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https://www.readbyqxmd.com/read/28340274/regularized-quantile-regression-applied-to-genome-enabled-prediction-of-quantitative-traits
#1
M Nascimento, F F E Silva, M D V de Resende, C D Cruz, A C C Nascimento, J M S Viana, C F Azevedo, L M A Barroso
Genomic selection (GS) is a variant of marker-assisted selection, in which genetic markers covering the whole genome predict individual genetic merits for breeding. GS increases the accuracy of breeding values (BV) prediction. Although a variety of statistical models have been proposed to estimate BV in GS, few methodologies have examined statistical challenges based on non-normal phenotypic distributions, e.g., skewed distributions. Traditional GS models estimate changes in the phenotype distribution mean, i...
March 22, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28340161/organizational-benchmarks-for-test-utilization-performance-an-example-based-on-positivity-rates-for-genetic-tests
#2
Joseph Rudolf, Brian R Jackson, Andrew R Wilson, Kristi J Smock, Robert L Schmidt
Objectives: Health care organizations are under increasing pressure to deliver value by improving test utilization management. Many factors, including organizational factors, could affect utilization performance. Past research has focused on the impact of specific interventions in single organizations. The impact of organizational factors is unknown. The objective of this study is to determine whether testing patterns are subject to organizational effects, ie, are utilization patterns for individual tests correlated within organizations...
March 15, 2017: American Journal of Clinical Pathology
https://www.readbyqxmd.com/read/28339748/genotype-based-gene-signature-of-glioma-risk
#3
Yen-Tsung Huang, Yi Zhang, Zhijin Wu, Dominique S Michaud
Background.: Glioma accounts for 80% of malignant brain tumors, but its etiologic determinants remain elusive. Despite genetic susceptibility loci identified by genome-wide association study (GWAS), the agnostic approach leaves open the possibility that other susceptibility genes remain to be discovered. Here we conduct a gene-centric integrative GWAS (iGWAS) of glioma risk that combines transcriptomics and genetics. Methods.: We synthesized a brain transcriptomics dataset (n = 354), a GWAS dataset (n = 4203), and an advanced glioma tumor transcriptomic dataset (n = 483) to conduct an iGWAS...
February 22, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/28335376/genetic-polymorphisms-contribute-to-the-individual-variations-of-imatinib-mesylate-plasma-levels-and-adverse-reactions-in-chinese-gist-patients
#4
Jing Liu, Zhiyu Chen, Hanmei Chen, Yingyong Hou, Weiqi Lu, Junyi He, Hanxing Tong, Yuhong Zhou, Weimin Cai
Imatinib mesylate (IM) has dramatically improved the outcomes of gastrointestinal stromal tumor (GIST) patients. However, the clinical responses of IM may considerably vary among single individuals. This study aimed to investigate the influences of genetic polymorphisms of drug-metabolizing enzyme (CYP3A4), transporters (ABCB1, ABCG2), and nuclear receptor (Pregnane X Receptor (PXR, encoded by NR1I2)) on IM plasma levels and related adverse reactions in Chinese GIST patients. A total of 68 Chinese GIST patients who have received IM 300-600 mg/day were genotyped for six single nucleotide polymorphisms (SNPs) (CYP3A4 rs2242480; ABCB1 rs1045642; ABCG2 rs2231137; NRI12 rs3814055, rs6785049, rs2276706), and the steady-state IM trough plasma concentrations were measured by a validated HPLC method...
March 13, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28335003/identification-of-genetic-variants-affecting-vitamin-d-receptor-binding-and-associations-with-autoimmune-disease
#5
Giuseppe Gallone, Wilfried Haerty, Giulio Disanto, Sreeram V Ramagopalan, Chris P Ponting, Antonio J Berlanga-Taylor
Large numbers of statistically significant associations between sentinel SNPs and case-control status have been replicated by genome-wide association studies. Nevertheless, few underlying molecular mechanisms of complex disease are currently known. We investigated whether variation in binding of a transcription factor, the vitamin D receptor (VDR) whose activating ligand vitamin D has been proposed as a modifiable factor in multiple disorders, could explain any of these associations. VDR modifies gene expression by binding DNA as a heterodimer with the Retinoid X receptor (RXR)...
March 9, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334822/posigene-automated-and-easy-to-use-pipeline-for-genome-wide-detection-of-positively-selected-genes
#6
Arne Sahm, Martin Bens, Matthias Platzer, Karol Szafranski
Many comparative genomics studies aim to find the genetic basis of species-specific phenotypic traits. A prevailing strategy is to search genome-wide for genes that evolved under positive selection based on the non-synonymous to synonymous substitution ratio. However, incongruent results largely due to high false positive rates indicate the need for standardization of quality criteria and software tools. Main challenges are the ortholog and isoform assignment, the high sensitivity of the statistical models to alignment errors and the imperative to parallelize large parts of the software...
March 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334803/statistical-analysis-of-genetic-interactions-in-tn-seq-data
#7
Michael A DeJesus, Subhalaxmi Nambi, Clare M Smith, Richard E Baker, Christopher M Sassetti, Thomas R Ioerger
Tn-Seq is an experimental method for probing the functions of genes through construction of complex random transposon insertion libraries and quantification of each mutant's abundance using next-generation sequencing. An important emerging application of Tn-Seq is for identifying genetic interactions, which involves comparing Tn mutant libraries generated in different genetic backgrounds (e.g. wild-type strain versus knockout strain). Several analytical methods have been proposed for analyzing Tn-Seq data to identify genetic interactions, including estimating relative fitness ratios and fitting a generalized linear model...
February 22, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334355/a-zoom-focus-algorithm-zfa-to-locate-the-optimal-testing-region-for-rare-variant-association-tests
#8
Maggie Haitian Wang, Haoyi Weng, Rui Sun, Jack Lee, William Ka Kei Wu, Ka Chun Chong, Benny Chung-Ying Zee
Motivation: Increasing amounts of whole exome or genome sequencing data present the challenge of analysing rare variants with extremely small minor allele frequencies. Various statistical tests have been proposed, which are specifically configured to increase power for rare variants by conducting the test within a certain bin, such as a gene or a pathway. However, a gene may contain from several to thousands of markers, and not all of them are related to the phenotype. Combining functional and non-functional variants in an arbitrary genomic region could impair the testing power...
March 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334312/efficient-inference-for-genetic-association-studies-with-multiple-outcomes
#9
Helene Ruffieux, Anthony C Davison, Jorg Hager, Irina Irincheeva
Combined inference for heterogeneous high-dimensional data is critical in modern biology, where clinical and various kinds of molecular data may be available from a single study. Classical genetic association studies regress a single clinical outcome on many genetic variants one by one, but there is an increasing demand for joint analysis of many molecular outcomes and genetic variants in order to unravel functional interactions. Unfortunately, most existing approaches to joint modeling are either too simplistic to be powerful or are impracticable for computational reasons...
March 16, 2017: Biostatistics
https://www.readbyqxmd.com/read/28334117/a-generalized-association-test-based-on-u-statistics
#10
Changshuai Wei, Qing Lu
Motivation: Second generation sequencing technologies are being increasingly used for genetic association studies, where the main research interest is to identify sets of genetic variants that contribute to various phenotypes. The phenotype can be univariate disease status, multivariate responses and even high-dimensional outcomes. Considering the genotype and phenotype as two complex objects, this also poses a general statistical problem of testing association between complex objects...
February 17, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334077/a-powerful-and-efficient-two-stage-method-for-detecting-gene-to-gene-interactions-in-gwas
#11
Jakub Pecanka, Marianne A Jonker, Zoltan Bochdanovits, Aad W Van Der Vaart
For over a decade functional gene-to-gene interaction (epistasis) has been suspected to be a determinant in the "missing heritability" of complex traits. However, searching for epistasis on the genome-wide scale has been challenging due to the prohibitively large number of tests which result in a serious loss of statistical power as well as computational challenges. In this article, we propose a two-stage method applicable to existing case-control data sets, which aims to lessen both of these problems by pre-assessing whether a candidate pair of genetic loci is involved in epistasis before it is actually tested for interaction with respect to a complex phenotype...
February 6, 2017: Biostatistics
https://www.readbyqxmd.com/read/28333527/reading-self-perceived-ability-enjoyment-and-achievement-a-genetically-informative-study-of-their-reciprocal-links-over-time
#12
Margherita Malanchini, Zhe Wang, Ivan Voronin, Victoria J Schenker, Robert Plomin, Stephen A Petrill, Yulia Kovas
Extant literature has established a consistent association between aspects of reading motivation, such as enjoyment and self-perceived ability, and reading achievement, in that more motivated readers are generally more skilled readers. However, the developmental etiology of this relation is yet to be investigated. The present study explores the development of the motivation-achievement association and its genetic and environmental underpinnings. Applying cross-lagged design in a sample of 13,825 twins, we examined the relative contribution of genetic and environmental factors to the association between reading enjoyment and self-perceived ability and reading achievement...
April 2017: Developmental Psychology
https://www.readbyqxmd.com/read/28333195/genome-wide-genetic-analyses-highlight-mitogen-activated-protein-kinase-mapk-signaling-in-the-pathogenesis-of-endometriosis
#13
Outi Uimari, Nilufer Rahmioglu, Dale R Nyholt, Katy Vincent, Stacey A Missmer, Christian Becker, Andrew P Morris, Grant W Montgomery, Krina T Zondervan
STUDY QUESTION: Do genome-wide association study (GWAS) data for endometriosis provide insight into novel biological pathways associated with its pathogenesis? SUMMARY ANSWER: GWAS analysis uncovered multiple pathways that are statistically enriched for genetic association signals, analysis of Stage A disease highlighted a novel variant in MAP3K4, while top pathways significantly associated with all endometriosis and Stage A disease included several mitogen-activated protein kinase (MAPK)-related pathways...
February 9, 2017: Human Reproduction
https://www.readbyqxmd.com/read/28332910/association-between-dietary-xanthophyll-lutein-and-zeaxanthin-intake-and-early-age-related-macular-degeneration-the-atherosclerosis-risk-in-communities-study
#14
Henry Lin, Julie A Mares, Michael J LaMonte, William E Brady, Michelle W Sahli, Ronald Klein, Barbara E K Klein, Jing Nie, Amy E Millen
PURPOSE: To examine the association between xanthophyll intake and prevalent early age-related macular degeneration (AMD) using data from the Atherosclerosis Risk in Communities Study (n = 10,295). Potential effect modification by genetic polymorphisms and biomarkers of high-density lipoprotein (HDL) metabolism was explored. METHODS: Xanthophyll intake was assessed at visit 1 (1987-1989) using food frequency questionnaires. Prevalent early AMD was assessed at visit 3 (1993-1995) via retinal photographs...
March 23, 2017: Ophthalmic Epidemiology
https://www.readbyqxmd.com/read/28332719/rs7968606-polymorphism-of-anks1b-is-associated-with-improvement-in-the-panss-general-score-of-schizophrenia-caused-by-amisulpride
#15
Seung-Gul Kang, Ik-Seung Chee, Kwanghun Lee, Jonghun Lee
A recent genome-wide pharmacogenomics study showed that the rs7968606 single-nucleotide polymorphism (SNP) of the ankyrin repeat and sterile alpha motif domain-containing protein 1B (ANKS1B) gene approached the threshold of statistical significance. The aim of this study was to determine the association between the rs7968606 SNP of ANKS1B and the treatment response to amisulpride in schizophrenia patients. In total, 154 participants were enrolled from six university hospitals in Korea. All the subjects were interviewed before and after 6 weeks of amisulpride treatment with the aid of the positive and negative syndrome scale and the clinical global impression-severity scale...
March 23, 2017: Human Psychopharmacology
https://www.readbyqxmd.com/read/28332560/evaluating-genetic-susceptibility-to-staphylococcus-aureus-bacteremia-in-african-americans-using-admixture-mapping
#16
D D Cyr, A S Allen, G-J Du, F Ruffin, C Adams, J T Thaden, S A Maskarinec, M Souli, S Guo, D M Dykxhoorn, W K Scott, V G Fowler
The incidence of Staphylococcus aureus bacteremia (SAB) is significantly higher in African American (AA) than in European-descended populations. We used admixture mapping (AM) to test the hypothesis that genomic variations with different frequencies in European and African ancestral genomes influence susceptibility to SAB in AAs. A total of 565 adult AAs (390 cases with SAB; 175 age-matched controls) were genotyped for AM analysis. A case-only admixture score and a mixed χ(2)(1df) score (MIX) to jointly evaluate both single-nucleotide polymorphism (SNP) and admixture association (P<5...
March 23, 2017: Genes and Immunity
https://www.readbyqxmd.com/read/28332369/gender-specific-associations-between-chgb-genetic-variants-and-schizophrenia-in-a-korean-population
#17
Joong Gon Shin, Jeong Hyun Kim, Chul Soo Park, Bong Jo Kim, Jae Won Kim, Ihn Geun Choi, Jaeuk Hwang, Hyoung Doo Shin, Sung Il Woo
PURPOSE: Schizophrenia is a devastating mental disorder and is known to be affected by genetic factors. The chromogranin B (CHGB), a member of the chromogranin gene family, has been proposed as a candidate gene associated with the risk of schizophrenia. The secretory pathway for peptide hormones and neuropeptides in the brain is regulated by chromogranin proteins. The aim of this study was to investigate the potential associations between genetic variants of CHGB and schizophrenia susceptibility...
May 2017: Yonsei Medical Journal
https://www.readbyqxmd.com/read/28332201/identification-of-novel-variants-in-hla-class-ii-region-related-to-hla-dpb1-expression-and-disease-progression-in-patients-with-chronic-hepatitis-c
#18
Katsushi Hiramatsu, Hidetaka Matsuda, Tomoyuki Nemoto, Takuto Nosaka, Yasushi Saito, Tatsushi Naito, Kazuto Takahashi, Kazuya Ofuji, Masahiro Ohtani, Hiroyuki Suto, Toshihiro Yasuda, Yukio Hida, Hideki Kimura, Yoshihiro Soya, Yasunari Nakamoto
BACKGROUND: Recent genome-wide studies have demonstrated that HLA class II gene may play an important role in viral hepatitis. We studied genetic polymorphism and RNA expression of HLA class II genes in HCV-related liver diseases. METHODS: The study was performed in groups consisting of 24 patients with HCV-related liver disease (12 of persistent normal ALT: PNALT group and 12 of advanced liver disease: ALD group) and 26 patients without HCV infection (control group)...
March 22, 2017: Journal of Medical Virology
https://www.readbyqxmd.com/read/28332164/polymorphism-in-xrcc1-gene-modulates-survival-and-clinical-outcomes-of-advanced-north-indian-lung-cancer-patients-treated-with-platinum-based-doublet-chemotherapy
#19
Amrita Singh, Navneet Singh, Digambar Behera, Siddharth Sharma
Survival in lung cancer patients is genetically determined. Single nucleotide polymorphisms (SNPs) in DNA repair genes are observed to play a critical role in survival as DNA repair itself can behave as double-edged sword. We aim to explore the association of DNA repair gene XRCC1 in survival and clinical outcomes for North Indian population. Blood sample from patients diagnosed with lung cancer was taken. DNA isolation and genotyping were performed for the SNPs of XRCC1 gene. Further, patients were followed up through telephonic conversation after every 2 months for 3 years...
April 2017: Medical Oncology
https://www.readbyqxmd.com/read/28331852/effects-of-fmo3-polymorphisms-on-pharmacokinetics-of-sulindac-in-chinese-healthy-male-volunteers
#20
Yong-Jun Tang, Kai Hu, Wei-Hua Huang, Chong-Zhi Wang, Zhi Liu, Yao Chen, Dong-Sheng Ouyang, Zhi-Rong Tan, Hong-Hao Zhou, Chun-Su Yuan
Sulindac is a nonsteroidal anti-inflammatory drug, which is clinically used for the ailments of various inflammations. This study investigated the allele frequencies of FMO3 E158K and E308G and evaluated the influences of these two genetic polymorphisms on the pharmacokinetics of sulindac and its metabolites in Chinese healthy male volunteers. Eight FMO3 wild-type (FMO3 HHDD) subjects and seven FMO3 homozygotes E158K and E308G mutant (FMO3 hhdd) subjects were recruited from 247 healthy male volunteers genotyped by PCR-RFLP method...
2017: BioMed Research International
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