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https://www.readbyqxmd.com/read/28917830/al-awadi-raas-rothschild-syndrome-with-dental-anomalies-and-a-novel-wnt7a-mutation
#1
Piranit Nik Kantaputra, Seema Kapoor, Prashant Verma, Massupa Kaewgahya, Katsushige Kawasaki, Atsushi Ohazama, James R Ketudat Cairns
Al-Awadi-Raas-Rothschild syndrome (AARRS; OMIM 276820) is a very rare autosomal recessive limb malformation syndrome caused by WNT7A mutations. AARRS is characterized by various degrees of limb aplasia and hypoplasia. Normal intelligence and malformations of urogenital system are frequent findings. Complete loss of WNT7A function has been shown to cause AARRS, however, its partial loss leads to the milder malformation, Fuhrmann syndrome. An Indian boy affected with AARRS is reported. A novel homozygous base substitution mutation c...
September 13, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/28916928/newborn-screening-in-the-era-of-precision-medicine
#2
Lan Yang, Jiajia Chen, Bairong Shen
As newborn screening success stories gained general confirmation during the past 50 years, scientists quickly discovered diagnostic tests for a host of genetic disorders that could be treated at birth. Outstanding progress in sequencing technologies over the last two decades has made it possible to comprehensively profile newborn screening (NBS) and identify clinically relevant genomic alterations. With the rapid developments in whole-genome sequencing (WGS) and whole-exome sequencing (WES) recently, we can detect newborns at the genomic level and be able to direct the appropriate diagnosis to the different individuals at the appropriate time, which is also encompassed in the concept of precision medicine...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28916840/a-novel-col1a2-c-propeptide-cleavage-site-mutation-causing-high-bone-mass-osteogenesis-imperfecta-with-a-regional-distribution-pattern
#3
T Rolvien, U Kornak, J Stürznickel, T Schinke, M Amling, S Mundlos, R Oheim
Osteogenesis imperfecta (OI) is typically characterized by low bone mass and increased bone fragility caused by heterozygous mutations in the type I procollagen genes (COL1A1/COL1A2). We report two cases of a 56-year-old woman and her 80-year-old mother who suffered from multiple vertebral and non-vertebral fractures with onset in early childhood. A full osteologic assessment including dual-energy X-ray absorptiometry (DXA), high-resolution peripheral quantitative computed tomography (HR-pQCT), and serum analyses pointed to a high bone mineral density (BMD) in the hip (DXA Z-score + 3...
September 15, 2017: Osteoporosis International
https://www.readbyqxmd.com/read/28916750/comprehensive-multiregional-analysis-of-molecular-heterogeneity-in-bladder-cancer
#4
Mathilde Borg Houlberg Thomsen, Iver Nordentoft, Philippe Lamy, Søren Vang, Line Reinert, Christophe Kamungu Mapendano, Søren Høyer, Torben F Ørntoft, Jørgen Bjerggaard Jensen, Lars Dyrskjøt
Genetic alterations identified in adjacent normal appearing tissue in bladder cancer patients are indicative of a field disease. Here we assessed normal urothelium transformation and intra-tumour heterogeneity (ITH) in four patients with bladder cancer. Exome sequencing identified private acquired mutations in a lymph node metastasis and local recurrences. Deep re-sequencing revealed presence of at least three and four subclones in two patients with multifocal disease, while no demarcation of subclones was identified in the two patients with unifocal disease...
September 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28916646/serac1-deficiency-causes-complicated-hsp-evidence-from-a-novel-splice-mutation-in-a-large-family
#5
Benjamin Roeben, Rebecca Schüle, Susanne Ruf, Benjamin Bender, Bader Alhaddad, Tanja Benkert, Thomas Meitinger, Selina Reich, Judith Böhringer, Claus-Dieter Langhans, Frédéric M Vaz, Saskia B Wortmann-Hagemann, Thorsten Marquardt, Tobias B Haack, Ingeborg Krägeloh-Mann, Ludger Schöls, Matthis Synofzik
OBJECTIVE: To demonstrate that mutations in the phosphatidylglycerol remodelling enzyme SERAC1 can cause juvenile-onset complicated hereditary spastic paraplegia (cHSP) clusters, thus adding SERAC1 to the increasing number of complex lipid cHSP genes. METHODS: Combined genomic and functional validation studies (whole-exome sequencing, mRNA, cDNA and protein), biomarker investigations (3-methyl-glutaconic acid, filipin staining and phosphatidylglycerols PG34:1/PG36:1), and clinical and imaging phenotyping were performed in six affected subjects from two different branches of a large consanguineous family...
September 15, 2017: Journal of Medical Genetics
https://www.readbyqxmd.com/read/28916491/controversy-and-debate-on-clinical-genomics-sequencing-paper-2-clinical-genome-wide-sequencing-don-t-throw-out-the-baby-with-the-bathwater
#6
Shelin Adam, Jan M Friedman
Genome-wide (exome or whole genome) sequencing with appropriate genetic counselling should be considered for any patient with a suspected mendelian disease that has not been identified by conventional testing.Clinical genome-wide sequencing provides a powerful and effective meansof identifying specific genetic causes of serious disease and improving clinical care.
September 12, 2017: Journal of Clinical Epidemiology
https://www.readbyqxmd.com/read/28915721/dramatic-response-of-ctnnb1-and-vegfr-2-mutant-temporal-bone-squamous-cell-carcinoma-to-bevacizumab-in-combination-with-pemetrexed
#7
Lai Wei, Lizhi Wang, Ziye Liu, Meiyi Wang, Weili Lu, Dewei Zhao, Bin Yang, Xuejun Kong, Yan Ding, Zhiqiang Wang
High recurrence rates and poor survival rates for late stage/advanced temporal bone squamous cell carcinoma with the standard treatments continues to be a significant challenge to otolaryngologists. Targeted therapy for temporal bone squamous cell carcinoma after relapse has not been reported. Here we present a 58-year-old man who was diagnosed with recurrent temporal bone squamous cell carcinoma and treated with a regimen developed using whole exome sequencing. Somatic mutations in genes encoding catenin beta 1 and vascular endothelial growth factor receptor 2 were identified in the patient's tumor sample compared to the normal tissue...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28915622/genomic-analysis-integrated-whole-exome-sequencing-of-neuroblastomas-identifies-genetic-mutations-in-axon-guidance-pathway
#8
Yuanyuan Li, Miki Ohira, Yong Zhou, Teng Xiong, Wen Luo, Chao Yang, Xiangchun Li, Zhibo Gao, Rui Zhou, Yohko Nakamura, Takehiko Kamijo, Yasuhiko Kaneko, Takeshi Taketani, Junichi Ueyama, Tatsuro Tajiri, Hongyan Zhang, Jian Wang, Huanming Yang, Ye Yin, Akira Nakagawara
Neuroblastoma (NB) is a childhood solid malignant tumor originating from precursor cells of the peripheral nervous system. We have previously established a risk classification system based on DNA copy number profiles. To further explore the pathogenesis of NBs in distinct risk groups, we performed whole-exome sequencing analysis of 57 primary and 7 recurrent/metastatic tumors with unique chromosomal aberration profiles as categorized by our genomic sub-grouping system. Overall, a low frequency of somatic mutations was found...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28915574/comparative-study-of-whole-genome-amplification-and-next-generation-sequencing-performance-of-single-cancer-cells
#9
Anna Babayan, Malik Alawi, Michael Gormley, Volkmar Müller, Harriet Wikman, Ryan P McMullin, Denis A Smirnov, Weimin Li, Maria Geffken, Klaus Pantel, Simon A Joosse
BACKGROUND: Whole genome amplification (WGA) is required for single cell genotyping. Effectiveness of currently available WGA technologies in combination with next generation sequencing (NGS) and material preservation is still elusive. RESULTS: In respect to the accuracy of SNP/mutation, indel, and copy number aberrations (CNA) calling, the HiSeq2000 platform outperformed IonProton in all aspects. Furthermore, more accurate SNP/mutation and indel calling was demonstrated using single tumor cells obtained from EDTA-collected blood in respect to CellSave-preserved blood, whereas CNA analysis in our study was not detectably affected by fixation...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28915250/multi-layered-mutation-in-hedgehog-related-genes-in-gorlin-syndrome-may-affect-the-phenotype
#10
Shoko Onodera, Akiko Saito, Daigo Hasegawa, Nana Morita, Katsuhito Watanabe, Takeshi Nomura, Takahiko Shibahara, Shinsuke Ohba, Akira Yamaguchi, Toshifumi Azuma
Gorlin syndrome is a genetic disorder of autosomal dominant inheritance that predisposes the affected individual to a variety of disorders that are attributed largely to heterozygous germline patched1 (PTCH1) mutations. PTCH1 is a hedgehog (Hh) receptor as well as a repressor, mutation of which leads to constitutive activation of Hh pathway. Hh pathway encompasses a wide variety of cellular signaling cascades, which involve several molecules; however, no associated genotype-phenotype correlations have been reported...
2017: PloS One
https://www.readbyqxmd.com/read/28914715/diffuse-staining-for-activated-notch1-correlates-with-notch1-mutation-status-and-is-associated-with-worse-outcome-in-adenoid-cystic-carcinoma
#11
Dipti P Sajed, William C Faquin, Chris Carey, Eric A Severson, Amir H Afrogheh, Carl A Johnson, Stephen C Blacklow, Nicole G Chau, Derrick T Lin, Jeffrey F Krane, Vickie Y Jo, Joaquín J Garcia, Lynette M Sholl, Jon C Aster
NOTCH1 is frequently mutated in adenoid cystic carcinoma (ACC). To test the idea that immunohistochemical (IHC) staining can identify ACCs with NOTCH1 mutations, we performed IHC for activated NOTCH1 (NICD1) in 197 cases diagnosed as ACC from 173 patients. NICD1 staining was positive in 194 cases (98%) in 2 major patterns: subset positivity, which correlated with tubular/cribriform histology; and diffuse positivity, which correlated with a solid histology. To determine the relationship between NICD1 staining and NOTCH1 mutational status, targeted exome sequencing data were obtained on 14 diffusely NICD1-positive ACC specimens from 11 patients and 15 subset NICD1-positive ACC specimens from 15 patients...
September 13, 2017: American Journal of Surgical Pathology
https://www.readbyqxmd.com/read/28914635/clinical-genetics-of-craniosynostosis
#12
Andrew O M Wilkie, David Johnson, Steven A Wall
PURPOSE OF REVIEW: When providing accurate clinical diagnosis and genetic counseling in craniosynostosis, the challenge is heightened by knowledge that etiology in any individual case may be entirely genetic, entirely environmental, or anything in between. This review will scope out how recent genetic discoveries from next-generation sequencing have impacted on the clinical genetic evaluation of craniosynostosis. RECENT FINDINGS: Survey of a 13-year birth cohort of patients treated at a single craniofacial unit demonstrates that a genetic cause of craniosynostosis can be identified in one quarter of cases...
September 14, 2017: Current Opinion in Pediatrics
https://www.readbyqxmd.com/read/28914269/looking-beyond-the-exome-a-phenotype-first-approach-to-molecular-diagnostic-resolution-in-rare-and-undiagnosed-diseases
#13
Loren D M Pena, Yong-Hui Jiang, Kelly Schoch, Rebecca C Spillmann, Nicole Walley, Nicholas Stong, Sarah Rapisardo Horn, Jennifer A Sullivan, Allyn McConkie-Rosell, Sujay Kansagra, Edward C Smith, Mays El-Dairi, Jane Bellet, Martha Ann Keels, Joan Jasien, Peter G Kranz, Richard Noel, Shashi K Nagaraj, Robert K Lark, Daniel S G Wechsler, Daniela Del Gaudio, Marco L Leung, Laura G Hendon, Collette C Parker, Kelly L Jones, David B Goldstein, Vandana Shashi
PurposeTo describe examples of missed pathogenic variants on whole-exome sequencing (WES) and the importance of deep phenotyping for further diagnostic testing.MethodsGuided by phenotypic information, three children with negative WES underwent targeted single-gene testing.ResultsIndividual 1 had a clinical diagnosis consistent with infantile systemic hyalinosis, although WES and a next-generation sequencing (NGS)-based ANTXR2 test were negative. Sanger sequencing of ANTXR2 revealed a homozygous single base pair insertion, previously missed by the WES variant caller software...
September 14, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28914264/comprehensive-use-of-extended-exome-analysis-improves-diagnostic-yield-in-rare-disease-a-retrospective-survey-in-1-059-cases
#14
Gaber Bergant, Ales Maver, Luca Lovrecic, Goran Čuturilo, Alenka Hodzic, Borut Peterlin
PurposeWe sought to determine the analytical sensitivity of several extended exome variation analysis approaches in terms of their contribution to diagnostic yield and their clinical feasibility.MethodsWe retrospectively analyzed the results of genetic testing in 1,059 distinct cases referred for exome sequencing to our institution. In these, we routinely employed extended exome analysis approaches in addition to basic variant analysis, including (i) copy-number variation (CNV) detection, (ii) nonconsensus splice defect detection, (ii) genomic breakpoint detection, (iv) homozygosity mapping, and (v) mitochondrial variant analysis...
September 14, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28913766/computational-modeling-and-treatment-identification-in-the-myelodysplastic-syndromes
#15
REVIEW
Leylah M Drusbosky, Christopher R Cogle
PURPOSE OF REVIEW: This review discusses the need for computational modeling in myelodysplastic syndromes (MDS) and early test results. RECENT FINDINGS: As our evolving understanding of MDS reveals a molecularly complicated disease, the need for sophisticated computer analytics is required to keep track of the number and complex interplay among the molecular abnormalities. Computational modeling and digital drug simulations using whole exome sequencing data input have produced early results showing high accuracy in predicting treatment response to standard of care drugs...
September 14, 2017: Current Hematologic Malignancy Reports
https://www.readbyqxmd.com/read/28913729/exome-array-analysis-identifies-etfb-as-a-novel-susceptibility-gene-for-anthracycline-induced-cardiotoxicity-in-cancer-patients
#16
Sara Ruiz-Pinto, Guillermo Pita, Miguel Martín, Teresa Alonso-Gordoa, Daniel R Barnes, María R Alonso, Belén Herraez, Purificación García-Miguel, Javier Alonso, Antonio Pérez-Martínez, Antonio J Cartón, Federico Gutiérrez-Larraya, José A García-Sáenz, Javier Benítez, Douglas F Easton, Ana Patiño-García, Anna González-Neira
PURPOSE: Anthracyclines are widely used chemotherapeutic drugs that can cause progressive and irreversible cardiac damage and fatal heart failure. Several genetic variants associated with anthracycline-induced cardiotoxicity (AIC) have been identified, but they explain only a small proportion of the interindividual differences in AIC susceptibility. METHODS: In this study, we evaluated the association of low-frequency variants with risk of chronic AIC using the Illumina HumanExome BeadChip array in a discovery cohort of 61 anthracycline-treated breast cancer patients with replication in a second independent cohort of 83 anthracycline-treated pediatric cancer patients, using gene-based tests (SKAT-O)...
September 14, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28913435/iba57-mutations-abrogate-iron-sulfur-cluster-assembly-leading-to-cavitating-leukoencephalopathy
#17
Akihiko Ishiyama, Chika Sakai, Yuichi Matsushima, Satoru Noguchi, Satomi Mitsuhashi, Yukari Endo, Yukiko K Hayashi, Yoshiaki Saito, Eiji Nakagawa, Hirofumi Komaki, Kenji Sugai, Masayuki Sasaki, Noriko Sato, Ikuya Nonaka, Yu-Ichi Goto, Ichizo Nishino
OBJECTIVE: To determine the molecular factors contributing to progressive cavitating leukoencephalopathy (PCL) to help resolve the underlying genotype-phenotype associations in the mitochondrial iron-sulfur cluster (ISC) assembly system. METHODS: The subjects were 3 patients from 2 families who showed no inconsistencies in either clinical or brain MRI findings as PCL. We used exome sequencing, immunoblotting, and enzyme activity assays to establish a molecular diagnosis and determine the roles of ISC-associated factors in PCL...
October 2017: Neurology. Genetics
https://www.readbyqxmd.com/read/28912018/association-between-germline-mutations-in-brf1-a-subunit-of-the-rna-polymerase-iii-transcription-complex-and-hereditary-colorectal-cancer
#18
Fernando Bellido, Nadine Sowada, Pilar Mur, Conxi Lázaro, Tirso Pons, Rafael Valdés-Mas, Marta Pineda, Gemma Aiza, Silvia Iglesias, José Luís Soto, Miguel Urioste, Trinidad Caldés, Milagros Balbín, Pilar Blay, Daniel Rueda, Mercedes Durán, Alfonso Valencia, Victor Moreno, Joan Brunet, Ignacio Blanco, Matilde Navarro, George A Calin, Guntram Borck, Xose S Puente, Gabriel Capellá, Laura Valle
BACKGROUND & AIMS: Although there is a genetic predisposition to colorectal cancer (CRC), few of the genes that affect risk have been identified. We performed whole-exome sequence analysis of individuals in a high-risk family without mutations in genes previously associated with CRC risk to identify variants associated with inherited CRC. METHODS: We collected blood samples from 3 relatives with CRC in Spain (65, 62 and 40 years old at diagnosis) and perfomed whole-exome sequence analyses...
September 11, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28911955/brief-report-somatic-mutations-and-ancestry-markers-in-hispanic-lung-cancer-patients
#19
Nicholas T Gimbrone, Bhaswati Sarcar, Edna R Gordian, Jason I Rivera, Christian Lopez, Sean J Yoder, Jamie K Teer, Eric A Welsh, Alberto A Chiaporri, Matthew B Schabath, Gary W Reuther, Julie Dutil, Miosotis Garcia, Ronald Ventosilla-Villanueva, Luis Vera-Valdivia, Alejandro Yabar-Berrocal, Rodrigo Motta-Guerrero, Pedro G Santiago-Cardona, Teresita Muñoz-Antonia, W Douglas Cress
INTRODUCTION: To address the lack of genomic data from Hispanic/Latino (H/L) patients with lung cancer, the Latino Lung Cancer Registry was established to collect patient data and biospecimens from these patients. METHODS: This retrospective observational study examined lung cancer tumor samples from 163 H/L patients, and tumor-derived DNA was subjected to targeted-exome sequencing (>1000 genes, including EGFR, KRAS, STK11, and TP53) and ancestry analysis. Mutation frequencies in this H/L cohort were compared with those in a similar cohort of non-Hispanic white (NHW) patients and were correlated with ancestry, sex, smoking status, and tumor histology...
September 11, 2017: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/28911203/mutations-of-conserved-non-coding-elements-of-pitx2-in-patients-with-ocular-dysgenesis-and-developmental-glaucoma
#20
Meredith E Protas, Eric Weh, Tim Footz, Jay Kasberger, Scott C Baraban, Alex V Levin, L Jay Katz, Robert Ritch, Michael A Walter, Elena V Semina, Douglas B Gould
Mutations in FOXC1 and PITX2 constitute the most common causes of ocular anterior segment dysgenesis (ASD), and confer a high risk for secondary glaucoma. The genetic causes underlying ASD in approximately half of patients remain unknown, despite many of them being screened by whole exome sequencing. Here, we performed whole genome sequencing on DNA from two affected individuals from a family with dominantly inherited ASD and glaucoma to identify a 748-kb deletion in a gene desert that contains conserved putative PITX2 regulatory elements...
September 15, 2017: Human Molecular Genetics
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