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https://www.readbyqxmd.com/read/28330138/vdap-gui-a-user-friendly-pipeline-for-variant-discovery-and-annotation-of-raw-next-generation-sequencing-data
#1
Ramesh Menon, Namrata V Patel, Amitbikram Mohapatra, Chaitanya G Joshi
Even though next-generation sequencing (NGS) has become an invaluable tool in molecular biology, several laboratories with NGS facilities lack trained Bioinformaticians for data analysis. Here, focusing on the variant detection application of NGS analysis, we have developed a fully automated pipeline, namely Variant Discovery and Annotation Tool-Graphical User Interface (VDAP-GUI), which detects and annotates single nucleotide polymorphisms and insertions/deletions from raw sequence reads. VDAP-GUI consolidates several proven methods in each step such as quality control, trimming, mapping, variant detection and annotation...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28329683/inactivation-of-ezh2-upregulates-gfi1-and-drives-aggressive-myc-driven-group-3-medulloblastoma
#2
BaoHan T Vo, Chunliang Li, Marc A Morgan, Ilan Theurillat, David Finkelstein, Shaela Wright, Judith Hyle, Stephanie M C Smith, Yiping Fan, Yong-Dong Wang, Gang Wu, Brent A Orr, Paul A Northcott, Ali Shilatifard, Charles J Sherr, Martine F Roussel
The most aggressive of four medulloblastoma (MB) subgroups are cMyc-driven group 3 (G3) tumors, some of which overexpress EZH2, the histone H3K27 mono-, di-, and trimethylase of polycomb-repressive complex 2. Ezh2 has a context-dependent role in different cancers as an oncogene or tumor suppressor and retards tumor progression in a mouse model of G3 MB. Engineered deletions of Ezh2 in G3 MBs by gene editing nucleases accelerated tumorigenesis, whereas Ezh2 re-expression reversed attendant histone modifications and slowed tumor progression...
March 21, 2017: Cell Reports
https://www.readbyqxmd.com/read/28329682/the-swi-snf-protein-pbrm1-restrains-vhl-loss-driven-clear-cell-renal-cell-carcinoma
#3
Amrita M Nargund, Can G Pham, Yiyu Dong, Patricia I Wang, Hatice U Osmangeyoglu, Yuchen Xie, Omer Aras, Song Han, Toshinao Oyama, Shugaku Takeda, Chelsea E Ray, Zhenghong Dong, Mathieu Berge, A Ari Hakimi, Sebastien Monette, Carl L Lekaye, Jason A Koutcher, Christina S Leslie, Chad J Creighton, Nils Weinhold, William Lee, Satish K Tickoo, Zhong Wang, Emily H Cheng, James J Hsieh
PBRM1 is the second most commonly mutated gene after VHL in clear cell renal cell carcinoma (ccRCC). However, the biological consequences of PBRM1 mutations for kidney tumorigenesis are unknown. Here, we find that kidney-specific deletion of Vhl and Pbrm1, but not either gene alone, results in bilateral, multifocal, transplantable clear cell kidney cancers. PBRM1 loss amplified the transcriptional outputs of HIF1 and STAT3 incurred by Vhl deficiency. Analysis of mouse and human ccRCC revealed convergence on mTOR activation, representing the third driver event after genetic inactivation of VHL and PBRM1...
March 21, 2017: Cell Reports
https://www.readbyqxmd.com/read/28329541/cowden-syndrome-presenting-with-trichilemmomas
#4
Elise Ng, Vitaly Terushkin, Shane A Meehan, Roger Ho, Miriam Keltz Pomeranz
Cowden syndrome (CS) is a genetic cancerpredisposition syndrome that is associated withgermline mutations in the phosphate and tensinhomologue deleted on chromosome ten (PTEN)tumor suppressor gene. It is characterizedby the formation of benign and malignanttumors. Characteristic benign tumors includetrichilemmommas, acral keratoses, mucocutaneousneuromas, and oral papillomas. The most commonmalignant condition include breast, thyroid, andendometrial cancers. We present a case of a30-year-old woman with CS, who initially presentedwith trichilemmomas that were misdiagnosed ascomedonal acne...
December 15, 2016: Dermatology Online Journal
https://www.readbyqxmd.com/read/28329049/surgical-treatment-of-pulmonary-atresia-with-major-aortopulmonary-collateral-arteries-in-83-consecutive-patients%C3%A2
#5
Oleksandr D Babliak, Yaroslav B Mykychak, Oleksandra O Motrechko, Illya M Yemets
OBJECTIVES: This article reports the safety and efficacy of a morphology-based algorithm for the surgical management of pulmonary atresia and ventricular septal defect with major aortopulmonary collateral arteries. METHODS: A total of 83 patients were operated from 2007 to 2014 using 3 surgical approaches: one-stage total repair, one-stage unifocalization with central shunt and delayed total repair and multistage unifocalization with subsequent total repair. Patients were divided into 2 groups depending on the surgical strategy used to choose the surgical approach...
March 2, 2017: European Journal of Cardio-thoracic Surgery
https://www.readbyqxmd.com/read/28328141/a-590-kb-deletion-caused-by-non-allelic-homologous-recombination-between-two-line-1-elements-in-a-patient-with-mesomelia-synostosis-syndrome
#6
Tomohiro Kohmoto, Takuya Naruto, Miki Watanabe, Yuji Fujita, Sae Ujiro, Nana Okamoto, Hideaki Horikawa, Kiyoshi Masuda, Issei Imoto
Mesomelia-synostoses syndrome (MSS) is a rare, autosomal-dominant, syndromal osteochondrodysplasia characterized by mesomelic limb shortening, acral synostoses, and multiple congenital malformations due to a non-recurrent deletion at 8q13 that always encompasses two coding-genes, SULF1 and SLCO5A1. To date, five unrelated patients have been reported worldwide, and MMS was previously proposed to not be a genomic disorder associated with deletions recurring from non-allelic homologous recombination (NAHR) in at least two analyzed cases...
April 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28328139/long-term-survival-of-a-patient-with-perlman-syndrome-due-to-novel-compound-heterozygous-missense-mutations-in-rnb-domain-of-dis3l2
#7
Noriko Soma, Ken Higashimoto, Masaru Imamura, Akihiko Saitoh, Hidenobu Soejima, Keisuke Nagasaki
Perlman syndrome is a rare overgrowth syndrome characterized by polyhydramnios, macrosomia, distinctive facial appearance, renal dysplasia, and a predisposition to Wilms' tumor. The syndrome is often associated with a high neonatal mortality rate and there are few reports of long-term survivors. We studied a 6-year-old Japanese female patient, who was diagnosed with Perlman syndrome, with novel compound heterozygous mutations in DIS3L2 (c.[367-2A > G];[1328T > A]), who has survived long term. Most reported DIS3L2 mutations have been the homozygous deletion of exon 6 or exon 9, and these mutations would certainly have caused the loss of both RNA binding and degradation activity...
April 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28328133/an-xq22-1q22-2-nullisomy-in-a-male-patient-with-severe-neurological-impairment
#8
Kentaro Shirai, Yuya Higashi, Keiko Shimojima, Toshiyuki Yamamoto
The proteolipid protein 1 gene (PLP1) is located on chromosome Xq22.2 and is related to X-linked recessive leukoencephalopathy (Pelizaeus-Merzbacher disease: PMD). Compared to PLP1 duplications, which are a major contributor to PMD, chromosomal deletions in this region are rare and only a few PMD patients with small deletions have been reported, suggesting that large deletions of this region would cause embryonic lethality. Previously, we have reported female patients, with chromosomal deletions in this region, who showed severe developmental delays and behavioral abnormalities...
April 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28328126/quantitative-phenotypic-and-network-analysis-of-1q44-microdeletion-for-microcephaly
#9
Nicholas Raun, Janette Mailo, Egidio Spinelli, Xu He, Sarah McAvena, Logan Brand, Julia O'Sullivan, John Andersen, Lawrence Richer, Richard Tang-Wai, Francois V Bolduc
As genome wide techniques become more common, an increasing proportion of patients with intellectual disability (ID) are found to have genetic defects allowing genotype-phenotype correlations. Previously, AKT3 deletion was suggested to be responsible for microcephaly in patients with 1q43-q44 deletion syndrome, but this does not correspond to all cases. We report a case of a de novo 1q44 deletion in an 8-year-old boy with microcephaly in whom AKT3 is not deleted. We used a systematic review of the literature, our patient, and network analysis to gain a better understanding of the genetic basis of microcephaly in 1q deletion patients...
April 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28328119/cover-image-volume-173a-number-4-april-2017
#10
Paul Kruszka, Yonit A Addissie, Daniel E McGinn, Antonio R Porras, Elijah Biggs, Matthew Share, T Blaine Crowley, Brian H Y Chung, Gary T K Mok, Christopher C Y Mak, Premala Muthukumarasamy, Meow-Keong Thong, Nirmala D Sirisena, Vajira H W Dissanayake, C Sampath Paththinige, L B Lahiru Prabodha, Rupesh Mishra, Vorasuk Shotelersuk, Ekanem Nsikak Ekure, Ogochukwu Jidechukwu Sokunbi, Nnenna Kalu, Carlos R Ferreira, Jordann-Mishael Duncan, Siddaramappa Jagdish Patil, Kelly L Jones, Julie D Kaplan, Omar A Abdul-Rahman, Annette Uwineza, Leon Mutesa, Angélica Moresco, María Gabriela Obregon, Antonio Richieri-Costa, Vera L Gil-da-Silva-Lopes, Adebowale A Adeyemo, Marshall Summar, Elaine H Zackai, Donna M McDonald-McGinn, Marius George Linguraru, Maximilian Muenke
The cover image, by Paul Kruszka et al., is based on the Original Article 22q11.2 deletion syndrome in diverse populations, DOI: 10.1002/ajmg.a.38199. Individual images are property of the National Human Genome Research Institute and are in the public domain.
April 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28328118/22q11-2-deletion-syndrome-in-diverse-populations
#11
Paul Kruszka, Yonit A Addissie, Daniel E McGinn, Antonio R Porras, Elijah Biggs, Matthew Share, T Blaine Crowley, Brian H Y Chung, Gary T K Mok, Christopher C Y Mak, Premala Muthukumarasamy, Meow-Keong Thong, Nirmala D Sirisena, Vajira H W Dissanayake, C Sampath Paththinige, L B Lahiru Prabodha, Rupesh Mishra, Vorasuk Shotelersuk, Ekanem Nsikak Ekure, Ogochukwu Jidechukwu Sokunbi, Nnenna Kalu, Carlos R Ferreira, Jordann-Mishael Duncan, Siddaramappa Jagdish Patil, Kelly L Jones, Julie D Kaplan, Omar A Abdul-Rahman, Annette Uwineza, Leon Mutesa, Angélica Moresco, María Gabriela Obregon, Antonio Richieri-Costa, Vera L Gil-da-Silva-Lopes, Adebowale A Adeyemo, Marshall Summar, Elaine H Zackai, Donna M McDonald-McGinn, Marius George Linguraru, Maximilian Muenke
22q11.2 deletion syndrome (22q11.2 DS) is the most common microdeletion syndrome and is underdiagnosed in diverse populations. This syndrome has a variable phenotype and affects multiple systems, making early recognition imperative. In this study, individuals from diverse populations with 22q11.2 DS were evaluated clinically and by facial analysis technology. Clinical information from 106 individuals and images from 101 were collected from individuals with 22q11.2 DS from 11 countries; average age was 11.7 and 47% were male...
April 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28327638/conditional-deletion-of-ndufs4-in-dopaminergic-neurons-promotes-parkinson-s-disease-like-non-motor-symptoms-without-loss-of-dopamine-neurons
#12
Won-Seok Choi, Hyung-Wook Kim, François Tronche, Richard D Palmiter, Daniel R Storm, Zhengui Xia
Reduction of mitochondrial complex I activity is one of the major hypotheses for dopaminergic neuron death in Parkinson's disease. However, reduction of complex I activity in all cells or selectively in dopaminergic neurons via conditional deletion of the Ndufs4 gene, a subunit of the mitochondrial complex I, does not cause dopaminergic neuron death or motor impairment. Here, we investigated the effect of reduced complex I activity on non-motor symptoms associated with Parkinson's disease using conditional knockout (cKO) mice in which Ndufs4 was selectively deleted in dopaminergic neurons (Ndufs4 cKO)...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28327618/the-transcriptional-repressor-hic1-regulates-intestinal-immune-homeostasis
#13
K Burrows, F Antignano, M Bramhall, A Chenery, S Scheer, V Korinek, T M Underhill, C Zaph
The intestine is a unique immune environment that must respond to infectious organisms but remain tolerant to commensal microbes and food antigens. However, the molecular mechanisms that regulate immune cell function in the intestine remain unclear. Here we identify the POK/ZBTB family transcription factor hypermethylated in cancer 1 (HIC1, ZBTB29) as a central component of immunity and inflammation in the intestine. HIC1 is specifically expressed in immune cells in the intestinal lamina propria (LP) in the steady state and mice with a T-cell-specific deletion of HIC1 have reduced numbers of T cells in the LP...
March 22, 2017: Mucosal Immunology
https://www.readbyqxmd.com/read/28327604/chymase-producing-cells-of-the-innate-immune-system-are-required-for-decidual-vascular-remodeling-and-fetal-growth
#14
Nicole Meyer, Katja Woidacki, Martin Knöfler, Gudrun Meinhardt, Désirée Nowak, Philipp Velicky, Jürgen Pollheimer, Ana C Zenclussen
Intrauterine growth restriction (IUGR) is caused by insufficient remodeling of spiral arteries (SAs). The mechanism underlying the relevance of natural killer cells (NKs) and mast cells (MCs) for SA remodeling and its effects on pregnancy outcome are not well understood. We show that NK depletion arrested SA remodeling without affecting pregnancy. MC depletion resulted in abnormally remodeled SAs and IUGR. Combined absence of NKs and MCs substantially affected SA remodeling and impaired fetal growth. We found that α-chymase mast cell protease (Mcpt) 5 mediates apoptosis of uterine smooth muscle cells, a key feature of SA remodeling...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28327596/genetic-polymorphisms-of-54-mitochondrial-dna-snp-loci-in-chinese-xibe-ethnic-minority-group
#15
Chun-Mei Shen, Li Hu, Chun-Hua Yang, Cai-Yong Yin, Zhi-Dan Li, Hao-Tian Meng, Yu-Xin Guo, Ting Mei, Feng Chen, Bo-Feng Zhu
We analyzed the genetic polymorphisms of 54 mitochondrial DNA (mtDNA) variants in Chinese Xibe ethnic minority group. A total of 137 unrelated healthy volunteers from Chinese Xibe group were the objects of our study. Among the selected loci, there were 51 variable positions including transitions and transversions, and single nucleotide transitions were common (83.93%) versus transversions. These variations defined 64 different mtDNA haplotypes exclusive of (CA)n and 9 bp deletion variation. The haplotype diversity and discrimination power in Xibe population were 0...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28326957/alk-gene-copy-number-gain-and-immunohistochemical-expression-status-using-three-antibodies-in-neuroblastoma
#16
Eun Kyung Kim, Sewha Kim
Anaplastic lymphoma kinase ( ALK) gene aberrations-such as mutations, amplifications, and copy number gains-represent a major genetic predisposition to neuroblastoma (NB). This study aimed to evaluate the correlation between ALK gene copy number status, ALK protein expression, and clinicopathological parameters. We retrospectively retrieved 30 cases of poorly differentiated NB and constructed tissue microarrays (TMAs). ALK copy number changes were assessed by fluorescence in situ hybridization (FISH) assays, and ALK immunohistochemistry (IHC) testing was performed using three different antibodies (ALK1, D5F3, and 5A4 clones)...
March 2017: Pediatric and Developmental Pathology
https://www.readbyqxmd.com/read/28326452/methyleugenol-dna-adducts-in-human-liver-are-associated-with-sult1a1-copy-number-variations-and-expression-levels
#17
Roman Tremmel, Kristin Herrmann, Wolfram Engst, Walter Meinl, Kathrin Klein, Hansruedi Glatt, Ulrich M Zanger
Methyleugenol is a rodent hepatocarcinogen occurring in many herbs and spices as well as essential oils used for flavoring. Following metabolic activation by cytochromes P450 (CYPs) and sulfotransferases (SULTs), methyleugenol can form DNA adducts. Previously, we showed that DNA adduct formation by methyleugenol in mouse liver is dependent on SULT1A1 expression and that methyleugenol DNA adducts are abundant in human liver specimens. In humans, SULT1A1 activity is affected by genetic polymorphisms, including single-nucleotide polymorphisms (SNPs) and copy number variations (CNVs)...
March 22, 2017: Archives of Toxicology
https://www.readbyqxmd.com/read/28326294/the-eukaryote-like-serine-threonine-kinase-stk-regulates-the-growth-and-metabolism-of-zoonotic-streptococcus-suis
#18
Chunyan Zhang, Wen Sun, Meifang Tan, Mengmeng Dong, Wanquan Liu, Ting Gao, Lu Li, Zhuofei Xu, Rui Zhou
Like eukaryotes, bacteria express one or more serine/threonine kinases (STKs) that initiate diverse signaling networks. The STK from Streptococcus suis is encoded by a single-copy stk gene, which is crucial in stress response and virulence. To further understand the regulatory mechanism of STK in S. suis, a stk deletion strain (Δstk) and its complementary strain (CΔstk) were constructed to systematically decode STK characteristics by applying whole transcriptome RNA sequencing (RNA-Seq) and phosphoproteomic analysis...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28326293/pily1-promotes-legionella-pneumophila-infection-of-human-lung-tissue-explants-and-contributes-to-bacterial-adhesion-host-cell-invasion-and-twitching-motility
#19
Julia Hoppe, Can M Ünal, Stefanie Thiem, Louisa Grimpe, Torsten Goldmann, Nikolaus Gaßler, Matthias Richter, Olga Shevchuk, Michael Steinert
Legionnaires' disease is an acute fibrinopurulent pneumonia. During infection Legionella pneumophila adheres to the alveolar lining and replicates intracellularly within recruited macrophages. Here we provide a sequence and domain composition analysis of the L. pneumophila PilY1 protein, which has a high homology to PilY1 of Pseudomonas aeruginosa. PilY1 proteins of both pathogens contain a von Willebrand factor A (vWFa) and a C-terminal PilY domain. Using cellular fractionation, we assigned the L. pneumophila PilY1 as an outer membrane protein that is only expressed during the transmissive stationary growth phase...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28326190/malat1-regulates-myogenic-differentiation-and-muscle-regeneration-through-modulating-myod-transcriptional-activity
#20
Xiaona Chen, Liangqiang He, Yu Zhao, Yuying Li, Suyang Zhang, Kun Sun, Karl So, Fengyuan Chen, Liang Zhou, Leina Lu, Lijun Wang, Xihua Zhu, Xichen Bao, Miguel A Esteban, Shinichi Nakagawa, Kannanganattu V Prasanth, Zhenguo Wu, Hao Sun, Huating Wang
Malat1 is one of the most abundant long non-coding RNAs in various cell types; its exact cellular function is still a matter of intense investigation. In this study we characterized the function of Malat1 in skeletal muscle cells and muscle regeneration. Utilizing both in vitro and in vivo assays, we demonstrate that Malat1 has a role in regulating gene expression during myogenic differentiation of myoblast cells. Specifically, we found that knockdown of Malat1 accelerates the myogenic differentiation in cultured cells...
2017: Cell Discovery
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