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https://www.readbyqxmd.com/read/28212192/genetic-control-of-erythropoiesis
#1
Laxminath Tumburu, Swee Lay Thein
PURPOSE OF REVIEW: The discovery of several genetic variants associated with erythroid traits and subsequent elucidation of their functional mechanisms are exemplars of the power of the new genetic and genomic technology. The present review highlights findings from recent genetic studies related to the control of erythropoiesis and dyserythropoiesis, and fetal hemoglobin, an erythroid-related trait. RECENT FINDINGS: Identification of the genetic modulators of erythropoiesis involved two approaches: genome-wide association studies (GWASs) using single nucleotide polymorphism (SNP) arrays that revealed the common genetic variants associated with erythroid phenotypes (hemoglobin, red cell count, MCV, MCH) and fetal hemoglobin; and massive parallel sequencing such as whole genome sequencing (WGS) and whole exome sequencing (WES) that led to the discovery of the rarer variants (GFI1B, SBDS, RPS19, PKLR, EPO, EPOR, KLF1, GATA1)...
February 15, 2017: Current Opinion in Hematology
https://www.readbyqxmd.com/read/28211974/whole-exome-sequencing-identified-1-base-pair-novel-deletion-in-bcl2-associated-athanogene-3-bag3-gene-associated-with-severe-dilated-cardiomyopathy-dcm-requiring-heart-transplant-in-multiple-family-members
#2
Muhammad Arshad Rafiq, Ayeshah Chaudhry, Melanie Care, Danna A Spears, Chantal F Morel, Robert M Hamilton
Dilated cardiomyopathy (DCM) is characterized by dilation and impaired contraction of the left ventricle or both ventricles. Among hereditary DCM, the genetic causes are heterogeneous, and include mutations encoding cytoskeletal, nucleoskeletal, mitochondrial, and calcium-handling proteins. We report three severely affected males, in a four-generation pedigree, with DCM phenotype who underwent cardiac transplant. Cardiomegaly with marked biventricular dilation and fibrosis were noticeable histopathological findings...
March 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28202063/next-generation-sequencing-in-familial-breast-cancer-patients-from-lebanon
#3
Nadine Jalkh, Eliane Chouery, Zahraa Haidar, Christina Khater, David Atallah, Hamad Ali, Makia J Marafie, Mohamed R Al-Mulla, Fahd Al-Mulla, Andre Megarbane
BACKGROUND: Familial breast cancer (BC) represents 5 to 10% of all BC cases. Mutations in two high susceptibility BRCA1 and BRCA2 genes explain 16-40% of familial BC, while other high, moderate and low susceptibility genes explain up to 20% more of BC families. The Lebanese reported prevalence of BRCA1 and BRCA2 deleterious mutations (5.6% and 12.5%) were lower than those reported in the literature. METHODS: In the presented study, 45 Lebanese patients with a reported family history of BC were tested using Whole Exome Sequencing (WES) technique followed by Sanger sequencing validation...
February 15, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28199897/real-world-utility-of-whole-exome-sequencing-with-targeted-gene-analysis-for-focal-epilepsy
#4
Piero Perucca, Ingrid E Scheffer, A Simon Harvey, Paul A James, Sebastian Lunke, Natalie Thorne, Clara Gaff, Brigid M Regan, John A Damiano, Michael S Hildebrand, Samuel F Berkovic, Terence J O'Brien, Patrick Kwan
OBJECTIVE: Driven by advances in genomic technology and reduction in costs, next-generation sequencing (NGS) is venturing into routine clinical care. The 'real-world' clinical utility of NGS remains to be determined in focal epilepsies, which account for 60% of all epilepsies and for which the importance of genetic factors is just beginning to emerge. We investigated the diagnostic yield and management implications of whole exome sequencing (WES)-based screening of selected genes in the routine care of common focal epilepsies suspected to have a genetic basis...
February 7, 2017: Epilepsy Research
https://www.readbyqxmd.com/read/28198391/mcm5-a-new-actor-in-the-link-between-dna-replication-and-meier-gorlin-syndrome
#5
Annalisa Vetro, Salvatore Savasta, Annalisa Russo Raucci, Cristina Cerqua, Geppo Sartori, Ivan Limongelli, Antonella Forlino, Silvia Maruelli, Paola Perucca, Debora Vergani, Giuliano Mazzini, Andrea Mattevi, Lucia Anna Stivala, Leonardo Salviati, Orsetta Zuffardi
Meier-Gorlin syndrome (MGORS) is a rare disorder characterized by primordial dwarfism, microtia, and patellar aplasia/hypoplasia. Recessive mutations in ORC1, ORC4, ORC6, CDT1, CDC6, and CDC45, encoding members of the pre-replication (pre-RC) and pre-initiation (pre-IC) complexes, and heterozygous mutations in GMNN, a regulator of cell-cycle progression and DNA replication, have already been associated with this condition. We performed whole-exome sequencing (WES) in a patient with a clinical diagnosis of MGORS and identified biallelic variants in MCM5...
February 15, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28193203/first-insight-into-the-somatic-mutation-burden-of-neurofibromatosis-type-2-associated-grade-i-and-grade-ii-meningiomas-a-case-report-comprehensive-genomic-study-of-two-cranial-meningiomas-with-vastly-different-clinical-presentation
#6
Ramita Dewan, Alexander Pemov, Amalia S Dutra, Evgenia D Pak, Nancy A Edwards, Abhik Ray-Chaudhury, Nancy F Hansen, Settara C Chandrasekharappa, James C Mullikin, Ashok R Asthagiri, John D Heiss, Douglas R Stewart, Anand V Germanwala
BACKGROUND: Neurofibromatosis type 2 (NF2) is a rare autosomal dominant nervous system tumor predisposition disorder caused by constitutive inactivation of one of the two copies of NF2. Meningiomas affect about one half of NF2 patients, and are associated with a higher disease burden. Currently, the somatic mutation landscape in NF2-associated meningiomas remains largely unexamined. CASE PRESENTATION: Here, we present an in-depth genomic study of benign and atypical meningiomas, both from a single NF2 patient...
February 13, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28190938/elucidation-of-the-anti-inflammatory-mechanisms-of-bupleuri-and-scutellariae-radix-using-system-pharmacological-analyses
#7
Xia Shen, Zhenyu Zhao, Hao Wang, Zihu Guo, Benxiang Hu, Gang Zhang
Objective. This study was aimed at elucidating the molecular mechanisms underlying the anti-inflammatory effect of the combined application of Bupleuri Radix and Scutellariae Radix and explored the potential therapeutic efficacy of these two drugs on inflammation-related diseases. Methods. After searching the databases, we collected the active ingredients of Bupleuri Radix and Scutellariae Radix and calculated their oral bioavailability (OB) and drug-likeness (DL) based on the absorption-distribution-metabolism-elimination (ADME) model...
2017: Mediators of Inflammation
https://www.readbyqxmd.com/read/28190455/who-s-who-detecting-and-resolving-sample-anomalies-in-human-dna-sequencing-studies-with-peddy
#8
Brent S Pedersen, Aaron R Quinlan
The potential for genetic discovery in human DNA sequencing studies is greatly diminished if DNA samples from a cohort are mislabeled, swapped, or contaminated or if they include unintended individuals. Unfortunately, the potential for such errors is significant since DNA samples are often manipulated by several protocols, labs, or scientists in the process of sequencing. We have developed a software package, peddy, to identify and facilitate the remediation of such errors via interactive visualizations and reports comparing the stated sex, relatedness, and ancestry to what is inferred from the individual genotypes derived from whole-genome (WGS) or whole-exome (WES) sequencing...
January 30, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28190454/somatic-map2k1-mutations-are-associated-with-extracranial-arteriovenous-malformation
#9
Javier A Couto, August Y Huang, Dennis J Konczyk, Jeremy A Goss, Steven J Fishman, John B Mulliken, Matthew L Warman, Arin K Greene
Arteriovenous malformation (AVM) is a fast-flow, congenital vascular anomaly that may arise anywhere in the body. AVMs typically progress, causing destruction of surrounding tissue and, sometimes, cardiac overload. AVMs are difficult to control; they often re-expand after embolization or resection, and pharmacologic therapy is unavailable. We studied extracranial AVMs in order to identify their biological basis. We performed whole-exome sequencing (WES) and whole-genome sequencing (WGS) on AVM tissue from affected individuals...
January 30, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28186598/-a-boy-with-meier-gorlin-syndrome-carrying-a-novel-orc6-mutation-and-uniparental-disomy-of-chromosome-16
#10
Juan Li, Yu Ding, Guoying Chang, Qing Cheng, Xin Li, Jian Wang, Xiumin Wang, Yiping Shen
OBJECTIVE: To identify the genetic cause for a 11-year-old Chinese boy with Meier-Gorlin syndrome (MGS). METHODS: Chromosomal microarray analysis (CMA) was used to detect potential variations, while whole exome sequencing (WES) was used to identify sequence variants. Sanger sequencing was used to confirm the suspected variants. RESULTS: The boy has featured short stature, microtia, small patella, slender body build, craniofacial anomalies, and small testes with normal gonadotropin...
February 10, 2017: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/28181551/whole-exome-sequencing-using-ion-proton-system-enables-reliable-genetic-diagnosis-of-inherited-retinal-dystrophies
#11
Marina Riera, Rafael Navarro, Sheila Ruiz-Nogales, Pilar Méndez, Anniken Burés-Jelstrup, Borja Corcóstegui, Esther Pomares
Inherited retinal dystrophies (IRD) comprise a wide group of clinically and genetically complex diseases that progressively affect the retina. Over recent years, the development of next-generation sequencing (NGS) methods has transformed our ability to diagnose heterogeneous diseases. In this work, we have evaluated the implementation of whole exome sequencing (WES) for the molecular diagnosis of IRD. Using Ion Proton(TM) system, we simultaneously analyzed 212 genes that are responsible for more than 25 syndromic and non-syndromic IRD...
February 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28179590/whole-exome-sequencing-identified-mutational-profiles-of-high-grade-colon-adenomas
#12
Sung Hak Lee, Seung Hyun Jung, Tae-Min Kim, Je-Keun Rhee, Hyeon-Chun Park, Min Sung Kim, Sung Soo Kim, Chang Hyeok An, Sug Hyung Lee, Yeun-Jun Chung
Although gene-to-gene analyses identified genetic alterations such as APC, KRAS and TP53 mutations in colon adenomas, it is largely unknown whether there are any others in them. Mutational profiling of high-grade colon adenoma (HGCA) that just precedes colon carcinoma might identify not only novel adenoma-specific genes but also critical genes for its progression to carcinoma. For this, we performed whole-exome sequencing (WES) of 12 HGCAs and identified 11 non-hypermutated and one hypermutated (POLE-mutated) cases...
January 24, 2017: Oncotarget
https://www.readbyqxmd.com/read/28174134/whole-exome-sequencing-reveals-severe-thrombophilia-in-acute-unprovoked-idiopathic-fatal-pulmonary-embolism
#13
Matt Halvorsen, Ying Lin, Barbara A Sampson, Dawei Wang, Bo Zhou, Lucy S Eng, Sung Yon Um, Orrin Devinsky, David B Goldstein, Yingying Tang
BACKGROUND: Acute unprovoked idiopathic fatal pulmonary embolism (IFPE) causes sudden death without an identifiable thrombogenic risk. We aimed to investigate the underlying genomic risks of IFPE through whole exome sequencing (WES). METHODS: We reviewed 14years of consecutive out-of-hospital fatal pulmonary embolism records (n=1478) from the ethnically diverse population of New York City. We selected 68 qualifying IFPE cases for WES. We compared the WES data of IFPE cases to those of 9332 controls to determine if there is an excess of rare damaging variants in the genome using ethnicity-matched controls in collapsing analyses...
January 31, 2017: EBioMedicine
https://www.readbyqxmd.com/read/28173822/an-example-of-the-utility-of-genomic-analysis-for-fast-and-accurate-clinical-diagnosis-of-complex-rare-phenotypes
#14
Polona Le Quesne Stabej, Chela James, Louise Ocaka, Mehmet Tekman, Stephanie Grunewald, Emma Clement, Horia C Stanescu, Robert Kleta, Deborah Morrogh, Alistair Calder, Hywel J Williams, Maria Bitner-Glindzicz
BACKGROUND: We describe molecular diagnosis in a complex consanguineous family: four offspring presented with combinations of three distinctive phenotypes; non-syndromic hearing loss (NSHL), an unusual skeletal phenotype comprising multiple fractures, cranial abnormalities and diaphyseal expansion, and significant developmental delay with microcephaly. We performed Chromosomal Microarray Analysis on the offspring with either the skeletal or developmental delay phenotypes, and linkage analysis and whole exome sequencing (WES) on all four children, parents and maternal aunt...
February 7, 2017: Orphanet Journal of Rare Diseases
https://www.readbyqxmd.com/read/28170084/debunking-occam-s-razor-diagnosing-multiple-genetic-diseases-in-families-by-whole-exome-sequencing
#15
Tugce B Balci, Taila Hartley, Yanwei Xi, David A Dyment, Chandree L Beaulieu, Francois P Bernier, Lucie Dupuis, Gabriella Horvath, Roberto Mendoza-Londono, Chitra Prasad, Julie Richer, Xiao-Ru Yang, Christine M Armour, Eric Bareke, Bridget A Fernandez, Hugh J McMillan, Ryan Lamont, Jacek Majewski, Jillian Parboosingh, A Narayan Prasad, Tony Rupar, Jeremy Schwartzentruber, Amanda C Smith, Martine Tétreault, A Micheil Innes, Kym M Boycott
Recent clinical whole exome sequencing (WES) cohorts have identified unanticipated multiple genetic diagnoses in single patients. However, the frequency of multiple genetic diagnoses in families is largely unknown. We set out to identify the rate of multiple genetic diagnoses in probands and their families referred for analysis in two national research programs in Canada. We retrospectively analyzed WES results for 802 undiagnosed probands referred over the past five years in either the FORGE or Care4Rare Canada WES sequencing initiatives...
February 7, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/28160876/neurology-individualized-medicine-when-to-use-next-generation-sequencing-panels
#16
REVIEW
Christopher J Klein, Tatiana M Foroud
Next-generation sequencing (NGS) is increasingly being applied to clinical testing. This practice is predicted to grow especially in neurology clinics because many of their patients have monogenetic causes for their "diagnostic odyssey." The cost of sequencing has been steadily decreasing, but the cost of DNA sequencing is a minor part of the total cost. Downstream data analysis, storage, and interpretation account for most of the total expense. In patients with nonspecific neurologic disorders in which an extensive number of genetic differential diagnoses exist, whole-genome sequencing (WGS) or whole-exome sequencing (WES) has shown promise in the identification of genetic causes...
February 2017: Mayo Clinic Proceedings
https://www.readbyqxmd.com/read/28155632/global-inference-of-disease-causing-single-nucleotide-variants-from-exome-sequencing-data
#17
Mengmeng Wu, Ting Chen, Rui Jiang
BACKGROUND: Whole exome sequencing (WES) has recently emerged as an effective approach for identifying genetic variants underlying human diseases. However, considerable time and labour is needed for careful investigation of candidate variants. Although filtration based on population frequencies and functional prediction scores could effectively remove common and neutral variants, hundreds or even thousands of rare deleterious variants still remain. In addition, current WES platforms also provide variant information in flanking noncoding regions, such as promoters, introns and splice sites...
December 23, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28153049/longitudinal-analysis-of-treatment-induced-genomic-alterations-in-gliomas
#18
E Zeynep Erson-Omay, Octavian Henegariu, S Bülent Omay, Akdes Serin Harmancı, Mark W Youngblood, Ketu Mishra-Gorur, Jie Li, Koray Özduman, Geneive Carrión-Grant, Victoria E Clark, Caner Çağlar, Mehmet Bakırcıoğlu, M Necmettin Pamir, Viviane Tabar, Alexander O Vortmeyer, Kaya Bilguvar, Katsuhito Yasuno, Lisa M DeAngelis, Joachim M Baehring, Jennifer Moliterno, Murat Günel
BACKGROUND: Glioblastoma multiforme (GBM) constitutes nearly half of all malignant brain tumors and has a median survival of 15 months. The standard treatment for these lesions includes maximal resection, radiotherapy, and chemotherapy; however, individual tumors display immense variability in their response to these approaches. Genomic techniques such as whole-exome sequencing (WES) provide an opportunity to understand the molecular basis of this variability. METHODS: Here, we report WES-guided treatment of a patient with a primary GBM and two subsequent recurrences, demonstrating the dynamic nature of treatment-induced molecular changes and their implications for clinical decision-making...
February 2, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28152038/exome-sequencing-covers-98-of-mutations-identified-on-targeted-next-generation-sequencing-panels
#19
Holly LaDuca, Kelly D Farwell, Huy Vuong, Hsiao-Mei Lu, Wenbo Mu, Layla Shahmirzadi, Sha Tang, Jefferey Chen, Shruti Bhide, Elizabeth C Chao
BACKGROUND: With the expanded availability of next generation sequencing (NGS)-based clinical genetic tests, clinicians seeking to test patients with Mendelian diseases must weigh the superior coverage of targeted gene panels with the greater number of genes included in whole exome sequencing (WES) when considering their first-tier testing approach. Here, we use an in silico analysis to predict the analytic sensitivity of WES using pathogenic variants identified on targeted NGS panels as a reference...
2017: PloS One
https://www.readbyqxmd.com/read/28151472/calcb-splice-region-pathogenic-variants-leading-to-plasma-cell-neurotropic-enrichment-in-type-1-autoimmune-pancreatitis
#20
Qi-Cai Liu, Falin Chen, Chao-Yang Wu, Feng Gao, Ze-Hao Zhuang, Jin-Tong Chen, Bin Cai, Tianming Zhang, Ling Guo, Li-Qing Lin, Cheng-Fei Zhao, Xin-Hua Lin
Recently, we have demonstrated that PRSS1 mutations cause ectopic trypsinogen activation and thereby result in type 1 autoimmune pancreatitis (AIP). However, the molecules involved in inducing obliterative vasculitis and perineural inflammation in the pancreas are not well-described. The present study applied whole-exome sequencing (WES) to determine the underlying etiology and revealed novel missense splice region variants, CALCB c.88T>C (p.Ser30Pro) and IR [1]-mutants, in 2 of the 3 families and 2 of 26 unrelated patients with type 1 AIP...
February 2, 2017: Cell Death & Disease
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