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https://www.readbyqxmd.com/read/28343372/east-of-the-andes-the-genetic-profile-of-the-peruvian-amazon-populations
#1
T Di Corcia, C Sanchez Mellado, T J Davila Francia, G Ferri, S Sarno, D Luiselli, O Rickards
OBJECTIVES: Assuming that the differences between the Andes and the Amazon rainforest at environmental and historical levels have influenced the distribution patterns of genes, languages, and cultures, the maternal and paternal genetic reconstruction of the Peruvian Amazon populations was used to test the relationships within and between these two extreme environments. MATERIALS AND METHODS: We analyzed four Peruvian Amazon communities (Ashaninka, Huambisa, Cashibo, and Shipibo) for both Y chromosome (17 STRs and 8 SNPs) and mtDNA data (control region sequences, two diagnostic sites of the coding region, and one INDEL), and we studied their variability against the rest of South America...
March 25, 2017: American Journal of Physical Anthropology
https://www.readbyqxmd.com/read/28343281/using-patterns-of-genetic-association-to-elucidate-shared-genetic-etiologies-across-psychiatric-disorders
#2
Seung Bin Cho, Fazil Aliev, Shaunna L Clark, Amy E Adkins, Howard J Edenberg, Kathleen K Bucholz, Bernice Porjesz, Danielle M Dick
Twin studies indicate that latent genetic factors overlap across comorbid psychiatric disorders. In this study, we used a novel approach to elucidate shared genetic factors across psychiatric outcomes by clustering single nucleotide polymorphisms based on their genome-wide association patterns. We applied latent profile analysis (LPA) to p-values resulting from genome-wide association studies across three phenotypes: symptom counts of alcohol dependence (AD), antisocial personality disorder (ASP), and major depression (MD), using the European-American case-control genome-wide association study subsample of the collaborative study on the genetics of alcoholism (N = 1399)...
March 25, 2017: Behavior Genetics
https://www.readbyqxmd.com/read/28343277/pancreatic-alpha-cell-selective-deletion-of-tcf7l2-impairs-glucagon-secretion-and-counter-regulatory-responses-to-hypoglycaemia-in-mice
#3
Gabriela da Silva Xavier, Angeles Mondragon, Vishnou Mourougavelou, Céline Cruciani-Guglielmacci, Jessica Denom, Pedro Luis Herrera, Christophe Magnan, Guy A Rutter
AIMS/HYPOTHESIS: Transcription factor 7-like 2 (TCF7L2) is a high mobility group (HMG) box-containing transcription factor and downstream effector of the Wnt signalling pathway. SNPs in the TCF7L2 gene have previously been associated with an increased risk of type 2 diabetes in genome-wide association studies. In animal studies, loss of Tcf7l2 function is associated with defective islet beta cell function and survival. Here, we explore the role of TCF7L2 in the control of the counter-regulatory response to hypoglycaemia by generating mice with selective deletion of the Tcf7l2 gene in pancreatic alpha cells...
March 25, 2017: Diabetologia
https://www.readbyqxmd.com/read/28343170/mirnas-single-nucleotide-polymorphisms-snps-and-age-related-macular-degeneration-amd
#4
John Paul SanGiovanni, Peter M SanGiovanni, Przemysław Sapieha, Vincent De Guire
Advanced age-related macular degeneration (AAMD) is a complex sight-threating disease of public health significance. Micro RNAs (miRNAs) have been proposed as biomarkers for AAMD. The presence of certain single nucleotide polymorphisms (SNPs) may influence the explanatory value of these biomarkers. Here we present findings from an integrated approach used to determine whether AAMD-associated SNPs have the capacity to influence miRNA-mRNA pairing and, if so, to what extent such pairing may be manifested in a discrete AAMD transcriptome...
March 27, 2017: Clinical Chemistry and Laboratory Medicine: CCLM
https://www.readbyqxmd.com/read/28343162/mesothelin-promoter-variants-are-associated-with-increased-soluble-mesothelin-related-peptide-levels-in-asbestos-exposed-individuals
#5
Chiara De Santi, Perla Pucci, Alessandra Bonotti, Ombretta Melaiu, Monica Cipollini, Roberto Silvestri, Veronika Vymetalkova, Elisa Barone, Elisa Paolicchi, Alda Corrado, Irene Lepori, Irene Dell'Anno, Lucia Pellè, Pavel Vodicka, Luciano Mutti, Rudy Foddis, Alfonso Cristaudo, Federica Gemignani, Stefano Landi
BACKGROUND: Soluble mesothelin-related peptide (SMRP) is a promising diagnostic biomarker for malignant pleural mesothelioma (MPM), but various confounders hinder its usefulness in surveillance programmes. We previously showed that a single nucleotide polymorphism (SNP) within the 3'untranslated region (3'UTR) of the mesothelin (MSLN) gene could affect the levels of SMRP. OBJECTIVES: To focus on SNPs located within MSLN promoter as possible critical genetic variables in determining SMRP levels...
March 25, 2017: Occupational and Environmental Medicine
https://www.readbyqxmd.com/read/28343097/strait-razor-v2s-advancing-sequence-based-str-allele-reporting-and-beyond-to-other-marker-systems
#6
Jonathan L King, Frank R Wendt, Jie Sun, Bruce Budowle
STRait Razor has provided the forensic community a free-to-use, open-source tool for short tandem repeat (STR) analysis of massively parallel sequencing (MPS) data. STRait Razor v2s (SRv2s) allows users to capture physically phased haplotypes within the full amplicon of both commercial (ForenSeq) and "early access" panels (PowerSeq, Mixture ID). STRait Razor v2s may be run in batch mode to facilitate population-level analysis and is supported by all Unix distributions (including MAC OS). Data are reported in tables in string (haplotype), length-based (e...
March 12, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28343093/influence-of-genetic-variants-of-cyp2d6-cyp2c9-cyp2c19-and-cyp3a4-on-antiepileptic-drug-metabolism-in-pediatric-patients-with-refractory-epilepsy
#7
Miguel A López-García, Iris A Feria-Romero, Héctor Serrano, Darío Rayo-Mares, Pietro Fagiolino, Marta Vázquez, Consuelo Escamilla-Núñez, Israel Grijalva, David Escalante-Santiago, Sandra Orozco-Suarez
BACKGROUND: Identified the polymorphisms of CYP2D6, CYP2C9, CYP2C19 and CYP3A4, within a rigorously selected population of pediatric patients with drug-resistant epilepsy. METHOD: The genomic DNA of 23 drug-resistant epilepsy patients and 7 patients with good responses were analyzed. Ten exons in these four genes were genotyped, and the drug concentrations in saliva and plasma were determined. RESULTS: The relevant SNPs with pharmacogenomics relations were CYP2D6*2 (rs16947) decreased your activity and CYP2D6*4 (rs1065852), CYP2C19*2 (rs4244285) and CYP3A4*1B (rs2740574) by association with poor metabolizer...
January 19, 2017: Pharmacological Reports: PR
https://www.readbyqxmd.com/read/28342798/allele-frequencies-and-other-forensic-parameters-of-the-hid-ion-ampliseq%C3%A2-identity-panel-markers-in-basques-using-the-ion-torrent-pgm%C3%A2-platform
#8
O García, A Soto, I Yurrebaso
The HID-Ion AmpliSeq™ Identity Panel amplifies 90 autosomal SNPs and 34 Y- SNPs with massively parallel sequencing (MPS) using the Ion Torrent PGM™ platform. In the present study, 105 Basques were analyzed to assess this panel. All loci were in Hardy-Weinberg equilibrium and no association between them was detected. Forensic parameters were calculated as 5.74×10(-36) for combined match probability and 99.99998% for combined power of exclusion. In conclusion, the HID Identity panel and the use of this new MPS technology are very promising tools for paternity testing and human identification in routine casework in the forensic field...
March 8, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28342452/contribution-of-genetic-factors-to-platinum-based-chemotherapy-sensitivity-and-prognosis-of-non-small-cell-lung-cancer
#9
REVIEW
Cristina Pérez-Ramírez, Marisa Cañadas-Garre, Miguel Ángel Molina, Ana I Robles, María José Faus-Dáder, Miguel Ángel Calleja-Hernández
Although platinum-based chemotherapy remains the standard treatment for advanced NSCLC patients, clinical outcomes are poor and most patients develop high-grade toxicities. Genetic factors, such as single nucleotide polymorphisms (SNPs) involved in platinum pharmacodynamics, metabolism and mechanism of action, may account for inter-individual differences shown in effectiveness and toxicity. Polymorphisms in genes involved in DNA repair and others such as PI3K/PTEN/AKT and TGF-β pathways have been demonstrated to be associated with response, survival and toxicity in advanced NSCLC patients treated with platinum-based chemotherapy...
January 2017: Mutation Research
https://www.readbyqxmd.com/read/28342449/a-systematic-review-and-meta-analysis-of-the-association-between-long-non-coding-rna-polymorphisms-and-cancer-risk
#10
REVIEW
Zhi Lv, Qian Xu, Yuan Yuan
It has been suggested that long non-coding RNA (lncRNA) gene polymorphisms are associated with cancer risk. In this article, we conducted a systematic review related to studies on the association between lncRNA single-nucleotide polymorphisms (SNPs) and the overall risk of cancer. A total 17 SNPs in four common lncRNA genes were included in the meta-analysis. In the lncRNA H19, the rs2735971 A/G, rs2839698C/T, and rs3024270 G/C polymorphisms, but not rs217727C/T, were correlated with overall cancer risk. The results also suggested that other SNPs were correlated with overall cancer risk, namely, two in HOTAIR (HOX transcript antisense RNA: rs920778C/T and rs7958904 G/C) and two in PRNCR1 (rs1016343C/T and rs16901946 A/G)...
January 2017: Mutation Research
https://www.readbyqxmd.com/read/28340513/mendelian-randomisation-implicates-hyperlipidaemia-as-a-risk-factor-for-colorectal-cancer
#11
Henry Rodriguez-Broadbent, Philip J Law, Amit Sud, Kimmo Palin, Sari Tuupanen, Alexandra Gylfe, Ulrika A Hänninen, Tatiana Cajuso, Tomas Tanskanen, Johanna Kondelin, Eevi Kaasinen, Antti-Pekka Sarin, Samuli Ripatti, Johan G Eriksson, Harri Rissanen, Paul Knekt, Eero Pukkala, Pekka Jousilahti, Veikko Salomaa, Aarno Palotie, Laura Renkonen-Sinisalo, Anna Lepistö, Jan Böhm, Jukka-Pekka Mecklin, Nada A Al-Tassan, Claire Palles, Lynn Martin, Ella Barclay, Susan M Farrington, Maria N Timofeeva, Brian F Meyer, Salma M Wakil, Harry Campbell, Christopher G Smith, Shelley Idziaszczyk, Timothy S Maughan, Richard Kaplan, Rachel Kerr, David Kerr, Michael N Passarelli, Jane C Figueiredo, Daniel D Buchanan, Aung K Win, John L Hopper, Mark A Jenkins, Noralane M Lindor, Polly A Newcomb, Steven Gallinger, David Conti, Fred Schumacher, Graham Casey, Lauri A Aaltonen, Jeremy P Cheadle, Ian P Tomlinson, Malcolm G Dunlop, Richard S Houlston
While elevated blood cholesterol has been associated with an increased risk of colorectal cancer (CRC) in observational studies, causality is uncertain. Here we apply a Mendelian randomisation (MR) analysis to examine the potential causal relationship between lipid traits and CRC risk. We used single nucleotide polymorphisms (SNPs) associated with blood levels of total cholesterol (TC), triglyceride (TG), low-density lipoprotein (LDL), and high-density lipoprotein (HDL) as instrumental variables (IV). We calculated MR estimates for each risk factor with CRC using SNP-CRC associations from 9,254 cases and 18,386 controls...
March 24, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28340422/the-clinicopathologic-relevance-of-reck-gene-polymorphisms-in-ameloblastoma
#12
Xudong Zhang, Jie Wang, Huijuan Liu, Yanning Zhang, Fusheng Dong
OBJECTIVE: To investigate the relationship between RECK gene polymorphisms and the clinicopathologic features of ameloblastoma. DESIGN: Normal gingival mucosa specimens were obtained from 10 healthy volunteers. Ameloblastomas were surgically removed from 30 patients and part of the tumor specimens were used to detect RECK gene polymorphisms by using PCR-single-strand conformation polymorphism (PCR-SSCP) and DNA sequencing analysis. Expression of RECK and MMP-9 protein was measured using western blot...
March 16, 2017: Archives of Oral Biology
https://www.readbyqxmd.com/read/28340271/snp-detection-using-rna-sequences-of-candidate-genes-associated-with-puberty-in-cattle
#13
M M Dias, A Cánovas, C Mantilla-Rojas, D G Riley, P Luna-Nevarez, S J Coleman, S E Speidel, R M Enns, A Islas-Trejo, J F Medrano, S S Moore, M R S Fortes, L T Nguyen, B Venus, I S D P Diaz, F R P Souza, L F S Fonseca, F Baldi, L G Albuquerque, M G Thomas, H N Oliveira
Fertility traits, such as heifer pregnancy, are economically important in cattle production systems, and are therefore, used in genetic selection programs. The aim of this study was to identify single nucleotide polymorphisms (SNPs) using RNA-sequencing (RNA-Seq) data from ovary, uterus, endometrium, pituitary gland, hypothalamus, liver, longissimus dorsi muscle, and adipose tissue in 62 candidate genes associated with heifer puberty in cattle. RNA-Seq reads were assembled to the bovine reference genome (UMD 3...
March 22, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28340265/association-of-runx2-and-tnfsf11-genes-with-production-traits-in-a-paternal-broiler-line
#14
N V Grupioni, N B Stafuzza, A B Carvajal, A M G Ibelli, J O Peixoto, M C Ledur, D P Munari
Intense selection for production traits has improved the genetic gain of important economic traits. However, selection for performance and carcass traits has led to the onset of locomotors problems and decreasing bone strength in broilers. Thus, genes associated with bone integrity traits have become candidates for genetic studies in order to reduce the impact of bone disorders in broilers. This study investigated the association of the RUNX2 and TNFSF11 genes with 79 traits related to performance, carcass composition, organs, and bone integrity in a paternal broiler line...
March 22, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28340264/identification-of-19-loci-for-reproductive-traits-in-a-local-chinese-chicken-by-genome-wide-study
#15
Q C Fan, P F Wu, G J Dai, G X Zhang, T Zhang, Q Xue, H Q Shi, J Y Wang
Reproductive traits have long been studied and have an important influence on chicken breeding. To identify quantitative trait loci affecting reproductive traits, a genome-wide analysis of a Chinese chicken breed was performed to analyze age at first egg body weight at first egg, first egg weight, egg weight at the age of 300 days, egg weight at the age of 462 days, egg number at the age of 300 days, egg number between the ages of 300 and 462 days and egg number at the age of 462 days. Nineteen SNPs related to reproductive traits were presented (P < 1...
March 22, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28339850/allelic-variation-in-tlr4-is-linked-to-resistance-to-salmonella-enteritidis-infection-in-chickens
#16
Peng Li, Huihua Wang, Xingwang Zhao, Zhongyong Gou, Ranran Liu, Yongmei Song, Qinghe Li, Maiqing Zheng, Huanxian Cui, Nadia Everaert, Guiping Zhao, Jie Wen
Salmonella Enteritidis (SE) is a foodborne pathogen that negatively affects both animal and human health. Polymorphisms of the TLR4 gene may affect recognition by Toll-like receptor 4 (TLR4) of bacterial lipopolysaccharide (LPS), leading to differences in host resistance to pathogenic infections. The present study has investigated polymorphic loci of chicken TLR4 (ChTLR4) in ten chicken breeds, electrostatic potentials of mutant structures of TLR4, and a linkage analysis between allelic variation and survival ratio to infection with SE in specific-pathogen-free (SPF) White Leghorns...
March 1, 2017: Poultry Science
https://www.readbyqxmd.com/read/28339549/further-investigation-of-a-quantitative-trait-locus-for-ascites-on-chromosome-9-in-broiler-chicken-lines
#17
Shatovisha Dey, Sriram Krishna, Nicholas B Anthony, Douglas D Rhoads
Previously, we reported a genome wide association study (GWAS) that had shown association of a region between 11.8 and 13.6 Mbp on chromosome 9 with ascites phenotype in broilers. We had used microsatellite loci to demonstrate an association of particular genotypes for this region with ascites in experimental ascites lines and commercial broiler breeder lines. We identified two potential candidate genes, AGTR1 and UTS2D, within that chromosomal region for mediating the quantitative effect. We have now extended our analysis using SNPs for these genes to assess association with resistance or susceptibility to ascites in these same broiler lines...
October 10, 2016: Poultry Science
https://www.readbyqxmd.com/read/28339471/expression-quantitative-trait-loci-for-pax8-contributes-to-the-prognosis-of-hepatocellular-carcinoma
#18
Shijie Ma, Jianshui Yang, Ci Song, Zijun Ge, Jing Zhou, Guoxin Zhang, Zhibin Hu
Paired-box family member PAX8 encodes a transcription factor that has a role in cell differentiation and cell growth and may participate in the prognosis of hepatocellular carcinoma (HCC). By bioinformatics analysis, we identified several single nucleotide polymorphisms (SNPs) within a newly identified long non-coding RNA (lncRNA) AC016683.6 as expression quantitative trait loci (eQTLs) for PAX8. Hence, we hypothesized that PAX8eQTLs in lncRNA AC016683.6 may influence the HCC prognosis. We then performed a case-only study to assess the association between the two SNPs as well as the prognosis of HCC in 331 HBV-positive HCC patients without surgical treatment...
2017: PloS One
https://www.readbyqxmd.com/read/28339009/identification-of-egflam-spatc1l-and-rnase13-as-novel-susceptibility-loci-for-aortic-aneurysm-in-japanese-individuals-by-exome-wide-association-studies
#19
Yoshiji Yamada, Jun Sakuma, Ichiro Takeuchi, Yoshiki Yasukochi, Kimihiko Kato, Mitsutoshi Oguri, Tetsuo Fujimaki, Hideki Horibe, Masaaki Muramatsu, Motoji Sawabe, Yoshinori Fujiwara, Yu Taniguchi, Shuichi Obuchi, Hisashi Kawai, Shoji Shinkai, Seijiro Mori, Tomio Arai, Masashi Tanaka
We performed an exome-wide association study (EWAS) to identify genetic variants - in particular, low‑frequency or rare variants with a moderate to large effect size - that confer susceptibility to aortic aneurysm with 8,782 Japanese subjects (456 patients with aortic aneurysm, 8,326 control individuals) and with the use of Illumina HumanExome-12 DNA Analysis BeadChip or Infinium Exome-24 BeadChip arrays. The correlation of allele frequencies for 41,432 single nucleotide polymorphisms (SNPs) that passed quality control to aortic aneurysm was examined with Fisher's exact test...
March 21, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28338924/a-nonsynonymous-snp-catalog-of-mycobacterium-tuberculosis-virulence-genes-and-its-use-for-detecting-new-potentially-virulent-sublineages
#20
N E Mikheecheva, M V Zaychikova, A V Melerzanov, V N Danilenko
Mycobacterium tuberculosis is divided into several distinct lineages, and various genetic markers such as IS-elements, VNTR, and SNPs are used for lineage identification. We propose an M. tuberculosis classification approach based on functional polymorphisms in virulence genes. An M. tuberculosis virulence genes catalog has been established, including 319 genes from various protein groups, such as proteases, cell wall proteins, fatty acid and lipid metabolism proteins, sigma factors, toxin-antitoxin systems...
March 11, 2017: Genome Biology and Evolution
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