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Exome sequencing

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https://www.readbyqxmd.com/read/29679388/somatic-slc35a2-variants-in-the-brain-are-associated-with-intractable-neocortical-epilepsy
#1
Melodie R Winawer, Nicole G Griffin, Jorge Samanamud, Evan H Baugh, Dinesh Rathakrishnan, Senthilmurugan Ramalingam, David Zagzag, Catherine A Schevon, Patricia Dugan, Manu Hegde, Sameer A Sheth, Guy M McKhann, Werner K Doyle, Gerald A Grant, Brenda E Porter, Mohamad A Mikati, Carrie R Muh, Colin D Malone, Ann Marie R Bergin, Jurriaan M Peters, Danielle K McBrian, Alison M Pack, Cigdem I Akman, Christopher M LaCoursiere, Katherine M Keever, Joseph R Madsen, Edward Yang, Hart G W Lidov, Catherine Shain, Andrew S Allen, Peter Canoll, Peter B Crino, Annapurna H Poduri, Erin L Heinzen
OBJECTIVE Somatic variants are a recognized cause of epilepsy-associated focal malformations of cortical development (MCD). We hypothesized that somatic variants may underlie a wider range of focal epilepsy, including non-lesional focal epilepsy (NLFE). Through genetic analysis of brain tissue, we evaluated the role of somatic variation in focal epilepsy with and without MCD. METHODS We identified somatic variants through high-depth exome and ultra-high-depth candidate gene sequencing of DNA from epilepsy surgery specimens and leukocytes from 18 individuals with NLFE and 38 with focal MCD...
April 20, 2018: Annals of Neurology
https://www.readbyqxmd.com/read/29679229/compromised-alveolar-bone-cells-in-a-patient-with-dentinogenesis-imperfecta-caused-by-dspp-mutation
#2
Thantrira Porntaveetus, Nunthawan Nowwarote, Thanaphum Osathanon, Thanakorn Theerapanon, Prasit Pavasant, Lawan Boonprakong, Kittisak Sanon, Sirivimol Srisawasdi, Kanya Suphapeetiporn, Vorasuk Shotelersuk
OBJECTIVES: Dentin sialophosphoprotein (DSPP) plays an important role in the mineralization of both dentin and bones. The Dspp null mice developed periodontal diseases. Patients with DSPP mutations have dentinogenesis imperfecta (DGI), but very little is known about their bone characteristics. This study aims to characterize alveolar bone cells of a DGI patient with DSPP mutation. MATERIALS AND METHODS: Pathogenic variants were identified by whole exome and sanger sequencing...
April 20, 2018: Clinical Oral Investigations
https://www.readbyqxmd.com/read/29678961/-capn1-mutations-broadening-the-hereditary-spastic-paraplegia-spinocerebellar-ataxia-phenotype
#3
Jeffrey Lambe, Bernadette Monaghan, Tudor Munteanu, Janice Redmond
Increasing availability of next-generation sequencing technologies has revealed several limitations of diagnosis-driven traditional clinicogenetic disease classifications, particularly among patients with an atypical or mixed phenotype. Hereditary spastic paraplegia (HSP) and spinocerebellar ataxia (SCA) are two such disease entities with an often overlapping presentation, in which next generation exome sequencing has played a key role in identification of genes causing disease along a continuum of ataxia and spasticity...
April 20, 2018: Practical Neurology
https://www.readbyqxmd.com/read/29677504/multi-regional-sequencing-elucidates-the-evolution-of-clear-cell-renal-cell-carcinoma
#4
Christopher J Ricketts, W Marston Linehan
Extensive multi-regional whole-genome and -exome sequencing performed in tumors from patients with localized, as well as metastatic, clear cell renal cell carcinoma provides a comprehensive description of the tumor origin, intratumoral heterogeneity, evolution, and route to metastasis, laying the foundation for the development of precision clinical management.
April 19, 2018: Cell
https://www.readbyqxmd.com/read/29675035/trio-clinical-exome-sequencing-in-a-patient-with-multicentric-carpotarsal-osteolysis-syndrome-first-case-report-in-the-balkans
#5
Aleksandra Stajkovska, Sanja Mehandziska, Margarita Stavrevska, Kristina Jakovleva, Natasha Nikchevska, Zan Mitrev, Ivan Kungulovski, Gjorgje Zafiroski, Velibor Tasic, Goran Kungulovski
Exome sequencing can interrogate thousands of genes simultaneously and it is becoming a first line diagnostic tool in genomic medicine. Herein, we applied trio clinical exome sequencing (CES) in a patient presenting with undiagnosed skeletal disorder, minor facial abnormalities, and kidney hypoplasia; her parents were asymptomatic. Testing the proband and her parents led to the identification of a de novo mutation c.188C>T (p.Pro63Leu) in the MAFB gene, which is known to cause multicentric carpotarsal osteolysis syndrome (MCTO)...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29674644/aggressive-natural-killer-cell-leukemia-mutational-landscape-and-drug-profiling-highlight-jak-stat-signaling-as-therapeutic-target
#6
Olli Dufva, Matti Kankainen, Tiina Kelkka, Nodoka Sekiguchi, Shady Adnan Awad, Samuli Eldfors, Bhagwan Yadav, Heikki Kuusanmäki, Disha Malani, Emma I Andersson, Paavo Pietarinen, Leena Saikko, Panu E Kovanen, Teija Ojala, Dean A Lee, Thomas P Loughran, Hideyuki Nakazawa, Junji Suzumiya, Ritsuro Suzuki, Young Hyeh Ko, Won Seog Kim, Shih-Sung Chuang, Tero Aittokallio, Wing C Chan, Koichi Ohshima, Fumihiro Ishida, Satu Mustjoki
Aggressive natural killer-cell (NK-cell) leukemia (ANKL) is an extremely aggressive malignancy with dismal prognosis and lack of targeted therapies. Here, we elucidate the molecular pathogenesis of ANKL using a combination of genomic and drug sensitivity profiling. We study 14 ANKL patients using whole-exome sequencing (WES) and identify mutations in STAT3 (21%) and RAS-MAPK pathway genes (21%) as well as in DDX3X (29%) and epigenetic modifiers (50%). Additional alterations include JAK-STAT copy gains and tyrosine phosphatase mutations, which we show recurrent also in extranodal NK/T-cell lymphoma, nasal type (NKTCL) through integration of public genomic data...
April 19, 2018: Nature Communications
https://www.readbyqxmd.com/read/29674500/novel-gpr34-and-ccr6-mutation-and-distinct-genetic-profiles-in-malt-lymphomas-of-different-sites
#7
Sarah Moody, Joe Sneath Thompson, Shih-Sung Chuang, Hongxiang Liu, Markus Raderer, George Vassiliou, Iwona Wlodarska, Fangtian Wu, Sergio Cogliatti, Alistair Robson, Margaret Ashton-Key, Yingwen Bi, John Goodlad, Ming-Qing Du
MALT lymphoma originates from a background of diverse chronic inflammatory disorders at various anatomic sites. The genetics underlying its development, particularly in those associated with autoimmune disorders, is poorly characterised. By whole exome sequencing of 21 cases of MALT lymphomas of the salivary gland and thyroid, we have identified recurrent somatic mutations in 2 G-protein coupled receptors (GPR34 and CCR6) not previously reported in human malignancies, 3 genes (PIK3CD, TET2, TNFRSF14) not previously implicated in MALT lymphoma, and a further 2 genes (TBL1XR1, NOTCH1) recently described in MALT lymphoma...
April 19, 2018: Haematologica
https://www.readbyqxmd.com/read/29673649/auto-immune-disorders-in-a-child-with-pik3cd-variant-and-22q13-deletion
#8
Kyoko Kiyota, Koh-Ichiro Yoshiura, Ryoko Houbara, Hiroaki Miyahara, Seigo Korematsu, Kenji Ihara
22q13 deletion syndrome is a genetic disorder caused by the deletion or disruption of the segment of the long arm of chromosome 22. The characteristic clinical features of this syndrome include delayed expressive speech, autistic behavior and hypotonia, and clinically severe complications associated with autoimmunity are rarely reported. We herein report a girl with 22q13 deletion syndrome complicated with multiple inflammatory and autoimmune diseases during early childhood. We performed whole-exome sequencing to identify the genes responsible for her autoimmune diseases and identified the de novo variant p...
April 16, 2018: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/29673582/in-silico-prediction-of-the-pathogenic-effect-of-a-novel-variant-of-bckdha-leading-to-classical-maple-syrup-urine-disease-identified-using-clinical-exome-sequencing
#9
Cynthia Fernández-Lainez, Carmen Aláez-Verson, Isabel Ibarra-González, Sergio Enríquez-Flores, Karol Carrillo-Sanchez, Leonardo Flores-Lagunes, Sara Guillén-López, Leticia Belmont-Martínez, Marcela Vela-Amieva
Maple syrup urine disease (MSUD) is a metabolic disorder caused by mutations in three of the branched-chain α-keto acid dehydrogenase complex (BCKDC) genes. Classical MSUD symptom can be observed immediately after birth and include ketoacidosis, irritability, lethargy, and coma, which can lead to death or irreversible neurodevelopmental delay in survivors. The molecular diagnosis of MSUD can be time-consuming and difficult to establish using conventional Sanger sequencing because it could be due to pathogenic variants of any of the BCKDC genes...
April 16, 2018: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/29673316/a-study-on-fast-calling-variants-from-next-generation-sequencing-data-using-decision-tree
#10
Zhentang Li, Yi Wang, Fei Wang
BACKGROUND: The rapid development of next-generation sequencing (NGS) technology has continuously been refreshing the throughput of sequencing data. However, due to the lack of a smart tool that is both fast and accurate, the analysis task for NGS data, especially those with low-coverage, remains challenging. RESULTS: We proposed a decision-tree based variant calling algorithm. Experiments on a set of real data indicate that our algorithm achieves high accuracy and sensitivity for SNVs and indels and shows good adaptability on low-coverage data...
April 19, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29672841/mutant-myo1f-alters-the-mitochondrial-network-and-induces-tumor-proliferation-in-thyroid-cancer
#11
Chiara Diquigiovanni, Christian Bergamini, Cecilia Evangelisti, Federica Isidori, Andrea Vettori, Natascia Tiso, Francesco Argenton, Anna Costanzini, Luisa Iommarini, Hima Anbunathan, Uberto Pagotto, Andrea Repaci, Giulia Babbi, Rita Casadio, Giorgio Lenaz, Kerry J Rhoden, Anna Maria Porcelli, Romana Fato, Anne Bowcock, Marco Seri, Giovanni Romeo, Elena Bonora
Familial aggregation is a significant risk factor for the development of thyroid cancer and Familial Non-Medullary Thyroid Cancer (FNMTC) accounts for 5-7% of all NMTC. Whole Exome Sequencing analysis in the family affected by FNMTC with oncocytic features where our group previously identified a predisposing locus on chromosome 19p13.2, revealed a novel heterozygous mutation (c.400G>A, NM_012335; p.Gly134Ser) in exon 5 of MYO1F, mapping to the linkage locus. In the thyroid FRTL-5 cell model stably expressing the mutant MYO1F p...
April 19, 2018: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29671961/tmtc2-variant-associated-with-sensorineural-hearing-loss-and-auditory-neuropathy-spectrum-disorder-in-a-family-dyad
#12
Hector Guillen-Ahlers, Christy B Erbe, Frédéric D Chevalier, Maria J Montoya, Kip D Zimmerman, Carl D Langefeld, Michael Olivier, Christina L Runge
BACKGROUND: Sensorineural hearing loss (SNHL) is a common form of hearing loss that can be inherited or triggered by environmental insults; auditory neuropathy spectrum disorder (ANSD) is a SNHL subtype with unique diagnostic criteria. The genetic factors associated with these impairments are vast and diverse, but causal genetic factors are rarely characterized. METHODS: A family dyad, both cochlear implant recipients, presented with a hearing history of bilateral, progressive SNHL, and ANSD...
April 19, 2018: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/29671888/whole-exome-sequencing-reveals-microsatellites-dna-markers-for-response-to-dofetilide-initiation-in-patients-with-persistent-atrial-fibrillation-a-pilot-study
#13
Nick Kinney, Timothy R Larsen, David M Kim, Robin T Varghese, Steven Poelzing, Harold R Garner, Soufian T AlMahameed
BACKGROUND: Dofetilide is a class III antiarrhythmic drug effective for the treatment of atrial fibrillation (AF). Dofetilide initiation (DI) associate with corrected QT (QTc) interval prolongation. Significant QTc prolongation during DI mandates dose adjustment or discontinuation of the drug. Microsatellite DNA are novel genetic markers associate with congenital and acquired health conditions. OBJECTIVE: The purpose of this study was to explore potential genetic markers for QTc prolongation in response to DI in patients with persistent AF METHODS: We performed Whole Exome sequencing in a cohort of patients with persistent AF undergoing DI...
April 19, 2018: Clinical Cardiology
https://www.readbyqxmd.com/read/29671837/analysis-of-17-genes-detects-mutations-in-81-of-811-patients-with-lissencephaly
#14
Nataliya Di Donato, Andrew E Timms, Kimberly A Aldinger, Ghayda M Mirzaa, James T Bennett, Sarah Collins, Carissa Olds, Davide Mei, Sara Chiari, Gemma Carvill, Candace T Myers, Jean-Baptiste Rivière, Maha S Zaki, Joseph G Gleeson, Andreas Rump, Valerio Conti, Elena Parrini, M Elizabeth Ross, David H Ledbetter, Renzo Guerrini, William B Dobyns
PurposeTo estimate diagnostic yield and genotype-phenotype correlations in a cohort of 811 patients with lissencephaly or subcortical band heterotopia.MethodsWe collected DNA from 756 children with lissencephaly over 30 years. Many were tested for deletion 17p13.3 and mutations of LIS1, DCX, and ARX, but few other genes. Among those tested, 216 remained unsolved and were tested by a targeted panel of 17 genes (ACTB, ACTG1, ARX, CRADD, DCX, LIS1, TUBA1A, TUBA8, TUBB2B, TUBB, TUBB3, TUBG1, KIF2A, KIF5C, DYNC1H1, RELN, and VLDLR) or by whole-exome sequencing...
April 19, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29671115/utility-of-dna-rna-protein-and-functional-approaches-to-solve-cryptic-immunodeficiencies
#15
Margot A Cousin, Matthew J Smith, Ashley N Sigafoos, Jay J Jin, Marine I Murphree, Nicole J Boczek, Patrick R Blackburn, Gavin R Oliver, Ross A Aleff, Karl J Clark, Eric D Wieben, Avni Y Joshi, Pavel N Pichurin, Roshini S Abraham, Eric W Klee
PURPOSE: We report a female infant identified by newborn screening for severe combined immunodeficiencies (NBS SCID) with T cell lymphopenia (TCL). The patient had persistently elevated alpha-fetoprotein (AFP) with IgA deficiency, and elevated IgM. Gene sequencing for a SCID panel was uninformative. We sought to determine the cause of the immunodeficiency in this infant. METHODS: We performed whole-exome sequencing (WES) on the patient and parents to identify a genetic diagnosis...
April 18, 2018: Journal of Clinical Immunology
https://www.readbyqxmd.com/read/29670293/no-novel-high-penetrant-gene-might-remain-to-be-found-in-japanese-patients-with-unknown-mody
#16
Yukio Horikawa, Kazuyoshi Hosomichi, Mayumi Enya, Hiroyuki Ishiura, Yutaka Suzuki, Shoji Tsuji, Sumio Sugano, Ituro Inoue, Jun Takeda
MODY 5 and 6 have been shown to be low-penetrant MODYs. As the genetic background of unknown MODY is assumed to be similar, a new analytical strategy is applied here to elucidate genetic predispositions to unknown MODY. We examined to find whether there are major MODY gene loci remaining to be identified using SNP linkage analysis in Japanese. Whole-exome sequencing was performed with seven families with typical MODY. Candidates for novel MODY genes were examined combined with in silico network analysis. Some peaks were found only in either parametric or non-parametric analysis; however, none of these peaks showed a LOD score greater than 3...
April 18, 2018: Journal of Human Genetics
https://www.readbyqxmd.com/read/29669943/whole-exome-sequencing-uncovers-oxidoreductases-dhtkd1-and-ogdhl-as-linkers-between-mitochondrial-dysfunction-and-eosinophilic-esophagitis
#17
Joseph D Sherrill, Kiran Kc, Xinjian Wang, Ting Wen, Adam Chamberlin, Emily M Stucke, Margaret H Collins, J Pablo Abonia, Yanyan Peng, Qiang Wu, Philip E Putnam, Phillip J Dexheimer, Bruce J Aronow, Leah C Kottyan, Kenneth M Kaufman, John B Harley, Taosheng Huang, Marc E Rothenberg
Eosinophilic esophagitis (EoE) is an allergic inflammatory esophageal disorder with a complex underlying genetic etiology often associated with other comorbidities. Using whole-exome sequencing (WES) of 63 patients with EoE and 60 unaffected family members and family-based trio analysis, we sought to uncover rare coding variants. WES analysis identified 5 rare, damaging variants in dehydrogenase E1 and transketolase domain-containing 1 (DHTKD1). Rare variant burden analysis revealed an overabundance of putative, potentially damaging DHTKD1 mutations in EoE (P = 0...
April 19, 2018: JCI Insight
https://www.readbyqxmd.com/read/29669941/activating-prkacb-somatic-mutation-in-cortisol-producing-adenomas
#18
Stéphanie Espiard, Matthias J Knape, Kerstin Bathon, Guillaume Assié, Marthe Rizk-Rabin, Simon Faillot, Windy Luscap-Rondof, Daniel Abid, Laurence Guignat, Davide Calebiro, Friedrich W Herberg, Constantine A Stratakis, Jérôme Bertherat
Mutations in the gene encoding the protein kinase A (PKA) catalytic subunit α have been found to be responsible for cortisol-producing adenomas (CPAs). In this study, we identified by whole-exome sequencing the somatic mutation p.S54L in the PRKACB gene, encoding the catalytic subunit β (Cβ) of PKA, in a CPA from a patient with severe Cushing syndrome. Bioluminescence resonance energy transfer and surface plasmon resonance assays revealed that the mutation hampers formation of type I holoenzymes and that these holoenzymes were highly sensitive to cAMP...
April 19, 2018: JCI Insight
https://www.readbyqxmd.com/read/29669692/identification-of-lbx2-as-a-novel-causal-gene-of-atrial-septal-defect
#19
Jing Wang, Jing Luo, Qiuhong Chen, Xi Wang, Jiangyan He, Wei Zhang, Zhan Yin, Fang Zheng, Hong Pan, Tengyan Li, Qiyong Lou, Binbin Wang
BACKGROUND: Atrial septal defect (ASD) is one of the most common cardiac malformations worldwide. Several genes have been identified so far, which can merely explain small proportion of all the cases, therefore, it is anticipated that there are additional genes causing ASD. The aims of this study were to identify the causal gene of ostium secundum atrial septal defect (ASDII) in a Chinese family. METHODS: Whole exome sequencing was performed in three affected members and one control in the ASDII family...
April 11, 2018: International Journal of Cardiology
https://www.readbyqxmd.com/read/29669557/discovery-biology-of-neuropsychiatric-syndromes-dbns-a-center-for-integrating-clinical-medicine-and-basic-science
#20
Biju Viswanath, Naren P Rao, Janardhanan C Narayanaswamy, Palanimuthu T Sivakumar, Arun Kandasamy, Muralidharan Kesavan, Urvakhsh Meherwan Mehta, Ganesan Venkatasubramanian, John P John, Odity Mukherjee, Meera Purushottam, Ramakrishnan Kannan, Bhupesh Mehta, Thennarasu Kandavel, B Binukumar, Jitender Saini, Deepak Jayarajan, A Shyamsundar, Sydney Moirangthem, K G Vijay Kumar, Jagadisha Thirthalli, Prabha S Chandra, Bangalore N Gangadhar, Pratima Murthy, Mitradas M Panicker, Upinder S Bhalla, Sumantra Chattarji, Vivek Benegal, Mathew Varghese, Janardhan Y C Reddy, Padinjat Raghu, Mahendra Rao, Sanjeev Jain
BACKGROUND: There is emerging evidence that there are shared genetic, environmental and developmental risk factors in psychiatry, that cut across traditional diagnostic boundaries. With this background, the Discovery biology of neuropsychiatric syndromes (DBNS) proposes to recruit patients from five different syndromes (schizophrenia, bipolar disorder, obsessive compulsive disorder, Alzheimer's dementia and substance use disorders), identify those with multiple affected relatives, and invite these families to participate in this study...
April 18, 2018: BMC Psychiatry
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