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https://www.readbyqxmd.com/read/29625023/identification-of-misclassified-clinvar-variants-via-disease-population-prevalence
#1
Naisha Shah, Ying-Chen Claire Hou, Hung-Chun Yu, Rachana Sainger, C Thomas Caskey, J Craig Venter, Amalio Telenti
There is a significant interest in the standardized classification of human genetic variants. We used whole-genome sequence data from 10,495 unrelated individuals to contrast population frequency of pathogenic variants to the expected population prevalence of the disease. Analyses included the ACMG-recommended 59 gene-condition sets for incidental findings and 463 genes associated with 265 OrphaNet conditions. A total of 25,505 variants were used to identify patterns of inflation (i.e., excess genetic risk and misclassification)...
April 5, 2018: American Journal of Human Genetics
https://www.readbyqxmd.com/read/29606097/mucopolysaccharidosis-iiib-and-mild-skeletal-anomalies-coexistence-of-naglu-and-cyp26b1-missense-variations-in-the-same-patient-in-a-chinese-family
#2
Jinliang Li, Han Xie, Yuwu Jiang
BACKGROUND: Sanfilippo type B syndrome (mucopolysac-charidosis type IIIB; MPS IIIB) is an autosomal recessive lysosomal storage disorder. It is caused by a critically reduced α-2-acetamido-2-deoxy-D-glucoside acetamidodeoxy glucohydrolase (α-N-acetylglucosaminidase or NAGLU) activity. Recently, an autosomal recessive disorder of skeletal dysplasia associated with CYP26B1 was reported in three families, in which the patients were all homozygous variations. However, the co-occurrence of two rare diseases in a person is very rare...
April 2, 2018: BMC Medical Genetics
https://www.readbyqxmd.com/read/29588952/gene-panel-analysis-for-nonsyndromic-cryptogenic-neonatal-infantile-epileptic-encephalopathy
#3
Cheuk-Wing Fung, Anna Ka-Yee Kwong, Virginia Chun-Nei Wong
Objective: Epileptic encephalopathy (EE) is a heterogeneous condition associated with deteriorations of cognitive, sensory and/or motor functions as a consequence of epileptic activity. The phenomenon is the most common and severe in infancy and early childhood. Genetic-based diagnosis in EE patients is challenging owing to genetic and phenotypic heterogeneity of numerous monogenic disorders and the fact that thousands of genes are involved in neurodevelopment. Therefore, high-throughput next-generation sequencing (NGS) was used to investigate the genetic causes of non-syndromic cryptogenic neonatal/infantile EE (NIEE)...
June 2017: Epilepsia Open
https://www.readbyqxmd.com/read/29581464/whole-exome-sequencing-helps-the-diagnosis-and-treatment-in-children-with-neurodevelopmental-delay-accompanied-unexplained-dyspnea
#4
Wenjia Tong, Yajian Wang, Yun Lu, Tongsheng Ye, Conglei Song, Yuanyuan Xu, Min Li, Jie Ding, Yuanyuan Duan, Le Zhang, Weiyue Gu, Xiaoling Zhao, Xiu-An Yang, Danqun Jin
Neurodevelopmental delay accompanied unexplained dyspnea is a highly lethal disease in clinic. This study is to investigate the performance characteristics of trio whole exome sequencing (Trio-WES) in a pediatric setting by presenting our patient cohort and displaying the diagnostic yield. A total of 31 pediatric patients showing neurodevelopmental delay accompanied unexplained dyspnea were admitted to our hospital and referred for molecular genetic testing using Trio-WES. Eight genes namely MMACHC, G6PC, G6PT, ETFDH, OTC, NDUFAF5, SLC22A5, and MAGEL2 were suspected to be responsible for the onset of the clinical symptoms and 6 variants were novel...
March 26, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29567486/genetic-evaluation-of-cardiomyopathy-a-heart-failure-society-of-america-practice-guideline
#5
Ray E Hershberger, Michael Givertz, Carolyn Y Ho, Daniel P Judge, Paul Kantor, Kim L McBride, Ana Morales, Matthew R G Taylor, Matteo Vatta, Stephanie M Ware
This guideline describes the approach and expertise needed for the genetic evaluation of cardiomyopathy. First published in 2009 by the Heart Failure Society of America (HFSA), this guidance has now been updated in collaboration with the American College of Medical Genetics and Genomics (ACMG). The writing group, composed of cardiologists and genetics professionals with expertise in adult and pediatric cardiomyopathy, reflects the emergence and increased clinical activity devoted to cardiovascular genetic medicine...
March 19, 2018: Journal of Cardiac Failure
https://www.readbyqxmd.com/read/29565417/pediatric-clinical-exome-genome-sequencing-and-the-engagement-process-encouraging-active-conversation-with-the-older-child-and-adolescent-points-to-consider-a-statement-of-the-american-college-of-medical-genetics-and-genomics-acmg
#6
Lynn W Bush, Louis E Bartoshesky, Karen L David, Benjamin Wilfond, Janet L Williams, Ingrid A Holm
Disclaimer: This article is designed primarily as an educational resource for medical geneticists and other health care providers to help them provide quality patient care. Adherence to the information contained in this article does not necessarily assure a successful medical outcome. This information and any associated recommendations should not be considered inclusive of all proper procedures and tests or exclusive of other procedures and tests that are reasonably directed to obtaining the same results. In determining the propriety of any specific procedure or test, each provider should apply his or her own professional judgment to the specific clinical circumstances presented by the individual patient...
March 22, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29543229/the-acmg-amp-reputable-source-criteria-for-the-interpretation-of-sequence-variants
#7
Leslie G Biesecker, Steven M Harrison
No abstract text is available yet for this article.
March 15, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29543224/laboratory-analysis-of-organic-acids-2018-update-a-technical-standard-of-the-american-college-of-medical-genetics-and-genomics-acmg
#8
Renata C Gallagher, Laura Pollard, Anna I Scott, Suzette Huguenin, Stephen Goodman, Qin Sun
Disclaimer: These ACMG Standards are intended as an educational resource for clinical laboratory geneticists to help them provide quality clinical laboratory genetic services. Adherence to these Standards is voluntary and does not necessarily assure a successful medical outcome. These Standards should not be considered inclusive of all proper procedures and tests, or exclusive of others that are reasonably directed to obtaining the same results. In determining the propriety of any specific procedure or test, clinical laboratory geneticists should apply their professional judgment to the specific circumstances presented by the patient or specimen...
March 15, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29541281/cdkn2a-founder-mutation-in-pancreatic-ductal-adenocarcinoma-patients-without-cutaneous-features-of-familial-atypical-multiple-mole-melanoma-fammm-syndrome
#9
Carol Cremin, Sarah Howard, Lyly Le, Aly Karsan, David F Schaeffer, Daniel Renouf, Kasmintan A Schrader
Background: Approximately 5% to 10% of pancreatic ductal adenocarcinoma (PDAC) has a hereditary basis. In most of these defined hereditary cancer syndromes, PDAC is not the predominant cancer type. Traditional criteria for publicly funded genetic testing typically require the presence of a set combination of the predominant syndrome-associated cancer types in the family history.We report the identification of a CDKN2A pathogenic variant in a PDAC-prone family without the cutaneous features of multiple moles or melanoma that are characteristic of the Familial Atypical Multiple Mole Melanoma (FAMMM) Syndrome identified in a universal testing algorithm for inherited mutations in pancreatic cancer patients...
2018: Hereditary Cancer in Clinical Practice
https://www.readbyqxmd.com/read/29538399/generalising-better-applying-deep-learning-to-integrate-deleteriousness-prediction-scores-for-whole-exome-snv-studies
#10
Ilia Korvigo, Andrey Afanasyev, Nikolay Romashchenko, Mikhail Skoblov
Many automatic classifiers were introduced to aid inference of phenotypical effects of uncategorised nsSNVs (nonsynonymous Single Nucleotide Variations) in theoretical and medical applications. Lately, several meta-estimators have been proposed that combine different predictors, such as PolyPhen and SIFT, to integrate more information in a single score. Although many advances have been made in feature design and machine learning algorithms used, the shortage of high-quality reference data along with the bias towards intensively studied in vitro models call for improved generalisation ability in order to further increase classification accuracy and handle records with insufficient data...
2018: PloS One
https://www.readbyqxmd.com/read/29493581/clingen-s-rasopathy-expert-panel-consensus-methods-for-variant-interpretation
#11
Bruce D Gelb, Hélène Cavé, Mitchell W Dillon, Karen W Gripp, Jennifer A Lee, Heather Mason-Suares, Katherine A Rauen, Bradley Williams, Martin Zenker, Lisa M Vincent
PurposeStandardized and accurate variant assessment is essential for effective medical care. To that end, Clinical Genome (ClinGen) Resource clinical domain working groups (CDWGs) are systematically reviewing disease-associated genes for sufficient evidence to support disease causality and creating disease-specific specifications of American College of Medical Genetics and Genomics-Association for Molecular Pathology (ACMG-AMP) guidelines for consistent and accurate variant classification.MethodsThe ClinGen RASopathy CDWG established an expert panel to curate gene information and generate gene- and disease-specific specifications to ACMG-AMP variant classification framework...
March 1, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29463208/the-vaast-variant-prioritizer-vvp-ultrafast-easy-to-use-whole-genome-variant-prioritization-tool
#12
Steven Flygare, Edgar Javier Hernandez, Lon Phan, Barry Moore, Man Li, Anthony Fejes, Hao Hu, Karen Eilbeck, Chad Huff, Lynn Jorde, Martin G Reese, Mark Yandell
BACKGROUND: Prioritization of sequence variants for diagnosis and discovery of Mendelian diseases is challenging, especially in large collections of whole genome sequences (WGS). Fast, scalable solutions are needed for discovery research, for clinical applications, and for curation of massive public variant repositories such as dbSNP and gnomAD. In response, we have developed VVP, the VAAST Variant Prioritizer. VVP is ultrafast, scales to even the largest variant repositories and genome collections, and its outputs are designed to simplify clinical interpretation of variants of uncertain significance...
February 20, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29429203/-bainbridge-ropers-syndrome-with-asxl3-gene-variation-in-a-child-and-literature-review
#13
R Zhang, X H He, H Y Lin, X H Yang
Objective: To investigate the clinical manifestations and genetic features of a child with Bainbridge-Ropers syndrome caused by ASXL3 gene variation and review the literature. Methods: Clinical data and genetic features were collected and analyzed from a child with Bainbridge-Ropers syndrome who was diagnosed in Bao'an Maternity and Child Health Hospital in November 2016. "ASXL3" and "Bainbridge-Ropers" were used as key words to search at China National Knowledge Infrastructure, Wangfang Data Knowledge Service Platform, PubMed and Human Gene Mutation Database up to June 2017...
February 2, 2018: Zhonghua Er Ke za Zhi. Chinese Journal of Pediatrics
https://www.readbyqxmd.com/read/29374474/genio-a-phenotype-genotype-analysis-web-server-for-clinical-genomics-of-rare-diseases
#14
Daniel Koile, Marta Cordoba, Maximiliano de Sousa Serro, Marcelo Andres Kauffman, Patricio Yankilevich
BACKGROUND: GenIO is a novel web-server, designed to assist clinical genomics researchers and medical doctors in the diagnostic process of rare genetic diseases. The tool identifies the most probable variants causing a rare disease, using the genomic and clinical information provided by a medical practitioner. Variants identified in a whole-genome, whole-exome or target sequencing studies are annotated, classified and filtered by clinical significance. Candidate genes associated with the patient's symptoms, suspected disease and complementary findings are identified to obtain a small manageable number of the most probable recessive and dominant candidate gene variants associated with the rare disease case...
January 27, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29372391/genotype-phenotype-correlation-and-frequency-of-distribution-in-a-cohort-of-chinese-charcot-marie-tooth-patients-associated-with-gdap1-mutations
#15
Pukar Singh Pakhrin, Yongzhi Xie, Zhengmao Hu, Xiaobo Li, Lei Liu, Shunxiang Huang, Binghao Wang, Zihan Yang, Jiejun Zhang, Xin Liu, Kun Xia, Beisha Tang, Ruxu Zhang
Mutations in ganglioside-induced differentiation-associated-protein 1 (GDAP1) have been associated with both subtypes of Charcot-Marie-Tooth (CMT) disease, autosomal recessive (CMT4A and AR-CMT2K) and autosomal dominant (AD-CMT2K). Over 80 different mutations have been identified so far. With the use of Sanger sequencing and Next Generation Sequencing (NGS) technologies, we screened a cohort of 306 unrelated Chinese CMT patients and identified 8 variants in the GDAP1 gene in 4 families, 5 of which were novel (R41H, N201Kfs*5, Q38X, V215I and Q38R)...
January 25, 2018: Journal of Neurology
https://www.readbyqxmd.com/read/29369293/cardioclassifier-disease-and-gene-specific-computational-decision-support-for-clinical-genome-interpretation
#16
Nicola Whiffin, Roddy Walsh, Risha Govind, Matthew Edwards, Mian Ahmad, Xiaolei Zhang, Upasana Tayal, Rachel Buchan, William Midwinter, Alicja E Wilk, Hanna Najgebauer, Catherine Francis, Sam Wilkinson, Thomas Monk, Laura Brett, Declan P O'Regan, Sanjay K Prasad, Deborah J Morris-Rosendahl, Paul J R Barton, Elizabeth Edwards, James S Ware, Stuart A Cook
PurposeInternationally adopted variant interpretation guidelines from the American College of Medical Genetics and Genomics (ACMG) are generic and require disease-specific refinement. Here we developed CardioClassifier (http://www.cardioclassifier.org), a semiautomated decision-support tool for inherited cardiac conditions (ICCs).MethodsCardioClassifier integrates data retrieved from multiple sources with user-input case-specific information, through an interactive interface, to support variant interpretation...
January 25, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29366874/novel-dcc-variants-in-congenital-mirror-movements-and-evaluation-of-disease-associated-missense-variants
#17
Tatjana Bierhals, Georg Christoph Korenke, Martina Baethmann, Laura López Marín, Martin Staudt, Kerstin Kutsche
Congenital mirror movements (CMM) are involuntary movements of one side of the body that mirror intentional movements of the other side. Heterozygous missense, frameshift and nonsense variants and small intragenic deletions in DCC cause CMM, isolated agenesis of the corpus callosum (ACC) or both. We report here the clinical phenotype and natural history of ten individuals with CMM carrying five different monoallelic DCC variants, including the missense variant p.(Trp273Arg), two duplications, one deletion and one deletion-insertion; all are novel and absent from databases...
February 2, 2018: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/29365859/systematic-review-of-ldlr-mutations-associated-to-familial-hypercholesterolaemia-evidence-of-functional-studies-and-application-of-acmg-guidelines-for-fh-diagnosis
#18
Joana Rita Chora, Ana Catarina Alves, Ana Margarida Medeiros, Mafalda Bourbon
No abstract text is available yet for this article.
August 2017: Atherosclerosis
https://www.readbyqxmd.com/read/29343803/targeted-next-generation-sequencing-in-a-young-population-with-suspected-inherited-malignant-cardiac-arrhythmias
#19
Anders Krogh Broendberg, Morten Krogh Christiansen, Jens Cosedis Nielsen, Lisbeth Noerum Pedersen, Henrik Kjaerulf Jensen
Aborted sudden cardiac death in the young often is due to inherited heart disease. However, the clinical phenotype in these patients is not always evident. The aim of this study was to identify pathogenic molecular genetic variants in a population with suspected inherited cardiac arrhythmias. Eligible patients were admitted to Aarhus University Hospital, Denmark during the period 1999-2013 with arrhythmias assumed caused by a hereditary heart disease, and in whom no genotype had been established. We used the Danish national pacemaker and ICD registry to identify this cohort...
January 17, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29339979/-brca1-and-brca2-mutation-spectrum-an-update-on-mutation-distribution-in-a-large-cancer-genetics-clinic-in-norway
#20
Cecilie Heramb, Teresia Wangensteen, Eli Marie Grindedal, Sarah Louise Ariansen, Sheba Lothe, Ketil Riddervold Heimdal, Lovise Mæhle
Background: Founder mutations in the two breast cancer genes, BRCA1 and BRCA2 , have been described in many populations, among these are Ashkenazi-Jewish, Polish, Norwegian and Icelandic. Founder mutation testing in patients with relevant ancestry has been a cost-efficient approach in such populations. Four Norwegian BRCA1 founder mutations were defined by haplotyping in 2001, and accounted for 68% of BRCA1 mutation carriers at the time. After 15 more years of genetic testing, updated knowledge on the mutation spectrum of both BRCA1 and BRCA2 in Norway is needed...
2018: Hereditary Cancer in Clinical Practice
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