1
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Palmgren M, Morth JP, Nissen P. TMEM94 cannot be called a P-type ATPase. Cell Calcium 2024; 123:102911. [PMID: 38879951 DOI: 10.1016/j.ceca.2024.102911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/18/2024]
Affiliation(s)
- Michael Palmgren
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark.
| | - Jens Preben Morth
- Department of Biotechnology & Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark.
| | - Poul Nissen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
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2
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Vishnu N, Venkatesan M, Madaris TR, Venkateswaran MK, Stanley K, Ramachandran K, Chidambaram A, Madesh AK, Yang W, Nair J, Narkunan M, Muthukumar T, Karanam V, Joseph LC, Le A, Osidele A, Aslam MI, Morrow JP, Malicdan MC, Stathopulos PB, Madesh M. ERMA (TMEM94) is a P-type ATPase transporter for Mg 2+ uptake in the endoplasmic reticulum. Mol Cell 2024; 84:1321-1337.e11. [PMID: 38513662 PMCID: PMC10997467 DOI: 10.1016/j.molcel.2024.02.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 10/16/2023] [Accepted: 02/27/2024] [Indexed: 03/23/2024]
Abstract
Intracellular Mg2+ (iMg2+) is bound with phosphometabolites, nucleic acids, and proteins in eukaryotes. Little is known about the intracellular compartmentalization and molecular details of Mg2+ transport into/from cellular organelles such as the endoplasmic reticulum (ER). We found that the ER is a major iMg2+ compartment refilled by a largely uncharacterized ER-localized protein, TMEM94. Conventional and AlphaFold2 predictions suggest that ERMA (TMEM94) is a multi-pass transmembrane protein with large cytosolic headpiece actuator, nucleotide, and phosphorylation domains, analogous to P-type ATPases. However, ERMA uniquely combines a P-type ATPase domain and a GMN motif for ERMg2+ uptake. Experiments reveal that a tyrosine residue is crucial for Mg2+ binding and activity in a mechanism conserved in both prokaryotic (mgtB and mgtA) and eukaryotic Mg2+ ATPases. Cardiac dysfunction by haploinsufficiency, abnormal Ca2+ cycling in mouse Erma+/- cardiomyocytes, and ERMA mRNA silencing in human iPSC-cardiomyocytes collectively define ERMA as an essential component of ERMg2+ uptake in eukaryotes.
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Affiliation(s)
- Neelanjan Vishnu
- Department of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Center for Mitochondrial Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Manigandan Venkatesan
- Department of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Center for Mitochondrial Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Travis R Madaris
- Department of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Center for Mitochondrial Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Mridula K Venkateswaran
- Department of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Center for Mitochondrial Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Kristen Stanley
- Department of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Center for Mitochondrial Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Karthik Ramachandran
- Department of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Center for Mitochondrial Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Adhishree Chidambaram
- Department of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Center for Mitochondrial Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Abitha K Madesh
- Department of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Center for Mitochondrial Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Wenli Yang
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jyotsna Nair
- Department of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Center for Mitochondrial Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Melanie Narkunan
- Department of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Center for Mitochondrial Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Tharani Muthukumar
- Department of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Center for Mitochondrial Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Varsha Karanam
- Department of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Center for Mitochondrial Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Leroy C Joseph
- Department of Medicine, College of Physicians and Surgeons of Columbia University, 650 W 168 Street, New York, NY 10032, USA
| | - Amy Le
- Department of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Center for Mitochondrial Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Ayodeji Osidele
- Department of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Center for Mitochondrial Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - M Imran Aslam
- Department of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Center for Mitochondrial Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - John P Morrow
- Department of Medicine, College of Physicians and Surgeons of Columbia University, 650 W 168 Street, New York, NY 10032, USA
| | - May C Malicdan
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; NIH Undiagnosed Diseases Program, Office of the Clinical Director, National Human Genome Research Institute, and the Common Fund, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter B Stathopulos
- Department of Physiology and Pharmacology, Western University, London, ON N6A 5C1, Canada
| | - Muniswamy Madesh
- Department of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA; Center for Mitochondrial Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA.
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3
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Smith LM, Harrison TM. Neurodevelopment in the Congenital Heart Disease Population as Framed by the Life Course Health Development Framework. J Cardiovasc Nurs 2024; 39:160-169. [PMID: 36752754 PMCID: PMC10406968 DOI: 10.1097/jcn.0000000000000977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
BACKGROUND Adverse neurodevelopment is a common comorbidity associated with congenital heart disease (CHD). The consequences of adverse neurodevelopment are seen across the life course. The cause of adverse neurodevelopment is multifactorial, and use of a life course perspective can assist with understanding and enhancing neurodevelopment in individuals with CHD. PURPOSE The purposes of this article are to (1) apply the Life Course Health Development framework to neurodevelopment in the population with CHD and (2) discuss how exposure to the pediatric cardiac intensive care unit (PCICU) environment during infancy is a point of intervention for improving neurodevelopmental outcomes. CONCLUSION Individuals with CHD are at an increased risk for adverse neurodevelopment across the life course. The PCICU environment is a point of intervention for improving neurodevelopmental outcomes. Stress can lead to changes in brain structure and function that are associated with negative outcomes in terms of outward behavioral and functional capacity, and the PCICU environment is a source of stressful stimuli. Infancy is a period of rapid brain growth, and the brain is more susceptible to stress during this period of the life course, putting infants receiving care in the PCICU at an increased risk of adverse neurodevelopment. CLINICAL IMPLICATIONS Interventions to support optimal neurodevelopment should focus on the PCICU environment during infancy. Developmentally supportive care models should be explored as a means of modifying the PCICU environment. In addition, more research is needed on the relationship between the PCICU and neurodevelopment. The conceptual model introduced can serve as a starting point for this research.
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Dutta D, Kanca O, Shridharan RV, Marcogliese PC, Steger B, Morimoto M, Frost FG, Macnamara E, Wangler MF, Yamamoto S, Jenny A, Adams D, Malicdan MC, Bellen HJ. Loss of the endoplasmic reticulum protein Tmem208 affects cell polarity, development, and viability. Proc Natl Acad Sci U S A 2024; 121:e2322582121. [PMID: 38381787 PMCID: PMC10907268 DOI: 10.1073/pnas.2322582121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 01/26/2024] [Indexed: 02/23/2024] Open
Abstract
Nascent proteins destined for the cell membrane and the secretory pathway are targeted to the endoplasmic reticulum (ER) either posttranslationally or cotranslationally. The signal-independent pathway, containing the protein TMEM208, is one of three pathways that facilitates the translocation of nascent proteins into the ER. The in vivo function of this protein is ill characterized in multicellular organisms. Here, we generated a CRISPR-induced null allele of the fruit fly ortholog CG8320/Tmem208 by replacing the gene with the Kozak-GAL4 sequence. We show that Tmem208 is broadly expressed in flies and that its loss causes lethality, although a few short-lived flies eclose. These animals exhibit wing and eye developmental defects consistent with impaired cell polarity and display mild ER stress. Tmem208 physically interacts with Frizzled (Fz), a planar cell polarity (PCP) receptor, and is required to maintain proper levels of Fz. Moreover, we identified a child with compound heterozygous variants in TMEM208 who presents with developmental delay, skeletal abnormalities, multiple hair whorls, cardiac, and neurological issues, symptoms that are associated with PCP defects in mice and humans. Additionally, fibroblasts of the proband display mild ER stress. Expression of the reference human TMEM208 in flies fully rescues the loss of Tmem208, and the two proband-specific variants fail to rescue, suggesting that they are loss-of-function alleles. In summary, our study uncovers a role of TMEM208 in development, shedding light on its significance in ER homeostasis and cell polarity.
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Affiliation(s)
- Debdeep Dutta
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX77030
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX77030
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX77030
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX77030
| | - Rishi V. Shridharan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX77030
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX77030
| | - Paul C. Marcogliese
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX77030
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX77030
| | - Benjamin Steger
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - Marie Morimoto
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - F. Graeme Frost
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - Ellen Macnamara
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | | | - Michael F. Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX77030
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX77030
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX77030
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX77030
| | - Andreas Jenny
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, New York, NY10461
- Department of Genetics, Albert Einstein College of Medicine, New York, NY10461
| | - David Adams
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - May C. Malicdan
- NIH Undiagnosed Diseases Program, National Human Genome Research Institute, NIH, Bethesda, MD20892
| | - Hugo J. Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX77030
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX77030
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5
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Narayan P, Richter F, Morton S. Genetics and etiology of congenital heart disease. Curr Top Dev Biol 2024; 156:297-331. [PMID: 38556426 DOI: 10.1016/bs.ctdb.2024.01.009] [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] [Indexed: 04/02/2024]
Abstract
Congenital heart disease (CHD) is the most common severe birth anomaly, affecting almost 1% of infants. Most CHD is genetic, but only 40% of patients have an identifiable genetic risk factor for CHD. Chromosomal variation contributes significantly to CHD but is not readily amenable to biological follow-up due to the number of affected genes and lack of evolutionary synteny. The first CHD genes were implicated in extended families with syndromic CHD based on the segregation of risk alleles in affected family members. These have been complemented by more CHD gene discoveries in large-scale cohort studies. However, fewer than half of the 440 estimated human CHD risk genes have been identified, and the molecular mechanisms underlying CHD genetics remains incompletely understood. Therefore, model organisms and cell-based models are essential tools for improving our understanding of cardiac development and CHD genetic risk. Recent advances in genome editing, cell-specific genetic manipulation of model organisms, and differentiation of human induced pluripotent stem cells have recently enabled the characterization of developmental stages. In this chapter, we will summarize the latest studies in CHD genetics and the strengths of various study methodologies. We identify opportunities for future work that will continue to further CHD knowledge and ultimately enable better diagnosis, prognosis, treatment, and prevention of CHD.
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Affiliation(s)
| | - Felix Richter
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Sarah Morton
- Boston Children's Hospital and Harvard Medical School, Boston, MA, United States.
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Mattijssen S, Kerkhofs K, Stephen J, Yang A, Han CG, Tadafumi Y, Iben JR, Mishra S, Sakhawala RM, Ranjan A, Gowda M, Gahl WA, Gu S, Malicdan MC, Maraia RJ. A POLR3B-variant reveals a Pol III transcriptome response dependent on La protein/SSB. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.05.577363. [PMID: 38410490 PMCID: PMC10896340 DOI: 10.1101/2024.02.05.577363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
RNA polymerase III (Pol III, POLR3) synthesizes tRNAs and other small non-coding RNAs. Human POLR3 pathogenic variants cause a range of developmental disorders, recapitulated in part by mouse models, yet some aspects of POLR3 deficiency have not been explored. We characterized a human POLR3B:c.1625A>G;p.(Asn542Ser) disease variant that was found to cause mis-splicing of POLR3B. Genome-edited POLR3B1625A>G HEK293 cells acquired the mis-splicing with decreases in multiple POLR3 subunits and TFIIIB, although display auto-upregulation of the Pol III termination-reinitiation subunit POLR3E. La protein was increased relative to its abundant pre-tRNA ligands which bind via their U(n)U-3'-termini. Assays for cellular transcription revealed greater deficiencies for tRNA genes bearing terminators comprised of 4Ts than of ≥5Ts. La-knockdown decreased Pol III ncRNA expression unlinked to RNA stability. Consistent with these effects, small-RNAseq showed that POLR3B1625A>G and patient fibroblasts express more tRNA fragments (tRFs) derived from pre-tRNA 3'-trailers (tRF-1) than from mature-tRFs, and higher levels of multiple miRNAs, relative to control cells. The data indicate that decreased levels of Pol III transcripts can lead to functional excess of La protein which reshapes small ncRNA profiles revealing new depth in the Pol III system. Finally, patient cell RNA analysis uncovered a strategy for tRF-1/tRF-3 as POLR3-deficiency biomarkers.
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Affiliation(s)
- Sandy Mattijssen
- Section on Molecular and Cell Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Kyra Kerkhofs
- Section on Molecular and Cell Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Joshi Stephen
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Acong Yang
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD, 21702 USA
| | - Chen G. Han
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Yokoyama Tadafumi
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - James R. Iben
- Molecular Genetics Core, NICHD, NIH, Bethesda, MD 20892, USA
| | - Saurabh Mishra
- Section on Molecular and Cell Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Rima M. Sakhawala
- Section on Molecular and Cell Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Amitabh Ranjan
- Section on Molecular and Cell Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Mamatha Gowda
- Department of Obstetrics & Gynaecology, Jawaharlal Institute of Post-Graduate Medical Education and Research, Puducherry, India
| | - William A. Gahl
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
- NIH Undiagnosed Diseases Program, NIH, Bethesda, MD 20892, USA
| | - Shuo Gu
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD, 21702 USA
| | - May C. Malicdan
- Section of Human Biochemical Genetics, Medical Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
- NIH Undiagnosed Diseases Program, NIH, Bethesda, MD 20892, USA
| | - Richard J. Maraia
- Section on Molecular and Cell Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD 20892, USA
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Htet M, Lei S, Bajpayi S, Zoitou A, Chamakioti M, Tampakakis E. The role of noncoding genetic variants in cardiomyopathy. Front Cardiovasc Med 2023; 10:1116925. [PMID: 37283586 PMCID: PMC10239966 DOI: 10.3389/fcvm.2023.1116925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 05/04/2023] [Indexed: 06/08/2023] Open
Abstract
Cardiomyopathies remain one of the leading causes of morbidity and mortality worldwide. Environmental risk factors and genetic predisposition account for most cardiomyopathy cases. As with all complex diseases, there are significant challenges in the interpretation of the molecular mechanisms underlying cardiomyopathy-associated genetic variants. Given the technical improvements and reduced costs of DNA sequence technologies, an increasing number of patients are now undergoing genetic testing, resulting in a continuously expanding list of novel mutations. However, many patients carry noncoding genetic variants, and although emerging evidence supports their contribution to cardiac disease, their role in cardiomyopathies remains largely understudied. In this review, we summarize published studies reporting on the association of different types of noncoding variants with various types of cardiomyopathies. We focus on variants within transcriptional enhancers, promoters, intronic sites, and untranslated regions that are likely associated with cardiac disease. Given the broad nature of this topic, we provide an overview of studies that are relatively recent and have sufficient evidence to support a significant degree of causality. We believe that more research with additional validation of noncoding genetic variants will provide further mechanistic insights on the development of cardiac disease, and noncoding variants will be increasingly incorporated in future genetic screening tests.
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Affiliation(s)
- Myo Htet
- Department of Medicine, Division of Cardiology, Johns Hopkins University, Baltimore, MD, United States
| | - Shunyao Lei
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States
| | - Sheetal Bajpayi
- Department of Medicine, Division of Cardiology, Johns Hopkins University, Baltimore, MD, United States
| | - Asimina Zoitou
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States
| | | | - Emmanouil Tampakakis
- Department of Medicine, Division of Cardiology, Johns Hopkins University, Baltimore, MD, United States
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, United States
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8
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Yüksel Ülker A, Uludağ Alkaya D, Çağlayan AO, Usluer E, Aykut A, Aslanger A, Vural M, Tüysüz B. An investigation of the etiology and follow-up findings in 35 children with overgrowth syndromes, including biallelic SUZ12 variant. Am J Med Genet A 2023; 191:1530-1545. [PMID: 36919607 DOI: 10.1002/ajmg.a.63180] [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: 08/03/2022] [Revised: 01/01/2023] [Accepted: 03/01/2023] [Indexed: 03/16/2023]
Abstract
Overgrowth-intellectual disability (OGID) syndromes are clinically and genetically heterogeneous group of disorders. The aim of this study was to examine the molecular etiology and long-term follow-up findings of Turkish OGID cohort. Thirty-five children with OGID were included in the study. Single gene sequencing, clinical exome analysis, chromosomal microarray analysis and whole exome sequencing were performed. Five pathogenic copy number variants were detected in the patients; three of them located on chromosome 5q35.2 (encompassing NSD1), others on 9q22.3 and 22q13.31. In 19 of 35 patients; we identified pathogenic variants in OGID genes associated with epigenetic regulation, NSD1 (n = 15), HIST1H1E (n = 1), SETD1B (n = 1), and SUZ12 (n = 2). The pathogenic variants in PIK3CA (n = 2), ABCC9 (n = 1), GPC4 (n = 2), FIBP (n = 1), and TMEM94 (n = 1) which had a role in other growth pathways were detected in seven patients. The diagnostic yield was 31/35(88%). Twelve pathogenic variants were novel. The common facial feature of the patients was prominent forehead. The patients with Sotos syndrome were observed to have milder intellectual disability than patients with other OGID syndromes. In conclusion, this study showed, for the first time, that biallelic variants of SUZ12 caused Imagawa-Matsumoto syndrome, monoallelic variants in SETDIB resulted in OGID. Besides expanded the phenotypes of very rare OGID syndromes caused by FIBP and TMEM94.
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Affiliation(s)
- Aylin Yüksel Ülker
- Department of Pediatric Genetics, Cerrahpasa Medical Faculty, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Dilek Uludağ Alkaya
- Department of Pediatric Genetics, Cerrahpasa Medical Faculty, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Ahmet Okay Çağlayan
- Departments of Neurosurgery, Neurobiology and Genetics, Yale School of Medicine, New Haven, Connecticut, USA
| | - Esra Usluer
- Department of Pediatric Genetics, Cerrahpasa Medical Faculty, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Ayça Aykut
- Department of Medical Genetics, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Ayça Aslanger
- Department of Medical Genetics, Bezmialem University, Istanbul, Turkey
| | - Mehmet Vural
- Department of Neonatology, Cerrahpasa Medical Faculty, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Beyhan Tüysüz
- Department of Pediatric Genetics, Cerrahpasa Medical Faculty, Istanbul University-Cerrahpasa, Istanbul, Turkey
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9
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Al-Mamari W, Idris AB, Al-Thihli K, Abdulrahim R, Jalees S, Al-Jabri M, Gabr A, Al Murshedi F, Al Kindy A, Al-Hadabi I, Bruwer Z, Islam MM, Alsayegh A. Applying whole exome sequencing in a consanguineous population with autism spectrum disorder. INTERNATIONAL JOURNAL OF DEVELOPMENTAL DISABILITIES 2023; 69:190-200. [PMID: 37025335 PMCID: PMC10071987 DOI: 10.1080/20473869.2021.1937000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
This study aimed to systematically assess the impact of clinical and demographic variables on the diagnostic yield of Whole Exome Sequencing (WES) when applied to children with Autism Spectrum Disorder (ASD) from a consanguineous population. Ninety-seven children were included in the analysis, 63% were male and 37% were females. 77.3% had a suspected syndromic aetiology of which 68% had co-existent central nervous system (CNS) clinical features, while 69% had other systems involved. The diagnostic yield of WES in our cohort with ASD was 34%. Children with seizures were more likely to have positive WES results (46% vs. 31%, p = 0.042). Probands with suspected syndromic ASD aetiology showed no significant differential impact on the diagnostic yield of WES.
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Affiliation(s)
- Watfa Al-Mamari
- Developmental Pediatric Unit, Child Health Department, Sultan Qaboos University Hospital, Muscat, Oman
- Correspondence to: Watfa Al-Mamari, Developmental Pediatric Unit, Child Health Department, Sultan Qaboos University Hospital, Muscat, Oman.
| | - Ahmed B. Idris
- Developmental Pediatric Unit, Child Health Department, Sultan Qaboos University Hospital, Muscat, Oman
| | - Khalid Al-Thihli
- Genetic Department, Sultan Qaboos University Hospital, Muscat, Oman
| | - Reem Abdulrahim
- Genetic Department, Sultan Qaboos University Hospital, Muscat, Oman
| | - Saquib Jalees
- Developmental Pediatric Unit, Child Health Department, Sultan Qaboos University Hospital, Muscat, Oman
| | - Muna Al-Jabri
- Department of Nursing, Sultan Qaboos University Hospital, Muscat, Oman
| | - Ahlam Gabr
- Developmental Pediatric Unit, Child Health Department, Sultan Qaboos University Hospital, Muscat, Oman
| | | | - Adila Al Kindy
- Genetic Department, Sultan Qaboos University Hospital, Muscat, Oman
| | - Intisar Al-Hadabi
- Department of Nursing, Sultan Qaboos University Hospital, Muscat, Oman
| | - Zandrè Bruwer
- Genetic Department, Sultan Qaboos University Hospital, Muscat, Oman
| | - M. Mazharul Islam
- Department of Statistics, College of Science, Sultan Qaboos University, Muscat, Oman
| | - Abeer Alsayegh
- Genetic Department, Sultan Qaboos University Hospital, Muscat, Oman
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10
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Vadgama N, Ameen M, Sundaram L, Gaddam S, Gifford C, Nasir J, Karakikes I. De novo and inherited variants in coding and regulatory regions in genetic cardiomyopathies. Hum Genomics 2022; 16:55. [PMID: 36357925 PMCID: PMC9647983 DOI: 10.1186/s40246-022-00420-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/24/2022] [Indexed: 11/11/2022] Open
Abstract
Abstract
Background
Cardiomyopathies are a leading cause of progressive heart failure and sudden cardiac death; however, their genetic aetiology remains poorly understood. We hypothesised that variants in noncoding regulatory regions and oligogenic inheritance mechanisms may help close the diagnostic gap.
Methods
We first analysed whole-genome sequencing data of 143 parent–offspring trios from Genomics England 100,000 Genomes Project. We used gene panel testing and a phenotype-based, variant prioritisation framework called Exomiser to identify candidate genes in trios. To assess the contribution of noncoding DNVs to cardiomyopathies, we intersected DNVs with open chromatin sequences from single-cell ATAC-seq data of cardiomyocytes. We also performed a case–control analysis in an exome-negative cohort, including 843 probands and 19,467 controls, to assess the association between noncoding variants in known cardiomyopathy genes and disease.
Results
In the trio analysis, a definite or probable genetic diagnosis was identified in 21 probands according to the American College of Medical Genetics guidelines. We identified novel DNVs in diagnostic-grade genes (RYR2, TNNT2, PTPN11, MYH7, LZR1, NKX2-5), and five cases harbouring a combination of prioritised variants, suggesting that oligogenic inheritance and genetic modifiers contribute to cardiomyopathies. Phenotype-based ranking of candidate genes identified in noncoding DNV analysis revealed JPH2 as the top candidate. Moreover, a case–control analysis revealed an enrichment of rare noncoding variants in regulatory elements of cardiomyopathy genes (p = .035, OR = 1.43, 95% Cl = 1.095–1.767) versus controls. Of the 25 variants associated with disease (p< 0.5), 23 are novel and nine are predicted to disrupt transcription factor binding motifs.
Conclusion
Our results highlight complex genetic mechanisms in cardiomyopathies and reveal novel genes for future investigations.
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GestaltMatcher facilitates rare disease matching using facial phenotype descriptors. Nat Genet 2022; 54:349-357. [PMID: 35145301 DOI: 10.1038/s41588-021-01010-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 12/16/2021] [Indexed: 12/15/2022]
Abstract
Many monogenic disorders cause a characteristic facial morphology. Artificial intelligence can support physicians in recognizing these patterns by associating facial phenotypes with the underlying syndrome through training on thousands of patient photographs. However, this 'supervised' approach means that diagnoses are only possible if the disorder was part of the training set. To improve recognition of ultra-rare disorders, we developed GestaltMatcher, an encoder for portraits that is based on a deep convolutional neural network. Photographs of 17,560 patients with 1,115 rare disorders were used to define a Clinical Face Phenotype Space, in which distances between cases define syndromic similarity. Here we show that patients can be matched to others with the same molecular diagnosis even when the disorder was not included in the training set. Together with mutation data, GestaltMatcher could not only accelerate the clinical diagnosis of patients with ultra-rare disorders and facial dysmorphism but also enable the delineation of new phenotypes.
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Luo J, Ramlau-Hansen CH, Kesmodel US, Xiao J, Vasiliou V, Deziel NC, Zhang Y, Olsen J, Liew Z. Prenatal Exposure to Per- and Polyfluoroalkyl Substances and Facial Features at 5 Years of Age: A Study from the Danish National Birth Cohort. ENVIRONMENTAL HEALTH PERSPECTIVES 2022; 130:17006. [PMID: 35080464 PMCID: PMC8791068 DOI: 10.1289/ehp9478] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
BACKGROUND Per- and polyfluoroalkyl substances (PFAS) are widespread persistent pollutants. Evidence regarding neurodevelopmental effects of PFAS have been mixed. The relation between PFAS exposure and anatomical markers that have been suggested to correlate with fetal brain development have not been studied. OBJECTIVES We investigated the association between prenatal PFAS exposures and three craniofacial features in children measured at 5 years of age. METHODS Measures of palpebral fissure length (PFL), philtrum groove, and upper-lip thickness were generated from standardized digital facial photographs from 656 children in the Danish National Birth Cohort. PFL was classified into two groups (shorter; normal), and the philtrum (grooved; smooth; normal) and upper-lip (thick; thin; normal) measures into three groups each. Six PFAS were measured in maternal plasma (median=8 gestational wk). Multinomial logistic regression was used to estimate the odds ratio (OR) and 95% confidence interval (CI) for each facial feature using the normal group as the reference according to log2-PFAS concentration (in nanograms per milliliter) or PFAS tertiles, adjusting for potential confounders, including maternal alcohol intake and smoking. Stratified analyses by maternal alcohol intake or child's sex were performed. RESULTS Prenatal exposure to each PFAS was associated with elevated odds for a shorter PFL, with the strongest association observed for perfluorodecanoic acid (PFDA; per doubling OR=2.02; 95% CI: 1.11, 3.70). Some nonlinear associations were found for philtrum measures: the second tertile of PFDA and perfluorononanoic acid were associated with grooved philtrum, whereas the second tertile of perfluoroheptane sulfonate with smooth philtrum. The associations between PFAS exposure and a shorter PFL were stronger among mothers who consumed alcohol in the first trimester, some sex-specific associations were noted for philtrum and upper-lip measures. DISCUSSION Prenatal PFAS exposures might influence fetal craniofacial development. A larger study is needed to replicate the potential modifying effects observed for alcohol exposure and to clarify whether associations of craniofacial markers observed reflect specific neurologic deficits. https://doi.org/10.1289/EHP9478.
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Affiliation(s)
- Jiajun Luo
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, Connecticut, USA
- Yale Center for Perinatal, Pediatric, and Environmental Epidemiology, Yale School of Public Health, New Haven, Connecticut, USA
| | | | - Ulrik Schiøler Kesmodel
- Department of Obstetrics and Gynaecology, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Jingyuan Xiao
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, Connecticut, USA
- Yale Center for Perinatal, Pediatric, and Environmental Epidemiology, Yale School of Public Health, New Haven, Connecticut, USA
| | - Vasilis Vasiliou
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, Connecticut, USA
| | - Nicole C. Deziel
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, Connecticut, USA
- Yale Center for Perinatal, Pediatric, and Environmental Epidemiology, Yale School of Public Health, New Haven, Connecticut, USA
| | - Yawei Zhang
- Department of Cancer Prevention and Control, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing
| | - Jørn Olsen
- Department of Clinical Epidemiology, Aarhus University Hospital, Aarhus, Denmark
| | - Zeyan Liew
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, Connecticut, USA
- Yale Center for Perinatal, Pediatric, and Environmental Epidemiology, Yale School of Public Health, New Haven, Connecticut, USA
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Jiang WF, Xu YJ, Zhao CM, Wang XH, Qiu XB, Liu X, Wu SH, Yang YQ. A novel TBX5 mutation predisposes to familial cardiac septal defects and atrial fibrillation as well as bicuspid aortic valve. Genet Mol Biol 2020; 43:e20200142. [PMID: 33306779 PMCID: PMC7783509 DOI: 10.1590/1678-4685-gmb-2020-0142] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 09/19/2020] [Indexed: 02/06/2023] Open
Abstract
TBX5 has been linked to Holt-Oram syndrome, with congenital heart defect (CHD) and atrial fibrillation (AF) being two major cardiac phenotypes. However, the prevalence of a TBX5 variation in patients with CHD and AF remains obscure. In this research, by sequencing analysis of TBX5 in 178 index patients with both CHD and AF, a novel heterozygous variation, NM_000192.3: c.577G>T; p.(Gly193*), was identified in one index patient with CHD and AF as well as bicuspid aortic valve (BAV), with an allele frequency of approximately 0.28%. Genetic analysis of the proband's pedigree showed that the variation co-segregated with the diseases. The pathogenic variation was not detected in 292 unrelated healthy subjects. Functional analysis by using a dual-luciferase reporter assay system showed that the Gly193*-mutant TBX5 protein failed to transcriptionally activate its target genes MYH6 and NPPA. Moreover, the mutation nullified the synergistic transactivation between TBX5 and GATA4 as well as NKX2-5. Additionally, whole-exome sequencing analysis showed no other genes contributing to the diseases. This investigation firstly links a pathogenic variant in the TBX5 gene to familial CHD and AF as well as BAV, suggesting that CHD and AF as well as BAV share a common developmental basis in a subset of patients.
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Affiliation(s)
- Wei-Feng Jiang
- Shanghai Jiao Tong University, Department of Cardiology, Shanghai Chest Hospital, Shanghai, China
| | - Ying-Jia Xu
- Fudan University, Department of Cardiology, Shanghai Fifth People's Hospital, Shanghai, China
| | - Cui-Mei Zhao
- Tongji University School of Medicine, Department of Cardiology, Tongji Hospital, Shanghai, China
| | - Xin-Hua Wang
- Shanghai Jiao Tong University School of Medicine, Department of Cardiology, Renji Hospital, Shanghai, China
| | - Xing-Biao Qiu
- Shanghai Jiao Tong University, Department of Cardiology, Shanghai Chest Hospital, Shanghai, China
| | - Xu Liu
- Shanghai Jiao Tong University, Department of Cardiology, Shanghai Chest Hospital, Shanghai, China
| | - Shao-Hui Wu
- Shanghai Jiao Tong University, Department of Cardiology, Shanghai Chest Hospital, Shanghai, China
| | - Yi-Qing Yang
- Fudan University, Department of Cardiology, Shanghai Fifth People's Hospital, Shanghai, China.,Fudan University, Cardiovascular Research Laboratory, Shanghai Fifth People's Hospital, Shanghai, China.,Fudan University, Central Laboratory, Shanghai Fifth People's Hospital, Shanghai, China
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Fetal Anomalies Associated with Novel Pathogenic Variants in TMEM94. Genes (Basel) 2020; 11:genes11090967. [PMID: 32825426 PMCID: PMC7565137 DOI: 10.3390/genes11090967] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/12/2020] [Accepted: 08/13/2020] [Indexed: 11/24/2022] Open
Abstract
Background: Intellectual developmental disorder with cardiac defects and dysmorphic facies (IDDCDF, MIM 618316) is a newly described disorder. It is characterized by global developmental delay, intellectual disability and speech delay, congenital cardiac malformations, and dysmorphic facial features. Biallelic pathogenic variants of TMEM94 are associated with IDDCDF. Methods and Results: In a prenatal setting, where fetal abnormalities were detected using antenatal sonography, we used trio-exome sequencing (trio-ES) in conjunction with chromosomal microarray analysis (CMA) to identify two novel homozygous loss of function variants in the TMEM94 gene (c.606dupG and c.2729-2A>G) in two unrelated Saudi Arabian families. Conclusions: This study provides confirmation that TMEM94 variants may cause IDDCDF. For the first time we describe the pathogenicity of TMEM94 defects detected during the prenatal period.
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Zhang Y, Sun YM, Xu YJ, Zhao CM, Yuan F, Guo XJ, Guo YH, Yang CX, Gu JN, Qiao Q, Wang J, Yang YQ. A New TBX5 Loss-of-Function Mutation Contributes to Congenital Heart Defect and Atrioventricular Block. Int Heart J 2020; 61:761-768. [DOI: 10.1536/ihj.19-650] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Yan Zhang
- Department of Cardiology, Shanghai Jing'an District Central Hospital, Fudan University
| | - Yu-Min Sun
- Department of Cardiology, Shanghai Jing'an District Central Hospital, Fudan University
| | - Ying-Jia Xu
- Department of Cardiology, Shanghai Fifth People's Hospital, Fudan University
- Center for Complex Cardiac Arrhythmias of Minhang District, Shanghai Fifth People's Hospital, Fudan University
- Cardiovascular Research Laboratory, Shanghai Fifth People's Hospital, Fudan University
| | - Cui-Mei Zhao
- Department of Cardiology, Tongji Hospital, Tongji University School of Medicine
| | - Fang Yuan
- Department of Cardiology, Shanghai Tongren Hospital, Shanghai Jiao Tong University School of Medicine
| | - Xiao-Juan Guo
- Department of Cardiology, Shanghai Fifth People's Hospital, Fudan University
- Center for Complex Cardiac Arrhythmias of Minhang District, Shanghai Fifth People's Hospital, Fudan University
- Cardiovascular Research Laboratory, Shanghai Fifth People's Hospital, Fudan University
| | - Yu-Han Guo
- Department of Cardiology, Shanghai Fifth People's Hospital, Fudan University
- Center for Complex Cardiac Arrhythmias of Minhang District, Shanghai Fifth People's Hospital, Fudan University
- Cardiovascular Research Laboratory, Shanghai Fifth People's Hospital, Fudan University
| | - Chen-Xi Yang
- Department of Cardiology, Shanghai Fifth People's Hospital, Fudan University
- Center for Complex Cardiac Arrhythmias of Minhang District, Shanghai Fifth People's Hospital, Fudan University
- Cardiovascular Research Laboratory, Shanghai Fifth People's Hospital, Fudan University
| | - Jia-Ning Gu
- Department of Cardiology, Shanghai Fifth People's Hospital, Fudan University
- Center for Complex Cardiac Arrhythmias of Minhang District, Shanghai Fifth People's Hospital, Fudan University
- Cardiovascular Research Laboratory, Shanghai Fifth People's Hospital, Fudan University
| | - Qi Qiao
- Department of Cardiology, Shanghai Fifth People's Hospital, Fudan University
- Center for Complex Cardiac Arrhythmias of Minhang District, Shanghai Fifth People's Hospital, Fudan University
- Cardiovascular Research Laboratory, Shanghai Fifth People's Hospital, Fudan University
| | - Jun Wang
- Department of Cardiology, Shanghai Jing'an District Central Hospital, Fudan University
| | - Yi-Qing Yang
- Department of Cardiology, Shanghai Fifth People's Hospital, Fudan University
- Center for Complex Cardiac Arrhythmias of Minhang District, Shanghai Fifth People's Hospital, Fudan University
- Cardiovascular Research Laboratory, Shanghai Fifth People's Hospital, Fudan University
- Central Laboratory, Shanghai Fifth People's Hospital, Fudan University
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Lee H, Nelson SF. The frontiers of sequencing in undiagnosed neurodevelopmental diseases. Curr Opin Genet Dev 2020; 65:76-83. [PMID: 32599523 DOI: 10.1016/j.gde.2020.05.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/07/2020] [Accepted: 05/01/2020] [Indexed: 12/24/2022]
Abstract
Characterized by impairments in brain and central nervous system development, neurodevelopmental diseases causes are highly heterogeneous. Although many of these diseases are individually rare, collectively more than 3% of the children are reported to be affected with a type of neurodevelopmental diseases worldwide, and many remain undiagnosed even with current genomic tools. Identifying the genetic causes of these diseases allows better clinical management and expands our understanding of human neurodevelopment. Over the past decade, expansion of genomic sequencing and some methodologic improvements have improved molecular diagnostic yield as well as the discovery of novel genetic causes for wide spectrum of neurodevelopmental diseases. Here we review the current diagnostic workflow and propose ways of improving the diagnostic yield.
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Affiliation(s)
- Hane Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Stanley F Nelson
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
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Wang H, Yue T, Yang J, Wu W, Xing EP. Deep mixed model for marginal epistasis detection and population stratification correction in genome-wide association studies. BMC Bioinformatics 2019; 20:656. [PMID: 31881907 PMCID: PMC6933893 DOI: 10.1186/s12859-019-3300-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 12/02/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Genome-wide Association Studies (GWAS) have contributed to unraveling associations between genetic variants in the human genome and complex traits for more than a decade. While many works have been invented as follow-ups to detect interactions between SNPs, epistasis are still yet to be modeled and discovered more thoroughly. RESULTS In this paper, following the previous study of detecting marginal epistasis signals, and motivated by the universal approximation power of deep learning, we propose a neural network method that can potentially model arbitrary interactions between SNPs in genetic association studies as an extension to the mixed models in correcting confounding factors. Our method, namely Deep Mixed Model, consists of two components: 1) a confounding factor correction component, which is a large-kernel convolution neural network that focuses on calibrating the residual phenotypes by removing factors such as population stratification, and 2) a fixed-effect estimation component, which mainly consists of an Long-short Term Memory (LSTM) model that estimates the association effect size of SNPs with the residual phenotype. CONCLUSIONS After validating the performance of our method using simulation experiments, we further apply it to Alzheimer's disease data sets. Our results help gain some explorative understandings of the genetic architecture of Alzheimer's disease.
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Affiliation(s)
- Haohan Wang
- Language Technologies Institute, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA USA
| | - Tianwei Yue
- Language Technologies Institute, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA USA
| | - Jingkang Yang
- Department of Electrical and Computer Engineering, Rice University, Houston, TX USA
| | - Wei Wu
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA USA
| | - Eric P. Xing
- Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA USA
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