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https://www.readbyqxmd.com/read/28651097/population-and-performance-analyses-of-four-major-populations-with-illumina-s-fgx-forensic-genomics-system
#1
Jennifer D Churchill, Nicole M M Novroski, Jonathan L King, Lay Hong Seah, Bruce Budowle
The MiSeq FGx Forensic Genomics System (Illumina) enables amplification and massively parallel sequencing of 59 STRs, 94 identity informative SNPs, 54 ancestry informative SNPs, and 24 phenotypic informative SNPs. Allele frequency and population statistics data were generated for the 172 SNP loci included in this panel on four major population groups (Chinese, African Americans, US Caucasians, and Southwest Hispanics). Single-locus and combined random match probability values were generated for the identity informative SNPs...
June 17, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28651015/acute-rejection-after-kidney-transplantation-promotes-graft-fibrosis-with-elevated-adenosine-level-in-rat
#2
Mingliang Li, Yingbo Dai, Jun Lei, Jin Tang, Yihong Zhou, Bing Xia, Yang Xia, Guangming Yin
AIMS: Chronic allograft nephropathy is a worldwide issue with the major feature of progressive allograft fibrosis, eventually ending with graft loss. Adenosine has been demonstrated to play an important role in process of fibrosis. Our study aimed to investigate the relationship between adenosine and fibrosis in renal allograft acute rejection in rat. MATERIALS AND METHODS: Wistar rats and SD rats were selected as experimental animals. Our study designed two groups...
2017: PloS One
https://www.readbyqxmd.com/read/28650965/epigenetic-adaptation-of-the-placental-serotonin-transporter-gene-slc6a4-to-gestational-diabetes-mellitus
#3
Sofia Blazevic, Marina Horvaticek, Maja Kesic, Peter Zill, Dubravka Hranilovic, Marina Ivanisevic, Gernot Desoye, Jasminka Stefulj
We tested the hypothesis that gestational diabetes mellitus (GDM) alters the DNA methylation pattern of the fetal serotonin transporter gene (SLC6A4), and examined the functional relevance of DNA methylation for regulation of the SLC6A4 expression in the human placenta. The study included 50 mother-infant pairs. Eighteen mothers were diagnosed with GDM and 32 had normal glucose tolerance (NGT). All neonates were of normal birth weight and born at term by planned Cesarean section. DNA and RNA were isolated from samples of tissue collected from the fetal side of the placenta immediately after delivery...
2017: PloS One
https://www.readbyqxmd.com/read/28649647/moonshots-and-metastatic-disease-the-need-for-a-multi-faceted-approach-when-studying-atypical-responses
#4
REVIEW
Kristine De La Torre, Elly Cohen, Anne Loeser, Marc Hurlbert
Clinical research generally focuses on results involving a statistical mean with little attention in trial design to patients who respond considerably better or worse than average. Exploring the reasons underlying an "atypical response" will increase understanding of the mechanisms involved in cancer progression and treatment resistance, accelerate biomarker identification, and improve precision medicine by allowing clinicians to prospectively select optimal treatments. Based on our review, we suggest two ways to move this field forward...
2017: NPJ Breast Cancer
https://www.readbyqxmd.com/read/28648753/association-of-increased-genotypes-risk-for-bipolar-disorder-with-brain-white-matter-integrity-investigated-with-tract-based-spatial-statistics
#5
REVIEW
L Squarcina, J Houenou, A C Altamura, J Soares, P Brambilla
BACKGROUND: Diffusion tensor imaging (DTI) studies, which allow the in-vivo investigation of brain tissue integrity, have shown that bipolar disorder (BD) patients present signs of white matter dysconnectivity. In parallel, genome-wide association studies (GWAS) identified several risk genetic variants for BD. I METHODS: In this mini-review, we summarized DTI studies coupling tract-based spatial statistics (TBSS), a reliable technique exploring white matter axon bundles, and genetics in BD...
June 15, 2017: Journal of Affective Disorders
https://www.readbyqxmd.com/read/28648286/yeast-diversity-during-the-fermentation-of-andean-chicha-a-comparison-of-high-throughput-sequencing-and-culture-dependent-approaches
#6
Lucía M Mendoza, Alexander Neef, Graciela Vignolo, Carmela Belloch
Diversity and dynamics of yeasts associated with the fermentation of Argentinian maize-based beverage chicha was investigated. Samples taken at different stages from two chicha productions were analyzed by culture-dependent and culture-independent methods. Five hundred and ninety six yeasts were isolated by classical microbiological methods and 16 species identified by RFLPs and sequencing of D1/D2 26S rRNA gene. Genetic typing of isolates from the dominant species, Saccharomyces cerevisiae, by PCR of delta elements revealed up to 42 different patterns...
October 2017: Food Microbiology
https://www.readbyqxmd.com/read/28646625/fluctuating-effects-of-genetic-and-plastic-changes-in-body-mass-on-population-dynamics-in-a-large-herbivore
#7
Gabriel Pigeon, Thomas H G Ezard, Marco Festa-Bianchet, David W Coltman, Fanie Pelletier
Recent studies suggest that evolutionary changes can occur on a contemporary time scale. Hence, evolution can influence ecology and vice-versa. To understand the importance of eco-evolutionary dynamics in population dynamics, we must quantify the relative contribution of ecological and evolutionary changes to population growth and other ecological processes. To date, however, most eco-evolutionary dynamics studies have not partitioned the relative contribution of plastic and evolutionary changes in traits on population, community and ecosystem processes...
June 24, 2017: Ecology
https://www.readbyqxmd.com/read/28646506/three-lessons-for-genetic-toxicology-from-baseball-analytics
#8
EDITORIAL
Stephen D Dertinger
In many respects the evolution of baseball statistics mirrors advances made in the field of genetic toxicology. From its inception, baseball and statistics have been inextricably linked. Generations of players and fans have used a number of relatively simple measurements to describe team and individual player's current performance, as well as for historical record-keeping purposes. Over the years, baseball analytics has progressed in several important ways. Early advances were based on deriving more meaningful metrics from simpler forerunners...
June 24, 2017: Environmental and Molecular Mutagenesis
https://www.readbyqxmd.com/read/28645536/imaging-genetics-of-schizophrenia-in-the-post-gwas-era
#9
REVIEW
Ayla Arslan
Imaging genetics is a research methodology studying the effect of genetic variation on brain structure, function, behavior, and risk for psychopathology. Since the early 2000s, imaging genetics has been increasingly used in the research of schizophrenia (SZ). SZ is a severe mental disorder with no precise knowledge of its underlying neurobiology, however, new genetic and neurobiological data generate a climate for new avenues. The accumulating data of genome wide association studies (GWAS) continuously decode SZ risk genes...
June 20, 2017: Progress in Neuro-psychopharmacology & Biological Psychiatry
https://www.readbyqxmd.com/read/28644137/analyses-of-germline-variants-associated-with-ovarian-cancer-survival-identify-functional-candidates-at-the-1q22-and-19p12-outcome-loci
#10
Dylan M Glubb, Sharon E Johnatty, Michael C J Quinn, Tracy A O'Mara, Jonathan P Tyrer, Bo Gao, Peter A Fasching, Matthias W Beckmann, Diether Lambrechts, Ignace Vergote, Digna R Velez Edwards, Alicia Beeghly-Fadiel, Javier Benitez, Maria J Garcia, Marc T Goodman, Pamela J Thompson, Thilo Dörk, Matthias Dürst, Francesmary Modungo, Kirsten Moysich, Florian Heitz, Andreas du Bois, Jacobus Pfisterer, Peter Hillemanns, Beth Y Karlan, Jenny Lester, Ellen L Goode, Julie M Cunningham, Stacey J Winham, Melissa C Larson, Bryan M McCauley, Susanne Krüger Kjær, Allan Jensen, Joellen M Schildkraut, Andrew Berchuck, Daniel W Cramer, Kathryn L Terry, Helga B Salvesen, Line Bjorge, Penny M Webb, Peter Grant, Tanja Pejovic, Melissa Moffitt, Claus K Hogdall, Estrid Hogdall, James Paul, Rosalind Glasspool, Marcus Bernardini, Alicia Tone, David Huntsman, Michelle Woo, Aocs Group, Anna deFazio, Catherine J Kennedy, Paul D P Pharoah, Stuart MacGregor, Georgia Chenevix-Trench
We previously identified associations with ovarian cancer outcome at five genetic loci. To identify putatively causal genetic variants and target genes, we prioritized two ovarian outcome loci (1q22 and 19p12) for further study. Bioinformatic and functional genetic analyses indicated that MEF2D and ZNF100 are targets of candidate outcome variants at 1q22 and 19p12, respectively. At 19p12, the chromatin interaction of a putative regulatory element with the ZNF100 promoter region correlated with candidate outcome variants...
June 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28643794/enrichment-of-low-frequency-functional-variants-revealed-by-whole-genome-sequencing-of-multiple-isolated-european-populations
#11
Yali Xue, Massimo Mezzavilla, Marc Haber, Shane McCarthy, Yuan Chen, Vagheesh Narasimhan, Arthur Gilly, Qasim Ayub, Vincenza Colonna, Lorraine Southam, Christopher Finan, Andrea Massaia, Himanshu Chheda, Priit Palta, Graham Ritchie, Jennifer Asimit, George Dedoussis, Paolo Gasparini, Aarno Palotie, Samuli Ripatti, Nicole Soranzo, Daniela Toniolo, James F Wilson, Richard Durbin, Chris Tyler-Smith, Eleftheria Zeggini
The genetic features of isolated populations can boost power in complex-trait association studies, and an in-depth understanding of how their genetic variation has been shaped by their demographic history can help leverage these advantageous characteristics. Here, we perform a comprehensive investigation using 3,059 newly generated low-depth whole-genome sequences from eight European isolates and two matched general populations, together with published data from the 1000 Genomes Project and UK10K. Sequencing data give deeper and richer insights into population demography and genetic characteristics than genotype-chip data, distinguishing related populations more effectively and allowing their functional variants to be studied more fully...
June 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28643760/validation-of-microsatellite-instability-histology-scores-with-bethesda-guidelines-in-hereditary-nonpolyposis-colorectal-cancer
#12
Mustafa Kaya, Fatih Basak, Abdullah Sisik, Mustafa Hasbahceci, Gurhan Bas, Orhan Alimoglu, Cumhur Selçuk Topal, Gozde Kir
AIMS: Hereditary nonpolyposis colorectal cancer (HNPCC) is a subgroup of colorectal cancer (CRC) which should be differentiated because of the high risk for additional cancers and risk evaluation for other family members, especially for CRC. It is not practical to perform genetic testing for all CRC patients; therefore, various prediction modalities, for example, Bethesda guideline (BG) were studied in the literature. We aimed to assess the association of microsatellite instability (MSI), histology scores, and BG for predicting HNPCC risk...
April 2017: Journal of Cancer Research and Therapeutics
https://www.readbyqxmd.com/read/28643617/preselection-statistics-and-random-forest-classification-identify-population-informative-single-nucleotide-polymorphisms-in-cosmopolitan-and-autochthonous-cattle-breeds
#13
F Bertolini, G Galimberti, G Schiavo, S Mastrangelo, R Di Gerlando, M G Strillacci, A Bagnato, B Portolano, L Fontanesi
Commercial single nucleotide polymorphism (SNP) arrays have been recently developed for several species and can be used to identify informative markers to differentiate breeds or populations for several downstream applications. To identify the most discriminating genetic markers among thousands of genotyped SNPs, a few statistical approaches have been proposed. In this work, we compared several methods of SNPs preselection (Delta, F st and principal component analyses (PCA)) in addition to Random Forest classifications to analyse SNP data from six dairy cattle breeds, including cosmopolitan (Holstein, Brown and Simmental) and autochthonous Italian breeds raised in two different regions and subjected to limited or no breeding programmes (Cinisara, Modicana, raised only in Sicily and Reggiana, raised only in Emilia Romagna)...
June 23, 2017: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/28642846/decreased-fitness-and-virulence-in-st10-escherichia-coli-harboring-blandm-5-and-mcr-1-against-a-st4981-strain-with-blandm-5
#14
Yawei Zhang, Kang Liao, Hua Gao, Qi Wang, Xiaojuan Wang, Henan Li, Ruobing Wang, Hui Wang
Although coexistence of blaNDM-5 and mcr-1 in Escherichia coli has been reported, little is known about the fitness and virulence of such strains. Three carbapenem-resistant Escherichia coli (GZ1, GZ2, and GZ3) successively isolated from one patient in 2015 were investigated for microbiological fitness and virulence. GZ1 and GZ2 were also resistant to colistin. To verify the association between plasmids and fitness, growth kinetics of the transconjugants were performed. We also analyzed genomic sequences of GZ2 and GZ3 using PacBio sequencing...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28642624/whole-exome-sequencing-to-identify-genetic-variants-associated-with-raised-atherosclerotic-lesions-in-young-persons
#15
James E Hixson, Goo Jun, Lawrence C Shimmin, Yizhi Wang, Guoqiang Yu, Chunhong Mao, Andrew S Warren, Timothy D Howard, Richard S Vander Heide, Jennifer Van Eyk, Yue Wang, David M Herrington
We investigated the influence of genetic variants on atherosclerosis using whole exome sequencing in cases and controls from the autopsy study "Pathobiological Determinants of Atherosclerosis in Youth (PDAY)". We identified a PDAY case group with the highest total amounts of raised lesions (n = 359) for comparisons with a control group with no detectable raised lesions (n = 626). In addition to the standard exome capture, we included genome-wide proximal promoter regions that contain sequences that regulate gene expression...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28642587/systematic-comparison-of-two-whole-genome-amplification-methods-for-targeted-next-generation-sequencing-using-frozen-and-ffpe-normal-and-cancer-tissues
#16
Pedro Mendez, Li Tai Fang, David M Jablons, Il-Jin Kim
Sequencing key cancer-driver genes using formalin-fixed, paraffin-embedded (FFPE) cancer tissues is becoming the standard for identifying the best treatment regimen. However, about 25% of all samples are rejected for genetic analyses for reasons that include too little tissue to extract enough high quality DNA. One way to overcome this is to do whole-genome amplification (WGA) in clinical samples, but only limited studies have tested different WGA methods in FFPE cancer specimens using targeted next-generation sequencing (NGS)...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28642457/human-mediated-secondary-contact-of-two-tortoise-lineages-results-in-sex-biased-introgression
#17
Eva Graciá, Roberto C Rodríguez-Caro, Ana C Andreu, Uwe Fritz, Andrés Giménez, Francisco Botella
Human-mediated secondary contact of recently diverged taxa offers valuable opportunities for studying the evolutionary mechanisms involved in the establishment and maintenance of genetic boundaries between taxa. We used mitochondrial and microsatellite markers to examine a recently introduced population of the spur-thighed tortoise (Testudo graeca) of mixed origin in the Doñana National Park (SW Spain). The earliest records of tortoises in Doñana trace back to the 18th century, but several population reinforcements in the 20th century with animals from Morocco are well-documented...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28642271/powerful-genetic-association-analysis-for-common-or-rare-variants-with-high-dimensional-structured-traits
#18
Xiang Zhan, Ni Zhao, Anna Plantinga, Timothy A Thornton, Karen N Conneely, Michael P Epstein, Michael C Wu
Many genetic association studies collect a wide range of complex traits. As these traits may be correlated and share a common genetic mechanism, joint analysis can be statistically more powerful and biologically more meaningful. However, most existing tests for multiple traits cannot be used for high-dimensional and possibly structured traits, such as network-structured transcriptomic pathway expressions. To overcome potential limitations, in this paper we propose the dual kernel-based association test (DKAT) for testing the association between multiple traits and multiple genetic variants, both common and rare...
June 22, 2017: Genetics
https://www.readbyqxmd.com/read/28641744/polygenic-risk-score-and-heritability-estimates-reveals-a-genetic-relationship-between-asd-and-ocd
#19
W Guo, J F Samuels, Y Wang, H Cao, M Ritter, P S Nestadt, J Krasnow, B D Greenberg, A J Fyer, J T McCracken, D A Geller, D L Murphy, J A Knowles, M A Grados, M A Riddle, S A Rasmussen, N C McLaughlin, E L Nurmi, K D Askland, B A Cullen, J Piacentini, D L Pauls, O J Bienvenu, S E Stewart, F S Goes, B Maher, A E Pulver, D Valle, M Mattheisen, J Qian, G Nestadt, Y Y Shugart
Obsessive-compulsive disorder (OCD) and Autism spectrum disorder (ASD) are both highly heritable neurodevelopmental disorders that conceivably share genetic risk factors. However, the underlying genetic determinants remain largely unknown. In this work, the authors describe a combined genome-wide association study (GWAS) of ASD and OCD. The OCD dataset includes 2998 individuals in nuclear families. The ASD dataset includes 6898 individuals in case-parents trios. GWAS summary statistics were examined for potential enrichment of functional variants associated with gene expression levels in brain regions...
July 2017: European Neuropsychopharmacology: the Journal of the European College of Neuropsychopharmacology
https://www.readbyqxmd.com/read/28641695/-relationship-between-egfr-mutations-and-pathological-classification-and-%C3%A2-specimen-of-lung-adenocarcinoma
#20
Lifei Kang, Jie Zheng, Xiang Zhu
BACKGROUND: With the development of genetic mutations and targeted drugs, accurate therapy of lung adenocarcinoma attracts much more attention, and more research is focued on epidermal growth factor receptor (EGFR). It is unclear whether the result of EGFR mutation and pathology type is consistent with different specimens. In our study, by comparing the relationship between EGFR mutations and pathological classification of lung adenocarcinoma in surgical resection of specimen and biopsy specimen, to discuss the relationship between EGFR mutations and pathological classification of and the influence of specimen type on EGFR gene detection...
June 20, 2017: Zhongguo Fei Ai za Zhi, Chinese Journal of Lung Cancer
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