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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/29215655/observed-frequency-and-challenges-of-variant-reclassification-in-a-hereditary-cancer-clinic
#1
Sarah Macklin, Nisha Durand, Paldeep Atwal, Stephanie Hines
PurposeEfforts have been made by the American College of Medical Genetics and Genomics and the Association for Molecular Pathology to make variant classification more uniform, but many limitations remain. Reclassification of a variant of uncertain significance (VUS) is expected, but other more certain calls, like pathogenic or benign, can also be reclassified once additional information is gathered. Variant reclassification can create difficult circumstances for both patients and clinicians.MethodsRetrospective review of all variant reclassifications in genes associated with hereditary cancer syndromes at one clinic between September 2013 and February 2017 was completed...
December 7, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29215654/age-and-perceived-risks-and-benefits-of-preventive-genomic-screening
#2
Margaret Waltz, R Jean Cadigan, Anya E R Prince, Debra Skinner, Gail E Henderson
PurposeAs genome sequencing moves from research to clinical practice, sequencing technologies focused on "medically actionable" targets are being promoted for preventive screening despite the dearth of systematic evidence of risks and benefits and of criteria for selection of screening subjects. This study investigates researchers' and research participants' perceptions of these issues within the context of a preventive genomic screening study, GeneScreen.MethodsWe recorded researcher deliberations regarding age eligibility criteria and the risks and benefits of screening, and conducted interviews with 50 GeneScreen participants about their motivations for joining and their perceptions of risks and benefits...
December 7, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29215653/prevalence-of-neurofibromatosis-type-1-in-the-finnish-population
#3
Roope A Kallionpää, Elina Uusitalo, Jussi Leppävirta, Minna Pöyhönen, Sirkku Peltonen, Juha Peltonen
PurposeThe incidence of neurofibromatosis 1 (NF1) is ~1/2,000 live births, but the current estimates of prevalence vary greatly. This retrospective total-population study was aimed at determining the prevalence of NF1 in Finland.MethodsAll secondary and tertiary referral centers of Finland were searched for NF1 patients. Patient records were manually reviewed and patients fulfilling the National Institutes of Health diagnostic criteria for NF1 were included. Prevalence on 31 December 2005 was determined. Data on incidence and survival were combined to refine the prevalence estimation...
December 7, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29215652/corrigendum-sources-of-discordance-among-germ-line-variant-classifications-in-clinvar
#4
Shan Yang, Stephen E Lincoln, Yuya Kobayashi, Keith Nykamp, Robert L Nussbaum, Scott Topper
This corrects the article DOI: 10.1038/gim.2017.60.
December 7, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29215651/mosaic-disorders-and-the-taxonomy-of-human-disease
#5
Leslie G Biesecker
No abstract text is available yet for this article.
December 7, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29215650/phenocopies-in-melanoma-prone-families-with-germ-line-cdkn2a-mutations
#6
Hildur Helgadottir, Håkan Olsson, Margaret A Tucker, Xiaohong R Yang, Veronica Höiom, Alisa M Goldstein
PurposeCarriers of CDKN2A mutations have high risks of melanoma and certain other cancers. In this study we examined the occurrence of tumors among CDKN2A wild type (wt) members of melanoma-prone families with CDKN2A mutations.MethodsSwedish and US melanoma-prone families with CDKN2A mutations were included. Data was collected on tumors diagnosed among family members. Among the CDKN2A mutated families, members with CDKN2A wt status who were diagnosed with melanoma were designated phenocopies.ResultsOf patients with melanoma in the CDKN2A mutated families (n = 266), 7...
December 7, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29215649/a-craniosynostosis-massively-parallel-sequencing-panel-study-in-309-australian-and-new-zealand-patients-findings-and-recommendations
#7
Eric Lee, Trang Le, Ying Zhu, George Elakis, Anne Turner, William Lo, Hanka Venselaar, Carol-Ann Verrenkamp, Nicole Snow, David Mowat, Edwin Philip Kirk, Rani Sachdev, Janine Smith, Natasha Jane Brown, Mathew Wallis, Chris Barnett, Fiona McKenzie, Mary-Louise Freckmann, Felicity Collins, Maya Chopra, Nerine Gregersen, Ian Hayes, Sulekha Rajagopalan, Tiong Yang Tan, Zornitza Stark, Ravi Savarirayan, Alison Yeung, Lesley Adès, Michael Gattas, Kate Gibson, Michael Gabbett, David John Amor, Wanda Lattanzi, Simeon Boyd, Eric Haan, Mark Gianoutsos, Timothy Chilton Cox, Michael Francis Buckley, Tony Roscioli
PurposeThe craniosynostoses are characterized by premature fusion of one or more cranial sutures. The relative contribution of previously reported genes to craniosynostosis in large cohorts is unclear. Here we report on the use of a massively parallel sequencing panel in individuals with craniosynostosis without a prior molecular diagnosis.MethodsA 20-gene panel was designed based on the genes' association with craniosynostosis, and clinically validated through retrospective testing of an Australian and New Zealand cohort of 233 individuals with craniosynostosis in whom previous testing had not identified a causative variant within FGFR1-3 hot-spot regions or the TWIST1 gene...
December 7, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29215648/happy-birthday-genetics-in-medicine
#8
James P Evans
No abstract text is available yet for this article.
December 7, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29215647/fragile-x-population-carrier-screening
#9
Sylvia A Metcalfe, Martin B Delatycki, Jonathan Cohen, Alison D Archibald, Jon D Emery
No abstract text is available yet for this article.
December 7, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29215646/follow-up-status-during-the-first-5-years-of-life-for-metabolic-disorders-on-the-federal-recommended-uniform-screening-panel
#10
Lisa Feuchtbaum, Juan Yang, Robert Currier
PurposeTo investigate the 5-year follow-up status for newborns diagnosed with metabolic disorders designated as "primary disorders" on the federal Recommended Uniform Screening Panel (RUSP).MethodsFollow-up status and demographic characteristics are described for 426 newborns diagnosed with one of 20 primary metabolic disorders on the RUSP between 2005 and 2009. Newborn screening program data were linked to birth certificate data. Follow-up status is described for each year through age 5 and by disorder type...
December 7, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29215645/cherchez-la-femme-maternal-incidental-findings-can-explain-discordant-prenatal-cell-free-dna-sequencing-results
#11
REVIEW
Diana W Bianchi
Circulating DNA fragments in a pregnant woman's plasma derive from three sources: placenta, maternal bone marrow, and fetus. Prenatal sequencing to noninvasively screen for fetal chromosome abnormalities is performed on this mixed sample; results can therefore reflect the maternal as well as the fetoplacental DNA. Although it is recommended that pretest counseling include the possibility of detecting maternal genomic imbalance, this seldom occurs. Maternal abnormalities that can affect a prenatal screening test result include disorders that affect the size and metabolism of DNA, such as B12 deficiency, autoimmune disease, and intrahepatic cholestasis of pregnancy...
December 7, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29189820/somatic-tp53-variants-frequently-confound-germ-line-testing-results
#12
Jeffrey N Weitzel, Elizabeth C Chao, Bita Nehoray, Lily R Van Tongeren, Holly LaDuca, Kathleen R Blazer, Thomas Slavin, D A B M D Facmg, Tina Pesaran, Christina Rybak, Ilana Solomon, Mariana Niell-Swiller, Jill S Dolinsky, Danielle Castillo, Aaron Elliott, Chia-Ling Gau, Virginia Speare, Kory Jasperson
PurposeBlood/saliva DNA is thought to represent the germ line in genetic cancer-risk assessment. Cases with pathogenic TP53 variants detected by multigene panel testing are often discordant with Li-Fraumeni syndrome, raising concern about misinterpretation of acquired aberrant clonal expansions (ACEs) with TP53 variants as germ-line results.MethodsPathogenic TP53 variants with abnormal next-generation sequencing metrics (e.g., decreased ratio (<25%) of mutant to wild-type allele, more than two detected alleles) were selected from a CLIA laboratory testing cohort...
November 30, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29144512/ashkenazi-jewish-genomic-variants-integrating-data-from-the-israeli-national-genetic-database-and-gnomad
#13
Joël Zlotogora, George P Patrinos, Vardiella Meiner
PurposeThe aim of the study was to compare the data for mutations related to clinical disorders reported among Ashkenazi Jewish patients in the Israeli National Genetic Database (INGD) with variants included in the Genome Aggregation Database (gnomAD).MethodsWe extracted data for mutations claimed to cause disorders reported among Ashkenazi Jews from the INGD and searched gnomAD for each of them. We compared the allele frequency of each variant in Ashkenazi Jews with that of other delineated populations.ResultsOf the 58 INGD-reported mutations related to autosomal-dominant disorders, 19 were present in gnomAD (32...
November 16, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29144511/evaluating-charge-syndrome-in-congenital-hypogonadotropic-hypogonadism-patients-harboring-chd7-variants
#14
Cheng Xu, Daniele Cassatella, Almer M van der Sloot, Richard Quinton, Michael Hauschild, Christian De Geyter, Christa Flück, Katrin Feller, Deborah Bartholdi, Attila Nemeth, Irene Halperin, Sandra Pekic Djurdjevic, Philippe Maeder, Georgios Papadakis, Andrew A Dwyer, Laura Marino, Lucie Favre, Duarte Pignatelli, Nicolas J Niederländer, James Acierno, Nelly Pitteloud
PurposeCongenital hypogonadotropic hypogonadism (CHH), a rare genetic disease caused by gonadotropin-releasing hormone deficiency, can also be part of complex syndromes (e.g., CHARGE syndrome). CHD7 mutations were reported in 60% of patients with CHARGE syndrome, and in 6% of CHH patients. However, the definition of CHD7 mutations was variable, and the associated CHARGE signs in CHH were not systematically examined.MethodsRare sequencing variants (RSVs) in CHD7 were identified through exome sequencing in 116 CHH probands, and were interpreted according to American College of Medical Genetics and Genomics guidelines...
November 16, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29144510/characterizing-reduced-coverage-regions-through-comparison-of-exome-and-genome-sequencing-data-across-10-centers
#15
Rashesh V Sanghvi, Christian J Buhay, Bradford C Powell, Ellen A Tsai, Michael O Dorschner, Celine S Hong, Matthew S Lebo, Ariella Sasson, David S Hanna, Sean McGee, Kevin M Bowling, Gregory M Cooper, David E Gray, Robert J Lonigro, Andrew Dunford, Christine A Brennan, Carrie Cibulskis, Kimberly Walker, Mauricio O Carneiro, Joshua Sailsbery, Lucia A Hindorff, Dan R Robinson, Avni Santani, Mahdi Sarmady, Heidi L Rehm, Leslie G Biesecker, Deborah A Nickerson, Carolyn M Hutter, Levi Garraway, Donna M Muzny, Nikhil Wagle
PurposeAs massively parallel sequencing is increasingly being used for clinical decision making, it has become critical to understand parameters that affect sequencing quality and to establish methods for measuring and reporting clinical sequencing standards. In this report, we propose a definition for reduced coverage regions and describe a set of standards for variant calling in clinical sequencing applications.MethodsTo enable sequencing centers to assess the regions of poor sequencing quality in their own data, we optimized and used a tool (ExCID) to identify reduced coverage loci within genes or regions of particular interest...
November 16, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29120461/risk-of-colorectal-cancer-for-carriers-of-a-germ-line-mutation-in-pole-or-pold1
#16
Daniel D Buchanan, Jenna R Stewart, Mark Clendenning, Christophe Rosty, Khalid Mahmood, Bernard J Pope, Mark A Jenkins, John L Hopper, Melissa C Southey, Finlay A Macrae, Ingrid M Winship, Aung Ko Win
BackgroundGerm-line mutations in the exonuclease domains of the POLE and POLD1 genes are associated with an increased, but yet unquantified, risk of colorectal cancer (CRC).MethodsWe identified families with POLE or POLD1 variants by searching PubMed for relevant studies prior to October 2016 and by genotyping 669 population-based CRC cases diagnosed in patients under 60 years of age, from the Australasian Colorectal Cancer Family Registry. We estimated the age-specific cumulative risks (penetrance) using a modified segregation analysis...
November 9, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29120460/prenatal-reflex-dna-screening-for-trisomies-21-18-and-13
#17
Nicholas J Wald, Wayne J Huttly, Jonathan P Bestwick, Robert Old, Joan K Morris, Ray Cheng, Joe Aquilina, Elisabeth Peregrine, Devender Roberts, Zarko Alfirevic
PurposeThe purpose of the study was to determine the screening performance of prenatal reflex DNA screening for trisomies 21 (T21), 18 (T18), and 13 (T13) as part of a routine service at five hospitals.MethodsWomen who accepted screening had a first-trimester combined test (pregnancy-associated plasma protein A, free β-human chorionic gonadotropin, nuchal translucency interpreted with maternal age). Those with a risk of having an affected pregnancy ≥1 in 800 were reflexed to a DNA sequencing test using stored plasma from the original blood sample, thereby avoiding the need to recall them...
November 9, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29120459/informative-priors-on-fetal-fraction-increase-power-of-the-noninvasive-prenatal-screen
#18
Hanli Xu, Shaowei Wang, Lin-Lin Ma, Shuai Huang, Lin Liang, Qian Liu, Yang-Yang Liu, Ke-Di Liu, Ze-Min Tan, Hao Ban, Yongtao Guan, Zuhong Lu
PurposeNoninvasive prenatal screening (NIPS) sequences a mixture of the maternal and fetal cell-free DNA. Fetal trisomy can be detected by examining chromosomal dosages estimated from sequencing reads. The traditional method uses the Z-test, which compares a subject against a set of euploid controls, where the information of fetal fraction is not fully utilized. Here we present a Bayesian method that leverages informative priors on the fetal fraction.MethodOur Bayesian method combines the Z-test likelihood and informative priors of the fetal fraction, which are learned from the sex chromosomes, to compute Bayes factors...
November 9, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29120458/precision-newborn-screening-for-lysosomal-disorders
#19
Melissa M Minter Baerg, Stephanie D Stoway, Jeremy Hart, Lea Mott, Dawn S Peck, Stephanie L Nett, Jason S Eckerman, Jean M Lacey, Coleman T Turgeon, Dimitar Gavrilov, Devin Oglesbee, Kimiyo Raymond, Silvia Tortorelli, Dietrich Matern, Lars Mørkrid, Piero Rinaldo
PurposeThe implementation of newborn screening for lysosomal disorders has uncovered overall poor specificity, psychosocial harm experienced by caregivers, and costly follow-up testing of false-positive cases. We report an informatics solution proven to minimize these issues.MethodsThe Kentucky Department for Public Health outsourced testing for mucopolysaccharidosis type I (MPS I) and Pompe disease, conditions recently added to the recommended uniform screening panel, plus Krabbe disease, which was added by legislative mandate...
November 9, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29095815/identification-of-balanced-chromosomal-rearrangements-previously-unknown-among-participants-in-the-1000-genomes-project-implications-for-interpretation-of-structural-variation-in-genomes-and-the-future-of-clinical-cytogenetics
#20
Zirui Dong, Huilin Wang, Haixiao Chen, Hui Jiang, Jianying Yuan, Zhenjun Yang, Wen-Jing Wang, Fengping Xu, Xiaosen Guo, Ye Cao, Zhenzhen Zhu, Chunyu Geng, Wan Chee Cheung, Yvonne K Kwok, Huanming Yang, Tak Yeung Leung, Cynthia C Morton, Sau Wai Cheung, Kwong Wai Choy
PurposeRecent studies demonstrate that whole-genome sequencing enables detection of cryptic rearrangements in apparently balanced chromosomal rearrangements (also known as balanced chromosomal abnormalities, BCAs) previously identified by conventional cytogenetic methods. We aimed to assess our analytical tool for detecting BCAs in the 1000 Genomes Project without knowing which bands were affected.MethodsThe 1000 Genomes Project provides an unprecedented integrated map of structural variants in phenotypically normal subjects, but there is no information on potential inclusion of subjects with apparent BCAs akin to those traditionally detected in diagnostic cytogenetics laboratories...
November 2, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
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