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Steyaert W, Sagath L, Demidov G, Yépez VA, Esteve-Codina A, Gagneur J, Ellwanger K, Derks R, Weiss M, den Ouden A, van den Heuvel S, Swinkels H, Zomer N, Steehouwer M, O'Gorman L, Astuti G, Neveling K, Schüle R, Xu J, Synofzik M, Beijer D, Hengel H, Schöls L, Claeys KG, Baets J, Van de Vondel L, Ferlini A, Selvatici R, Morsy H, Saeed Abd Elmaksoud M, Straub V, Müller J, Pini V, Perry L, Sarkozy A, Zaharieva I, Muntoni F, Bugiardini E, Polavarapu K, Horvath R, Reid E, Lochmüller H, Spinazzi M, Savarese M, Matalonga L, Laurie S, Brunner HG, Graessner H, Beltran S, Ossowski S, Vissers LELM, Gilissen C, Hoischen A. Unravelling undiagnosed rare disease cases by HiFi long-read genome sequencing. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.03.24305331. [PMID: 38746462 PMCID: PMC11092722 DOI: 10.1101/2024.05.03.24305331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Solve-RD is a pan-European rare disease (RD) research program that aims to identify disease-causing genetic variants in previously undiagnosed RD families. We utilised 10-fold coverage HiFi long-read sequencing (LRS) for detecting causative structural variants (SVs), single nucleotide variants (SNVs), insertion-deletions (InDels), and short tandem repeat (STR) expansions in extensively studied RD families without clear molecular diagnoses. Our cohort includes 293 individuals from 114 genetically undiagnosed RD families selected by European Rare Disease Network (ERN) experts. Of these, 21 families were affected by so-called 'unsolvable' syndromes for which genetic causes remain unknown, and 93 families with at least one individual affected by a rare neurological, neuromuscular, or epilepsy disorder without genetic diagnosis despite extensive prior testing. Clinical interpretation and orthogonal validation of variants in known disease genes yielded thirteen novel genetic diagnoses due to de novo and rare inherited SNVs, InDels, SVs, and STR expansions. In an additional four families, we identified a candidate disease-causing SV affecting several genes including an MCF2 / FGF13 fusion and PSMA3 deletion. However, no common genetic cause was identified in any of the 'unsolvable' syndromes. Taken together, we found (likely) disease-causing genetic variants in 13.0% of previously unsolved families and additional candidate disease-causing SVs in another 4.3% of these families. In conclusion, our results demonstrate the added value of HiFi long-read genome sequencing in undiagnosed rare diseases.
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Licata L, Via A, Turina P, Babbi G, Benevenuta S, Carta C, Casadio R, Cicconardi A, Facchiano A, Fariselli P, Giordano D, Isidori F, Marabotti A, Martelli PL, Pascarella S, Pinelli M, Pippucci T, Russo R, Savojardo C, Scafuri B, Valeriani L, Capriotti E. Resources and tools for rare disease variant interpretation. Front Mol Biosci 2023; 10:1169109. [PMID: 37234922 PMCID: PMC10206239 DOI: 10.3389/fmolb.2023.1169109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
Collectively, rare genetic disorders affect a substantial portion of the world's population. In most cases, those affected face difficulties in receiving a clinical diagnosis and genetic characterization. The understanding of the molecular mechanisms of these diseases and the development of therapeutic treatments for patients are also challenging. However, the application of recent advancements in genome sequencing/analysis technologies and computer-aided tools for predicting phenotype-genotype associations can bring significant benefits to this field. In this review, we highlight the most relevant online resources and computational tools for genome interpretation that can enhance the diagnosis, clinical management, and development of treatments for rare disorders. Our focus is on resources for interpreting single nucleotide variants. Additionally, we present use cases for interpreting genetic variants in clinical settings and review the limitations of these results and prediction tools. Finally, we have compiled a curated set of core resources and tools for analyzing rare disease genomes. Such resources and tools can be utilized to develop standardized protocols that will enhance the accuracy and effectiveness of rare disease diagnosis.
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Affiliation(s)
- Luana Licata
- Department of Biology, University of Rome Tor Vergata, Roma, Italy
| | - Allegra Via
- Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome “La Sapienza”, Roma, Italy
| | - Paola Turina
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Giulia Babbi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | | | - Claudio Carta
- National Centre for Rare Diseases, Istituto Superiore di Sanità, Roma, Italy
| | - Rita Casadio
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Andrea Cicconardi
- Department of Physics, University of Genova, Genova, Italy
- Italiano di Tecnologia—IIT, Genova, Italy
| | - Angelo Facchiano
- National Research Council, Institute of Food Science, Avellino, Italy
| | - Piero Fariselli
- Department of Medical Sciences, University of Torino, Torino, Italy
| | - Deborah Giordano
- National Research Council, Institute of Food Science, Avellino, Italy
| | - Federica Isidori
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Anna Marabotti
- Department of Chemistry and Biology “A. Zambelli”, University of Salerno, Fisciano, SA, Italy
| | - Pier Luigi Martelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Stefano Pascarella
- Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome “La Sapienza”, Roma, Italy
| | - Michele Pinelli
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Napoli, Italy
| | - Tommaso Pippucci
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Roberta Russo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Napoli, Italy
- CEINGE Biotecnologie Avanzate Franco Salvatore, Napoli, Italy
| | - Castrense Savojardo
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Bernardina Scafuri
- Department of Chemistry and Biology “A. Zambelli”, University of Salerno, Fisciano, SA, Italy
| | | | - Emidio Capriotti
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
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Boycott KM, Hartley T, Kernohan KD, Dyment DA, Howley H, Innes AM, Bernier FP, Brudno M. Care4Rare Canada: Outcomes from a decade of network science for rare disease gene discovery. Am J Hum Genet 2022; 109:1947-1959. [PMID: 36332610 PMCID: PMC9674964 DOI: 10.1016/j.ajhg.2022.10.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 10/04/2022] [Indexed: 11/06/2022] Open
Abstract
The past decade has witnessed a rapid evolution in rare disease (RD) research, fueled by the availability of genome-wide (exome and genome) sequencing. In 2011, as this transformative technology was introduced to the research community, the Care4Rare Canada Consortium was launched: initially as FORGE, followed by Care4Rare, and Care4Rare SOLVE. Over what amounted to three eras of diagnosis and discovery, the Care4Rare Consortium used exome sequencing and, more recently, genome and other 'omic technologies to identify the molecular cause of unsolved RDs. We achieved a diagnostic yield of 34% (623/1,806 of participating families), including the discovery of deleterious variants in 121 genes not previously associated with disease, and we continue to study candidate variants in novel genes for 145 families. The Consortium has made significant contributions to RD research, including development of platforms for data collection and sharing and instigating a Canadian network to catalyze functional characterization research of novel genes. The Consortium was instrumental to implementing genome-wide sequencing as a publicly funded test for RD diagnosis in Canada. Despite the successes of the past decade, the challenge of solving all RDs remains enormous, and the work is far from over. We must leverage clinical and 'omic data for secondary use, develop tools and policies to support safe data sharing, continue to explore the utility of new and emerging technologies, and optimize research protocols to delineate complex disease mechanisms. Successful approaches in each of these realms is required to offer diagnostic clarity to all families with RDs.
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Affiliation(s)
- Kym M. Boycott
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada,Corresponding author
| | - Taila Hartley
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Kristin D. Kernohan
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - David A. Dyment
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Heather Howley
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - A. Micheil Innes
- Department of Medical Genetics and Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Francois P. Bernier
- Department of Medical Genetics and Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada
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4
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Cohen ASA, Farrow EG, Abdelmoity AT, Alaimo JT, Amudhavalli SM, Anderson JT, Bansal L, Bartik L, Baybayan P, Belden B, Berrios CD, Biswell RL, Buczkowicz P, Buske O, Chakraborty S, Cheung WA, Coffman KA, Cooper AM, Cross LA, Curran T, Dang TTT, Elfrink MM, Engleman KL, Fecske ED, Fieser C, Fitzgerald K, Fleming EA, Gadea RN, Gannon JL, Gelineau-Morel RN, Gibson M, Goldstein J, Grundberg E, Halpin K, Harvey BS, Heese BA, Hein W, Herd SM, Hughes SS, Ilyas M, Jacobson J, Jenkins JL, Jiang S, Johnston JJ, Keeler K, Korlach J, Kussmann J, Lambert C, Lawson C, Le Pichon JB, Leeder JS, Little VC, Louiselle DA, Lypka M, McDonald BD, Miller N, Modrcin A, Nair A, Neal SH, Oermann CM, Pacicca DM, Pawar K, Posey NL, Price N, Puckett LMB, Quezada JF, Raje N, Rowell WJ, Rush ET, Sampath V, Saunders CJ, Schwager C, Schwend RM, Shaffer E, Smail C, Soden S, Strenk ME, Sullivan BR, Sweeney BR, Tam-Williams JB, Walter AM, Welsh H, Wenger AM, Willig LK, Yan Y, Younger ST, Zhou D, Zion TN, Thiffault I, Pastinen T. Genomic answers for children: Dynamic analyses of >1000 pediatric rare disease genomes. Genet Med 2022; 24:1336-1348. [PMID: 35305867 DOI: 10.1016/j.gim.2022.02.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 02/05/2022] [Accepted: 02/07/2022] [Indexed: 12/17/2022] Open
Abstract
PURPOSE This study aimed to provide comprehensive diagnostic and candidate analyses in a pediatric rare disease cohort through the Genomic Answers for Kids program. METHODS Extensive analyses of 960 families with suspected genetic disorders included short-read exome sequencing and short-read genome sequencing (srGS); PacBio HiFi long-read genome sequencing (HiFi-GS); variant calling for single nucleotide variants (SNV), structural variant (SV), and repeat variants; and machine-learning variant prioritization. Structured phenotypes, prioritized variants, and pedigrees were stored in PhenoTips database, with data sharing through controlled access the database of Genotypes and Phenotypes. RESULTS Diagnostic rates ranged from 11% in patients with prior negative genetic testing to 34.5% in naive patients. Incorporating SVs from genome sequencing added up to 13% of new diagnoses in previously unsolved cases. HiFi-GS yielded increased discovery rate with >4-fold more rare coding SVs compared with srGS. Variants and genes of unknown significance remain the most common finding (58% of nondiagnostic cases). CONCLUSION Computational prioritization is efficient for diagnostic SNVs. Thorough identification of non-SNVs remains challenging and is partly mitigated using HiFi-GS sequencing. Importantly, community research is supported by sharing real-time data to accelerate gene validation and by providing HiFi variant (SNV/SV) resources from >1000 human alleles to facilitate implementation of new sequencing platforms for rare disease diagnoses.
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Affiliation(s)
- Ana S A Cohen
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO
| | - Emily G Farrow
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | | | - Joseph T Alaimo
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO
| | - Shivarajan M Amudhavalli
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | - John T Anderson
- Department of Orthopaedic Surgery, Children's Mercy Kansas City, Kansas City, MO
| | - Lalit Bansal
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Lauren Bartik
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | | | - Bradley Belden
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | | | - Rebecca L Biswell
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | | | | | | | - Warren A Cheung
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Keith A Coffman
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Ashley M Cooper
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Laura A Cross
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | - Tom Curran
- Children's Mercy Research Institute, Kansas City, MO
| | - Thuy Tien T Dang
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Mary M Elfrink
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | | | - Erin D Fecske
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Cynthia Fieser
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Keely Fitzgerald
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Emily A Fleming
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | - Randi N Gadea
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | | | - Rose N Gelineau-Morel
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Margaret Gibson
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Jeffrey Goldstein
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Elin Grundberg
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Kelsee Halpin
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Brian S Harvey
- Department of Orthopaedic Surgery, Children's Mercy Kansas City, Kansas City, MO
| | - Bryce A Heese
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | - Wendy Hein
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Suzanne M Herd
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Susan S Hughes
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | - Mohammed Ilyas
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Jill Jacobson
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Janda L Jenkins
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | | | | | - Kathryn Keeler
- Department of Orthopaedic Surgery, Children's Mercy Kansas City, Kansas City, MO
| | - Jonas Korlach
- Pacific Biosciences of California, Inc, Menlo Park, CA
| | | | | | - Caitlin Lawson
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | | | | | - Vicki C Little
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | | | | | | | - Neil Miller
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Division of Allergy Immunology Pulmonary and Sleep Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Ann Modrcin
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Annapoorna Nair
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Shelby H Neal
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | | | - Donna M Pacicca
- Department of Orthopaedic Surgery, Children's Mercy Kansas City, Kansas City, MO
| | - Kailash Pawar
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Nyshele L Posey
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Nigel Price
- Department of Orthopaedic Surgery, Children's Mercy Kansas City, Kansas City, MO
| | - Laura M B Puckett
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Julio F Quezada
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Nikita Raje
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Division of Neonatology, Children's Mercy Kansas City, Kansas City, MO
| | | | - Eric T Rush
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Division of Genetics, Children's Mercy Kansas City, Kansas City, MO; Department of Internal Medicine, University of Kansas School of Medicine, Kansas City, MO
| | - Venkatesh Sampath
- Division of Neonatology, Children's Mercy Hospital Kansas City, Kansas City, MO
| | - Carol J Saunders
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO
| | - Caitlin Schwager
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | - Richard M Schwend
- Department of Orthopaedic Surgery, Children's Mercy Kansas City, Kansas City, MO
| | - Elizabeth Shaffer
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Craig Smail
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Sarah Soden
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Meghan E Strenk
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | | | - Brooke R Sweeney
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | | | - Adam M Walter
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Holly Welsh
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | | | - Laurel K Willig
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Yun Yan
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Scott T Younger
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Dihong Zhou
- Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | - Tricia N Zion
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Division of Genetics, Children's Mercy Kansas City, Kansas City, MO
| | - Isabelle Thiffault
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO.
| | - Tomi Pastinen
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO; Children's Mercy Research Institute, Kansas City, MO.
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5
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Baxter SM, Posey JE, Lake NJ, Sobreira N, Chong JX, Buyske S, Blue EE, Chadwick LH, Coban-Akdemir ZH, Doheny KF, Davis CP, Lek M, Wellington C, Jhangiani SN, Gerstein M, Gibbs RA, Lifton RP, MacArthur DG, Matise TC, Lupski JR, Valle D, Bamshad MJ, Hamosh A, Mane S, Nickerson DA, Rehm HL, O'Donnell-Luria A. Centers for Mendelian Genomics: A decade of facilitating gene discovery. Genet Med 2022; 24:784-797. [PMID: 35148959 PMCID: PMC9119004 DOI: 10.1016/j.gim.2021.12.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 12/08/2021] [Accepted: 12/12/2021] [Indexed: 12/27/2022] Open
Abstract
PURPOSE Mendelian disease genomic research has undergone a massive transformation over the past decade. With increasing availability of exome and genome sequencing, the role of Mendelian research has expanded beyond data collection, sequencing, and analysis to worldwide data sharing and collaboration. METHODS Over the past 10 years, the National Institutes of Health-supported Centers for Mendelian Genomics (CMGs) have played a major role in this research and clinical evolution. RESULTS We highlight the cumulative gene discoveries facilitated by the program, biomedical research leveraged by the approach, and the larger impact on the research community. Beyond generating a list of gene-phenotype relationships and participating in widespread data sharing, the CMGs have created resources, tools, and training for the larger community to foster understanding of genes and genome variation. The CMGs have participated in a wide range of data sharing activities, including deposition of all eligible CMG data into the Analysis, Visualization, and Informatics Lab-space (AnVIL), sharing candidate genes through the Matchmaker Exchange and the CMG website, and sharing variants in Genotypes to Mendelian Phenotypes (Geno2MP) and VariantMatcher. CONCLUSION The work is far from complete; strengthening communication between research and clinical realms, continued development and sharing of knowledge and tools, and improving access to richly characterized data sets are all required to diagnose the remaining molecularly undiagnosed patients.
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Affiliation(s)
- Samantha M Baxter
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA.
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Nicole J Lake
- Department of Genetics, Yale School of Medicine, New Haven, CT; Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Nara Sobreira
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Jessica X Chong
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA; Brotman Baty Institute for Precision Medicine, Seattle, WA
| | - Steven Buyske
- Department of Statistics, Rutgers University, Piscataway, NJ; Department of Genetics, Rutgers University, Piscataway, NJ
| | - Elizabeth E Blue
- Brotman Baty Institute for Precision Medicine, Seattle, WA; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA
| | - Lisa H Chadwick
- Division of Genome Sciences, National Human Genome Research Institute, Bethesda, MD
| | - Zeynep H Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX
| | - Kimberly F Doheny
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Colleen P Davis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA
| | - Monkol Lek
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Genetics, Yale School of Medicine, New Haven, CT
| | | | | | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Richard P Lifton
- Department of Genetics, Yale School of Medicine, New Haven, CT; Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY
| | - Daniel G MacArthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, New South Wales, Australia; Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Tara C Matise
- Department of Genetics, Rutgers University, Piscataway, NJ
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX; Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - David Valle
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Michael J Bamshad
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA; Brotman Baty Institute for Precision Medicine, Seattle, WA; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA
| | - Ada Hamosh
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Shrikant Mane
- Department of Genetics, Yale School of Medicine, New Haven, CT
| | - Deborah A Nickerson
- Brotman Baty Institute for Precision Medicine, Seattle, WA; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA.
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA; Department of Pediatrics, Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA.
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6
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Innes AM, Lynch DC. Fifty years of recognizable patterns of human malformation: Insights and opportunities. Am J Med Genet A 2021; 185:2653-2669. [PMID: 33951288 DOI: 10.1002/ajmg.a.62240] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/05/2021] [Accepted: 04/09/2021] [Indexed: 12/11/2022]
Abstract
Now in its 7th edition, Smith's Recognizable Patterns of Human Malformation was first published in 1970. This 1st edition comprised 135 "dysmorphic syndromes of multiple primary defects" and 12 "single syndromic malformations resulting in secondary defects." Of the former, other than a few chromosomal and environmental disorders, most were heritable conditions of then unknown etiology. In 2021, the majority of these conditions are now "solved," a notable exception is Hallermann-Streiff syndrome. The "solved" conditions were typically clinically delineated decades prior to understanding the underlying etiology, which rarely required recent technologies such as exome sequencing (ES) to elucidate. The 7th edition includes nearly 300 syndromes, sequences, and associations. An increasing number of conditions first appearing in the latest editions are sporadic, with many solved using either array CGH or ES. We have reviewed all syndromes that have appeared in "Smith's" with a focus on inheritance, heterogeneity, and year and method of etiologic discovery. Several themes emerge. Genetic heterogeneity and pleiotropy of genes are frequent. Several of the currently "unresolved" syndromes are clinically diverse such as Dubowitz syndrome. Multiple recurrent constellations of embryonic malformations, with VACTERL association as a paradigm, are increasingly likely to have a shared pathogenesis requiring further study.
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Affiliation(s)
- A Micheil Innes
- Department of Medical Genetics, Alberta Children's Hospital Research Institute, Calgary, Alberta, Canada.,Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Danielle C Lynch
- Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
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Amodeo ME, Inzaghi E, Deodati A, Cianfarani S. Endocrinological features of a patient with 14q microdeletion and Dubowitz phenotype. Mol Genet Genomic Med 2021; 9:e1644. [PMID: 33788412 PMCID: PMC8172207 DOI: 10.1002/mgg3.1644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/24/2020] [Accepted: 02/19/2021] [Indexed: 11/29/2022] Open
Abstract
Background Dubowitz syndrome (DS) is a complex and rare condition characterized by postnatal growth retardation, microcephaly, short stature, mild developmental delay, facial dysmorphism, skin eruption and bone marrow failure. Though approximately 200 cases have been described so far, no specific genetic analysis, laboratory tests or radiological exams are available to confirm the diagnosis which is still based on clinical and facial features. Although short stature is a major feature of the syndrome, no endocrine alterations have been reported so far and scant data are available about the efficacy and safety of GH treatment in these patients. Methods A 13‐year‐old male patient was referred to our attention for short stature. Endocrinological evaluation including GH axis, adrenal and gonadal functions were assessed. aCGH was performed. Results 14q terminal microdeletion associated with Dubowitz phenotype was found. Endocrinological investigations revealed the presence of hypopituitarism which showed a satisfactory response to short‐term growth hormone therapy. The subject also started glucocorticoid replacement therapy. Disorders in pubertal progression and gonadal function were noted. Conclusions Dubowitz syndrome (DS) includes different clinical findings variably occurring. Subjects with a Dubowitz phenotype should be carefully monitored for endocrinological anomalies. The prompt recognition of potential life‐threatening endocrinological condition for example adrenal insufficiency is mandatory in order to start an adequate and early treatment.
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Affiliation(s)
- Maria Elisa Amodeo
- Dipartimento Pediatrico Universitario Ospedaliero, IRCCS "Bambino Gesù" Children's Hospital, Rome, Italy.,Department of Systems Medicine, Tor Vergata University, Rome, Italy
| | - Elena Inzaghi
- Dipartimento Pediatrico Universitario Ospedaliero, IRCCS "Bambino Gesù" Children's Hospital, Rome, Italy
| | - Annalisa Deodati
- Dipartimento Pediatrico Universitario Ospedaliero, IRCCS "Bambino Gesù" Children's Hospital, Rome, Italy
| | - Stefano Cianfarani
- Dipartimento Pediatrico Universitario Ospedaliero, IRCCS "Bambino Gesù" Children's Hospital, Rome, Italy.,Department of Systems Medicine, Tor Vergata University, Rome, Italy.,Department of Women's and Children's Health, Karolinska Institutet and University Hospital, Stockholm, Sweden
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Stevenson RE. Common pathogenesis for sirenomelia, OEIS complex, limb-body wall defect, and other malformations of caudal structures. Am J Med Genet A 2021; 185:1379-1387. [PMID: 33522143 DOI: 10.1002/ajmg.a.62103] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 01/11/2023]
Abstract
Decades of clinical, pathological, and epidemiological study and the recent application of advanced microarray and gene sequencing technologies have led to an understanding of the causes and pathogenesis of most recognized patterns of malformation. Still, there remain a number of patterns of malformation whose pathogenesis has not been established. Six such patterns of malformation are sirenomelia, VACTERL association, OEIS complex, limb-body wall defect (LBWD), urorectal septum malformation (URSM) sequence, and MURCS association, all of which predominantly affect caudal structures. On the basis of the overlap of the component malformations, the co-occurrence in individual fetuses, and the findings on fetal examination, a common pathogenesis is proposed for these patterns of malformation. The presence of a single artery in the umbilical cord provides a visible clue to the pathogenesis of all cases of sirenomelia and 30%-50% of cases of VACTERL association, OEIS complex, URSM sequence, and LBWD. The single artery is formed by a coalescence of arteries that supply the yolk sac, arises from the descending aorta high in the abdominal cavity, and redirects blood flow from the developing caudal structures of the embryo to the placenta. This phenomenon during embryogenesis is termed vitelline vascular steal.
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Affiliation(s)
- Roger E Stevenson
- Greenwood Genetic Center, J. C. Self Research Institute of Human Genetics, Greenwood, South Carolina, USA
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Adam AP, Curry CJ, Hall JG, Keppler-Noreuil KM, Adam MP, Dobyns WB. Recurrent constellations of embryonic malformations re-conceptualized as an overlapping group of disorders with shared pathogenesis. Am J Med Genet A 2020; 182:2646-2661. [PMID: 32924308 DOI: 10.1002/ajmg.a.61847] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/12/2020] [Accepted: 08/12/2020] [Indexed: 12/17/2022]
Abstract
Several recurrent malformation associations affecting the development of the embryo have been described in which a genetic etiology has not been found, including LBWC, MURCS, OAVS, OEIS, POC, VACTERL, referred to here as "recurrent constellations of embryonic malformations" (RCEM). All are characterized by an excess of reported monozygotic discordant twins and lack of familial recurrence. We performed a comprehensive review of published twin data across all six phenotypes to allow a more robust assessment of the association with twinning and potential embryologic timing of a disruptive event. We recorded the type of twinning, any overlapping features of another RCEM, maternal characteristics, and the use of ART. Statistically significant associations included an excess of monozygotic twins and 80% discordance rate for the phenotype across all twins. There was an 18.5% rate of ART and no consistently reported maternal adverse events during pregnancy. We found 24 instances of co-occurrence of two RCEM, suggesting a shared pathogenesis across all RCEM phenotypes. We hypothesize the following timing for RCEM phenotypes from the earliest perturbation in development to the latest: LBWC, POC, OEIS, VACTERL, OAVS, then MURCS. The RCEM group of conditions should be considered a spectrum that could be studied as a group.
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Affiliation(s)
- Aaron P Adam
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Cynthia J Curry
- Genetic Medicine, Department of Pediatrics, University of California San Francisco, Fresno, California, USA
| | - Judith G Hall
- Pediatrics and Medical Genetics, Children's and Women's Health Center of BC, UBC, Vancouver, British Columbia, Canada.,Department of Medical Genetics, BC Children's Hospital, Vancouver, British Columbia, Canada
| | - Kim M Keppler-Noreuil
- Division of Genetics and Metabolism, Rare Disease Institute, Children's National, Washington, District of Columbia, USA
| | - Margaret P Adam
- Divison of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - William B Dobyns
- Division of Genetics and Metabolism, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA
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Boycott KM, Hartley T, Biesecker LG, Gibbs RA, Innes AM, Riess O, Belmont J, Dunwoodie SL, Jojic N, Lassmann T, Mackay D, Temple IK, Visel A, Baynam G. A Diagnosis for All Rare Genetic Diseases: The Horizon and the Next Frontiers. Cell 2020; 177:32-37. [PMID: 30901545 DOI: 10.1016/j.cell.2019.02.040] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The introduction of exome sequencing in the clinic has sparked tremendous optimism for the future of rare disease diagnosis, and there is exciting opportunity to further leverage these advances. To provide diagnostic clarity to all of these patients, however, there is a critical need for the field to develop and implement strategies to understand the mechanisms underlying all rare diseases and translate these to clinical care.
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Affiliation(s)
- Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Leslie G Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX, USA
| | - A Micheil Innes
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - John Belmont
- Illumina, Madison, WI, USA; Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Sally L Dunwoodie
- Victor Chang Cardiac Research Institute, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | | | - Timo Lassmann
- Telethon Kids Institute, University of Western Australia, Nedlands, WA, Australia
| | - Deborah Mackay
- Department of Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, Hampshire, UK
| | - I Karen Temple
- Department of Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, Hampshire, UK
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, CA, USA; DOE Joint Genome Institute, CA, USA; The University of California at Merced, CA, USA
| | - Gareth Baynam
- Faculty of Health and Medical Sciences, University of Western Australia Medical School, Perth, WA, Australia; Western Australian Register of Developmental Anomalies, Genetic Services of Western Australia, Perth, WA, Australia; Office of Population Health Genomics, Western Australian Department of Health, Perth, WA, Australia
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Two Cases of Oculofaciocardiodental (OFCD) Syndrome due to X-Linked BCOR Mutations Presenting with Infantile Hemangiomas: Phenotypic Overlap with PHACE Syndrome. Case Rep Genet 2020; 2019:9382640. [PMID: 31956451 PMCID: PMC6949664 DOI: 10.1155/2019/9382640] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 12/07/2019] [Indexed: 01/16/2023] Open
Abstract
Background Oculofaciocardiodental (OFCD) syndrome is due to mutations in BCOR (BCL-6 corepressor). OFCD has phenotypic overlaps with PHACE syndrome (Posterior fossa anomalies, Hemangioma, Arterial anomalies, Cardiac defects, Eye anomalies). Infantile hemangiomas are a key diagnostic criterion for PHACE, but not for OFCD. A previous study reported two cases of infantile hemangiomas in OFCD, but the authors could not exclude chance association. Case Presentation We describe two novel cases of female patients (one initially diagnosed with PHACE syndrome), both of whom had infantile hemangiomas. Ophthalmological findings were consistent with oculofaciocardiodental (OFCD) syndrome. Upon genetic testing, these two females were determined to have X-linked BCOR mutations confirming OFCD syndrome diagnoses. Conclusion These case reports add support to the hypothesis that infantile hemangiomas may be a feature of OFCD. BCOR may potentially be within a pathway of genes involved in PHACE syndrome and/or in infantile hemangioma formation.
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