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Next generation sequencing review

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https://www.readbyqxmd.com/read/28818953/new-horizons-for-precision-medicine-in-biliary-tract-cancers
#1
REVIEW
Juan W Valle, Angela Lamarca, Lipika Goyal, Jorge Barriuso, Andrew X Zhu
Biliary tract cancers (BTC), including cholangiocarcinoma and gallbladder cancer, are poor-prognosis and low-incidence cancers, although the incidence of intrahepatic cholangiocarcinoma is rising. A minority of patients present with resectable disease but relapse rates are high; benefit from adjuvant capecitabine chemotherapy has been demonstrated. Cisplatin/gemcitabine combination chemotherapy has emerged as the reference first-line treatment regimen; there is no standard second-line therapy. Selected patients may be suitable for liver-directed therapy (e...
August 17, 2017: Cancer Discovery
https://www.readbyqxmd.com/read/28815469/metagenome-analysis-a-powerful-tool-for-enzyme-bioprospecting
#2
Aravind Madhavan, Raveendran Sindhu, Binod Parameswaran, Rajeev K Sukumaran, Ashok Pandey
Microorganisms are found throughout every corner of nature, and vast number of microorganisms is difficult to cultivate by classical microbiological techniques. The advent of metagenomics has revolutionized the field of microbial biotechnology. Metagenomics allow the recovery of genetic material directly from environmental niches without any cultivation techniques. Currently, metagenomic tools are widely employed as powerful tools to isolate and identify enzymes with novel biocatalytic activities from the uncultivable component of microbial communities...
August 16, 2017: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/28812256/the-potential-for-emerging-microbiome-mediated-therapeutics-in-asthma
#3
REVIEW
Ayse Bilge Ozturk, Benjamin Arthur Turturice, David L Perkins, Patricia W Finn
PURPOSE OF REVIEW: In terms of immune regulating functions, analysis of the microbiome has led the development of therapeutic strategies that may be applicable to asthma management. This review summarizes the current literature on the gut and lung microbiota in asthma pathogenesis with a focus on the roles of innate molecules and new microbiome-mediated therapeutics. RECENT FINDINGS: Recent clinical and basic studies to date have identified several possible therapeutics that can target innate immunity and the microbiota in asthma...
August 10, 2017: Current Allergy and Asthma Reports
https://www.readbyqxmd.com/read/28811299/twenty-years-of-menin-emerging-opportunities-for-restoration-of-transcription-in-men1
#4
Koen M A Dreijerink, Marc Timmers, Myles Brown
Since the discovery of the multiple endocrine neoplasia type 1 (MEN1) gene in 1997, elucidation of the molecular function of its protein product, menin, has been a challenge. Biochemical, proteomics, genetics and genomics approaches have identified various potential roles, which converge on gene expression regulation. The most consistent findings show that menin connects transcription factors and chromatin modifying enzymes, in particular the histone H3K4 methyltransferase complexes MLL1 and MLL2. Chromatin immunoprecipitation combined with next generation sequencing has enabled studying genome-wide dynamics of chromatin binding by menin...
August 15, 2017: Endocrine-related Cancer
https://www.readbyqxmd.com/read/28808977/skeletal-dysplasias-what-every-bone-health-clinician-needs-to-know
#5
REVIEW
Sarah M Nikkel
PURPOSE OF REVIEW: This review highlights how skeletal dysplasias are diagnosed and how our understanding of some of these conditions has now translated to treatment options. RECENT FINDINGS: The use of multigene panels, using next-generation sequence technology, has improved our ability to quickly identify the genetic etiology, which can impact management. There are successes with the use of growth hormone in individuals with SHOX deficiencies, asfotase alfa in hypophosphatasia, and some promising data for c-type natriuretic peptide for those with achondroplasia...
August 14, 2017: Current Osteoporosis Reports
https://www.readbyqxmd.com/read/28807546/epigenetic-drivers-of-tumourigenesis-and-cancer-metastasis
#6
REVIEW
Aniruddha Chatterjee, Euan J Rodger, Michael R Eccles
Since the completion of the first human genome sequence and the advent of next generation sequencing technologies, remarkable progress has been made in understanding the genetic basis of cancer. These studies have mainly defined genetic changes as either causal, providing a selective advantage to the cancer cell (a driver mutation) or consequential with no selective advantage (not directly causal, a passenger mutation). A vast unresolved question is how a primary cancer cell becomes metastatic and what are the molecular events that underpin this process...
August 11, 2017: Seminars in Cancer Biology
https://www.readbyqxmd.com/read/28805986/histiocytic-sarcoma-new-insights-into-fna-cytomorphology-and-molecular-characteristics
#7
Yin P Hung, Scott B Lovitch, Xiaohua Qian
BACKGROUND: Histiocytic sarcoma (HS) is a rare malignant neoplasm showing morphologic and immunophenotypic features of histiocytes. Molecular characteristics of HS and fine-needle aspiration (FNA) criteria for its diagnosis have not been established. METHODS: A case series of HS in 8 FNA samples from 6 patients was reviewed along with histopathologic and clinical data. Immunohistochemistry was performed on cell blocks (3 cases), core biopsies (5 cases), and surgical specimens (4 cases)...
August 2017: Cancer
https://www.readbyqxmd.com/read/28805638/nonretroviral-integrated-rna-viruses-in-arthropod-vectors-an-occasional-event-or-something-more
#8
REVIEW
Ken E Olson, Mariangela Bonizzoni
With few exceptions, all arthropod-borne viruses (arboviruses) are nonretroviral RNA viruses (NRVs). Despite NRVs do not encode reverse transcriptases and integrases, NRVs-DNA fragments are detected in mosquito cells and mosquitoes at early stages of infection as episomal DNA forms. Additionally, next generation sequencing and bioinformatics analyses have convincingly shown NRVs-vDNA integrated in vector genomes. We hypothesize vDNA role may be linked to host immunity and viral persistence. Key questions remain about nonretroviral integrated RNA virus sequences (NIRVS) in mosquitoes such as what is driving vDNA synthesis from NRVs, how does integration occur and what is their biological function...
August 2017: Current Opinion in Insect Science
https://www.readbyqxmd.com/read/28801731/molecular-mapping-and-genomics-of-soybean-seed-protein-a-review-and-perspective-for-the-future
#9
REVIEW
Gunvant Patil, Rouf Mian, Tri Vuong, Vince Pantalone, Qijian Song, Pengyin Chen, Grover J Shannon, Tommy C Carter, Henry T Nguyen
Genetic improvement of soybean protein meal is a complex process because of negative correlation with oil, yield, and temperature. This review describes the progress in mapping and genomics, identifies knowledge gaps, and highlights the need of integrated approaches. Meal protein derived from soybean [Glycine max (L) Merr.] seed is the primary source of protein in poultry and livestock feed. Protein is a key factor that determines the nutritional and economical value of soybean. Genetic improvement of soybean seed protein content is highly desirable, and major quantitative trait loci (QTL) for soybean protein have been detected and repeatedly mapped on chromosomes (Chr...
August 11, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28798766/toward-genomics-based-breeding-in-c3-cool-season-perennial-grasses
#10
REVIEW
Shyamal K Talukder, Malay C Saha
Most important food and feed crops in the world belong to the C3 grass family. The future of food security is highly reliant on achieving genetic gains of those grasses. Conventional breeding methods have already reached a plateau for improving major crops. Genomics tools and resources have opened an avenue to explore genome-wide variability and make use of the variation for enhancing genetic gains in breeding programs. Major C3 annual cereal breeding programs are well equipped with genomic tools; however, genomic research of C3 cool-season perennial grasses is lagging behind...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28796964/can-minimal-residual-disease-determination-in-acute-myeloid-leukemia-be-used-in-clinical-practice
#11
Marlise R Luskin, Richard M Stone
In acute myeloid leukemia (AML) that is in complete remission, minimal residual disease (MRD) is presumed to be present, though not morphologically evident. Advances in diagnostics now permit the detection and quantification of MRD in AML by several techniques. The level of MRD after induction and consolidation therapy correlates with disease sensitivity to chemotherapy and has greater power to predict long-term survival than patient and disease characteristics that are available at diagnosis, including genetic information...
August 2017: Journal of Oncology Practice
https://www.readbyqxmd.com/read/28794806/recent-developments-in-the-treatment-of-metastatic-colorectal-cancer
#12
REVIEW
Jonathan M Loree, Scott Kopetz
Over the past decade there have been significant advances in the molecular characterization of colorectal cancer (CRC) that are driving treatment decisions. Expanded RAS testing beyond KRAS exon 2 was established as crucial for identifying patients who will respond to anti-epidermal growth factor receptor (EGFR) therapies and low-frequency mutations in RAS/tumor heterogeneity are gaining recognition as potential mechanisms of resistance. Despite this progress, the fact that we do not understand why left-sided but not right-sided tumors have improved outcomes following anti-EGFR therapy highlights our superficial understanding of this disease...
August 2017: Therapeutic Advances in Medical Oncology
https://www.readbyqxmd.com/read/28793149/genotypic-and-phenotypic-features-of-bap1-cancer-syndrome-a-report-of-8-new-families-and-review-of-cases-in-the-literature
#13
Alexandra M Haugh, Ching-Ni Njauw, Jeffrey A Bubley, Anna Elisa Verzì, Bin Zhang, Emily Kudalkar, Timothy VandenBoom, Kara Walton, Brian L Swick, Raj Kumar, Huma Q Rana, Sarah Cochrane, Shelley R McCormick, Christopher R Shea, Hensin Tsao, Pedram Gerami
Importance: Patients with germline mutations in BAP1 may develop several flesh-colored melanocytic BAP1-mutated atypical intradermal tumors (MBAITs). These tumors generally develop earlier than other BAP1-associated tumors, highlighting an important role for dermatologists in identifying and screening patients with a history suggestive of a germline mutation. Objective: To describe 8 new families with germline mutations in BAP1 and provide a comprehensive review of reported cases...
August 9, 2017: JAMA Dermatology
https://www.readbyqxmd.com/read/28791010/uses-of-next-generation-sequencing-technologies-for-the-diagnosis-of-primary-immunodeficiencies
#14
REVIEW
Michael Seleman, Rodrigo Hoyos-Bachiloglu, Raif S Geha, Janet Chou
Primary immunodeficiencies (PIDs) are genetic disorders impairing host immunity, leading to life-threatening infections, autoimmunity, and/or malignancies. Genomic technologies have been critical for expediting the discovery of novel genetic defects underlying PIDs, expanding our knowledge of the complex clinical phenotypes associated with PIDs, and in shifting paradigms of PID pathogenesis. Once considered Mendelian, monogenic, and completely penetrant disorders, genomic studies have redefined PIDs as a heterogeneous group of diseases found in the global population that may arise through multigenic defects, non-germline transmission, and with variable penetrance...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28790837/rucaparib-the-past-present-and-future-of-a-newly-approved-parp-inhibitor-for-ovarian-cancer
#15
REVIEW
L E Dockery, C C Gunderson, K N Moore
Rucaparib camsylate (CO-338, AG-014699, PF-01367338) is a potent PARP-1, PARP-2, and PARP-3 inhibitor. Phase I and II studies demonstrated clinical efficacy in both BRCA-mutated (inclusive of germline and somatic) ovarian tumors and ovarian tumors with homologous recombination deficiency (HRD) loss of heterozygosity (LOH). Rucaparib has received the US Food and Drug Administration (FDA) approval for patients with deleterious BRCA mutation (germline and/or somatic)-associated advanced ovarian cancer who have been treated with two or more chemotherapies...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/28782984/review-of-clinical-next-generation-sequencing
#16
Sophia Yohe, Bharat Thyagarajan
CONTEXT: - Next-generation sequencing (NGS) is a technology being used by many laboratories to test for inherited disorders and tumor mutations. This technology is new for many practicing pathologists, who may not be familiar with the uses, methodology, and limitations of NGS. OBJECTIVE: - To familiarize pathologists with several aspects of NGS, including current and expanding uses; methodology including wet bench aspects, bioinformatics, and interpretation; validation and proficiency; limitations; and issues related to the integration of NGS data into patient care...
August 7, 2017: Archives of Pathology & Laboratory Medicine
https://www.readbyqxmd.com/read/28777494/clinico-radiological-features-and-next-generation-sequencing-of-pulmonary-epithelioid-hemangioendothelioma-a-case-report-and-review-of-literature
#17
Xiaoyong Mao, Zibin Liang, Fidelis Chibhabha, Wei Ou, Ning Li, Pengfei Xu, Siyu Wang
Epithelioid hemangioendothelioma is a very rare, vascular, low-grade malignant tumor found in the lungs, liver, bone, and other soft tissues. Most patients with pulmonary epithelioid hemangioendothelioma (PEH) are asymptomatic but usually present with multiple bilateral nodular lesions in the lungs. Currently, surgical lung biopsy, histology, and immunohistochemical methods are essential for diagnosis. However, there is no standard therapy for the treatment for PEH. Our paper describes the clinico-radiologic features and genomics of PEH based on next-generation sequencing (NGS) in a 43-year-old male we encountered...
August 4, 2017: Thoracic Cancer
https://www.readbyqxmd.com/read/28776307/genetic-basis-of-adult-onset-nephrotic-syndrome-and-focal-segmental-glomerulosclerosis
#18
REVIEW
Jian Liu, Weiming Wang
Nephrotic syndrome (NS) is one of the most common glomerular diseases with signs of nephrosis, heavy proteinuria, hypoalbuminemia, and edema. Dysfunction of glomerular filtration barrier causes protein loss through the kidneys. Focal segmental glomerulosclerosis (FSGS) accounts for nearly 20% of NS among children and adults. Adult-onset FSGS/NS is often associated with low response to steroid treatment and immunosuppressive medication and poor renal survival. Several genes involved in NS and FSGS have been identified by linkage analysis and next-generation sequencing...
August 3, 2017: Frontiers of Medicine
https://www.readbyqxmd.com/read/28771233/impact-of-germline-and-somatic-brca1-2-mutations-tumor-spectrum-and-detection-platforms
#19
REVIEW
H Wu, X Wu, Z Liang
The BRCA1/2 genes are long and complex and mutation carriers are at risk of developing malignancies, mainly of gynecological origin. Various mutations arise in these genes and their characterization is a time consuming, cost intensive, complicated process. Tumors of BRCA1/2 origin have distinct molecular and histological features that can impact responses to therapy. Therefore, detection of these mutations constitutes an important step in the risk assessment, prevention strategy and treatment of subjects. Although Sanger sequencing is the gold standard for the detection of genetic mutations, several next generation sequencing-based high throughput platforms have been developed and adapted for the detection of BRCA1/2 mutations...
August 3, 2017: Gene Therapy
https://www.readbyqxmd.com/read/28768485/a-systematic-review-of-genetic-mutations-in-pulmonary-arterial-hypertension
#20
Gerardo Garcia-Rivas, Carlos Jerjes-Sánchez, David Rodriguez, José Garcia-Pelaez, Victor Trevino
BACKGROUND: Pulmonary arterial hypertension (PAH) is a group of vascular diseases that produce right ventricular dysfunction, heart failure syndrome, and death. Although the majority of patients appear idiopathic, accumulated research work combined with current sequencing technology show that many gene variants could be an important component of the disease. However, current guidelines, clinical practices, and available gene panels focus the diagnosis of PAH on a relatively low number of genes and variants associated with the bone morphogenic proteins and transforming Growth Factor-β pathways, such as the BMPR2, ACVRL1, CAV1, ENG, and SMAD9...
August 2, 2017: BMC Medical Genetics
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