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https://www.readbyqxmd.com/read/28535585/good-laboratory-standards-for-clinical-next-generation-sequencing-cancer-panel-tests
#1
REVIEW
Jihun Kim, Woong-Yang Park, Nayoung K D Kim, Se Jin Jang, Sung-Min Chun, Chang-Ohk Sung, Jene Choi, Young-Hyeh Ko, Yoon-La Choi, Hyo Sup Shim, Jae-Kyung Won
Next-generation sequencing (NGS) has recently emerged as an essential component of personalized cancer medicine due to its high throughput and low per-base cost. However, no sufficient guidelines for implementing NGS as a clinical molecular pathology test are established in Korea. To ensure clinical grade quality without inhibiting adoption of NGS, a taskforce team assembled by the Korean Society of Pathologists developed laboratory guidelines for NGS cancer panel testing procedures and requirements for clinical implementation of NGS...
May 2017: Journal of Pathology and Translational Medicine
https://www.readbyqxmd.com/read/28534836/differentiation-and-structure-in-sulfolobus-islandicus-rod-shaped-virus-populations
#2
Maria A Bautista, Jesse A Black, Nicholas D Youngblut, Rachel J Whitaker
In the past decade, molecular surveys of viral diversity have revealed that viruses are the most diverse and abundant biological entities on Earth. In culture, however, most viral isolates that infect microbes are represented by a few variants isolated on type strains, limiting our ability to study how natural variation affects virus-host interactions in the laboratory. We screened a set of 137 hot spring samples for viruses that infect a geographically diverse panel of the hyperthemophilic crenarchaeon Sulfolobus islandicus...
May 19, 2017: Viruses
https://www.readbyqxmd.com/read/28534687/role-of-molecular-markers-in-thyroid-nodule-management-then-and-now
#3
Yuri E Nikiforov
OBJECTIVE: To describe the evolution and clinical utility of molecular testing for thyroid nodules and cancer achieved over the last two decades. METHODS: Scientific reports on thyroid cancer genetics and molecular diagnostics in thyroid nodules. RESULTS: Over the last two decades, our understanding of the genetic mechanisms of thyroid cancer has dramatically expanded, such that most thyroid cancers now have known gene driver events. This knowledge provides the basis for establishing and further improving molecular tests for thyroid nodules and cancer and for the introduction of new entities such as non-invasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP)...
May 23, 2017: Endocrine Practice
https://www.readbyqxmd.com/read/28534081/power-of-pedigree-likelihood-analysis-in-extended-pedigrees-to-classify-rare-variants-of-uncertain-significance-in-cancer-risk-genes
#4
Elisabeth A Rosenthal, John Michael O Ranola, Brian H Shirts
Rare and private variants of uncertain significance (VUS) are routinely identified in clinical panel, exome, and genome sequencing. We investigated the power of single family co-segregation analysis to aid classification of VUS. We simulated thousands of pedigrees using demographics in China and the United States, segregating benign and pathogenic variants. Genotypes and phenotypes were simulated using penetrance models for Lynch syndrome and breast/ovarian cancer. We calculated LOD scores adjusted for proband ascertainment (LODadj), to determine power to yield quantitative evidence for, or against, pathogenicity of the VUS...
May 22, 2017: Familial Cancer
https://www.readbyqxmd.com/read/28533224/microrna-196b-5p-regulates-colorectal-cancer-cell-migration-and-metastases-through-interaction-of-hoxb7-and-galnt5
#5
Verena Stiegelbauer, Petra Vychytilova-Faltejskova, Michael Karbiener, Anna-Maria Pehserl, Cristina Ivan, Marc D Bullock, Hui Ling, Alexander Ja Deutsch, Annika Wulf-Goldenberg, Jan Basri Adiprasito, Herbert Stöger, Johannes Haybaeck, Marek Svoboda, Michael Stotz, Gerald Höfler, Ondrej Slaby, George A Calin, Armin Gerger, Martin Pichler, Ellen Heitzer, Margit Resel, Andreas Reicher
Purpose: MicroRNA-196b-5p (miR-196b-5p) has been previously implicated in malignant transformation, however, its role in colorectal cancer (CRC) has not been fully explored. In the current study, we examine the clinical and biological relevance of miR-196b-5p, and the molecular pathways regulated by miR-196b-5p in CRC. <p>Experimental design: MiR-196b-5p expression was quantitated by qRT-PCR in two independent cohorts comprised of 292 CRC patients in total, to explore its biomarker potential. Transient and stable gain and loss of function experiments were conducted in a panel of CRC cell lines and mice, to evaluate the impact of miR-196b-5p on proliferation, chemo-sensitivity, migration/invasion and metastases formation in vitro and in vivo The molecular pathways influenced by miR-196b-5p were characterized using whole transcriptome profiling, in-silico target prediction tools, luciferase-interaction assays, and pheno-copy/rescue gene knock-down experiments...
May 22, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28532774/genotype-positive-long-qt-syndrome-in-patients-with-coexisting-congenital-heart-disease
#6
Mohammed A Ebrahim, Matthew R Williams, Suzanne Shepard, James C Perry
Congenital long QT syndrome (LQTS) is characterized by QT prolongation with predisposition to life-threatening arrhythmia. There have been sporadic reports of LQTS coexisting with more common forms of congenital heart disease (CHD). However, the diagnosis of LQTS when CHD is present may be confounded by several common variables including postoperative electromechanical factors predisposing to ventricular arrhythmia, intrinsic, and postoperative QRS abnormalities. This report documents a single-center experience with patients who have both genetically confirmed LQTS and CHD to examine their modes of presentation and factors associated with making the diagnosis of LQTS in this patient population, as well as potential confounding variables that may mask or delay both LQTS diagnosis and initiation of therapy...
April 27, 2017: American Journal of Cardiology
https://www.readbyqxmd.com/read/28532474/detection-of-ikk%C3%AE%C2%B5-by-immunohistochemistry-in-primary-breast-cancer-association-with-egfr-expression-and-absence-of-lymph-node-metastasis
#7
Virginie Williams, Andrée-Anne Grosset, Natalia Zamorano Cuervo, Yves St-Pierre, Marie-Pierre Sylvestre, Louis Gaboury, Nathalie Grandvaux
BACKGROUND: IKKε is an oncogenic kinase that was found amplified and overexpressed in a substantial percentage of human breast cancer cell lines and primary tumors using genomic and gene expression analyses. Molecular studies have provided the rational for a key implication of IKKε in breast cancer cells proliferation and invasiveness through the phosphorylation of several substrates. METHODS: Here, we performed immunohistochemical detection of IKKε expression on tissue microarrays constituted of 154 characterized human breast cancer tumors...
May 22, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28530140/associations-of-nasopharyngeal-metabolome-and-microbiome-with-severity-among-infants-with-bronchiolitis-a-multi-omic-analysis
#8
Christopher J Stewart, Jonathan M Mansbach, Matthew C Wong, Nadim J Ajami, Joseph F Petrosino, Carlos A Camargo, Kohei Hasegawa
RATIONALE: Bronchiolitis is the most common lower respiratory infection in infants; however, it remains unclear which infants with bronchiolitis will develop severe illness. In addition, while emerging evidence indicates associations of the upper-airway microbiome with bronchiolitis severity, little is known about the mechanisms linking airway microbes and host response to disease severity. OBJECTIVES: To determine the relations among the nasopharyngeal airway metabolome profiles, microbiome profiles, and severity in infants with bronchiolitis...
May 21, 2017: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/28529006/validation-of-a-next-generation-sequencing-pipeline-for-the-molecular-diagnosis-of-multiple-inherited-cancer-predisposing-syndromes
#9
Paula Paulo, Pedro Pinto, Ana Peixoto, Catarina Santos, Carla Pinto, Patrícia Rocha, Isabel Veiga, Gabriela Soares, Catarina Machado, Fabiana Ramos, Manuel R Teixeira
Despite the growing knowledge of the genetic background behind the cancers that occur in a context of hereditary predisposition, personal or family cancer history may not be clear enough to support directional gene testing. Defined targeted next-generation sequencing gene panels allow identification of the causative disease mutations of multigene syndromes and differential diagnosis for syndromes with phenotypically overlapping characteristics. Herein, we established a next-generation sequencing analysis pipeline for the molecular diagnosis of multiple inherited cancer predisposing syndromes using the commercially available target sequencing panel TruSight Cancer...
May 18, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28528518/a-multi-gene-panel-study-in-hereditary-breast-and-ovarian-cancer-in-colombia
#10
A M Cock-Rada, C A Ossa, H I Garcia, L R Gomez
Germline mutations in BRCA1 and BRCA2 account for approximately 50% of inherited breast and ovarian cancers. Three founder mutations in BRCA1/2 have been reported in Colombia, but the pattern of mutations in other cancer susceptibility genes is unknown. This study describes the frequency and type of germline mutations in hereditary breast and/or ovarian cancer genes in a referral cancer center in Colombia. Eighty-five women referred to the oncogenetics unit of the Instituto de Cancerologia Las Americas in Medellin (Colombia), meeting testing criteria for hereditary breast and ovarian cancer syndrome (NCCN 2015), who had germline testing with a commercial 25-gene hereditary cancer panel, were included in the analysis...
May 20, 2017: Familial Cancer
https://www.readbyqxmd.com/read/28526081/comprehensive-detection-of-germline-variants-by-msk-impact-a-clinical-diagnostic-platform-for-solid-tumor-molecular-oncology-and-concurrent-cancer-predisposition-testing
#11
Donavan T Cheng, Meera Prasad, Yvonne Chekaluk, Ryma Benayed, Justyna Sadowska, Ahmet Zehir, Aijazuddin Syed, Yan Elsa Wang, Joshua Somar, Yirong Li, Zarina Yelskaya, Donna Wong, Mark E Robson, Kenneth Offit, Michael F Berger, Khedoudja Nafa, Marc Ladanyi, Liying Zhang
BACKGROUND: The growing number of Next Generation Sequencing (NGS) tests is transforming the routine clinical diagnosis of hereditary cancers. Identifying whether a cancer is the result of an underlying disease-causing mutation in a cancer predisposition gene is not only diagnostic for a cancer predisposition syndrome, but also has significant clinical implications in the clinical management of patients and their families. METHODS: Here, we evaluated the performance of MSK-IMPACT (Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets) in detecting genetic alterations in 76 genes implicated in cancer predisposition syndromes...
May 19, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28525363/targeted-sequencing-of-tonsillar-and-base-of-tongue-cancer-and-human-papillomavirus-positive-unknown-primary-of-the-head-and-neck-reveals-prognostic-effects-of-mutated-fgfr3
#12
Cinzia Bersani, Lars Sivars, Linnea Haeggblom, Sebastian DiLorenzo, Michael Mints, Andreas Ährlund-Richter, Nikolaos Tertipis, Eva Munck-Wikland, Anders Näsman, Torbjörn Ramqvist, Tina Dalianis
BACKGROUND: Human papillomavirus positive (HPV+) tonsillar cancer (TSCC), base of tongue cancer (BOTSCC) and unknown primary cancer of the head and neck (HNCUP) have better outcome than corresponding HPV- cancers. To find predictive markers for response to treatment, and correlations and differences in mutated oncogenes and suppressor genes between HPV+ TSCC/BOTSSCC and HPV+ HNCUP and HPV- TSCC/BOTSCC targeted next-generation sequencing was performed of frequently mutated regions in 50 cancer related genes...
February 9, 2017: Oncotarget
https://www.readbyqxmd.com/read/28524363/donor-transmitted-mutation-of-the-abcb11-gene-and-ensuing-intra-hepatic-cholestasis-of-pregnancy-in-a-liver-transplant-recipient
#13
Tiong Yeng Lim, Iona Coltart, Pierre Foskett, Richard Thompson, Sandra Strautnieks, Leonie Penna, Catherine Williamson, Rosa Miquel, Michael A Heneghan
In liver transplant (LT) recipients, the cause of graft dysfunction in pregnancy is often difficult to ascertain. Moreover, a liver biopsy in late pregnancy is often avoided as a consequence of patient and physician factors. Management of graft dysfunction can be difficult in this setting. We report a 30-year-old female LT recipient who developed acutely deranged liver biochemistry during the third trimester of her first pregnancy. At 29 weeks gestation, her liver function test (LFT) became abnormal; AST peaked at 978 IU/L (normal range 10-50), GGT 25 IU/L (normal range 1-55), bilirubin 1...
May 19, 2017: Liver Transplantation
https://www.readbyqxmd.com/read/28524223/-infantile-epileptic-encephalopathies-what-matters-is-genetics
#14
J J Garcia-Penas, M Jimenez-Legido
INTRODUCTION: Epileptic encephalopathies in infancy are defined as conditions where the sustained epileptic activity itself may contribute to the severe neurological and cognitive impairment. These epileptic encephalopathies include Ohtahara syndrome, early myoclonic epileptic encephalopathy, West syndrome, Dravet syndrome, and malignant migrating epilepsy in infancy. These syndromes result from identifiable primary causes, such as structural, neurodegenerative, metabolic, or genetic defects...
May 17, 2017: Revista de Neurologia
https://www.readbyqxmd.com/read/28523639/association-mapping-of-yield-and-yield-related-traits-under-reproductive-stage-drought-stress-in-rice-oryza-sativa-l
#15
B P Mallikarjuna Swamy, Noraziyah Abd Aziz Shamsudin, Site Noorzuraini Abd Rahman, Ramil Mauleon, Wickneswari Ratnam, Ma Teressa Sta Cruz, Arvind Kumar
BACKGROUND: The identification and introgression of major-effect QTLs for grain yield under drought are some of the best and well-proven approaches for improving the drought tolerance of rice varieties. In the present study, we characterized Malaysian rice germplasm for yield and yield-related traits and identified significant trait marker associations by structured association mapping. RESULTS: The drought screening was successful in screening germplasm with a yield reduction of up to 60% and heritability for grain yield under drought was up to 78%...
December 2017: Rice
https://www.readbyqxmd.com/read/28523222/olfaction-in-parkin-carriers-in-chinese-patients-with-parkinson-disease
#16
Ying Wang, Jian-Jun Wu, Feng-Tao Liu, Kui Chen, Chen Chen, Su-Shan Luo, Yi-Xuan Wang, Da-Ke Li, Rong-Yuan Guan, Yu-Jie Yang, Yu An, Jian Wang, Yi-Min Sun
BACKGROUND: Olfactory identification was reported to be better among PD (Parkinson disease) patients with Parkin mutations, but previous studies didn't eliminate the interference of other PD related genes on olfaction, and whether olfaction of Parkin mutations patients was better in Chinese population was still unknown. OBJECTIVE: To assess olfaction function among PD patients with Parkin mutations in Chinese population. MATERIALS AND METHODS: A total of 226 PD patients with a positive family history or an early-onset age (<50 years) were enrolled for genetic testing of PD related genes by target sequencing and multiple ligation-dependent probe amplification...
May 2017: Brain and Behavior
https://www.readbyqxmd.com/read/28523199/de-novo-pten-mutation-in-a-young-boy-with-cutaneous-vasculitis
#17
Angela Mauro, Ebun Omoyinmi, Neil James Sebire, Angela Barnicoat, Paul Brogan
Phosphatase and tensin homolog (PTEN) is the protein encoded by the PTEN gene (10q23.3). PTEN mutations are related to a variety of rare diseases referred to collectively as PTEN hamartoma tumor syndromes (PHTS), which include Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome, Proteus Syndrome, and Proteus-like syndrome. These diseases are associated with an increased risk of malignancy and for this reason an accurate and early diagnosis is essential in order to institute cancer surveillance. PTEN is a regulator of growth and homeostasis in immune system cells, although there are limited data describing immune dysregulation caused by PTEN mutations...
2017: Case Reports in Pediatrics
https://www.readbyqxmd.com/read/28523047/alpha-thalassemia-deletions-found-in-suspected-cases-of-beta-thalassemia-major-in-pakistani-population
#18
Saba Shahid, Muhammad Nadeem, Danish Zahid, Jawad Hassan, Saqib Ansari, Tahir Shamsi
BACKGROUND & OBJECTIVE: Alpha (α) thalassemia is a hereditary disorder and is caused by deletions or mutations in globin genes. It is present in two clinically significant forms: hemoglobin Bart hydrops fetalis (Hb Bart) syndrome and hemoglobin H (HbH) disease. It is highly prevalent in South-East Asia or Mediterranean countries. The most common deletion reported in alpha thalassemia in Pakistani population was -α(3.7) with a frequency of 8.3%, and the rare forms were -α(4.2) (0.2%) and ααα(anti3...
March 2017: Pakistan Journal of Medical Sciences Quarterly
https://www.readbyqxmd.com/read/28521441/the-context-of-prostate-cancer-genomics-in-personalized-medicine
#19
Yanling Liu
Prostate cancer is one of the most common types of cancer in males. Heterogeneous genomic aberrations may lead to prostate cancer onset, progression and metastasis. This heterogeneity also contributes to the variety in cancer risk and outcomes, different drug responses and progression, observed between individual patients. Classical prognostic factors, including prostate-specific antigen, Gleason Score and clinical tumor staging, are not sufficient to portray the complexity of a clinically relevant cancer diagnosis, risk prognosis, treatment choice and therapy monitoring...
May 2017: Oncology Letters
https://www.readbyqxmd.com/read/28521416/a-proposed-method-for-the-relative-quantification-of-levels-of-circulating-micrornas-in-the-plasma-of-gastric-cancer-patients
#20
Mayra-Cecilia Suárez-Arriaga, Javier Torres, Margarita Camorlinga-Ponce, Alejandro Gómez-Delgado, Patricia Piña-Sánchez, Hilda-Alicia Valdez-Salazar, Rosa-María Ribas-Aparicio, Ezequiel M Fuentes-Pananá, Martha-Eugenia Ruiz-Tachiquín
Gastric cancer (GC) is the fifth most common type of malignancy and the third leading cause of cancer-associated mortality worldwide. It is necessary to identify novel methods aimed at improving the early diagnosis and treatment of GC. MicroRNA expression profiles in the plasma of patients with GC have demonstrated a potential use in the opportune diagnosis of this neoplasm. However, there are currently no standardized targets for use in the normalization of microRNA Cq values for different neoplasms. The present study tested two normalization approaches while analyzing plasma derived from patients with GC and non-atrophic gastritis...
May 2017: Oncology Letters
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