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https://www.readbyqxmd.com/read/29145603/accuracy-of-next-generation-sequencing-for-molecular-diagnosis-in-patients-with-infantile-nystagmus-syndrome
#1
John Hoon Rim, Seung-Tae Lee, Heon Yung Gee, Byung Joo Lee, Jong Rak Choi, Hye Won Park, Sueng-Han Han, Jinu Han
Importance: Infantile nystagmus syndrome (INS) is a group of disorders presenting with genetic and clinical heterogeneities that have challenged the genetic and clinical diagnoses of INS. Precise molecular diagnosis in early infancy may result in more accurate genetic counseling and improved patient management. Objective: To assess the accuracy of genomic data from next-generation sequencing (NGS) and phenotypic data to enhance the definitive diagnosis of INS. Design, Setting, and Participants: A single-center retrospective case series was conducted in 48 unrelated, consecutive patients with INS, with or without associated ocular or systemic conditions, who underwent genetic testing between June 1, 2015, and January 31, 2017...
November 16, 2017: JAMA Ophthalmology
https://www.readbyqxmd.com/read/29145573/human-papillomavirus-hpv-and-somatic-egfr-mutations-are-essential-mutually-exclusive-oncogenic-mechanisms-for-inverted-sinonasal-papillomas-and-associated-sinonasal-squamous-cell-carcinomas
#2
A M Udager, J B McHugh, C M Goudsmit, H C Weigelin, M S Lim, K S J Elenitoba-Johnson, B L Betz, T E Carey, N A Brown
Background: Inverted sinonasal papilloma (ISP) is a locally aggressive neoplasm often associated with sinonasal squamous cell carcinoma (SNSCC). While the etiology of ISP is not well understood, human papillomavirus (HPV) has been detected in a subset of cases. Our group recently identified activating somatic EGFR mutations in the majority of ISP and ISP-associated SNSCC. However, the relationship between EGFR mutations and HPV infection has not been explored. Patients and Methods: We evaluated 58 ISP and 22 ISP-associated SNSCC (including 13 patients with matched ISP/SNSCC samples), as well as 14 SNSCC without clinical or pathologic evidence of an associated ISP...
November 14, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29145572/difference-in-clinical-course-genetics-and-the-microbiome-between-familial-and-sporadic-inflammatory-bowel-diseases
#3
Nienke Z Borren, Grace Conway, John J Garber, Hamed Khalili, Shrish Budree, Himel Mallick, Vijay Yajnik, Ramnik J Xavier, Ashwin N Ananthakrishnan
Objective: Family history is the strongest risk factor for developing Crohn's disease (CD) or ulcerative colitis (UC). We investigated whether the proximity of relationship with the affected relative and concordance for type of IBD modifies the effect of family history on phenotype and disease severity. Design: This cross-sectional study included patients with a confirmed diagnosis of IBD in a clinical registry. Family history of IBD was assessed by a questionnaire ascertaining presence of disease in a 1 st degree, 2 nd degree or a distant relative...
November 14, 2017: Journal of Crohn's & Colitis
https://www.readbyqxmd.com/read/29145505/spontaneous-development-of-epstein-barr-virus-associated-human-lymphomas-in-a-prostate-cancer-xenograft-program
#4
Alberto J Taurozzi, Ramprakash Beekharry, Michelle Wantoch, Marie-Christine Labarthe, Hannah F Walker, Robert I Seed, Matthew Simms, Greta Rodrigues, James Bradford, Geertje van der Horst, Gabri van der Pluijm, Anne T Collins
Prostate cancer research is hampered by the lack of in vivo preclinical models that accurately reflect patient tumour biology and the clinical heterogeneity of human prostate cancer. To overcome these limitations we propagated and characterised a new collection of patient-derived prostate cancer xenografts. Tumour fragments from 147 unsupervised, surgical prostate samples were implanted subcutaneously into immunodeficient Rag2-/-γC-/- mice within 24 hours of surgery. Histologic and molecular characterisation of xenografts was compared with patient characteristics, including androgen-deprivation therapy, and exome sequencing...
2017: PloS One
https://www.readbyqxmd.com/read/29145046/genetic-and-clinical-characteristics-of-phyllodes-tumors-of-the-breast
#5
Ji-Yeon Kim, Jong Han Yu, Seok Jin Nam, Seok Won Kim, Se Kyung Lee, Woong-Yang Park, Dong-Young Noh, Do-Hyun Nam, Yeon Hee Park, Wonshik Han, Jeong Eon Lee
PURPOSE: Phyllodes tumors (PTs) of the breast are rare, accounting for less than 1% of all breast tumors. Among PTs, malignant PTs (MPTs) have malignant characteristics and distant metastases occur in about 20% to 30% of MPTs. However, there is no effective treatment for MPTs with distant metastasis, resulting in an abject prognosis. We performed targeted deep sequencing on PTs to identify the associations between genetic alterations and clinical prognosis. METHODS: We performed targeted deep sequencing to evaluate the genetic characteristics of PTs and analyzed the relationships between clinical and genetic characteristics...
November 12, 2017: Translational Oncology
https://www.readbyqxmd.com/read/29144541/genetic-landscape-of-papillary-thyroid-carcinoma-in-the-chinese-population
#6
Jialong Liang, Wanshi Cai, Dongdong Feng, Huajing Teng, Fengbiao Mao, Yi Jiang, Shanshan Hu, Xianfeng Li, Yujie Zhang, Baoguo Liu, Zhong Sheng Sun
Improvement in the clinical outcome of human cancers requires characterization of genetic alterations underlying their pathogenesis. Large-scale genomic and transcriptomic characterization of papillary thyroid carcinomas (PTCs) in Western populations has revealed multiple oncogenic drivers which are essential for understanding pathogenic mechanisms of this disease; while so far, the genetic landscape in Chinese patients with PTC remains uncharacterized. Here, we conducted a largescale genetic analysis of PTCs from patients in China to determine the mutational landscape of this cancer...
November 16, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/29144511/evaluating-charge-syndrome-in-congenital-hypogonadotropic-hypogonadism-patients-harboring-chd7-variants
#7
Cheng Xu, Daniele Cassatella, Almer M van der Sloot, Richard Quinton, Michael Hauschild, Christian De Geyter, Christa Flück, Katrin Feller, Deborah Bartholdi, Attila Nemeth, Irene Halperin, Sandra Pekic Djurdjevic, Philippe Maeder, Georgios Papadakis, Andrew A Dwyer, Laura Marino, Lucie Favre, Duarte Pignatelli, Nicolas J Niederländer, James Acierno, Nelly Pitteloud
PurposeCongenital hypogonadotropic hypogonadism (CHH), a rare genetic disease caused by gonadotropin-releasing hormone deficiency, can also be part of complex syndromes (e.g., CHARGE syndrome). CHD7 mutations were reported in 60% of patients with CHARGE syndrome, and in 6% of CHH patients. However, the definition of CHD7 mutations was variable, and the associated CHARGE signs in CHH were not systematically examined.MethodsRare sequencing variants (RSVs) in CHD7 were identified through exome sequencing in 116 CHH probands, and were interpreted according to American College of Medical Genetics and Genomics guidelines...
November 16, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29144510/characterizing-reduced-coverage-regions-through-comparison-of-exome-and-genome-sequencing-data-across-10-centers
#8
Rashesh V Sanghvi, Christian J Buhay, Bradford C Powell, Ellen A Tsai, Michael O Dorschner, Celine S Hong, Matthew S Lebo, Ariella Sasson, David S Hanna, Sean McGee, Kevin M Bowling, Gregory M Cooper, David E Gray, Robert J Lonigro, Andrew Dunford, Christine A Brennan, Carrie Cibulskis, Kimberly Walker, Mauricio O Carneiro, Joshua Sailsbery, Lucia A Hindorff, Dan R Robinson, Avni Santani, Mahdi Sarmady, Heidi L Rehm, Leslie G Biesecker, Deborah A Nickerson, Carolyn M Hutter, Levi Garraway, Donna M Muzny, Nikhil Wagle
PurposeAs massively parallel sequencing is increasingly being used for clinical decision making, it has become critical to understand parameters that affect sequencing quality and to establish methods for measuring and reporting clinical sequencing standards. In this report, we propose a definition for reduced coverage regions and describe a set of standards for variant calling in clinical sequencing applications.MethodsTo enable sequencing centers to assess the regions of poor sequencing quality in their own data, we optimized and used a tool (ExCID) to identify reduced coverage loci within genes or regions of particular interest...
November 16, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29143897/anaplastic-lymphoma-kinase-testing-ihc-vs-fish-vs-ngs
#9
REVIEW
Xiaomin Niu, Jody C Chuang, Gerald J Berry, Heather A Wakelee
Personalized targeted therapy has emerged as a promising strategy in lung cancer treatment, with current attention focused on elucidation and detection of oncogenic drivers responsible for tumor initiation and maintenance and development of drug resistance. In lung cancer, several oncogenic drivers have been reported, triggering the application of tyrosine kinase inhibitors (TKIs) to target these dysfunctional genes. The anaplastic lymphoma kinase (ALK) rearrangement is responsible for about 4-7% of all non-small cell lung cancers (NSCLCs) and perhaps as high as a third in specific patient populations such as younger, male, non-smokers with advanced stage, epidermal growth factor receptor (EGFR) and Kirsten rat sarcoma viral oncogene (KRAS) wild type, and signet ring cell adenocarcinoma with abundant intracytoplasmic mucin...
November 16, 2017: Current Treatment Options in Oncology
https://www.readbyqxmd.com/read/29143887/diagnosis-and-treatment-of-aplastic-anemia
#10
REVIEW
Scott A Peslak, Timothy Olson, Daria V Babushok
Acquired aplastic anemia (AA) is a rare, life-threatening bone marrow failure (BMF) disorder that affects patients of all ages and is caused by lymphocyte destruction of early hematopoietic cells. Diagnosis of AA requires a comprehensive approach with prompt evaluation for inherited and secondary causes of bone marrow aplasia, while providing aggressive supportive care. The choice of frontline therapy is determined by a number of factors including AA severity, age of the patient, donor availability, and access to optimal therapies...
November 16, 2017: Current Treatment Options in Oncology
https://www.readbyqxmd.com/read/29143804/telomeres-and-telomerase-in-hematopoietic-dysfunction-prognostic-implications-and-pharmacological-interventions
#11
REVIEW
Theresa Vasko, Andrea Kaifie, Matthias B Stope, Thomas Kraus, Patrick Ziegler
Leukocyte telomere length (TL) has been suggested as a marker of biological age in healthy individuals, but can also reflect inherited and acquired hematopoietic dysfunctions or indicate an increased turnover of the hematopoietic stem and progenitor cell compartment. In addition, TL is able to predict the response rate of tyrosine kinase inhibitor therapy in chronic myeloid leukemia (CML), indicates clinical outcomes in chronic lymphocytic leukemia (CLL), and can be used as screening tool for genetic sequencing of selected genes in patients with inherited bone marrow failure syndromes (BMFS)...
October 28, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29143727/characterization-of-clinically-isolated-thymidine-dependent-small-colony-variants-of-escherichia-coli-producing-extended-spectrum-%C3%AE-lactamase
#12
Tatsuya Negishi, Takehisa Matsumoto, Kazuki Horiuchi, Eriko Kasuga, Tatsuya Natori, Mina Matsuoka, Naoko Ogiwara, Mitsutoshi Sugano, Takeshi Uehara, Noriyuki Nagano, Takayuki Honda
PURPOSE: Thymidine-dependent small-colony variants (TD-SCVs) are difficult to detect or test for antimicrobial susceptibility. We investigated the characteristics of clonal TD-SCVs of Escherichia coli, both with and without blaCTX-M-3, isolated from a patient. METHODOLOGY: Mutation in the thyA gene was analysed by sequencing, and morphological abnormalities in the colonies and cells of the isolates were examined. Additionally, conjugational transfer experiments were performed to prove the horizontal transferability of plasmids harbouring resistance genes...
November 16, 2017: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/29143720/epidemiological-investigation-of-a-severe-rumen-fluke-outbreak-on-an-irish-dairy-farm
#13
James O'Shaughnessy, Andres Garcia-Campos, Conor G McAloon, Seamus Fagan, Theo de Waal, Maire McElroy, Micheal Casey, Barbara Good, Grace Mulcahy, John Fagan, Denise Murphy, Annetta Zintl
Although the rumen fluke, Calicophoron daubneyi is now very common and widespread throughout Western Europe, reports of clinical cases are still rare. This study explores the epidemiological background to a severe rumen fluke outbreak in 6-month-old heifers on a dairy farm in Ireland. Sequence analysis of the cytochrome oxidase subunit 1 (Cox1) gene of the rumen fluke metacercariae on pasture failed to identify predominant, possibly pathogenic subtypes. However, estimates of metacercarial load indicated that the animals were exposed to a daily dose of about 5334 C...
November 16, 2017: Parasitology
https://www.readbyqxmd.com/read/29143629/from-erasure-to-opportunity-a-qualitative-study-of-the-experiences-of-transgender-men-around-pregnancy-and-recommendations-for-providers
#14
Alexis Hoffkling, Juno Obedin-Maliver, Jae Sevelius
BACKGROUND: Some transgender men retain their uterus, get pregnant, and give birth. However, societal attitudes about gender have erected barriers to openly being pregnant and giving birth as a transgender man. Little research exists regarding transgender men's reproductive needs. Anecdotal observations suggest that social change and increasing empowerment of transgender men may result in increasing frequency and openness about pregnancy and birth. Specific needs around conception, pregnancy, and newborn care may arise from transphobia, exogenous testosterone exposure, or from having had (or desiring) gender-affirming surgery...
November 8, 2017: BMC Pregnancy and Childbirth
https://www.readbyqxmd.com/read/29143560/induced-pluripotent-stem-cells-derived-from-human-amnion-in-chemically-defined-conditions
#15
Jaroslav Slamecka, Steven McClellan, Anna Wilk, Javier Laurini, Elizabeth Manci, Simon P Hoerstrup, Benedikt Weber, Laurie Owen
Fetal stem cells are a unique type of adult stem cells that have been suggested to be broadly multipotent with some features of pluripotency. Their clinical potential has been documented but their upgrade to full pluripotency could open up a wide range of cell-based therapies particularly suited for pediatric tissue engineering, longitudinal studies or disease modeling. Here we describe episomal reprogramming of mesenchymal stem cells from the human amnion to pluripotency (AM-iPSC) in chemically defined conditions...
November 16, 2017: Cell Cycle
https://www.readbyqxmd.com/read/29143492/molecular-epidemiological-survey-and-phylogenetic-analysis-of-bovine-influenza-d-virus-in-japan
#16
H Mekata, M Yamamoto, S Hamabe, H Tanaka, T Omatsu, T Mizutani, B M Hause, T Okabayashi
The influenza D virus, a new member of the Orthomyxoviridae family, is predominantly found in cattle. Although viral pathology and clinical disease in cattle appear mild, this virus plays an important role as a trigger of bovine respiratory disease (BRD). BRD is a costly illness worldwide. Thus, epidemiological surveys of the influenza D virus are necessary. Here, we conducted a molecular epidemiological survey for the influenza D virus in healthy and respiratory-diseased cattle in Japan. We found that 2.1% (8/377) of the cattle were infected with influenza D...
November 16, 2017: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/29143313/polyglucosan-myopathy-and-functional-characterization-of-a-novel-gyg1-mutation
#17
C Hedberg-Oldfors, A Mensch, K Visuttijai, G Stoltenburg, D Stoevesandt, T Kraya, A Oldfors, S Zierz
OBJECTIVES: Disorders of glycogen metabolism include rare hereditary muscle glycogen storage diseases with polyglucosan, which are characterized by storage of abnormally structured glycogen in muscle in addition to exercise intolerance or muscle weakness. In this study, we investigated the etiology and pathogenesis of a late-onset myopathy associated with glycogenin-1 deficiency. MATERIALS AND METHODS: A family with two affected siblings, 64- and 66-year-olds, was studied...
November 15, 2017: Acta Neurologica Scandinavica
https://www.readbyqxmd.com/read/29143190/role-of-magnetic-resonance-imaging-in-the-management-of-perianal-crohn-s-disease
#18
REVIEW
Jose C Gallego, Ana Echarri
Perianal fistulas are a major problem in many patients with Crohn's disease. These are usually complex fistulas that adversely affect patients' quality of life, and their clinical management is difficult. Medical treatment sometimes achieves cessation of discharge and closure of the external opening; however, it is difficult to assess the status of the rest of the fistula tract. Magnetic resonance imaging is the method of choice with which to evaluate the condition of perianal fistulas and allows for assessment of the status of inaccessible areas...
November 15, 2017: Insights Into Imaging
https://www.readbyqxmd.com/read/29143063/translating-aetiological-insight-into-sustainable-management-of-type-2-diabetes
#19
REVIEW
Roy Taylor, Alison C Barnes
Using a low-energy diet as a tool, it has been possible to elucidate the sequence of pathophysiological changes that lead to the onset of type 2 diabetes. Negative energy balance in type 2 diabetes causes a profound fall in liver fat content resulting in normalisation of hepatic insulin sensitivity within 7 days. As the period of negative energy balance extends and liver fat levels fall to low normal, the rate of export of triacylglycerol from the liver falls. Consequent to this, the raised pancreas fat content falls and in early type 2 diabetes, normal first-phase insulin secretion becomes re-established with normal plasma glucose control...
November 15, 2017: Diabetologia
https://www.readbyqxmd.com/read/29142786/extraordinary-clinical-benefit-to-sequential-treatment-with-targeted-therapy-and-immunotherapy-of-a-braf-v600e-and-pd-l1-positive-metastatic-lung-adenocarcinoma
#20
Shuyu D Li, Annia Martial, Alexa B Schrock, Jane J Liu
Background: The treatment algorithm for metastatic non-small cell lung cancers (NSCLCs) has been evolving rapidly due to the development of new therapeutic agents. Although guidelines are provided by National Comprehensive Cancer Network (NCCN) for treatment options according to biomarker testing results, sequentially applying the three main modalities (chemotherapy, targeted therapy and immunotherapy) remains an ad hoc practice in clinic. In light of recent FDA approval of dabrafenib and trametinib combination for metastatic NSCLCs with BRAF V600E mutation, one question arises due to insufficient clinical data is if the targeted therapy should be used before immunotherapy in patients with both BRAF V600E and PD-L1 expression...
2017: Experimental Hematology & Oncology
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