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https://www.readbyqxmd.com/read/29777910/differentially-expressed-novel-alternatively-spliced-transcript-variant-of-tumor-suppressor-stk11-gene-in-mouse
#1
Hassan Mubarak Ishqi, Tarique Sarwar, Mohammed Amir Husain, Sayeed Ur Rehman, Mohammad Tabish
Serine/threonine kinase 11 (STK11) is a protein kinase that is encoded by Stk11 gene located on chromosome 19 and 10 in humans and mouse respectively. It acts as a master kinase of adenine monophosphate-activated protein kinase (AMPK) pathway that coordinates the regulation of cellular energy metabolism and cell division. STK11 exerts effect by activating more than 14 kinases including AMPK and AMPK-related kinases. It is also known to regulate cell polarity and acts as tumor suppressor. Alternative splicing of pre-mRNA is a mechanism which results in multiple transcript variants of a single gene...
May 16, 2018: Gene
https://www.readbyqxmd.com/read/29777376/comprehensive-molecular-diagnosis-of-epstein-barr-virus-associated-lymphoproliferative-diseases-using-next-generation-sequencing
#2
Shintaro Ono, Manabu Nakayama, Hirokazu Kanegane, Akihiro Hoshino, Saeko Shimodera, Hirofumi Shibata, Hisanori Fujino, Takahiro Fujino, Yuta Yunomae, Tsubasa Okano, Motoi Yamashita, Takahiro Yasumi, Kazushi Izawa, Masatoshi Takagi, Kohsuke Imai, Kejian Zhang, Rebecca Marsh, Capucine Picard, Sylvain Latour, Osamu Ohara, Tomohiro Morio
Epstein-Barr virus (EBV) is associated with several life-threatening diseases, such as lymphoproliferative disease (LPD), particularly in immunocompromised hosts. Some categories of primary immunodeficiency diseases (PIDs) including X-linked lymphoproliferative syndrome (XLP), are characterized by susceptibility and vulnerability to EBV infection. The number of genetically defined PIDs is rapidly increasing, and clinical genetic testing plays an important role in establishing a definitive diagnosis. Whole-exome sequencing is performed for diagnosing rare genetic diseases, but is both expensive and time-consuming...
May 18, 2018: International Journal of Hematology
https://www.readbyqxmd.com/read/29774580/evaluation-of-hoxc8-in-crested-swiss-chicken
#3
S Joller, P Ammann, C Flury, C Drögemüller
The crest in chicken consists of elongated and upraised feathers, as seen in various breeds such as the Silkie chicken. Recently, the still unknown causative mutation for the crest phenotype was assigned to chromosome 33 and an ectopic expression of HOXC8 was shown. The aim this study was to evaluate whether the crest phenotype in a local Swiss chicken breed, the Appenzeller Spitzhaubenhuhn, is associated with HOXC8. Three previously reported crest-associated flanking markers at the HOXC8 locus were genotyped in cohorts of this breed and two other local breeds without the crest phenotype...
May 18, 2018: Animal Genetics
https://www.readbyqxmd.com/read/29774201/investigation-of-experimental-factors-that-underlie-brca1-2-mrna-isoform-expression-variation-recommendations-for-utilizing-targeted-rna-sequencing-to-evaluate-potential-spliceogenic-variants
#4
Vanessa L Lattimore, John F Pearson, Margaret J Currie, Amanda B Spurdle, Bridget A Robinson, Logan C Walker
PCR-based RNA splicing assays are commonly used in diagnostic and research settings to assess the potential effects of variants of uncertain clinical significance in BRCA1 and BRCA2 . The Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) consortium completed a multicentre investigation to evaluate differences in assay design and the integrity of published data, raising a number of methodological questions associated with cell culture conditions and PCR-based protocols. We utilized targeted RNA-seq to re-assess BRCA1 and BRCA2 mRNA isoform expression patterns in lymphoblastoid cell lines (LCLs) previously used in the multicentre ENIGMA study...
2018: Frontiers in Oncology
https://www.readbyqxmd.com/read/29774030/changes-in-the-tcr%C3%AE-repertoire-and-tumor-immune-signature-from-a-cutaneous-melanoma-patient-immunized-with-the-csf-470-vaccine-a-case-report
#5
Mariana Aris, Alicia Inés Bravo, María Betina Pampena, Paula Alejandra Blanco, Ibel Carri, Daniel Koile, Patricio Yankilevich, Estrella Mariel Levy, María Marcela Barrio, José Mordoh
The allogeneic therapeutic vaccine CSF-470 has demonstrated a significant benefit over medium-dose IFNα2b in the distant metastasis-free survival for stages IIB-IIC-III cutaneous melanoma patients in a randomized phase II/III clinical trial (CASVAC-0401, NCT01729663). At the end of the 2-year CSF-470 immunization protocol, patient #006 developed several lung and one subcutaneous melanoma metastases; this later was excised. In this report, we analyzed the changes throughout vaccination of immune populations in blood and in the tumor tissue, with special focus on the T-cell repertoire...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29773329/mutation-screening-of-the-tia1-gene-in-chinese-patients-with-amyotrophic-lateral-sclerosis-frontotemporal-dementia
#6
XiaoJing Gu, YongPing Chen, QianQian Wei, Bei Cao, RuWei Ou, XiaoQin Yuan, YanBin Hou, LingYu Zhang, Hui Liu, XuePing Chen, Hui-Fang Shang
Mutations in the low-complexity domain (LCD) of T-cell intracellular antigen-1 (TIA1) have been reported to be associated with amyotrophic lateral sclerosis/frontotemporal dementia (ALS/FTD) in the Caucasian population. In the present study, we aimed to screen mutations in the LCD (exon 11-13) of TIA1 and determine the mutation frequency in Chinese ALS/FTD patients. A total of 740 ALS patients, including 721 sporadic ALS (sALS), 19 familial ALS, 24 FTD patients, and 501 healthy controls, were directly sequenced...
April 24, 2018: Neurobiology of Aging
https://www.readbyqxmd.com/read/29772757/fine-mapping-and-candidate-gene-prediction-for-white-immature-fruit-skin-in-cucumber-cucumis-sativus-l
#7
Hong-Yu Tang, Xu Dong, Jian-Ke Wang, Jun-Hui Xia, Fei Xie, Yu Zhang, Xuan Yao, Yue-Jin Xu, Zheng-Jie Wang
In this study, a single recessive gene (designated w ₀) was identified to control the white immature fruit color. Genetic mapping with simple sequence repeats (SSR) markers located the w₀ gene in the distal region of cucumber chromosome 3 (Chr.3). Fine mapping was then conducted using the method of draft genome scaffold-assisted chromosome walking with 7304 F₂ individuals, which allowed for the assignment of the gene locus to a 100.3 kb genomic DNA region with two flanking markers, Q138 and Q193. Thirteen candidate genes were predicted in the 100...
May 17, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29772374/evolution-expression-and-characterisation-of-liver-expressed-antimicrobial-peptide-genes-in-ancient-chondrostean-sturgeons
#8
Shuhuan Zhang, Qiaoqing Xu, Hao Du, Zhitao Qi, Youshen Li, Jun Huang, Jun Di, Qiwei Wei
Liver-expressed antimicrobial peptide 2 (leap-2) is an evolutionarily ancient molecule that acts as the key component in vertebrate innate immunity against invading pathogens. Leap-2 has been identified and characterised in several teleosts, but not yet in chondrosteans. Herein, the complete coding sequences of leap-2b and leap-2c were identified from expressed sequence tags (ESTs) isolated from Dabry's sturgeon (Acipenser dabryanus) and Chinese sturgeon (A. sinensis), designated as adleap-2b, adleap-2c, asleap-2b, and asleap-2c, respectively...
May 14, 2018: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29771377/alternative-splicing-analysis-in-human-monocytes-and-macrophages-reveals-mbnl1-as-major-regulator
#9
Hongfei Liu, Paolo A Lorenzini, Fan Zhang, Shaohai Xu, Mei Su M Wong, Jie Zheng, Xavier Roca
We report the detailed transcriptomic profiles of human innate myeloid cells using RNA sequencing. Monocytes migrate from blood into infected or wounded tissue to differentiate into macrophages, and control inflammation via phagocytosis or cytokine secretion. We differentiated culture primary monocytes with either GM- or M-CSF to obtain pro- or anti-inflammatory macrophages, and respectively activated them with either LPS/IFNγ or anti-inflammatory cytokines. We also treated the THP-1 monocytic cell line with PMA and similar cytokines to mimic differentiation and activation...
May 16, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29771280/identification-and-characterization-of-moonlighting-long-non-coding-rnas-based-on-rna-and-protein-interactome
#10
Lixin Cheng, Kwong-Sak Leung
Motivation: Moonlighting proteins are a class of proteins having multiple distinct functions, which play essential roles in a variety of cellular and enzymatic functioning systems. Although there have long been calls for computational algorithms for the identification of moonlighting proteins, research on approaches to identify moonlighting long non-coding RNAs (lncRNAs) has never been undertaken. Here, we introduce a novel methodology, MoonFinder, for the identification of moonlighting lncRNAs...
May 16, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29770457/abo-genotyping-with-next-generation-sequencing-to-resolve-heterogeneity-in-donors-with-serology-discrepancies
#11
Ping Chun Wu, Yin-Hung Lin, Lei Fang Tsai, Ming Hung Chen, Pei-Lung Chen, Shun-Chung Pai
BACKGROUND: ABO subtypes are characterized by the alteration of antigens present and their expression levels on red blood cells and many are linked to genetic changes in the ABO gene. Weakened expression of antigens should be identified to prevent transfusion reactions or ABO-incompatible transplantations. Genotyping can be applied to identify subtypes to complement serologic testing. Next-generation sequencing (NGS) has shown to provide sensitive and accurate genotyping results as well as valuable cis/trans information...
May 16, 2018: Transfusion
https://www.readbyqxmd.com/read/29770143/a-census-of-tandemly-repeated-polymorphic-loci-in-genic-regions-through-the-comparative-integration-of-human-genome-assemblies
#12
Loredana M Genovese, Filippo Geraci, Lucia Corrado, Eleonora Mangano, Romina D'Aurizio, Roberta Bordoni, Marco Severgnini, Giovanni Manzini, Gianluca De Bellis, Sandra D'Alfonso, Marco Pellegrini
Polymorphic Tandem Repeat (PTR) is a common form of polymorphism in the human genome. A PTR consists in a variation found in an individual (or in a population) of the number of repeating units of a Tandem Repeat (TR) locus of the genome with respect to the reference genome. Several phenotypic traits and diseases have been discovered to be strongly associated with or caused by specific PTR loci. PTR are further distinguished in two main classes: Short Tandem Repeats (STR) when the repeating unit has size up to 6 base pairs, and Variable Number Tandem Repeats (VNTR) for repeating units of size above 6 base pairs...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29769567/genomic-alterations-of-ground-glass-nodular-lung-adenocarcinoma
#13
Hyun Lee, Je-Gun Joung, Hyun-Tae Shin, Duk-Hwan Kim, Yujin Kim, Hojoong Kim, O Jung Kwon, Young Mog Shim, Ho Yun Lee, Kyung Soo Lee, Yoon-La Choi, Woong-Yang Park, D Neil Hayes, Sang-Won Um
In-depth molecular pathogenesis of ground-glass nodular lung adenocarcinoma has not been well understood. The objectives of this study were to identify genomic alterations in ground-glass nodular lung adenocarcinomas and to investigate whether viral transcripts were detected in these tumors. Nine patients with pure (n = 4) and part-solid (n = 5) ground-glass nodular adenocarcinomas were included. Six were females with a median age of 58 years. We performed targeted exon sequencing and RNA sequencing...
May 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29769358/resolving-the-phylogenetic-position-of-darwin-s-extinct-ground-sloth-mylodon-darwinii-using-mitogenomic-and-nuclear-exon-data
#14
Frédéric Delsuc, Melanie Kuch, Gillian C Gibb, Jonathan Hughes, Paul Szpak, John Southon, Jacob Enk, Ana T Duggan, Hendrik N Poinar
Mylodon darwinii is the extinct giant ground sloth named after Charles Darwin, who first collected its remains in South America. We have successfully obtained a high-quality mitochondrial genome at 99-fold coverage using an Illumina shotgun sequencing of a 12 880-year-old bone fragment from Mylodon Cave in Chile. Low level of DNA damage showed that this sample was exceptionally well preserved for an ancient subfossil, probably the result of the dry and cold conditions prevailing within the cave. Accordingly, taxonomic assessment of our shotgun metagenomic data showed a very high percentage of endogenous DNA with 22% of the assembled metagenomic contigs assigned to Xenarthra...
May 16, 2018: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29766417/the-fto-gene-is-associated-with-growth-and-omega-3-6-ratio-in-asian-seabass
#15
Fei Sun, Rongjian Tu, Jun Hong Xia, Xiao Jun Liu, Gen Hua Yue
Polymorphisms in the FTO gene are associated with obesity and body mass index in humans and livestock. Little information of whether FTO plays an important role in aquaculture fish species is available. We cloned and characterized the FTO gene in an economically important food fish species: Asian seabass (Lates calcarifer). The full-length cDNA of the gene is 3679 bp, containing an ORF of 1935 bp encoding 644 amino acids, a 216 bp 5' UTR and a 1538 bp 3' UTR. The gene consisted of nine exons and eight introns and was 117,679 bp in length...
May 16, 2018: Marine Biotechnology
https://www.readbyqxmd.com/read/29765525/clinical-characteristics-of-non-small-cell-lung-cancer-harboring-mutations-in-exon-20-of-egfr-or-her2
#16
Masayuki Takeda, Kazuko Sakai, Hidetoshi Hayashi, Kaoru Tanaka, Junko Tanizaki, Takayuki Takahama, Koji Haratani, Kazuto Nishio, Kazuhiko Nakagawa
Unlike common epidermal growth factor receptor gene ( EGFR ) mutations that confer sensitivity to tyrosine kinase inhibitors (TKIs) in non-small cell lung cancer (NSCLC), mutations in exon 20 of either EGFR or the human EGFR2 gene ( HER2 ) are associated with insensitivity to EGFR-TKIs, with treatment options for patients with such mutations being limited. Clinical characteristics, outcome of EGFR-TKI or nivolumab treatment, and the presence of coexisting mutations were reviewed for NSCLC patients with exon-20 mutations of EGFR or HER2 as detected by routine application of an amplicon-based next-generation sequencing panel...
April 20, 2018: Oncotarget
https://www.readbyqxmd.com/read/29765451/sequencing-of-exons-4-5-12-of-coch-gene-in-patients-with-postlingual-sensorineural-hearing-loss-accompanied-by-vestibular-lesion
#17
Marzena Mielczarek, Jurek Olszewski, Piotr Pietkiewicz
Introduction: Mutations at the DFNA9 locus on chromosome 14q12 are the third most common form of DFNA hearing loss, which is clinically characterized by late onset (in adulthood) progressive sensorineural hearing loss accompanied by vestibular dysfunction. The aim of the study was to search for COCH gene mutations (P51S, V66G, G87W, G88E, V104del, I109N, W117R, A119T, M512T, C542Y) in patients with severe or profound sensorineural hearing loss accompanied by a vestibular lesion. Material and methods: The study was based on a group of 30 patients...
April 2018: Archives of Medical Science: AMS
https://www.readbyqxmd.com/read/29765250/genetic-variants-in-the-exon-region-of-versican-predict-survival-of-patients-with-resected-early-stage-hepatitis-b-virus-associated-hepatocellular-carcinoma
#18
Xiaoguang Liu, Chuangye Han, Xiwen Liao, Long Yu, Guangzhi Zhu, Hao Su, Wei Qin, Sicong Lu, Xinping Ye, Tao Peng
Background: The upregulated expression of versican (VCAN) promotes the proliferation, invasion, and metastasis of various types of human cancer cells, including hepatocellular carcinoma (HCC) cells. Patients and methods: In this study, genetic variants in the exon region of VCAN were genotyped by DNA sequencing. Prognostic values of VCAN exon single nucleotide polymorphisms (SNPs) were assessed by Kaplan-Meier with the log-rank test, and uni- and multivariate Cox proportional hazard regression model...
2018: Cancer Management and Research
https://www.readbyqxmd.com/read/29765099/one-novel-representation-of-dna-sequence-based-on-the-global-and-local-position-information
#19
Zhiyi Mo, Wen Zhu, Yi Sun, Qilin Xiang, Ming Zheng, Min Chen, Zejun Li
One novel representation of DNA sequence combining the global and local position information of the original sequence has been proposed to distinguish the different species. First, for the sufficient exploitation of global information, one graphical representation of DNA sequence has been formulated according to the curve of Fermat spiral. Then, for the consideration of local characteristics of DNA sequence, attaching each point in the curve of Fermat spiral with the related mass has been applied based on the relationships of neighboring four nucleotides...
May 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29764576/-nipbl-gene-mutations-in-two-children-with-cornelia-de-lange-syndrome
#20
Yun-Jing Zhao, Hong-Wei Ma
Both children (one boy and one girl) experienced disease onset in infancy and visited the hospital due to growth retardation. They had unusual facies including thick hair, arched and confluent eyebrows, long and curly eyelashes, short nose, and micrognathia. Patient 1 had congenital heart disease (atrial septal defect and pulmonary stenosis) and special dermatoglyph (a single palmar crease). Patient 2 had cleft palate and moderate-to-severe deafness. Clinical features suggested Cornelia de Lange syndrome in both children...
May 2018: Zhongguo Dang Dai Er Ke za Zhi, Chinese Journal of Contemporary Pediatrics
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