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1. Structural brain abnormalities in Pallister-Killian syndrome: a neuroimaging study of 31 children

Author

Anna Fetta, Francesco Toni, Ilaria Pettenuzzo, Emilia Ricci, Alessandro Rocca, Caterina Gambi, Luca Soliani, Veronica Di Pisa, Silvia Martini, Giacomo Sperti, Valeria Cagnazzo, Patrizia Accorsi, Emanuele Bartolini, Domenica Battaglia, Pia Bernardo, Maria Paola Canevini, Anna Rita Ferrari, Lucio Giordano, Chiara Locatelli, Margherita Mancardi, Alessandro Orsini, Tommaso Pippucci, Dario Pruna, Anna Rosati, Agnese Suppiej, Sara Tagliani, Alessandro Vaisfeld, Aglaia Vignoli, Kosuke Izumi, Ian Krantz, and Duccio Maria Cordelli

Subjects
Medicine
Abstract

Abstract Background Pallister-Killian syndrome (PKS) is a rare genetic disorder caused by mosaic tetrasomy of 12p with wide neurological involvement. Intellectual disability, developmental delay, behavioral problems, epilepsy, sleep disturbances, and brain malformations have been described in most individuals, with a broad phenotypic spectrum. This observational study, conducted through brain MRI scan analysis on a cohort of patients with genetically confirmed PKS, aims to systematically investigate the neuroradiological features of this syndrome and identify the possible existence of a typical pattern. Moreover, a literature review differentiating the different types of neuroimaging data was conducted for comparison with our population. Results Thirty-one individuals were enrolled (17 females/14 males; age range 0.1–17.5 years old at first MRI). An experienced pediatric neuroradiologist reviewed brain MRIs, blindly to clinical data. Brain abnormalities were observed in all but one individual (compared to the 34% frequency found in the literature review). Corpus callosum abnormalities were found in 20/30 (67%) patients: 6 had callosal hypoplasia; 8 had global hypoplasia with hypoplastic splenium; 4 had only hypoplastic splenium; and 2 had a thin corpus callosum. Cerebral hypoplasia/atrophy was found in 23/31 (74%) and ventriculomegaly in 20/31 (65%). Other frequent features were the enlargement of the cisterna magna in 15/30 (50%) and polymicrogyria in 14/29 (48%). Conversely, the frequency of the latter was found to be 4% from the literature review. Notably, in our population, polymicrogyria was in the perisylvian area in all 14 cases, and it was bilateral in 10/14. Conclusions Brain abnormalities are very common in PKS and occur much more frequently than previously reported. Bilateral perisylvian polymicrogyria was a main aspect of our population. Our findings provide an additional tool for early diagnosis.Further studies to investigate the possible correlations with both genotype and phenotype may help to define the etiopathogenesis of the neurologic phenotype of this syndrome.

Published
2024
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2. Heterozygous loss-of-function SMC3 variants are associated with variable growth and developmental features

Author

Morad Ansari, Kamli N.W. Faour, Akiko Shimamura, Graeme Grimes, Emeline M. Kao, Erica R. Denhoff, Ana Blatnik, Daniel Ben-Isvy, Lily Wang, Benjamin M. Helm, Helen Firth, Amy M. Breman, Emilia K. Bijlsma, Aiko Iwata-Otsubo, Thomy J.L. de Ravel, Vincent Fusaro, Alan Fryer, Keith Nykamp, Lara G. Stühn, Tobias B. Haack, G. Christoph Korenke, Panayiotis Constantinou, Kinga M. Bujakowska, Karen J. Low, Emily Place, Jennifer Humberson, Melanie P. Napier, Jessica Hoffman, Jane Juusola, Matthew A. Deardorff, Wanqing Shao, Shira Rockowitz, Ian Krantz, Maninder Kaur, Sarah Raible, Victoria Dortenzio, Sabine Kliesch, Moriel Singer-Berk, Emily Groopman, Stephanie DiTroia, Sonia Ballal, Siddharth Srivastava, Kathrin Rothfelder, Saskia Biskup, Jessica Rzasa, Jennifer Kerkhof, Haley McConkey, Bekim Sadikovic, Sarah Hilton, Siddharth Banka, Frank Tüttelmann, Donald F. Conrad, Anne O’Donnell-Luria, Michael E. Talkowski, David R. FitzPatrick, and Philip M. Boone

Subjects
Cornelia de Lange syndrome, SMC3, loss-of-function, cohesin, CdLS3, LoF, Genetics, QH426-470
Abstract

Summary: Heterozygous missense variants and in-frame indels in SMC3 are a cause of Cornelia de Lange syndrome (CdLS), marked by intellectual disability, growth deficiency, and dysmorphism, via an apparent dominant-negative mechanism. However, the spectrum of manifestations associated with SMC3 loss-of-function variants has not been reported, leading to hypotheses of alternative phenotypes or even developmental lethality. We used matchmaking servers, patient registries, and other resources to identify individuals with heterozygous, predicted loss-of-function (pLoF) variants in SMC3, and analyzed population databases to characterize mutational intolerance in this gene. Here, we show that SMC3 behaves as an archetypal haploinsufficient gene: it is highly constrained against pLoF variants, strongly depleted for missense variants, and pLoF variants are associated with a range of developmental phenotypes. Among 14 individuals with SMC3 pLoF variants, phenotypes were variable but coalesced on low growth parameters, developmental delay/intellectual disability, and dysmorphism, reminiscent of atypical CdLS. Comparisons to individuals with SMC3 missense/in-frame indel variants demonstrated an overall milder presentation in pLoF carriers. Furthermore, several individuals harboring pLoF variants in SMC3 were nonpenetrant for growth, developmental, and/or dysmorphic features, and some had alternative symptomatologies with rational biological links to SMC3. Analyses of tumor and model system transcriptomic data and epigenetic data in a subset of cases suggest that SMC3 pLoF variants reduce SMC3 expression but do not strongly support clustering with functional genomic signatures of typical CdLS. Our finding of substantial population-scale LoF intolerance in concert with variable growth and developmental features in subjects with SMC3 pLoF variants expands the scope of cohesinopathies, informs on their allelic architecture, and suggests the existence of additional clearly LoF-constrained genes whose disease links will be confirmed only by multilayered genomic data paired with careful phenotyping.

Published
2024
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4. PheNominal: an EHR-integrated web application for structured deep phenotyping at the point of care

Author

James M. Havrilla, Anbumalar Singaravelu, Dennis M. Driscoll, Leonard Minkovsky, Ingo Helbig, Livija Medne, Kai Wang, Ian Krantz, and Bimal R. Desai

Subjects
EHR, EMR, Phenotype, Epic healthcare, Health record data, Computer applications to medicine. Medical informatics, R858-859.7
Abstract

Abstract Background Clinical phenotype information greatly facilitates genetic diagnostic interpretations pipelines in disease. While post-hoc extraction using natural language processing on unstructured clinical notes continues to improve, there is a need to improve point-of-care collection of patient phenotypes. Therefore, we developed “PheNominal”, a point-of-care web application, embedded within Epic electronic health record (EHR) workflows, to permit capture of standardized phenotype data. Methods Using bi-directional web services available within commercial EHRs, we developed a lightweight web application that allows users to rapidly browse and identify relevant terms from the Human Phenotype Ontology (HPO). Selected terms are saved discretely within the patient’s EHR, permitting reuse both in clinical notes as well as in downstream diagnostic and research pipelines. Results In the 16 months since implementation, PheNominal was used to capture discrete phenotype data for over 1500 individuals and 11,000 HPO terms during clinic and inpatient encounters for a genetic diagnostic consultation service within a quaternary-care pediatric academic medical center. An average of 7 HPO terms were captured per patient. Compared to a manual workflow, the average time to enter terms for a patient was reduced from 15 to 5 min per patient, and there were fewer annotation errors. Conclusions Modern EHRs support integration of external applications using application programming interfaces. We describe a practical application of these interfaces to facilitate deep phenotype capture in a discrete, structured format within a busy clinical workflow. Future versions will include a vendor-agnostic implementation using FHIR. We describe pilot efforts to integrate structured phenotyping through controlled dictionaries into diagnostic and research pipelines, reducing manual effort for phenotype documentation and reducing errors in data entry.

Published
2022
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5. Rare variants create synthetic genome-wide associations.

Author

Samuel P Dickson, Kai Wang, Ian Krantz, Hakon Hakonarson, and David B Goldstein

Subjects
Biology (General), QH301-705.5
Abstract

Genome-wide association studies (GWAS) have now identified at least 2,000 common variants that appear associated with common diseases or related traits (http://www.genome.gov/gwastudies), hundreds of which have been convincingly replicated. It is generally thought that the associated markers reflect the effect of a nearby common (minor allele frequency >0.05) causal site, which is associated with the marker, leading to extensive resequencing efforts to find causal sites. We propose as an alternative explanation that variants much less common than the associated one may create "synthetic associations" by occurring, stochastically, more often in association with one of the alleles at the common site versus the other allele. Although synthetic associations are an obvious theoretical possibility, they have never been systematically explored as a possible explanation for GWAS findings. Here, we use simple computer simulations to show the conditions under which such synthetic associations will arise and how they may be recognized. We show that they are not only possible, but inevitable, and that under simple but reasonable genetic models, they are likely to account for or contribute to many of the recently identified signals reported in genome-wide association studies. We also illustrate the behavior of synthetic associations in real datasets by showing that rare causal mutations responsible for both hearing loss and sickle cell anemia create genome-wide significant synthetic associations, in the latter case extending over a 2.5-Mb interval encompassing scores of "blocks" of associated variants. In conclusion, uncommon or rare genetic variants can easily create synthetic associations that are credited to common variants, and this possibility requires careful consideration in the interpretation and follow up of GWAS signals.

Published
2010
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7. Dosage effects of cohesin regulatory factor PDS5 on mammalian development: implications for cohesinopathies.

Author

Bin Zhang, Jufang Chang, Ming Fu, Jie Huang, Rakesh Kashyap, Ezequiel Salavaggione, Sanjay Jain, Shashikant Kulkarni, Matthew A Deardorff, Maria L Giovannucci Uzielli, Dale Dorsett, David C Beebe, Patrick Y Jay, Robert O Heuckeroth, Ian Krantz, and Jeffrey Milbrandt

Subjects
Medicine, Science
Abstract

Cornelia de Lange syndrome (CdLS), a disorder caused by mutations in cohesion proteins, is characterized by multisystem developmental abnormalities. PDS5, a cohesion protein, is important for proper chromosome segregation in lower organisms and has two homologues in vertebrates (PDS5A and PDS5B). Pds5B mutant mice have developmental abnormalities resembling CdLS; however the role of Pds5A in mammals and the association of PDS5 proteins with CdLS are unknown. To delineate genetic interactions between Pds5A and Pds5B and explore mechanisms underlying phenotypic variability, we generated Pds5A-deficient mice. Curiously, these mice exhibit multiple abnormalities that were previously observed in Pds5B-deficient mice, including cleft palate, skeletal patterning defects, growth retardation, congenital heart defects and delayed migration of enteric neuron precursors. They also frequently display renal agenesis, an abnormality not observed in Pds5B(-/-) mice. While Pds5A(-/-) and Pds5B(-/-) mice die at birth, embryos harboring 3 mutant Pds5 alleles die between E11.5 and E12.5 most likely of heart failure, indicating that total Pds5 gene dosage is critical for normal development. In addition, characterization of these compound homozygous-heterozygous mice revealed a severe abnormality in lens formation that does not occur in either Pds5A(-/-) or Pds5B(-/-) mice. We further identified a functional missense mutation (R1292Q) in the PDS5B DNA-binding domain in a familial case of CdLS, in which affected individuals also develop megacolon. This study shows that PDS5A and PDS5B functions other than those involving chromosomal dynamics are important for normal development, highlights the sensitivity of key developmental processes on PDS5 signaling, and provides mechanistic insights into how PDS5 mutations may lead to CdLS.

Published
2009
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8. Expanding the reproductive organ phenotype of CHD7 ‐spectrum disorder

Author

Tomoki T. Nomakuchi, Melinda Danowitz, Blythe Stewart, Jacqueline Leonard, Kosuke Izumi, Ian Krantz, Thomas F. Kolon, David Langdon, Cara Skraban, Jason Van Batavia, Elaine Zackai, Kai Jiao, Rebecca Linn, Caitlin Alexander, Mark Zaontz, Maria G. Vogiatzi, and Louise C. Pyle

Subjects
Genetics, Genetics (clinical)
Published
2023
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9. Activating RAC1 variants in the switch II region cause a developmental syndrome and alter neuronal morphology

Author

Siddharth Banka, Abigail Bennington, Martin J Baker, Ellen Rijckmans, Giuliana D Clemente, Nurhuda Mohamad Ansor, Hilary Sito, Pritha Prasad, Kwame Anyane-Yeboa, Lauren Badalato, Boyan Dimitrov, David Fitzpatrick, Anna C E Hurst, Anna C Jansen, Melissa A Kelly, Ian Krantz, Claudine Rieubland, Meredith Ross, Natasha L Rudy, Javier Sanz, Katrien Stouffs, Zhuo Luan Xu, Angeliki Malliri, Marcelo G Kazanietz, Tom H Millard, Public Health Sciences, Pediatrics, Faculty of Medicine and Pharmacy, Clinical sciences, Medical Genetics, Mental Health and Wellbeing research group, Neurogenetics, Neuroprotection & Neuromodulation, and Reproduction and Genetics

Subjects
Neurons, Manchester Cancer Research Centre, ResearchInstitutes_Networks_Beacons/mcrc, WAVE regulatory complex, 610 Medicine & health, small GTPases, Megalencephaly, Mice, Neurodevelopmental Disorders, intellectual disability, NIH 3T3 Cells, Animals, Neurology (clinical), polymicrogyria, RAC1, Signal Transduction
Abstract

RAC1 is a highly conserved Rho GTPase critical for many cellular and developmental processes. De novo missense RAC1 variants cause a highly variable neurodevelopmental disorder. Some of these variants have previously been shown to have a dominant negative effect. Most previously reported patients with this disorder have either severe microcephaly or severe macrocephaly. Here, we describe eight patients with pathogenic missense RAC1 variants affecting residues between Q61 and R68 within the switch II region of RAC1. These patients display variable combinations of developmental delay, intellectual disability, brain anomalies such as polymicrogyria and cardiovascular defects with normocephaly or relatively milder micro- or macrocephaly. Pulldown assays, NIH3T3 fibroblast spreading assays and staining for activated PAK1/2/3 and WAVE2 suggest that these variants increase RAC1 activity and over-activate downstream signalling targets. Axons of neurons isolated from Drosophila embryos expressing the most common of the activating variants are significantly shorter, with an increased density of filopodial protrusions. In vivo, these embryos exhibit frequent defects in axonal organization. Class IV dendritic arborization neurons expressing this variant exhibit a significant reduction in the total area of the dendritic arbour, increased branching and failure of self-avoidance. RNAi knock down of the WAVE regulatory complex component Cyfip significantly rescues these morphological defects. These results establish that activating substitutions affecting residues Q61–R68 within the switch II region of RAC1 cause a developmental syndrome. Our findings reveal that these variants cause altered downstream signalling, resulting in abnormal neuronal morphology and reveal the WAVE regulatory complex/Arp2/3 pathway as a possible therapeutic target for activating RAC1 variants. These insights also have the potential to inform the mechanism and therapy for other disorders caused by variants in genes encoding other Rho GTPases, their regulators and downstream effectors.

Published
2022
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10. Disease-specific ACMG/AMP guidelines improve sequence variant interpretation for hearing loss

Author

Mayher J. Patel, Marina T. DiStefano, Andrea M. Oza, Madeline Y. Hughes, Emma H. Wilcox, Sarah E. Hemphill, Brandon J. Cushman, Andrew R. Grant, Rebecca K. Siegert, Jun Shen, Alex Chapin, Nicole J. Boczek, Lisa A. Schimmenti, Kiyomitsu Nara, Margaret Kenna, Hela Azaiez, Kevin T. Booth, Karen B. Avraham, Hannie Kremer, Andrew J. Griffith, Heidi L. Rehm, Sami S. Amr, Ahmad N. Abou Tayoun, Sonia Abdelhak, John Alexander, Zippora Brownstein, Rachel Burt, Byung Yoon Choi, Lilian Downie, Thomas Friedman, Anne Giersch, John Greinwald, Jeffrey Holt, Makoto Hosoya, Un-Kyung Kim, Ian Krantz, Suzanne Leal, Saber Masmoudi, Tatsuo Matsunaga, Matías Morín, Cynthia Morton, Hideki Mutai, Arti Pandya, Richard Smith, Mustafa Tekin, Shin-Ichi Usami, Guy Van Camp, Kazuki Yamazawa, Hui-Jun Yuan, Elizabeth Black-Zeigelbein, and Kejian Zhang

Subjects
Disease specific, medicine.medical_specialty, Hearing loss, Molecular pathology, business.industry, Genome, Human, Genetic Variation, Computational biology, Sensory disorders Donders Center for Medical Neuroscience [Radboudumc 12], Human genetics, Article, medicine, Medical genetics, Humans, Genetic Testing, medicine.symptom, business, Hearing Loss, Uncertain significance, Genetics (clinical), Likely pathogenic, Sequence (medicine)
Abstract

Contains fulltext : 243959.pdf (Publisher’s version ) (Closed access) PURPOSE: The ClinGen Variant Curation Expert Panels (VCEPs) provide disease-specific rules for accurate variant interpretation. Using the hearing loss-specific American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guidelines, the Hearing Loss VCEP (HL VCEP) illustrates the utility of expert specifications in variant interpretation. METHODS: A total of 157 variants across nine HL genes, previously submitted to ClinVar, were curated by the HL VCEP. The curation process involved collecting published and unpublished data for each variant by biocurators, followed by bimonthly meetings of an expert curation subgroup that reviewed all evidence and applied the HL-specific ACMG/AMP guidelines to reach a final classification. RESULTS: Before expert curation, 75% (117/157) of variants had single or multiple variants of uncertain significance (VUS) submissions (17/157) or had conflicting interpretations in ClinVar (100/157). After applying the HL-specific ACMG/AMP guidelines, 24% (4/17) of VUS and 69% (69/100) of discordant variants were resolved into benign (B), likely benign (LB), likely pathogenic (LP), or pathogenic (P). Overall, 70% (109/157) variants had unambiguous classifications (B, LB, LP, P). We quantify the contribution of the HL-specified ACMG/AMP codes to variant classification. CONCLUSION: Expert specification and application of the HL-specific ACMG/AMP guidelines effectively resolved discordant interpretations in ClinVar. This study highlights the utility of ClinGen VCEPs in supporting more consistent clinical variant interpretation.

Published
2021

11. Genome-first approach to rare EYA4 variants and cardio-auditory phenotypes in adults

Author

Shadi, Ahmadmehrabi, Binglan, Li, Joseph, Park, Batsal, Devkota, Marijana, Vujkovic, Yi-An, Ko, David, Van Wagoner, W H Wilson, Tang, Ian, Krantz, Marylyn, Ritchie, Jason, Brant, Michael J, Ruckenstein, Douglas J, Epstein, and Daniel J, Rader

Subjects
Male, Genome, Human, Black People, Gene Expression, Pennsylvania, Severity of Illness Index, White People, Electrocardiography, Phenotype, Audiometry, Echocardiography, Mutation, Exome Sequencing, Trans-Activators, Humans, Cardiomyopathies, Hearing Loss, Biological Specimen Banks
Abstract

While newborns and children with hearing loss are routinely offered genetic testing, adults are rarely clinically tested for a genetic etiology. One clinically actionable result from genetic testing in children is the discovery of variants in syndromic hearing loss genes. EYA4 is a known hearing loss gene which is also involved in important pathways in cardiac tissue. The pleiotropic effects of rare EYA4 variants are poorly understood and their prevalence in a large cohort has not been previously reported. We investigated cardio-auditory phenotypes in 11,451 individuals in a large biobank using a rare variant, genome-first approach to EYA4. We filtered 256 EYA4 variants carried by 6737 participants to 26 rare and predicted deleterious variants carried by 42 heterozygotes. We aggregated predicted deleterious EYA4 gene variants into a combined variable (i.e. "gene burden") and performed association studies across phenotypes compared to wildtype controls. We validated findings with replication in three independent cohorts and human tissue expression data. EYA4 gene burden was significantly associated with audiometric-proven HL (p = [Formula: see text], Mobitz Type II AV block (p = [Formula: see text]) and the syndromic presentation of HL and primary cardiomyopathy (p = 0.0194). Analyses on audiogram, echocardiogram, and electrocardiogram data validated these associations. Prior reports have focused on identifying variants in families with severe or syndromic phenotypes. In contrast, we found, using a genotype-first approach, that gene burden in EYA4 is associated with more subtle cardio-auditory phenotypes in an adult medical biobank population, including cardiac conduction disorders which have not been previously reported. We show the value of using a focused approach to uncover human disease related to pleiotropic gene variants and suggest a role for genetic testing in adults presenting with hearing loss.

Published
2020

12. ClinGen Expert Clinical Validity Curation of 164 Hearing Loss Gene-Disease Pairs

Author

Marina T. DiStefano, Sarah E. Hemphill, Andrea M. Oza, Rebecca K. Siegert, Andrew R. Grant, Madeline Y. Hughes, Brandon J. Cushman, Hela Azaiez, Kevin T. Booth, Alex Chapin, Hatice Duzkale, Tatsuo Matsunaga, Jun Shen, Wenying Zhang, Margaret Kenna, Lisa A. Schimmenti, Mustafa Tekin, Heidi L. Rehm, Ahmad N. Abou Tayoun, Sami S. Amr, Sonia Abdelhak, John Alexander, Karen Avraham, Neha Bhatia, Donglin Bai, Nicole Boczek, Zippora Brownstein, Rachel Burt, Yasmin Bylstra, Ignacio del Castillo, Byung Yoon Choi, Lilian Downie, Thomas Friedman, Anne Giersch, Jasmine Goh, John Greinwald, Andrew J. Griffith, Amy Hernandez, Jeffrey Holt, Makoto Hosoya, Lim Jiin Ying, Kanika Jain, Un-Kyung Kim, Hannie Kremer, Ian Krantz, Suzanne Leal, Morag Lewis, Xue Zhong Liu, Wendy Low, Yu Lu, Minjie Luo, Saber Masmoudi, Tan Yuen Ming, Miguel Angel Moreno-Pelayo, Matías Morín, Cynthia Morton, Jaclyn Murray, Hideki Mutai, Kiyomitsu Nara, Arti Pandya, Sylvia Kam Pei-Rong, Richard J.H. Smith, Saumya Shekhar Jamuar, Funda Elif Suer, Shin-Ichi Usami, Guy Van Camp, Kazuki Yamazawa, Hui-Jun Yuan, Elizabeth Black-Zeigelbein, Keijan Zhang, and ClinGen Hearing Loss Clinical Domain Working Group

Subjects
ClinGen, Hearing loss, Medical laboratory, Computational biology, Disease, Deafness, gene curation, Genome, Sensory disorders Donders Center for Medical Neuroscience [Radboudumc 12], Article, genetic diagnosis, 03 medical and health sciences, 0302 clinical medicine, Databases, Genetic, Humans, Medicine, Genetic Testing, Hearing Loss, Biology, Gene, Genetics (clinical), Data Curation, 030304 developmental biology, Genetic testing, 0303 health sciences, medicine.diagnostic_test, Genome, Human, business.industry, Genetic Variation, Reproducibility of Results, Genomics, Medical decision making, Human genetics, Mutation, Clinical validity, Human medicine, medicine.symptom, business, 030217 neurology & neurosurgery
Abstract

PurposeProper interpretation of genomic variants is critical to successful medical decision making based on genetic testing results. A fundamental prerequisite to accurate variant interpretation is the clear understanding of the clinical validity of gene-disease relationships. The Clinical Genome Resource (ClinGen) has developed a semi-quantitative framework to assign clinical validity to gene-disease relationships.MethodsThe ClinGen Hearing Loss Gene Curation Expert Panel (HL GCEP) uses this framework to perform evidence-based curations of genes present on testing panels from 17 clinical laboratories in the Genetic Testing Registry. The HL GCEP curated and reviewed 142 genes and 164 gene-disease pairs, including 105 nonsyndromic and 59 syndromic forms of hearing loss.ResultsThe final outcome included 82 Definitive (50%), 12 Strong (7%), 25 Moderate (15%), 32 Limited (20%), 10 Disputed (6%), and 3 Refuted (2%) classifications. The summary of each curation is date stamped with the HL GCEP approval, is live, and will be kept up-to-date on the ClinGen website (https://search.clinicalgenome.org/kb/gene-validity).ConclusionThis gene curation approach serves to optimize the clinical sensitivity of genetic testing while reducing the rate of uncertain or ambiguous test results caused by the interrogation of genes with insufficient evidence of a disease link.

Published
2019
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13. Correction: ClinGen expert clinical validity curation of 164 hearing loss gene–disease pairs

Author

Marina T. DiStefano, Sarah E. Hemphill, Andrea M. Oza, Rebecca K. Siegert, Andrew R. Grant, Madeline Y. Hughes, Brandon J. Cushman, Hela Azaiez, Kevin T. Booth, Alex Chapin, Hatice Duzkale, Tatsuo Matsunaga, Jun Shen, Wenying Zhang, Margaret Kenna, Lisa A. Schimmenti, Mustafa Tekin, Heidi L. Rehm, Ahmad N. Abou Tayoun, Sami S. Amr, Sonia Abdelhak, John Alexander, Karen Avraham, Neha Bhatia, Donglin Bai, Nicole Boczek, Zippora Brownstein, Rachel Burt, Yasmin Bylstra, Ignacio del Castillo, Byung Yoon Choi, Lilian Downie, Thomas Friedman, Anne Giersch, Jasmine Goh, John Greinwald, Andrew J. Griffith, Amy Hernandez, Jeffrey Holt, Makoto Hosoya, Lim Jiin Ying, Kanika Jain, Un-Kyung Kim, Hannie Kremer, Ian Krantz, Suzanne Leal, Morag Lewis, Xue Zhong Liu, Wendy Low, Yu Lu, Minjie Luo, Saber Masmoudi, Tan Yuen Ming, Miguel Angel Moreno-Pelayo, Matías Morín, Cynthia Morton, Jaclyn Murray, Hideki Mutai, Kiyomitsu Nara, Arti Pandya, Sylvia Kam Pei-Rong, Richard J.H. Smith, Saumya Shekhar Jamuar, Funda Elif Suer, Shin-Ichi Usami, Guy Van Camp, Kazuki Yamazawa, Hui-Jun Yuan, Elizabeth Black-Zeigelbein, and Keijan Zhang

Subjects
medicine.medical_specialty, Text mining, business.industry, Hearing loss, Published Erratum, Clinical validity, MEDLINE, medicine, Disease, Audiology, medicine.symptom, business, Genetics (clinical)
Published
2019
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14. Clinical Sequencing Exploratory Research Consortium: Accelerating Evidence-Based Practice of Genomic Medicine

Author

Robert C. Green, Katrina A.B. Goddard, Gail P. Jarvik, Laura M. Amendola, Paul S. Appelbaum, Jonathan S. Berg, Barbara A. Bernhardt, Leslie G. Biesecker, Sawona Biswas, Carrie L. Blout, Kevin M. Bowling, Kyle B. Brothers, Wylie Burke, Charlisse F. Caga-anan, Arul M. Chinnaiyan, Wendy K. Chung, Ellen W. Clayton, Gregory M. Cooper, Kelly East, James P. Evans, Stephanie M. Fullerton, Levi A. Garraway, Jeremy R. Garrett, Stacy W. Gray, Gail E. Henderson, Lucia A. Hindorff, Ingrid A. Holm, Michelle Huckaby Lewis, Carolyn M. Hutter, Pasi A. Janne, Steven Joffe, David Kaufman, Bartha M. Knoppers, Barbara A. Koenig, Ian D. Krantz, Teri A. Manolio, Laurence McCullough, Jean McEwen, Amy McGuire, Donna Muzny, Richard M. Myers, Deborah A. Nickerson, Jeffrey Ou, Donald W. Parsons, Gloria M. Petersen, Sharon E. Plon, Heidi L. Rehm, J. Scott Roberts, Dan Robinson, Joseph S. Salama, Sarah Scollon, Richard R. Sharp, Brian Shirts, Nancy B. Spinner, Holly K. Tabor, Peter Tarczy-Hornoch, David L. Veenstra, Nikhil Wagle, Karen Weck, Benjamin S. Wilfond, Kirk Wilhelmsen, Susan M. Wolf, Julia Wynn, Joon-Ho Yu, Michelle Amaral, Laura Amendola, Samuel J. Aronson, Shubhangi Arora, Danielle R. Azzariti, Greg S. Barsh, E.M. Bebin, Barbara B. Biesecker, Brian L. Brown, Amber A. Burt, Peter H. Byers, Muge G. Calikoglu, Sara J. Carlson, Nizar Chahin, Kurt D. Christensen, Wendy Chung, Allison L. Cirino, Ellen Clayton, Laura K. Conlin, Greg M. Cooper, David R. Crosslin, James V. Davis, Kelly Davis, Matthew A. Deardorff, Batsal Devkota, Raymond De Vries, Pamela Diamond, Michael O. Dorschner, Noreen P. Dugan, Dmitry Dukhovny, Matthew C. Dulik, Kelly M. East, Edgar A. Rivera-Munoz, Barbara Evans, Jessica Everett, Nicole Exe, Zheng Fan, Lindsay Z. Feuerman, Kelly Filipski, Candice R. Finnila, Kristen Fishler, Bob Ghrundmeier, Karen Giles, Marian J. Gilmore, Zahra S. Girnary, Katrina Goddard, Steven Gonsalves, Adam S. Gordon, Michele C. Gornick, William M. Grady, David E. Gray, Robert Green, Robert S. Greenwood, Amanda M. Gutierrez, Paul Han, Ragan Hart, Patrick Heagerty, Naomi Hensman, Susan M. Hiatt, Patricia Himes, Fuki M. Hisama, Carolyn Y. Ho, Lily B. Hoffman-Andrews, Celine Hong, Martha J. Horike-Pyne, Sara Hull, Seema Jamal, Brian C. Jensen, Steve Joffe, Jennifer Johnston, Dean Karavite, Tia L. Kauffman, Dave Kaufman, Whitley Kelley, Jerry H. Kim, Christine Kirby, William Klein, Bartha Knoppers, Sek Won Kong, Ian Krantz, Joel B. Krier, Neil E. Lamb, Michele P. Lambert, Lan Q. Le, Matthew S. Lebo, Alexander Lee, Kaitlyn B. Lee, Niall Lennon, Michael C. Leo, Kathleen A. Leppig, Katie Lewis, Michelle Lewis, Neal I. Lindeman, Nicole Lockhart, Bob Lonigro, Edward J. Lose, Philip J. Lupo, Laura Lyman Rodriguez, Frances Lynch, Kalotina Machini, Calum MacRae, Daniel S. Marchuk, Josue N. Martinez, Aaron Masino, Heather M. McLaughlin, Carmit McMullen, Piotr A. Mieczkowski, Jeff Miller, Victoria A. Miller, Rajen Mody, Sean D. Mooney, Elizabeth G. Moore, Elissa Morris, Michael Murray, David Ng, Nelly M. Oliver, Will Parsons, Donald L. Patrick, Jeffrey Pennington, Denise L. Perry, Gloria Petersen, Sharon Plon, Katie Porter, Bradford C. Powell, Sumit Punj, Carmen Radecki Breitkopf, Robin A. Raesz-Martinez, Wendy H. Raskind, Dean A. Reigar, Jacob A. Reiss, Carla A. Rich, Carolyn Sue Richards, Christine Rini, Scott Roberts, Peggy D. Robertson, Jill O. Robinson, Marguerite E. Robinson, Myra I. Roche, Edward J. Romasko, Elisabeth A. Rosenthal, Joseph Salama, Maria I. Scarano, Jennifer Schneider, Christine E. Seidman, Bryce A. Seifert, Brian H. Shirts, Lynette M. Sholl, Javed Siddiqui, Elian Silverman, Shirley Simmons, Janae V. Simons, Debra Skinner, Elena Stoffel, Natasha T. Strande, Shamil Sunyaev, Virginia P. Sybert, Jennifer Taber, Deanne M. Taylor, Christian R. Tilley, Ashley Tomlinson, Susan Trinidad, Ellen Tsai, Peter Ubel, Eliezer M. Van Allen, Jason L. Vassy, Pankaj Vats, Victoria L. Vetter, Raymond D. Vries, Sarah A. Walser, Rebecca C. Walsh, Allison Werner-Lin, Jana Whittle, Ben Wilfond, Kirk C. Wilhelmsen, Yaping Yang, Carol Young, and Brian J. Zikmund-Fisher

Subjects
0301 basic medicine, Adult, Evidence-based practice, Biomedical Research, Best practice, Exploratory research, MEDLINE, Genomics, Computational biology, 030105 genetics & heredity, Bioinformatics, Polymorphism, Single Nucleotide, Article, 03 medical and health sciences, Population Groups, Genetics, Medicine, Genomic medicine, Humans, Genetics(clinical), Exome, Child, Genetics (clinical), Exome sequencing, Medical education, Clinical Trials as Topic, business.industry, Genome, Human, Correction, High-Throughput Nucleotide Sequencing, Human genetics, United States, 3. Good health, National Human Genome Research Institute (U.S.), 030104 developmental biology, Cardiovascular Diseases, Evidence-Based Practice, Human genome, business, Psychology, Software
Abstract

Despite rapid technical progress and demonstrable effectiveness for some types of diagnosis and therapy, much remains to be learned about clinical genome and exome sequencing (CGES) and its role within the practice of medicine. The Clinical Sequencing Exploratory Research (CSER) consortium includes 18 extramural research projects, one National Human Genome Research Institute (NHGRI) intramural project, and a coordinating center funded by the NHGRI and National Cancer Institute. The consortium is exploring analytic and clinical validity and utility, as well as the ethical, legal, and social implications of sequencing via multidisciplinary approaches; it has thus far recruited 5,577 participants across a spectrum of symptomatic and healthy children and adults by utilizing both germline and cancer sequencing. The CSER consortium is analyzing data and creating publically available procedures and tools related to participant preferences and consent, variant classification, disclosure and management of primary and secondary findings, health outcomes, and integration with electronic health records. Future research directions will refine measures of clinical utility of CGES in both germline and somatic testing, evaluate the use of CGES for screening in healthy individuals, explore the penetrance of pathogenic variants through extensive phenotyping, reduce discordances in public databases of genes and variants, examine social and ethnic disparities in the provision of genomics services, explore regulatory issues, and estimate the value and downstream costs of sequencing. The CSER consortium has established a shared community of research sites by using diverse approaches to pursue the evidence-based development of best practices in genomic medicine.

Published
2016

15. Correction: Novel findings with reassessment of exome data: implications for validation testing and interpretation of genomic data

Author

Kristin McDonald, Gibson, Addie, Nesbitt, Kajia, Cao, Zhenming, Yu, Elizabeth, Denenberg, Elizabeth, DeChene, Qiaoning, Guan, Elizabeth, Bhoj, Xiangdong, Zhou, Bo, Zhang, Chao, Wu, Holly, Dubbs, Alisha, Wilkens, Livija, Medne, Emma, Bedoukian, Peter S, White, Jeffrey, Pennington, Minjie, Luo, Laura, Conlin, Dimitri, Monos, Mahdi, Sarmady, Eric, Marsh, Elaine, Zackai, Nancy, Spinner, Ian, Krantz, Matt, Deardorff, and Avni, Santani

Subjects
Genetics (clinical)
Abstract

In the published version of this article, the name of the 18th author was misspelled as Minjie Lou. The correct name is Minjie Luo. The authors regret the error.

Published
2018
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17. Return of genomic results to research participants: the floor, the ceiling, and the choices in between

Author

Gail P. Jarvik, Laura M. Amendola, Jonathan S. Berg, Kyle Brothers, Ellen W. Clayton, Wendy Chung, Barbara J. Evans, James P. Evans, Stephanie M. Fullerton, Carlos J. Gallego, Nanibaa’ A. Garrison, Stacy W. Gray, Ingrid A. Holm, Iftikhar J. Kullo, Lisa Soleymani Lehmann, Cathy McCarty, Cynthia A. Prows, Heidi L. Rehm, Richard R. Sharp, Joseph Salama, Saskia Sanderson, Sara L. Van Driest, Marc S. Williams, Susan M. Wolf, Wendy A. Wolf, Wylie Burke, John Harley, Melanie Myers, Bahram Namjou, Sander Vinks, John Connolly, Brendan Keating, Glenn Gerhard, Agnes Sundaresan, Gerard Tromp, David Crosslin, Kathy Leppig, Cathy Wicklund, Christopher Chute, John Lynch, Mariza De Andrade, John Heit, Jen McCormick, Murray Brilliant, Terrie Kitchner, Marylyn Ritchie, Erwin Böttinger, Inga Peter, Stephen Persell, Laura Rasmussen-Torvik, Tracy McGregor, Dan Roden, Armand Antommaria, Rosetta Chiavacci, Andy Faucett, David Ledbetter, Janet Williams, Andrea Hartzler, Carolyn R. Rohrer Vitek, Norm Frost, Kadija Ferryman, Carol Horowitz, Rosamond Rhodes, Randi Zinberg, Sharon Aufox, Vivian Pan, Rochelle Long, Erin Ramos, Jackie Odgis, Anastasia Wise, Sara Hull, Jonathan Gitlin, Robert Green, Danielle Metterville, Amy McGuire, Sek Won Kong, Sue Trinidad, David Veenstra, Myra Roche, Debra Skinner, Kelly Raspberry, Julianne O’Daniel, Will Parsons, Christine Eng, Susan Hilsenbeck, Dean Karavite, Laura Conlin, Nancy Spinner, Ian Krantz, Marni Falk, Avni Santani, Elizabeth Dechene, Matthew Dulik, Barbara Bernhardt, Scott Schuetze, Jessica Everett, Michele Caroline Gornick, Ben Wilfond, Holly Tabor, Amy A. Lemke, Sue Richards, Katrina Goddard, Greg Cooper, Kelly East, Greg Barsh, Barbara Koenig, Eliezer Van Allen, Judy Garber, Jeremy Garrett, Ma’n Zawati, Michelle Lewis, Sarah Savage, Maureen Smith, Sameek Roychowdhury, Alice Bailey, Benjamin Berkman, Charlisse Caga Anan, Lucia Hindorff, Carolyn Hutter, Rosalind King, Rongling Li, Nicole Lockhart, Jean McEwen, Derek Scholes, Sheri Schully, and Kathie Sun

Subjects
Societies, Scientific, Biomedical Research, Referral, Genetics, Medical, Exploratory research, MEDLINE, Disclosure, Bioinformatics, Article, Population Groups, Research participant, Genetics, Humans, Genetics(clinical), Genetic Privacy, Genetics (clinical), Receipt, Medical education, Patient Access to Records, Genome, Human, Medical record, High-Throughput Nucleotide Sequencing, Genomics, 3. Good health, Return of results, Psychology, Medical ethics
Abstract

As more research studies incorporate next-generation sequencing (including whole-genome or whole-exome sequencing), investigators and institutional review boards face difficult questions regarding which genomic results to return to research participants and how. An American College of Medical Genetics and Genomics 2013 policy paper suggesting that pathogenic mutations in 56 specified genes should be returned in the clinical setting has raised the question of whether comparable recommendations should be considered in research settings. The Clinical Sequencing Exploratory Research (CSER) Consortium and the Electronic Medical Records and Genomics (eMERGE) Network are multisite research programs that aim to develop practical strategies for addressing questions concerning the return of results in genomic research. CSER and eMERGE committees have identified areas of consensus regarding the return of genomic results to research participants. In most circumstances, if results meet an actionability threshold for return and the research participant has consented to return, genomic results, along with referral for appropriate clinical follow-up, should be offered to participants. However, participants have a right to decline the receipt of genomic results, even when doing so might be viewed as a threat to the participants’ health. Research investigators should be prepared to return research results and incidental findings discovered in the course of their research and meeting an actionability threshold, but they have no ethical obligation to actively search for such results. These positions are consistent with the recognition that clinical research is distinct from medical care in both its aims and its guiding moral principles.

Published
2014

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