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Nawaz K, Alifah N, Hussain T, Hameed H, Ali H, Hamayun S, Mir A, Wahab A, Naeem M, Zakria M, Pakki E, Hasan N. From genes to therapy: A comprehensive exploration of congenital heart disease through the lens of genetics and emerging technologies. Curr Probl Cardiol 2024; 49:102726. [PMID: 38944223 DOI: 10.1016/j.cpcardiol.2024.102726] [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: 06/20/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024]
Abstract
Congenital heart disease (CHD) affects approximately 1 % of live births worldwide, making it the most common congenital anomaly in newborns. Recent advancements in genetics and genomics have significantly deepened our understanding of the genetics of CHDs. While the majority of CHD etiology remains unclear, evidence consistently indicates that genetics play a significant role in its development. CHD etiology holds promise for enhancing diagnosis and developing novel therapies to improve patient outcomes. In this review, we explore the contributions of both monogenic and polygenic factors of CHDs and highlight the transformative impact of emerging technologies on these fields. We also summarized the state-of-the-art techniques, including targeted next-generation sequencing (NGS), whole genome and whole exome sequencing (WGS, WES), single-cell RNA sequencing (scRNA-seq), human induced pluripotent stem cells (hiPSCs) and others, that have revolutionized our understanding of cardiovascular disease genetics both from diagnosis perspective and from disease mechanism perspective in children and young adults. These molecular diagnostic techniques have identified new genes and chromosomal regions involved in syndromic and non-syndromic CHD, enabling a more defined explanation of the underlying pathogenetic mechanisms. As our knowledge and technologies continue to evolve, they promise to enhance clinical outcomes and reduce the CHD burden worldwide.
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Affiliation(s)
- Khalid Nawaz
- Department of Medical Laboratory Technology, Khyber Medical University, Peshawar, 25100, Khyber Pakhtunkhwa, Pakistan
| | - Nur Alifah
- Faculty of Pharmacy, Universitas Hasanuddin, Jl. Perintis Kemerdekaan Km 10, Makassar, 90245, Republic of Indonesia
| | - Talib Hussain
- Women Dental College, Khyber Medical University, Abbottabad, 22080, Khyber Pakhtunkhwa, Pakistan
| | - Hamza Hameed
- Department of Cardiology, Pakistan Institute of Medical Sciences (PIMS), Islamabad, 04485, Punjab, Pakistan
| | - Haider Ali
- Department of Pharmacy, Kohat University of Science and Technology, Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Shah Hamayun
- Department of Cardiology, Pakistan Institute of Medical Sciences (PIMS), Islamabad, 04485, Punjab, Pakistan
| | - Awal Mir
- Department of Medical Laboratory Technology, Khyber Medical University, Peshawar, 25100, Khyber Pakhtunkhwa, Pakistan
| | - Abdul Wahab
- Department of Pharmacy, Kohat University of Science and Technology, Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Naeem
- Department of Biological Sciences, National University of Medical Sciences (NUMS), Rawalpindi, Punjab, Pakistan
| | - Mohammad Zakria
- Advanced Center for Genomic Technologies, Khyber Medical University, Peshawar, 25100, Khyber Pakhtunkhwa, Pakistan
| | - Ermina Pakki
- Faculty of Pharmacy, Universitas Hasanuddin, Jl. Perintis Kemerdekaan Km 10, Makassar, 90245, Republic of Indonesia
| | - Nurhasni Hasan
- Faculty of Pharmacy, Universitas Hasanuddin, Jl. Perintis Kemerdekaan Km 10, Makassar, 90245, Republic of Indonesia.
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Miller DT, Adam MP, Aradhya S, Biesecker LG, Brothman AR, Carter NP, Church DM, Crolla JA, Eichler EE, Epstein CJ, Faucett WA, Feuk L, Friedman JM, Hamosh A, Jackson L, Kaminsky EB, Kok K, Krantz ID, Kuhn RM, Lee C, Ostell JM, Rosenberg C, Scherer SW, Spinner NB, Stavropoulos DJ, Tepperberg JH, Thorland EC, Vermeesch JR, Waggoner DJ, Watson MS, Martin CL, Ledbetter DH. Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet 2010; 86:749-64. [PMID: 20466091 PMCID: PMC2869000 DOI: 10.1016/j.ajhg.2010.04.006] [Citation(s) in RCA: 1815] [Impact Index Per Article: 129.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Revised: 04/12/2010] [Accepted: 04/19/2010] [Indexed: 12/11/2022] Open
Abstract
Chromosomal microarray (CMA) is increasingly utilized for genetic testing of individuals with unexplained developmental delay/intellectual disability (DD/ID), autism spectrum disorders (ASD), or multiple congenital anomalies (MCA). Performing CMA and G-banded karyotyping on every patient substantially increases the total cost of genetic testing. The International Standard Cytogenomic Array (ISCA) Consortium held two international workshops and conducted a literature review of 33 studies, including 21,698 patients tested by CMA. We provide an evidence-based summary of clinical cytogenetic testing comparing CMA to G-banded karyotyping with respect to technical advantages and limitations, diagnostic yield for various types of chromosomal aberrations, and issues that affect test interpretation. CMA offers a much higher diagnostic yield (15%-20%) for genetic testing of individuals with unexplained DD/ID, ASD, or MCA than a G-banded karyotype ( approximately 3%, excluding Down syndrome and other recognizable chromosomal syndromes), primarily because of its higher sensitivity for submicroscopic deletions and duplications. Truly balanced rearrangements and low-level mosaicism are generally not detectable by arrays, but these are relatively infrequent causes of abnormal phenotypes in this population (<1%). Available evidence strongly supports the use of CMA in place of G-banded karyotyping as the first-tier cytogenetic diagnostic test for patients with DD/ID, ASD, or MCA. G-banded karyotype analysis should be reserved for patients with obvious chromosomal syndromes (e.g., Down syndrome), a family history of chromosomal rearrangement, or a history of multiple miscarriages.
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Affiliation(s)
- David T. Miller
- Division of Genetics and Department of Laboratory Medicine, Children's Hospital Boston and Harvard Medical School, Boston, MA, USA
| | - Margaret P. Adam
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Leslie G. Biesecker
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Arthur R. Brothman
- Department of Pediatrics, Human Genetics, Pathology and ARUP Laboratories, University of Utah School of Medicine, Salt Lake City, UT, USA
| | | | - Deanna M. Church
- National Center for Biotechnology Information, Bethesda, MD, USA
| | - John A. Crolla
- National Genetics Reference Laboratory (Wessex), Salisbury UK
| | - Evan E. Eichler
- Department of Genome Sciences and Howard Hughes Medical Institute, University of Washington School of Medicine, Seattle, WA, USA
| | - Charles J. Epstein
- Institute for Human Genetics and Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - W. Andrew Faucett
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Lars Feuk
- Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Jan M. Friedman
- Department of Medical Genetics, University of British Columbia, and Child & Family Research Institute, Vancouver, British Columbia, Canada
| | - Ada Hamosh
- Department of Pediatrics and McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Laird Jackson
- Department of Obstetrics and Gynecology, Drexel University College of Medicine and Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Erin B. Kaminsky
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Klaas Kok
- Department of Genetics, University Medical Centre Groningen, University of Groningen, The Netherlands
| | - Ian D. Krantz
- Department of Pediatrics/Human Genetics, The Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Robert M. Kuhn
- Center for Biomolecular Science and Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Charles Lee
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - James M. Ostell
- National Center for Biotechnology Information, Bethesda, MD, USA
| | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, University Sao Paulo, Brazil
| | - Stephen W. Scherer
- The Centre for Applied Genomics and Program in Genetics and Genetic Biology, The Hospital for Sick Children and Department of Molecular Genetics, University of Toronto, Ontario, Canada
| | - Nancy B. Spinner
- Department of Pediatrics/Human Genetics, The Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Dimitri J. Stavropoulos
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Erik C. Thorland
- Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Darrel J. Waggoner
- Department of Human Genetics and Pediatrics, University of Chicago, Chicago, IL, USA
| | | | - Christa Lese Martin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - David H. Ledbetter
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
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Colella S, Yau C, Taylor JM, Mirza G, Butler H, Clouston P, Bassett AS, Seller A, Holmes CC, Ragoussis J. QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data. Nucleic Acids Res 2007; 35:2013-25. [PMID: 17341461 PMCID: PMC1874617 DOI: 10.1093/nar/gkm076] [Citation(s) in RCA: 450] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Array-based technologies have been used to detect chromosomal copy number changes (aneuploidies) in the human genome. Recent studies identified numerous copy number variants (CNV) and some are common polymorphisms that may contribute to disease susceptibility. We developed, and experimentally validated, a novel computational framework (QuantiSNP) for detecting regions of copy number variation from BeadArray SNP genotyping data using an Objective Bayes Hidden-Markov Model (OB-HMM). Objective Bayes measures are used to set certain hyperparameters in the priors using a novel re-sampling framework to calibrate the model to a fixed Type I (false positive) error rate. Other parameters are set via maximum marginal likelihood to prior training data of known structure. QuantiSNP provides probabilistic quantification of state classifications and significantly improves the accuracy of segmental aneuploidy identification and mapping, relative to existing analytical tools (Beadstudio, Illumina), as demonstrated by validation of breakpoint boundaries. QuantiSNP identified both novel and validated CNVs. QuantiSNP was developed using BeadArray SNP data but it can be adapted to other platforms and we believe that the OB-HMM framework has widespread applicability in genomic research. In conclusion, QuantiSNP is a novel algorithm for high-resolution CNV/aneuploidy detection with application to clinical genetics, cancer and disease association studies.
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Affiliation(s)
- Stefano Colella
- Genomics Laboratory and Bioinformatics, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, Life Science Interface Doctoral Training Centre, Wolfson Building, Parks Road, Oxford OX1 3QD, Henry Wellcome Centre for Gene Function, Department of Statistics, University of Oxford, Oxford, OX1 3TG, Oxford Medical Genetics Laboratories, The Churchill Hospital, Oxford, OX3 7LJ, UK, Centre for Addiction & Mental Health, University of Toronto, 1001 Queen Street West, Toronto, Ontario M6J 1H4, Canada and MRC Mammalian Genetics Unit, Medical Research Council, Harwell, Oxford, OX11 0RD
| | - Christopher Yau
- Genomics Laboratory and Bioinformatics, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, Life Science Interface Doctoral Training Centre, Wolfson Building, Parks Road, Oxford OX1 3QD, Henry Wellcome Centre for Gene Function, Department of Statistics, University of Oxford, Oxford, OX1 3TG, Oxford Medical Genetics Laboratories, The Churchill Hospital, Oxford, OX3 7LJ, UK, Centre for Addiction & Mental Health, University of Toronto, 1001 Queen Street West, Toronto, Ontario M6J 1H4, Canada and MRC Mammalian Genetics Unit, Medical Research Council, Harwell, Oxford, OX11 0RD
| | - Jennifer M. Taylor
- Genomics Laboratory and Bioinformatics, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, Life Science Interface Doctoral Training Centre, Wolfson Building, Parks Road, Oxford OX1 3QD, Henry Wellcome Centre for Gene Function, Department of Statistics, University of Oxford, Oxford, OX1 3TG, Oxford Medical Genetics Laboratories, The Churchill Hospital, Oxford, OX3 7LJ, UK, Centre for Addiction & Mental Health, University of Toronto, 1001 Queen Street West, Toronto, Ontario M6J 1H4, Canada and MRC Mammalian Genetics Unit, Medical Research Council, Harwell, Oxford, OX11 0RD
| | - Ghazala Mirza
- Genomics Laboratory and Bioinformatics, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, Life Science Interface Doctoral Training Centre, Wolfson Building, Parks Road, Oxford OX1 3QD, Henry Wellcome Centre for Gene Function, Department of Statistics, University of Oxford, Oxford, OX1 3TG, Oxford Medical Genetics Laboratories, The Churchill Hospital, Oxford, OX3 7LJ, UK, Centre for Addiction & Mental Health, University of Toronto, 1001 Queen Street West, Toronto, Ontario M6J 1H4, Canada and MRC Mammalian Genetics Unit, Medical Research Council, Harwell, Oxford, OX11 0RD
| | - Helen Butler
- Genomics Laboratory and Bioinformatics, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, Life Science Interface Doctoral Training Centre, Wolfson Building, Parks Road, Oxford OX1 3QD, Henry Wellcome Centre for Gene Function, Department of Statistics, University of Oxford, Oxford, OX1 3TG, Oxford Medical Genetics Laboratories, The Churchill Hospital, Oxford, OX3 7LJ, UK, Centre for Addiction & Mental Health, University of Toronto, 1001 Queen Street West, Toronto, Ontario M6J 1H4, Canada and MRC Mammalian Genetics Unit, Medical Research Council, Harwell, Oxford, OX11 0RD
| | - Penny Clouston
- Genomics Laboratory and Bioinformatics, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, Life Science Interface Doctoral Training Centre, Wolfson Building, Parks Road, Oxford OX1 3QD, Henry Wellcome Centre for Gene Function, Department of Statistics, University of Oxford, Oxford, OX1 3TG, Oxford Medical Genetics Laboratories, The Churchill Hospital, Oxford, OX3 7LJ, UK, Centre for Addiction & Mental Health, University of Toronto, 1001 Queen Street West, Toronto, Ontario M6J 1H4, Canada and MRC Mammalian Genetics Unit, Medical Research Council, Harwell, Oxford, OX11 0RD
| | - Anne S. Bassett
- Genomics Laboratory and Bioinformatics, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, Life Science Interface Doctoral Training Centre, Wolfson Building, Parks Road, Oxford OX1 3QD, Henry Wellcome Centre for Gene Function, Department of Statistics, University of Oxford, Oxford, OX1 3TG, Oxford Medical Genetics Laboratories, The Churchill Hospital, Oxford, OX3 7LJ, UK, Centre for Addiction & Mental Health, University of Toronto, 1001 Queen Street West, Toronto, Ontario M6J 1H4, Canada and MRC Mammalian Genetics Unit, Medical Research Council, Harwell, Oxford, OX11 0RD
| | - Anneke Seller
- Genomics Laboratory and Bioinformatics, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, Life Science Interface Doctoral Training Centre, Wolfson Building, Parks Road, Oxford OX1 3QD, Henry Wellcome Centre for Gene Function, Department of Statistics, University of Oxford, Oxford, OX1 3TG, Oxford Medical Genetics Laboratories, The Churchill Hospital, Oxford, OX3 7LJ, UK, Centre for Addiction & Mental Health, University of Toronto, 1001 Queen Street West, Toronto, Ontario M6J 1H4, Canada and MRC Mammalian Genetics Unit, Medical Research Council, Harwell, Oxford, OX11 0RD
| | - Christopher C. Holmes
- Genomics Laboratory and Bioinformatics, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, Life Science Interface Doctoral Training Centre, Wolfson Building, Parks Road, Oxford OX1 3QD, Henry Wellcome Centre for Gene Function, Department of Statistics, University of Oxford, Oxford, OX1 3TG, Oxford Medical Genetics Laboratories, The Churchill Hospital, Oxford, OX3 7LJ, UK, Centre for Addiction & Mental Health, University of Toronto, 1001 Queen Street West, Toronto, Ontario M6J 1H4, Canada and MRC Mammalian Genetics Unit, Medical Research Council, Harwell, Oxford, OX11 0RD
| | - Jiannis Ragoussis
- Genomics Laboratory and Bioinformatics, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, Life Science Interface Doctoral Training Centre, Wolfson Building, Parks Road, Oxford OX1 3QD, Henry Wellcome Centre for Gene Function, Department of Statistics, University of Oxford, Oxford, OX1 3TG, Oxford Medical Genetics Laboratories, The Churchill Hospital, Oxford, OX3 7LJ, UK, Centre for Addiction & Mental Health, University of Toronto, 1001 Queen Street West, Toronto, Ontario M6J 1H4, Canada and MRC Mammalian Genetics Unit, Medical Research Council, Harwell, Oxford, OX11 0RD
- *To whom correspondence should be addressed. +44-(0)1865 287526+44-(0)1865 287533
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