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Genetics in Medicine: Official Journal of the American College of Medical Genetics

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https://www.readbyqxmd.com/read/28617419/utilization-of-genomic-sequencing-for-population-screening-of-immunodeficiencies-in-the-newborn
#1
Ashleigh R Pavey, Dale L Bodian, Thierry Vilboux, Alina Khromykh, Natalie S Hauser, Kathi Huddleston, Elisabeth Klein, Aaron Black, Megan S Kane, Ramaswamy K Iyer, John E Niederhuber, Benjamin D Solomon
PurposeImmunodeficiency screening has been added to many state-directed newborn screening programs. The current methodology is limited to screening for severe T-cell lymphopenia disorders. We evaluated the potential of genomic sequencing to augment current newborn screening for immunodeficiency, including identification of non-T cell disorders.MethodsWe analyzed whole-genome sequencing (WGS) and clinical data from a cohort of 1,349 newborn-parent trios by genotype-first and phenotype-first approaches. For the genotype-first approach, we analyzed predicted protein-impacting variants in 329 immunodeficiency-related genes in the WGS data...
June 15, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28617418/medical-genetics-and-genomics-education-how-do-we-define-success-where-do-we-focus-our-resources
#2
Robin L Bennett, Darrel Waggoner, Miriam G Blitzer
No abstract text is available yet for this article.
June 15, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28617417/a-cohort-of-17-patients-with-kyphoscoliotic-ehlers-danlos-syndrome-caused-by-biallelic-mutations-in-fkbp14-expansion-of-the-clinical-and-mutational-spectrum-and-description-of-the-natural-history
#3
Cecilia Giunta, Matthias Baumann, Christine Fauth, Uschi Lindert, Ebtesam M Abdalla, Angela F Brady, James Collins, Jahannaz Dastgir, Sandra Donkervoort, Neeti Ghali, Diana S Johnson, Ariana Kariminejad, Johannes Koch, Marius Kraenzlin, Nayana Lahiri, Bernarda Lozic, Adnan Y Manzur, Jenny E V Morton, Jacek Pilch, Rebecca C Pollitt, Gudrun Schreiber, Nora L Shannon, Glenda Sobey, Anthony Vandersteen, Fleur S van Dijk, Martina Witsch-Baumgartner, Johannes Zschocke, F Michael Pope, Carsten G Bönnemann, Marianne Rohrbach
PurposeIn 2012 we reported in six individuals a clinical condition almost indistinguishable from PLOD1-kyphoscoliotic Ehlers-Danlos syndrome (PLOD1-kEDS), caused by biallelic mutations in FKBP14, and characterized by progressive kyphoscoliosis, myopathy, and hearing loss in addition to connective tissue abnormalities such as joint hypermobility and hyperelastic skin. FKBP14 is an ER-resident protein belonging to the family of FK506-binding peptidyl-prolyl cis-trans isomerases (PPIases); it catalyzes the folding of type III collagen and interacts with type III, type VI, and type X collagens...
June 15, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28617416/genome-wide-cfdna-screening-clinical-laboratory-experience-with-the-first-10-000-cases
#4
Mathias Ehrich, John Tynan, Amin Mazloom, Eyad Almasri, Ron McCullough, Theresa Boomer, Daniel Grosu, Jason Chibuk
PurposeInvasive diagnostic prenatal testing can provide the most comprehensive information about the genetic status of a fetus. Noninvasive prenatal screening methods, especially when using cell-free DNA (cfDNA), are often limited to reporting only on trisomies 21, 18, and 13 and sex chromosome aneuploidies. This can leave a significant number of chromosomal and subchromosomal copy-number variations undetected. In 2015, we launched a new genome-wide cfDNA screening test that has the potential to narrow this detection gap...
June 15, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28617415/oral-d-galactose-supplementation-in-pgm1-cdg
#5
Sunnie Yan-Wai Wong, Therese Gadomski, Monique van Scherpenzeel, Tomas Honzik, Hana Hansikova, Katja S Brocke Holmefjord, Marit Mork, Francis Bowling, Jolanta Sykut-Cegielska, Dieter Koch, Jozef Hertecant, Graeme Preston, Jaak Jaeken, Nicole Peeters, Stefanie Perez, David Do Nguyen, Kea Crivelly, Tim Emmerzaal, K Michael Gibson, Kimiyo Raymond, Nurulamin Abu Bakar, Francois Foulquier, Gernot Poschet, Amanda M Ackermann, Miao He, Dirk J Lefeber, Christian Thiel, Tamas Kozicz, Eva Morava
PurposePhosphoglucomutase-1 deficiency is a subtype of congenital disorders of glycosylation (PGM1-CDG). Previous casereports in PGM1-CDG patients receiving oral D-galactose (D-gal) showed clinical improvement. So far no systematic in vitro and clinical studies have assessed safety and benefits of D-gal supplementation. In a prospective pilot study, we evaluated the effects of oral D-gal in nine patients.MethodsD-gal supplementation was increased to 1.5 g/kg/day (maximum 50 g/day) in three increments over 18 weeks...
June 15, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28569743/sources-of-discordance-among-germ-line-variant-classifications-in-clinvar
#6
Shan Yang, Stephen E Lincoln, Yuya Kobayashi, Keith Nykamp, Robert L Nussbaum, Scott Topper
PurposeClinVar is increasingly used as a resource for both genetic variant interpretation and clinical practice. However, controversies exist regarding the consistency of classifications in ClinVar, and questions remain about how best to use these data. Our study systematically examined ClinVar to identify common sources of discordance and thus inform ongoing practices.MethodsWe analyzed variants that had multiple classifications in ClinVar, excluding benign polymorphisms. Classifications were categorized by potential actionability and pathogenicity...
June 1, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28541281/revisiting-the-prevalence-of-nonclassic-congenital-adrenal-hyperplasia-in-us-ashkenazi-jews-and-caucasians
#7
Fady Hannah-Shmouni, Rachel Morissette, Ninet Sinaii, Meredith Elman, Toni R Prezant, Wuyan Chen, Ann Pulver, Deborah P Merke
PurposeNonclassic 21-hydroxylase deficiency, a mild form of congenital adrenal hyperplasia (CAH), is estimated to be the most common autosomal recessive condition, with an especially high prevalence in Ashkenazi Jews (3.7% affected, 30.9% carriers), based on a 1985 HLA-B linkage study of affected families. Affected individuals, especially women, may suffer from hyperandrogenism and infertility. State-of-the-art genetic studies have not been done to confirm these remarkable rates.MethodsCYP21A2 genotyping was performed in 200 unrelated healthy Ashkenazi Jewish subjects and 200 random US Caucasians who did not self-identify as a specific ethnicity using multiplex minisequencing, real-time polymerase chain reaction and junction site analysis...
May 25, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28541280/a-quantitative-csmart-assay-for-noninvasive-prenatal-screening-of-autosomal-recessive-nonsyndromic-hearing-loss-caused-by-gjb2-and-slc26a4-mutations
#8
Mingyu Han, Zhifeng Li, Wenlu Wang, Shasha Huang, Yanping Lu, Zhiying Gao, Longxia Wang, Dongyang Kang, Linwei Li, Yiqian Liu, Mengnan Xu, David S Cram, Pu Dai
PurposeThe aim of this study was to assess the performance of a noninvasive prenatal screening (NIPS) assay for accurate fetal genotyping of pregnancies at genetic risk for autosomal recessive nonsyndromic hearing loss (ARNSHL).MethodsA total of 80 pregnant couples carrying known mutations in either the GJB2 or SLC26A4 genes associated with a risk for ARNSHL were recruited to the study. Fetal amniocyte samples were genotyped by invasive prenatal screening (IPS), whereas the cell-free fetal DNA present in maternal plasma samples was genotyped using a novel NIPS method based on circulating single-molecule amplification and resequencing technology (cSMART)...
May 25, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28541279/do-the-data-really-support-ordering-fragile-x-testing-as-a-first-tier-test-without-clinical-features
#9
Veronique Weinstein, Pranoot Tanpaiboon, Kimberly A Chapman, Nicholas Ah Mew, Sean Hofherr
PurposeCurrent guidelines recommend first-tier chromosome microarray analysis (CMA) and fragile X syndrome (FX) testing for males with isolated intellectual disabilities/learning delay (ID/LD) and autism spectrum disorders (ASDs).MethodsMales in our clinic with ID/LD or ASD (310) were analyzed for positive results from CMA and/or FX testing.ResultsCMA detected abnormalities in 29% of males with ID/LD and only 9% of males with ASD (including variants of uncertain significance and absence of heterozygosity). When males with ID/LD were tested for FX, the detection rate was 2...
May 25, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28541278/sharing-data-under-the-21st-century-cures-act
#10
REVIEW
Mary A Majumder, Christi J Guerrini, Juli M Bollinger, Robert Cook-Deegan, Amy L McGuire
On 13 December 2016, President Obama signed the 21st Century Cures Act ("the Act") into law. Many of its provisions support the creation of an "Information Commons," an ecosystem of separate but interconnected initiatives that facilitate open and responsible sharing of genomic and other data for research and clinical purposes. For example, the Act supports the National Institutes of Health in mandating data sharing, provides funding and guidance for the large national cohort program now known as All of Us, expresses congressional support for a global pediatric study network, and strengthens patient access to health information...
May 25, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28518170/prenatal-exome-sequencing-in-anomalous-fetuses-new-opportunities-and-challenges
#11
Neeta L Vora, Bradford Powell, Alicia Brandt, Natasha Strande, Emily Hardisty, Kelly Gilmore, Ann Katherine M Foreman, Kirk Wilhelmsen, Chris Bizon, Jason Reilly, Phil Owen, Cynthia M Powell, Debra Skinner, Christine Rini, Anne D Lyerly, Kim A Boggess, Karen Weck, Jonathan S Berg, James P Evans
PurposeWe investigated the diagnostic and clinical performance of exome sequencing in fetuses with sonographic abnormalities with normal karyotype and microarray and, in some cases, normal gene-specific sequencing.MethodsExome sequencing was performed on DNA from 15 anomalous fetuses and from the peripheral blood of their parents. Parents provided consent to be informed of diagnostic results in the fetus, medically actionable findings in the parents, and their identification as carrier couples for significant autosomal recessive conditions...
May 18, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28518169/population-based-impact-of-noninvasive-prenatal-screening-on-screening-and-diagnostic-testing-for-fetal-aneuploidy
#12
Lisa Hui, Briohny Hutchinson, Alice Poulton, Jane Halliday
PurposeTo assess the population-wide impact of noninvasive prenatal screening (NIPS) on combined first-trimester screening (CFTS), early ultrasound (11-13 weeks), and invasive prenatal diagnosis in a state with over 73,000 births per year.MethodsAnalysis of population-based data from 2000 to 2015 including (i) invasive prenatal tests, (ii) CFTS uptake, and (iii) total births. Utilization of early ultrasound was analyzed before and after NIPS (2010-2015).ResultsInvasive testing decreased significantly by 39...
May 18, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28518168/using-high-resolution-variant-frequencies-to-empower-clinical-genome-interpretation
#13
Nicola Whiffin, Eric Minikel, Roddy Walsh, Anne H O'Donnell-Luria, Konrad Karczewski, Alexander Y Ing, Paul J R Barton, Birgit Funke, Stuart A Cook, Daniel MacArthur, James S Ware
PurposeWhole-exome and whole-genome sequencing have transformed the discovery of genetic variants that cause human Mendelian disease, but discriminating pathogenic from benign variants remains a daunting challenge. Rarity is recognized as a necessary, although not sufficient, criterion for pathogenicity, but frequency cutoffs used in Mendelian analysis are often arbitrary and overly lenient. Recent very large reference datasets, such as the Exome Aggregation Consortium (ExAC), provide an unprecedented opportunity to obtain robust frequency estimates even for very rare variants...
May 18, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28492536/quantifying-family-dissemination-and-identifying-barriers-to-communication-of-risk-information-in-australian-brca-families
#14
Emma Healey, Natalie Taylor, Sian Greening, Claire E Wakefield, Linda Warwick, Rachel Williams, Kathy Tucker
PurposeRecommendations for BRCA1 and BRCA2 mutation carriers to disseminate information to at-risk relatives pose significant challenges. This study aimed to quantify family dissemination, to explain the differences between fully informed families (all relatives informed verbally or in writing) and partially informed families (at least one relative uninformed), and to identify dissemination barriers.MethodsBRCA1 and BRCA2 mutation carriers identified from four Australian hospitals (n=671) were invited to participate in the study...
May 11, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28492535/response-to-laissue-et-al
#15
Katharine Press, Joann Bodurtha
No abstract text is available yet for this article.
May 11, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28492534/response-to-de-vries-et-al
#16
Mrudu Herbert, Zoheb B Kazi, Susan Richards, Amy S Rosenberg, Priya S Kishnani
No abstract text is available yet for this article.
May 11, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28492533/gene-patents-still-alive-and-kicking-their-impact-on-provision-of-genetic-testing-for-long-qt-syndrome-in-the-canadian-public-health-care-system
#17
Sarah E Ali-Khan, E Richard Gold
PurposeAlthough the Supreme Court of the United States limited their availability in Association for Molecular Pathology v. Myriad Genetics, gene patents remain important around the world. We examine the situation in Canada, where gene patents continue to exist, in light of recent litigation relating to familial long QT syndrome (LQTS).MethodsWe conducted in-depth semistructured interviews with 25 stakeholders across five Canadian provinces and supplemented this with a case analysis of the litigation.ResultsThe majority of LQTS testing was carried out outside Canada...
May 11, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28492532/sherloc-a-comprehensive-refinement-of-the-acmg-amp-variant-classification-criteria
#18
Keith Nykamp, Michael Anderson, Martin Powers, John Garcia, Blanca Herrera, Yuan-Yuan Ho, Yuya Kobayashi, Nila Patil, Janita Thusberg, Marjorie Westbrook, Scott Topper
PurposeThe 2015 American College of Medical Genetics and Genomics-Association for Molecular Pathology (ACMG-AMP) guidelines were a major step toward establishing a common framework for variant classification. In practice, however, several aspects of the guidelines lack specificity, are subject to varied interpretations, or fail to capture relevant aspects of clinical molecular genetics. A simple implementation of the guidelines in their current form is insufficient for consistent and comprehensive variant classification...
May 11, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28492531/improving-the-evaluation-of-milestones-for-students-completing-a-clinical-genetics-elective
#19
Paul Laissue, Carlos M Restrepo, Angela María Ortiz
No abstract text is available yet for this article.
May 11, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28471438/electronic-health-record-phenotype-in-subjects-with-genetic-variants-associated-with-arrhythmogenic-right-ventricular-cardiomyopathy-a-study-of-30-716-subjects-with-exome-sequencing
#20
Christopher M Haggerty, Cynthia A James, Hugh Calkins, Crystal Tichnell, Joseph B Leader, Dustin N Hartzel, Christopher D Nevius, Sarah A Pendergrass, Thomas N Person, Marci Schwartz, Marylyn D Ritchie, David J Carey, David H Ledbetter, Marc S Williams, Frederick E Dewey, Alexander Lopez, John Penn, John D Overton, Jeffrey G Reid, Matthew Lebo, Heather Mason-Suares, Christina Austin-Tse, Heidi L Rehm, Brian P Delisle, Daniel J Makowski, Vishal C Mehra, Michael F Murray, Brandon K Fornwalt
PurposeArrhythmogenic right ventricular cardiomyopathy (ARVC) is an inherited heart disease. Clinical follow-up of incidental findings in ARVC-associated genes is recommended. We aimed to determine the prevalence of disease thus ascertained.MethodsIndividuals (n = 30,716) underwent exome sequencing. Variants in PKP2, DSG2, DSC2, DSP, JUP, TMEM43, or TGFβ3 that were database-listed as pathogenic or likely pathogenic were identified and evidence-reviewed. For subjects with putative loss-of-function (pLOF) variants or variants of uncertain significance (VUS), electronic health records (EHR) were reviewed for ARVC diagnosis, diagnostic criteria, and International Classification of Diseases (ICD-9) codes...
May 4, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
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