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https://www.readbyqxmd.com/read/28912426/deconvolution-of-dna-methylation-identifies-differentially-methylated-gene-regions-on-1p36-across-breast-cancer-subtypes
#1
Alexander J Titus, Gregory P Way, Kevin C Johnson, Brock C Christensen
Breast cancer is a complex disease consisting of four distinct molecular subtypes. DNA methylation-based (DNAm) studies in tumors are complicated further by disease heterogeneity. In the present study, we compared DNAm in breast tumors with normal-adjacent breast samples from The Cancer Genome Atlas (TCGA). We constructed models stratified by tumor stage and PAM50 molecular subtype and performed cell-type reference-free deconvolution to control for cellular heterogeneity. We identified nineteen differentially methylated gene regions (DMGRs) in early stage tumors across eleven genes (AGRN, C1orf170, FAM41C, FLJ39609, HES4, ISG15, KLHL17, NOC2L, PLEKHN1, SAMD11, WASH5P)...
September 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28905115/clinical-application-of-snp-array-analysis-in-fetuses-with-ventricular-septal-defects-and-normal-karyotypes
#2
Fang Fu, Qiong Deng, Ting-Ying Lei, Ru Li, Xiang-Yi Jing, Xin Yang, Can Liao
PURPOSE: The present study aims to evaluate the utility of high-resolution single-nucleotide polymorphism (SNP) arrays in fetuses with ventricular septal defects (VSDs) with or without other structural anomalies but with normal karyotypes and to investigate the outcomes of cases of prenatal VSDs via clinical follow-up. METHODS: We analyzed 144 fetuses with VSDs and normal karyotypes using Affymetrix CytoScan HD arrays and the analyses were carried out a year after birth...
September 13, 2017: Archives of Gynecology and Obstetrics
https://www.readbyqxmd.com/read/28901666/clinicopathological-and-molecular-characteristics-of-pediatric-meningiomas
#3
Sudha Battu, Anupam Kumar, Pankaj Pathak, Suvendu Purkait, Linchi Dhawan, Mehar C Sharma, Ashish Suri, Manmohan Singh, Chitra Sarkar, Vaishali Suri
Molecular and clinical characteristics of pediatric meningiomas are poorly defined. Therefore, we analyzed clinical, morphological and molecular profiles of pediatric meningiomas. Forty pediatric meningiomas from January 2002 to June 2015 were studied. 1p36, 14q32 and 22q-deletion were assessed by fluorescent in situ hybridization and mutations of most relevant exons of AKT, SMO, KLF4, TRAF and pTERT using sequencing. Expression of GAB1, stathmin, progesterone receptor (PR), p53 along with MIB-1 LI was examined using immunohistochemistry...
September 13, 2017: Neuropathology: Official Journal of the Japanese Society of Neuropathology
https://www.readbyqxmd.com/read/28814241/the-emerging-picture-of-cdk11-genetic-functional-and-medicinal-aspects
#4
Nikolas Ferreira Dos Santos Paparidis, Fernanda Canduri
Cyclin-dependent kinase 11 is a relatively neglected member of the transcriptional CDKs subfamily, despite possibly being the most versatile CDK in this group. Different CDK11 variants are known to play essential roles in major cellular processes as mRNA transcription (CDK11p110), mitosis (CDK11p58), and apoptosis (CDK11p46 and CDK11p60). Each CDK11 species targets a particular set of substrates related to its functional background, but all isoforms originate from the CDC2L gene complex in human chromosome 1p36...
August 14, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/28811188/familial-1p36-3-microduplication-resulting-from-a-1p-9q-non-reciprocal-translocation
#5
Valentine Marquet, Sylvie Bourthoumieu, Amelia Dobrescu, Cécile Laroche-Raynaud, Catherine Yardin
Unlike the 1p36 microdeletion syndrome, which has been extensively described, 1p36 microduplications have rarely been reported. We describe a three years old boy presenting with a severe global developmental delay and a few dysmorphic features. Cytogenetic analyses revealed a maternally inherited 3.35 Mb microduplication of chromosomal band 1p36.3. The maternal grandfather is also carrier of the same chromosomal rearrangement. Interestingly, the duplicated 1p36.3 segment was found to be localized at the telomeric end of the long arms of a chromosome 9, probably deriving from a 1p36...
August 12, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/28791793/early-transition-from-insulin-to-sulfonylureas-in-neonatal-diabetes-and-follow-up-experience-from-china
#6
Xiuzhen Li, Aijing Xu, Huiying Sheng, Tzer Hwu Ting, Xiaojian Mao, Xinjiang Huang, Minyan Jiang, Jing Cheng, Li Liu
BACKGROUND: Sulfonylurea therapy can improve glycemic control and ameliorate neurodevelopmental outcomes in patients suffering from neonatal diabetes mellitus (NDM) with KCNJ11 or ABCC8 mutations. As genetic testing results are often delayed, it remains controversial whether sulfonylurea treatment should be attempted immediately at diagnosis or doctors should await genetic confirmation. OBJECTIVE: This study aimed to investigate the effectiveness and safety of sulfonylurea therapy in Chinese NDM patients during infancy before genetic testing results were available...
August 8, 2017: Pediatric Diabetes
https://www.readbyqxmd.com/read/28770103/subclonal-analysis-in-a-lobular-breast-cancer-with-classical-and-solid-growth-pattern-mimicking-a-solid-papillary-carcinoma
#7
Matthias Christgen, Stephan Bartels, Jana Lisa van Luttikhuizen, Maximilian Schieck, Stefanie Pertschy, Sudip Kundu, Ulrich Lehmann, Bjoern Sander, Enrico Pelz, Florian Länger, Brigitte Schlegelberger, Doris Steinemann, Hans Kreipe
Recently, a new variant of invasive lobular breast cancer (ILBC) with solid-papillary-like growth pattern has been described. We present a case of ILBC with solid-papillary-like growth pattern in the main tumour mass and classical invasive lobular growth pattern in adjacent satellite foci. The two tumour components were subjected to comprehensive molecular analyses. Both components were ER/PR-positive, HER2-negative, and showed a complete loss of E-cadherin and beta-catenin protein expression, as determined by immunohistochemistry...
July 2017: Journal of Pathology. Clinical Research
https://www.readbyqxmd.com/read/28696552/clinical-experience-with-a-single-nucleotide-polymorphism-based-noninvasive-prenatal-test-for-five-clinically-significant-microdeletions
#8
Kimberly Martin, Sushma Iyengar, Akshita Kalyan, Christine Lan, Alexander L Simon, Melissa Stosic, Katie Kobara, Harini Ravi, Tina Truong, Allison Ryan, Zachary P Demko, Peter Benn
Single-nucleotide polymorphism (SNP)-based noninvasive prenatal testing (NIPT) can currently predict a subset of submicroscopic abnormalities associated with severe clinical manifestations. We retrospectively analyzed the performance of SNP-based NIPT in 80,449 referrals for 22q11.2 deletion syndrome and 42,326 referrals for 1p36, cri-du-chat, Prader-Willi, and Angelman microdeletion syndromes over a one-year period, and compared the original screening protocol with a revision that reflexively sequenced high-risk calls at a higher depth of read...
July 11, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/28683472/comprehensive-analysis-of-copy-number-aberrations-in-microsatellite-stable-colon-cancer-in-view-of-stromal-component
#9
M Henar Alonso, Susanna Aussó, Adriana Lopez-Doriga, David Cordero, Elisabet Guinó, Xavier Solé, Mercè Barenys, Javier de Oca, Gabriel Capella, Ramón Salazar, Rebeca Sanz-Pamplona, Victor Moreno
BACKGROUND: Somatic copy number aberrations (CNAs) are common acquired changes in cancer cells having an important role in the progression of colon cancer (colorectal cancer, CRC). This study aimed to perform a characterisation of CNA and their impact in gene expression. METHODS: Copy number aberrations were inferred from SNP array data in a series of 99 CRC. Copy number aberration events were calculated and used to assess the association between copy number dosage, clinical and molecular characteristics of the tumours, and gene expression changes...
July 25, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28673192/association-between-clinicopathological-factors-and-genomic-abnormalities-detected-by-fish-analysis-in-epithelioid-diffuse-malignant-pleural-mesothelioma
#10
Maiko Takeda, Takahiko Kasai, Kinta Hatakeyama, Tokiko Nakai, Hiroe Itami, Tomoko Uchiyama, Norishige IIzuka, Hiroshi Maruyama, Chiho Ohbayashi
BACKGROUND: Abnormality of genes including 9p21 is known in malignant mesothelioma and we have examined the frequency of gene deletion and amplification using the fluorescence in situ hybridization (FISH) method. We formerly reported that abnormality of the genes was more common in the sarcomatoid type than epithelioid type. In this study, we compared the clinicopathological factors including nuclear grade (NG) and genomic abnormality in epithelioid malignant pleural mesothelioma (MPM)...
June 1, 2017: International Journal of Surgical Pathology
https://www.readbyqxmd.com/read/28645799/genotype-phenotype-evaluation-of-med13l-defects-in-the-light-of-a-novel-truncating-and-a-recurrent-missense-mutation
#11
Reza Asadollahi, Markus Zweier, Laura Gogoll, Raphael Schiffmann, Heinrich Sticht, Katharina Steindl, Anita Rauch
A decade after the designation of MED13L as a gene and its link to intellectual disability (ID) and dextro-looped transposition of great arteries in 2003, we previously described a recognizable syndrome due to MED13L haploinsufficiency. Subsequent reports of 22 further patients diagnosed by genome-wide testing further delineated the syndrome with expansion of the phenotypic spectrum and showed reduced penetrance for congenital heart defects. We now report two novel patients identified by whole exome sequencing, one with a de novo MED13L truncating mutation and the other with a de novo missense mutation...
June 21, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/28637693/neuroblast-differentiation-during-development-and-in-neuroblastoma-requires-kif1b%C3%AE-mediated-transport-of-trka
#12
Stuart M Fell, Shuijie Li, Karin Wallis, Anna Kock, Olga Surova, Vilma Rraklli, Carolin S Höfig, Wenyu Li, Jens Mittag, Marie Arsenian Henriksson, Rajappa S Kenchappa, Johan Holmberg, Per Kogner, Susanne Schlisio
We recently identified pathogenic KIF1Bβ mutations in sympathetic nervous system malignancies that are defective in developmental apoptosis. Here we deleted KIF1Bβ in the mouse sympathetic nervous system and observed impaired sympathetic nervous function and misexpression of genes required for sympathoadrenal lineage differentiation. We discovered that KIF1Bβ is required for nerve growth factor (NGF)-dependent neuronal differentiation through anterograde transport of the NGF receptor TRKA. Moreover, pathogenic KIF1Bβ mutations identified in neuroblastoma impair TRKA transport...
May 15, 2017: Genes & Development
https://www.readbyqxmd.com/read/28594133/diagnostic-value-of-stmn1-lmo2-hgal-aid-expression-and-1p36-chromosomal-abnormalities-in-primary-cutaneous-b-cell-lymphomas
#13
Evelyne Verdanet, Olivier Dereure, Céline René, Ariane Tempier, Assia Benammar-Hafidi, Mathieu Gallo, Eric Frouin, Luc Durand, Isabelle Gazagne, Valérie Costes-Martineau, Valère Cacheux, Vanessa Szablewski
AIMS: Distinction between primary cutaneous follicular lymphoma (PCFL) and primary cutaneous marginal zone lymphoma (PCMZL) is challenging, as clear-cut immunophenotypical and cytogenetic criteria to segregate both entities are lacking. METHODS AND RESULTS: To characterize PCFL and PCMZL more clearly and to define criteria helpful for the differential diagnosis, we compared expression of immunohistochemical markers [LIM-only transcription factor 2 (LMO2), human germinal centre-associated lymphoma (HGAL), stathmin 1 (STMN1), activation-induced cytidine deaminase (AID), myeloid cell nuclear differentiation antigen (MNDA)] and the presence of cytogenetic abnormalities described previously in nodal follicular lymphoma [B cell lymphoma 2 (BCL2) and BCL6 breaks, 1p36 chromosomal region deletion (del 1p36)] in a series of 48 cutaneous follicular and marginal zone lymphomas [cutaneous follicular lymphoma (CFL) and cutaneous marginal zone lymphoma (CMZL)]...
June 8, 2017: Histopathology
https://www.readbyqxmd.com/read/28570402/genetic-factors-involved-in-mandibular-prognathism
#14
Anna Doraczynska-Kowalik, Kamil H Nelke, Wojciech Pawlak, Maria M Sasiadek, Hanna Gerber
Mandibular prognathism is defined as an abnormal forward projection of the mandible beyond the standard relation to the cranial base and it is usually categorized as both a skeletal Class III pattern and Angle Class III malocclusion. The etiology of mandibular prognathism is still uncertain, with various genetic, epigenetic, and environmental factors possibly involved. However, many reports on its coexistence in both twins and segregation in families suggest the importance of genetic influences. A multifactorial and polygenic background with a threshold for expression or an autosomal dominant mode with incomplete penetrance and variable expressivity are the most probable inheritance patterns...
May 31, 2017: Journal of Craniofacial Surgery
https://www.readbyqxmd.com/read/28516910/genetic-architecture-of-epigenetic-and-neuronal-ageing-rates-in-human-brain-regions
#15
Ake T Lu, Eilis Hannon, Morgan E Levine, Eileen M Crimmins, Katie Lunnon, Jonathan Mill, Daniel H Geschwind, Steve Horvath
Identifying genes regulating the pace of epigenetic ageing represents a new frontier in genome-wide association studies (GWASs). Here using 1,796 brain samples from 1,163 individuals, we carry out a GWAS of two DNA methylation-based biomarkers of brain age: the epigenetic ageing rate and estimated proportion of neurons. Locus 17q11.2 is significantly associated (P=4.5 × 10(-9)) with the ageing rate across five brain regions and harbours a cis-expression quantitative trait locus for EFCAB5 (P=3.4 × 10(-20))...
May 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28459463/mycn-induces-neuroblastoma-in-primary-neural-crest-cells
#16
R R Olsen, J H Otero, J García-López, K Wallace, D Finkelstein, J E Rehg, Z Yin, Y-D Wang, K W Freeman
Neuroblastoma (NBL) is an embryonal cancer of the sympathetic nervous system (SNS), which causes 15% of pediatric cancer deaths. High-risk NBL is characterized by N-Myc amplification and segmental chromosomal gains and losses. Owing to limited disease models, the etiology of NBL is largely unknown, including both the cell of origin and the majority of oncogenic drivers. We have established a novel system for studying NBL based on the transformation of neural crest cells (NCCs), the progenitor cells of the SNS, isolated from mouse embryonic day 9...
August 31, 2017: Oncogene
https://www.readbyqxmd.com/read/28433800/chromosomal-alterations-and-gene-expression-changes-associated-with-the-progression-of-leukoplakia-to-advanced-gingivobuccal-cancer
#17
Priyanka G Bhosale, Simona Cristea, Srikant Ambatipudi, Rajiv S Desai, Rajiv Kumar, Asawari Patil, Shubhada Kane, Anita M Borges, Alejandro A Schäffer, Niko Beerenwinkel, Manoj B Mahimkar
We present an integrative genome-wide analysis that can be used to predict the risk of progression from leukoplakia to oral squamous cell carcinoma (OSCC) arising in the gingivobuccal complex (GBC). We find that the genomic and transcriptomic profiles of leukoplakia resemble those observed in later stages of OSCC and that several changes are associated with this progression, including amplification of 8q24.3, deletion of 8p23.2, and dysregulation of DERL3, EIF5A2, ECT2, HOXC9, HOXC13, MAL, MFAP5 and NELL2. Comparing copy number profiles of primary tumors with and without lymph-node metastasis, we identify alterations associated with metastasis, including amplifications of 3p26...
June 2017: Translational Oncology
https://www.readbyqxmd.com/read/28288578/case-report-of-pierre-robin-sequence-with-severe-upper-airway-obstruction-who-was-rescued-by-fiberoptic-nasotracheal-intubation
#18
Satoru Takeshita, Hiroko Ueda, Tatenobu Goto, Daisuke Muto, Hiroki Kakita, Kazuo Oshima, Takahisa Tainaka, Takayuki Ono, Yoshiaki Kazaoka, Yasumasa Yamada
BACKGROUND: Pierre Robin sequence (PRS) refers to the association of micrognathia, glossoptosis, and airway obstruction. Cases with severe dyspnea due to upper airway obstruction immediately after birth are very rare. We here report two cases with PRS who developed severe dyspnea due to morphological abnormality immediately after birth and were rescued by fiberoptic nasotracheal intubation. CASE PRESENTATION: The patient in case 1 had micrognathia and cleft palate, and his tongue protruded into the nasal cavity via a cleft palate...
March 14, 2017: BMC Anesthesiology
https://www.readbyqxmd.com/read/28171565/endometriosis-risk-alleles-at-1p36-12-act-through-inverse-regulation-of-cdc42-and-linc00339
#19
Joseph E Powell, Jenny N Fung, Konstantin Shakhbazov, Yadav Sapkota, Nicole Cloonan, Gibran Hemani, Kristine M Hillman, Susanne Kaufmann, Hien T Luong, Lisa Bowdler, Jodie N Painter, Sarah J Holdsworth-Carson, Peter M Visscher, Marcel E Dinger, Martin Healey, Dale R Nyholt, Juliet D French, Stacey L Edwards, Peter A W Rogers, Grant W Montgomery
No abstract text is available yet for this article.
November 15, 2016: Human Molecular Genetics
https://www.readbyqxmd.com/read/28165464/genome-wide-association-analysis-implicates-dysregulation-of-immunity-genes-in-chronic-lymphocytic-leukaemia
#20
Philip J Law, Sonja I Berndt, Helen E Speedy, Nicola J Camp, Georgina P Sava, Christine F Skibola, Amy Holroyd, Vijai Joseph, Nicola J Sunter, Alexandra Nieters, Silvia Bea, Alain Monnereau, David Martin-Garcia, Lynn R Goldin, Guillem Clot, Lauren R Teras, Inés Quintela, Brenda M Birmann, Sandrine Jayne, Wendy Cozen, Aneela Majid, Karin E Smedby, Qing Lan, Claire Dearden, Angela R Brooks-Wilson, Andrew G Hall, Mark P Purdue, Tryfonia Mainou-Fowler, Claire M Vajdic, Graham H Jackson, Pierluigi Cocco, Helen Marr, Yawei Zhang, Tongzhang Zheng, Graham G Giles, Charles Lawrence, Timothy G Call, Mark Liebow, Mads Melbye, Bengt Glimelius, Larry Mansouri, Martha Glenn, Karen Curtin, W Ryan Diver, Brian K Link, Lucia Conde, Paige M Bracci, Elizabeth A Holly, Rebecca D Jackson, Lesley F Tinker, Yolanda Benavente, Paolo Boffetta, Paul Brennan, Marc Maynadie, James McKay, Demetrius Albanes, Stephanie Weinstein, Zhaoming Wang, Neil E Caporaso, Lindsay M Morton, Richard K Severson, Elio Riboli, Paolo Vineis, Roel C H Vermeulen, Melissa C Southey, Roger L Milne, Jacqueline Clavel, Sabine Topka, John J Spinelli, Peter Kraft, Maria Grazia Ennas, Geoffrey Summerfield, Giovanni M Ferri, Robert J Harris, Lucia Miligi, Andrew R Pettitt, Kari E North, David J Allsup, Joseph F Fraumeni, James R Bailey, Kenneth Offit, Guy Pratt, Henrik Hjalgrim, Chris Pepper, Stephen J Chanock, Chris Fegan, Richard Rosenquist, Silvia de Sanjose, Angel Carracedo, Martin J S Dyer, Daniel Catovsky, Elias Campo, James R Cerhan, James M Allan, Nathanial Rothman, Richard Houlston, Susan Slager
Several chronic lymphocytic leukaemia (CLL) susceptibility loci have been reported; however, much of the heritable risk remains unidentified. Here we perform a meta-analysis of six genome-wide association studies, imputed using a merged reference panel of 1,000 Genomes and UK10K data, totalling 6,200 cases and 17,598 controls after replication. We identify nine risk loci at 1p36.11 (rs34676223, P=5.04 × 10(-13)), 1q42.13 (rs41271473, P=1.06 × 10(-10)), 4q24 (rs71597109, P=1.37 × 10(-10)), 4q35.1 (rs57214277, P=3...
February 6, 2017: Nature Communications
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