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Next generation sequencing review

Kelly M Zatopek, Andrew F Gardner, Zvi Kelman
DNA replication and repair are essential biological processes needed for the survival of all organisms. Although these processes are fundamentally conserved in the three domains, Archaea, Bacteria and Eukarya, the proteins and complexes involved differ. The genetic and biophysical tools developed for archaea in the last several years have accelerated the study of DNA replication and repair in this domain. In this review, the current knowledge of DNA replication and repair processes in archaea will be summarized, with emphasis on the contribution of genetics and other recently developed biophysical and molecular tools, including capillary gel electrophoresis, next-generation sequencing and single-molecule approaches...
April 18, 2018: FEMS Microbiology Reviews
Christina D Moon, Wayne Young, Paul H Maclean, Adrian L Cookson, Emma N Bermingham
Interests in the impact of the gastrointestinal microbiota on health and wellbeing have extended from humans to that of companion animals. While relatively fewer studies to date have examined canine and feline gut microbiomes, analysis of the metagenomic DNA from fecal communities using next-generation sequencing technologies have provided insights into the microbes that are present, their function, and potential to contribute to overall host nutrition and health. As carnivores, healthy dogs and cats possess fecal microbiomes that reflect the generally higher concentrations of protein and fat in their diets, relative to omnivores and herbivores...
June 17, 2018: MicrobiologyOpen
Sebastian Mondaca, Rona Yaeger
The widespread use of next generation sequencing (NGS) has led to a refined understanding of the genomics of colorectal cancer (CRC). However, progress in the use of molecular biomarkers in standard practice has been slow, and there is no approved targeted therapy for CRC based on a positive predictive marker yet. In this review, we will first summarize biomarkers with clinical utility in standard practice or targeted therapy trials and then consider how to rationally design clinical trials to more effectively target CRC...
May 2018: Annals of Translational Medicine
Tessa van Dijk, Frank Baas, Peter G Barth, Bwee Tien Poll-The
BACKGROUND: Pontocerebellar hypoplasia (PCH) describes a rare, heterogeneous group of neurodegenerative disorders mainly with a prenatal onset. Patients have severe hypoplasia or atrophy of cerebellum and pons, with variable involvement of supratentorial structures, motor and cognitive impairments. Based on distinct clinical features and genetic causes, current classification comprises 11 types of PCH. MAIN TEXT: In this review we describe the clinical, neuroradiological and genetic characteristics of the different PCH subtypes, summarize the differential diagnosis and reflect on potential disease mechanisms in PCH...
June 15, 2018: Orphanet Journal of Rare Diseases
Frank U Weiss, Mariya E Skube, Markus M Lerch
PURPOSE OF REVIEW: Genetic mutations in genes within and outside of the trypsin-dependent pathologic pathway have been found to be associated with chronic pancreatitis. This review highlights recent developments. RECENT FINDINGS: CTRB1-CTRB2 has been identified as a new risk locus for chronic pancreatitis and the disease mechanism may involve trypsin degradation. Misfolding mutations in PRSS1, CPA1, and CEL, as well as environmental stress factors like tobacco and alcohol can trigger endoplasmic reticulum stress (ER-Stress)...
June 8, 2018: Current Opinion in Gastroenterology
Minghui Pang, Yijun Liu, Xiaolin Hou, Jialiang Yang, Xuelai He, Nengyi Hou, Peixi Liu, Luo Liang, Junwen Fu, Kang Wang, Zimeng Ye, Bo Gong
Familial adenomatous polyposis (FAP), an autosomal dominant disease, is a colon cancer predisposition syndrome that manifests as a large number of adenomatous polyps. Mutations in the Adenomatous polyposis coli (APC) gene are responsible for the majority of cases of FAP. The purpose of the present study was to report the clinical features of a Chinese family with FAP and screen for novel mutations using the targeted next‑generation sequencing technology. Among the 29 family members, 12 were diagnosed of FAP...
June 5, 2018: Molecular Medicine Reports
Yang Shao, Hui Li, Ran Du, Jiao Meng, Gong Yang
Ovarian cancer (OC) is the most lethal gynecological malignancy, with a low 5-year survival rate. Most patients with ovarian cancer are diagnosed in late-stages. A rising number of non-coding RNAs (ncRNAs) have been found to act as key regulators of gene expression by applying novel high-thought methods, such as next generation sequencing (NGS). Non-coding RNAs not only play important roles in carcinogenesis, but also affect the clinical treatment strategies. One of the biggest challenge in OC treatment was chemoresistance, which causes poor prognosis and high recurrence rate after applying traditional remedies...
2018: Journal of Cancer
Na He, Zhi-Jian Lin, Jie Wang, Feng Wei, Heng Meng, Xiao-Rong Liu, Qian Chen, Tao Su, Yi-Wu Shi, Yong-Hong Yi, Wei-Ping Liao
Epileptic encephalopathies comprise a group of catastrophic epilepsies with heterogeneous genetic etiology. Although next-generation sequencing techniques can reveal a number of de novo variants in epileptic encephalopathies, evaluating the pathogenicity of these variants can be challenging. Determining the pathogenic potential of genes in epileptic encephalopathies is critical before evaluating the pathogenicity of variants identified in an individual. We reviewed de novo variants in epileptic encephalopathies, including their genotypes and functional consequences...
June 12, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
Jian-Woon Chen, Yin Yin Lau, Thiba Krishnan, Kok-Gan Chan, Chien-Yi Chang
Pseudomonas aeruginosa is a rod-shaped Gram-negative bacterium which is notably known as a pathogen in humans, animals, and plants. Infections caused by P. aeruginosa especially in hospitalized patients are often life-threatening and rapidly increasing worldwide throughout the years. Recently, multidrug-resistant P. aeruginosa has taken a toll on humans' health due to the inefficiency of antimicrobial agents. Therefore, the rapid and advanced diagnostic techniques to accurately detect this bacterium particularly in clinical samples are indeed necessary to ensure timely and effective treatments and to prevent outbreaks...
2018: Frontiers in Microbiology
Agda Karina Eterovic, Ossama M Maher, Joya Chandra, Ken Chen, Jason Huse, Wafik Zaky
Metachronous neoplasms have rarely been reported in patients with neuroblastoma. This report presents the clinical case of a 23-month-old child who was diagnosed with an anaplastic medulloblastoma 5 months after completing treatment for stage IV neuroblastoma. The patient was treated with complete surgical resection and adjuvant chemoradiation followed by maintenance chemotherapy at an outside institution and came to our institution for further management. A pathologic diagnosis and review of both the suprarenal and posterior fossa masses were performed, as well as a genetic analysis of both cerebellar tumor tissue and blood using next-generation gene sequencing...
June 2018: Journal of the National Comprehensive Cancer Network: JNCCN
An Boudewyns, Jenneke van den Ende, Manou Sommen, Wim Wuyts, Nils Peeters, Paul Van de Heyning, Guy Van Camp
OBJECTIVES: The purpose of this study is to report the results of a comprehensive etiological work-up for congenitally deaf children including targeted next generation sequencing. STUDY DESIGN: Retrospective case review. SETTING: Tertiary referral center. PATIENTS: Fifty children with congenital, bilateral profound hearing loss (HL) (>90 dBnHL). INTERVENTIONS: Etiological work-up included testing for pathogenic variants in GJB2, a phenotype driven genetic analysis, screening for congenital infections and imaging...
July 2018: Otology & Neurotology
Vassiliki Saloura, Theodore Vougiouklakis, Cem Sievers, Kyunghee Burkitt, Yusuke Nakamura, Gordon Hager, Carter van Waes
Squamous cell carcinoma of the head and neck is a lethal disease with suboptimal survival outcomes and standard therapies with significant comorbidities. Whole exome sequencing data recently revealed an abundance of genetic and expression alterations in a family of enzymes known as protein methyltransferases in a variety of cancer types, including squamous cell carcinoma of the head and neck. These enzymes are mostly known for their chromatin-modifying functions through methylation of various histone substrates, though evidence supports their function also through methylation of non-histone substrates...
June 2018: Oral Oncology
Márton Münz, Shazia Mahamdallie, Shawn Yost, Andrew Rimmer, Emma Poyastro-Pearson, Ann Strydom, Sheila Seal, Elise Ruark, Nazneen Rahman
Quality assurance and quality control are essential for robust next generation sequencing (NGS). Here we present CoverView, a fast, flexible, user-friendly quality evaluation tool for NGS data. CoverView processes mapped sequencing reads and user-specified regions to report depth of coverage, base and mapping quality metrics with increasing levels of detail from a chromosome-level summary to per-base profiles. CoverView can flag regions that do not fulfil user-specified quality requirements, allowing suboptimal data to be systematically and automatically presented for review...
2018: Wellcome Open Research
Anna R Hemnes
Pulmonary arterial hypertension (PAH) is a devastating disease for which there is no cure. Presently this condition is differentiated from other diseases of the pulmonary vasculature by a practitioner's history, physical examination, and clinical studies with clinical markers of disease severity primarily guiding therapeutic choices. New technologies such as next generation DNA sequencing, high throughput RNA sequencing, metabolomics and proteomics have greatly enhanced the amount of data that can be studied efficiently in patients with PAH and other rare diseases...
2018: Frontiers in Medicine
Christina Tsigalou, Elisavet Stavropoulou, Eugenia Bezirtzoglou
Sjogren's syndrome (SS) is an autoimmune disease, among the most common ones, that targets mainly the exocrine glands as well as extra-glandular epithelial tissues. Their lymphocytic infiltration leads to manifestations from other organs (e.g., kidneys, lungs, liver, or thyroid), apart from sicca symptoms (xerostomia and keratoconjunctivitis). SS is more prevalent in women than in men (9:1). Moreover, p.SS patients are in increased risk to develop lymphoma. Certain autoantibodies (e.g., antibodies against ribonucleoprotein autoantigens Ro-SSA and La-SSB) are ultimate hallmarks for the disease...
2018: Frontiers in Immunology
Michal Pawlak, Katarzyna Niescierowicz, Cecilia Lanny Winata
: Vertebrate organs develop through a complex process which involves interaction between multiple signaling pathways at the molecular, cell, and tissue levels. Heart development is an example of such complex process which, when disrupted, results in congenital heart disease (CHD). This complexity necessitates a holistic approach which allows the visualization of genome-wide interaction networks, as opposed to assessment of limited subsets of factors. Genomics offers a powerful solution to address the problem of biological complexity by enabling the observation of molecular processes at a genome-wide scale...
June 7, 2018: Genes
Luca Persani, Tiziana de Filippis, Carla Colombo, Davide Gentilini
The technological advancements in genetics produced a profound impact on the research and diagnostics of non-communicable diseases. The availability of Next Generation Sequencing (NGS) allowed the identification of novel candidate genes but also an in depth modification of the understanding of the architecture of several endocrine diseases. Several different NGS approaches are available allowing the sequencing of several regions of interest or the whole exome or genome (WGS, WES, or targeted NGS), with highly variable costs, potentials and limitations that should be clearly known before designing the experiment...
June 7, 2018: European Journal of Endocrinology
Donatella Lucchetti, Andrea Fattorossi, Alessandro Sgambato
Background The possibility to study solid tumors through the analysis of extracellular vesicles in biological fluids is one of the most exciting and rapidly advancing field in cancer research. The extracellular vesicles are tiny sacs released in both physiological and pathological conditions and could be used to monitor the evolution of several pathological states, including neoplastic diseases. Indeed, these vesicles carry biological informations and can affect the behavior of recipient cells by transferring proteins, DNA, RNA and microRNA...
June 7, 2018: Biotechnology Journal
Ichiro Hanamura, Shinsuke Iida
Proteasome inhibitors and immunomodulatory drugs have substantially improved the clinical outcomes in patients with multiple myeloma (MM) since 2000. In 2015, the new monoclonal antibodies, daratumumab and elotuzumab, were approved for treating relapsed and/or refractory MM (RRMM). Furthermore, venetoclax, a selective BCL-2 inhibitor, and chimeric antigen receptor (CAR) T-cell therapy that work against B-cell maturation antigen (BCMA) have reportedly shown great efficacy in phase 1 studies. The efficacy of venetoclax has been observed in RRMM with t (11;14) and higher BCL-2/BCL-XL expression...
2018: [Rinshō Ketsueki] the Japanese Journal of Clinical Hematology
Fumihiko Hayakawa
For a long time, treatment for adult acute lymphoblastic leukemia (ALL) lacked significant improvements. Since 2000, new approaches, such as the treatments of adolescent and young adult ALL using pediatric-like protocols and Ph+ ALL treatments using tyrosine kinase inhibitor-combined chemotherapies. Further improvements are expected from the use of pediatric-like protocols to whole adults, and the use of newly approved anti-cancer drugs, such as inotuzumab ozogamicin and blinatumomab. Furthermore, comprehensive genetic analyses using next generation sequencing technology have recently discovered new recurrent fusion genes of ALL, such as DUX4 fusion genes, ZNF384 fusion genes, and MEF2D fusion genes...
2018: [Rinshō Ketsueki] the Japanese Journal of Clinical Hematology
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