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https://www.readbyqxmd.com/read/29858661/association-analysis-of-copy-number-variations-in-type-2-diabetes-related-susceptible-genes-in-a-chinese-population
#1
Yu-Xiang Yan, Jia-Jiang-Hui Li, Huan-Bo Xiao, Shuo Wang, Yan He, Li-Juan Wu
AIMS: Copy number variations (CNVs) have been implicated as an important genetic marker of common disease. In this study, we explored genetic effects of common CNVs in Type 2 diabetes (T2D) related susceptible genes in Chinese population. METHODS: Seven common CNV loci were selected from genes enclosing the susceptible single nucleotide polymorphisms (SNPs) of T2D confirmed by genome-wide association studies (GWAS) and replication studies conducted in east Asia population...
June 1, 2018: Acta Diabetologica
https://www.readbyqxmd.com/read/29844865/identification-of-different-mutational-profiles-in-cancers-arising-in-specific-colon-segments-by-next-generation-sequencing
#2
Duarte Mendes Oliveira, Carmelo Laudanna, Simona Migliozzi, Pietro Zoppoli, Gianluca Santamaria, Katia Grillone, Laura Elia, Chiara Mignogna, Flavia Biamonte, Rosario Sacco, Francesco Corcione, Giuseppe Viglietto, Donatella Malanga, Antonia Rizzuto
The objective of this study was to investigate the mutational profiles of cancers arising in different colon segments. To this aim, we have analyzed 37 colon cancer samples by use of the Ion AmpliSeq™ Comprehensive Cancer Panel. Overall, we have found 307 mutated genes, most of which already implicated in the development of colon cancer. Among these, 15 genes were mutated in tumors originating in all six colon segments and were defined "common genes" (i.e. APC, PIK3CA, TP53) whereas 13 genes were preferentially mutated in tumors originating only in specific colon segments and were defined "site-associated genes" (i...
May 8, 2018: Oncotarget
https://www.readbyqxmd.com/read/29774586/genome-wide-association-study-reveals-novel-genes-for-the-ear-size-in-sheep-ovis-aries
#3
L Gao, S-S Xu, J-Q Yang, M Shen, M-H Li
Variations in ear size can be observed in livestock such as sheep; however, the genetic basis of variable ear size in sheep is still poorly understood. To investigate causative genes associated with ear size in sheep, a genome-wide association study was performed in 115 adult Duolang sheep with different-sized floppy ears using the Ovine Infinium HD BeadChip. We found 38 significant SNPs at the genome-wide or chromosome-wise 5% significance level after Bonferroni correction. The most significant association (P = 1...
May 18, 2018: Animal Genetics
https://www.readbyqxmd.com/read/29730043/identifying-the-genetic-risk-factors-for-treatment-response-to-lurasidone-by-genome-wide-association-study-a-meta-analysis-of-samples-from-three-independent-clinical-trials
#4
Jiang Li, Antony Loebel, Herbert Y Meltzer
A genome-wide association study (GWAS) of response of schizophrenia patients to the atypical antipsychotic drug, lurasidone, based on two double-blind registration trials, identified SNPs from four classes of genes as predictors of efficacy, but none were genome wide significant (GWS). After inclusion of data from a third lurasidone trial, meta-analysis identified a GWS marker and other findings consistent with our first study. The primary end-point was change in Total Positive and Negative Syndrome Scale (PANSS) between baseline and last observation carried forward...
May 2, 2018: Schizophrenia Research
https://www.readbyqxmd.com/read/29657712/recent-advances-in-understanding-the-biology-of-marginal-zone-lymphoma
#5
REVIEW
Francesco Bertoni, Davide Rossi, Emanuele Zucca
There are three different marginal zone lymphomas (MZLs): the extranodal MZL of mucosa-associated lymphoid tissue (MALT) type (MALT lymphoma), the splenic MZL, and the nodal MZL. The three MZLs share common lesions and deregulated pathways but also present specific alterations that can be used for their differential diagnosis. Although trisomies of chromosomes 3 and 18, deletions at 6q23, deregulation of nuclear factor kappa B, and chromatin remodeling genes are frequent events in all of them, the three MZLs differ in the presence of recurrent translocations, mutations affecting the NOTCH pathway, and the transcription factor Kruppel like factor 2 ( KLF2) or the receptor-type protein tyrosine phosphatase delta ( PTPRD )...
2018: F1000Research
https://www.readbyqxmd.com/read/29608257/genetic-overlap-between-endometriosis-and-endometrial-cancer-evidence-from-cross-disease-genetic-correlation-and-gwas-meta-analyses
#6
Jodie N Painter, Tracy A O'Mara, Andrew P Morris, Timothy H T Cheng, Maggie Gorman, Lynn Martin, Shirley Hodson, Angela Jones, Nicholas G Martin, Scott Gordon, Anjali K Henders, John Attia, Mark McEvoy, Elizabeth G Holliday, Rodney J Scott, Penelope M Webb, Peter A Fasching, Matthias W Beckmann, Arif B Ekici, Alexander Hein, Matthias Rübner, Per Hall, Kamila Czene, Thilo Dörk, Matthias Dürst, Peter Hillemanns, Ingo Runnebaum, Diether Lambrechts, Frederic Amant, Daniela Annibali, Jeroen Depreeuw, Adriaan Vanderstichele, Ellen L Goode, Julie M Cunningham, Sean C Dowdy, Stacey J Winham, Jone Trovik, Erling Hoivik, Henrica M J Werner, Camilla Krakstad, Katie Ashton, Geoffrey Otton, Tony Proietto, Emma Tham, Miriam Mints, Shahana Ahmed, Catherine S Healey, Mitul Shah, Paul D P Pharoah, Alison M Dunning, Joe Dennis, Manjeet K Bolla, Kyriaki Michailidou, Qin Wang, Jonathan P Tyrer, John L Hopper, Julian Peto, Anthony J Swerdlow, Barbara Burwinkel, Hermann Brenner, Alfons Meindl, Hiltrud Brauch, Annika Lindblom, Jenny Chang-Claude, Fergus J Couch, Graham G Giles, Vessela N Kristensen, Angela Cox, Krina T Zondervan, Dale R Nyholt, Stuart MacGregor, Grant W Montgomery, Ian Tomlinson, Douglas F Easton, Deborah J Thompson, Amanda B Spurdle
Epidemiological, biological, and molecular data suggest links between endometriosis and endometrial cancer, with recent epidemiological studies providing evidence for an association between a previous diagnosis of endometriosis and risk of endometrial cancer. We used genetic data as an alternative approach to investigate shared biological etiology of these two diseases. Genetic correlation analysis of summary level statistics from genomewide association studies (GWAS) using LD Score regression revealed moderate but significant genetic correlation (rg  = 0...
May 2018: Cancer Medicine
https://www.readbyqxmd.com/read/29581789/integrated-oncogenomic-profiling-of-copy-numbers-and-gene-expression-in-lung-adenocarcinomas-without-egfr-mutations-or-alk-fusion
#7
Yanzhuo Luo, Bingjin Li, Guangxin Zhang, Yuxiao He, Jeeyoo Hope Bae, Fengping Hu, Ranji Cui, Runhua Liu, Zhou Wang, Lizhong Wang
Targeted therapies based on EGFR mutations or on the ALK fusion oncogene have become the standard treatment for certain patients with lung adenocarcinoma (LUAD). However, most LUAD patients have no EGFR mutation or ALK fusion, and their oncogenetic alterations remain to be characterized. Here we conducted an integrated analysis of public datasets to assess the genomic alterations of 23 highly lung cancer-associated genes. The copy numbers of these genes were measured in ten micro-dissected, paired tumors and normal lung tissues of LUAD patients without EGFR mutations or ALK fusion...
2018: Journal of Cancer
https://www.readbyqxmd.com/read/29536759/genome-wide-analysis-of-nuclear-magnetic-resonance-metabolites-revealed-parent-of-origin-effect-on-triglycerides-in-medium-very-low-density-lipoprotein-in-ptprd-gene
#8
N Pervjakova, V Kukushkina, T Haller, S Kasela, A Joensuu, K Kristiansson, T Annilo, M Perola, V Salomaa, P Jousilahti, A Metspalu, R Mägi
AIM: The aim of the study was to explore the parent-of-origin effects (POEs) on a range of human nuclear magnetic resonance metabolites. MATERIALS & METHODS: We search for POEs in 14,815 unrelated individuals from Estonian and Finnish cohorts using POE method for the genotype data imputed with 1000 G reference panel and 82 nuclear magnetic resonance metabolites. RESULTS: Meta-analysis revealed the evidence of POE for the variant rs1412727 in PTPRD gene for the metabolite: triglycerides in medium very low-density lipoprotein...
May 2018: Biomarkers in Medicine
https://www.readbyqxmd.com/read/29483675/nature-vs-nurture-in-human-sociality-multi-level-genomic-analyses-of-social-conformity
#9
Biqing Chen, Zijian Zhu, Yingying Wang, Xiaohu Ding, Xiaobo Guo, Mingguang He, Wan Fang, Qin Zhou, Shanbi Zhou, Han Lei, Ailong Huang, Tingmei Chen, Dongsheng Ni, Yuping Gu, Jianing Liu, Yi Rao
Social conformity is fundamental to human societies and has been studied for more than six decades, but our understanding of its mechanisms remains limited. Individual differences in conformity have been attributed to social and cultural environmental influences, but not to genes. Here we demonstrate a genetic contribution to conformity after analyzing 1,140 twins and single-nucleotide polymorphism (SNP)-based studies of 2,130 young adults. A two-step genome-wide association study (GWAS) revealed replicable associations in 9 genomic loci, and a meta-analysis of three GWAS with a sample size of ~2,600 further confirmed one locus, corresponding to the NAV3 (Neuron Navigator 3) gene which encodes a protein important for axon outgrowth and guidance...
May 2018: Journal of Human Genetics
https://www.readbyqxmd.com/read/29360682/ontogeny-related-pharmacogene-changes-in-the-pediatric-liver-transcriptome
#10
Richard Meier, Chengpeng Bi, Roger Gaedigk, Daniel P Heruth, Shui Qing Ye, J Steven Leeder, Brooke L Fridley
OBJECTIVES: The majority of drug dosing studies are based on adult populations, with modification of the dosing for children based on size and weight. This rudimentary approach for drug dosing children is limited, as biologically a child can differ from an adult in far more aspects than just size and weight. Specifically, understanding the ontogeny of childhood liver development is critical in dosing drugs that are metabolized through the liver, as the rate of metabolism determines the duration and intensity of a drug's pharmacologic action...
March 2018: Pharmacogenetics and Genomics
https://www.readbyqxmd.com/read/29230811/whole-exome-sequencing-of-oral-mucosal-melanoma-reveals-mutational-profile-and-therapeutic-targets
#11
Jiong Lyu, Zhijian Song, Jianhua Chen, Matthew J Shepard, Hao Song, Guoxin Ren, Zhiqiang Li, Wei Guo, Zhengping Zhuang, Yongyong Shi
Oral mucosal melanoma (OMM) is a rare and aggressive subtype of melanoma with little known about its pathogenesis or carcinogenesis. We therefore performed whole-exome sequencing (WES) on 19 matched OMM tumor/normal pairs in order to gain insight into potential genetic drivers of tumor formation. For the first time, we describe the comprehensive mutational profile of OMM. Our data suggest that the genetic background of OMM differs from those of other melanoma subtypes. We identified recurrent mutations involving KIT, POLE, PTPRD, PTCHD2, and DMXL2...
March 2018: Journal of Pathology
https://www.readbyqxmd.com/read/29228728/protein-tyrosine-phosphatase-receptor-type-%C3%AE-acts-as-a-negative-regulator-suppressing-breast-cancer
#12
Xiaotang Yu, Fan Zhang, Jun Mao, Ying Lu, Jiazhi Li, Wei Ma, Shujun Fan, Chunying Zhang, Qing Li, Bo Wang, Bo Song, Lianhong Li
Protein tyrosine phosphatase receptor-type δ (PTPRD) is frequently inactivated in human cancers. This study investigated the role of PTPRD in the regulation of stemness, epithelial-mesenchymal transition (EMT), and migration and invasion in breast cancer cells. In vitro , PTPRD silencing using siRNA enhanced the stem cell-like properties of breast cancer cells, including their mammosphere- and holoclone-forming abilities, and it promoted tumorigenicity in vivo . PTPRD knockdown also increased the CD44+ /CD24- breast cancer stem cell (BCSC) population and the expression of the stem cell markers ALDH1 and OCT4...
November 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29187730/genome-wide-analysis-in-uk-biobank-identifies-four-loci-associated-with-mood-instability-and-genetic-correlation-with-major-depressive-disorder-anxiety-disorder-and-schizophrenia
#13
Joey Ward, Rona J Strawbridge, Mark E S Bailey, Nicholas Graham, Amy Ferguson, Donald M Lyall, Breda Cullen, Laura M Pidgeon, Jonathan Cavanagh, Daniel F Mackay, Jill P Pell, Michael O'Donovan, Valentina Escott-Price, Daniel J Smith
Mood instability is a core clinical feature of affective and psychotic disorders. In keeping with the Research Domain Criteria approach, it may be a useful construct for identifying biology that cuts across psychiatric categories. We aimed to investigate the biological validity of a simple measure of mood instability and evaluate its genetic relationship with several psychiatric disorders, including major depressive disorder (MDD), bipolar disorder (BD), schizophrenia, attention deficit hyperactivity disorder (ADHD), anxiety disorder and post-traumatic stress disorder (PTSD)...
November 30, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/29033051/genetics-of-restless-legs-syndrome-an-update
#14
REVIEW
Félix J Jiménez-Jiménez, Hortensia Alonso-Navarro, Elena García-Martín, José A G Agúndez
A major role of genetic factors in the risk of developing restless legs syndrome (RLS) is supported by the high frequency of positive family history of RLS in patients affected with this disease, and the higher concordance rates in monozygotic twins compared with dizygotic ones in twin studies. In this review we have focused on those reports describing inheritance patterns of RLS, genetic anticipation, the results of studies performed on positivity of family history of RLS, twin studies, linkage studies in familial RLS, genome-wide association studies (GWAS), exome sequencing studies, and case-control association studies on candidate genes in RLS...
June 2018: Sleep Medicine Reviews
https://www.readbyqxmd.com/read/28977839/genetic-defects-of-the-irf1-mediated-major-histocompatibility-complex-class-i-antigen-presentation-pathway-occur-prevalently-in-the-jak2-gene-in-non-small-cell-lung-cancer
#15
Tao Shen, Zhengming Chen, Zhizhuang Joe Zhao, Jie Wu
Recognition of major histocompatibility complex (MHC) class I antigens on tumor cells by cytotoxic T cells is involved in T cell-mediated tumor immune surveillance and immune checkpoint therapy. The interferon-γ (IFNγ)-IRF1 signaling pathway regulates MHC class I antigen presentation. To examine genetic defects of the IFNγ-IRF1 pathway in non-small cell lung cancer (NSCLC), we analyzed The Cancer Genome Atlas (TCGA) lung adenocarcinoma (LuAd) and lung squamous cell carcinoma (LuSc) data. Loss-of-function (LOF) genetic alterations of the IFNγ-IRF1 pathway genes (IFNGR1, IFNGR2, JAK1, JAK2, STAT1, IRF1) were found in 64 (6...
September 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28968711/spectrum-of-germline-mutations-in-smokers-and-non-smokers-in-brazilian-non-small-cell-lung-cancer-nsclc-patients
#16
Patrícia P Couto, Luciana Bastos-Rodrigues, Hagit Schayek, Flavia M Melo, Raony G C Lisboa, Debora M Miranda, Alyne Vilhena, Allen E Bale, Eitan Friedman, Luiz De Marco
Lung cancer (LC) is a leading cause of cancer-related mortality. Although smoking is the major risk factor, ~15% of all cases occur in never-smokers, suggesting that genetic factors play a role in LC predisposition. Indeed, germline mutations in the TP53 gene predispose to multiple cancer types, including LC. To date, few studies compared the somatic and germline mutational profiles of LC cases by smoking status, and none was reported in Brazilians. Whole-exome sequencing (WES) was performed on two pools (seven smokers and six non-smokers) of tumor-derived DNA using the Illumina HiSeq2000 platform...
October 26, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/28859360/targeted-next-generation-sequencing-of-commonly-mutated-genes-in-esophageal-adenocarcinoma-patients-with-long-term-survival
#17
E Visser, I A Franken, L A A Brosens, W W J de Leng, E Strengman, J A Offerhaus, J P Ruurda, R van Hillegersberg
Survival of patients with esophageal adenocarcinoma remains poor and individual differences in prognosis remain unexplained. This study investigated whether gene mutations can explain why patients with high-risk (pT3-4, pN+) esophageal adenocarcinoma survive past 5 years after esophagectomy. Six long-term survivors (LTS) (≥5 years survival without recurrence) and six short-term survivors (STS) (<2 years survival due to recurrence) who underwent resection without neoadjuvant therapy for high-risk esophageal adenocarcinoma were included...
September 1, 2017: Diseases of the Esophagus: Official Journal of the International Society for Diseases of the Esophagus
https://www.readbyqxmd.com/read/28802642/prognostic-value-of-tert-alterations-mutational-and-copy-number-alterations-burden-in-urothelial-carcinoma
#18
Sumit Isharwal, François Audenet, Esther Drill, Eugene J Pietzak, Gopa Iyer, Irina Ostrovnaya, Eugene Cha, Timothy Donahue, Maria Arcila, Gowtham Jayakumaran, Michael F Berger, Jonathan E Rosenberg, Dean F Bajorin, Jonathan Coleman, Guido Dalbagni, Victor E Reuter, Bernard H Bochner, David B Solit, Hikmat A Al-Ahmadie
Point mutations in the TERT gene promoter occur at high frequency in multiple cancers, including urothelial carcinoma (UC). However, the relationship between TERT promoter mutations and UC patient outcomes is unclear due to conflicting reports in the literature. In this study, we examined the association of TERT alterations, tumor mutational burden per megabase (Mb), and copy number alteration (CNA) burden with clinical parameters and their prognostic value in a cohort of 398 urothelial tumors. The majority of TERT mutations were located at two promoter region hotspots (chromosome 5, 1 295 228 C>T and 1 295 250 C>T)...
August 10, 2017: European Urology Focus
https://www.readbyqxmd.com/read/28761083/revealing-the-complex-genetic-architecture-of-obsessive-compulsive-disorder-using-meta-analysis
#19
(no author information available yet)
Two obsessive-compulsive disorder (OCD) genome-wide association studies (GWASs) have been published by independent OCD consortia, the International Obsessive-Compulsive Disorder Foundation Genetics Collaborative (IOCDF-GC) and the OCD Collaborative Genetics Association Study (OCGAS), but many of the top-ranked signals were supported in only one study. We therefore conducted a meta-analysis from the two consortia, investigating a total of 2688 individuals of European ancestry with OCD and 7037 genomically matched controls...
May 2018: Molecular Psychiatry
https://www.readbyqxmd.com/read/28615674/meta-analysis-of-genome-wide-snp-and-pathway-based-associations-for-facets-of-neuroticism
#20
Song E Kim, Han-Na Kim, Yeo-Jun Yun, Seong Gu Heo, Juhee Cho, Min-Jung Kwon, Yoosoo Chang, Seungho Ryu, Hocheol Shin, Chol Shin, Nam H Cho, Yeon Ah Sung, Hyung-Lae Kim
Neuroticism is a heritable personality trait that is comprised of distinct sub-factors, or facets. Sub-factors of neuroticism are linked to different emotional states or psychiatric symptoms and studying the genetic variants associated with these facets may help reveal the biological mechanisms underlying psychiatric disorders. In the present study, a meta-analysis of genome-wide association studies for six facets of neuroticism was performed in 5584 participants from three cohorts. Additionally, a Gene Set Enrichment Analysis was conducted to find biological pathways associated with each facet...
October 2017: Journal of Human Genetics
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