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Ungar RA, Goddard PC, Jensen TD, Degalez F, Smith KS, Jin CA, Bonner DE, Bernstein JA, Wheeler MT, Montgomery SB. Impact of genome build on RNA-seq interpretation and diagnostics. Am J Hum Genet 2024; 111:1282-1300. [PMID: 38834072 PMCID: PMC11267525 DOI: 10.1016/j.ajhg.2024.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 05/04/2024] [Accepted: 05/06/2024] [Indexed: 06/06/2024] Open
Abstract
Transcriptomics is a powerful tool for unraveling the molecular effects of genetic variants and disease diagnosis. Prior studies have demonstrated that choice of genome build impacts variant interpretation and diagnostic yield for genomic analyses. To identify the extent genome build also impacts transcriptomics analyses, we studied the effect of the hg19, hg38, and CHM13 genome builds on expression quantification and outlier detection in 386 rare disease and familial control samples from both the Undiagnosed Diseases Network and Genomics Research to Elucidate the Genetics of Rare Disease Consortium. Across six routinely collected biospecimens, 61% of quantified genes were not influenced by genome build. However, we identified 1,492 genes with build-dependent quantification, 3,377 genes with build-exclusive expression, and 9,077 genes with annotation-specific expression across six routinely collected biospecimens, including 566 clinically relevant and 512 known OMIM genes. Further, we demonstrate that between builds for a given gene, a larger difference in quantification is well correlated with a larger change in expression outlier calling. Combined, we provide a database of genes impacted by build choice and recommend that transcriptomics-guided analyses and diagnoses are cross referenced with these data for robustness.
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Affiliation(s)
- Rachel A Ungar
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA; Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Pagé C Goddard
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA; Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Tanner D Jensen
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA; Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | | | - Kevin S Smith
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Christopher A Jin
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Devon E Bonner
- Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA, USA; Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
| | - Jonathan A Bernstein
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
| | - Matthew T Wheeler
- Department of Cardiovascular Medicine, School of Medicine, Stanford University, Stanford, CA, USA
| | - Stephen B Montgomery
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA; Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
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Ungar RA, Goddard PC, Jensen TD, Degalez F, Smith KS, Jin CA, Bonner DE, Bernstein JA, Wheeler MT, Montgomery SB. Impact of genome build on RNA-seq interpretation and diagnostics. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.11.24301165. [PMID: 38260490 PMCID: PMC10802764 DOI: 10.1101/2024.01.11.24301165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Transcriptomics is a powerful tool for unraveling the molecular effects of genetic variants and disease diagnosis. Prior studies have demonstrated that choice of genome build impacts variant interpretation and diagnostic yield for genomic analyses. To identify the extent genome build also impacts transcriptomics analyses, we studied the effect of the hg19, hg38, and CHM13 genome builds on expression quantification and outlier detection in 386 rare disease and familial control samples from both the Undiagnosed Diseases Network (UDN) and Genomics Research to Elucidate the Genetics of Rare Disease (GREGoR) Consortium. We identified 2,800 genes with build-dependent quantification across six routinely-collected biospecimens, including 1,391 protein-coding genes and 341 known rare disease genes. We further observed multiple genes that only have detectable expression in a subset of genome builds. Finally, we characterized how genome build impacts the detection of outlier transcriptomic events. Combined, we provide a database of genes impacted by build choice, and recommend that transcriptomics-guided analyses and diagnoses are cross-referenced with these data for robustness.
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Affiliation(s)
- Rachel A. Ungar
- Department of Genetics, School of Medicine, Stanford University
- Department of Pathology, School of Medicine, Stanford University
| | - Pagé C. Goddard
- Department of Genetics, School of Medicine, Stanford University
- Department of Pathology, School of Medicine, Stanford University
| | - Tanner D. Jensen
- Department of Genetics, School of Medicine, Stanford University
- Department of Pathology, School of Medicine, Stanford University
| | | | - Kevin S. Smith
- Department of Pathology, School of Medicine, Stanford University
| | | | | | - Devon E. Bonner
- Department of Pediatrics, School of Medicine, Stanford University
- Stanford Center for Undiagnosed Diseases, Stanford University
| | | | - Matthew T. Wheeler
- Department of Cardiovascular Medicine, School of Medicine, Stanford University
| | - Stephen B. Montgomery
- Department of Genetics, School of Medicine, Stanford University
- Department of Pathology, School of Medicine, Stanford University
- Department of Biomedical Data Science, Stanford University
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Ludwig K, Wu Z, Bardai G, Mason P, Ward LM, Moffatt P, Rauch F. RNA Sequencing of Urine-Derived Cells for the Characterization and Diagnosis of Osteogenesis Imperfecta. J Bone Miner Res 2023; 38:1125-1134. [PMID: 37293821 DOI: 10.1002/jbmr.4865] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/23/2023] [Accepted: 06/06/2023] [Indexed: 06/10/2023]
Abstract
DNA sequencing is a reliable tool for identifying genetic variants in osteogenesis imperfecta (OI) but cannot always establish pathogenicity, particularly in variants altering splicing. RNA sequencing can provide functional evidence of the effect of a variant on the transcript but requires cells expressing the relevant genes. Here, we used urine-derived cells (UDC) to characterize genetic variants in patients with suspected or confirmed OI and provide evidence on the pathogenicity of variants of uncertain significance (VUS). Urine samples were obtained from 45 children and adolescents; UDC culture was successful in 40 of these participants (age range 4-20 years, 21 females), including 18 participants with OI or suspected OI who had a candidate variant or VUS on DNA sequencing. RNA was extracted from UDC and sequenced on an Illumina NextSeq550 device. Principal component analysis showed that the gene expression profiles of UDC and fibroblasts (based on Genotype Tissue Expression [GTEx] Consortium data) clustered close together and had less variability than those of whole blood cells. Transcript abundance was sufficient for analysis by RNA sequencing (defined as a median gene expression level of ≥10 transcripts per million) for 25 of the 32 bone fragility genes (78%) that were included in our diagnostic DNA sequencing panel. These results were similar to GTEx data for fibroblasts. Abnormal splicing was identified in 7 of the 8 participants with pathogenic or likely pathogenic variants in the splice region or deeper within the intron. Abnormal splicing was also observed in 2 VUS (COL1A1 c.2829+5G>A and COL1A2 c.693+6T>G), but no splice abnormality was observed in 3 other VUS. Abnormal deletions and duplications could also be observed in UDC transcripts. In conclusion, UDC are suitable for RNA transcript analysis in patients with suspected OI and can provide functional evidence for pathogenicity, in particular of variants affecting splicing. © 2023 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Karissa Ludwig
- Shriners Hospital for Children - Canada, Montreal, Canada
| | - Zenghui Wu
- Shriners Hospital for Children - Canada, Montreal, Canada
| | - Ghalib Bardai
- Shriners Hospital for Children - Canada, Montreal, Canada
| | - Patrizia Mason
- Shriners Hospital for Children - Canada, Montreal, Canada
| | - Leanne M Ward
- Department of Pediatrics, University of Ottawa and Division of Endocrinology, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Pierre Moffatt
- Shriners Hospital for Children - Canada, Montreal, Canada
| | - Frank Rauch
- Shriners Hospital for Children - Canada, Montreal, Canada
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Nugent D, Acharya SS, Baumann KJ, Bedrosian C, Bialas R, Brown K, Corzo D, Haidar A, Hayward CPM, Marks P, Menegatti M, Miller ME, Nammacher K, Palla R, Peltier S, Pruthi RK, Recht M, Sørensen B, Tarantino M, Wolberg AS, Shapiro AD. Building the foundation for a community-generated national research blueprint for inherited bleeding disorders: research priorities for ultra-rare inherited bleeding disorders. Expert Rev Hematol 2023; 16:55-70. [PMID: 36920862 PMCID: PMC10020868 DOI: 10.1080/17474086.2023.2175661] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/30/2023] [Indexed: 03/16/2023]
Abstract
BACKGROUND Ultra-rare inherited bleeding disorders (BDs) present important challenges for generating a strong evidence foundation for optimal diagnosis and management. Without disorder-appropriate treatment, affected individuals potentially face life-threatening bleeding, delayed diagnosis, suboptimal management of invasive procedures, psychosocial distress, pain, and decreased quality-of-life. RESEARCH DESIGN AND METHODS The National Hemophilia Foundation (NHF) and the American Thrombosis and Hemostasis Network identified the priorities of people with inherited BDs and their caregivers, through extensive inclusive community consultations, to inform a blueprint for future decades of research. Multidisciplinary expert Working Group (WG) 3 distilled highly feasible transformative ultra-rare inherited BD research opportunities from the community-identified priorities. RESULTS WG3 identified three focus areas with the potential to advance the needs of all people with ultra-rare inherited BDs and scored the feasibility, impact, and risk of priority initiatives, including 13 in systems biology and mechanistic science; 2 in clinical research, data collection, and research infrastructure; and 5 in the regulatory process for novel therapeutics and required data collection. CONCLUSIONS Centralization and expansion of expertise and resources, flexible innovative research and regulatory approaches, and inclusion of all people with ultra-rare inherited BDs and their health care professionals will be essential to capitalize on the opportunities outlined herein.
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Affiliation(s)
- Diane Nugent
- Center for Inherited Blood Disorders, Orange, California, USA
- Children’s Hospital of Orange County, University of California at Irvine, Irvine, California, USA
| | - Suchitra S. Acharya
- Hemostasis and Thrombosis Center, Northwell Health, New Hyde Park, New York, New York, USA
| | - Kimberly J. Baumann
- Center for Bleeding and Clotting Disorders, M Health Fairview, Minneapolis, Minnesota, USA
| | | | - Rebeca Bialas
- Plasminogen Deficiency Foundation, Durham, North Carolina, USA
| | - Kai Brown
- National Hemophilia Foundation, New York, New York, USA
| | - Deya Corzo
- Sigilon Therapeutics, Cambridge, Massachusetts, USA
| | - Amar Haidar
- Patient author, Lived Experience Expert, Dearborn, Michigan, USA
| | - Catherine P. M. Hayward
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Ontario, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Peter Marks
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Marzia Menegatti
- Angelo Bianchi Bonomi Hemophilia and Thrombosis Center and Fondazione Luigi Villa, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | | | - Roberta Palla
- Angelo Bianchi Bonomi Hemophilia and Thrombosis Center and Fondazione Luigi Villa, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Skye Peltier
- Center for Bleeding and Clotting Disorders, M Health Fairview, Minneapolis, Minnesota, USA
| | - Rajiv K. Pruthi
- Comprehensive Hemophilia Center, Division of Hematology, Mayo Clinic, Rochester, Minnesota, USA
| | - Michael Recht
- American Thrombosis and Hemostasis Network, Rochester, New York, USA
- The Hemophilia Center, Oregon Health & Science University, Portland, Oregon, USA
| | | | | | - Alisa S. Wolberg
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- UNC Blood Research Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Amy D. Shapiro
- Indiana Hemophilia and Thrombosis Center, Indianapolis, Indiana, USA
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Wang G, Wang Y, Gao C, Xie W. Novel compound heterozygous variants in EMC1 associated with global developmental delay: a lesson from a non-silent synonymous exonic mutation. Front Mol Neurosci 2023; 16:1153156. [PMID: 37187958 PMCID: PMC10175691 DOI: 10.3389/fnmol.2023.1153156] [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: 01/29/2023] [Accepted: 04/10/2023] [Indexed: 05/17/2023] Open
Abstract
Background The endoplasmic reticulum-membrane protein complex (EMC) as a molecular chaperone is required for the proper synthesis, folding and traffic of several transmembrane proteins. Variants in the subunit 1 of EMC (EMC1) have been implicated in neurodevelopmental disorders. Methods Whole exome sequencing (WES) with Sanger sequencing validation was performed for a Chinese family, including the proband (a 4-year-old girl who displayed global developmental delay, severe hypotonia and visual impairment), her affected younger sister and her non-consanguineous parents. RT-PCR assay and Sanger sequencing were used to detect abnormal RNA splicing. Results Novel compound heterozygous variants in EMC1, including the maternally inherited chr1: 19566812_1956800delinsATTCTACTT[hg19];NM_015047.3:c.765_777delins ATTCTACTT;p.(Leu256fsTer10) and the paternally inherited chr1:19549890G> A[hg19];NM_015047.3:c.2376G>A;p.(Val792=) are identified in the proband and her affected sister. RT-PCR assay followed by Sanger sequencing reveals that the c.2376G>A variant leads to aberrant splicing, with retention of intron 19 (561bp) in the mature mRNA, which is presumed to introduce a premature translational termination codon (p.(Val792fsTer31)). Conclusion Novel compound heterozygous variants in EMC1 have been identified in individuals with global developmental delay. Non-silent synonymous mutations should be kept in mind in genetic analysis.
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Affiliation(s)
- Ge Wang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yanli Wang
- Department of Rehabilitation Medicine, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou, China
| | - Chao Gao
- Department of Rehabilitation Medicine, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou, China
- *Correspondence: Chao Gao
| | - Wanqin Xie
- National Health Committee Key Laboratory of Birth Defects for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
- Wanqin Xie
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De Novo Somatic Mosaicism of CYBB Caused by Intronic LINE-1 Element Insertion Resulting in Chronic Granulomatous Disease. J Clin Immunol 2023; 43:88-100. [PMID: 35997928 DOI: 10.1007/s10875-022-01347-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/10/2022] [Indexed: 01/21/2023]
Abstract
Chronic granulomatosis disease (CGD) is a rare inborn error of immunity, characterized by phagocytic respiratory outbreak dysfunction. Mutations causing CGD occur in CYBB on the X chromosome and in the autosomal genes CYBA, NCF1, NCF2, NCF4, RAC2, and CYBC1. Nevertheless, some patients are clinically diagnosed with CGD, due to abnormal respiratory outbursts, while the pathogenic gene mutation is unidentified. Here, we report a patient with CGD who first presented with Bacillus Calmette-Guérin disease and had recurrent pneumonia. He was diagnosed with CGD by nitro blue tetrazolium and respiratory burst tests. Detailed assessment of neutrophil activity revealed that patient neutrophils were almost entirely nonfunctional. Sanger sequencing detected a 6-kb insertion of a LINE-1 transposable element in the third intron of CYBB, leading to abnormal splicing and pseudoexon insertion, as well as introduction of a premature termination codon, resulting in predicted protein truncation. Clonal analysis demonstrated that the patient had somatic mosaicism, and the phagocytes were almost all variant CYBB, while the mosaicism rate of PBMC was about 65%. Finally, deep RNA sequencing and gp91phox expression analysis confirmed the pathogenicity of the mutation. In conclusion, we demonstrate that insertion of a LINE-1 transposon in a CYBB intron was responsible for CGD in our patient. Intron LINE-1 transposon element insertion should be examined in CGD patients without any known disease-causing gene mutation, in addition to identification of new genes.
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Dohi E, Matsui H. The Utility of Small Fishes for the Genetic Study of Human Age-Related Disorders. Front Genet 2022; 13:928597. [PMID: 35910227 PMCID: PMC9335361 DOI: 10.3389/fgene.2022.928597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/08/2022] [Indexed: 11/13/2022] Open
Abstract
Animal models have been used to model human diseases, and among them, small fishes have been highlighted for their usefulness in various ways, such as the low cost of maintenance, ease of genetic modification, small size for easy handling, and strength in imaging studies due to their relative transparency. Recently, the use of turquoise killifish, Nothobranchius furzeri, which is known to exhibit various aging phenotypes in a short period, has attracted attention in research on aging and age-related diseases. However, when using animal models, it is important to keep their genetic background and interspecies differences in mind for translating them into human diseases. In this article, we obtained the gene symbols of protein-coding genes of turquoise killifish, medaka, zebrafish, and humans from NCBI datasets and extracted common shared genes among four species to explore the potential of interspecies translational research and to apply small fish models for human age-related disorders. Common shared protein-coding genes were analyzed with the Reactome Pathway Database to determine the coverage of these genes in each pathway in humans. We applied common shared genes to the Orphanet database to establish a list of human diseases that contain common shared genes among the four species. As examples, the senescence-related pathways and some pathways of human age-related diseases, such as Alzheimer’s disease, Parkinson’s disease, frontotemporal dementia, nonalcoholic fatty liver disease, progeria, hepatocellular carcinoma, and renal cell carcinoma, were extracted from the curated pathway and disease list to discuss the further utility of fish models for human age-related disorders.
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