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https://www.readbyqxmd.com/read/28802642/prognostic-value-of-tert-alterations-and-mutational-and-copy-number-alteration-burden-in-urothelial-carcinoma
#1
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
Missense 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 9, 2017: European Urology Focus
https://www.readbyqxmd.com/read/28761083/revealing-the-complex-genetic-architecture-of-obsessive-compulsive-disorder-using-meta-analysis
#2
(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...
August 1, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28615674/meta-analysis-of-genome-wide-snp-and-pathway-based-associations-for-facets-of-neuroticism
#3
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...
June 15, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28537924/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
#4
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...
May 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/28497593/polymorphism-of-receptor-type-tyrosine-protein-phosphatase-delta-gene-in-the-development-of-non-alcoholic-fatty-liver-disease
#5
Shunsuke Nakajima, Hiroki Tanaka, Koji Sawada, Hidemi Hayashi, Takumu Hasebe, Masami Abe, Chitomi Hasebe, Mikihiro Fujiya, Toshikatsu Okumura
BACKGROUND AND AIM: Some single nucleotide polymorphisms (SNPs) are associated with the development of non-alcoholic fatty liver disease (NAFLD). As one of the genetic factors, PNPLA3 rs738409 (I148M) is important to associate with pathogenesis of NAFLD. Since other SNPs remain unclear in Japan, we performed high-throughput sequencing, which targeted more than 1,000 genes to identify a novel genetic variant in Japanese patients with NAFLD. METHODS: The present study in 36 NAFLD patients and 27 healthy volunteers (HVs) was performed...
May 11, 2017: Journal of Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/28433457/spatial-and-temporal-expression-patterns-of-genes-around-nine-neuroticism-associated-loci
#6
Kazutaka Ohi, Takamitsu Shimada, Toshiki Yasuyama, Kohei Kimura, Takashi Uehara, Yasuhiro Kawasaki
Neuroticism is a high-order personality trait. Individuals with higher neuroticism have increased risks of various psychiatric disorders and physical health outcomes. Neuroticism is related to physiological differences in the brain. A recent genome-wide association study identified nine distinct genomic loci that contribute to neuroticism. Brain development and function depend on the precise regulation of gene expression, which is differentially regulated across brain regions and developmental stages. Using multiple publicly available human post-mortem databases, we investigated, in brain and non-brain tissues and across several developmental life stages, the spatial and temporal expression patterns of genes arising from nine neuroticism-associated loci...
April 19, 2017: Progress in Neuro-psychopharmacology & Biological Psychiatry
https://www.readbyqxmd.com/read/28431800/genetic-predictors-of-antipsychotic-response-to-lurasidone-identified-in-a-genome-wide-association-study-and-by-schizophrenia-risk-genes
#7
Jiang Li, Akane Yoshikawa, Mark D Brennan, Timothy L Ramsey, Herbert Y Meltzer
Biomarkers which predict response to atypical antipsychotic drugs (AAPDs) increases their benefit/risk ratio. We sought to identify common variants in genes which predict response to lurasidone, an AAPD, by associating genome-wide association study (GWAS) data and changes (Δ) in Positive And Negative Syndrome Scale (PANSS) scores from two 6-week randomized, placebo-controlled trials of lurasidone in schizophrenia (SCZ) patients. We also included SCZ risk SNPs identified by the Psychiatric Genomics Consortium using a polygenic risk analysis...
April 18, 2017: Schizophrenia Research
https://www.readbyqxmd.com/read/28426752/somatic-copy-number-alterations-in-gastric-adenocarcinomas-among-asian-and-western-patients
#8
Steven E Schumacher, Byoung Yong Shim, Giovanni Corso, Min-Hee Ryu, Yoon-Koo Kang, Franco Roviello, Gordon Saksena, Shouyong Peng, Ramesh A Shivdasani, Adam J Bass, Rameen Beroukhim
Gastric cancer, a leading worldwide cause of cancer mortality, shows high geographic and ethnic variation in incidence rates, which are highest in East Asia. The anatomic locations and clinical behavior also differ by geography, leading to the controversial idea that Eastern and Western forms of the disease are distinct. In view of these differences, we investigated whether gastric cancers from Eastern and Western patients show distinct genomic profiles. We used high-density profiling of somatic copy-number aberrations to analyze the largest collection to date of gastric adenocarcinomas and utilized genotyping data to rigorously annotate ethnic status...
2017: PloS One
https://www.readbyqxmd.com/read/28345455/recurrent-epigenetic-silencing-of-the-ptprd-tumor-suppressor-in-laryngeal-squamous-cell-carcinoma
#9
Marcin Szaumkessel, Sonia Wojciechowska, Joanna Janiszewska, Natalia Zemke, Ewa Byzia, Katarzyna Kiwerska, Magdalena Kostrzewska-Poczekaj, Adam Ustaszewski, Malgorzata Jarmuz-Szymczak, Reidar Grenman, Malgorzata Wierzbicka, Anna Bartochowska, Krzysztof Szyfter, Maciej Giefing
Cellular processes like differentiation, mitotic cycle, and cell growth are regulated by tyrosine kinases with known oncogenic potential and tyrosine phosphatases that downmodulate the first. Therefore, tyrosine phosphatases are recurrent targets of gene alterations in human carcinomas. We and others suggested recently a tumor suppressor function of the PTPRD tyrosine phosphatase and reported homozygous deletions of the PTPRD locus in laryngeal squamous cell carcinoma. In this study, we investigated other gene-inactivating mechanisms potentially targeting PTPRD, including loss-of-function mutations and also epigenetic alterations like promoter DNA hypermethylation...
March 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28329290/association-of-btbd9-and-map2k5-skor1-with-restless-legs-syndrome-in-chinese-population
#10
Gen Li, Huidong Tang, Cheng Wang, Xuemei Qi, Jie Chen, Shengdi Chen, Jianfang Ma
Study Objectives: The aim of the study was to investigate the relationship between genetic factors and primary restless legs syndrome (RLS) in Chinese population. Methods: A total of 116 RLS patients and 200 controls were recruited and the diagnosis of RLS was based on the criteria of International RLS Study Group. Polymer chain reaction (PCR) and sequencing were used to detect 19 single nucleotide polymorphisms (SNPs) in six genetic loci (MEIS1, BTBD9, PTPRD, MAP2K5/SKOR1, TOX3, and Intergenic region of 2p14)...
April 1, 2017: Sleep
https://www.readbyqxmd.com/read/28322283/susceptibility-to-neurofibrillary-tangles-role-of-the-ptprd-locus-and-limited-pleiotropy-with-other-neuropathologies
#11
L B Chibnik, C C White, S Mukherjee, T Raj, L Yu, E B Larson, T J Montine, C D Keene, J Sonnen, J A Schneider, P K Crane, J M Shulman, D A Bennett, P L De Jager
Tauopathies, including Alzheimer's disease (AD) and other neurodegenerative conditions, are defined by a pathological hallmark: neurofibrillary tangles (NFTs). NFT accumulation is thought to be closely linked to cognitive decline in AD. Here, we perform a genome-wide association study for NFT pathologic burden and report the association of the PTPRD locus (rs560380, P=3.8 × 10(-8)) in 909 prospective autopsies. The association is replicated in an independent data set of 369 autopsies. The association of PTPRD with NFT is not dependent on the accumulation of amyloid pathology...
March 21, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28235956/genomic-complexity-and-targeted-genes-in-anaplastic-thyroid-cancer-cell-lines
#12
Eleanor L Woodward, Andrea Biloglav, Naveen Ravi, Minjun Yang, Lars Ekblad, Johan Wennerberg, Kajsa Paulsson
Anaplastic thyroid cancer (ATC) is a highly malignant disease with a very short median survival time. Few studies have addressed the underlying somatic mutations, and the genomic landscape of ATC thus remains largely unknown. In the present study, we have ascertained copy number aberrations, gene fusions, gene expression patterns, and mutations in early-passage cells from ten newly established ATC cell lines using single nucleotide polymorphism (SNP) array analysis, RNA sequencing and whole exome sequencing...
May 2017: Endocrine-related Cancer
https://www.readbyqxmd.com/read/28235828/independent-maternal-and-fetal-genetic-effects-on-midgestational-circulating-levels-of-environmental-pollutants
#13
Michela Traglia, Lisa A Croen, Kristen Lyall, Gayle C Windham, Marty Kharrazi, Gerald N DeLorenze, Anthony R Torres, Lauren A Weiss
Maternal exposure to environmental pollutants could affect fetal brain development and increase autism spectrum disorder (ASD) risk in conjunction with differential genetic susceptibility. Organohalogen congeners measured in maternal midpregnancy blood samples have recently shown significant, but negative associations with offspring ASD outcome. We report the first large-scale maternal and fetal genetic study of the midpregnancy serum levels of a set of 21 organohalogens in a subset of 790 genotyped women and 764 children collected in California by the Early Markers for Autism (EMA) Project...
April 3, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28159835/mir-135a-5p-mediated-downregulation-of-protein-tyrosine-phosphatase-receptor-delta-is-a-candidate-driver-of-hcv-associated-hepatocarcinogenesis
#14
Nicolaas Van Renne, Armando Andres Roca Suarez, Francois H T Duong, Claire Gondeau, Diego Calabrese, Nelly Fontaine, Amina Ababsa, Simonetta Bandiera, Tom Croonenborghs, Nathalie Pochet, Vito De Blasi, Patrick Pessaux, Tullio Piardi, Daniele Sommacale, Atsushi Ono, Kazuaki Chayama, Masashi Fujita, Hidewaki Nakagawa, Yujin Hoshida, Mirjam B Zeisel, Markus H Heim, Thomas F Baumert, Joachim Lupberger
BACKGROUND AND AIMS: HCV infection is a leading risk factor of hepatocellular carcinoma (HCC). However, even after viral clearance, HCC risk remains elevated. HCV perturbs host cell signalling to maintain infection, and derailed signalling circuitry is a key driver of carcinogenesis. Since protein phosphatases are regulators of signalling events, we aimed to identify phosphatases that respond to HCV infection with relevance for hepatocarcinogenesis. METHODS: We assessed mRNA and microRNA (miRNA) expression profiles in primary human hepatocytes, liver biopsies and resections of patients with HCC, and analysed microarray and RNA-seq data from paired liver biopsies of patients with HCC...
February 3, 2017: Gut
https://www.readbyqxmd.com/read/28099906/genomic-characteristics-of-pancreatic-squamous-cell-carcinoma-an-investigation-by-using-high-throughput-sequencing-after-in-solution-hybrid-capture
#15
Meng-Dan Xu, Shu-Ling Liu, Yi-Zhong Feng, Qiang Liu, Meng Shen, Qiaoming Zhi, Zeyi Liu, Dong-Mei Gu, Jie Yu, Liu-Mei Shou, Fei-Ran Gong, Qi Zhu, Weiming Duan, Kai Chen, Junning Zhang, Meng-Yao Wu, Min Tao, Wei Li
Squamous cell carcinoma (SCC) of pancreas is a rare histotype of pancreatic ductal carcinoma which is distinct from pancreatic adenocarcinoma (AC). Although there are standard treatments for pancreatic AC, no precise therapies exist for pancreatic SCC. Here, we screened 1033 cases of pancreatic cancer and identified 2 cases of pure SCC, which were pathologically diagnosed on the basis of finding definite intercellular bridges and/or focal keratin peal formation in the tumor cells. Immunohistochemistry assay confirmed the positive expression of CK5/6 and p63 in pancreatic SCC...
February 28, 2017: Oncotarget
https://www.readbyqxmd.com/read/27777633/uncovering-obsessive-compulsive-disorder-risk-genes-in-a-pediatric-cohort-by-high-resolution-analysis-of-copy-number-variation
#16
Matthew J Gazzellone, Mehdi Zarrei, Christie L Burton, Susan Walker, Mohammed Uddin, S M Shaheen, Julie Coste, Rageen Rajendram, Reva J Schachter, Marlena Colasanto, Gregory L Hanna, David R Rosenberg, Noam Soreni, Kate D Fitzgerald, Christian R Marshall, Janet A Buchanan, Daniele Merico, Paul D Arnold, Stephen W Scherer
BACKGROUND: Obsessive-compulsive disorder (OCD) is a heterogeneous neuropsychiatric condition, thought to have a significant genetic component. When onset occurs in childhood, affected individuals generally exhibit different characteristics from adult-onset OCD, including higher prevalence in males and increased heritability. Since neuropsychiatric conditions are associated with copy number variations (CNVs), we considered their potential role in the etiology of OCD. METHODS: We genotyped 307 unrelated pediatric probands with idiopathic OCD (including 174 that were part of complete parent-child trios) and compared their genotypes with those of 3861 population controls, to identify rare CNVs (<0...
2016: Journal of Neurodevelopmental Disorders
https://www.readbyqxmd.com/read/27738328/genetic-variants-in-ptprd-and-risk-of-gestational-diabetes-mellitus
#17
Ting Chen, Juan Xu, Guangquan Liu, Heng Liu, Minjian Chen, Yufeng Qin, Wei Wu, Yankai Xia, Chenbo Ji, Xirong Guo, Juan Wen, Xinru Wang
Genome-wide association studies (GWASs) showed that two single nucleotide polymorphisms (SNPs) (rs17584499 and rs649891) in the protein tyrosine phosphatase receptor type D (PTPRD) were associated with type 2 diabetes (T2D). We sought to determine the influence of the PTPRD variants on the gestational diabetes mellitus (GDM) risk. In this research, two SNPs in PTPRD reported in T2D GWASs and six PTPRD expression-related SNPs were genotyped in 964 GDM cases and 1,021 controls using the Sequenom platform. Logistic regression analyses in additive models showed consistently significant associations of PTPRD rs10511544 A>C, rs10756026 T>A and rs10809070 C>G with a decreased risk of GDM [adjusted OR (95% CI) = 0...
November 15, 2016: Oncotarget
https://www.readbyqxmd.com/read/27539027/connectome-and-molecular-pharmacological-differences-in-the-dopaminergic-system-in-restless-legs-syndrome-rls-plastic-changes-and-neuroadaptations-that-may-contribute-to-augmentation
#18
REVIEW
Christopher J Earley, George R Uhl, Stefan Clemens, Sergi Ferré
Restless legs syndrome (RLS) is primarily treated with levodopa and dopaminergics that target the inhibitory dopamine receptor subtypes D3 and D2. The initial success of this therapy led to the idea of a hypodopaminergic state as the mechanism underlying RLS. However, multiple lines of evidence suggest that this simplified concept of a reduced dopamine function as the basis of RLS is incomplete. Moreover, long-term medication with the D2/D3 agonists leads to a reversal of the initial benefits of dopamine agonists and augmentation, which is a worsening of symptoms under therapy...
March 2017: Sleep Medicine
https://www.readbyqxmd.com/read/27335277/the-genetics-of-nodal-marginal-zone-lymphoma
#19
Valeria Spina, Hossein Khiabanian, Monica Messina, Sara Monti, Luciano Cascione, Alessio Bruscaggin, Elisa Spaccarotella, Antony B Holmes, Luca Arcaini, Marco Lucioni, Fabrizio Tabbò, Sakellarios Zairis, Fary Diop, Michaela Cerri, Sabina Chiaretti, Roberto Marasca, Maurilio Ponzoni, Silvia Deaglio, Antonio Ramponi, Enrico Tiacci, Laura Pasqualucci, Marco Paulli, Brunangelo Falini, Giorgio Inghirami, Francesco Bertoni, Robin Foà, Raul Rabadan, Gianluca Gaidano, Davide Rossi
Nodal marginal zone lymphoma (NMZL) is a rare, indolent B-cell tumor that is distinguished from splenic marginal zone lymphoma (SMZL) by the different pattern of dissemination. NMZL still lacks distinct markers and remains orphan of specific cancer gene lesions. By combining whole-exome sequencing, targeted sequencing of tumor-related genes, whole-transcriptome sequencing, and high-resolution single nucleotide polymorphism array analysis, we aimed at disclosing the pathways that are molecularly deregulated in NMZL and we compare the molecular profile of NMZL with that of SMZL...
September 8, 2016: Blood
https://www.readbyqxmd.com/read/27087860/array-based-molecular-karyotyping-in-fetuses-with-isolated-brain-malformations-identifies-disease-causing-cnvs
#20
Madita Schumann, Andrea Hofmann, Sophia K Krutzke, Alina C Hilger, Florian Marsch, Dietlinde Stienen, Ulrich Gembruch, Michael Ludwig, Waltraut M Merz, Heiko Reutter
BACKGROUND: The overall birth prevalence for congenital malformations of the central nervous system (CNS) among Europeans may be as high as 1 in 100 live births. The etiological factors remain largely unknown. The aim of this study was to detect causative copy number variations (CNVs) in fetuses of terminated pregnancies with prenatally detected isolated brain malformations. METHODS: Array-based molecular karyotyping was performed in a cohort of 35 terminated fetuses with isolated CNS malformations...
2016: Journal of Neurodevelopmental Disorders
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