nucleotide polymorphism (SNPs) associated with both MI and HC is not firmly established, and whether there are modulate and modified effects (interactions of genetic and known environmental factors) on either HC or MI, and whether these joint effects improve the predictions of MI, is understudied...
September 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28904993/abnormalities-of-signal-transduction-networks-in-chronic-schizophrenia
#17
Jennifer L McGuire, Erica A Depasquale, Adam J Funk, Sinead M O'Donnovan, Kathryn Hasselfeld, Shruti Marwaha, John H Hammond, Vahram Hartounian, James H Meador-Woodruff, Jarek Meller, Robert E McCullumsmith
Schizophrenia is a serious neuropsychiatric disorder characterized by disruptions of brain cell metabolism, microstructure, and neurotransmission. All of these processes require coordination of multiple kinase-mediated signaling events. We hypothesize that imbalances in kinase activity propagate through an interconnected network of intracellular signaling with potential to simultaneously contribute to many or all of the observed deficits in schizophrenia. We established a workflow distinguishing schizophrenia-altered kinases in anterior cingulate cortex using a previously published kinome array data set...
2017: NPJ Schizophrenia
https://www.readbyqxmd.com/read/28904015/sasquatch-predicting-the-impact-of-regulatory-snps-on-transcription-factor-binding-from-cell-and-tissue-specific-dnase-footprints
#18
Ron Schwessinger, Maria C Suciu, Simon J McGowan, Jelena Telenius, Stephen Taylor, Doug R Higgs, Jim R Hughes
In the era of genome-wide association studies (GWAS) and personalized medicine, predicting the impact of single nucleotide polymorphisms (SNPs) in regulatory elements is an important goal. Current approaches to determine the potential of regulatory SNPs depend on inadequate knowledge of cell-specific DNA binding motifs. Here, we present Sasquatch, a new computational approach that uses DNase footprint data to estimate and visualize the effects of noncoding variants on transcription factor binding. Sasquatch performs a comprehensive k-mer-based analysis of DNase footprints to determine any k-mer's potential for protein binding in a specific cell type and how this may be changed by sequence variants...
September 13, 2017: Genome Research
https://www.readbyqxmd.com/read/28902459/exome-sequences-of-multiplex-multigenerational-families-reveal-schizophrenia-risk-loci-with-potential-implications-for-neurocognitive-performance
#19
Mark Z Kos, Melanie A Carless, Juan Peralta, Joanne E Curran, Ellen E Quillen, Marcio Almeida, August Blackburn, Lucy Blondell, David R Roalf, Michael F Pogue-Geile, Ruben C Gur, Harald H H Göring, Vishwajit L Nimgaonkar, Raquel E Gur, Laura Almasy
Schizophrenia is a serious mental illness, involving disruptions in thought and behavior, with a worldwide prevalence of about one percent. Although highly heritable, much of the genetic liability of schizophrenia is yet to be explained. We searched for susceptibility loci in multiplex, multigenerational families affected by schizophrenia, targeting protein-altering variation with in silico predicted functional effects. Exome sequencing was performed on 136 samples from eight European-American families, including 23 individuals diagnosed with schizophrenia or schizoaffective disorder...
September 13, 2017: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
https://www.readbyqxmd.com/read/28901420/bioinformatics-analysis-of-genetic-variants-of-endoplasmic-reticulum-aminopeptidase-1-in-ankylosing-spondylitis
#20
Xiaoli Wang, Jie Ma, Jianbing Ma, Yurong Wen, Liesu Meng, Hao Yang, Rui Zhang, Dingjun Hao
According to the results of the first genome-wide association study of ankylosing spondylitis (AS), endoplasmic reticulum aminopeptidase 1 (ERAP1) may serve an important role. However, a number of case-control studies have not been able to replicate this result using the same genetic markers. In the present study, the role of common genetic variants of ERAP1 in AS was investigated using two-stage bioinformatics analysis. In the first stage, a classical meta-analysis was performed to assess AS susceptibility markers in ERAP1 using data from available published case-control association studies...
August 31, 2017: Molecular Medicine Reports
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