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https://www.readbyqxmd.com/read/29342065/diagnosis-of-periprosthetic-joint-infection-the-potential-of-next-generation-sequencing
#1
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
#2
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/29341343/small-heat-shock-protein-b3-hspb3-mutation-in-an-axonal-charcot-marie-tooth-disease-family
#3
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/29341164/patient-derived-organoid-models-help-define-personalized-management-of-gastrointestinal-cancer
#4
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/29341110/eurogin-roadmap-2017-triage-strategies-for-the-management-of-hpv-positive-women-in-cervical-screening-programmes
#5
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/29340697/genetic-and-clinical-evidence-of-mitochondrial-dysfunction-in-autism-spectrum-disorder-and-intellectual-disability
#6
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
#7
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/29340115/hypermutation-and-microsatellite-instability-in-gastrointestinal-cancers
#8
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
#9
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/29339441/allele-specific-droplet-digital-pcr-combined-with-a-next-generation-sequencing-based-algorithm-for-diagnostic-copy-number-analysis-in-genes-with-high-homology-proof-of-concept-using-stereocilin
#10
Sami S Amr, Elissa Murphy, Elizabeth Duffy, Rojeen Niazi, Jorune Balciuniene, Minjie Luo, Heidi L Rehm, Ahmad N Abou Tayoun
BACKGROUND: Copy number variants (CNVs) can substantially contribute to the pathogenic variant spectrum in several disease genes. The detection of this type of variant is complicated in genes with high homology to other genomic sequences, yet such genomics regions are more likely to lead to CNVs, making it critical to address detection in these settings. METHODS: We developed a copy number analysis approach for high homology genes/regions that consisted of next-generation sequencing (NGS)-based dosage analysis accompanied by allele-specific droplet digital PCR (ddPCR) confirmatory testing...
January 16, 2018: Clinical Chemistry
https://www.readbyqxmd.com/read/29337640/molecular-determinants-of-response-to-anti-programmed-cell-death-pd-1-and-anti-programmed-death-ligand-pd-l-ligand-1-blockade-in-patients-with-non-small-cell-lung-cancer-profiled-with-targeted-next-generation-sequencing
#11
Hira Rizvi, Francisco Sanchez-Vega, Konnor La, Walid Chatila, Philip Jonsson, Darragh Halpenny, Andrew Plodkowski, Niamh Long, Jennifer L Sauter, Natasha Rekhtman, Travis Hollmann, Kurt A Schalper, Justin F Gainor, Ronglai Shen, Ai Ni, Kathryn C Arbour, Taha Merghoub, Jedd Wolchok, Alexandra Snyder, Jamie E Chaft, Mark G Kris, Charles M Rudin, Nicholas D Socci, Michael F Berger, Barry S Taylor, Ahmet Zehir, David B Solit, Maria E Arcila, Marc Ladanyi, Gregory J Riely, Nikolaus Schultz, Matthew D Hellmann
Purpose Treatment of advanced non-small-cell lung cancer with immune checkpoint inhibitors (ICIs) is characterized by durable responses and improved survival in a subset of patients. Clinically available tools to optimize use of ICIs and understand the molecular determinants of response are needed. Targeted next-generation sequencing (NGS) is increasingly routine, but its role in identifying predictors of response to ICIs is not known. Methods Detailed clinical annotation and response data were collected for patients with advanced non-small-cell lung cancer treated with anti-programmed death-1 or anti-programmed death-ligand 1 [anti-programmed cell death (PD)-1] therapy and profiled by targeted NGS (MSK-IMPACT; n = 240)...
January 16, 2018: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/29336709/novel-mutation-of-the-dystrophin-gene-in-a-child-with-duchenne-muscular-dystrophy
#12
Jingjing Jiang, Tiejia Jiang, Jialu Xu, Jue Shen, Feng Gao
INTRODUCTION: Duchenne muscular dystrophy (DMD) is an X-linked autosomal recessive genetic disorder caused by mutations in DMD gene. Approximately 70% of the mutations are caused by deletions or duplications of DMD exons, while the remaining were minor mutations. CASE REPORT: We present a 5-year-old boy with typical clinical features of DMD. A novel mutation was identified as a c.9358_9359insA of DMD gene by next-generation sequencing. This mutation which was origined from mother, generated a frameshift mutation and resulted in abnormal synthesis of protein polypeptide chains...
January 16, 2018: Fetal and Pediatric Pathology
https://www.readbyqxmd.com/read/29336669/first-line-treatment-of-apatinib-in-elderly-patient-of-advanced-gastric-carcinoma-a-case-report-of-ngs-driven-targeted-therapy
#13
Yan Yang, Wuqiong Zhang, Jinghao Yao, Jing Liu, Shukui Qin, Qiong Wu
Gastric carcinoma (GC) is a common gastrointestinal malignancy with high incidence and mortality worldwide, and most patients are diagnosed in the late stages of disease. Palliative chemotherapy provides a survival benefit for patients with inoperable advanced GC. However, elderly patients who are unable to tolerate chemotherapy had worse prognosis due to lack of effective treatment. Herein we reported a Chinese elderly GC patient using next generation sequencing (NGS)-based tumor DNA analysis. Valuable gene variants of vascular endothelial growth factor (VEGF) A gene amplification were detected...
January 16, 2018: Cancer Biology & Therapy
https://www.readbyqxmd.com/read/29335834/genetics-of-osteopetrosis
#14
REVIEW
Eleonora Palagano, Ciro Menale, Cristina Sobacchi, Anna Villa
PURPOSE OF REVIEW: The term osteopetrosis refers to a group of rare skeletal diseases sharing the hallmark of a generalized increase in bone density owing to a defect in bone resorption. Osteopetrosis is clinically and genetically heterogeneous, and a precise molecular classification is relevant for prognosis and treatment. Here, we review recent data on the pathogenesis of this disorder. RECENT FINDINGS: Novel mutations in known genes as well as defects in new genes have been recently reported, further expanding the spectrum of molecular defects leading to osteopetrosis...
January 15, 2018: Current Osteoporosis Reports
https://www.readbyqxmd.com/read/29334134/a-comprehensive-next-generation-sequencing-assay-for-the-diagnosis-of-epidermolysis-bullosa
#15
Anne W Lucky, Neha Dagaonkar, Karen Lammers, Ammar Husami, Diane Kissell, Kejian Zhang
BACKGROUND: Historically, diagnosis of epidermolysis bullosa has required skin biopsies for electron microscopy, direct immunofluorescence to determine which gene(s) to choose for genetic testing, or both. METHODS: To avoid these invasive tests, we developed a high-throughput next-generation sequencing (NGS)-based diagnostic assay called EBSEQ that allows simultaneous detection of mutations in 21 genes with known roles in epidermolysis bullosa pathogenicity. Mutations are confirmed with traditional Sanger sequencing...
January 15, 2018: Pediatric Dermatology
https://www.readbyqxmd.com/read/29332123/braf-nras-and-gnaq-mutations-in-conjunctival-melanocytic-nevi
#16
Jasmine H Francis, Hans E Grossniklaus, Larissa A Habib, Brian Marr, David H Abramson, Klaus J Busam
Purpose: To evaluate BRAF, NRAS, and GNAQ mutations in surgical specimens of common and blue conjunctival melanocytic nevi. Methods: Surgical specimens from 25 conjunctival melanocytic nevi (23 common and 2 blue) of 25 patients were evaluated. All common nevi were analyzed immunohistochemically for the expression of BRAF V600E or NRAS Q61R. One lesion with negative immunoreactivity and for all blue nevi, a hybridization capture-based next-generation sequencing method was employed for mutation analysis...
January 1, 2018: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/29331079/lmod3-associated-nemaline-myopathy-prenatal-ultrasonographic-pathologic-and-molecular-findings
#17
Michal Berkenstadt, Ben Pode-Shakked, Ortal Barel, Hila Barash, Reuven Achiron, Yinon Gilboa, Dvora Kidron, Annick Raas-Rothschild
To describe the prenatal presentation, including ultrasonographic, histologic, and molecular findings, in 2 fetuses affected with LMOD3-related nemaline myopathy. Prenatal ultrasonographic examinations and histopathologic studies were performed on 2 fetuses with evidence of nemaline myopathy. To establish a molecular diagnosis, whole-exome sequencing was pursued for the affected fetuses. Nemaline myopathy is a common form of congenital myopathy manifesting with nonprogressive generalized muscle weakness, hypotonia, and electron-dense protein inclusions in skeletal myofibers...
January 13, 2018: Journal of Ultrasound in Medicine: Official Journal of the American Institute of Ultrasound in Medicine
https://www.readbyqxmd.com/read/29330365/engineered-nanointerfaces-for-microfluidic-isolation-and-molecular-profiling-of-tumor-specific-extracellular-vesicles
#18
Eduardo Reátegui, Kristan E van der Vos, Charles P Lai, Mahnaz Zeinali, Nadia A Atai, Berent Aldikacti, Frederick P Floyd, Aimal H Khankhel, Vishal Thapar, Fred H Hochberg, Lecia V Sequist, Brian V Nahed, Bob S Carter, Mehmet Toner, Leonora Balaj, David T Ting, Xandra O Breakefield, Shannon L Stott
Extracellular vesicles (EVs) carry RNA, DNA, proteins, and lipids. Specifically, tumor-derived EVs have the potential to be utilized as disease-specific biomarkers. However, a lack of methods to isolate tumor-specific EVs has limited their use in clinical settings. Here we report a sensitive analytical microfluidic platform (EVHB-Chip) that enables tumor-specific EV-RNA isolation within 3 h. Using the EVHB-Chip, we achieve 94% tumor-EV specificity, a limit of detection of 100 EVs per μL, and a 10-fold increase in tumor RNA enrichment in comparison to other methods...
January 12, 2018: Nature Communications
https://www.readbyqxmd.com/read/29330115/pediatric-onset-evans-syndrome-heterogeneous-presentation-and-high-frequency-of-monogenic-disorders-including-lrba-and-ctla4-mutations
#19
Caroline Besnard, Eva Levy, Nathalie Aladjidi, Marie-Claude Stolzenberg, Aude Magerus-Chatinet, Olivier Alibeu, Patrick Nitschke, Stéphane Blanche, Olivier Hermine, Eric Jeziorski, Judith Landman-Parker, Guy Leverger, Nizar Mahlaoui, Gérard Michel, Isabelle Pellier, Felipe Suarez, Isabelle Thuret, Geneviève de Saint-Basile, Capucine Picard, Alain Fischer, Bénédicte Neven, Frédéric Rieux-Laucat, Pierre Quartier
Evans syndrome (ES) is defined by the combination of autoimmune hemolytic anemia and immune thrombocytopenia. Clinical presentation includes manifestations of immune dysregulation, found in primary immune deficiencies, autoimmune lymphoproliferative syndrome with FAS (ALPS-FAS), Cytotoxic T Lymphocyte Antigen-4 (CTLA-4) and Lipopolysaccharide-Responsive vesicle trafficking Beige-like and Anchor protein (LRBA) defects. We report the clinical history and genetic results of 18 children with ES after excluding ALPS-FAS...
January 9, 2018: Clinical Immunology: the Official Journal of the Clinical Immunology Society
https://www.readbyqxmd.com/read/29327718/epithelioid-fibrous-histiocytoma-molecular-characterization-of-alk-fusion-partners-in-23-cases
#20
Brendan C Dickson, David Swanson, George S Charames, Christopher Dm Fletcher, Jason L Hornick
Epithelioid fibrous histiocytoma is a rare and distinctive cutaneous neoplasm. Most cases harbor ALK rearrangement and show ALK overexpression, which distinguish this neoplasm from conventional cutaneous fibrous histiocytoma and variants. SQSTM1 and VCL have previously been shown to partner with ALK in one case each of epithelioid fibrous histiocytoma. The purpose of this study was to examine a large cohort of epithelioid fibrous histiocytomas by next-generation sequencing to characterize the nature and prevalence of ALK fusion partners...
January 12, 2018: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
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