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https://read.qxmd.com/read/30776697/gene-mutational-analysis-in-a-cohort-of-chinese-children-with-unexplained-epilepsy-identification-of-a-new-kcnd3-phenotype-and-novel-genes-causing-dravet-syndrome
#1
Jiaping Wang, Yongxin Wen, Qingping Zhang, Shujie Yu, Yan Chen, Xiru Wu, YueHua Zhang, Xinhua Bao
PURPOSE: This study aimed to investigate the genetic etiology of epilepsy in a cohort of Chinese children. METHODS: Targeted next-generation sequencing (NGS) was performed for 120 patients with unexplained epilepsy, including 71 patients with early-onset epileptic encephalopathies, and 16 patients with Dravet syndrome (including three patients with a Dravet-like phenotype) but without SCN1A pathogenic variants. RESULTS: Pathogenic variants of 14 genes were discovered in 22 patients (18%)...
January 28, 2019: Seizure: the Journal of the British Epilepsy Association
https://read.qxmd.com/read/30776545/strengthening-laboratory-surveillance-of-viral-pathogens-experiences-and-lessons-learned-building-next-generation-sequencing-capacity-in-ghana
#2
Rachel L Marine, Nana Afia Asante Ntim, Christina J Castro, Keren O Attiku, Deborah Pratt, Ewurabena Duker, Esinam Agbosu, Terry Fei Fan Ng, Wangeci Gatei, Evangeline Obodai, John Kofi Odoom, Chastity L Walker, Paul A Rota, M Steven Oberste, William Kwabena Ampofo, S Arunmozhi Balajee
OBJECTIVES: To demonstrate the feasibility of applying next-generation sequencing (NGS) in medium-resource reference laboratories in Africa to enhance global disease surveillance. METHODS: A training program was developed to support implementation of NGS at Noguchi Memorial Institute for Medical Research (NMIMR), University of Ghana. The program was divided into two training stages, first at the Centers for Disease Control and Prevention (CDC) in Atlanta, GA, followed by on-site training at NMIMR for a larger cohort of scientists...
February 15, 2019: International Journal of Infectious Diseases: IJID
https://read.qxmd.com/read/30776361/endometriosis-associated-ovarian-cancer-what-have-we-learned-so-far
#3
REVIEW
M Herreros-Villanueva, Chih-Chieh Chen, Eing-Mei Tsai, Tze-Kiong Er
Endometriosis is defined as the presence of ectopic endometrial tissue outside of the uterine cavity, most commonly in the ovaries and peritoneum. It is a complex disease that is influenced by multiple factors. It is also a common gynecological disorder and affects approximately 10-15% of all women of reproductive age. Recent molecular and pathological studies indicate that endometriosis may serve as a precursor of ovarian cancer (endometriosis-associated ovarian cancer, EAOC), particularly endometrioid and clear cell ovarian cancers...
February 15, 2019: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://read.qxmd.com/read/30776175/somatic-alterations-of-tp53-erbb2-pik3ca-and-ccnd1-were-associated-with-chemosensitivity-for-breast-cancers
#4
Libo Yang, Feng Ye, Longlong Bao, Xiaoyan Zhou, Zhe Wang, Peizhen Hu, Nengtai Ouyang, Xiaojuan Li, Yi Shi, Gang Chen, Peiyi Xia, Meiying Chui, Wencai Li, Ying Jia, Liu Yueping, Junjun Liu, Junyi Ye, Zhe Zhang, Hong Bu
The correlation of genetic alterations with responding to neoadjuvant chemotherapy (NAC) is not fully revealed. In this study, we enrolled 247 breast cancers receiving anthracycline-taxane-based NAC treatment. Next generation sequencing (NGS) panel containing 36 hot spot breast cancer related genes was used in this study. Two different extent of pathologic complete response (pCR) standards, which were ypT0/isypN0 and ypT0/is, were used as indicators for NAC treatment. TP53 mutation (n = 149, 60.3%), PIK3CA mutation (n = 109, 44...
February 18, 2019: Cancer Science
https://read.qxmd.com/read/30775878/a-myelodysplastic-syndrome-with-concurrent-basophilia-and-eosinophilia-lacking-oncogenic-mutations-in-54-relevant-genes
#5
Miyoung Kim, Dae Young Zang, Boram Han, Jiwon Lee, Yousun Chung, Chan-Jeoung Park, Young Kyung Lee
Myelodysplastic syndromes (MDS) with basophilia or eosinophilia are very rare and portend poor prognoses. We present a rare patient who had MDS with excess blasts as well as peripheral basophilia and concurrent bone marrow (BM) basophilia/eosinophilia. She had a complex karyotype including 5q and 7q deletions; however, no oncogenic mutations were observed on next-generation sequencing of 54 genes known to be frequently mutated in acute myeloid leukemia/MDS. Peripheral basophilia resolved after decitabine treatment...
January 1, 2019: Clinical Laboratory
https://read.qxmd.com/read/30775047/a-novel-de-novo-frameshift-mutation-in-kat6a-identified-by-whole-exome-sequencing
#6
Asem Alkhateeb, Wafa Alazaizeh
Intellectual disability is a common condition with multiple etiologies. The number of monogenic causes has increased steadily in recent years due to the implementation of next generation sequencing. Here, we describe a 2-year-old boy with global developmental delay and intellectual disability. The child had feeding difficulties since birth. He had delayed motor skills and muscular hypotonia. Brain magnetic resonance imaging revealed diffuse white matter loss and thinning of the corpus callosum. Banded karyotype and comparative genomic hybridization (CGH) array were normal...
March 2019: Journal of Pediatric Genetics
https://read.qxmd.com/read/30774650/metastatic-tumor-cells-genotypes-and-phenotypes
#7
Dingcheng Gao, Vivek Mittal, Yi Ban, Ana Rita Lourenco, Shira Yomtoubian, Sharrell Lee
BACKGROUND: Metastasis is the primary cause of mortality in cancer patients. Therefore, elucidating the genetics and epigenetics of metastatic tumor cells and the mechanisms by which tumor cells acquire metastatic properties constitute significant challenges in cancer research. OBJECTIVE: To summarize the current understandings of the specific genotype and phenotype of the metastatic tumor cells. METHOD and RESULT: In-depth genetic analysis of tumor cells, especially with advances in the next-generation sequencing, have revealed insights of the genotypes of metastatic tumor cells...
August 2018: Frontiers in Biology
https://read.qxmd.com/read/30774647/systems-biology-approaches-toward-understanding-primary-mitochondrial-diseases
#8
REVIEW
Elaina M Maldonado, Fatma Taha, Joyeeta Rahman, Shamima Rahman
Primary mitochondrial diseases form one of the most common and severe groups of genetic disease, with a birth prevalence of at least 1 in 5000. These disorders are multi-genic and multi-phenotypic (even within the same gene defect) and span the entire age range from prenatal to late adult onset. Mitochondrial disease typically affects one or multiple high-energy demanding organs, and is frequently fatal in early life. Unfortunately, to date there are no known curative therapies, mostly owing to the rarity and heterogeneity of individual mitochondrial diseases, leading to diagnostic odysseys and difficulties in clinical trial design...
2019: Frontiers in Genetics
https://read.qxmd.com/read/30774400/alternative-eradication-regimens-for-helicobacter-pylori-infection-in-indonesian-regions-with-high-metronidazole-and-levofloxacin-resistance
#9
Muhammad Miftahussurur, Langgeng Agung Waskito, Ari Fahrial Syam, Iswan Abbas Nusi, Gontar Siregar, Marselino Richardo, Achmad Fuad Bakry, Yudith Annisa Ayu Rezkitha, I Dewa Nyoman Wibawa, Yoshio Yamaoka
Background: The prevalence of Helicobacter pylori resistance to metronidazole and clarithromycin is high in Indonesia. Moreover, the increasing levofloxacin resistance rates in the absence of bismuth treatment in Indonesia has led to the use of other antibiotics as alternative regimens. Methods: We determined the minimum inhibitory concentrations (MICs) of five alternative antibiotics for H. pylori (rifaximin, rifabutin, furazolidone, garenoxacin, and sitafloxacin) using the agar dilution method and assessed mutations associated with antibiotic resistance using next-generation sequencing...
2019: Infection and Drug Resistance
https://read.qxmd.com/read/30774126/using-in-vitro-and-in-cell-shape-to-investigate-small-molecule-induced-pre-mrna-structural-changes
#10
Jingxin Wang, John Hammond, Kristen A Johnson
In the process of drug development of RNA-targeting small molecules, elucidating the structural changes upon their interactions with target RNA sequences is desired. We herein provide a detailed in vitro and in-cell selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) protocol to study the RNA structural change in the presence of an experimental drug for spinal muscular atrophy (SMA), survival of motor neuron (SMN)-C2, and in exon 7 of the pre-mRNA of the SMN2 gene. In in vitro SHAPE, an RNA sequence of 140 nucleotides containing SMN2 exon 7 is transcribed by T7 RNA polymerase, folded in the presence of SMN-C2, and subsequently modified by a mild 2'-OH acylation reagent, 2-methylnicotinic acid imidazolide (NAI)...
January 30, 2019: Journal of Visualized Experiments: JoVE
https://read.qxmd.com/read/30773826/identification-of-a-novel-hla-b-40-variant-allele-b-40-405-by-next-generation-sequencing
#11
Shinae Yu, Jae Houn Shim, Kwang Jun Park, So-Jung Choi, Kyung Ran Jun
The new allele, HLA-B*40:405 differs from B*40:02:01:01 by one nucleotide substitution at codon 304. This article is protected by copyright. All rights reserved.
February 18, 2019: HLA
https://read.qxmd.com/read/30773800/homozygous-variant-in-otx2-and-possible-genetic-modifiers-identified-in-a-patient-with-combined-pituitary-hormone-deficiency-ocular-involvement-myopathy-ataxia-and-mitochondrial-impairment
#12
Alessia Catania, Andrea Legati, Lorenzo Peverelli, Lorenzo Nanetti, Silvia Marchet, Nadia Zanetti, Costanza Lamperti, Daniele Ghezzi
Here we report on a singleton patient affected by a complicated congenital syndrome characterized by growth delay, retinal dystrophy, sensorineural deafness, myopathy, ataxia, combined pituitary hormone deficiency, associated with mitochondrial impairment. Targeted clinical exome sequencing led to the identification of a homozygous missense variant in OTX2. Since only dominant mutations within OTX2 have been associated with cases of syndromic microphthalmia, retinal dystrophy with or without pituitary dysfunctions, this represents the first report of an OTX2 recessive mutation...
February 17, 2019: American Journal of Medical Genetics. Part A
https://read.qxmd.com/read/30773302/distinctive-subpopulations-of-the-intestinal-microbiota-are-present-in-women-with-unexplained-chronic-anovulation
#13
Hiroyuki Sasaki, Kazuhiro Kawamura, Toshihiro Kawamura, Toshitaka Odamaki, Noriko Katsumata, Jin-Zhong Xiao, Nao Suzuki, Mamoru Tanaka
RESEARCH QUESTION: Do gut microbiota associate with the ovulatory cycle in women showing normogonadotrophic anovulation? In humans, the gut microbiota affects diverse physiological functions and dysbiosis (microbial imbalance) may lead to pathological syndromes. However, there is comparatively little information on the relevance of gut microbiota to reproductive functions in women. Here, a group of women with idiopathic chronic anovulation were examined, who do not exhibit any apparent endocrinological disorder, as they are suitable for investigating the relationship between intestinal bacteria and ovulatory disorders...
December 22, 2018: Reproductive Biomedicine Online
https://read.qxmd.com/read/30772567/unmasking-the-identity-of-toxigenic-cyanobacteria-driving-a-multi-toxin-bloom-by-high-throughput-sequencing-of-cyanotoxins-genes-and-16s-rrna-metabarcoding
#14
María Cristina Casero, David Velázquez, Miguel Medina-Cobo, Antonio Quesada, Samuel Cirés
Cyanobacterial harmful algal blooms (CyanoHABs) are complex communities that include coexisting toxic and non-toxic strains only distinguishable by genetic methods. This study shows a water-management oriented use of next generation sequencing (NGS) to specifically pinpoint toxigenic cyanobacteria within a bloom simultaneously containing three of the most widespread cyanotoxins (the hepatotoxins microcystins, MCs; and the neurotoxins anatoxin-a, ATX, and saxitoxins, STXs). The 2013 summer bloom in Rosarito reservoir (Spain) comprised 33 cyanobacterial OTUs based on 16S rRNA metabarcoding, 7 of which accounted for as much as 96...
February 6, 2019: Science of the Total Environment
https://read.qxmd.com/read/30772474/atm-mutation-spectrum-in-russian-children-with-ataxia-telangiectasia
#15
Evgeny Suspitsin, Anna Sokolenko, Ilya Bizin, Anastasia Tumakova, Marina Guseva, Natalia Sokolova, Svetlana Vakhlyarskaya, Irina Kondratenko, Evgeny Imyanitov
Ataxia-telangiectasia (AT) is a severe autosomal recessive orphan disease characterized by a number of peculiar clinical manifestations. Genetic diagnosis of AT is complicated due to a large size of the causative gene, ATM. We used next-generation sequencing (NGS) technology for the ATM analysis in 17 children with the clinical diagnosis of AT. Biallelic mutations in the ATM gene were identified in all studied subjects; these lesions included one large gene rearrangement, which was reliably detected by NGS and validated by multiplex ligation-dependent probe amplification (MLPA)...
February 14, 2019: European Journal of Medical Genetics
https://read.qxmd.com/read/30772141/a-novel-approach-to-detect-programed-death-ligand-1-pd-l1-status-and-multiple-tumor-mutations-using-a-single-non-small-cell-lung-cancer-nsclc-bronchoscopy-specimen
#16
Amanda Vannitamby, Shona Hendry, Tanvi Makadia, Janine Danks, John Slavin, Louis Irving, Daniel Steinfort, Steven Bozinovski
Multiple biomarkers are under evaluation to guide the use of immune checkpoint inhibitors in non-small-cell lung cancer (NSCLC), including programed death ligand 1 (PD-L1) tumor cell staining. We have developed a new approach that accurately quantifies PD-L1 status and identifies multiple mutations by using a single bronchoscopy specimen. A novel molecular marker was identified to detect the presence of malignant cells in radial endobronchial ultrasound bronchial brushings from NSCLC (n = 15) and benign (n = 13) nodules by quantitative real-time RT-PCR (RT-qPCR)...
February 8, 2019: Journal of Molecular Diagnostics: JMD
https://read.qxmd.com/read/30771719/microbial-species-and-biodiversity-in-settling-dust-within-and-between-pig-farms
#17
John Kerr White, Jeppe Lund Nielsen, Anne Mette Madsen
The airborne fungal and bacterial species present in pig farm dust have not been well characterised even though these bioaerosols are known to cause inflammation and other airway maladies. In this study, the microbial species and composition in airborne dust within and between pig farms were investigated. Passively sedimenting dust from six pig farms were collected using electrostatic dust collectors. The bacterial and fungal species were identified using matrix-assisted laser desorption-ionisation time-of-flight mass spectrometry (MALDI-TOF MS) and next generation sequencing (NGS)...
January 6, 2019: Environmental Research
https://read.qxmd.com/read/30770994/unusual-radiological-and-histological-presentation-of-a-diffuse-leptomeningeal-glioneuronal-tumor-dlgnt-in-a-13-year-old-girl
#18
Nishant Tiwari, Benita Tamrazi, Nathan Robison, Mark Krieger, Jianling Ji, Di Tian
Diffuse leptomeningeal glioneuronal tumors (DLGNTs) are newly recognized as an entity in the 2016 revision of the WHO Classification of tumors of the central nervous system. They typically present as diffuse leptomeningeal infiltrates along the neuraxis with focal and superficial involvement of the parenchyma. Here, we report a DLGNT with unusual radiological and histological features. A 13-year-old girl presented with scoliosis and back pain. Magnetic resonance imaging demonstrated a syrinx from C2 to T11 and an intramedullary mass from T6 to T9-10...
February 15, 2019: Child's Nervous System: ChNS: Official Journal of the International Society for Pediatric Neurosurgery
https://read.qxmd.com/read/30770747/next-generation-sequencing-identified-two-novel-mutations-in-nipbl-and-a-frame-shift-mutation-in-crebbp-in-three-chinese-children
#19
Hui Tang, Jing Guo, Siyuan Linpeng, Lingqian Wu
BACKGROUND: Cornelia de Lange syndrome (CdLS) and Rubinstein-Taybi syndrome (RSTS) are both rare congenital multiple malformation disorders caused by genes associated with transcription. They share a number of similar features clinically. In addition, it is difficult to make a molecular diagnosis rapidly and detect the mosaic mutation when only sanger sequencing is taken. This study aims to report three novel mutations in three Chinese children identified by next generation sequencing...
February 15, 2019: Orphanet Journal of Rare Diseases
https://read.qxmd.com/read/30770598/divergent-mitochondrial-lineages-arose-within-a-large-panmictic-population-of-the-savannah-sparrow-passerculus-sandwichensis
#20
Phred M Benham, Zachary A Cheviron
Unusual patterns of mtDNA diversity can reveal interesting aspects of a species' biology. However, making such inferences requires discerning among the many alternative scenarios that could underlie any given mtDNA pattern. Next-generation sequencing methods provide large, multi-locus datasets with increased power to resolve unusual mtDNA patterns. A mtDNA-based phylogeography of the Savannah sparrow (Passerculus sandwichensis) previously identified two sympatric, but divergent (~2%) clades within the nominate subspecies group and a third clade that consisted of birds sampled from northwest Mexico...
February 15, 2019: Molecular Ecology
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