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Next generation sequencing review

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https://www.readbyqxmd.com/read/28528510/immunogenomics-using-genomics-to-personalize-cancer-immunotherapy
#1
Rance C Siniard, Shuko Harada
While the use of genomic data has the potential to revolutionize patient care, there is still much work to be done with regard to the transformation of host-tumor interactions into favorable clinical outcomes for our patients. High-throughput technologies, such as next-generation sequencing (NGS), have rapidly advanced our understanding of oncology, and we are learning that most tumors do not simply possess consistently mutated genes that are responsible for tumorigenesis, facilitating the need for personalized cancer therapy...
May 20, 2017: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/28526922/advances-in-systemic-therapy-for-metastatic-breast-cancer-future-perspectives
#2
REVIEW
S P Corona, N Sobhani, A Ianza, G Roviello, G Mustacchi, M Bortul, F Zanconati, D Generali
Breast cancer (BC) is the most common cancer in women worldwide. One in eight women will develop the disease in her lifetime. Notwithstanding the incredible progress made in this field, BC still represents the second most common cause of cancer-related death in women. Targeted drugs have revolutionised breast cancer treatment and improved the prognosis as well as the life expectancy of millions of women. However, the phenomenon of primary and secondary pharmacological resistance is becoming increasingly evident, limiting the efficacy of these agents and calling for a better in-depth knowledge and understanding of the biology as well as the biochemical crosstalk underlying the disease...
July 2017: Medical Oncology
https://www.readbyqxmd.com/read/28524730/recent-advances-in-genetic-testing-for-familial-hypercholesterolemia
#3
Michael A Iacocca, Robert A Hegele
Familial hypercholesterolemia (FH) is a common genetic cause of premature coronary heart disease that is widely underdiagnosed and undertreated. To improve the identification of FH and initiate timely and appropriate treatment strategies, genetic testing is becoming increasingly offered worldwide as a central part of diagnosis. Areas covered: Recent advances have been propelled by an improved understanding of the genetic determinants of FH together with substantially reduced costs of appropriate screening strategies...
May 19, 2017: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/28520864/from-chromatogram-to-analyte-to-metabolite-how-to-pick-horses-for-courses-from-the-massive-web-resources-for-mass-spectral-plant-metabolomics
#4
Leonardo Perez de Souza, Thomas Naake, Takayuki Tohge, Alisdair R Fernie
The grand challenge currently facing metabolomics is the expansion of the coverage of the metabolome from a minor percentage of the metabolic complement of the cell towards the level of coverage afforded by other post-genomic technologies such as transcriptomics and proteomics. In plants this problem is exacerbated by the sheer diversity of chemicals that constitute the metabolome with the number of metabolites in the plant kingdom generally being considered to be in excess of 200 000. In this review we focus on web-resources that can be exploited in order to improve analyte and ultimately metabolite identification and quantification...
May 17, 2017: GigaScience
https://www.readbyqxmd.com/read/28520527/open-label-multicenter-phase-ii-study-of-ceritinib-in-patients-with-non-small-cell-lung-cancer-harboring-ros1-rearrangement
#5
Sun Min Lim, Hye Ryun Kim, Jong-Seok Lee, Ki Hyeong Lee, Yun-Gyoo Lee, Young Joo Min, Eun Kyung Cho, Sung Sook Lee, Bong-Seog Kim, Moon Young Choi, Hyo Sup Shim, Jin-Haeng Chung, Yoon La Choi, Min Jeong Lee, Maria Kim, Joo-Hang Kim, Siraj M Ali, Myung-Ju Ahn, Byoung Chul Cho
Purpose ROS1 rearrangement is a distinct molecular subset of non-small-cell lung cancer (NSCLC). We investigated the efficacy and safety of ceritinib in patients with ROS1-rearranged NSCLC. Patients and Methods We enrolled 32 patients with advanced NSCLC who tested positive for ROS1 rearrangement by fluorescent in situ hybridization. Ceritinib 750 mg was administered once daily. The primary end point was objective response rate. The secondary end points were disease control rate; duration of response; progression-free survival; overall survival; toxicity; and concordance among fluorescent in situ hybridization, immunohistochemistry, and next-generation sequencing...
May 18, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28519717/phytophthora-cinnamomi
#6
Adrienne R Hardham, Leila M Blackman
Phytophthora cinnamomi is one of the most devastating plant pathogens in the world. It infects close to 5,000 species of plants, including many of importance in agriculture, forestry and horticulture. Inadvertent introduction of P. cinnamomi into natural ecosystems, including a number of recognised Global Biodiversity Hotspots, has disastrous consequences for the environment and biodiversity of flora and fauna. The genus Phytophthora belongs to the Class Oomycetes, a group of fungus-like organisms that initiate plant disease through the production of motile zoospores...
May 18, 2017: Molecular Plant Pathology
https://www.readbyqxmd.com/read/28510119/genetic-epidemiology-of-titin-truncating-variants-in-the-etiology-of-dilated-cardiomyopathy
#7
REVIEW
Ali M Tabish, Valerio Azzimato, Aris Alexiadis, Byambajav Buyandelger, Ralph Knöll
Heart failure (HF) is a complex clinical syndrome defined by the inability of the heart to pump enough blood to meet the body's metabolic demands. Major causes of HF are cardiomyopathies (diseases of the myocardium associated with mechanical and/or electrical dysfunction), among which the most common form is dilated cardiomyopathy (DCM). DCM is defined by ventricular chamber enlargement and systolic dysfunction with normal left ventricular wall thickness, which leads to progressive HF. Over 60 genes are linked to the etiology of DCM...
May 5, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/28509937/next-generation-sequencing-is-informing-phenotype-a-tp53-example
#8
R O'Shea, R Clarke, E Berkley, C Giffney, M Farrell, E O'Donovan, D J Gallagher
The increased availability of next generation sequencing (NGS) and multi gene panel testing has resulted in more frequent TP53 testing of families that do not meet classic testing criteria. We investigated testing criteria, family history and result outcome in a cohort of Irish probands undergoing TP53 full sequencing. All TP53 test requests processed through the national genetic testing laboratory between 2012 and 2014 were retrospectively reviewed. Personal and family cancer histories were collected, including tumour type and age at diagnosis, from two adult cancer genetic services in Ireland...
May 16, 2017: Familial Cancer
https://www.readbyqxmd.com/read/28509786/igg4-related-disease-of-the-biliary-tract-and-pancreas-clinical-and-experimental-advances
#9
Lowiek M Hubers, Ulrich Beuers
PURPOSE OF REVIEW: IgG4-related disease (IgG4-RD) is an immune-mediated disease of unknown cause. It predominantly affects the biliary tract [IgG4-associated cholangitis (IAC)] and pancreas [autoimmune pancreatitis (AIP)] of mostly elderly men. Accurate diagnostic tests are lacking. Patients benefit from predniso(lo)ne treatment. However, disease relapse is often seen. This review will address pathophysiological aspects and advances in diagnostic and therapeutic strategies. RECENT FINDINGS: The role of IgG1 and IgG4 in the pathophysiology of IgG4-RD was studied in mice which showed more intense organ damage of pancreas and salivary glands when IgG1 rather than IgG4 of patients with IgG4-RD was injected...
May 13, 2017: Current Opinion in Gastroenterology
https://www.readbyqxmd.com/read/28509679/the-impact-of-next-generation-sequencing-in-immunogenetics-current-status-and-future-directions
#10
Valia Bravo-Egana, Dimitri Monos
PURPOSE OF REVIEW: Next-generation sequencing (NGS) has now been established, and widely recognized, to be the preferred choice for human leukocyte antigen (HLA) typing. This transformation is based upon the many scientific, operational and economic benefits this technology affords. In this report, we review the major advantages, existing limitations and significant promise derived from adopting this technology in immunogenetics. RECENT FINDINGS: Significant benefits have emerged from the usage of NGS in a relatively short period, whereby we realize that this technology not only helps addressing the technical and operational problems we have had with the legacy methods for HLA typing, but equally important, it also allows for creative applications in stem cell and organ transplantation, new ways to investigate associations of the major histocompatibility complex (MHC) with many diseases and enhance our understanding regarding the MHC and non-MHC genomic interactions...
May 13, 2017: Current Opinion in Organ Transplantation
https://www.readbyqxmd.com/read/28509669/genetic-advances-in-systemic-lupus-erythematosus-an-update
#11
Lingyan Chen, David L Morris, Timothy J Vyse
PURPOSE OF REVIEW: More than 80 susceptibility loci are now reported to show robust genetic association with systemic lupus erythematosus (SLE). The differential functional effects of the risk alleles for the majority of these loci remain to be defined. Here, we review current SLE association findings and the recent progress in the annotation of noncoding regions of the human genome as well as the new technologies and statistical methods that can be applied to further the understanding of SLE genetics...
May 15, 2017: Current Opinion in Rheumatology
https://www.readbyqxmd.com/read/28506110/evaluation-of-chemical-mutagenicity-using-next-generation-sequencing-a-review
#12
Hua Du, Bohu Pan, Tao Chen
Mutations are heritable changes in the nucleotide sequence of DNA that can lead to many adverse effects. Genotoxicity assays have been used to identify chemical mutagenicity. Recently, next generation sequencing (NGS) has been used for this purpose. In this review, we present the progress in NGS application for assessing mutagenicity of chemicals, including the methods used for detecting the induced mutations, bioinformatics tools for analyzing the sequencing data, and chemicals whose mutagenicity has been evaluated using NGS...
May 16, 2017: Journal of Environmental Science and Health. Part C, Environmental Carcinogenesis & Ecotoxicology Reviews
https://www.readbyqxmd.com/read/28505974/state-of-play-in-alzheimer-s-disease-genetics
#13
Jin-Bao Zhu, Chen-Chen Tan, Lan Tan, Jin-Tai Yu
Alzheimer's disease (AD), the main form of dementia in the elderly, is the most common progressive neurodegenerative disease characterized by rapidly progressive cognitive dysfunction and behavior impairment. AD exhibits a considerable heritability and great advances have been made in approaches to searching the genetic etiology of AD. In AD genetic studies, methods have developed from classic linkage-based and candidate-gene-based association studies to genome-wide association studies (GWAS) and next generation sequencing...
May 11, 2017: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/28505061/novel-ofd1-frameshift-mutation-in-a-chinese-boy-with-joubert-syndrome-a-case-report-and-literature-review
#14
Kaihui Zhang, Chen Meng, Jing Ma, Min Gao, Yuqiang Lv, Yi Liu, Zhongtao Gai
Joubert syndrome (JBTS) is a clinically and genetically heterogeneous group of ciliopathy with a key diagnostic feature of 'molar tooth sign' in brain MRI. So far, over 20 causative genes have been identified, but only one gene (OFD1) results in X-linked Joubert syndrome 10 (JBTS10). Six mutations in the OFD1 gene have been found to cause JBTS10. In this study, we identified a novel OFD1 mutation of c.2843_2844 delAA (p.Lys948ArgfsX) in a 3-month-old boy with a 'molar tooth sign' and clinical features of JBTS using targeted exome next-generation sequencing...
May 12, 2017: Clinical Dysmorphology
https://www.readbyqxmd.com/read/28504904/application-of-panel-based-tests-for-inherited-risk-of-cancer
#15
Payal D Shah, Katherine L Nathanson
Next-generation or massively parallel sequencing has transformed the landscape of genetic testing for cancer susceptibility. Panel-based genetic tests evaluate multiple genes simultaneously and rapidly. Because these tests are frequently offered in clinical settings, understanding their clinical validity and utility is critical. When evaluating the inherited risk of breast and ovarian cancers, panel-based tests provide incremental benefit compared with BRCA1/2 genetic testing. For inherited risk of other cancers, such as colon cancer and pheochromocytoma-paraganglioma, the clinical utility and yield of panel-based testing are higher; in fact, simultaneous evaluation of multiple genes has been the historical standard for these diseases...
May 15, 2017: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/28502730/overgrowth-syndromes-caused-by-somatic-variants-in-the-phosphatidylinositol-3-kinase-akt-mammalian-target-of-rapamycin-pathway
#16
REVIEW
Gozde Akgumus, Fengqi Chang, Marilyn M Li
Somatic variants have been well described in tumorigenesis; however, they are only recently appreciated in other human disorders, such as mosaic overgrowth syndromes. Although overgrowth is a manifestation in many genetic syndromes, not all overgrowth syndromes are inherited. Mosaic somatic variants have been lately described in several overgrowth disorders, such as Proteus syndrome, CLOVES (congenital, lipomatous, overgrowth, vascular malformations, epidermal nevi, and spinal/skeletal anomalies and/or scoliosis) syndrome, megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome, and megalencephaly-capillary malformation-polymicrogyria syndrome...
May 11, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28502422/preimplantation-genetic-diagnosis-for-monogenic-diseases
#17
REVIEW
Vivian Chi Yan Lee, Judy F C Chow, William Shu Biu Yeung, Pak Chung Ho
Preimplantation genetic diagnosis (PGD) was first reported in 1990. Thereafter, more and more indications for PGD, including monogenic diseases (MGD) and translocations, are presently available, and the list of indications of PGD is expanding from early-onset and serious conditions to late-onset diseases. Polymerase chain reaction has been used for PGD of MGD, while newer techniques, including karyomapping and next-generation sequencing, emerge in recent decade. The limitations of various methods for PGD are discussed in this review...
April 15, 2017: Best Practice & Research. Clinical Obstetrics & Gynaecology
https://www.readbyqxmd.com/read/28498723/advances-in-preimplantation-genetic-testing-for-monogenic-disease-and-aneuploidy
#18
Nathan R Treff, Rebekah S Zimmerman
Genetic testing of preimplantation embryos promises to prevent monogenic disease in children born to at-risk couples, the transfer of unbalanced embryos to patients carrying a balanced translocation, and the use of aneuploid embryos created during in vitro fertilization. Technologies have evolved from fluorescence in situ hybridization to next-generation-sequencing-based aneuploidy screening and allow for simultaneous testing of multiple genetic abnormalities in a single biopsy. The field has also shifted away from polar body or blastomere biopsy and toward trophectoderm biopsy as the new standard...
May 12, 2017: Annual Review of Genomics and Human Genetics
https://www.readbyqxmd.com/read/28497172/deep-intronic-mutations-and-human-disease
#19
REVIEW
Rita Vaz-Drago, Noélia Custódio, Maria Carmo-Fonseca
Next-generation sequencing has revolutionized clinical diagnostic testing. Yet, for a substantial proportion of patients, sequence information restricted to exons and exon-intron boundaries fails to identify the genetic cause of the disease. Here we review evidence from mRNA analysis and entire genomic sequencing indicating that pathogenic mutations can occur deep within the introns of over 75 disease-associated genes. Deleterious DNA variants located more than 100 base pairs away from exon-intron junctions most commonly lead to pseudo-exon inclusion due to activation of non-canonical splice sites or changes in splicing regulatory elements...
May 12, 2017: Human Genetics
https://www.readbyqxmd.com/read/28497038/epigenetics-and-vascular-diseases-influence-of-non-coding-rnas-and-their-clinical-implications
#20
REVIEW
Leonardo Elia, Manuela Quintavalle
Epigenetics refers to heritable mechanisms able to modulate gene expression that do not involve alteration of the genomic DNA sequence. Classically, mechanisms such as DNA methylation and histone modifications were part of this classification. Today, this field of study has been expanded and includes also the large class of non-coding RNAs (ncRNAs). Indeed, with the extraordinary possibilities introduced by the next-generation sequencing approaches, our knowledge of the mammalian transcriptome has greatly improved...
2017: Frontiers in Cardiovascular Medicine
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