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Varzari A, Deyneko IV, Bruun GH, Dembic M, Hofmann W, Cebotari VM, Ginda SS, Andresen BS, Illig T. Candidate genes and sequence variants for susceptibility to mycobacterial infection identified by whole-exome sequencing. Front Genet 2022; 13:969895. [PMID: 36338958 PMCID: PMC9632272 DOI: 10.3389/fgene.2022.969895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 10/04/2022] [Indexed: 11/13/2022] Open
Abstract
Inborn errors of immunity are known to influence susceptibility to mycobacterial infections. The aim of this study was to characterize the genetic profile of nine patients with mycobacterial infections (eight with BCGitis and one with disseminated tuberculosis) from the Republic of Moldova using whole-exome sequencing. In total, 12 variants in eight genes known to be associated with Mendelian Susceptibility to Mycobacterial Disease (MSMD) were detected in six out of nine patients examined. In particular, a novel splice site mutation c.373–2A>C in STAT1 gene was found and functionally confirmed in a patient with disseminated tuberculosis. Trio analysis was possible for seven out of nine patients, and resulted in 23 candidate variants in 15 novel genes. Four of these genes - GBP2, HEATR3, PPP1R9B and KDM6A were further prioritized, considering their elevated expression in immune-related tissues. Compound heterozygosity was found in GBP2 in a single patient, comprising a maternally inherited missense variant c.412G>A/p.(Ala138Thr) predicted to be deleterious and a paternally inherited intronic mutation c.1149+14T>C. Functional studies demonstrated that the intronic mutation affects splicing and the level of transcript. Finally, we analyzed pathogenicity of variant combinations in gene pairs and identified five patients with putative oligogenic inheritance. In summary, our study expands the spectrum of genetic variation contributing to susceptibility to mycobacterial infections in children and provides insight into the complex/oligogenic disease-causing mode.
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Affiliation(s)
- Alexander Varzari
- Laboratory of Human Genetics, Chiril Draganiuc Institute of Phthisiopneumology, Kishinev, Moldova
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
- *Correspondence: Alexander Varzari,
| | - Igor V. Deyneko
- Laboratory of Functional Genomics, Timiryazev Institute of Plant Physiology Russian Academy of Sciences, Moscow, Russia
| | - Gitte Hoffmann Bruun
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
- The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Maja Dembic
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
- The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | - Winfried Hofmann
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Victor M. Cebotari
- Municipal Hospital of Phthisiopneumology, Department of Pediatrics, Kishinev, Moldova
| | - Sergei S. Ginda
- Laboratory of Immunology and Allergology, Chiril Draganiuc Institute of Phthisiopneumology, Kishinev, Moldova
| | - Brage S. Andresen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
- The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Thomas Illig
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
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2
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Boycott KM, Azzariti DR, Hamosh A, Rehm HL. Seven years since the launch of the Matchmaker Exchange: The evolution of genomic matchmaking. Hum Mutat 2022; 43:659-667. [PMID: 35537081 PMCID: PMC9133175 DOI: 10.1002/humu.24373] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 03/22/2022] [Indexed: 11/09/2022]
Abstract
The Matchmaker Exchange (MME) was launched in 2015 to provide a robust mechanism to discover novel disease-gene relationships. It operates as a federated network connecting databases holding relevant data using a common application programming interface, where two or more users are looking for a match for the same gene (two-sided matchmaking). Seven years from its launch, it is clear that the MME is making outstanding contributions to understanding the morbid anatomy of the genome. The number of unique genes present across the MME has steadily increased over time; there are currently >13,520 unique genes (~68% of all protein-coding genes) connected across the MME's eight genomic matchmaking nodes, GeneMatcher, DECIPHER, PhenomeCentral, MyGene2, seqr, Initiative on Rare and Undiagnosed Disease, PatientMatcher, and the RD-Connect Genome-Phenome Analysis Platform. The collective data set accessible across the MME currently includes more than 120,000 cases from over 12,000 contributors in 98 countries. The discovery of potential new disease-gene relationships is happening daily and international collaborative teams are moving these advances forward to publication, now numbering well over 500. Expansion of data sharing into routine clinical practice by clinicians, genetic counselors, and clinical laboratories has ensured access to discovery for even more individuals with undiagnosed rare genetic diseases. Tens of thousands of patients and their family members have been directly or indirectly impacted by the discoveries facilitated by two-sided genomic matchmaking. MME supports further connections to the literature (PubCaseFinder) and to human and model organism resources (Monarch Initiative) and scientists (ModelMatcher). Efforts are now underway to explore additional approaches to matchmaking at the gene or variant level where there is only one querier (one-sided matchmaking). Genomic matchmaking has proven its utility over the past 7 years and will continue to facilitate discoveries in the years to come.
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Affiliation(s)
- Kym M. Boycott
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Danielle R. Azzariti
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Ada Hamosh
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Heidi L. Rehm
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
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3
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Ouahed J, Kelsen JR, Spessott WA, Kooshesh K, Sanmillan ML, Dawany N, Sullivan KE, Hamilton KE, Slowik V, Nejentsev S, Neves JF, Flores H, Chung WK, Wilson A, Anyane-Yeboa K, Wou K, Jain P, Field M, Tollefson S, Dent MH, Li D, Naito T, McGovern DPB, Kwong AC, Taliaferro F, Ordovas-Montanes J, Horwitz BH, Kotlarz D, Klein C, Evans J, Dorsey J, Warner N, Elkadri A, Muise AM, Goldsmith J, Thompson B, Engelhardt KR, Cant AJ, Hambleton S, Barclay A, Toth-Petroczy A, Vuzman D, Carmichael N, Bodea C, Cassa CA, Devoto M, Maas RL, Behrens EM, Giraudo CG, Snapper SB. Variants in STXBP3 are Associated with Very Early Onset Inflammatory Bowel Disease, Bilateral Sensorineural Hearing Loss and Immune Dysregulation. J Crohns Colitis 2021; 15:1908-1919. [PMID: 33891011 PMCID: PMC8575043 DOI: 10.1093/ecco-jcc/jjab077] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
BACKGROUND AND AIMS Very early onset inflammatory bowel disease [VEOIBD] is characterized by intestinal inflammation affecting infants and children less than 6 years of age. To date, over 60 monogenic aetiologies of VEOIBD have been identified, many characterized by highly penetrant recessive or dominant variants in underlying immune and/or epithelial pathways. We sought to identify the genetic cause of VEOIBD in a subset of patients with a unique clinical presentation. METHODS Whole exome sequencing was performed on five families with ten patients who presented with a similar constellation of symptoms including medically refractory infantile-onset IBD, bilateral sensorineural hearing loss and, in the majority, recurrent infections. Genetic aetiologies of VEOIBD were assessed and Sanger sequencing was performed to confirm novel genetic findings. Western analysis on peripheral blood mononuclear cells and functional studies with epithelial cell lines were employed. RESULTS In each of the ten patients, we identified damaging heterozygous or biallelic variants in the Syntaxin-Binding Protein 3 gene [STXBP3], a protein known to regulate intracellular vesicular trafficking in the syntaxin-binding protein family of molecules, but not associated to date with either VEOIBD or sensorineural hearing loss. These mutations interfere with either intron splicing or protein stability and lead to reduced STXBP3 protein expression. Knock-down of STXBP3 in CaCo2 cells resulted in defects in cell polarity. CONCLUSION Overall, we describe a novel genetic syndrome and identify a critical role for STXBP3 in VEOIBD, sensorineural hearing loss and immune dysregulation.
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Affiliation(s)
- Jodie Ouahed
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children's Hospital, and Harvard Medical School, Boston, MA, 02115, USA
| | - Judith R Kelsen
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Waldo A Spessott
- Department of Microbiology and Immunology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Kameron Kooshesh
- Brigham Genomic Medicine Program, Division of Genetics, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Maria L Sanmillan
- Department of Microbiology and Immunology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Noor Dawany
- Department of Biomedical Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Kathleen E Sullivan
- Division of Allergy and Immunology, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kathryn E Hamilton
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Voytek Slowik
- Department of Medicine, Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sergey Nejentsev
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Mercy Kansas City, Kansas City, MO, 64108, USA.,Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - João Farela Neves
- Department of Molecular Cell Biology and Immunology, Amsterdam University Medical Centers, Amsterdam, the Netherlands.,Primary Immunodeficiencies Unit; Hospital Dona Estefânia-CHLC, EPE, Lisbon, 1169, Portugal
| | - Helena Flores
- CEDOC, Chronic Diseases Research Center, NOVA Medical School, Lisbon, 1150, Portugal
| | - Wendy K Chung
- Gastroenterology Unit, Hospital Dona Estefânia-CHLC, EPE, Lisbon, 1169, Portugal
| | - Ashley Wilson
- Gastroenterology Unit, Hospital Dona Estefânia-CHLC, EPE, Lisbon, 1169, Portugal
| | - Kwame Anyane-Yeboa
- Gastroenterology Unit, Hospital Dona Estefânia-CHLC, EPE, Lisbon, 1169, Portugal
| | - Karen Wou
- Gastroenterology Unit, Hospital Dona Estefânia-CHLC, EPE, Lisbon, 1169, Portugal
| | - Preti Jain
- Department of Pediatrics, Columbia University Medical Center, New York, NY, 10032, USA.,Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Michael Field
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children's Hospital, and Harvard Medical School, Boston, MA, 02115, USA
| | - Sophia Tollefson
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children's Hospital, and Harvard Medical School, Boston, MA, 02115, USA
| | - Maiah H Dent
- Department of Genetics, Yale University, New Haven, CT, 06510, USA
| | - Dalin Li
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Takeo Naito
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Andrew C Kwong
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children's Hospital, and Harvard Medical School, Boston, MA, 02115, USA.,Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Faith Taliaferro
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children's Hospital, and Harvard Medical School, Boston, MA, 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Jose Ordovas-Montanes
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children's Hospital, and Harvard Medical School, Boston, MA, 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Program in Immunology, Harvard Medical School, Boston, MA, 02115, USA.,Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | - Bruce H Horwitz
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children's Hospital, and Harvard Medical School, Boston, MA, 02115, USA.,Division of Emergency Medicine, Department of Pediatrics, Boston Children's Hospital, and Harvard Medical School, Boston, MA, 02115, USA
| | - Daniel Kotlarz
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children's Hospital, and Harvard Medical School, Boston, MA, 02115, USA.,Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital LMU Munich, Munich, 80337, Germany
| | - Christoph Klein
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital LMU Munich, Munich, 80337, Germany
| | - Jonathan Evans
- Department of Pediatrics, Nemours Children's Specialty Care, Jacksonville, FL 32207, USA
| | - Jill Dorsey
- Department of Pediatrics, Nemours Children's Specialty Care, Jacksonville, FL 32207, USA
| | - Neil Warner
- SickKids Inflammatory Bowel Disease Center and Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON, Canada.,Department of Pediatrics and Biochemistry, University of Toronto, Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
| | - Abdul Elkadri
- SickKids Inflammatory Bowel Disease Center and Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON, Canada.,Department of Pediatrics and Biochemistry, University of Toronto, Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
| | - Aleixo M Muise
- SickKids Inflammatory Bowel Disease Center and Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON, Canada.,Department of Pediatrics and Biochemistry, University of Toronto, Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada
| | - Jeffrey Goldsmith
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Benjamin Thompson
- Primary Immunodeficiency Group, III Theme, Institute of Cellular Medicine, Newcastle University, Newcastle, NE2 4HH, UK
| | - Karin R Engelhardt
- Primary Immunodeficiency Group, III Theme, Institute of Cellular Medicine, Newcastle University, Newcastle, NE2 4HH, UK
| | - Andrew J Cant
- Primary Immunodeficiency Group, III Theme, Institute of Cellular Medicine, Newcastle University, Newcastle, NE2 4HH, UK.,Children's Immunology Service, Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, NE1 4LP, UK
| | - Sophie Hambleton
- Primary Immunodeficiency Group, III Theme, Institute of Cellular Medicine, Newcastle University, Newcastle, NE2 4HH, UK.,Children's Immunology Service, Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, NE1 4LP, UK
| | - Andrew Barclay
- Department of Paediatric Gastroenterology, Royal Hospital for Children, Glasgow, G51 4TF, UK
| | - Agnes Toth-Petroczy
- Brigham Genomic Medicine Program, Division of Genetics, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.,Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Center for Systems Biology Dresden, Dresden, Germany
| | - Dana Vuzman
- Brigham Genomic Medicine Program, Division of Genetics, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Nikkola Carmichael
- Brigham Genomic Medicine Program, Division of Genetics, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Corneliu Bodea
- Brigham Genomic Medicine Program, Division of Genetics, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Christopher A Cassa
- Brigham Genomic Medicine Program, Division of Genetics, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Marcella Devoto
- Division of Human Genetics, The Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Translational and Precision Medicine, University Sapienza, Rome 00185, Italy.,CNR-IRGB, Cagliari 09042, Italy
| | - Richard L Maas
- Brigham Genomic Medicine Program, Division of Genetics, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Edward M Behrens
- Division of Rheumatology, The Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Claudio G Giraudo
- Department of Microbiology and Immunology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Scott B Snapper
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children's Hospital, and Harvard Medical School, Boston, MA, 02115, USA.,Division of Gastroenterology, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
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4
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Miller DB, Piccolo SR. A Survey of Compound Heterozygous Variants in Pediatric Cancers and Structural Birth Defects. Front Genet 2021; 12:640242. [PMID: 33828584 PMCID: PMC8019969 DOI: 10.3389/fgene.2021.640242] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/24/2021] [Indexed: 11/13/2022] Open
Abstract
Compound heterozygous (CH) variants occur when two recessive alleles are inherited and the variants are located at different loci within the same gene in a given individual. CH variants are important contributors to many different types of recessively inherited diseases. However, many studies overlook CH variants because identification of this type of variant requires knowing the parent of origin for each nucleotide. Using computational methods, haplotypes can be inferred using a process called "phasing," which estimates the chromosomal origin of most nucleotides. In this paper, we used germline, phased, whole-genome sequencing (WGS) data to identify CH variants across seven pediatric diseases (adolescent idiopathic scoliosis: n = 16, congenital heart defects: n = 709, disorders of sex development: n = 79, ewing sarcoma: n = 287, neuroblastoma: n = 259, orofacial cleft: n = 107, and syndromic cranial dysinnervation: n = 172), available as parent-child trios in the Gabriella Miller Kids First Data Resource Center. Relatively little is understood about the genetic underpinnings of these diseases. We classified CH variants as "potentially damaging" based on minor allele frequencies (MAF), Combined Annotation Dependent Depletion scores, variant impact on transcription or translation, and gene-level frequencies in the disease group compared to a healthy population. For comparison, we also identified homozygous alternate (HA) variants, which affect both gene copies at a single locus; HA variants represent an alternative mechanism of recessive disease development and do not require phasing. Across all diseases, 2.6% of the samples had a potentially damaging CH variant and 16.2% had a potentially damaging HA variant. Of these samples with potentially damaging variants, the average number of genes per sample was 1 with a CH variant and 1.25 with a HA variant. Across all samples, 5.1 genes per disease had a CH variant, while 35.6 genes per disease had a HA variant; on average, only 4.3% of these variants affected common genes. Therefore, when seeking to identify potentially damaging variants of a putatively recessive disease, CH variants should be considered as potential contributors to disease development. If CH variants are excluded from analysis, important candidate genes may be overlooked.
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Affiliation(s)
| | - Stephen R. Piccolo
- Department of Biology, Brigham Young University, Provo, UT, United States
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5
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Liu F, Zhao Y, Beier S, Jiang Y, Thorwarth P, H. Longin CF, Ganal M, Himmelbach A, Reif JC, Schulthess AW. Exome association analysis sheds light onto leaf rust (Puccinia triticina) resistance genes currently used in wheat breeding (Triticum aestivum L.). PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1396-1408. [PMID: 31782598 PMCID: PMC7207002 DOI: 10.1111/pbi.13303] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/06/2019] [Accepted: 11/17/2019] [Indexed: 05/18/2023]
Abstract
Resistance breeding is crucial for a sustainable control of leaf rust (Puccinia triticina) in wheat (Triticum aestivum L.) while directly targeting functional variants is the Holy Grail for efficient marker-assisted selection and map-based cloning. We assessed the limits and prospects of exome association analysis for severity of leaf rust in a large hybrid wheat population of 1574 single-crosses plus their 133 parents. After imputation and quality control, exome sequencing revealed 202 875 single-nucleotide polymorphisms (SNPs) covering 19.7% of the high-confidence annotated gene space. We performed intensive data mining and found significant associations for 2171 SNPs corresponding to 50 different loci. Some of these associations mapped in the proximity of the already known resistance genes Lr21, Lr34-B, Lr1 and Lr10, while other associated genomic regions, such as those on chromosomes 1A and 3D, harboured several annotated genes putatively involved in resistance. Validation with an independent population helped to narrow down the list of putative resistance genes that should be targeted by fine-mapping. We expect that the proposed strategy of intensive data mining coupled with validation will significantly influence research in plant genetics and breeding.
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Affiliation(s)
- Fang Liu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt SeelandGermany
| | - Yusheng Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt SeelandGermany
| | - Sebastian Beier
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt SeelandGermany
| | - Yong Jiang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt SeelandGermany
| | - Patrick Thorwarth
- State Plant Breeding InstituteUniversity of HohenheimStuttgartGermany
| | | | | | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt SeelandGermany
| | - Jochen C. Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt SeelandGermany
| | - Albert W. Schulthess
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt SeelandGermany
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6
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Pontikos N, Murphy C, Moghul I, Arno G, Fujinami K, Fujinami Y, Sumodhee D, Downes S, Webster A, Yu J. Phenogenon: Gene to phenotype associations for rare genetic diseases. PLoS One 2020; 15:e0230587. [PMID: 32271766 PMCID: PMC7144978 DOI: 10.1371/journal.pone.0230587] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 03/03/2020] [Indexed: 11/30/2022] Open
Abstract
As high-throughput sequencing is increasingly applied to the molecular diagnosis of rare Mendelian disorders, a large number of patients with diverse phenotypes have their genetic and phenotypic data pooled together to uncover new gene-phenotype relations. We introduce Phenogenon, a statistical tool that combines, Human Phenotype Ontology (HPO) annotated patient phenotypes, gnomAD allele population frequency, and Combined Annotation Dependent Depletion (CADD) score for variant pathogenicity, in order to jointly predict the mode of inheritance and gene-phenotype associations. We ran Phenogenon on our cohort of 3,290 patients who had undergone whole exome sequencing. Among the top associations, we recapitulated previously known, such as "SRD5A3—Abnormal full-field electroretinogram—recessive" and "GRHL2 –Nail dystrophy—recessive", and discovered one potentially novel, “RRAGA–Abnormality of the skin—dominant”. We also developed an interactive web interface available at https://phenogenon.phenopolis.org to visualise and explore the results.
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Affiliation(s)
- Nikolas Pontikos
- UCL Genetics Institute, University College London, London, United Kingdom
- Institute of Ophthalmology, University College London, London, United Kingdom
- Moorfields Eye Hospital, London, United Kingdom
| | - Cian Murphy
- UCL Genetics Institute, University College London, London, United Kingdom
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Ismail Moghul
- UCL Cancer Institute, University College London, London, United Kingdom
| | - Gavin Arno
- Institute of Ophthalmology, University College London, London, United Kingdom
- Moorfields Eye Hospital, London, United Kingdom
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | - Kaoru Fujinami
- Institute of Ophthalmology, University College London, London, United Kingdom
- Moorfields Eye Hospital, London, United Kingdom
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
- Department of Ophthalmology, Keio University School of Medicine, Tokyo, Japan
| | - Yu Fujinami
- Graduate School of Health Management, Keio University, Tokyo, Japan
- Division of Public Health, Yokokawa Clinic, Osaka, Japan
| | - Dayyanah Sumodhee
- Queen Mary University, Mile End Road, Bethnal Green, London, United Kingdom
| | - Susan Downes
- Oxford Eye Hospital, West Wing, John Radcliffe Hospital, Oxford, United Kingdom
- Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Andrew Webster
- Institute of Ophthalmology, University College London, London, United Kingdom
- Moorfields Eye Hospital, London, United Kingdom
| | - Jing Yu
- Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- * E-mail:
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7
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Nellåker C, Alkuraya FS, Baynam G, Bernier RA, Bernier FP, Boulanger V, Brudno M, Brunner HG, Clayton-Smith J, Cogné B, Dawkins HJ, deVries BB, Douzgou S, Dudding-Byth T, Eichler EE, Ferlaino M, Fieggen K, Firth HV, FitzPatrick DR, Gration D, Groza T, Haendel M, Hallowell N, Hamosh A, Hehir-Kwa J, Hitz MP, Hughes M, Kini U, Kleefstra T, Kooy RF, Krawitz P, Küry S, Lees M, Lyon GJ, Lyonnet S, Marcadier JL, Meyn S, Moslerová V, Politei JM, Poulton CC, Raymond FL, Reijnders MR, Robinson PN, Romano C, Rose CM, Sainsbury DC, Schofield L, Sutton VR, Turnovec M, Van Dijck A, Van Esch H, Wilkie AO. Enabling Global Clinical Collaborations on Identifiable Patient Data: The Minerva Initiative. Front Genet 2019; 10:611. [PMID: 31417602 PMCID: PMC6681681 DOI: 10.3389/fgene.2019.00611] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 06/12/2019] [Indexed: 01/25/2023] Open
Abstract
The clinical utility of computational phenotyping for both genetic and rare diseases is increasingly appreciated; however, its true potential is yet to be fully realized. Alongside the growing clinical and research availability of sequencing technologies, precise deep and scalable phenotyping is required to serve unmet need in genetic and rare diseases. To improve the lives of individuals affected with rare diseases through deep phenotyping, global big data interrogation is necessary to aid our understanding of disease biology, assist diagnosis, and develop targeted treatment strategies. This includes the application of cutting-edge machine learning methods to image data. As with most digital tools employed in health care, there are ethical and data governance challenges associated with using identifiable personal image data. There are also risks with failing to deliver on the patient benefits of these new technologies, the biggest of which is posed by data siloing. The Minerva Initiative has been designed to enable the public good of deep phenotyping while mitigating these ethical risks. Its open structure, enabling collaboration and data sharing between individuals, clinicians, researchers and private enterprise, is key for delivering precision public health.
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Affiliation(s)
- Christoffer Nellåker
- Nuffield Department of Women’s and Reproductive Health, University of Oxford, Oxford, United Kingdom
- Big Data Institute, University of Oxford, Oxford, United Kingdom
- Institute for Biomedical Engineering, University of Oxford, Oxford, United Kingdom
| | - Fowzan S. Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies, and Genetic Services of Western Australia, King Edward Memorial, Subiaco, WA, Australia
- Telethon Kids Institute and School of Paediatrics and Child Health, University of Western Australia, Perth, WA, Australia
- Spatial Sciences, Science and Engineering, Curtin University, Perth, WA, Australia
| | - Raphael A. Bernier
- Department of Psychiatry & Behavioral Science, University of Washington School of Medicine, Seattle, WA, United States
| | | | - Vanessa Boulanger
- National Organization for Rare Disorders, Danbury, CT, United States
| | - Michael Brudno
- Department of Computer Science, University of Toronto and the Hospital for Sick Children, Toronto, Canada
| | - Han G. Brunner
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Jill Clayton-Smith
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, MAHSC, Saint Mary’s Hospital, Manchester, United Kingdom
| | - Benjamin Cogné
- CHU Nantes, Service de Génétique Médicale, Nantes, France
| | - Hugh J.S. Dawkins
- Office of Population Health Genomics, Public and Aboriginal Health Division, Department of Health Government of Western Australia, Perth, WA, Australia
- Sir Walter Murdoch School of Policy and International Affairs, Murdoch University
- Centre for Population Health Research, Curtin University of Technology, Perth, WA, Australia
| | - Bert B.A. deVries
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Sofia Douzgou
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, MAHSC, Saint Mary’s Hospital, Manchester, United Kingdom
| | | | - Evan E. Eichler
- Department of Genome Science, University of Washington School of Medicine, Seattle, WA, United States
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, United States
| | - Michael Ferlaino
- Nuffield Department of Women’s and Reproductive Health, University of Oxford, Oxford, United Kingdom
- Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Karen Fieggen
- Division of Human Genetics, Level 3, Wernher and Beit North, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa
| | - Helen V. Firth
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - David R. FitzPatrick
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Dylan Gration
- Genetic Services of Western Australia, King Edward Memorial Hospital, Subiaco, WA, Australia
| | - Tudor Groza
- The Garvan Institute, Sydney, NSW, Australia
| | - Melissa Haendel
- Oregon Health & Science University, Portland, OR, United States
| | - Nina Hallowell
- Big Data Institute, University of Oxford, Oxford, United Kingdom
- Wellcome Centre for Ethics and Humanities, University of Oxford, Oxford, United Kingdom
- Ethox Centre, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Jayne Hehir-Kwa
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Marc-Phillip Hitz
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein–Campus Kiel, Kiel, Germany
| | - Mark Hughes
- Department of Clinical Neurosciences, Western General Hospital, Edinburgh, United Kingdom
| | - Usha Kini
- Oxford Centre for Genomic Medicine, Oxford, United Kingdom
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Peter Krawitz
- Institut für Genomische Statistik und Bioinformatik, Universitätsklinikum Bonn, Rheinische-Friedrich-Wilhelms-Universität, Bonn, Germany
| | - Sébastien Küry
- CHU Nantes, Service de Génétique Médicale, Nantes, France
| | - Melissa Lees
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Gholson J. Lyon
- George A. Jervis Clinic and Institute for Basic Research in Developmental Disabilities (IBR), Staten Island, NY, United States
| | | | | | - Stephen Meyn
- Department of Computer Science, University of Toronto and the Hospital for Sick Children, Toronto, Canada
| | - Veronika Moslerová
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University and University Hospital, Prague, Czechia
| | - Juan M. Politei
- Laboratorio Chamoles, Errores Congénitos del Metabolismo, Buenos Aires, Argentina
| | - Cathryn C. Poulton
- Department of Paediatrics and Neonates, Fiona Stanley Hospital, Perth, WA, Australia
| | - F Lucy Raymond
- CIMR (Wellcome Trust/MRC Building), Cambridge, United Kingdom
| | - Margot R.F. Reijnders
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | | | | | - Catherine M. Rose
- Victorian Clinical Genetics Service and Murdoch Childrens Research Institute, The Royal Children’s Hospital, Parkville, VIC, Australia
| | - David C.G. Sainsbury
- Northern & Yorkshire Cleft Lip and Palate Service, Royal Victoria Infirmary, Newcastle upon Tyne, United Kingdom
| | - Lyn Schofield
- Genetic Services of Western Australia, King Edward Memorial Hospital, Subiaco, WA, Australia
| | - Vernon R. Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Marek Turnovec
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University and University Hospital, Prague, Czechia
| | - Anke Van Dijck
- Department of Medical Genetics, University and University Hospital Antwerp, Antwerp, Belgium
| | - Hilde Van Esch
- Center for Human Genetics, University Hospitals Leuven, University of Leuven, Leuven, Belgium
| | - Andrew O.M. Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
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8
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Rao AR, Nelson SF. Calculating the statistical significance of rare variants causal for Mendelian and complex disorders. BMC Med Genomics 2018; 11:53. [PMID: 29898714 PMCID: PMC6001062 DOI: 10.1186/s12920-018-0371-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 05/25/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND With the expanding use of next-gen sequencing (NGS) to diagnose the thousands of rare Mendelian genetic diseases, it is critical to be able to interpret individual DNA variation. To calculate the significance of finding a rare protein-altering variant in a given gene, one must know the frequency of seeing a variant in the general population that is at least as damaging as the variant in question. METHODS We developed a general method to better interpret the likelihood that a rare variant is disease causing if observed in a given gene or genic region mapping to a described protein domain, using genome-wide information from a large control sample. Based on data from 2504 individuals in the 1000 Genomes Project dataset, we calculated the number of individuals who have a rare variant in a given gene for numerous filtering threshold scenarios, which may be used for calculating the significance of an observed rare variant being causal for disease. Additionally, we calculated mutational burden data on the number of individuals with rare variants in genic regions mapping to protein domains. RESULTS We describe methods to use the mutational burden data for calculating the significance of observing rare variants in a given proportion of sequenced individuals. We present SORVA, an implementation of these methods as a web tool, and we demonstrate application to 20 relevant but diverse next-gen sequencing studies. Specifically, we calculate the statistical significance of findings involving multi-family studies with rare Mendelian disease and a large-scale study of a complex disorder, autism spectrum disorder. If we use the frequency counts to rank genes based on intolerance for variation, the ranking correlates well with pLI scores derived from the Exome Aggregation Consortium (ExAC) dataset (ρ = 0.515), with the benefit that the scores are directly interpretable. CONCLUSIONS We have presented a strategy that is useful for vetting candidate genes from NGS studies and allows researchers to calculate the significance of seeing a variant in a given gene or protein domain. This approach is an important step towards developing a quantitative, statistics-based approach for presenting clinical findings.
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Affiliation(s)
- Aliz R Rao
- Department of Human Genetics, University of California, Los Angeles, California, Los Angeles, USA.
| | - Stanley F Nelson
- Department of Human Genetics, University of California, Los Angeles, California, Los Angeles, USA.,Department of Psychiatry and Biobehavioral Sciences at the David Geffen School of Medicine, University of California, Los Angeles, California, Los Angeles, USA.,Department of Pathology and Laboratory Medicine, University of California, Los Angeles, California, Los Angeles, USA
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9
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Townend GS, Ehrhart F, van Kranen HJ, Wilkinson M, Jacobsen A, Roos M, Willighagen EL, van Enckevort D, Evelo CT, Curfs LMG. MECP2 variation in Rett syndrome-An overview of current coverage of genetic and phenotype data within existing databases. Hum Mutat 2018; 39:914-924. [PMID: 29704307 PMCID: PMC6033003 DOI: 10.1002/humu.23542] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 04/18/2018] [Accepted: 04/23/2018] [Indexed: 12/30/2022]
Abstract
Rett syndrome (RTT) is a monogenic rare disorder that causes severe neurological problems. In most cases, it results from a loss-of-function mutation in the gene encoding methyl-CPG-binding protein 2 (MECP2). Currently, about 900 unique MECP2 variations (benign and pathogenic) have been identified and it is suspected that the different mutations contribute to different levels of disease severity. For researchers and clinicians, it is important that genotype-phenotype information is available to identify disease-causing mutations for diagnosis, to aid in clinical management of the disorder, and to provide counseling for parents. In this study, 13 genotype-phenotype databases were surveyed for their general functionality and availability of RTT-specific MECP2 variation data. For each database, we investigated findability and interoperability alongside practical user functionality, and type and amount of genetic and phenotype data. The main conclusions are that, as well as being challenging to find these databases and specific MECP2 variants held within, interoperability is as yet poorly developed and requires effort to search across databases. Nevertheless, we found several thousand online database entries for MECP2 variations and their associated phenotypes, diagnosis, or predicted variant effects, which is a good starting point for researchers and clinicians who want to provide, annotate, and use the data.
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Affiliation(s)
- Gillian S Townend
- Rett Expertise Centre Netherlands - GKC, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Friederike Ehrhart
- Rett Expertise Centre Netherlands - GKC, Maastricht University Medical Center, Maastricht, The Netherlands.,Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
| | - Henk J van Kranen
- Rett Expertise Centre Netherlands - GKC, Maastricht University Medical Center, Maastricht, The Netherlands.,Institute for Public Health Genomics, Maastricht University, Maastricht, The Netherlands
| | - Mark Wilkinson
- Center for Plant Biotechnology and Genomics, Universidad Politécnica de Madrid, Madrid, Spain
| | - Annika Jacobsen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Marco Roos
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Egon L Willighagen
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
| | - David van Enckevort
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Chris T Evelo
- Rett Expertise Centre Netherlands - GKC, Maastricht University Medical Center, Maastricht, The Netherlands.,Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
| | - Leopold M G Curfs
- Rett Expertise Centre Netherlands - GKC, Maastricht University Medical Center, Maastricht, The Netherlands
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10
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Cassa CA, Akle S, Jordan DM, Rosenfeld JA. When " N of 2" is not enough: integrating statistical and functional data in gene discovery. Cold Spring Harb Mol Case Stud 2017; 3:a001099. [PMID: 28487880 PMCID: PMC5411689 DOI: 10.1101/mcs.a001099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The expanding use of genomic sequencing promises to improve clinical diagnostics and to drive the discovery of new disease genes. Candidate genes are increasingly being identified through recurrent cases (e.g., two or more independent cases [“N of 2”] in which variants are present in the same gene). These second case hits provide statistical evidence of an association, which may then be combined with functional validation or familial segregation studies to bolster the evidence that a gene is truly causal. Here, we discuss how to integrate different forms of functional evidence with human genetics case and segregation data to improve the significance of new disease–gene associations.
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Affiliation(s)
- Christopher A Cassa
- Brigham and Women's Hospital, Division of Genetics, Boston, Massachusetts 02115, USA.,Harvard Medical School, Department of Medicine, Boston, Massachusetts 02115, USA
| | - Sebastian Akle
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Daniel M Jordan
- Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
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11
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Boycott KM, Rath A, Chong JX, Hartley T, Alkuraya FS, Baynam G, Brookes AJ, Brudno M, Carracedo A, den Dunnen JT, Dyke SOM, Estivill X, Goldblatt J, Gonthier C, Groft SC, Gut I, Hamosh A, Hieter P, Höhn S, Hurles ME, Kaufmann P, Knoppers BM, Krischer JP, Macek M, Matthijs G, Olry A, Parker S, Paschall J, Philippakis AA, Rehm HL, Robinson PN, Sham PC, Stefanov R, Taruscio D, Unni D, Vanstone MR, Zhang F, Brunner H, Bamshad MJ, Lochmüller H. International Cooperation to Enable the Diagnosis of All Rare Genetic Diseases. Am J Hum Genet 2017; 100:695-705. [PMID: 28475856 PMCID: PMC5420351 DOI: 10.1016/j.ajhg.2017.04.003] [Citation(s) in RCA: 245] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Provision of a molecularly confirmed diagnosis in a timely manner for children and adults with rare genetic diseases shortens their "diagnostic odyssey," improves disease management, and fosters genetic counseling with respect to recurrence risks while assuring reproductive choices. In a general clinical genetics setting, the current diagnostic rate is approximately 50%, but for those who do not receive a molecular diagnosis after the initial genetics evaluation, that rate is much lower. Diagnostic success for these more challenging affected individuals depends to a large extent on progress in the discovery of genes associated with, and mechanisms underlying, rare diseases. Thus, continued research is required for moving toward a more complete catalog of disease-related genes and variants. The International Rare Diseases Research Consortium (IRDiRC) was established in 2011 to bring together researchers and organizations invested in rare disease research to develop a means of achieving molecular diagnosis for all rare diseases. Here, we review the current and future bottlenecks to gene discovery and suggest strategies for enabling progress in this regard. Each successful discovery will define potential diagnostic, preventive, and therapeutic opportunities for the corresponding rare disease, enabling precision medicine for this patient population.
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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.
| | - Ana Rath
- Orphanet, Institut National de la Santé et de la Recherche Médicale US14, 75014 Paris, France
| | - Jessica X Chong
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Research Center, Riyadh 11211, Saudi Arabia; Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
| | - Gareth Baynam
- Genetic Services of Western Australia, Perth, WA 6008, Australia
| | - Anthony J Brookes
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto M5S 1A1, Canada
| | - Angel Carracedo
- Genomic Medicine Group, Galician Foundation of Genomic Medicine and University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Johan T den Dunnen
- Departments of Human Genetics and Clinical Genetics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Stephanie O M Dyke
- Centre of Genomics and Policy, Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, QC H3A 1A4, Canada
| | - Xavier Estivill
- Experimental Division, Sidra Medical and Research Center, PO Box 26999, Doha, Qatar; Genetics Unit, Dexeus Woman's Health, 08028 Barcelona, Spain
| | - Jack Goldblatt
- Genetic Services of Western Australia, Perth, WA 6008, Australia
| | - Catherine Gonthier
- Orphanet, Institut National de la Santé et de la Recherche Médicale US14, 75014 Paris, France
| | - Stephen C Groft
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892-4874, USA
| | - Ivo Gut
- Centre Nacional d'Anàlisi Genòmica, Center for Genomic Regulation, Barcelona Institute of Science and Technology, Universitat Pompeu Fabra, 08028 Barcelona, Spain
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21286, USA
| | - Philip Hieter
- Michael Smith Laboratories, Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Sophie Höhn
- Orphanet, Institut National de la Santé et de la Recherche Médicale US14, 75014 Paris, France
| | - Matthew E Hurles
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Petra Kaufmann
- Office of Rare Diseases Research, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892-4874, USA
| | - Bartha M Knoppers
- Centre of Genomics and Policy, Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, QC H3A 1A4, Canada
| | - Jeffrey P Krischer
- University of South Florida Health Informatics Institute, Tampa, FL 33620, USA
| | - Milan Macek
- Department of Biology and Medical Genetics, Second Faculty of Medicine, Charles University and University Hospital Motol, 150 06 Prague 5, Czech Republic
| | - Gert Matthijs
- Center for Human Genetics, University of Leuven, 3000 Leuven, Belgium
| | - Annie Olry
- Orphanet, Institut National de la Santé et de la Recherche Médicale US14, 75014 Paris, France
| | | | - Justin Paschall
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | | | - Heidi L Rehm
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Peter N Robinson
- Institut für Medizinische Genetik und Humangenetik, Charité Universitätsmdizin Berlin, 13353 Berlin, Germany; Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Pak-Chung Sham
- Centre for Genomic Sciences, University of Hong Kong, Hong Kong, China
| | - Rumen Stefanov
- Department of Social Medicine and Public Health, Faculty of Public Health, Medical University of Plovdiv, Plovdiv 4002, Bulgaria
| | - Domenica Taruscio
- National Centre for Rare Diseases, Istituto Superiore di Sanità, Rome 299-00161, Italy
| | - Divya Unni
- Orphanet, Institut National de la Santé et de la Recherche Médicale US14, 75014 Paris, France
| | - Megan R Vanstone
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Feng Zhang
- WuXi AppTec, Waigaoqiao Free Trade Zone, Shanghai 200131, China; WuXi NextCODE, Cambridge, MA 02142, USA
| | - Han Brunner
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands; Maastricht University Medical Center, Department of Clinical Genetics, 6229 GT Maastricht, the Netherlands
| | - Michael J Bamshad
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Hanns Lochmüller
- John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
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12
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Vulto-van Silfhout AT, Gilissen C, Goeman JJ, Jansen S, van Amen-Hellebrekers CJM, van Bon BWM, Koolen DA, Sistermans EA, Brunner HG, de Brouwer APM, de Vries BBA. Quantification of Phenotype Information Aids the Identification of Novel Disease Genes. Hum Mutat 2017; 38:594-599. [PMID: 28074630 DOI: 10.1002/humu.23176] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 01/09/2017] [Indexed: 01/10/2023]
Abstract
Next-generation sequencing led to the identification of many potential novel disease genes. The presence of mutations in the same gene in multiple unrelated patients is, however, a priori insufficient to establish that these genes are truly involved in the respective disease. Here, we show how phenotype information can be incorporated within statistical approaches to provide additional evidence for the causality of mutations. We developed a broadly applicable statistical model that integrates gene-specific mutation rates, cohort size, mutation type, and phenotype frequency information to assess the chance of identifying de novo mutations affecting the same gene in multiple patients with shared phenotype features. We demonstrate our approach based on the frequency of phenotype features present in a unique cohort of 6,149 patients with intellectual disability. We show that our combined approach can decrease the number of patients required to identify novel disease genes, especially for patients with combinations of rare phenotypes. In conclusion, we show how integrating genotype-phenotype information can aid significantly in the interpretation of de novo mutations in potential novel disease genes.
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Affiliation(s)
| | - Christian Gilissen
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Jelle J Goeman
- Department for Health Evidence, Radboud university medical center, Nijmegen, The Netherlands.,Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
| | - Sandra Jansen
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | | | - Bregje W M van Bon
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - David A Koolen
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Erik A Sistermans
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Han G Brunner
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Arjan P M de Brouwer
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Bert B A de Vries
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
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13
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Gene discovery for Mendelian conditions via social networking: de novo variants in KDM1A cause developmental delay and distinctive facial features. Genet Med 2015; 18:788-95. [PMID: 26656649 PMCID: PMC4902791 DOI: 10.1038/gim.2015.161] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 09/30/2015] [Indexed: 01/09/2023] Open
Abstract
PURPOSE The pace of Mendelian gene discovery is slowed by the "n-of-1 problem"-the difficulty of establishing the causality of a putatively pathogenic variant in a single person or family. Identification of an unrelated person with an overlapping phenotype and suspected pathogenic variant in the same gene can overcome this barrier, but it is often impeded by lack of a convenient or widely available way to share data on candidate variants/genes among families, clinicians, and researchers. METHODS Social networking among families, clinicians, and researchers was used to identify three children with variants of unknown significance in KDM1A and similar phenotypes. RESULTS De novo variants in KDM1A underlie a new syndrome characterized by developmental delay and distinctive facial features. CONCLUSION Social networking is a potentially powerful strategy to discover genes for rare Mendelian conditions, particularly those with nonspecific phenotypic features. To facilitate the efforts of families to share phenotypic and genomic information with each other, clinicians, and researchers, we developed the Repository for Mendelian Genomics Family Portal (RMD-FP; http://uwcmg.org/#/family). Design and development of MyGene2 (http://www.mygene2.org), a Web-based tool that enables families, clinicians, and researchers to search for gene matches based on analysis of phenotype and exome data deposited into the RMD-FP, is under way.Genet Med 18 8, 788-795.
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14
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Philippakis AA, Azzariti DR, Beltran S, Brookes AJ, Brownstein CA, Brudno M, Brunner HG, Buske OJ, Carey K, Doll C, Dumitriu S, Dyke SO, den Dunnen JT, Firth HV, Gibbs RA, Girdea M, Gonzalez M, Haendel MA, Hamosh A, Holm IA, Huang L, Hurles ME, Hutton B, Krier JB, Misyura A, Mungall CJ, Paschall J, Paten B, Robinson PN, Schiettecatte F, Sobreira NL, Swaminathan GJ, Taschner PE, Terry SF, Washington NL, Züchner S, Boycott KM, Rehm HL. The Matchmaker Exchange: a platform for rare disease gene discovery. Hum Mutat 2015; 36:915-21. [PMID: 26295439 PMCID: PMC4610002 DOI: 10.1002/humu.22858] [Citation(s) in RCA: 345] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 07/21/2015] [Indexed: 12/21/2022]
Abstract
There are few better examples of the need for data sharing than in the rare disease community, where patients, physicians, and researchers must search for "the needle in a haystack" to uncover rare, novel causes of disease within the genome. Impeding the pace of discovery has been the existence of many small siloed datasets within individual research or clinical laboratory databases and/or disease-specific organizations, hoping for serendipitous occasions when two distant investigators happen to learn they have a rare phenotype in common and can "match" these cases to build evidence for causality. However, serendipity has never proven to be a reliable or scalable approach in science. As such, the Matchmaker Exchange (MME) was launched to provide a robust and systematic approach to rare disease gene discovery through the creation of a federated network connecting databases of genotypes and rare phenotypes using a common application programming interface (API). The core building blocks of the MME have been defined and assembled. Three MME services have now been connected through the API and are available for community use. Additional databases that support internal matching are anticipated to join the MME network as it continues to grow.
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Affiliation(s)
- Anthony A. Philippakis
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Cardiology, Brigham & Women's Hospital,
Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Danielle R. Azzariti
- Laboratory for Molecular Medicine, Partners Personalized
Medicine, Boston, MA USA
| | - Sergi Beltran
- Centro Nacional de Análisis Genómico, Barcelona,
Spain
| | | | - Catherine A. Brownstein
- Harvard Medical School, Boston, MA, USA
- Division of Genetics and Genomics and the Manton Center for
Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto,
Canada
- Genetics and Genome Biology Program, The Hospital for Sick
Children, Toronto, Canada
- Centre for Computational Medicine, The Hospital for Sick
Children, Toronto, Canada
| | - Han G. Brunner
- Radboud University Medical Center,Department of Human
Genetics, PO Box 9101, 6500HB Nijmegen, The Netherlands
- Maastricht University Medical Center, Department of Clinical
Genetics,PO Box 5800, 6202AZ Maastricht, The Netherlands
| | - Orion J. Buske
- Department of Computer Science, University of Toronto, Toronto,
Canada
- Genetics and Genome Biology Program, The Hospital for Sick
Children, Toronto, Canada
- Centre for Computational Medicine, The Hospital for Sick
Children, Toronto, Canada
| | | | | | - Sergiu Dumitriu
- Centre for Computational Medicine, The Hospital for Sick
Children, Toronto, Canada
| | - Stephanie O.M. Dyke
- Centre of Genomics and Policy, Faculty of Medicine, McGill
University, Canada
| | - Johan T. den Dunnen
- Human and Clinical Genetics, Leiden University Medical Center,
Leiden, Nederland
| | - Helen V. Firth
- East Anglian Medical Genetics Service, Box 134, Cambridge
University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, CB2 0QQ,
UK
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine,
Houston, Tx 77030, U.S.A
| | - Marta Girdea
- Department of Computer Science, University of Toronto, Toronto,
Canada
- Centre for Computational Medicine, The Hospital for Sick
Children, Toronto, Canada
| | | | - Melissa A. Haendel
- Department of Medical Informatics and Clinical Epidemiology,
Oregon Health & Science University, Portland, OR, USA
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins
University, Baltimore, MD, USA
| | - Ingrid A. Holm
- Harvard Medical School, Boston, MA, USA
- Division of Genetics and Genomics and the Manton Center for
Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Lijia Huang
- The Children's Hospital of Eastern Ontario Research Institute,
Ottawa, ON, Canada
| | - Matthew E. Hurles
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus,
Hinxton CB10 1SA, U.K
| | - Ben Hutton
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus,
Hinxton CB10 1SA, U.K
| | - Joel B. Krier
- Division of Genetics, Department of Medicine, Brigham and
Women's Hospital, 41 Avenue Louis Pasteur, Suite 301, Boston, MA 02115, USA
| | - Andriy Misyura
- Centre for Computational Medicine, The Hospital for Sick
Children, Toronto, Canada
| | | | - Justin Paschall
- European Molecular Biology Laboratory - European
Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD,
UK
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, 1156 High Street, Santa
Cruz, CA, USA
| | - Peter N. Robinson
- Institute for Medical Genetics and Human Genetics,
Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
- Max Planck Institute for Molecular Genetics, 14195 Berlin,
Germany
- Institute for Bioinformatics, Department of Mathematics and
Computer Science, Freie Universität Berlin, 14195 Berlin, Germany
- Berlin Brandenburg Center for Regenerative Therapies, 13353
Berlin, Germany
| | | | - Nara L. Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins
University, Baltimore, MD, USA
| | - Ganesh J. Swaminathan
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus,
Hinxton CB10 1SA, U.K
| | - Peter E. Taschner
- Department of Medical Informatics and Clinical Epidemiology,
Oregon Health & Science University, Portland, OR, USA
- Division of Genetics, Department of Medicine, Brigham and
Women's Hospital, 41 Avenue Louis Pasteur, Suite 301, Boston, MA 02115, USA
| | | | | | - Stephan Züchner
- Dr. John T. Macdonald Foundation Department of Human Genetics
and John P. Hussman Institute for Human Genomics, University of Miami Miller School of
Medicine, Miami, FL, USA
| | - Kym M. Boycott
- Department of Genetics, Children's Hospital of Eastern
Ontario, Ottawa, Ontario, Canada
| | - Heidi L. Rehm
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Laboratory for Molecular Medicine, Partners Personalized
Medicine, Boston, MA USA
- Department of Pathology, Brigham & Women's Hospital, Boston,
MA, USA
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