51
|
Poszewiecka B, Pienkowski VM, Nowosad K, Robin JD, Gogolewski K, Gambin A. TADeus2: a web server facilitating the clinical diagnosis by pathogenicity assessment of structural variations disarranging 3D chromatin structure. Nucleic Acids Res 2022; 50:W744-W752. [PMID: 35524567 PMCID: PMC9252839 DOI: 10.1093/nar/gkac318] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/12/2022] [Accepted: 04/21/2022] [Indexed: 01/01/2023] Open
Abstract
In recent years great progress has been made in identification of structural variants (SV) in the human genome. However, the interpretation of SVs, especially located in non-coding DNA, remains challenging. One of the reasons stems in the lack of tools exclusively designed for clinical SVs evaluation acknowledging the 3D chromatin architecture. Therefore, we present TADeus2 a web server dedicated for a quick investigation of chromatin conformation changes, providing a visual framework for the interpretation of SVs affecting topologically associating domains (TADs). This tool provides a convenient visual inspection of SVs, both in a continuous genome view as well as from a rearrangement’s breakpoint perspective. Additionally, TADeus2 allows the user to assess the influence of analyzed SVs within flaking coding/non-coding regions based on the Hi-C matrix. Importantly, the SVs pathogenicity is quantified and ranked using TADA, ClassifyCNV tools and sampling-based P-value. TADeus2 is publicly available at https://tadeus2.mimuw.edu.pl.
Collapse
Affiliation(s)
- Barbara Poszewiecka
- Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, 2 Banacha street, 02-097 Warsaw, Poland
| | - Victor Murcia Pienkowski
- Aix Marseille Univ, INSERM, Marseille Medical Genetics, MMG, Marseille, France.,Department of Medical Genetics, Medical University of Warsaw, Adolfa Pawińskiego 3c, 02-106 Warsaw, Poland
| | - Karol Nowosad
- Department of Cell Biology, Erasmus Medical Center, Doctor Molewaterplein 40, 3015 GD Rotterdam, Netherlands.,Department of Biomedical Sciences, Laboratory of Molecular Genetics, Medical University of Lublin, Doktora Witolda Chodźki 1, 20-400 Lublin, Poland.,The Postgraduate School of Molecular Medicine, Medical University of Warsaw, Żwirki i Wigury 61, 02-091 Warsaw, Poland
| | - Jérôme D Robin
- Aix Marseille Univ, INSERM, Marseille Medical Genetics, MMG, Marseille, France
| | - Krzysztof Gogolewski
- Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, 2 Banacha street, 02-097 Warsaw, Poland
| | - Anna Gambin
- Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, 2 Banacha street, 02-097 Warsaw, Poland
| |
Collapse
|
52
|
Sheardown E, Mech AM, Petrazzini MEM, Leggieri A, Gidziela A, Hosseinian S, Sealy IM, Torres-Perez JV, Busch-Nentwich EM, Malanchini M, Brennan CH. Translational relevance of forward genetic screens in animal models for the study of psychiatric disease. Neurosci Biobehav Rev 2022; 135:104559. [PMID: 35124155 PMCID: PMC9016269 DOI: 10.1016/j.neubiorev.2022.104559] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 12/10/2021] [Accepted: 02/01/2022] [Indexed: 12/16/2022]
Abstract
Psychiatric disorders represent a significant burden in our societies. Despite the convincing evidence pointing at gene and gene-environment interaction contributions, the role of genetics in the etiology of psychiatric disease is still poorly understood. Forward genetic screens in animal models have helped elucidate causal links. Here we discuss the application of mutagenesis-based forward genetic approaches in common animal model species: two invertebrates, nematodes (Caenorhabditis elegans) and fruit flies (Drosophila sp.); and two vertebrates, zebrafish (Danio rerio) and mice (Mus musculus), in relation to psychiatric disease. We also discuss the use of large scale genomic studies in human populations. Despite the advances using data from human populations, animal models coupled with next-generation sequencing strategies are still needed. Although with its own limitations, zebrafish possess characteristics that make them especially well-suited to forward genetic studies exploring the etiology of psychiatric disorders.
Collapse
Affiliation(s)
- Eva Sheardown
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England, UK
| | - Aleksandra M Mech
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England, UK
| | | | - Adele Leggieri
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England, UK
| | - Agnieszka Gidziela
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England, UK
| | - Saeedeh Hosseinian
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England, UK
| | - Ian M Sealy
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Jose V Torres-Perez
- UK Dementia Research Institute at Imperial College London and Department of Brain Sciences, Imperial College London, 86 Wood Lane, London W12 0BZ, UK
| | - Elisabeth M Busch-Nentwich
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England, UK
| | - Margherita Malanchini
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England, UK
| | - Caroline H Brennan
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, England, UK.
| |
Collapse
|
53
|
Ulaganathan VK. Membrane anchorage-induced (MAGIC) knock-down of non-synonymous point mutations. Chembiochem 2022; 23:e202100637. [PMID: 35352864 DOI: 10.1002/cbic.202100637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/24/2022] [Indexed: 11/08/2022]
Abstract
The promise of personalized medicine for monogenic and complex polygenic diseases depends on the availability of strategies for targeted inhibition of disease-associated polymorphic protein variants. A large majority of disease-causing genetic alterations are non-synonymous single nucleotide genetic variations (nsSNVs). Yet a general strategy for inhibiting the expression of nsSNVs without editing the human genome is currently lacking. Here, we reveal that upon intracellular delivery of lipid conjugated point mutation-specific monoclonal antibodies, a target-specific knockdown of gene expression at both mRNA and protein levels is observed. By harnessing the phenomenon of m embrane a nchorage i ndu c ed (MAGIC) knock-down of epitope-containing protein targets, we reveal a novel approach for inhibiting the expression of amino acid-altering point mutations. This approach opens up a new opportunity for the therapeutic inhibition of undruggable protein variants as well as paves the way for interrogating the nsSNVs in the human genome.
Collapse
Key Words
- membrane anchorage-induced knockdown, nsSNV, 18:0-14:0 PC, lipid-anchor, phospholipid-conjugated mAbs, SNP, SNV, genetic variants, allele varaints, rare variants, common variants, pathogenic mutations, point mutation knockdown, mRNA knockdown
Collapse
Affiliation(s)
- Vijay Kumar Ulaganathan
- University of Lorraine: Universite de Lorraine, NGERE Unit, Faculté de Médecine, Bâtiment C - 2ème étage, 54505, Nancy, FRANCE
| |
Collapse
|
54
|
Tan M, Brusgaard K, Gerdes AM, Larsen MJ, Mortensen MB, Detlefsen S, de Muckadell OBS, Joergensen MT. Whole genome sequencing identifies rare genetic variants in familial pancreatic cancer patients. Ann Hum Genet 2022; 86:195-206. [PMID: 35312039 PMCID: PMC9313800 DOI: 10.1111/ahg.12464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/25/2022] [Accepted: 03/03/2022] [Indexed: 11/27/2022]
Affiliation(s)
- Ming Tan
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Department of Medical Gastroenterology, Odense University Hospital, Odense, Denmark.,Odense Pancreas Center (OPAC), Odense University Hospital, Odense, Denmark
| | - Klaus Brusgaard
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Anne-Marie Gerdes
- Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark
| | - Martin Jakob Larsen
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Michael Bau Mortensen
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Odense Pancreas Center (OPAC), Odense University Hospital, Odense, Denmark.,Department of Surgery, Odense University Hospital, Odense, Denmark
| | - Sönke Detlefsen
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Odense Pancreas Center (OPAC), Odense University Hospital, Odense, Denmark.,Department of Pathology, Odense University Hospital, Odense, Denmark
| | - Ove B Schaffalitzky de Muckadell
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Department of Medical Gastroenterology, Odense University Hospital, Odense, Denmark.,Odense Pancreas Center (OPAC), Odense University Hospital, Odense, Denmark
| | - Maiken Thyregod Joergensen
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Department of Medical Gastroenterology, Odense University Hospital, Odense, Denmark.,Odense Pancreas Center (OPAC), Odense University Hospital, Odense, Denmark
| |
Collapse
|
55
|
Boddy S, Islam M, Moll T, Kurz J, Burrows D, McGown A, Bhargava A, Julian TH, Harvey C, Marshall JNG, Hall BPC, Allen SP, Kenna KP, Sanderson E, Zhang S, Ramesh T, Snyder MP, Shaw PJ, McDermott C, Cooper-Knock J. Unbiased metabolome screen leads to personalized medicine strategy for amyotrophic lateral sclerosis. Brain Commun 2022; 4:fcac069. [PMID: 35441136 PMCID: PMC9010771 DOI: 10.1093/braincomms/fcac069] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 11/29/2021] [Accepted: 03/15/2022] [Indexed: 11/17/2022] Open
Abstract
Amyotrophic lateral sclerosis is a rapidly progressive neurodegenerative disease that affects 1/350 individuals in the United Kingdom. The cause of amyotrophic lateral sclerosis is unknown in the majority of cases. Two-sample Mendelian randomization enables causal inference between an exposure, such as the serum concentration of a specific metabolite, and disease risk. We obtained genome-wide association study summary statistics for serum concentrations of 566 metabolites which were population matched with a genome-wide association study of amyotrophic lateral sclerosis. For each metabolite, we performed Mendelian randomization using an inverse variance weighted estimate for significance testing. After stringent Bonferroni multiple testing correction, our unbiased screen revealed three metabolites that were significantly linked to the risk of amyotrophic lateral sclerosis: Estrone-3-sulphate and bradykinin were protective, which is consistent with literature describing a male preponderance of amyotrophic lateral sclerosis and a preventive effect of angiotensin-converting enzyme inhibitors which inhibit the breakdown of bradykinin. Serum isoleucine was positively associated with amyotrophic lateral sclerosis risk. All three metabolites were supported by robust Mendelian randomization measures and sensitivity analyses; estrone-3-sulphate and isoleucine were confirmed in a validation amyotrophic lateral sclerosis genome-wide association study. Estrone-3-sulphate is metabolized to the more active estradiol by the enzyme 17β-hydroxysteroid dehydrogenase 1; further, Mendelian randomization demonstrated a protective effect of estradiol and rare variant analysis showed that missense variants within HSD17B1, the gene encoding 17β-hydroxysteroid dehydrogenase 1, modify risk for amyotrophic lateral sclerosis. Finally, in a zebrafish model of C9ORF72-amyotrophic lateral sclerosis, we present evidence that estradiol is neuroprotective. Isoleucine is metabolized via methylmalonyl-CoA mutase encoded by the gene MMUT in a reaction that consumes vitamin B12. Multivariable Mendelian randomization revealed that the toxic effect of isoleucine is dependent on the depletion of vitamin B12; consistent with this, rare variants which reduce the function of MMUT are protective against amyotrophic lateral sclerosis. We propose that amyotrophic lateral sclerosis patients and family members with high serum isoleucine levels should be offered supplementation with vitamin B12.
Collapse
Affiliation(s)
- Sarah Boddy
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Mahjabin Islam
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Tobias Moll
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Julian Kurz
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - David Burrows
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Alexander McGown
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Anushka Bhargava
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Thomas H Julian
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Calum Harvey
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Jack NG Marshall
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Benjamin PC Hall
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Scott P Allen
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Kevin P Kenna
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Eleanor Sanderson
- Medical Research Council (MRC) Integrative Epidemiology Unit (IEU), University of Bristol, Bristol, UK
| | - Sai Zhang
- Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Tennore Ramesh
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Michael P Snyder
- Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Pamela J Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Christopher McDermott
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Johnathan Cooper-Knock
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| |
Collapse
|
56
|
Chen C, Parejo M, Momeni J, Langa J, Nielsen RO, Shi W, Vingborg R, Kryger P, Bouga M, Estonba A, Meixner M. Population Structure and Diversity in European Honey Bees ( Apismellifera L.)-An Empirical Comparison of Pool and Individual Whole-Genome Sequencing. Genes (Basel) 2022; 13:182. [PMID: 35205227 PMCID: PMC8872436 DOI: 10.3390/genes13020182] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 12/27/2021] [Accepted: 12/30/2021] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Whole-genome sequencing has become routine for population genetic studies. Sequencing of individuals provides maximal data but is rather expensive and fewer samples can be studied. In contrast, sequencing a pool of samples (pool-seq) can provide sufficient data, while presenting less of an economic challenge. Few studies have compared the two approaches to infer population genetic structure and diversity in real datasets. Here, we apply individual sequencing (ind-seq) and pool-seq to the study of Western honey bees (Apis mellifera). METHODS We collected honey bee workers that belonged to 14 populations, including 13 subspecies, totaling 1347 colonies, who were individually (139 individuals) and pool-sequenced (14 pools). We compared allele frequencies, genetic diversity estimates, and population structure as inferred by the two approaches. RESULTS Pool-seq and ind-seq revealed near identical population structure and genetic diversities, albeit at different costs. While pool-seq provides genome-wide polymorphism data at considerably lower costs, ind-seq can provide additional information, including the identification of population substructures, hybridization, or individual outliers. CONCLUSIONS If costs are not the limiting factor, we recommend using ind-seq, as population genetic structure can be inferred similarly well, with the advantage gained from individual genetic information. Not least, it also significantly reduces the effort required for the collection of numerous samples and their further processing in the laboratory.
Collapse
Affiliation(s)
- Chao Chen
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China;
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture and Rural Affairs, Beijing 100093, China
| | - Melanie Parejo
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain; (J.L.); (A.E.)
- Swiss Bee Research Center, Agroscope, 3003 Bern, Switzerland
| | - Jamal Momeni
- Eurofins Genomics, 8200 Aarhus, Denmark; (J.M.); (R.O.N.); (R.V.)
| | - Jorge Langa
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain; (J.L.); (A.E.)
| | | | - Wei Shi
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China;
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture and Rural Affairs, Beijing 100093, China
| | | | - Rikke Vingborg
- Eurofins Genomics, 8200 Aarhus, Denmark; (J.M.); (R.O.N.); (R.V.)
| | - Per Kryger
- Department of Agroecology, Aarhus University, 4200 Slagelse, Denmark;
| | - Maria Bouga
- Lab of Agricultural Zoology and Entomology, Agricultural University of Athens, 11855 Athens, Greece;
| | - Andone Estonba
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain; (J.L.); (A.E.)
| | | |
Collapse
|
57
|
Khani M, Gibbons E, Bras J, Guerreiro R. Challenge accepted: uncovering the role of rare genetic variants in Alzheimer's disease. Mol Neurodegener 2022; 17:3. [PMID: 35000612 PMCID: PMC8744312 DOI: 10.1186/s13024-021-00505-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 12/06/2021] [Indexed: 12/11/2022] Open
Abstract
The search for rare variants in Alzheimer's disease (AD) is usually deemed a high-risk - high-reward situation. The challenges associated with this endeavor are real. Still, the application of genome-wide technologies to large numbers of cases and controls or to small, well-characterized families has started to be fruitful.Rare variants associated with AD have been shown to increase risk or cause disease, but also to protect against the development of AD. All of these can potentially be targeted for the development of new drugs.Multiple independent studies have now shown associations of rare variants in NOTCH3, TREM2, SORL1, ABCA7, BIN1, CLU, NCK2, AKAP9, UNC5C, PLCG2, and ABI3 with AD and suggested that they may influence disease via multiple mechanisms. These genes have reported functions in the immune system, lipid metabolism, synaptic plasticity, and apoptosis. However, the main pathway emerging from the collective of genes harboring rare variants associated with AD is the Aβ pathway. Associations of rare variants in dozens of other genes have also been proposed, but have not yet been replicated in independent studies. Replication of this type of findings is one of the challenges associated with studying rare variants in complex diseases, such as AD. In this review, we discuss some of these primary challenges as well as possible solutions.Integrative approaches, the availability of large datasets and databases, and the development of new analytical methodologies will continue to produce new genes harboring rare variability impacting AD. In the future, more extensive and more diverse genetic studies, as well as studies of deeply characterized families, will enhance our understanding of disease pathogenesis and put us on the correct path for the development of successful drugs.
Collapse
Affiliation(s)
- Marzieh Khani
- School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Elizabeth Gibbons
- Department of Neurodegenerative Science, Van Andel Institute, 333 Bostwick Ave. N.E., Grand Rapids, Michigan 49503-2518 USA
| | - Jose Bras
- Department of Neurodegenerative Science, Van Andel Institute, 333 Bostwick Ave. N.E., Grand Rapids, Michigan 49503-2518 USA
- Division of Psychiatry and Behavioral Medicine, Michigan State University College of Human Medicine, Grand Rapids, MI USA
| | - Rita Guerreiro
- Department of Neurodegenerative Science, Van Andel Institute, 333 Bostwick Ave. N.E., Grand Rapids, Michigan 49503-2518 USA
- Division of Psychiatry and Behavioral Medicine, Michigan State University College of Human Medicine, Grand Rapids, MI USA
| |
Collapse
|
58
|
Cohen A, Hostyk J, Baugh EH, Buchovecky CM, Aggarwal VS, Recker RR, Lappe JM, Dempster DW, Zhou H, Kamanda-Kosseh M, Bucovsky M, Stubby J, Goldstein DB, Shane E. Whole exome sequencing reveals potentially pathogenic variants in a small subset of premenopausal women with idiopathic osteoporosis. Bone 2022; 154:116253. [PMID: 34743040 PMCID: PMC8671293 DOI: 10.1016/j.bone.2021.116253] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 10/30/2021] [Accepted: 11/01/2021] [Indexed: 01/03/2023]
Abstract
Osteoporosis in premenopausal women with intact gonadal function and no known secondary cause of bone loss is termed idiopathic osteoporosis (IOP). Women with IOP diagnosed in adulthood have profound bone structural deficits and often report adult and childhood fractures, and family history of osteoporosis. Some have very low bone formation rates (BFR/BS) suggesting osteoblast dysfunction. These features led us to investigate potential genetic etiologies of bone fragility. In 75 IOP women (aged 20-49) with low trauma fractures and/or very low BMD who had undergone transiliac bone biopsies, we performed Whole Exome Sequencing (WES) using our variant analysis pipeline to select candidate rare and novel variants likely to affect known disease genes. We ran rare-variant burden analyses on all genes individually and on phenotypically-relevant gene sets. For particular genes implicated in osteoporosis, we also assessed the frequency of all (including common) variants in subjects versus 6540 non-comorbid female controls. The variant analysis pipeline identified 4 women with 4 heterozygous variants in LRP5 and PLS3 that were considered to contribute to osteoporosis. All 4 women had adult fractures, and 3 women also had multiple fractures, childhood fractures and a family history of osteoporosis. Two women presented during pregnancy/lactation. In an additional 4 subjects, 4 different relevant Variants of Uncertain Significance (VUS) were detected in the genes FKBP10, SLC34A3, and HGD. Of the subjects with VUS, 2 had multiple adult fractures, childhood fractures, and presented during pregnancy/lactation, and 2 had nephrolithiasis. BFR/BS varied among the 8 subjects with identified variants; BFR/BS was quite low in those with variants that are likely to have adverse effects on bone formation. The analysis pipeline did not discover candidate variants in COL1A1, COL1A2, WNT, or ALPL. Although we found several novel and rare variants in LRP5, cases did not have an increased burden of common LRP5 variants compared to controls. Cohort-wide collapsing analysis did not reveal any novel disease genes with genome-wide significance for qualifying variants between controls and our 75 cases. In summary, WES revealed likely pathogenic variants or relevant VUS in 8 (11%) of 75 women with IOP. Notably, the genetic variants identified were consistent with the affected women's diagnostic evaluations that revealed histological evidence of low BFR/BS or biochemical evidence of increased bone resorption and urinary calcium excretion. These results, and the fact that the majority of the women had no identifiable genetic etiology, also suggest that the pathogenesis of and mechanisms leading to osteoporosis in this cohort are heterogeneous. Future research is necessary to identify both new genetic and non-genetic etiologies of early-onset osteoporosis.
Collapse
Affiliation(s)
- Adi Cohen
- Department of Medicine, Columbia University Vagelos College of Physicians & Surgeons, New York, NY, USA.
| | - Joseph Hostyk
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Evan H Baugh
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Christie M Buchovecky
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Vimla S Aggarwal
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Robert R Recker
- Department of Medicine, Creighton University Medical Center, Omaha, NE, USA
| | - Joan M Lappe
- Department of Medicine, Creighton University Medical Center, Omaha, NE, USA
| | - David W Dempster
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians & Surgeons, New York, NY, USA
| | - Hua Zhou
- Regional Bone Center, Helen Hayes Hospital, West Haverstraw, New York, NY, USA
| | - Mafo Kamanda-Kosseh
- Department of Medicine, Columbia University Vagelos College of Physicians & Surgeons, New York, NY, USA
| | - Mariana Bucovsky
- Department of Medicine, Columbia University Vagelos College of Physicians & Surgeons, New York, NY, USA
| | - Julie Stubby
- Department of Medicine, Creighton University Medical Center, Omaha, NE, USA
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Elizabeth Shane
- Department of Medicine, Columbia University Vagelos College of Physicians & Surgeons, New York, NY, USA
| |
Collapse
|
59
|
Zhang K, Rodriguez L, Cheng LY, Wang M, Zhang DY. Single-Tube qPCR Detection and Quantitation of Hotspot Mutations Down to 0.01% Variant Allele Fraction. Anal Chem 2021; 94:934-943. [PMID: 34932306 DOI: 10.1021/acs.analchem.1c03716] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Clinically and biologically, rare DNA sequence variants are significant and informative. However, existing common detection technologies are either complex and time-consuming in workflow, or restricted in the limit of detection (LoD), or do not allow for multiplexing. Blocker displacement amplification (BDA) method can stably and effectively detect and enrich multiple rare variants with LoD around 0.1% variant allele fraction (VAF). Nonetheless, the detailed mutation information has to be identified by additional sequencing technologies. Here, we present allele-specific BDA (As-BDA), a method combining BDA with allele-specific TaqMan (As-TaqMan) probes for effective variant enrichment and simultaneous single nucleotide variant or small insertions and deletions (INDELs) profiling. We demonstrated that As-BDA could detect mutations down to 0.01% VAF. Further, As-BDA could detect up to four mutations with low to 0.1% VAF per reaction using only 15 ng DNA input. The median error of As-BDA in VAF determination is approximately 9.1%. Comparison experiments using As-BDA and droplet digital PCR on peripheral blood mononuclear cell clinical samples showed 100% concordance for samples with mutations at ≥ 0.1% VAF. Hence, we have shown that As-BDA can achieve simultaneous enrichment and identification of multiple targeted mutations within the same reaction with high clinical sensitivity and specificity, thus helpful for clinical diagnosis.
Collapse
Affiliation(s)
- Kerou Zhang
- Bioengineering, Rice University, Houston, Texas 77030, United States
| | | | | | - Michael Wang
- Bioengineering, Rice University, Houston, Texas 77030, United States
| | | |
Collapse
|
60
|
Liu TY, Lin CF, Wu HT, Wu YL, Chen YC, Liao CC, Chou YP, Chao D, Chang YS, Lu HF, Chang JG, Hsu KC, Tsai FJ. Comparison of multiple imputation algorithms and verification using whole-genome sequencing in the CMUH genetic biobank. Biomedicine (Taipei) 2021; 11:57-65. [PMID: 35223420 PMCID: PMC8823485 DOI: 10.37796/2211-8039.1302] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 03/09/2021] [Accepted: 04/08/2021] [Indexed: 11/13/2022] Open
Abstract
A genome-wide association study (GWAS) can be conducted to systematically analyze the contributions of genetic factors to a wide variety of complex diseases. Nevertheless, existing GWASs have provided highly ethnic specific data. Accordingly, to provide data specific to Taiwan, we established a large-scale genetic database in a single medical institution at the China Medical University Hospital. With current technological limitations, microarray analysis can detect only a limited number of single-nucleotide polymorphisms (SNPs) with a minor allele frequency of >1%. Nevertheless, imputation represents a useful alternative means of expanding data. In this study, we compared four imputation algorithms in terms of various metrics. We observed that among the compared algorithms, Beagle5.2 achieved the fastest calculation speed, smallest storage space, highest specificity, and highest number of high-quality variants. We obtained 15,277,414 high-quality variants in 175,871 people by using Beagle5.2. In our internal verification process, Beagle5.2 exhibited an accuracy rate of up to 98.75%. We also conducted external verification. Our imputed variants had a 79.91% mapping rate and 90.41% accuracy. These results will be combined with clinical data in future research. We have made the results available for researchers to use in formulating imputation algorithms, in addition to establishing a complete SNP database for GWAS and PRS researchers. We believe that these data can help improve overall medical capabilities, particularly precision medicine, in Taiwan.
Collapse
Affiliation(s)
- Ting-Yuan Liu
- Center for Precision Medicine, China Medical University Hospital, Taichung, 40447,
Taiwan
| | - Chih-Fan Lin
- Artificial Intelligence Center for Medical Diagnosis, China Medical University Hospital, Taichung, 40447,
Taiwan
| | - Hsing-Tsung Wu
- Artificial Intelligence Center for Medical Diagnosis, China Medical University Hospital, Taichung, 40447,
Taiwan
| | - Ya-Lun Wu
- Artificial Intelligence Center for Medical Diagnosis, China Medical University Hospital, Taichung, 40447,
Taiwan
| | - Yu-Chia Chen
- Center for Precision Medicine, China Medical University Hospital, Taichung, 40447,
Taiwan
| | - Chi-Chou Liao
- Center for Precision Medicine, China Medical University Hospital, Taichung, 40447,
Taiwan
| | - Yu-Pao Chou
- Center for Precision Medicine, China Medical University Hospital, Taichung, 40447,
Taiwan
| | - Dysan Chao
- Center for Precision Medicine, China Medical University Hospital, Taichung, 40447,
Taiwan
| | - Ya-Sian Chang
- Center for Precision Medicine, China Medical University Hospital, Taichung, 40447,
Taiwan
- Epigenome Research Center, China Medical University Hospital, Taichung, 40447,
Taiwan
| | - Hsing-Fang Lu
- Million-person Precision Medicine Initiative, China Medical University Hospital, Taichung, 40447,
Taiwan
| | - Jan-Gowth Chang
- Center for Precision Medicine, China Medical University Hospital, Taichung, 40447,
Taiwan
- Epigenome Research Center, China Medical University Hospital, Taichung, 40447,
Taiwan
| | - Kai-Cheng Hsu
- Artificial Intelligence Center for Medical Diagnosis, China Medical University Hospital, Taichung, 40447,
Taiwan
- Department of Medicine, China Medical University, Taichung,
Taiwan
- Department of Neurology, China Medical University Hospital, Taichung,
Taiwan
| | - Fuu-Jen Tsai
- Department of Medical Research, China Medical University Hospital, Taichung, 40402,
Taiwan
- School of Chinese Medicine, China Medical University, Taichung, 40402,
Taiwan
- Division of Pediatric Genetics, Children’s Hospital of China Medical University, Taichung, 40447,
Taiwan
- Department of Biotechnology and Bioinformatics, Asia University, Taichung, 41354,
Taiwan
| |
Collapse
|
61
|
Prediction of genetic alteration of phospholipase C isozymes in brain disorders: Studies with deep learning. Adv Biol Regul 2021; 82:100833. [PMID: 34773889 DOI: 10.1016/j.jbior.2021.100833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 11/22/2022]
Abstract
Genetic mutations leading to the development of various diseases, such as cancer, diabetes, and neurodegenerative disorders, can be attributed to multiple mechanisms and exposure to diverse environments. These disorders further increase gene mutation rates and affect the activity of translated proteins, both phenomena associated with cellular responses. Therefore, maintaining the integrity of genetic and epigenetic information is critical for disease suppression and prevention. With the advent of genome sequencing technologies, large-scale genomic data-based machine learning tools, including deep learning, have been used to predict and identify somatic inactivation or negative dominant expression of target genes in various diseases. Although deep learning studies have recently been highlighted for their ability to distinguish between the genetic information of diseases, conventional wisdom is also necessary to explain the correlation between genotype and phenotype. Herein, we summarize the current understanding of phosphoinositide-specific phospholipase C isozymes (PLCs) and an overview of their associations with genetic variation, as well as their emerging roles in several diseases. We also predicted and discussed new findings of cryptic PLC splice variants by deep learning and the clinical implications of the PLC genetic variations predicted using these tools.
Collapse
|
62
|
Sun TH, Shao YHJ, Mao CL, Hung MN, Lo YY, Ko TM, Hsiao TH. A Novel Quality-Control Procedure to Improve the Accuracy of Rare Variant Calling in SNP Arrays. Front Genet 2021; 12:736390. [PMID: 34764980 PMCID: PMC8577504 DOI: 10.3389/fgene.2021.736390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/21/2021] [Indexed: 12/16/2022] Open
Abstract
Background: Single-nucleotide polymorphism (SNP) arrays are an ideal technology for genotyping genetic variants in mass screening. However, using SNP arrays to detect rare variants [with a minor allele frequency (MAF) of <1%] is still a challenge because of noise signals and batch effects. An approach that improves the genotyping quality is needed for clinical applications. Methods: We developed a quality-control procedure for rare variants which integrates different algorithms, filters, and experiments to increase the accuracy of variant calling. Using data from the TWB 2.0 custom Axiom array, we adopted an advanced normalization adjustment to prevent false calls caused by splitting the cluster and a rare het adjustment which decreases false calls in rare variants. The concordance of allelic frequencies from array data was compared to those from sequencing datasets of Taiwanese. Finally, genotyping results were used to detect familial hypercholesterolemia (FH), thrombophilia (TH), and maturity-onset diabetes of the young (MODY) to assess the performance in disease screening. All heterozygous calls were verified by Sanger sequencing or qPCR. The positive predictive value (PPV) of each step was estimated to evaluate the performance of our procedure. Results: We analyzed SNP array data from 43,433 individuals, which interrogated 267,247 rare variants. The advanced normalization and rare het adjustment methods adjusted genotyping calling of 168,134 variants (96.49%). We further removed 3916 probesets which were discordant in MAFs between the SNP array and sequencing data. The PPV for detecting pathogenic variants with 0.01%10,000 are available. The results demonstrated our procedure could perform correct genotype calling of rare variants. It provides a solution of pathogenic variant detection through SNP array. The approach brings tremendous promise for implementing precision medicine in medical practice.
Collapse
Affiliation(s)
- Ting-Hsuan Sun
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Yu-Hsuan Joni Shao
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- Clinical Big Data Research Center, Taipei Medical University Hospital, Taipei, Taiwan
| | - Chien-Lin Mao
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Miao-Neng Hung
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Yi-Yun Lo
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Tai-Ming Ko
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Tzu-Hung Hsiao
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
- Department of Public Health, Fu Jen Catholic University, New Taipei City, Taiwan
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan
- Research Center for Biomedical Science and Engineering, National Tsing Hua University, Hsinchu, Taiwan
| |
Collapse
|
63
|
Gupta PK. GWAS for genetics of complex quantitative traits: Genome to pangenome and SNPs to SVs and k-mers. Bioessays 2021; 43:e2100109. [PMID: 34486143 DOI: 10.1002/bies.202100109] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/21/2021] [Accepted: 08/23/2021] [Indexed: 12/22/2022]
Abstract
The development of improved methods for genome-wide association studies (GWAS) for genetics of quantitative traits has been an active area of research during the last 25 years. This activity initially started with the use of mixed linear model (MLM), which was variously modified. During the last decade, however, with the availability of high throughput next generation sequencing (NGS) technology, development and use of pangenomes and novel markers including structural variations (SVs) and k-mers for GWAS has taken over as a new thrust area of research. Pangenomes and SVs are now available in humans, livestock, and a number of plant species, so that these resources along with k-mers are being used in GWAS for exploring additional genetic variation that was hitherto not available for analysis. These developments have resulted in significant improvement in GWAS methodology for detection of marker-trait associations (MTAs) that are relevant to human healthcare and crop improvement.
Collapse
Affiliation(s)
- Pushpendra K Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University Meerut, Meerut, Uttar Pradesh, India
| |
Collapse
|
64
|
Genetic Ancestry Inference and Its Application for the Genetic Mapping of Human Diseases. Int J Mol Sci 2021; 22:ijms22136962. [PMID: 34203440 PMCID: PMC8269095 DOI: 10.3390/ijms22136962] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 12/21/2022] Open
Abstract
Admixed populations arise when two or more ancestral populations interbreed. As a result of this admixture, the genome of admixed populations is defined by tracts of variable size inherited from these parental groups and has particular genetic features that provide valuable information about their demographic history. Diverse methods can be used to derive the ancestry apportionment of admixed individuals, and such inferences can be leveraged for the discovery of genetic loci associated with diseases and traits, therefore having important biomedical implications. In this review article, we summarize the most common methods of global and local genetic ancestry estimation and discuss the use of admixture mapping studies in human diseases.
Collapse
|
65
|
Tutukova S, Tarabykin V, Hernandez-Miranda LR. The Role of Neurod Genes in Brain Development, Function, and Disease. Front Mol Neurosci 2021; 14:662774. [PMID: 34177462 PMCID: PMC8221396 DOI: 10.3389/fnmol.2021.662774] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/11/2021] [Indexed: 01/14/2023] Open
Abstract
Transcriptional regulation is essential for the correct functioning of cells during development and in postnatal life. The basic Helix-loop-Helix (bHLH) superfamily of transcription factors is well conserved throughout evolution and plays critical roles in tissue development and tissue maintenance. A subgroup of this family, called neural lineage bHLH factors, is critical in the development and function of the central nervous system. In this review, we will focus on the function of one subgroup of neural lineage bHLH factors, the Neurod family. The Neurod family has four members: Neurod1, Neurod2, Neurod4, and Neurod6. Available evidence shows that these four factors are key during the development of the cerebral cortex but also in other regions of the central nervous system, such as the cerebellum, the brainstem, and the spinal cord. We will also discuss recent reports that link the dysfunction of these transcription factors to neurological disorders in humans.
Collapse
Affiliation(s)
- Svetlana Tutukova
- Institute of Neuroscience, Lobachevsky University of Nizhny Novgorod, Nizhny Novgorod, Russia.,Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute for Cell- and Neurobiology, Berlin, Germany
| | - Victor Tarabykin
- Institute of Neuroscience, Lobachevsky University of Nizhny Novgorod, Nizhny Novgorod, Russia.,Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute for Cell- and Neurobiology, Berlin, Germany
| | - Luis R Hernandez-Miranda
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute for Cell- and Neurobiology, Berlin, Germany
| |
Collapse
|
66
|
Lin TY, Chang YC, Hsiao YJ, Chien Y, Jheng YC, Wu JR, Ching LJ, Hwang DK, Hsu CC, Lin TC, Chou YB, Huang YM, Chen SJ, Yang YP, Tsai PH. Identification of Novel Genomic-Variant Patterns of OR56A5, OR52L1, and CTSD in Retinitis Pigmentosa Patients by Whole-Exome Sequencing. Int J Mol Sci 2021; 22:ijms22115594. [PMID: 34070492 PMCID: PMC8198027 DOI: 10.3390/ijms22115594] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 12/24/2022] Open
Abstract
Inherited retinal dystrophies (IRDs) are rare but highly heterogeneous genetic disorders that affect individuals and families worldwide. However, given its wide variability, its analysis of the driver genes for over 50% of the cases remains unexplored. The present study aims to identify novel driver genes, disease-causing variants, and retinitis pigmentosa (RP)-associated pathways. Using family-based whole-exome sequencing (WES) to identify putative RP-causing rare variants, we identified a total of five potentially pathogenic variants located in genes OR56A5, OR52L1, CTSD, PRF1, KBTBD13, and ATP2B4. Of the variants present in all affected individuals, genes OR56A5, OR52L1, CTSD, KBTBD13, and ATP2B4 present as missense mutations, while PRF1 and CTSD present as frameshift variants. Sanger sequencing confirmed the presence of the novel pathogenic variant PRF1 (c.124_128del) that has not been reported previously. More causal-effect or evidence-based studies will be required to elucidate the precise roles of these SNPs in the RP pathogenesis. Taken together, our findings may allow us to explore the risk variants based on the sequencing data and upgrade the existing variant annotation database in Taiwan. It may help detect specific eye diseases such as retinitis pigmentosa in East Asia.
Collapse
Affiliation(s)
- Ting-Yi Lin
- College of Medicine, Kaohsiung Medical University, Kaohsiung 807378, Taiwan;
| | - Yun-Chia Chang
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei 112304, Taiwan; (Y.-C.C.); (D.-K.H.); (C.-C.H.); (T.-C.L.); (Y.-B.C.); (Y.-M.H.); (S.-J.C.)
| | - Yu-Jer Hsiao
- College of Medicine, National Yang-Ming Chiao-Tung University, Taipei 11217, Taiwan;
| | - Yueh Chien
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (Y.C.); (Y.-C.J.); (J.-R.W.); (L.-J.C.)
- Institute of Pharmacology, National Yang-Ming Chiao Tung University, Taipei 112304, Taiwan
| | - Ying-Chun Jheng
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (Y.C.); (Y.-C.J.); (J.-R.W.); (L.-J.C.)
- School of Medicine, National Yang-Ming Chiao Tung University, Taipei 112304, Taiwan
- Big Data Center, Taipei Veterans General Hospital, Taipei 112201, Taiwan
| | - Jing-Rong Wu
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (Y.C.); (Y.-C.J.); (J.-R.W.); (L.-J.C.)
| | - Lo-Jei Ching
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (Y.C.); (Y.-C.J.); (J.-R.W.); (L.-J.C.)
| | - De-Kuang Hwang
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei 112304, Taiwan; (Y.-C.C.); (D.-K.H.); (C.-C.H.); (T.-C.L.); (Y.-B.C.); (Y.-M.H.); (S.-J.C.)
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (Y.C.); (Y.-C.J.); (J.-R.W.); (L.-J.C.)
- School of Medicine, National Yang-Ming Chiao Tung University, Taipei 112304, Taiwan
- Institute of Clinical Medicine, National Yang-Ming Chiao Tung University, Taipei 112304, Taiwan
| | - Chih-Chien Hsu
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei 112304, Taiwan; (Y.-C.C.); (D.-K.H.); (C.-C.H.); (T.-C.L.); (Y.-B.C.); (Y.-M.H.); (S.-J.C.)
| | - Tai-Chi Lin
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei 112304, Taiwan; (Y.-C.C.); (D.-K.H.); (C.-C.H.); (T.-C.L.); (Y.-B.C.); (Y.-M.H.); (S.-J.C.)
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (Y.C.); (Y.-C.J.); (J.-R.W.); (L.-J.C.)
- School of Medicine, National Yang-Ming Chiao Tung University, Taipei 112304, Taiwan
- Institute of Clinical Medicine, National Yang-Ming Chiao Tung University, Taipei 112304, Taiwan
| | - Yu-Bai Chou
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei 112304, Taiwan; (Y.-C.C.); (D.-K.H.); (C.-C.H.); (T.-C.L.); (Y.-B.C.); (Y.-M.H.); (S.-J.C.)
| | - Yi-Ming Huang
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei 112304, Taiwan; (Y.-C.C.); (D.-K.H.); (C.-C.H.); (T.-C.L.); (Y.-B.C.); (Y.-M.H.); (S.-J.C.)
| | - Shih-Jen Chen
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei 112304, Taiwan; (Y.-C.C.); (D.-K.H.); (C.-C.H.); (T.-C.L.); (Y.-B.C.); (Y.-M.H.); (S.-J.C.)
- School of Medicine, National Yang-Ming Chiao Tung University, Taipei 112304, Taiwan
| | - Yi-Ping Yang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (Y.C.); (Y.-C.J.); (J.-R.W.); (L.-J.C.)
- School of Medicine, National Yang-Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Internal Medicine, Taipei Veterans General Hospital, Taipei 112201, Taiwan
- Critical Center, Taipei Veterans General Hospital, Taipei 112201, Taiwan
- Correspondence: (Y.-P.Y.); (P.H.T.); Tel.: +886-2-2875-7394 (Y.-P.Y.); +886-2-2875-7394 (P.H.T.)
| | - Ping-Hsing Tsai
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (Y.C.); (Y.-C.J.); (J.-R.W.); (L.-J.C.)
- Institute of Pharmacology, National Yang-Ming Chiao Tung University, Taipei 112304, Taiwan
- Correspondence: (Y.-P.Y.); (P.H.T.); Tel.: +886-2-2875-7394 (Y.-P.Y.); +886-2-2875-7394 (P.H.T.)
| |
Collapse
|
67
|
Grazioli S, Petris G. Synthetic genomics for curing genetic diseases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 182:477-520. [PMID: 34175051 DOI: 10.1016/bs.pmbts.2021.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
From the beginning of the genome sequencing era, it has become increasingly evident that genetics plays a role in all diseases, of which only a minority are single-gene disorders, the most common target of current gene therapies. However, the majority of people have some kind of health problems resulting from congenital genetic mutations (over 6000 diseases have been associated to genes, https://www.omim.org/statistics/geneMap) and most genetic disorders are rare and only incompletely understood. The vision and techniques applied to the synthesis of genomes may help to address unmet medical needs from a chromosome and genome-scale perspective. In this chapter, we address the potential therapy of genetic diseases from a different outlook, in which we no longer focus on small gene corrections but on higher-order tools for genome manipulation. These will play a crucial role in the next years, as they prelude to a much deeper understanding of the architecture of the human genome and a more accurate modeling of human diseases, offering new therapeutic opportunities.
Collapse
Affiliation(s)
| | - Gianluca Petris
- Medical Research Council Laboratory of Molecular Biology (MRC LMB), Cambridge, United Kingdom.
| |
Collapse
|
68
|
Masoero L, Camerlenghi F, Favaro S, Broderick T. More for less: predicting and maximizing genomic variant discovery via Bayesian nonparametrics. Biometrika 2021. [DOI: 10.1093/biomet/asab012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Summary
While the cost of sequencing genomes has decreased dramatically in recent years, this expense often remains nontrivial. Under a fixed budget, scientists face a natural trade-off between quantity and quality: spending resources to sequence a greater number of genomes or spending resources to sequence genomes with increased accuracy. Our goal is to find the optimal allocation of resources between quantity and quality. Optimizing resource allocation promises to reveal as many new variations in the genome as possible. We introduce a Bayesian nonparametric methodology to predict the number of new variants in a follow-up study based on a pilot study. When experimental conditions are kept constant between the pilot and follow-up, we find that our prediction is competitive with the best existing methods. Unlike current methods, though, our new method allows practitioners to change experimental conditions between the pilot and the follow-up. We demonstrate how this distinction allows our method to be used for more realistic predictions and for optimal allocation of a fixed budget between quality and quantity. We validate our method on cancer and human genomics data.
Collapse
|
69
|
Germenis AE, Rijavec M, Veronez CL. Leveraging Genetics for Hereditary Angioedema: A Road Map to Precision Medicine. Clin Rev Allergy Immunol 2021; 60:416-428. [PMID: 33507496 DOI: 10.1007/s12016-021-08836-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2021] [Indexed: 12/25/2022]
Abstract
Biochemical studies performed during the last decades resulted in the development of various innovative medicinal products for hereditary angioedema (HAE). These therapeutic agents target the production or the function of bradykinin-the main mediator of HAE due to C1-inhibitor (C1-INH) deficiency. However, despite these remarkable achievements, current knowledge cannot provide convincing explanations for the clinical variability of the disease. As a consequence, treatment indications apply for drugs available for C1-INH deficiency. The advent of high-throughput next-generation sequencing technologies may assist in covering the missing part of our understanding of HAE pathogenesis. During the last 3 years alone, several new entities were added to the already described genotypes. The recent discovery of four novel target genes expands our understanding of other causes which may explain recurrent angioedema in individuals and families with normal C1-INH activity. Furthermore, new genetic technologies allowed the recognition of deep intronic variants associated with the disease, and elegant functional studies characterized new variants for the C1-INH gene. Thus, evidence has been provided regarding pathogenetic aspects remaining obscure for many years, such as the defective intracellular transport of mutant C1-INH, and environmental effect on the disease expression. Therefore, it seems that the stage for Precision Medicine era in HAE management is ready. Disease endotypes are expected to be uncovered and specified targets for therapeutic intervention will be detected, promising a more effective, individualized management of the disease.
Collapse
Affiliation(s)
- Anastasios E Germenis
- Department of Immunology and Histocompatibility, School of Medicine, University of Thessaly, 3 Panepistimiou Street, GR-41500, Biopolis Larissa, Greece.
| | - Matija Rijavec
- University Clinic of Respiratory and Allergic Diseases Golnik, Golnik, Slovenia
| | - Camila Lopes Veronez
- Department of Medicine, Division of Rheumatology, Allergy and Immunology, University of California San Diego, San Diego, CA, USA.,Research Service, San Diego Veterans Affairs Healthcare, San Diego, CA, USA
| |
Collapse
|
70
|
Seo JH, Kim TY, Kim SJ, Choi JH, So HS, Kang JI. Possible Association of Polymorphisms in Ubiquitin Specific Peptidase 46 Gene With Post-traumatic Stress Disorder. Front Psychiatry 2021; 12:663647. [PMID: 34456759 PMCID: PMC8385240 DOI: 10.3389/fpsyt.2021.663647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/14/2021] [Indexed: 11/13/2022] Open
Abstract
Introduction: Dynamic proteolysis, through the ubiquitin-proteasome system, has an important role in DNA transcription and cell cycle, and is considered to modulate cell stress response and synaptic plasticity. We investigated whether genetic variants in the ubiquitin carboxyl-terminal hydrolase 46 (USP46) would be associated with post-traumatic stress disorder (PTSD) in people with exposure to combat trauma using a case-control candidate gene association design. Methods: Korean male veterans exposed to the Vietnam War were grouped into those with (n = 128) and without (n = 128) PTSD. Seven tagging SNPs of USP46 were selected, and single-marker and haplotype-based association analyses were performed. All analyses were adjusted for sociodemographic factors and levels of combat exposure severity and alcohol problem. Results: One single-marker (rs2244291) showed nominal evidence of association with PTSD status and with the "re-experiencing" cluster, although the association was not significant after Bonferroni correction. No significant association with the other SNPs or the haplotypes was detected. Conclusion: The present finding suggests preliminarily that genetic vulnerability regarding the ubiquitin-proteasome system may be related to fear memory processes and the development of PTSD symptoms after trauma exposure. Further studies with a larger sample size will be needed to examine the role of the ubiquitin-proteasome system including USP46 in PTSD.
Collapse
Affiliation(s)
- Jun Ho Seo
- Institute of Behavioral Science in Medicine and Department of Psychiatry, Yonsei University College of Medicine, Seoul, South Korea
| | - Tae Yong Kim
- Institute of Behavioral Science in Medicine and Department of Psychiatry, Yonsei University College of Medicine, Seoul, South Korea.,Department of Neuropsychiatry, Veterans Health Service Medical Center, Seoul, South Korea
| | - Se Joo Kim
- Institute of Behavioral Science in Medicine and Department of Psychiatry, Yonsei University College of Medicine, Seoul, South Korea
| | - Jin Hee Choi
- Department of Neuropsychiatry, Veterans Health Service Medical Center, Seoul, South Korea
| | - Hyung Seok So
- Department of Neuropsychiatry, Veterans Health Service Medical Center, Seoul, South Korea
| | - Jee In Kang
- Institute of Behavioral Science in Medicine and Department of Psychiatry, Yonsei University College of Medicine, Seoul, South Korea
| |
Collapse
|