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https://www.readbyqxmd.com/read/29342213/circulating-neutrophil-transcriptome-may-reveal-intracranial-aneurysm-signature
#1
Vincent M Tutino, Kerry E Poppenberg, Kaiyu Jiang, James N Jarvis, Yijun Sun, Ashish Sonig, Adnan H Siddiqui, Kenneth V Snyder, Elad I Levy, John Kolega, Hui Meng
BACKGROUND: Unruptured intracranial aneurysms (IAs) are typically asymptomatic and undetected except for incidental discovery on imaging. Blood-based diagnostic biomarkers could lead to improvements in IA management. This exploratory study examined circulating neutrophils to determine whether they carry RNA expression signatures of IAs. METHODS: Blood samples were collected from patients receiving cerebral angiography. Eleven samples were collected from patients with IAs and 11 from patients without IAs as controls...
2018: PloS One
https://www.readbyqxmd.com/read/29342065/diagnosis-of-periprosthetic-joint-infection-the-potential-of-next-generation-sequencing
#2
Majd Tarabichi, Noam Shohat, Karan Goswami, Abtin Alvand, Randi Silibovsky, Katherine Belden, Javad Parvizi
BACKGROUND: Next-generation sequencing is a well-established technique for sequencing of DNA and has recently gained attention in many fields of medicine. Our aim was to evaluate the accuracy of next-generation sequencing in identifying the causative organism(s) in patients with periprosthetic joint infection. METHODS: In this prospective study, samples were collected from 65 revision arthroplasties (39 knees and 26 hips) and 17 primary arthroplasties (9 hips and 8 knees)...
January 17, 2018: Journal of Bone and Joint Surgery. American Volume
https://www.readbyqxmd.com/read/29341956/microbiome-associated-with-denture-malodour
#3
S Yitzhaki, L Reshef, U Gophna, M Rosenberg, N Sterer
In the past, our inability to cultivate most of the oral microorganisms has limited our view of this complex ecosystem. In the present study, we utilized next generation deep sequencing techniques to revisit the microbiome associated with denture malodour, a growing field with the rise in life expectancy. The study population comprised 26 full dentures patients (mean age 71 ± 6.4, 10 males, 16 females) who visited the Tel Aviv University dental geriatric clinic. Denture malodour was rated organoleptically by a single odour judge, and dentures scoring 2 and above were considered malodour positive...
January 17, 2018: Journal of Breath Research
https://www.readbyqxmd.com/read/29341374/validation-of-the-digital-pcr-system-in-tyrosine-kinase-inhibitor-resistant-egfr-mutant-non-small-cell-lung-cancer
#4
Katsuhiro Masago, Shiro Fujita, Akito Hata, Chiyuki Okuda, Yuko Yoshizumi, Reiko Kaji, Nobuyuki Katakami, Yukio Hirata, Yasushi Yatabe
The aim of this study was to compare the accuracy of the QuantStudio 3D Digital polymerase chain reaction (dPCR) system and a PCR-based next generation sequencing (NGS) system for detecting a secondary mutation in the epidermal growth factor receptor (EGFR) gene T790M in non-small cell lung cancer (NSCLC) patients previously diagnosed with EGFR-activating mutations. Twenty-five patients with NSCLC previously treated with EGFR-TKIs were examined. The patients were treated daily with either erlotinib or gefitinib...
January 17, 2018: Pathology International
https://www.readbyqxmd.com/read/29341343/small-heat-shock-protein-b3-hspb3-mutation-in-an-axonal-charcot-marie-tooth-disease-family
#5
Da Eun Nam, Soo Hyun Nam, Ah Jin Lee, Young Bin Hong, Byung-Ok Choi, Ki Wha Chung
HSPB3 gene encodes a small heat-shock protein 27-like protein which has a high sequence homology with HSPB1. A mutation in the HSPB3 was reported as the putative underlying cause of distal hereditary motor neuropathy 2C (dHMN2C) in 2010. We identified a heterozygous mutation (c.352T>C, p.Tyr118His) in the HSPB3 from a Charcot-Marie-Tooth disease type 2 (CMT2) family by the method of targeted next generation sequencing. The mutation was located in the well conserved alpha-crystalline domain, and several in silico predictions indicated a pathogenic effect of the mutation...
January 17, 2018: Journal of the Peripheral Nervous System: JPNS
https://www.readbyqxmd.com/read/29341259/child-syndrome-mimicking-verrucous-nevus-in-a-chinese-patient-responded-well-to-the-topical-therapy-of-compound-of-simvastatin-and-cholesterol
#6
Xia Yu, Jia Zhang, Yan Gu, Dan Deng, Zhouwei Wu, Lei Bao, Ming Li, Zhirong Yao
BACKGROUND: Congenital hemidysplasia with ichthyosiform erythroderma and limb defects (CHILD) syndrome is a rare X-linked dominant disorder characterized by peculiar cutaneous presentations and ipsilateral skeletal abnormalities. CHILD syndrome is caused by mutations in NSDHL gene, which involves in cholesterol synthesis. OBJECTIVES: To verify the diagnosis of CHILD syndrome and seek effective pathogenesis-based therapy with little side effects. METHOD: We comprehensively evaluated the patient's conditions...
January 17, 2018: Journal of the European Academy of Dermatology and Venereology: JEADV
https://www.readbyqxmd.com/read/29341164/patient-derived-organoid-models-help-define-personalized-management-of-gastrointestinal-cancer
#7
REVIEW
M R Aberle, R A Burkhart, H Tiriac, S W M Olde Damink, C H C Dejong, D A Tuveson, R M van Dam
BACKGROUND: The prognosis of patients with different gastrointestinal cancers varies widely. Despite advances in treatment strategies, such as extensive resections and the addition of new drugs to chemotherapy regimens, conventional treatment strategies have failed to improve survival for many tumours. Although promising, the clinical application of molecularly guided personalized treatment has proven to be challenging. This narrative review focuses on the personalization of cancer therapy using patient-derived three-dimensional 'organoid' models...
January 2018: British Journal of Surgery
https://www.readbyqxmd.com/read/29341151/gut-microbiome-influences-on-anastomotic-leak-and-recurrence-rates-following-colorectal-cancer-surgery
#8
REVIEW
S Gaines, C Shao, N Hyman, J C Alverdy
BACKGROUND: The pathogenesis of colorectal cancer recurrence after a curative resection remains poorly understood. A yet-to-be accounted for variable is the composition and function of the microbiome adjacent to the tumour and its influence on the margins of resection following surgery. METHODS: PubMed was searched for historical as well as current manuscripts dated between 1970 and 2017 using the following keywords: 'colorectal cancer recurrence', 'microbiome', 'anastomotic leak', 'anastomotic failure' and 'mechanical bowel preparation'...
January 2018: British Journal of Surgery
https://www.readbyqxmd.com/read/29341110/eurogin-roadmap-2017-triage-strategies-for-the-management-of-hpv-positive-women-in-cervical-screening-programmes
#9
REVIEW
K Cuschieri, G Ronco, A Lorincz, L Smith, G Ogilvie, L Mirabello, F Carozzi, H Cubie, N Wentzensen, P Snijders, M Arbyn, J Monsonego J, S Franceschi
Cervical cancer screening will rely, increasingly, on HPV testing as a primary screen. The requirement for triage tests which can delineate clinically significant infection is thus prescient. In this EUROGIN 2017 roadmap, justification behind the most evidenced triages is outlined, as are challenges for implementation. Cytology is the triage with the most follow-up data; the existence of an HR-HPV positive, cytology negative group presents a challenge and re-testing intervals for this group (and choice of re-test) require careful consideration...
January 17, 2018: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29340846/novel-isoforms-of-n16-and-n19-families-implicated-for-the-nacreous-layer-formation-in-the-pearl-oyster-pinctada-fucata
#10
Fumito Ohmori, Shigeharu Kinoshita, Daisuke Funabara, Hiroki Koyama, Kiyohito Nagai, Kaoru Maeyama, Kikuhiko Okamoto, Shuichi Asakawa, Shugo Watabe
Although a wide variety of proteins and genes possibly related to the shell formation in bivalve have been identified, their functions have been only partially approved. We have recently performed deep sequencing of expressed sequence tags (ESTs) from the pearl oyster Pinctada fucata using a next-generation sequencer, identifying a dozen of novel gene candidates which are possibly associated with the nacreous layer formation. Among the ESTs, we focused on three novel isoforms (N16-6, N16-7, and N19-2) of N16 and N19 families with reference to five known genes in the families and determined the full-length cDNA sequences of these isoforms...
January 16, 2018: Marine Biotechnology
https://www.readbyqxmd.com/read/29340714/taxonomical-resolution-and-distribution-of-bacterioplankton-along-the-vertical-gradient-reveals-pronounced-spatiotemporal-patterns-in-contrasted-temperate-freshwater-lakes
#11
J Keshri, A S Pradeep Ram, P A Nana, T Sime-Ngando
We examined the relationship between viruses and co-occurring bacterial communities across spatiotemporal scale in two contrasting freshwater lakes, namely meromictic Lake Pavin and dimictic Lake Aydat (Central France). Next-generation sequencing of 16S rRNA genes suggested distinct patterns in bacterioplankton community composition (BCC) between the lakes over depths and seasons. BCC were generally dominated by members of Actinobacteria, Proteobacteria, and Bacteroidetes covering about 95% of all sequences...
January 16, 2018: Microbial Ecology
https://www.readbyqxmd.com/read/29340697/genetic-and-clinical-evidence-of-mitochondrial-dysfunction-in-autism-spectrum-disorder-and-intellectual-disability
#12
Alba Valiente-Pallejà, Helena Torrell, Gerard Muntané, Maria J Cortés, Rafael Martínez-Leal, Nerea Abasolo, Yolanda Alonso, Elisabet Vilella, Lourdes Martorell
Clinical conditions commonly associated with mitochondrial disorders (CAMDs) are often present in autism spectrum disorders (ASD) and intellectual disability (ID). Therefore, the mitochondrial dysfunction hypothesis has been proposed as a transversal mechanism that may function in both disorders. Here, we investigated the presence of conditions associated with mitochondrial disorders and mitochondrial DNA (mtDNA) alterations in 122 subjects who presented ASD with ID (ASD group), 115 subjects who presented ID but not ASD (ID group) and 112 healthy controls (HC group)...
January 11, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29340642/identifying-corneal-infections-in-formalin-fixed-specimens-using-next-generation-sequencing
#13
Zhigang Li, Florian P Breitwieser, Jennifer Lu, Albert S Jun, Laura Asnaghi, Steven L Salzberg, Charles G Eberhart
Purpose: We test the ability of next-generation sequencing, combined with computational analysis, to identify a range of organisms causing infectious keratitis. Methods: This retrospective study evaluated 16 cases of infectious keratitis and four control corneas in formalin-fixed tissues from the pathology laboratory. Infectious cases also were analyzed in the microbiology laboratory using culture, polymerase chain reaction, and direct staining. Classified sequence reads were analyzed with two different metagenomics classification engines, Kraken and Centrifuge, and visualized using the Pavian software tool...
January 1, 2018: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/29340239/fastviromeexplorer-a-pipeline-for-virus-and-phage-identification-and-abundance-profiling-in-metagenomics-data
#14
Saima Sultana Tithi, Frank O Aylward, Roderick V Jensen, Liqing Zhang
With the increase in the availability of metagenomic data generated by next generation sequencing, there is an urgent need for fast and accurate tools for identifying viruses in host-associated and environmental samples. In this paper, we developed a stand-alone pipeline called FastViromeExplorer for the detection and abundance quantification of viruses and phages in large metagenomic datasets by performing rapid searches of virus and phage sequence databases. Both simulated and real data from human microbiome and ocean environmental samples are used to validate FastViromeExplorer as a reliable tool to quickly and accurately identify viruses and their abundances in large datasets...
2018: PeerJ
https://www.readbyqxmd.com/read/29340115/hypermutation-and-microsatellite-instability-in-gastrointestinal-cancers
#15
REVIEW
Kizuki Yuza, Masayuki Nagahashi, Satoshi Watanabe, Kazuaki Takabe, Toshifumi Wakai
Recent progress in cancer genome analysis using next-generation sequencing has revealed a high mutation burden in some tumors. The particularly high rate of somatic mutation in these tumors correlates with the generation of neo-antigens capable of eliciting an immune response. Identification of hypermutated tumors is therefore clinically valuable for selecting patients suitable for immunotherapy treatment. There are several known causes of hypermutation in tumors, such as ultraviolet light in melanoma, tobacco smoke in lung cancer, and excessive APOBEC (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like) activity in breast and gastric cancer...
December 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29340099/a-plasma-mirna-signature-for-lung-cancer-early-detection
#16
Qixin Leng, Yanli Lin, Fangran Jiang, Cheng-Ju Lee, Min Zhan, HongBin Fang, Yue Wang, Feng Jiang
The early detection of lung cancer continues to be a major clinical challenge. Using whole-transcriptome next-generation sequencing to analyze lung tumor and the matched noncancerous tissues, we previously identified 54 lung cancer-associated microRNAs (miRNAs). The objective of this study was to investigate whether the miRNAs could be used as plasma biomarkers for lung cancer. We determined expressions of the lung tumor-miRNAs in plasma of a development cohort of 180 subjects by using reverse transcription PCR to develop biomarkers...
December 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29340083/next-generation-sequencing-based-microrna-profiling-of-mice-testis-subjected-to-transient-heat-stress
#17
Meng Rao, Zhengyan Zeng, Li Tang, Guiping Cheng, Wei Xia, Changhong Zhu
This study aimed to investigate the role of microRNA (miRNA) in heat stress-induced spermatogenic impairment. Testes from 15 adult ICR mice subjected to testicular hyperthermia at 43°C for 30 min and from 15 control mice were collected and pooled into 3 samples. Isolated RNA from these samples was subjected to small RNA high-throughput sequencing, and differentially expressed miRNAs were identified and validated using RT-PCR. The identified miRNAs were further subjected to Gene Ontology and KEGG analyses, which revealed significant enrichment for pathways potentially involved in heat stress-induced spermatogenic impairment...
December 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29340061/analysis-of-the-mutational-landscape-of-classic-hodgkin-lymphoma-identifies-disease-heterogeneity-and-potential-therapeutic-targets
#18
Elena Mata, Antonio Díaz-López, Ana M Martín-Moreno, Margarita Sánchez-Beato, Ignacio Varela, María J Mestre, Carlos Santonja, Fernando Burgos, Javier Menárguez, Mónica Estévez, Mariano Provencio, Beatriz Sánchez-Espiridión, Eva Díaz, Carlos Montalbán, Miguel A Piris, Juan F García
Defining the mutational landscape of classic Hodgkin lymphoma is still a major research goal. New targeted next-generation sequencing (NGS) techniques may identify pathogenic mechanisms and new therapeutic opportunities related to this disease. We describe the mutational profile of a series of 57 cHL cases, enriched in Hodgkin and Reed-Sternberg (HRS) cells. Overall, the results confirm the presence of strong genomic heterogeneity. However, several variants were consistently detected in genes related to relevant signaling pathways, such as GM-CSF/IL-3, CBP/EP300, JAK/STAT, NF-kappaB, and numerous variants of genes affecting the B-cell receptor (BCR) pathway, such as BTK, CARD11, BCL10, among others...
December 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29340028/high-resolution-microbiome-profiling-uncovers-fusobacterium-nucleatum-lactobacillus-gasseri-johnsonii-and-lactobacillus-vaginalis-associated-to-oral-and-oropharyngeal-cancer-in-saliva-from-hpv-positive-and-hpv-negative-patients-treated-with-surgery-and-chemo
#19
Rafael Guerrero-Preston, James Robert White, Filipa Godoy-Vitorino, Arnold Rodríguez-Hilario, Kelvin Navarro, Herminio González, Christina Michailidi, Anne Jedlicka, Sierra Canapp, Jessica Bondy, Amanda Dziedzic, Barbara Mora-Lagos, Gustavo Rivera-Alvarez, Carmen Ili-Gangas, Priscilla Brebi-Mieville, William Westra, Wayne Koch, Hyunseok Kang, Luigi Marchionni, Young Kim, David Sidransky
Microbiome studies show altered microbiota in head and neck squamous cell carcinoma (HNSCC), both in terms of taxonomic composition and metabolic capacity. These studies utilized a traditional bioinformatics methodology, which allows for accurate taxonomic assignment down to the genus level, but cannot accurately resolve species level membership. We applied Resphera Insight, a high-resolution methodology for 16S rRNA taxonomic assignment that is able to provide species-level context in its assignments of 16S rRNA next generation sequencing (NGS) data...
December 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29339753/efficient-isolation-on-vero-dogslamtag-cells-and-full-genome-characterization-of-dolphin-morbillivirus-dmv-by-next-generation-sequencing
#20
Simone Peletto, Claudio Caruso, Francesco Cerutti, Paola Modesto, Cristina Biolatti, Alessandra Pautasso, Carla Grattarola, Federica Giorda, Sandro Mazzariol, Walter Mignone, Loretta Masoero, Cristina Casalone, Pier Luigi Acutis
The Dolphin Morbillivirus (DMV) genome from the first Mediterranean epidemic (1990-'92) is the only cetacean Morbillivirus that has been completely sequenced. Here, we report the first application of next generation sequencing (NGS) to morbillivirus infection of aquatic mammals. A viral isolate, representative of the 2006-'08 Mediterranean epidemic (DMV_IZSPLV_2008), efficiently grew on Vero.DogSLAMtag cells and was submitted to whole genome characterization by NGS. The final genome length was 15,673 nucleotides, covering 99...
January 16, 2018: Scientific Reports
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