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the next generation sequence

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https://www.readbyqxmd.com/read/29232568/prior-systemic-treatment-increased-the-incidence-of-somatic-mutations-in-metastatic-breast-cancer
#1
Takeo Fujii, Naoko Matsuda, Miho Kono, Kenichi Harano, Huiqin Chen, Rajyalakshmi Luthra, Sinchita Roy-Chowdhuri, Aysegul A Sahin, Chetna Wathoo, Aron Y Joon, Debu Tripathy, Funda Meric-Bernstam, Naoto T Ueno
BACKGROUND: Understanding the biology of breast cancer is important for guiding treatment strategies and revealing resistance mechanisms. Our objectives were to investigate the relationship between previous systemic therapy exposure and mutational spectrum in metastatic breast cancer and to identify clinicopathological factors associated with identified frequent somatic mutations. METHODS: Archival tissues of patients with metastatic breast cancer were subjected to hotspot molecular testing by next-generation sequencing...
December 9, 2017: European Journal of Cancer
https://www.readbyqxmd.com/read/29232328/novel-cyp2a6-diplotypes-identified-through-next-generation-sequencing-are-associated-with-in-vitro-and-in-vivo-nicotine-metabolism
#2
Julie-Anne Tanner, Andy Z Zhu, Katrina G Claw, Bhagwat Prasad, Viktoriya Korchina, Jianhong Hu, HarshaVardhan Doddapaneni, Donna M Muzny, Erin G Schuetz, Caryn Lerman, Kenneth E Thummel, Steven E Scherer, Rachel F Tyndale
OBJECTIVES: Smoking patterns and cessation rates vary widely across smokers and can be influenced by variation in rates of nicotine metabolism [i.e. cytochrome P450 2A6 (CYP2A6), enzyme activity]. There is high heritability of CYP2A6-mediated nicotine metabolism (60-80%) owing to known and unidentified genetic variation in the CYP2A6 gene. We aimed to identify and characterize additional genetic variants at the CYP2A6 gene locus. METHODS: A new CYP2A6-specific sequencing method was used to investigate genetic variation in CYP2A6...
January 2018: Pharmacogenetics and Genomics
https://www.readbyqxmd.com/read/29232304/rapid-braf-mutation-tests-in-patients-with-advanced-melanoma-comparison-of-immunohistochemistry-droplet-digital-pcr-and-the-idylla-mutation-platform
#3
Cornelis Bisschop, Arja Ter Elst, Lisette J Bosman, Inge Platteel, Mathilde Jalving, Anke van den Berg, Arjan Diepstra, Bettien van Hemel, Gilles F H Diercks, Geke A P Hospers, Ed Schuuring
BRAF mutational testing has become a common practice in the diagnostic process of patients with advanced melanoma. Although time-consuming, DNA sequencing techniques are the current gold standard for mutational testing. However, in certain clinical situations, a rapid test result is required. In this study, the performance of three rapid BRAF mutation tests was compared. Thirty-nine formalin-fixed paraffin-embedded melanoma tissue samples collected between 2007 and 2014 at a single center were included. These samples were analyzed by immunohistochemistry using the anti-BRAF-V600E (VE1) mouse monocolonal antibody (BRAF-VE1 IHC), a V600E-specific Droplet Digital PCR Test, and the Idylla BRAF- Mutation Test (Idylla)...
December 11, 2017: Melanoma Research
https://www.readbyqxmd.com/read/29231896/differential-expression-of-serum-micrornas-supports-cd4%C3%A2-%C2%BA-t-cell-differentiation-into-th2-th17-cells-in-severe-equine-asthma
#4
Alicja Pacholewska, Matthias F Kraft, Vincent Gerber, Vidhya Jagannathan
MicroRNAs (miRNAs) regulate post-transcriptional gene expression and may be exported from cells via exosomes or in partnership with RNA-binding proteins. MiRNAs in body fluids can act in a hormone-like manner and play important roles in disease initiation and progression. Hence, miRNAs are promising candidates as biomarkers. To identify serum miRNA biomarkers in the equine model of asthma we investigated small RNA derived from the serum of 34 control and 37 asthmatic horses. These samples were used for next generation sequencing, novel miRNA identification and differential miRNA expression analysis...
December 12, 2017: Genes
https://www.readbyqxmd.com/read/29230833/causes-of-iron-overload-in-blood-donors-a-clinical-study
#5
A H Laursen, O W Bjerrum, L Friis-Hansen, T O Hansen, J L Marott, K Magnussen
BACKGROUND AND OBJECTIVES: Despite the obligate iron loss from blood donation, some donors present with hyperferritinaemia that can result from a wide range of acute and chronic conditions including hereditary haemochromatosis (HH). The objective of our study was to investigate the causes of hyperferritinaemia in the blood donor population and explore the value of extensive HH mutational analyses. MATERIALS AND METHODS: Forty-nine consecutive donors (f = 6, m = 43) were included prospectively from the Capital Regional Blood Center...
December 12, 2017: Vox Sanguinis
https://www.readbyqxmd.com/read/29230532/rna-mediated-transgenerational-inheritance-in-ciliates-and-plants
#6
REVIEW
Zachary T Neeb, Mariusz Nowacki
In the age of next-generation sequencing (NGS) and with the availability of whole sequenced genomes and epigenomes, some attention has shifted from purely sequence-based studies to those of heritable epigenetic modifications. Transgenerational inheritance can be defined as heritable changes to the state of DNA that may be passed on to subsequent generations without alterations to the underlying DNA sequence. Although this phenomenon has been extensively studied in many systems, studies of transgenerational inheritance in mammals and other higher-level eukaryotes may be complicated by the fact that many epigenetic marks are reprogrammed during sexual reproduction...
December 11, 2017: Chromosoma
https://www.readbyqxmd.com/read/29230253/barriers-to-clinical-adoption-of-next-generation-sequencing-a-policy-delphi-panel-s-solutions
#7
Donna A Messner, Pei Koay, Jennifer Al Naber, Robert Cook-Deegan, Mary Majumder, Gail Javitt, Rachel Dvoskin, Juli Bollinger, Margaret Curnutte, Amy L McGuire
Aim: Identify solutions to the most important policy barriers to the clinical adoption of next-generation sequencing. Materials & methods: Four-round modified policy Delphi with a multistakeholder panel of 48 experts. The panel deliberated policy solutions to (previously reported) challenges deemed most important to address. Results: The group advocated using consensus panels to promote consistency in payer policies and to standardize test reporting, and favored making genomic data-sharing a condition of regulatory clearance, certification, or accreditation processes...
2017: Personalized Medicine
https://www.readbyqxmd.com/read/29230161/a-homozygous-missense-variant-in-inpp5e-associated-with-joubert-syndrome-and-related-disorders
#8
Mitesh Shetty, Nimmy Ramdas, Shubhi Sahni, Nandita Mullapudi, Sridevi Hegde
Joubert syndrome and related disorders (JSRD; ORPHA 140874) is a complex set of neurodevelopmental disorders with multiple organ involvement. JSRD is a type of ciliopathy which is caused by the presence of defective primary cilia in an individual. JSRD is commonly inherited in an autosomal recessive pattern, and more than 23 genes are known to be associated with JSRD. We report a novel homozygous mutation identified in the INPP5E gene, c.1303C>T, which leads to a change of an amino acid from arginine to tryptophan at residue 435 in the protein chain...
November 2017: Molecular Syndromology
https://www.readbyqxmd.com/read/29230066/functional-and-evolutionary-analysis-of-korean-bob-tailed-native-dog-using-whole-genome-sequencing-data
#9
Daehwan Lee, Dajeong Lim, Daehong Kwon, Juyeon Kim, Jongin Lee, Mikang Sim, Bong-Hwan Choi, Seog-Gyu Choi, Jaebum Kim
Rapid and cost effective production of large-scale genome data through next-generation sequencing has enabled population-level studies of various organisms to identify their genotypic differences and phenotypic consequences. This is also used to study indigenous animals with historical and economical values, although they are less studied than model organisms. The objective of this study was to perform functional and evolutionary analysis of Korean bob-tailed native dog Donggyeong with distinct tail and agility phenotype using whole-genome sequencing data by using population and comparative genomics approaches...
December 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29229980/molecular-cloning-of-novel-transcripts-of-human-kallikrein-related-peptidases-5-6-7-8-and-9-klk5-klk9-using-next-generation-sequencing
#10
Panagiotis G Adamopoulos, Christos K Kontos, Andreas Scorilas
Alternative splicing of cancer-related genes is a common cellular mechanism accounting for cancer cell transcriptome complexity and affecting cell cycle control, proliferation, apoptosis, angiogenesis, invasion, and metastasis. In this study, we describe the discovery and molecular cloning of thirty novel transcripts of the human KLK5, KLK6, KLK7, KLK8 and KLK9 genes, using 3' rapid amplification of cDNA ends (3' RACE) and NGS technology, as well as their expression analysis in many established cell lines, originating from several distinct cancerous and normal tissues...
December 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29228723/an-ngs-based-approach-for-the-identification-of-sex-specific-markers-in-snakehead-channa-argus
#11
Mi Ou, Cheng Yang, Qing Luo, Rong Huang, Ai-Di Zhang, Lan-Jie Liao, Yong-Ming Li, Li-Bo He, Zuo-Yan Zhu, Kun-Ci Chen, Ya-Ping Wang
We described a next generation sequencing (NGS)-based approach to identify sex-specific markers and subsequently determine whether a species has male or female heterogamety. To test the accuracy of this technique, we examined the snakehead (Channa argus), which is economically important freshwater fish in China. Males grow faster than females, and there is significant interest in developing methods to skew breeding towards all-males to increase biomass yields. NGS was conducted on DNAs of individual female and male, the male reads were spitted into 60 bp K-mers and aligned to the female reference genome assembled by female reads, unaligned male K-mers-60 were kept in next filter process...
November 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29228654/lack-of-chemopreventive-effects-of-p2x7r-inhibitors-against-pancreatic-cancer
#12
Altaf Mohammed, Naveena B Janakiram, Venkateshwar Madka, Gopal Pathuri, Qian Li, Rebekah Ritchie, Laura Biddick, Hannah Kutche, Yuting Zhang, Anil Singh, Hariprasad Gali, Stan Lightfoot, Vernon E Steele, Chen S Suen, Chinthalapally V Rao
Pancreatic cancer (PC) is an almost uniformly lethal disease with inflammation playing an important role in its progression. Sustained stimulation of purinergic receptor P2X7 drives induction of NLRP inflammasome activation. To understand the role of P2X7 receptor and inflammasome, we performed transcriptomic analysis of p48Cre/+-LSL-KrasG12D/+ mice pancreatic tumors by next generation sequencing. Results showed that P2X7R's key inflammasome components, IL-1β and caspase-1 are highly expressed (p < 0.05) in pancreatic tumors...
November 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29228650/ultrasensitive-plasma-ctdna-kras-assay-for-detection-prognosis-and-assessment-of-therapeutic-response-in-patients-with-unresectable-pancreatic-ductal-adenocarcinoma
#13
Inna Chen, Victoria M Raymond, Jennifer A Geis, Eric A Collisson, Benny V Jensen, Kirstine L Hermann, Mark G Erlander, Margaret Tempero, Julia S Johansen
Precision oncology requires sensitive and specific clinical biomarkers. Carbohydrate Antigen 19-9 (CA19-9) is widely used in pancreatic ductal adenocarcinoma (PDA) but lacks sensitivity and specificity. Nearly all PDAs harbor somatic KRAS mutations, nominating circulating tumor DNA (ctDNA) KRAS as an alternative disease biomarker, however, variable clinical performance has limited its clinical utility. We applied an ultrasensitive, PCR mutation enrichment, next generation sequencing ctDNA KRAS assay in a large cohort of patients with unresectable PDA (N = 189) recruited to the BIOPAC study between 2008-2015...
November 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29228571/identification-of-a-novel-de-novo-ank1-r1426-nonsense-mutation-in-a-chinese-family-with-hereditary-spherocytosis-by-ngs
#14
Xiong Wang, Bin Yi, Ketao Mu, Na Shen, Yaowu Zhu, Qun Hu, Yanjun Lu
Hereditary spherocytosis (HS) is an inherited heterogeneous hemolytic anemia, characterized by the presence of spherical-shaped erythrocytes on the peripheral blood smear, and the clinical manifestation ranges from asymptomatic to severely anemic, and transfusion-dependent patients. Mutations in at least five genes (ANK1, EPB42, SLC4A1, SPTA1, and SPTB) have been identified so far, and mutations of ANK1 gene are responsible for the majority of all HS cases. In this study, targeted next generation sequencing (NGS) was applied to identify a novel de novo ANK1 c...
November 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/29228562/clinical-mutational-profiling-of-1006-lung-cancers-by-next-generation-sequencing
#15
Peter B Illei, Deborah Belchis, Li-Hui Tseng, Doreen Nguyen, Federico De Marchi, Lisa Haley, Stacy Riel, Katie Beierl, Gang Zheng, Julie R Brahmer, Frederic B Askin, Christopher D Gocke, James R Eshleman, Patrick M Forde, Ming-Tseh Lin
Analysis of lung adenocarcinomas for actionable mutations has become standard of care. Here, we report our experience using next generation sequencing (NGS) to examine AKT1, BRAF, EGFR, ERBB2, KRAS, NRAS, and PIK3CA genes in 1006 non-small cell lung cancers in a clinical diagnostic setting. NGS demonstrated high sensitivity. Among 760 mutations detected, the variant allele frequency (VAF) was 2-5% in 33 (4.3%) mutations and 2-10% in 101 (13%) mutations. A single bioinformatics pipeline using Torrent Variant Caller, however, missed a variety of EGFR mutations...
November 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/29228394/the-psychiatric-risk-gene-transcription-factor-4-tcf4-regulates-neurodevelopmental-pathways-associated-with-schizophrenia-autism-and-intellectual-disability
#16
Marc P Forrest, Matthew J Hill, David H Kavanagh, Katherine E Tansey, Adrian J Waite, Derek J Blake
Background: Common genetic variants in and around the gene encoding transcription factor 4 (TCF4) are associated with an increased risk of schizophrenia. Conversely, rare damaging TCF4 mutations cause Pitt-Hopkins syndrome and have also been found in individuals with intellectual disability (ID) and autism spectrum disorder (ASD). Methods: Chromatin immunoprecipitation and next generation sequencing were used to identify the genomic targets of TCF4. These data were integrated with expression, epigenetic and disease gene sets using a range of computational tools...
December 8, 2017: Schizophrenia Bulletin
https://www.readbyqxmd.com/read/29228370/a-nf-%C3%AE%C2%BAb-signature-predicts-low-grade-glioma-prognosis-a-precision-medicine-approach-based-on-patient-derived-stem-cells
#17
Tamara Ius, Yari Ciani, Maria Elisabetta Ruaro, Miriam Isola, Marisa Sorrentino, Michela Bulfoni, Veronica Candotti, Cecilia Correcig, Evgenia Bourkoula, Ivana Manini, Enrico Pegolo, Damiano Mangoni, Stefania Marzinotto, Slobodanka Radovic, Barbara Toffoletto, Federica Caponnetto, Andrea Zanello, Laura Mariuzzi, Carla Di Loreto, Antonio Paolo Beltrami, Silvano Piazza, Miran Skrap, Daniela Cesselli
Background: While recent genome wide association studies have suggested novel low-grade glioma (LGG) stratification models based on a molecular classification, we explored the potential clinical utility of patient-derived cells. Specifically, we assayed glioma-associated stem cells (GASC) that are patient-derived stem cells representative of the glioma microenvironment. Methods: By next generation sequencing, we analyzed the transcriptional profile of GASC derived from patients that underwent anaplastic transformation either within 48 months (GASC-BAD) or ≥7 years (GASC-GOOD) after surgery...
December 7, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/29227985/low-frequency-of-fabry-disease-in-patients-with-common-heart-disease
#18
Raphael Schiffmann, Caren Swift, Nathan McNeill, Elfrida R Benjamin, Jeffrey P Castelli, Jay Barth, Lawrence Sweetman, Xuan Wang, Xiaoyang Wu
PurposeTo test the hypothesis that undiagnosed patients with Fabry disease exist among patients affected by common heart disease.MethodsGlobotriaosylceramide in random whole urine using tandem mass spectroscopy, α-galactosidase A activity in dried blood spots, and next-generation sequencing of pooled or individual genomic DNA samples supplemented by Sanger sequencing.ResultsWe tested 2,256 consecutive patients: 852 women (median age 65 years (19-95)) and 1,404 men (median age 65 years (21-92)). The primary diagnoses were coronary artery disease (n = 994), arrhythmia (n = 607), cardiomyopathy (n = 138), and valvular disease (n = 568)...
October 26, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29227558/rna-sequencing-identifies-gene-regulatory-networks-controlling-extracellular-matrix-synthesis-in-intervertebral-disk-tissues
#19
Scott M Riester, Yang Lin, Wei Wang, Lin Cong, Abdel-Moneim Mohamed Ali, Sun H Peck, Lachlan J Smith, Bradford L Currier, Michelle Clark, Paul Huddleston, William Krauss, Michael J Yaszemski, Mark E Morrey, Matthew P Abdel, Mohamad Bydon, Wenchun Qu, A Noelle Larson, Andre J van Wijnen, Ahmad Nassr
Degenerative disk disease of the spine is a major cause of back pain and disability. Optimization of regenerative medical therapies for degenerative disk disease requires a deep mechanistic understanding of the factors controlling the structural integrity of spinal tissues. In this investigation, we sought to identify candidate regulatory genes controlling extracellular matrix synthesis in spinal tissues. To achieve this goal we performed high throughput next generation RNA sequencing on 39 annulus fibrosus and 21 nucleus pulposus human tissue samples...
December 11, 2017: Journal of Orthopaedic Research: Official Publication of the Orthopaedic Research Society
https://www.readbyqxmd.com/read/29227308/medical-bioinformatics-in-melanoma
#20
Phil F Cheng
PURPOSE OF REVIEW: Bioinformatic insights from next-generation sequencing has been integral in understanding melanoma biology, resistance to treatment and provided new avenues for melanoma treatment. Whole-genome sequencing, whole-exome sequencing and RNA sequencing has redefined the molecular classification of melanoma, revealed distinct genetic aberrations that define clinical subtypes of melanoma and uncovered the diverse heterogeneity that resides in an individual tumor. RECENT FINDINGS: In this review, we will summarize the recent whole-genome study that catalogs the genomic landscape across many melanoma subtypes, the single-cell RNA sequencing studies that interrogates tumor heterogeneity and the personalized vaccine approaches to melanoma treatment...
December 8, 2017: Current Opinion in Oncology
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