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Chen Y, Dawes R, Kim HC, Stenton SL, Walker S, Ljungdahl A, Lord J, Ganesh VS, Ma J, Martin-Geary AC, Lemire G, D'Souza EN, Dong S, Ellingford JM, Adams DR, Allan K, Bakshi M, Baldwin EE, Berger SI, Bernstein JA, Brown NJ, Burrage LC, Chapman K, Compton AG, Cunningham CA, D'Souza P, Délot EC, Dias KR, Elias ER, Evans CA, Ewans L, Ezell K, Fraser JL, Gallacher L, Genetti CA, Grant CL, Haack T, Kuechler A, Lalani SR, Leitão E, Fevre AL, Leventer RJ, Liebelt JE, Lockhart PJ, Ma AS, Macnamara EF, Maurer TM, Mendez HR, Montgomery SB, Nassogne MC, Neumann S, O'Leary M, Palmer EE, Phillips J, Pitsava G, Pysar R, Rehm HL, Reuter CM, Revencu N, Riess A, Rius R, Rodan L, Roscioli T, Rosenfeld JA, Sachdev R, Simons C, Sisodiya SM, Snell P, Clair LS, Stark Z, Tan TY, Tan NB, Temple SE, Thorburn DR, Tifft CJ, Uebergang E, VanNoy GE, Vilain E, Viskochil DH, Wedd L, Wheeler MT, White SM, Wojcik M, Wolfe LA, Wolfenson Z, Xiao C, Zocche D, Rubenstein JL, Markenscoff-Papadimitriou E, Fica SM, Baralle D, Depienne C, MacArthur DG, Howson JM, Sanders SJ, O'Donnell-Luria A, Whiffin N. De novo variants in the non-coding spliceosomal snRNA gene RNU4-2 are a frequent cause of syndromic neurodevelopmental disorders. medRxiv 2024:2024.04.07.24305438. [PMID: 38645094 PMCID: PMC11030480 DOI: 10.1101/2024.04.07.24305438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Around 60% of individuals with neurodevelopmental disorders (NDD) remain undiagnosed after comprehensive genetic testing, primarily of protein-coding genes 1 . Increasingly, large genome-sequenced cohorts are improving our ability to discover new diagnoses in the non-coding genome. Here, we identify the non-coding RNA RNU4-2 as a novel syndromic NDD gene. RNU4-2 encodes the U4 small nuclear RNA (snRNA), which is a critical component of the U4/U6.U5 tri-snRNP complex of the major spliceosome 2 . We identify an 18 bp region of RNU4-2 mapping to two structural elements in the U4/U6 snRNA duplex (the T-loop and Stem III) that is severely depleted of variation in the general population, but in which we identify heterozygous variants in 119 individuals with NDD. The vast majority of individuals (77.3%) have the same highly recurrent single base-pair insertion (n.64_65insT). We estimate that variants in this region explain 0.41% of individuals with NDD. We demonstrate that RNU4-2 is highly expressed in the developing human brain, in contrast to its contiguous counterpart RNU4-1 and other U4 homologs, supporting RNU4-2 's role as the primary U4 transcript in the brain. Overall, this work underscores the importance of non-coding genes in rare disorders. It will provide a diagnosis to thousands of individuals with NDD worldwide and pave the way for the development of effective treatments for these individuals.
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Krysov VA, Wilson RH, Ten NS, Youlton N, De Jong HN, Sutton S, Huang Y, Reuter CM, Grove ME, Wheeler MT, Ashley EA, Parikh VN. Regional Variation in Cardiovascular Genes Enables a Tractable Genome Editing Strategy. Circ Genom Precis Med 2024; 17:e004370. [PMID: 38506054 PMCID: PMC11020015 DOI: 10.1161/circgen.123.004370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 03/10/2024] [Indexed: 03/21/2024]
Abstract
BACKGROUND To realize the potential of genome engineering therapeutics, tractable strategies must be identified that balance personalized therapy with the need for off-the-shelf availability. We hypothesized that regional clustering of pathogenic variants can inform the design of rational prime editing therapeutics to treat the majority of genetic cardiovascular diseases with a limited number of reagents. METHODS We collated 2435 high-confidence pathogenic/likely pathogenic (P/LP) variants in 82 cardiovascular disease genes from ClinVar. We assessed the regional density of these variants by defining a regional clustering index. We then combined a highly active base editor with prime editing to demonstrate the feasibility of a P/LP hotspot-directed genome engineering therapeutic strategy in vitro. RESULTS P/LP variants in cardiovascular disease genes display higher regional density than rare variants found in the general population. P/LP missense variants displayed higher average regional density than P/LP truncating variants. Following hypermutagenesis at a pathogenic hotspot, mean prime editing efficiency across introduced variants was 57±27%. CONCLUSIONS Designing therapeutics that target pathogenic hotspots will not only address known missense P/LP variants but also novel P/LP variants identified in these hotspots as well. Moreover, the clustering of P/LP missense rather than truncating variants in these hotspots suggests that prime editing technology is particularly valuable for dominant negative disease. Although prime editing technology in relation to cardiac health continues to improve, this study presents an approach to targeting the most impactful regions of the genome for inherited cardiovascular disease.
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Affiliation(s)
- Vikki A. Krysov
- Division of Cardiovascular Medicine (V.A.K., R.H.W., N.S.T., N.Y., H.N.D.J., S.S., Y.H., C.M.R., M.T.W., E.A.A., V.N.P.)
- University of California, Davis School of Medicine, Sacramento, CA (V.A.K.)
| | - Rachel H. Wilson
- Division of Cardiovascular Medicine (V.A.K., R.H.W., N.S.T., N.Y., H.N.D.J., S.S., Y.H., C.M.R., M.T.W., E.A.A., V.N.P.)
| | - Nicholas S. Ten
- Division of Cardiovascular Medicine (V.A.K., R.H.W., N.S.T., N.Y., H.N.D.J., S.S., Y.H., C.M.R., M.T.W., E.A.A., V.N.P.)
| | - Nathan Youlton
- Division of Cardiovascular Medicine (V.A.K., R.H.W., N.S.T., N.Y., H.N.D.J., S.S., Y.H., C.M.R., M.T.W., E.A.A., V.N.P.)
| | - Hannah N. De Jong
- Division of Cardiovascular Medicine (V.A.K., R.H.W., N.S.T., N.Y., H.N.D.J., S.S., Y.H., C.M.R., M.T.W., E.A.A., V.N.P.)
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA (H.N.D.J., E.A.A.)
- Maze Therapeutics, Inc., San Francisco, CA (H.N.D.J.)
| | - Shirley Sutton
- Division of Cardiovascular Medicine (V.A.K., R.H.W., N.S.T., N.Y., H.N.D.J., S.S., Y.H., C.M.R., M.T.W., E.A.A., V.N.P.)
| | - Yong Huang
- Division of Cardiovascular Medicine (V.A.K., R.H.W., N.S.T., N.Y., H.N.D.J., S.S., Y.H., C.M.R., M.T.W., E.A.A., V.N.P.)
| | - Chloe M. Reuter
- Division of Cardiovascular Medicine (V.A.K., R.H.W., N.S.T., N.Y., H.N.D.J., S.S., Y.H., C.M.R., M.T.W., E.A.A., V.N.P.)
- Color Health, Burlingame, CA (C.M.R., M.E.G.)
| | | | - Matthew T. Wheeler
- Division of Cardiovascular Medicine (V.A.K., R.H.W., N.S.T., N.Y., H.N.D.J., S.S., Y.H., C.M.R., M.T.W., E.A.A., V.N.P.)
- Stanford Center for Inherited Cardiovascular Disease, Stanford Medicine, CA (M.T.W., E.A.A., V.N.P.)
| | - Euan A. Ashley
- Division of Cardiovascular Medicine (V.A.K., R.H.W., N.S.T., N.Y., H.N.D.J., S.S., Y.H., C.M.R., M.T.W., E.A.A., V.N.P.)
- Department of Genetics, Stanford University School of Medicine, Palo Alto, CA (H.N.D.J., E.A.A.)
- Stanford Center for Inherited Cardiovascular Disease, Stanford Medicine, CA (M.T.W., E.A.A., V.N.P.)
| | - Victoria N. Parikh
- Division of Cardiovascular Medicine (V.A.K., R.H.W., N.S.T., N.Y., H.N.D.J., S.S., Y.H., C.M.R., M.T.W., E.A.A., V.N.P.)
- Stanford Center for Inherited Cardiovascular Disease, Stanford Medicine, CA (M.T.W., E.A.A., V.N.P.)
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3
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Jensen TD, Ni B, Reuter CM, Gorzynski JE, Fazal S, Bonner D, Ungar RA, Goddard PC, Raja A, Ashley EA, Bernstein JA, Zuchner S, Greicius MD, Montgomery SB, Schatz MC, Wheeler MT, Battle A. Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease. medRxiv 2024:2024.03.22.24304565. [PMID: 38585781 PMCID: PMC10996727 DOI: 10.1101/2024.03.22.24304565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Rare structural variants (SVs) - insertions, deletions, and complex rearrangements - can cause Mendelian disease, yet they remain difficult to accurately detect and interpret. We sequenced and analyzed Oxford Nanopore long-read genomes of 68 individuals from the Undiagnosed Disease Network (UDN) with no previously identified diagnostic mutations from short-read sequencing. Using our optimized SV detection pipelines and 571 control long-read genomes, we detected 716 long-read rare (MAF < 0.01) SV alleles per genome on average, achieving a 2.4x increase from short-reads. To characterize the functional effects of rare SVs, we assessed their relationship with gene expression from blood or fibroblasts from the same individuals, and found that rare SVs overlapping enhancers were enriched (LOR = 0.46) near expression outliers. We also evaluated tandem repeat expansions (TREs) and found 14 rare TREs per genome; notably these TREs were also enriched near overexpression outliers. To prioritize candidate functional SVs, we developed Watershed-SV, a probabilistic model that integrates expression data with SV-specific genomic annotations, which significantly outperforms baseline models that don't incorporate expression data. Watershed-SV identified a median of eight high-confidence functional SVs per UDN genome. Notably, this included compound heterozygous deletions in FAM177A1 shared by two siblings, which were likely causal for a rare neurodevelopmental disorder. Our observations demonstrate the promise of integrating long-read sequencing with gene expression towards improving the prioritization of functional SVs and TREs in rare disease patients.
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4
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Wojcik MH, Reuter CM, Marwaha S, Mahmoud M, Duyzend MH, Barseghyan H, Yuan B, Boone PM, Groopman EE, Délot EC, Jain D, Sanchis-Juan A, Starita LM, Talkowski M, Montgomery SB, Bamshad MJ, Chong JX, Wheeler MT, Berger SI, O'Donnell-Luria A, Sedlazeck FJ, Miller DE. Beyond the exome: What's next in diagnostic testing for Mendelian conditions. Am J Hum Genet 2023; 110:1229-1248. [PMID: 37541186 PMCID: PMC10432150 DOI: 10.1016/j.ajhg.2023.06.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 08/06/2023] Open
Abstract
Despite advances in clinical genetic testing, including the introduction of exome sequencing (ES), more than 50% of individuals with a suspected Mendelian condition lack a precise molecular diagnosis. Clinical evaluation is increasingly undertaken by specialists outside of clinical genetics, often occurring in a tiered fashion and typically ending after ES. The current diagnostic rate reflects multiple factors, including technical limitations, incomplete understanding of variant pathogenicity, missing genotype-phenotype associations, complex gene-environment interactions, and reporting differences between clinical labs. Maintaining a clear understanding of the rapidly evolving landscape of diagnostic tests beyond ES, and their limitations, presents a challenge for non-genetics professionals. Newer tests, such as short-read genome or RNA sequencing, can be challenging to order, and emerging technologies, such as optical genome mapping and long-read DNA sequencing, are not available clinically. Furthermore, there is no clear guidance on the next best steps after inconclusive evaluation. Here, we review why a clinical genetic evaluation may be negative, discuss questions to be asked in this setting, and provide a framework for further investigation, including the advantages and disadvantages of new approaches that are nascent in the clinical sphere. We present a guide for the next best steps after inconclusive molecular testing based upon phenotype and prior evaluation, including when to consider referral to research consortia focused on elucidating the underlying cause of rare unsolved genetic disorders.
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Affiliation(s)
- Monica H Wojcik
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Chloe M Reuter
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shruti Marwaha
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Michael H Duyzend
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Hayk Barseghyan
- Center for Genetics Medicine Research, Children's National Research Institute, Children's National Hospital, Washington, DC 20010, USA; Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037, USA
| | - Bo Yuan
- Department of Molecular and Human Genetics and Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Philip M Boone
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Emily E Groopman
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Emmanuèle C Délot
- Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037, USA; Center for Genetics Medicine Research, Children's National Research and Innovation Campus, Washington, DC, USA; Department of Pediatrics, George Washington University, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037, USA
| | - Deepti Jain
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA 98195, USA
| | - Alba Sanchis-Juan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Lea M Starita
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Michael Talkowski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephen B Montgomery
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael J Bamshad
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jessica X Chong
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA; Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | - Matthew T Wheeler
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Seth I Berger
- Center for Genetics Medicine Research and Rare Disease Institute, Children's National Hospital, Washington, DC 20010, USA
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Department of Computer Science, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Danny E Miller
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA; Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA.
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5
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Srivastava S, Shaked HM, Gable K, Gupta SD, Pan X, Somashekarappa N, Han G, Mohassel P, Gotkine M, Doney E, Goldenberg P, Tan QKG, Gong Y, Kleinstiver B, Wishart B, Cope H, Pires CB, Stutzman H, Spillmann RC, Sadjadi R, Elpeleg O, Lee CH, Bellen HJ, Edvardson S, Eichler F, Dunn TM, Dai H, Dhar SU, Emrick LT, Goldman AM, Hanchard NA, Jamal F, Karaviti L, Lalani SR, Lee BH, Lewis RA, Marom R, Moretti PM, Murdock DR, Nicholas SK, Orengo JP, Posey JE, Potocki L, Rosenfeld JA, Samson SL, Scott DA, Tran AA, Vogel TP, Wangler MF, Yamamoto S, Eng CM, Liu P, Ward PA, Behrens E, Deardorff M, Falk M, Hassey K, Sullivan K, Vanderver A, Goldstein DB, Cope H, McConkie-Rosell A, Schoch K, Shashi V, Smith EC, Spillmann RC, Sullivan JA, Tan QKG, Walley NM, Agrawal PB, Beggs AH, Berry GT, Briere LC, Cobban LA, Coggins M, Cooper CM, Fieg EL, High F, Holm IA, Korrick S, Krier JB, Lincoln SA, Loscalzo J, Maas RL, MacRae CA, Pallais JC, Rao DA, Rodan LH, Silverman EK, Stoler JM, Sweetser DA, Walker M, Walsh CA, Esteves C, Kelley EG, Kohane IS, LeBlanc K, McCray AT, Nagy A, Dasari S, Lanpher BC, Lanza IR, Morava E, Oglesbee D, Bademci G, Barbouth D, Bivona S, Carrasquillo O, Chang TCP, Forghani I, Grajewski A, Isasi R, Lam B, Levitt R, Liu XZ, McCauley J, Sacco R, Saporta M, Schaechter J, Tekin M, Telischi F, Thorson W, Zuchner S, Colley HA, Dayal JG, Eckstein DJ, Findley LC, Krasnewich DM, Mamounas LA, Manolio TA, Mulvihill JJ, LaMoure GL, Goldrich MP, Urv TK, Doss AL, Acosta MT, Bonnenmann C, D’Souza P, Draper DD, Ferreira C, Godfrey RA, Groden CA, Macnamara EF, Maduro VV, Markello TC, Nath A, Novacic D, Pusey BN, Toro C, Wahl CE, Baker E, Burke EA, Adams DR, Gahl WA, Malicdan MCV, Tifft CJ, Wolfe LA, Yang J, Power B, Gochuico B, Huryn L, Latham L, Davis J, Mosbrook-Davis D, Rossignol F, Solomon B, MacDowall J, Thurm A, Zein W, Yousef M, Adam M, Amendola L, Bamshad M, Beck A, Bennett J, Berg-Rood B, Blue E, Boyd B, Byers P, Chanprasert S, Cunningham M, Dipple K, Doherty D, Earl D, Glass I, Golden-Grant K, Hahn S, Hing A, Hisama FM, Horike-Pyne M, Jarvik GP, Jarvik J, Jayadev S, Lam C, Maravilla K, Mefford H, Merritt JL, Mirzaa G, Nickerson D, Raskind W, Rosenwasser N, Scott CR, Sun A, Sybert V, Wallace S, Wener M, Wenger T, Ashley EA, Bejerano G, Bernstein JA, Bonner D, Coakley TR, Fernandez L, Fisher PG, Fresard L, Hom J, Huang Y, Kohler JN, Kravets E, Majcherska MM, Martin BA, Marwaha S, McCormack CE, Raja AN, Reuter CM, Ruzhnikov M, Sampson JB, Smith KS, Sutton S, Tabor HK, Tucker BM, Wheeler MT, Zastrow DB, Zhao C, Byrd WE, Crouse AB, Might M, Nakano-Okuno M, Whitlock J, Brown G, Butte MJ, Dell’Angelica EC, Dorrani N, Douine ED, Fogel BL, Gutierrez I, Huang A, Krakow D, Lee H, Loo SK, Mak BC, Martin MG, Martínez-Agosto JA, McGee E, Nelson SF, Nieves-Rodriguez S, Palmer CGS, Papp JC, Parker NH, Renteria G, Signer RH, Sinsheimer JS, Wan J, Wang LK, Perry KW, Woods JD, Alvey J, Andrews A, Bale J, Bohnsack J, Botto L, Carey J, Pace L, Longo N, Marth G, Moretti P, Quinlan A, Velinder M, Viskochi D, Bayrak-Toydemir P, Mao R, Westerfield M, Bican A, Brokamp E, Duncan L, Hamid R, Kennedy J, Kozuira M, Newman JH, PhillipsIII JA, Rives L, Robertson AK, Solem E, Cogan JD, Cole FS, Hayes N, Kiley D, Sisco K, Wambach J, Wegner D, Baldridge D, Pak S, Schedl T, Shin J, Solnica-Krezel L, Sadjadi R, Elpeleg O, Lee CH, Bellen HJ, Edvardson S, Eichler F, Dunn TM. SPTSSA variants alter sphingolipid synthesis and cause a complex hereditary spastic paraplegia. Brain 2023; 146:1420-1435. [PMID: 36718090 PMCID: PMC10319774 DOI: 10.1093/brain/awac460] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 11/03/2022] [Accepted: 11/19/2022] [Indexed: 02/01/2023] Open
Abstract
Sphingolipids are a diverse family of lipids with critical structural and signalling functions in the mammalian nervous system, where they are abundant in myelin membranes. Serine palmitoyltransferase, the enzyme that catalyses the rate-limiting reaction of sphingolipid synthesis, is composed of multiple subunits including an activating subunit, SPTSSA. Sphingolipids are both essential and cytotoxic and their synthesis must therefore be tightly regulated. Key to the homeostatic regulation are the ORMDL proteins that are bound to serine palmitoyltransferase and mediate feedback inhibition of enzymatic activity when sphingolipid levels become excessive. Exome sequencing identified potential disease-causing variants in SPTSSA in three children presenting with a complex form of hereditary spastic paraplegia. The effect of these variants on the catalytic activity and homeostatic regulation of serine palmitoyltransferase was investigated in human embryonic kidney cells, patient fibroblasts and Drosophila. Our results showed that two different pathogenic variants in SPTSSA caused a hereditary spastic paraplegia resulting in progressive motor disturbance with variable sensorineural hearing loss and language/cognitive dysfunction in three individuals. The variants in SPTSSA impaired the negative regulation of serine palmitoyltransferase by ORMDLs leading to excessive sphingolipid synthesis based on biochemical studies and in vivo studies in Drosophila. These findings support the pathogenicity of the SPTSSA variants and point to excessive sphingolipid synthesis due to impaired homeostatic regulation of serine palmitoyltransferase as responsible for defects in early brain development and function.
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Affiliation(s)
- Siddharth Srivastava
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, BostonChildren's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hagar Mor Shaked
- Department of Genetics, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Kenneth Gable
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Sita D Gupta
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Xueyang Pan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Niranjanakumari Somashekarappa
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Gongshe Han
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Payam Mohassel
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20814, USA
| | - Marc Gotkine
- Department of Genetics, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | | | - Paula Goldenberg
- Department of Pediatrics, Section on Medical Genetics, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Queenie K G Tan
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Yi Gong
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Benjamin Kleinstiver
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Brian Wishart
- Physical Medicine and Rehabilitation, Spaulding Rehabilitation Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Heidi Cope
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Claudia Brito Pires
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Hannah Stutzman
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Rebecca C Spillmann
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, NC 27710, USA
| | | | - Reza Sadjadi
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Orly Elpeleg
- Department of Genetics, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Chia-Hsueh Lee
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Simon Edvardson
- Pediatric Neurology Unit, Hadassah University Hospital, Mount Scopus, Jerusalem 91240, Israel
| | - Florian Eichler
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Teresa M Dunn
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Reza Sadjadi
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School , Boston, MA 02114 , USA
| | - Orly Elpeleg
- Department of Genetics, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem , Jerusalem 91120 , Israel
| | - Chia-Hsueh Lee
- Department of Structural Biology, St. Jude Children’s Research Hospital , Memphis, TN 38105 , USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine , Houston, TX 77030 , USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital , Houston, TX 77030 , USA
| | - Simon Edvardson
- Pediatric Neurology Unit, Hadassah University Hospital, Mount Scopus , Jerusalem 91240 , Israel
| | - Florian Eichler
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School , Boston, MA 02114 , USA
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School , Boston, MA 02114 , USA
| | - Teresa M Dunn
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences , Bethesda, MD 20814 , USA
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6
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Nguyen Dolphyn TT, Ormond KE, Weissman SM, Kim HJ, Reuter CM. Patient experiences with clinical confirmatory genetic testing after using direct-to-consumer raw DNA and third-party genetic interpretation services. Transl Behav Med 2023; 13:104-114. [PMID: 36327324 DOI: 10.1093/tbm/ibac083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The availability of raw DNA and genetic interpretation tools allow individuals to access genetic health risk information, where analytical false-positives exist. Little is known about the experience of individuals who receive pathogenic or likely pathogenic variant(s) through raw DNA interpretation and follow-up with clinical confirmatory genetic testing. This qualitative study set out to describe the experiences of individuals who pursued clinical confirmatory genetic testing, including their perception of the process. Participants were recruited from social media and eligible if they discovered a potential pathogenic or likely pathogenic variant in a raw DNA interpretation report, completed clinical confirmatory genetic testing in the U.S., and provided documentation of those results. Individuals participated in semi-structured interviews, which were transcribed and inductively coded to identify themes. Of the 12 participants, 3 received clinical genetic testing results that confirmed pathogenic or likely pathogenic variants noted in raw DNA interpretation reports (confirmation positive), and 9 were not confirmed. Nearly all (n = 11) participants described emotional distress and information-seeking behavior as a coping mechanism after discovering a pathogenic or likely pathogenic variant in raw DNA interpretation. When pursuing confirmatory genetic testing, many (n = 9) faced challenges with finding knowledgeable healthcare providers and obtaining insurance coverage. Despite reporting concerns over raw DNA interpretation and a desire for more safeguards, almost all (n = 10) participants stated interest in using the service again. Overall, participants' experiences reveal they find personal utility in raw DNA interpretation results and provide insight into opportunities for patient and provider education.
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Affiliation(s)
- Tiffany T Nguyen Dolphyn
- Department of Genetics, Stanford School of Medicine, Stanford University, Stanford, California, 94305USA.,Stanford Medicine Clinical Genomics Program, Stanford School of Medicine, Stanford University, Stanford, California, 94305, USA
| | - Kelly E Ormond
- Department of Genetics, Stanford School of Medicine, Stanford University, Stanford, California, 94305USA.,Department of Genetics and Stanford Center for Biomedical Ethics, Stanford School of Medicine, Stanford University, Stanford, California, 94305, USA.,Health Ethics and Policy Lab, Department of Health Science and Technology, ETH Zurich, 8092 Zurich, Switzerland
| | | | - Helen J Kim
- Department of Genetics, Stanford School of Medicine, Stanford University, Stanford, California, 94305USA
| | - Chloe M Reuter
- Stanford Center for Inherited Cardiovascular Disease, Stanford Health Care, Stanford, California, 94305, USA
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7
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Morimoto M, Bhambhani V, Gazzaz N, Davids M, Sathiyaseelan P, Macnamara EF, Lange J, Lehman A, Zerfas PM, Murphy JL, Acosta MT, Wang C, Alderman E, Reichert S, Thurm A, Adams DR, Introne WJ, Gorski SM, Boerkoel CF, Gahl WA, Tifft CJ, Malicdan MCV, Baldridge D, Bale J, Bamshad M, Barbouth D, Bayrak-Toydemir P, Beck A, Beggs AH, Behrens E, Bejerano G, Bellen HJ, Bennett J, Berg-Rood B, Bernstein JA, Berry GT, Bican A, Bivona S, Blue E, Bohnsack J, Bonner D, Botto L, Boyd B, Briere LC, Brokamp E, Brown G, Burke EA, Burrage LC, Butte MJ, Byers P, Byrd WE, Carey J, Carrasquillo O, Cassini T, Chang TCP, Chanprasert S, Chao HT, Clark GD, Coakley TR, Cobban LA, Cogan JD, Coggins M, Cole FS, Colley HA, Cooper CM, Cope H, Craigen WJ, Crouse AB, Cunningham M, D’Souza P, Dai H, Dasari S, Davis J, Dayal JG, Dell’Angelica EC, Dipple K, Doherty D, Dorrani N, Doss AL, Douine ED, Duncan L, Earl D, Eckstein DJ, Emrick LT, Eng CM, Esteves C, Falk M, Fieg EL, Fisher PG, Fogel BL, Forghani I, Glass I, Gochuico B, Goddard PC, Godfrey RA, Golden-Grant K, Grajewski A, Gutierrez I, Hadley D, Hahn S, Halley MC, Hamid R, Hassey K, Hayes N, High F, Hing A, Hisama FM, Holm IA, Hom J, Horike-Pyne M, Huang A, Hutchison S, Introne WJ, Isasi R, Izumi K, Jamal F, Jarvik GP, Jarvik J, Jayadev S, Jean-Marie O, Jobanputra V, Karaviti L, Kennedy J, Ketkar S, Kiley D, Kilich G, Kobren SN, Kohane IS, Kohler JN, Korrick S, Kozuira M, Krakow D, Krasnewich DM, Kravets E, Lalani SR, Lam B, Lam C, Lanpher BC, Lanza IR, LeBlanc K, Lee BH, Levitt R, Lewis RA, Liu P, Liu XZ, Longo N, Loo SK, Loscalzo J, Maas RL, MacRae CA, Maduro VV, Mahoney R, Mak BC, Mamounas LA, Manolio TA, Mao R, Maravilla K, Marom R, Marth G, Martin BA, Martin MG, Martínez-Agosto JA, Marwaha S, McCauley J, McConkie-Rosell A, McCray AT, McGee E, Mefford H, Merritt JL, Might M, Mirzaa G, Morava E, Moretti P, Nakano-Okuno M, Nelson SF, Newman JH, Nicholas SK, Nickerson D, Nieves-Rodriguez S, Novacic D, Oglesbee D, Orengo JP, Pace L, Pak S, Pallais JC, Palmer CGS, Papp JC, Parker NH, Phillips JA, Posey JE, Potocki L, Pusey Swerdzewski BN, Quinlan A, Rao DA, Raper A, Raskind W, Renteria G, Reuter CM, Rives L, Robertson AK, Rodan LH, Rosenfeld JA, Rosenwasser N, Rossignol F, Ruzhnikov M, Sacco R, Sampson JB, Saporta M, Schaechter J, Schedl T, Schoch K, Scott DA, Scott CR, Shashi V, Shin J, Silverman EK, Sinsheimer JS, Sisco K, Smith EC, Smith KS, Solem E, Solnica-Krezel L, Solomon B, Spillmann RC, Stoler JM, Sullivan K, Sullivan JA, Sun A, Sutton S, Sweetser DA, Sybert V, Tabor HK, Tan QKG, Tan ALM, Tekin M, Telischi F, Thorson W, Toro C, Tran AA, Ungar RA, Urv TK, Vanderver A, Velinder M, Viskochil D, Vogel TP, Wahl CE, Walker M, Wallace S, Walley NM, Wambach J, Wan J, Wang LK, Wangler MF, Ward PA, Wegner D, Weisz Hubshman M, Wener M, Wenger T, Wesseling Perry K, Westerfield M, Wheeler MT, Whitlock J, Wolfe LA, Worley K, Xiao C, Yamamoto S, Yang J, Zhang Z, Zuchner S, Reichert S, Thurm A, Adams DR, Introne WJ, Gorski SM, Boerkoel CF, Gahl WA, Tifft CJ, Malicdan MCV. Bi-allelic ATG4D variants are associated with a neurodevelopmental disorder characterized by speech and motor impairment. NPJ Genom Med 2023; 8:4. [PMID: 36765070 PMCID: PMC9918471 DOI: 10.1038/s41525-022-00343-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 12/06/2022] [Indexed: 02/12/2023] Open
Abstract
Autophagy regulates the degradation of damaged organelles and protein aggregates, and is critical for neuronal development, homeostasis, and maintenance, yet few neurodevelopmental disorders have been associated with pathogenic variants in genes encoding autophagy-related proteins. We report three individuals from two unrelated families with a neurodevelopmental disorder characterized by speech and motor impairment, and similar facial characteristics. Rare, conserved, bi-allelic variants were identified in ATG4D, encoding one of four ATG4 cysteine proteases important for autophagosome biogenesis, a hallmark of autophagy. Autophagosome biogenesis and induction of autophagy were intact in cells from affected individuals. However, studies evaluating the predominant substrate of ATG4D, GABARAPL1, demonstrated that three of the four ATG4D patient variants functionally impair ATG4D activity. GABARAPL1 is cleaved or "primed" by ATG4D and an in vitro GABARAPL1 priming assay revealed decreased priming activity for three of the four ATG4D variants. Furthermore, a rescue experiment performed in an ATG4 tetra knockout cell line, in which all four ATG4 isoforms were knocked out by gene editing, showed decreased GABARAPL1 priming activity for the two ATG4D missense variants located in the cysteine protease domain required for priming, suggesting that these variants impair the function of ATG4D. The clinical, bioinformatic, and functional data suggest that bi-allelic loss-of-function variants in ATG4D contribute to the pathogenesis of this syndromic neurodevelopmental disorder.
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Affiliation(s)
- Marie Morimoto
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Vikas Bhambhani
- grid.418506.e0000 0004 0629 5022Department of Medical Genetics, Children’s Hospitals and Clinics of Minnesota, Minneapolis, MN 55404 USA
| | - Nour Gazzaz
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada ,grid.414137.40000 0001 0684 7788Provincial Medical Genetics Program, British Columbia Women’s and Children’s Hospital, Vancouver, BC V6H 3N1 Canada ,grid.412125.10000 0001 0619 1117Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mariska Davids
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Paalini Sathiyaseelan
- grid.434706.20000 0004 0410 5424Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3 Canada ,grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Ellen F. Macnamara
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | | | - Anna Lehman
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada
| | - Patricia M. Zerfas
- grid.94365.3d0000 0001 2297 5165Diagnostic and Research Services Branch, Office of Research Services, National Institutes of Health, Bethesda, MD 20892 USA
| | - Jennifer L. Murphy
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Maria T. Acosta
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Camille Wang
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Emily Alderman
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada ,grid.414137.40000 0001 0684 7788Provincial Medical Genetics Program, British Columbia Women’s and Children’s Hospital, Vancouver, BC V6H 3N1 Canada
| | | | - Sara Reichert
- grid.418506.e0000 0004 0629 5022Department of Medical Genetics, Children’s Hospitals and Clinics of Minnesota, Minneapolis, MN 55404 USA
| | - Audrey Thurm
- grid.94365.3d0000 0001 2297 5165Neurodevelopmental and Behavioral Phenotyping Service, Office of the Clinical Director, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892 USA
| | - David R. Adams
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Wendy J. Introne
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Sharon M. Gorski
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada ,grid.434706.20000 0004 0410 5424Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3 Canada ,grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Cornelius F. Boerkoel
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada ,grid.414137.40000 0001 0684 7788Provincial Medical Genetics Program, British Columbia Women’s and Children’s Hospital, Vancouver, BC V6H 3N1 Canada
| | - William A. Gahl
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Cynthia J. Tifft
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - May Christine V. Malicdan
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
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8
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Floyd BJ, Weile J, Kannankeril PJ, Glazer AM, Reuter CM, MacRae CA, Ashley EA, Roden DM, Roth FP, Parikh VN. Proactive Variant Effect Mapping Aids Diagnosis in Pediatric Cardiac Arrest. Circ Genom Precis Med 2023; 16:e003792. [PMID: 36716194 PMCID: PMC9974880 DOI: 10.1161/circgen.122.003792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Brendan J. Floyd
- Division of Cardiology, Dept of Pediatrics, Stanford University Medical School, Stanford, CA
| | - Jochen Weile
- Lunenfeld-Tanenbaum Research Institute, Sinai Health
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Depts of Molecular Genetics & Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Prince J. Kannankeril
- Center for Pediatric Precision Medicine, Dept of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Andrew M. Glazer
- Division of Clinical Pharmacology, Dept of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Chloe M. Reuter
- Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, Stanford University, Stanford, CA
| | - Calum A. MacRae
- Dept of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Euan A. Ashley
- Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, Stanford University, Stanford, CA
- Dept of Genetics, Stanford University, Stanford, CA
| | - Dan M. Roden
- Division of Clinical Pharmacology, Dept of Medicine, Vanderbilt University Medical Center, Nashville, TN
- Division of Cardiovascular Medicine, Dept of Medicine, Vanderbilt University Medical Center, Nashville, TN
- Dept of Pharmacology, Vanderbilt University Medical Center, Nashville, TN
- Dept of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN
| | - Frederick P. Roth
- Lunenfeld-Tanenbaum Research Institute, Sinai Health
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Depts of Molecular Genetics & Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Victoria N. Parikh
- Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, Stanford University, Stanford, CA
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9
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Wojcik MH, Reuter CM, Marwaha S, Mahmoud M, Duyzend MH, Barseghyan H, Yuan B, Boone PM, Groopman EE, Délot EC, Jain D, Sanchis-Juan A, Starita LM, Talkowski M, Montgomery SB, Bamshad MJ, Chong JX, Wheeler MT, Berger SI, O’Donnell-Luria A, Sedlazeck FJ, Miller DE. Beyond the exome: what's next in diagnostic testing for Mendelian conditions. ArXiv 2023:arXiv:2301.07363v1. [PMID: 36713248 PMCID: PMC9882576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Despite advances in clinical genetic testing, including the introduction of exome sequencing (ES), more than 50% of individuals with a suspected Mendelian condition lack a precise molecular diagnosis. Clinical evaluation is increasingly undertaken by specialists outside of clinical genetics, often occurring in a tiered fashion and typically ending after ES. The current diagnostic rate reflects multiple factors, including technical limitations, incomplete understanding of variant pathogenicity, missing genotype-phenotype associations, complex gene-environment interactions, and reporting differences between clinical labs. Maintaining a clear understanding of the rapidly evolving landscape of diagnostic tests beyond ES, and their limitations, presents a challenge for non-genetics professionals. Newer tests, such as short-read genome or RNA sequencing, can be challenging to order and emerging technologies, such as optical genome mapping and long-read DNA or RNA sequencing, are not available clinically. Furthermore, there is no clear guidance on the next best steps after inconclusive evaluation. Here, we review why a clinical genetic evaluation may be negative, discuss questions to be asked in this setting, and provide a framework for further investigation, including the advantages and disadvantages of new approaches that are nascent in the clinical sphere. We present a guide for the next best steps after inconclusive molecular testing based upon phenotype and prior evaluation, including when to consider referral to a consortium such as GREGoR, which is focused on elucidating the underlying cause of rare unsolved genetic disorders.
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Affiliation(s)
- Monica H. Wojcik
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115 USA
- Division of Newborn Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Chloe M. Reuter
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Shruti Marwaha
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston TX 77030 USA
| | - Michael H. Duyzend
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115 USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114 USA
| | - Hayk Barseghyan
- Center for Genetics Medicine Research, Children’s National Research Institute, Children’s National Hospital, Washington, DC 20010 USA
- Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037 USA
| | - Bo Yuan
- Department of Molecular and Human Genetics and Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston TX 77030 USA
| | - Philip M. Boone
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115 USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114 USA
| | - Emily E. Groopman
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115 USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114 USA
| | - Emmanuèle C. Délot
- Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037 USA
- Center for Genetics Medicine Research, Children’s National Research and Innovation Campus, Washington, DC, USA
- Department of Pediatrics, George Washington University, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037 USA
| | - Deepti Jain
- Department of Biostatistics, School of Public Health, University of Washington, Seattle WA 98195 USA
| | - Alba Sanchis-Juan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114 USA
| | | | - Lea M. Starita
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195 USA
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195 USA
| | - Michael Talkowski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114 USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Stephen B. Montgomery
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305 USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Michael J. Bamshad
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195 USA
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195 USA
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195 USA
| | - Jessica X. Chong
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195 USA
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195 USA
| | - Matthew T. Wheeler
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Seth I. Berger
- Center for Genetics Medicine Research and Rare Disease Institute, Children’s National Hospital, Washington, DC 20010 USA
| | - Anne O’Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115 USA
- Center for Genomic Medicine, Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114 USA
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston TX 77030 USA
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX, 77005 USA
| | - Danny E. Miller
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195 USA
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195 USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195 USA
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10
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Miller IM, Yashar BM, Macnamara EF, Adams DR, Agrawal PB, Alvey J, Amendola L, Andrews A, Ashley EA, Azamian MS, Bacino CA, Bademci G, Baker E, Balasubramanyam A, Baldridge D, Bale J, Bamshad M, Barbouth D, Bayrak-Toydemir P, Beck A, Beggs AH, Behrens E, Bejerano G, Bellen HJ, Bennett J, Berg-Rood B, Bernstein JA, Berry GT, Bican A, Bivona S, Blue E, Bohnsack J, Bonnenmann C, Bonner D, Botto L, Boyd B, Briere LC, Brokamp E, Brown G, Burke EA, Burrage LC, Butte MJ, Byers P, Byrd WE, Carey J, Carrasquillo O, Chang TCP, Chanprasert S, Chao HT, Clark GD, Coakley TR, Cobban LA, Cogan JD, Coggins M, Cole FS, Colley HA, Cooper CM, Cope H, Craigen WJ, Crouse AB, Cunningham M, D’Souza P, Dai H, Dasari S, Davis J, Dayal JG, Dell’Angelica EC, Dipple K, Doherty D, Dorrani N, Doss AL, Douine ED, Draper DD, Duncan L, Earl D, Eckstein DJ, Emrick LT, Eng CM, Esteves C, Falk M, Fernandez L, Ferreira C, Fieg EL, Findley LC, Fisher PG, Fogel BL, Forghani I, Gahl WA, Glass I, Gochuico B, Godfrey RA, Golden-Grant K, Goldrich MP, Goldstein DB, Grajewski A, Groden CA, Gutierrez I, Hahn S, Hamid R, Hassey K, Hayes N, High F, Hing A, Hisama FM, Holm IA, Hom J, Horike-Pyne M, Huang Y, Huang A, Huryn L, Isasi R, Izumi K, Jamal F, Jarvik GP, Jarvik J, Jayadev S, Karaviti L, Kennedy J, Ketkar S, Kiley D, Kilich G, Kobren SN, Kohane IS, Kohler JN, Korrick S, Kozuira M, Krakow D, Krasnewich DM, Kravets E, Krier JB, Lalani SR, Lam B, Lam C, LaMoure GL, Lanpher BC, Lanza IR, Latham L, LeBlanc K, Lee BH, Lee H, Levitt R, Lewis RA, Lincoln SA, Liu P, Liu XZ, Longo N, Loo SK, Loscalzo J, Maas RL, MacDowall J, Macnamara EF, MacRae CA, Maduro VV, Mahoney R, Mak BC, Malicdan MCV, Mamounas LA, Manolio TA, Mao R, Maravilla K, Markello TC, Marom R, Marth G, Martin BA, Martin MG, Martfnez-Agosto JA, Marwaha S, McCauley J, McConkie-Rosell A, McCray AT, McGee E, Mefford H, Merritt JL, Might M, Mirzaa G, Morava E, Moretti PM, Moretti P, Mosbrook-Davis D, Mulvihill JJ, Nakano-Okuno M, Nath A, Nelson SF, Newman JH, Nicholas SK, Nickerson D, Nieves-Rodriguez S, Novacic D, Oglesbee D, Orengo JP, Pace L, Pak S, Pallais JC, Palmer CGS, Papp JC, Parker NH, Phillips JA, Posey JE, Potocki L, Power B, Pusey BN, Quinlan A, Raja AN, Rao DA, Raper A, Raskind W, Renteria G, Reuter CM, Rives L, Robertson AK, Rodan LH, Rosenfeld JA, Rosenwasser N, Rossignol F, Ruzhnikov M, Sacco R, Sampson JB, Saporta M, Schaechter J, Schedl T, Schoch K, Scott DA, Scott CR, Shashi V, Shin J, Signer RH, Silverman EK, Sinsheimer JS, Sisco K, Smith EC, Smith KS, Solem E, Solnica-Krezel L, Solomon B, Spillmann RC, Stoler JM, Sullivan K, Sullivan JA, Sun A, Sutton S, Sweetser DA, Sybert V, Tabor HK, Tan QKG, Tan ALM, Tekin M, Telischi F, Thorson W, Thurm A, Tifft CJ, Toro C, Tran AA, Tucker BM, Urv TK, Vanderver A, Velinder M, Viskochil D, Vogel TP, Wahl CE, Walker M, Wallace S, Walley NM, Walsh CA, Wambach J, Wan J, Wang LK, Wangler MF, Ward PA, Wegner D, Hubshman MW, Wener M, Wenger T, Perry KW, Westerfield M, Wheeler MT, Whitlock J, Wolfe LA, Woods JD, Worley K, Yamamoto S, Yang J, Yousef M, Zastrow DB, Zein W, Zhang Z, Zhao C, Zuchner S, Macnamara EF. Continuing a search for a diagnosis: the impact of adolescence and family dynamics. Orphanet J Rare Dis 2023; 18:6. [PMID: 36624503 PMCID: PMC9830697 DOI: 10.1186/s13023-022-02598-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 12/14/2022] [Indexed: 01/11/2023] Open
Abstract
The "diagnostic odyssey" describes the process those with undiagnosed conditions undergo to identify a diagnosis. Throughout this process, families of children with undiagnosed conditions have multiple opportunities to decide whether to continue or stop their search for a diagnosis and accept the lack of a diagnostic label. Previous studies identified factors motivating a family to begin searching, but there is limited information about the decision-making process in a prolonged search and how the affected child impacts a family's decision. This study aimed to understand how families of children with undiagnosed diseases decide whether to continue to pursue a diagnosis after standard clinical testing has failed. Parents who applied to the Undiagnosed Disease Network (UDN) at the National Institutes of Health (NIH) were recruited to participate in semi-structured interviews. The 2015 Supportive Care Needs model by Pelenstov, which defines critical needs in families with rare/undiagnosed diseases, provided a framework for interview guide development and transcript analysis (Pelentsov et al in Disabil Health J 8(4):475-491, 2015. https://doi.org/10.1016/J.DHJO.2015.03.009 ). A deductive, iterative coding approach was used to identify common unifying themes. Fourteen parents from 13 families were interviewed. The average child's age was 11 years (range 3-18) and an average 63% of their life had been spent searching for a diagnosis. Our analysis found that alignment or misalignment of parent and child needs impact the trajectory of the diagnostic search. When needs and desires align, reevaluation of a decision to pursue a diagnosis is limited. However, when there is conflict between parent and child desires, there is reevaluation, and often a pause, in the search. This tension is exacerbated when children are adolescents and attempting to balance their dependence on parents for medical care with a natural desire for independence. Our results provide novel insights into the roles of adolescents in the diagnostic odyssey. The tension between desired and realistic developmental outcomes for parents and adolescents impacts if, and how, the search for a diagnosis progresses.
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Affiliation(s)
- Ilana M. Miller
- grid.239560.b0000 0004 0482 1586Children’s National Medical Center, Rare Disease Institute, 7125 13th Place NW, DC 20012 Washington, USA ,grid.214458.e0000000086837370Department of Human Genetics, University of Michigan, 4909 Buhl Building, Catherine St, Ann Arbor, MI 48109 USA
| | - Beverly M. Yashar
- grid.214458.e0000000086837370Department of Human Genetics, University of Michigan, 4909 Buhl Building, Catherine St, Ann Arbor, MI 48109 USA
| | | | - Ellen F. Macnamara
- grid.453125.40000 0004 0533 8641National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD USA
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11
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Deuitch N, Beckman E, Halley MC, Young JL, Reuter CM, Kohler J, Bernstein JA, Wheeler MT, Ormond KE, Tabor HK. "Doctors can read about it, they can know about it, but they've never lived with it": How parents use social media throughout the diagnostic odyssey. J Genet Couns 2021; 30:1707-1718. [PMID: 34096130 PMCID: PMC8777467 DOI: 10.1002/jgc4.1438] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 04/24/2021] [Accepted: 05/01/2021] [Indexed: 11/08/2022]
Abstract
Parents of children with undiagnosed conditions struggle to obtain information about how to treat and support their children. It can be particularly challenging to find communities and other parents who share their experiences and can provide emotional and informational support. This study sought to characterize how parents use social media, both throughout the diagnostic odyssey and post-diagnosis, to meet their informational, social, and emotional support needs. We conducted qualitative semi-structured interviews with 14 parents from the Stanford site of the Undiagnosed Diseases Network (UDN), including five whose children had received a diagnosis through study participation. Interview recordings were analyzed using inductive, team-based coding and thematic analysis based in grounded theory using Dedoose qualitative analysis software. Through this process, we identified four key themes related to social media use. First, parents struggled to find the "right" community, often seeking out groups of similar patients based on symptoms or similar conditions. Second, though they found much valuable information through social media about caring for their child, they also struggled to interpret the relevance of the information to their own child's condition. Third, the social support and access to other patients' and families' lived experiences were described as both highly valued and emotionally challenging, particularly in the case of poor outcomes for similar families. Finally, parents expressed the need to balance concerns about their child's privacy with the value of transparency and data sharing for diagnosis. Our results suggest that the needs and experiences of undiagnosed patients and families differ from those with diagnosed diseases and highlight the need for support in best utilizing social media resources at different stages of the diagnostic odyssey.
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Affiliation(s)
- Natalie Deuitch
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Erika Beckman
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Meghan C. Halley
- Stanford Center for Biomedical Ethics, Stanford University School of Medicine, Stanford, CA
| | - Jennifer L. Young
- Stanford Center for Biomedical Ethics, Stanford University School of Medicine, Stanford, CA
| | - Chloe M. Reuter
- Stanford Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA
| | - Jennefer Kohler
- Stanford Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA
| | - Jonathan A. Bernstein
- Stanford Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pediatrics, Stanford, University School of Medicine, Stanford, CA
| | - Matthew T. Wheeler
- Department of Pediatrics, Stanford, University School of Medicine, Stanford, CA
- Division of Cardiovascular Medicine, Department of Medicine Stanford University School of Medicine, Stanford, CA
| | | | - Kelly E. Ormond
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- These authors contributed equally to this work
| | - Holly K. Tabor
- Stanford Center for Biomedical Ethics, Stanford University School of Medicine, Stanford, CA
- Stanford Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA
- These authors contributed equally to this work
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12
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Dries AM, Kirillova A, Reuter CM, Garcia J, Zouk H, Hawley M, Murray B, Tichnell C, Pilichou K, Protonotarios A, Medeiros-Domingo A, Kelly MA, Baras A, Ingles J, Semsarian C, Bauce B, Celeghin R, Basso C, Jongbloed JDH, Nussbaum RL, Funke B, Cerrone M, Mestroni L, Taylor MRG, Sinagra G, Merlo M, Saguner AM, Elliott PM, Syrris P, van Tintelen JP, James CA, Haggerty CM, Parikh VN. Correction to: The genetic architecture of Plakophilin 2 cardiomyopathy. Genet Med 2021; 23:2014. [PMID: 34408292 PMCID: PMC8486651 DOI: 10.1038/s41436-021-01298-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Annika M Dries
- Stanford Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Anna Kirillova
- Stanford Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Chloe M Reuter
- Stanford Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Hana Zouk
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA, USA.,Dept. Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Megan Hawley
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA, USA.,Dept. Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Brittney Murray
- Division of Cardiology, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Crystal Tichnell
- Division of Cardiology, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Kalliopi Pilichou
- Dept. of Cardiac-Thoracic-Vascular Sciences and Public Health, University of Padua, Padua, Italy
| | - Alexandros Protonotarios
- Centre for Heart Muscle Disease, Institute of Cardiovascular Science, University College London, London, UK
| | | | | | - Aris Baras
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Jodie Ingles
- Cardio Genomics Program at Centenary Institute, The University of Sydney, Sydney, Australia
| | - Christopher Semsarian
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, University of Sydney, Sydney, Australia
| | - Barbara Bauce
- Dept. of Cardiac-Thoracic-Vascular Sciences and Public Health, University of Padua, Padua, Italy
| | - Rudy Celeghin
- Dept. of Cardiac-Thoracic-Vascular Sciences and Public Health, University of Padua, Padua, Italy
| | - Cristina Basso
- Dept. of Cardiac-Thoracic-Vascular Sciences and Public Health, University of Padua, Padua, Italy
| | - Jan D H Jongbloed
- University of Groningen Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Birgit Funke
- Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, Cambridge, MA, USA.,Dept. Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Marina Cerrone
- Leon H. Charney Division of Cardiology, NYU School of Medicine, New York, NY, US
| | - Luisa Mestroni
- University of Colorado Anschutz Medical Campus, Aurora, CO, US
| | | | - Gianfranco Sinagra
- Cardiovascular Department, Azienda Sanitaria-Universitaria Giuliano Isontina (ASUGI), Trieste, Italy
| | - Marco Merlo
- Cardiovascular Department, Azienda Sanitaria-Universitaria Giuliano Isontina (ASUGI), Trieste, Italy
| | - Ardan M Saguner
- Department of Cardiology, University Heart Center, University Hospital, Zurich, Switzerland
| | - Perry M Elliott
- Centre for Heart Muscle Disease, Institute of Cardiovascular Science, University College London, London, UK
| | - Petros Syrris
- Centre for Heart Muscle Disease, Institute of Cardiovascular Science, University College London, London, UK
| | - J Peter van Tintelen
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands.,Netherlands Heart Institute, Utrecht, the Netherlands
| | | | - Cynthia A James
- Division of Cardiology, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | | | - Victoria N Parikh
- Stanford Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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13
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Mao D, Reuter CM, Ruzhnikov MR, Beck AE, Farrow EG, Emrick LT, Rosenfeld JA, Mackenzie KM, Robak L, Wheeler MT, Burrage LC, Jain M, Liu P, Calame D, Küry S, Sillesen M, Schmitz-Abe K, Tonduti D, Spaccini L, Iascone M, Genetti CA, Koenig MK, Graf M, Tran A, Alejandro M, Lee BH, Thiffault I, Agrawal PB, Bernstein JA, Bellen HJ, Chao HT, Acosta MT, Adam M, Adams DR, Agrawal PB, Alejandro ME, Allard P, Alvey J, Amendola L, Andrews A, Ashley EA, Azamian MS, Bacino CA, Bademci G, Baker E, Balasubramanyam A, Baldridge D, Bale J, Bamshad M, Barbouth D, Batzli GF, Bayrak-Toydemir P, Beck A, Beggs AH, Bejerano G, Bellen HJ, Bennet J, Berg-Rood B, Bernier R, Bernstein JA, Berry GT, Bican A, Bivona S, Blue E, Bohnsack J, Bonnenmann C, Bonner D, Botto L, Briere LC, Brokamp E, Burke EA, Burrage LC, Butte MJ, Byers P, Carey J, Carrasquillo O, Chang TCP, Chanprasert S, Chao HT, Clark GD, Coakley TR, Cobban LA, Cogan JD, Cole FS, Colley HA, Cooper CM, Cope H, Craigen WJ, Cunningham M, D’Souza P, Dai H, Dasari S, Davids M, Dayal JG, Dell’Angelica EC, Dhar SU, Dipple K, Doherty D, Dorrani N, Douine ED, Draper DD, Duncan L, Earl D, Eckstein DJ, Emrick LT, Eng CM, Esteves C, Estwick T, Fernandez L, Ferreira C, Fieg EL, Fisher PG, Fogel BL, Forghani I, Fresard L, Gahl WA, Glass I, Godfrey RA, Golden-Grant K, Goldman AM, Goldstein DB, Grajewski A, Groden CA, Gropman AL, Hahn S, Hamid R, Hanchard NA, Hayes N, High F, Hing A, Hisama FM, Holm IA, Hom J, Horike-Pyne M, Huang A, Huang Y, Isasi R, Jamal F, Jarvik GP, Jarvik J, Jayadev S, Jiang YH, Johnston JM, Karaviti L, Kelley EG, Kiley D, Kohane IS, Kohler JN, Krakow D, Krasnewich DM, Korrick S, Koziura M, Krier JB, Lalani SR, Lam B, Lam C, Lanpher BC, Lanza IR, Lau CC, LeBlanc K, Lee BH, Lee H, Levitt R, Lewis RA, Lincoln SA, Liu P, Liu XZ, Longo N, Loo SK, Loscalzo J, Maas RL, Macnamara EF, MacRae CA, Maduro VV, Majcherska MM, Malicdan MCV, Mamounas LA, Manolio TA, Mao R, Maravilla K, Markello TC, Marom R, Marth G, Martin BA, Martin MG, Martínez-Agosto JA, Marwaha S, McCauley J, McConkie-Rosell A, McCormack CE, McCray AT, Mefford H, Merritt JL, Might M, Mirzaa G, Morava-Kozicz E, Moretti PM, Morimoto M, Mulvihill JJ, Murdock DR, Nath A, Nelson SF, Newman JH, Nicholas SK, Nickerson D, Novacic D, Oglesbee D, Orengo JP, Pace L, Pak S, Pallais JC, Palmer CG, Papp JC, Parker NH, Phillips JA, Posey JE, Postlethwait JH, Potocki L, Pusey BN, Quinlan A, Raskind W, Raja AN, Renteria G, Reuter CM, Rives L, Robertson AK, Rodan LH, Rosenfeld JA, Rowley RK, Ruzhnikov M, Sacco R, Sampson JB, Samson SL, Saporta M, Scott CR, Schaechter J, Schedl T, Schoch K, Scott DA, Shakachite L, Sharma P, Shashi V, Shin J, Signer R, Sillari CH, Silverman EK, Sinsheimer JS, Sisco K, Smith KS, Solnica-Krezel L, Spillmann RC, Stoler JM, Stong N, Sullivan JA, Sun A, Sutton S, Sweetser DA, Sybert V, Tabor HK, Tamburro CP, Tan QKG, Tekin M, Telischi F, Thorson W, Tifft CJ, Toro C, Tran AA, Urv TK, Velinder M, Viskochil D, Vogel TP, Wahl CE, Wallace S, Walley NM, Walsh CA, Walker M, Wambach J, Wan J, Wang LK, Wangler MF, Ward PA, Wegner D, Wener M, Westerfield M, Wheeler MT, Wise AL, Wolfe LA, Woods JD, Yamamoto S, Yang J, Yoon AJ, Yu G, Zastrow DB, Zhao C, Zuchner S. De novo EIF2AK1 and EIF2AK2 Variants Are Associated with Developmental Delay, Leukoencephalopathy, and Neurologic Decompensation. Am J Hum Genet 2020; 106:570-583. [PMID: 32197074 PMCID: PMC7118694 DOI: 10.1016/j.ajhg.2020.02.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 02/28/2020] [Indexed: 02/03/2023] Open
Abstract
EIF2AK1 and EIF2AK2 encode members of the eukaryotic translation initiation factor 2 alpha kinase (EIF2AK) family that inhibits protein synthesis in response to physiologic stress conditions. EIF2AK2 is also involved in innate immune response and the regulation of signal transduction, apoptosis, cell proliferation, and differentiation. Despite these findings, human disorders associated with deleterious variants in EIF2AK1 and EIF2AK2 have not been reported. Here, we describe the identification of nine unrelated individuals with heterozygous de novo missense variants in EIF2AK1 (1/9) or EIF2AK2 (8/9). Features seen in these nine individuals include white matter alterations (9/9), developmental delay (9/9), impaired language (9/9), cognitive impairment (8/9), ataxia (6/9), dysarthria in probands with verbal ability (6/9), hypotonia (7/9), hypertonia (6/9), and involuntary movements (3/9). Individuals with EIF2AK2 variants also exhibit neurological regression in the setting of febrile illness or infection. We use mammalian cell lines and proband-derived fibroblasts to further confirm the pathogenicity of variants in these genes and found reduced kinase activity. EIF2AKs phosphorylate eukaryotic translation initiation factor 2 subunit 1 (EIF2S1, also known as EIF2α), which then inhibits EIF2B activity. Deleterious variants in genes encoding EIF2B proteins cause childhood ataxia with central nervous system hypomyelination/vanishing white matter (CACH/VWM), a leukodystrophy characterized by neurologic regression in the setting of febrile illness and other stressors. Our findings indicate that EIF2AK2 missense variants cause a neurodevelopmental syndrome that may share phenotypic and pathogenic mechanisms with CACH/VWM.
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14
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Reuter CM, Kohler JN, Bonner D, Zastrow D, Fernandez L, Dries A, Marwaha S, Davidson J, Brokamp E, Herzog M, Hong J, Macnamara E, Rosenfeld JA, Schoch K, Spillmann R, Loscalzo J, Krier J, Stoler J, Sweetser D, Palmer CGS, Phillips JA, Shashi V, Adams DA, Yang Y, Ashley EA, Fisher PG, Mulvihill JJ, Bernstein JA, Wheeler MT. Yield of whole exome sequencing in undiagnosed patients facing insurance coverage barriers to genetic testing. J Genet Couns 2019; 28:1107-1118. [PMID: 31478310 DOI: 10.1002/jgc4.1161] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 07/12/2019] [Accepted: 07/27/2019] [Indexed: 01/02/2023]
Abstract
BACKGROUND Despite growing evidence of diagnostic yield and clinical utility of whole exome sequencing (WES) in patients with undiagnosed diseases, there remain significant cost and reimbursement barriers limiting access to such testing. The diagnostic yield and resulting clinical actions of WES for patients who previously faced insurance coverage barriers have not yet been explored. METHODS We performed a retrospective descriptive analysis of clinical WES outcomes for patients facing insurance coverage barriers prior to clinical WES and who subsequently enrolled in the Undiagnosed Diseases Network (UDN). Clinical WES was completed as a result of participation in the UDN. Payer type, molecular diagnostic yield, and resulting clinical actions were evaluated. RESULTS Sixty-six patients in the UDN faced insurance coverage barriers to WES at the time of enrollment (67% public payer, 26% private payer). Forty-two of 66 (64%) received insurance denial for clinician-ordered WES, 19/66 (29%) had health insurance through a payer known not to cover WES, and 5/66 (8%) had previous payer denial of other genetic tests. Clinical WES results yielded a molecular diagnosis in 23 of 66 patients (35% [78% pediatric, 65% neurologic indication]). Molecular diagnosis resulted in clinical actions in 14 of 23 patients (61%). CONCLUSIONS These data demonstrate that a substantial proportion of patients who encountered insurance coverage barriers to WES had a clinically actionable molecular diagnosis, supporting the notion that WES has value as a covered benefit for patients who remain undiagnosed despite objective clinical findings.
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Affiliation(s)
- Chloe M Reuter
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA.,Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
| | - Jennefer N Kohler
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA.,Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
| | - Devon Bonner
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA.,Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
| | - Diane Zastrow
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA.,Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
| | - Liliana Fernandez
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA.,Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
| | - Annika Dries
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA.,Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
| | - Shruti Marwaha
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA.,Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
| | - Jean Davidson
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA.,Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
| | - Elly Brokamp
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Matthew Herzog
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA
| | - Joyce Hong
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | - Ellen Macnamara
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Kelly Schoch
- Department of Pediatrics, Duke University Medical Center, Durham, NC
| | - Rebecca Spillmann
- Department of Pediatrics, Duke University Medical Center, Durham, NC
| | | | - Joseph Loscalzo
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | - Joel Krier
- Department of Medicine, Brigham and Women's Hospital, Boston, MA
| | - Joan Stoler
- Division of Genetics, Boston Children's Hospital, Boston, MA
| | - David Sweetser
- Division of Medical Genetics and Metabolism, Department of Pediatrics, Massachusetts General Hospital, Boston, MA
| | - Christina G S Palmer
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA.,Psychiatry & Biobehavioral Sciences, University of California Los Angeles, Los Angeles, CA.,Institute for Society & Genetics, University of California Los Angeles, Los Angeles, CA
| | - John A Phillips
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN
| | - Vandana Shashi
- Department of Pediatrics, Duke University Medical Center, Durham, NC
| | - David A Adams
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Euan A Ashley
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA.,Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Paul G Fisher
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA.,Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA.,Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - John J Mulvihill
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD
| | - Jonathan A Bernstein
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA.,Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Matthew T Wheeler
- Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA.,Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA
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15
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Nguyen CT, Reuter CM, Hudson T, Li J. Evaluation of surgical site infection antibiotic prophylaxis among patients receiving antibiotics for active infection. J Hosp Infect 2019; 103:354-355. [PMID: 31185251 DOI: 10.1016/j.jhin.2019.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 06/03/2019] [Indexed: 11/16/2022]
Affiliation(s)
- C T Nguyen
- Department of Pharmacy, University of Chicago Medicine, Chicago, IL, USA.
| | - C M Reuter
- Department of Specialty Pharmacy, Ochsner Health System, New Orleans, LA, USA
| | - T Hudson
- Department of Pharmacy, FirstHealth of the Carolinas, Troy, NC, USA
| | - J Li
- Department of Pharmacy, Southeast Louisiana Veteran Health Care System, New Orleans, LA, USA
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16
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Frésard L, Smail C, Ferraro NM, Teran NA, Li X, Smith KS, Bonner D, Kernohan KD, Marwaha S, Zappala Z, Balliu B, Davis JR, Liu B, Prybol CJ, Kohler JN, Zastrow DB, Reuter CM, Fisk DG, Grove ME, Davidson JM, Hartley T, Joshi R, Strober BJ, Utiramerur S, Lind L, Ingelsson E, Battle A, Bejerano G, Bernstein JA, Ashley EA, Boycott KM, Merker JD, Wheeler MT, Montgomery SB. Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts. Nat Med 2019; 25:911-919. [PMID: 31160820 PMCID: PMC6634302 DOI: 10.1038/s41591-019-0457-8] [Citation(s) in RCA: 174] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 04/15/2019] [Indexed: 02/08/2023]
Abstract
It is estimated that 350 million individuals worldwide suffer from rare diseases, which are predominantly caused by mutation in a single gene1. The current molecular diagnostic rate is estimated at 50%, with whole-exome sequencing (WES) among the most successful approaches2-5. For patients in whom WES is uninformative, RNA sequencing (RNA-seq) has shown diagnostic utility in specific tissues and diseases6-8. This includes muscle biopsies from patients with undiagnosed rare muscle disorders6,9, and cultured fibroblasts from patients with mitochondrial disorders7. However, for many individuals, biopsies are not performed for clinical care, and tissues are difficult to access. We sought to assess the utility of RNA-seq from blood as a diagnostic tool for rare diseases of different pathophysiologies. We generated whole-blood RNA-seq from 94 individuals with undiagnosed rare diseases spanning 16 diverse disease categories. We developed a robust approach to compare data from these individuals with large sets of RNA-seq data for controls (n = 1,594 unrelated controls and n = 49 family members) and demonstrated the impacts of expression, splicing, gene and variant filtering strategies on disease gene identification. Across our cohort, we observed that RNA-seq yields a 7.5% diagnostic rate, and an additional 16.7% with improved candidate gene resolution.
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Affiliation(s)
- Laure Frésard
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA.
| | - Craig Smail
- Biomedical Informatics Program, Stanford University, Stanford, CA, USA
| | - Nicole M Ferraro
- Biomedical Informatics Program, Stanford University, Stanford, CA, USA
| | - Nicole A Teran
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Xin Li
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Kevin S Smith
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Devon Bonner
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
| | - Kristin D Kernohan
- Newborn Screening Ontario (NSO), Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Shruti Marwaha
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
- Stanford Cardiovascular Institute, School of Medicine, Stanford University, Stanford, CA, USA
| | - Zachary Zappala
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Brunilda Balliu
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Joe R Davis
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Boxiang Liu
- Department of Biology, School of Humanities and Sciences, Stanford University, Stanford, CA, USA
| | - Cameron J Prybol
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Jennefer N Kohler
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
| | - Diane B Zastrow
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
| | - Chloe M Reuter
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
| | - Dianna G Fisk
- Stanford Medicine Clinical Genomics Program, School of Medicine, Stanford University, Stanford, CA, USA
| | - Megan E Grove
- Stanford Medicine Clinical Genomics Program, School of Medicine, Stanford University, Stanford, CA, USA
| | - Jean M Davidson
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Ruchi Joshi
- Stanford Medicine Clinical Genomics Program, School of Medicine, Stanford University, Stanford, CA, USA
| | - Benjamin J Strober
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Sowmithri Utiramerur
- Stanford Medicine Clinical Genomics Program, School of Medicine, Stanford University, Stanford, CA, USA
| | - Lars Lind
- Department of Medical Sciences, Cardiovascular Epidemiology, Uppsala University, Uppsala, Sweden
| | - Erik Ingelsson
- Stanford Cardiovascular Institute, School of Medicine, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, School of Medicine, Stanford University, Stanford, CA, USA
| | - Alexis Battle
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Gill Bejerano
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, School of Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, CA, USA
| | - Jonathan A Bernstein
- Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Euan A Ashley
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, School of Medicine, Stanford University, Stanford, CA, USA
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Jason D Merker
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
- Stanford Medicine Clinical Genomics Program, School of Medicine, Stanford University, Stanford, CA, USA
- Departments of Pathology and Laboratory Medicine & Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina School Medicine, Chapel Hill, NC, USA
| | - Matthew T Wheeler
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
- Stanford Cardiovascular Institute, School of Medicine, Stanford University, Stanford, CA, USA
| | - Stephen B Montgomery
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA.
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA.
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17
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Zastrow DB, Kohler JN, Bonner D, Reuter CM, Fernandez L, Grove ME, Fisk DG, Yang Y, Eng CM, Ward PA, Bick D, Worthey EA, Fisher PG, Ashley EA, Bernstein JA, Wheeler MT. A toolkit for genetics providers in follow-up of patients with non-diagnostic exome sequencing. J Genet Couns 2019; 28:213-228. [PMID: 30964584 PMCID: PMC7385984 DOI: 10.1002/jgc4.1119] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 03/01/2019] [Accepted: 03/04/2019] [Indexed: 12/11/2022]
Abstract
There are approximately 7,000 rare diseases affecting 25-30 million Americans, with 80% estimated to have a genetic basis. This presents a challenge for genetics practitioners to determine appropriate testing, make accurate diagnoses, and conduct up-to-date patient management. Exome sequencing (ES) is a comprehensive diagnostic approach, but only 25%-41% of the patients receive a molecular diagnosis. The remaining three-fifths to three-quarters of patients undergoing ES remain undiagnosed. The Stanford Center for Undiagnosed Diseases (CUD), a clinical site of the Undiagnosed Diseases Network, evaluates patients with undiagnosed and rare diseases using a combination of methods including ES. Frequently these patients have non-diagnostic ES results, but strategic follow-up techniques identify diagnoses in a subset. We present techniques used at the CUD that can be adopted by genetics providers in clinical follow-up of cases where ES is non-diagnostic. Solved case examples illustrate different types of non-diagnostic results and the additional techniques that led to a diagnosis. Frequent approaches include segregation analysis, data reanalysis, genome sequencing, additional variant identification, careful phenotype-disease correlation, confirmatory testing, and case matching. We also discuss prioritization of cases for additional analyses.
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Affiliation(s)
- Diane B Zastrow
- Center for Undiagnosed Diseases, Stanford University, Stanford, California
| | - Jennefer N Kohler
- Center for Undiagnosed Diseases, Stanford University, Stanford, California
| | - Devon Bonner
- Center for Undiagnosed Diseases, Stanford University, Stanford, California
| | - Chloe M Reuter
- Center for Undiagnosed Diseases, Stanford University, Stanford, California
| | - Liliana Fernandez
- Center for Undiagnosed Diseases, Stanford University, Stanford, California
| | - Megan E Grove
- Clinical Genomics Program, Stanford Health Care, Stanford, California
| | - Dianna G Fisk
- Clinical Genomics Program, Stanford Health Care, Stanford, California
| | | | | | | | - David Bick
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | | | - Paul G Fisher
- Center for Undiagnosed Diseases, Stanford University, Stanford, California
- Department of Neurology, Stanford University School of Medicine, Stanford, California
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Euan A Ashley
- Center for Undiagnosed Diseases, Stanford University, Stanford, California
- Clinical Genomics Program, Stanford Health Care, Stanford, California
- Department of Genetics, Stanford University School of Medicine, Stanford, California
- Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Jonathan A Bernstein
- Center for Undiagnosed Diseases, Stanford University, Stanford, California
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Matthew T Wheeler
- Center for Undiagnosed Diseases, Stanford University, Stanford, California
- Department of Medicine, Stanford University School of Medicine, Stanford, California
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18
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Grove ME, White S, Fisk DG, Rego S, Dagan-Rosenfeld O, Kohler JN, Reuter CM, Bonner D, Wheeler MT, Bernstein JA, Ormond KE, Hanson-Kahn AK. Developing a genomics rotation: Practical training around variant interpretation for genetic counseling students. J Genet Couns 2019; 28:466-476. [PMID: 30706981 PMCID: PMC6456376 DOI: 10.1002/jgc4.1094] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/23/2018] [Accepted: 12/23/2018] [Indexed: 11/11/2022]
Abstract
With the wide adoption of next-generation sequencing (NGS)-based genetic tests, genetic counselors require increased familiarity with NGS technology, variant interpretation concepts, and variant assessment tools. The use of exome and genome sequencing in clinical care has expanded the reach and diversity of genetic testing. Regardless of the setting where genetic counselors are performing variant interpretation or reporting, most of them have learned these skills from colleagues, while on the job. Though traditional, lecture-based learning around these topics is important, there has been growing need for the inclusion of case-based, experiential training of genomics and variant interpretation for genetic counseling students, with the goal of creating a strong foundation in variant interpretation for new genetic counselors, regardless of what area of practice they enter. To address this need, we established a genomics and variant interpretation rotation for Stanford's genetic counseling training program. In response to changes in the genomics landscape, this has now evolved into three unique rotation experiences, each focused on variant interpretation in the context of various genomic settings, including clinical laboratory, research laboratory, and healthy genomic analysis studies. Here, we describe the goals and learning objectives that we have developed for these variant interpretation rotations, and illustrate how these concepts are applied in practice.
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Affiliation(s)
- Megan E Grove
- Stanford Clinical Genomics Program, Stanford Health Care, Stanford, California
| | - Shana White
- Stanford Clinical Genomics Program, Stanford Health Care, Stanford, California
| | - Dianna G Fisk
- Stanford Clinical Genomics Program, Stanford Health Care, Stanford, California
| | - Shannon Rego
- Department of Genetics, Stanford University School of Medicine, Stanford, California
- Institute for Human Genetics, University of California-San Francisco, San Francisco, California
| | - Orit Dagan-Rosenfeld
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Jennefer N Kohler
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, California
| | - Chloe M Reuter
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, California
- Stanford Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, Stanford School of Medicine, Stanford, California
| | - Devon Bonner
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, California
| | - Matthew T Wheeler
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, California
- Stanford Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, Stanford School of Medicine, Stanford, California
- Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Jonathan A Bernstein
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, California
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Kelly E Ormond
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Andrea K Hanson-Kahn
- Department of Genetics, Stanford University School of Medicine, Stanford, California
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California
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19
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Machol K, Rousseau J, Ehresmann S, Garcia T, Nguyen TTM, Spillmann RC, Sullivan JA, Shashi V, Jiang YH, Stong N, Fiala E, Willing M, Pfundt R, Kleefstra T, Cho MT, McLaughlin H, Rosello Piera M, Orellana C, Martínez F, Caro-Llopis A, Monfort S, Roscioli T, Nixon CY, Buckley MF, Turner A, Jones WD, van Hasselt PM, Hofstede FC, van Gassen KL, Brooks AS, van Slegtenhorst MA, Lachlan K, Sebastian J, Madan-Khetarpal S, Sonal D, Sakkubai N, Thevenon J, Faivre L, Maurel A, Petrovski S, Krantz ID, Tarpinian JM, Rosenfeld JA, Lee BH, Campeau PM, Adams DR, Alejandro ME, Allard P, Azamian MS, Bacino CA, Balasubramanyam A, Barseghyan H, Batzli GF, Beggs AH, Behnam B, Bican A, Bick DP, Birch CL, Bonner D, Boone BE, Bostwick BL, Briere LC, Brown DM, Brush M, Burke EA, Burrage LC, Chen S, Clark GD, Coakley TR, Cogan JD, Cooper CM, Cope H, Craigen WJ, D’Souza P, Davids M, Dayal JG, Dell’Angelica EC, Dhar SU, Dillon A, Dipple KM, Donnell-Fink LA, Dorrani N, Dorset DC, Douine ED, Draper DD, Eckstein DJ, Emrick LT, Eng CM, Eskin A, Esteves C, Estwick T, Ferreira C, Fogel BL, Friedman ND, Gahl WA, Glanton E, Godfrey RA, Goldstein DB, Gould SE, Gourdine JPF, Groden CA, Gropman AL, Haendel M, Hamid R, Hanchard NA, Handley LH, Herzog MR, Holm IA, Hom J, Howerton EM, Huang Y, Jacob HJ, Jain M, Jiang YH, Johnston JM, Jones AL, Kohane IS, Krasnewich DM, Krieg EL, Krier JB, Lalani SR, Lau CC, Lazar J, Lee BH, Lee H, Levy SE, Lewis RA, Lincoln SA, Lipson A, Loo SK, Loscalzo J, Maas RL, Macnamara EF, MacRae CA, Maduro VV, Majcherska MM, Malicdan MCV, Mamounas LA, Manolio TA, Markello TC, Marom R, Martínez-Agosto JA, Marwaha S, May T, McConkie-Rosell A, McCormack CE, McCray AT, Might M, Moretti PM, Morimoto M, Mulvihill JJ, Murphy JL, Muzny DM, Nehrebecky ME, Nelson SF, Newberry JS, Newman JH, Nicholas SK, Novacic D, Orange JS, Pallais JC, Palmer CG, Papp JC, Parker NH, Pena LD, Phillips JA, Posey JE, Postlethwait JH, Potocki L, Pusey BN, Reuter CM, Robertson AK, Rodan LH, Rosenfeld JA, Sampson JB, Samson SL, Schoch K, Schroeder MC, Scott DA, Sharma P, Shashi V, Signer R, Silverman EK, Sinsheimer JS, Smith KS, Spillmann RC, Splinter K, Stoler JM, Stong N, Sullivan JA, Sweetser DA, Tifft CJ, Toro C, Tran AA, Urv TK, Valivullah ZM, Vilain E, Vogel TP, Wahl CE, Walley NM, Walsh CA, Ward PA, Waters KM, Westerfield M, Wise AL, Wolfe LA, Worthey EA, Yamamoto S, Yang Y, Yu G, Zastrow DB, Zheng A. Expanding the Spectrum of BAF-Related Disorders: De Novo Variants in SMARCC2 Cause a Syndrome with Intellectual Disability and Developmental Delay. Am J Hum Genet 2019; 104:164-178. [PMID: 30580808 DOI: 10.1016/j.ajhg.2018.11.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 11/14/2018] [Indexed: 12/22/2022] Open
Abstract
SMARCC2 (BAF170) is one of the invariable core subunits of the ATP-dependent chromatin remodeling BAF (BRG1-associated factor) complex and plays a crucial role in embryogenesis and corticogenesis. Pathogenic variants in genes encoding other components of the BAF complex have been associated with intellectual disability syndromes. Despite its significant biological role, variants in SMARCC2 have not been directly associated with human disease previously. Using whole-exome sequencing and a web-based gene-matching program, we identified 15 individuals with variable degrees of neurodevelopmental delay and growth retardation harboring one of 13 heterozygous variants in SMARCC2, most of them novel and proven de novo. The clinical presentation overlaps with intellectual disability syndromes associated with other BAF subunits, such as Coffin-Siris and Nicolaides-Baraitser syndromes and includes prominent speech impairment, hypotonia, feeding difficulties, behavioral abnormalities, and dysmorphic features such as hypertrichosis, thick eyebrows, thin upper lip vermilion, and upturned nose. Nine out of the fifteen individuals harbor variants in the highly conserved SMARCC2 DNA-interacting domains (SANT and SWIRM) and present with a more severe phenotype. Two of these individuals present cardiac abnormalities. Transcriptomic analysis of fibroblasts from affected individuals highlights a group of differentially expressed genes with possible roles in regulation of neuronal development and function, namely H19, SCRG1, RELN, and CACNB4. Our findings suggest a novel SMARCC2-related syndrome that overlaps with neurodevelopmental disorders associated with variants in BAF-complex subunits.
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20
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Marcogliese PC, Shashi V, Spillmann RC, Stong N, Rosenfeld JA, Koenig MK, Martínez-Agosto JA, Herzog M, Chen AH, Dickson PI, Lin HJ, Vera MU, Salamon N, Graham JM, Ortiz D, Infante E, Steyaert W, Dermaut B, Poppe B, Chung HL, Zuo Z, Lee PT, Kanca O, Xia F, Yang Y, Smith EC, Jasien J, Kansagra S, Spiridigliozzi G, El-Dairi M, Lark R, Riley K, Koeberl DD, Golden-Grant K, Yamamoto S, Wangler MF, Mirzaa G, Hemelsoet D, Lee B, Nelson SF, Goldstein DB, Bellen HJ, Pena LD, Callens S, Coucke P, Dermaut B, Hemelsoet D, Poppe B, Steyaert W, Terryn W, Van Coster R, Adams DR, Alejandro ME, Allard P, Azamian MS, Bacino CA, Balasubramanyam A, Barseghyan H, Batzli GF, Beggs AH, Behnam B, Bican A, Bick DP, Birch CL, Bonner D, Boone BE, Bostwick BL, Briere LC, Brown DM, Brush M, Burke EA, Burrage LC, Chen S, Clark GD, Coakley TR, Cogan JD, Cooper CM, Cope H, Craigen WJ, D’Souza P, Davids M, Dayal JG, Dell’Angelica EC, Dhar SU, Dillon A, Dipple KM, Donnell-Fink LA, Dorrani N, Dorset DC, Douine ED, Draper DD, Eckstein DJ, Emrick LT, Eng CM, Eskin A, Esteves C, Estwick T, Ferreira C, Fogel BL, Friedman ND, Gahl WA, Glanton E, Godfrey RA, Goldstein DB, Gould SE, Gourdine JPF, Groden CA, Gropman AL, Haendel M, Hamid R, Hanchard NA, Handley LH, Herzog MR, Holm IA, Hom J, Howerton EM, Huang Y, Jacob HJ, Jain M, Jiang YH, Johnston JM, Jones AL, Kohane IS, Krasnewich DM, Krieg EL, Krier JB, Lalani SR, Lau CC, Lazar J, Lee BH, Lee H, Levy SE, Lewis RA, Lincoln SA, Lipson A, Loo SK, Loscalzo J, Maas RL, Macnamara EF, MacRae CA, Maduro VV, Majcherska MM, Malicdan MCV, Mamounas LA, Manolio TA, Markello TC, Marom R, Martínez-Agosto JA, Marwaha S, May T, McConkie-Rosell A, McCormack CE, McCray AT, Might M, Moretti PM, Morimoto M, Mulvihill JJ, Murphy JL, Muzny DM, Nehrebecky ME, Nelson SF, Newberry JS, Newman JH, Nicholas SK, Novacic D, Orange JS, Pallais JC, Palmer CG, Papp JC, Parker NH, Pena LD, Phillips JA, Posey JE, Postlethwait JH, Potocki L, Pusey BN, Reuter CM, Robertson AK, Rodan LH, Rosenfeld JA, Sampson JB, Samson SL, Schoch K, Schroeder MC, Scott DA, Sharma P, Shashi V, Signer R, Silverman EK, Sinsheimer JS, Smith KS, Spillmann RC, Splinter K, Stoler JM, Stong N, Sullivan JA, Sweetser DA, Tifft CJ, Toro C, Tran AA, Urv TK, Valivullah ZM, Vilain E, Vogel TP, Wahl CE, Walley NM, Walsh CA, Ward PA, Waters KM, Westerfield M, Wise AL, Wolfe LA, Worthey EA, Yamamoto S, Yang Y, Yu G, Zastrow DB, Zheng A. IRF2BPL Is Associated with Neurological Phenotypes. Am J Hum Genet 2018; 103:456. [PMID: 30193138 PMCID: PMC6128320 DOI: 10.1016/j.ajhg.2018.08.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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21
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Reuter CM, Brimble E, DeFilippo C, Dries AM, Enns GM, Ashley EA, Bernstein JA, Fisher PG, Wheeler MT. A New Approach to Rare Diseases of Children: The Undiagnosed Diseases Network. J Pediatr 2018; 196:291-297.e2. [PMID: 29331327 PMCID: PMC5924635 DOI: 10.1016/j.jpeds.2017.12.029] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 11/09/2017] [Accepted: 12/14/2017] [Indexed: 10/18/2022]
Affiliation(s)
- Chloe M. Reuter
- Stanford Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, 94305, USA,Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Elise Brimble
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Colette DeFilippo
- Department of Pediatrics, Division of Medical Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA,Stanford Children’s Health, Palo Alto, CA, 94304, USA
| | - Annika M. Dries
- Stanford Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, 94305, USA,Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Gregory M. Enns
- Department of Pediatrics, Division of Medical Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Euan A. Ashley
- Stanford Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, 94305, USA,Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA,Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Jonathan A. Bernstein
- Stanford Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, 94305, USA,Department of Pediatrics, Division of Medical Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA,Stanford Children’s Health, Palo Alto, CA, 94304, USA
| | - Paul Graham Fisher
- Stanford Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, 94305, USA,Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, 94305, USA,Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Matthew T. Wheeler
- Stanford Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, 94305, USA,Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
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