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Vona B, Regele S, Rad A, Strenzke N, Pater JA, Neumann K, Sturm M, Haack TB, Am Zehnhoff-Dinnesen AG. Unraveling haplotype errors in the DFNA33 locus. Front Genet 2023; 14:1214736. [PMID: 37671045 PMCID: PMC10475583 DOI: 10.3389/fgene.2023.1214736] [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: 05/02/2023] [Accepted: 08/04/2023] [Indexed: 09/07/2023] Open
Abstract
Genetic heterogeneity makes it difficult to identify the causal genes for hearing loss. Studies from previous decades have mapped numerous genetic loci, providing critical supporting evidence for gene discovery studies. Despite widespread sequencing accessibility, many historically mapped loci remain without a causal gene. The DFNA33 locus was mapped in 2009 and coincidentally contains ATP11A, a gene recently associated with autosomal dominant hearing loss and auditory neuropathy type 2. In a rare opportunity, we genome-sequenced a member of the original family to determine whether the DFNA33 locus may also be assigned to ATP11A. We identified a deep intronic variant in ATP11A that showed evidence of functionally normal splicing. Furthermore, we re-assessed haplotypes from the originally published DFNA33 family and identified two double recombination events and one triple recombination event in the pedigree, a highly unlikely occurrence, especially at this scale. This brief research report also serves as a call to the community to revisit families who have previously been involved in gene mapping studies, provide closure, and resolve these historical loci.
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Affiliation(s)
- Barbara Vona
- Tübingen Hearing Research Centre, Department of Otolaryngology, Head and Neck Surgery, Eberhard Karls University Tübingen, Tübingen, Germany
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany
| | - Sabrina Regele
- Department of Phoniatrics and Pedaudiology, University Hospital Münster, University of Münster, Münster, Germany
| | - Aboulfazl Rad
- Tübingen Hearing Research Centre, Department of Otolaryngology, Head and Neck Surgery, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Nicola Strenzke
- Auditory Systems Physiology Group, Department of Otolaryngology and Institute for Auditory Neuroscience, University Medical Center Göttingen, Göttingen, Germany
| | - Justin A. Pater
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, United States
- Health Sciences Centre, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
| | - Katrin Neumann
- Department of Phoniatrics and Pedaudiology, University Hospital Münster, University of Münster, Münster, Germany
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Tobias B. Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
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Kocaaga A, Aköz İÖ, Demir NU, Paksoy B. Identification of novel variants in retinitis pigmentosa genes by whole-exome sequencing. REVISTA DA ASSOCIACAO MEDICA BRASILEIRA (1992) 2023; 69:e20221073. [PMID: 37222315 DOI: 10.1590/1806-9282.20221073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/23/2023] [Indexed: 05/25/2023]
Abstract
OBJECTIVE Retinitis pigmentosa is an inherited degenerative disorder causing severe retinal dystrophy and visual impairment, mainly with onset in the first or second decades. The next-generation sequencing has become an efficient tool to identify disease-causing mutations in retinitis pigmentosa. The aim of this retrospective study was to investigate novel gene variants and evaluate the utility of whole-exome sequencing in patients with retinitis pigmentosa. METHODS The medical records of 20 patients with retinitis pigmentosa at Eskişehir City Hospital between September 2019 and February 2022 were analyzed retrospectively. Peripheral venous blood was obtained, followed by the extraction of genomic DNAs. The medical and ophthalmic histories were collected, and ophthalmological examinations were performed. Whole-exome sequencing was performed to determine the genetic etiology of the patients. RESULTS The proportion of genetically solved cases was 75% (15/20) in the patients with retinitis pigmentosa. Molecular genetic testing identified 13 biallelic and 4 monoallelic mutations in known retinitis pigmentosa genes, including 11 novel variants. According to in silico prediction tools, nine variants were predicted as pathogenic or possibly pathogenic. We identified six previously reported mutations to be associated with retinitis pigmentosa. The age of onset of the patients ranged from 3 to 19, with a mean age of onset of 11.6. All patients had a loss of central vision. CONCLUSION As the first study of the application of whole-exome sequencing among patients with retinitis pigmentosa in a Turkish cohort, our results may contribute to the characterization of the spectrum of variants related to retinitis pigmentosa in the Turkish population. Future population-based studies will enable us to reveal the detailed genetic epidemiology of retinitis pigmentosa.
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Affiliation(s)
- Ayca Kocaaga
- Eskişehir City Hospital, Department of Medical Genetics - Eskişehir, Turkey
| | - İrem Öztürk Aköz
- Eskişehir City Hospital, Department of Ophthalmology - Eskişehir, Turkey
| | - Nihal Ulus Demir
- Eskişehir City Hospital, Department of Ophthalmology - Eskişehir, Turkey
| | - Bariş Paksoy
- Antalya Eğitim ve Araştırma Hastanesi, Department of Medical Genetics - Antalya, Turkey
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Abstract
Our understanding of genetic disease(s) has increased exponentially since the completion of human genome sequencing and the development of numerous techniques to detect genetic variants. These techniques have not only allowed us to diagnose genetic disease, but in so doing, also provide increased understanding of the pathogenesis of these diseases to aid in developing appropriate therapeutic options. Additionally, the advent of next-generation or massively parallel sequencing (NGS/MPS) is increasingly being used in the clinical setting, as it can detect a number of abnormalities from point mutations to chromosomal rearrangements as well as aberrations within the transcriptome. In this article, we will discuss the use of multiple techniques that are used in genetic diagnosis. © 2020 by John Wiley & Sons, Inc.
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Affiliation(s)
- Rashmi S Goswami
- Department of Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada.,Sunnybrook Research Institute, Biological Sciences, Odette Cancer Research Program, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Shuko Harada
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama
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4
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Du Q, Zhang D, Zhuang Y, Xia Q, Wen T, Jia H. The Molecular Genetics of Marfan Syndrome. Int J Med Sci 2021; 18:2752-2766. [PMID: 34220303 PMCID: PMC8241768 DOI: 10.7150/ijms.60685] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 05/18/2021] [Indexed: 12/27/2022] Open
Abstract
Marfan syndrome (MFS) is a complex connective tissue disease that is primarily characterized by cardiovascular, ocular and skeletal systems disorders. Despite its rarity, MFS severely impacts the quality of life of the patients. It has been shown that molecular genetic factors serve critical roles in the pathogenesis of MFS. FBN1 is associated with MFS and the other genes such as FBN2, transforming growth factor beta (TGF-β) receptors (TGFBR1 and TGFBR2), latent TGF-β-binding protein 2 (LTBP2) and SKI, amongst others also have their associated syndromes, however high overlap may exist between these syndromes and MFS. Abnormalities in the TGF-β signaling pathway also contribute to the development of aneurysms in patients with MFS, although the detailed molecular mechanism remains unclear. Mutant FBN1 protein may cause unstableness in elastic structures, thereby perturbing the TGF-β signaling pathway, which regulates several processes in cells. Additionally, DNA methylation of FBN1 and histone acetylation in an MFS mouse model demonstrated that epigenetic factors play a regulatory role in MFS. The purpose of the present review is to provide an up-to-date understanding of MFS-related genes and relevant assessment technologies, with the aim of laying a foundation for the early diagnosis, consultation and treatment of MFS.
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Affiliation(s)
- Qiu Du
- Marfan Research Group, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, Sichuan, China
| | - Dingding Zhang
- Marfan Research Group, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, Sichuan, China.,Sichuan Provincial Key Laboratory for Genetic Disease, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 611731, Sichuan, China
| | - Yue Zhuang
- Department of Rheumatology and Immunology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 611731, Sichuan, China
| | - Qiongrong Xia
- Marfan Research Group, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, Sichuan, China
| | - Taishen Wen
- Sichuan Provincial Key Laboratory for Genetic Disease, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 611731, Sichuan, China
| | - Haiping Jia
- Department of Immunology, North Sichuan Medical College, Nanchong, 637100, Sichuan, China
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5
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Kanzi AM, San JE, Chimukangara B, Wilkinson E, Fish M, Ramsuran V, de Oliveira T. Next Generation Sequencing and Bioinformatics Analysis of Family Genetic Inheritance. Front Genet 2020; 11:544162. [PMID: 33193618 PMCID: PMC7649788 DOI: 10.3389/fgene.2020.544162] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 09/21/2020] [Indexed: 12/29/2022] Open
Abstract
Mendelian and complex genetic trait diseases continue to burden and affect society both socially and economically. The lack of effective tests has hampered diagnosis thus, the affected lack proper prognosis. Mendelian diseases are caused by genetic mutations in a singular gene while complex trait diseases are caused by the accumulation of mutations in either linked or unlinked genomic regions. Significant advances have been made in identifying novel diseases associated mutations especially with the introduction of next generation and third generation sequencing. Regardless, some diseases are still without diagnosis as most tests rely on SNP genotyping panels developed from population based genetic analyses. Analysis of family genetic inheritance using whole genomes, whole exomes or a panel of genes has been shown to be effective in identifying disease-causing mutations. In this review, we discuss next generation and third generation sequencing platforms, bioinformatic tools and genetic resources commonly used to analyze family based genomic data with a focus on identifying inherited or novel disease-causing mutations. Additionally, we also highlight the analytical, ethical and regulatory challenges associated with analyzing personal genomes which constitute the data used for family genetic inheritance.
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Affiliation(s)
- Aquillah M. Kanzi
- Kwazulu-Natal Research and Innovation Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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6
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Zhou J, Gao J, Zhang H, Zhao D, Li A, Iqbal F, Shi Q, Zhang Y. PedMiner: a tool for linkage analysis-based identification of disease-associated variants using family based whole-exome sequencing data. Brief Bioinform 2020; 22:5835558. [PMID: 32393981 PMCID: PMC8138824 DOI: 10.1093/bib/bbaa077] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 04/13/2020] [Accepted: 04/17/2020] [Indexed: 12/22/2022] Open
Abstract
With the advances of next-generation sequencing technology, the field of disease research has been revolutionized. However, pinpointing the disease-causing variants from millions of revealed variants is still a tough task. Here, we have reviewed the existing linkage analysis tools and presented PedMiner, a web-based application designed to narrow down candidate variants from family based whole-exome sequencing (WES) data through linkage analysis. PedMiner integrates linkage analysis, variant annotation and prioritization in one automated pipeline. It provides graphical visualization of the linked regions along with comprehensive annotation of variants and genes within these linked regions. This efficient and comprehensive application will be helpful for the scientific community working on Mendelian inherited disorders using family based WES data.
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Affiliation(s)
| | | | | | | | | | | | - Qinghua Shi
- Qinghua Shi, The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at the Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, School of Life Sciences, University of Science and Technology of China, 443 Huangshan Road, Shushan District, Hefei 230027, China. Tel: +86-551-63600442; Fax: +86-551-63600344; E-mail:
| | - Yuanwei Zhang
- Corresponding author: Yuanwei Zhang, The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at the Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, School of Life Sciences, University of Science and Technology of China, 443 Huangshan Road, Shushan District, Hefei 230027, China. Tel: +86-551-63600442; Fax: +86-551-63600344; E-mail:
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Wysocki T, Olesińska M, Paradowska-Gorycka A. Current Understanding of an Emerging Role of HLA-DRB1 Gene in Rheumatoid Arthritis-From Research to Clinical Practice. Cells 2020; 9:cells9051127. [PMID: 32370106 PMCID: PMC7291248 DOI: 10.3390/cells9051127] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/28/2020] [Accepted: 04/30/2020] [Indexed: 12/22/2022] Open
Abstract
Rheumatoid arthritis (RA) is an autoimmune disease with an unclear pathogenic mechanism. However, it has been proven that the key underlying risk factor is a genetic predisposition. Association studies of the HLA-DRB1 gene clearly indicate its importance in RA morbidity. This review presents the current state of knowledge on the impact of HLA-DRB1 gene, functioning both as a component of the patient’s genome and as an environmental risk factor. The impact of known HLA-DRB1 risk variants on the specific structure of the polymorphic HLA-DR molecule, and epitope binding affinity, is presented. The issues of the potential influence of HLA-DRB1 on the occurrence of non-articular disease manifestations and response to treatment are also discussed. A deeper understanding of the role of the HLA-DRB1 gene is essential to explore the complex nature of RA, which is a result of multiple contributing factors, including genetic, epigenetic and environmental factors. It also creates new opportunities to develop modern and personalized forms of therapy.
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Affiliation(s)
- Tomasz Wysocki
- Department of Systemic Connective Tissue Diseases, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartańska 1, 02-637 Warsaw, Poland; or
- Correspondence:
| | - Marzena Olesińska
- Department of Systemic Connective Tissue Diseases, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartańska 1, 02-637 Warsaw, Poland; or
| | - Agnieszka Paradowska-Gorycka
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartańska 1, 02-637 Warsaw, Poland; or
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8
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Angural A, Spolia A, Mahajan A, Verma V, Sharma A, Kumar P, Dhar MK, Pandita KK, Rai E, Sharma S. Review: Understanding Rare Genetic Diseases in Low Resource Regions Like Jammu and Kashmir - India. Front Genet 2020; 11:415. [PMID: 32425985 PMCID: PMC7203485 DOI: 10.3389/fgene.2020.00415] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 04/01/2020] [Indexed: 12/11/2022] Open
Abstract
Rare diseases (RDs) are the clinical conditions affecting a few percentage of individuals in a general population compared to other diseases. Limited clinical information and a lack of reliable epidemiological data make their timely diagnosis and therapeutic management difficult. Emerging Next-Generation DNA Sequencing technologies have enhanced our horizons on patho-physiological understanding of many of the RDs and ushered us into an era of diagnostic and therapeutic research related to this ignored health challenge. Unfortunately, relevant research is meager in developing countries which lack a reliable estimate of the exact burden of most of the RDs. India is to be considered as the "Pandora's Box of genetic disorders." Owing to its huge population heterogeneity and high inbreeding or endogamy rates, a higher burden of rare recessive genetic diseases is expected and supported by the literature findings that endogamy is highly detrimental to health as it enhances the degree of homozygosity of recessive alleles in the general population. The population of a low resource region Jammu and Kashmir (J&K) - India, is highly inbred. Some of its population groups variably practice consanguinity. In context with the region's typical geographical topography, highly inbred population structure and unique but heterogeneous gene pool, a huge burden of known and uncharacterized genetic disorders is expected. Unfortunately, many suspected cases of genetic disorders remain undiagnosed or misdiagnosed due to lack of appropriate clinical as well as diagnostic resources in the region, causing patients to face a huge psycho-socio-economic crisis and many a time suffer life-long with their ailment. In this review, the major challenges associated with RDs are highlighted in general and an account on the methods that can be adopted for conducting fruitful molecular genetic studies in genetically vulnerable and low resource regions is also provided, with an example of a region like J&K - India.
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Affiliation(s)
- Arshia Angural
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Akshi Spolia
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Ankit Mahajan
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Vijeshwar Verma
- Bioinformatics Infrastructure Facility, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Ankush Sharma
- Shri Mata Vaishno Devi Narayana Superspeciality Hospital, Katra, India
| | - Parvinder Kumar
- Institute of Human Genetics, University of Jammu, Jammu, India
| | | | - Kamal Kishore Pandita
- Shri Mata Vaishno Devi Narayana Superspeciality Hospital, Katra, India
- Independent Researcher, Health Clinic, Jammu, India
| | - Ekta Rai
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Swarkar Sharma
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
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9
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Garnai SJ, Brinkmeier ML, Emery B, Aleman TS, Pyle LC, Veleva-Rotse B, Sisk RA, Rozsa FW, Ozel AB, Li JZ, Moroi SE, Archer SM, Lin CM, Sheskey S, Wiinikka-Buesser L, Eadie J, Urquhart JE, Black GC, Othman MI, Boehnke M, Sullivan SA, Skuta GL, Pawar HS, Katz AE, Huryn LA, Hufnagel RB, Camper SA, Richards JE, Prasov L. Variants in myelin regulatory factor (MYRF) cause autosomal dominant and syndromic nanophthalmos in humans and retinal degeneration in mice. PLoS Genet 2019; 15:e1008130. [PMID: 31048900 PMCID: PMC6527243 DOI: 10.1371/journal.pgen.1008130] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 05/20/2019] [Accepted: 04/09/2019] [Indexed: 01/11/2023] Open
Abstract
Nanophthalmos is a rare, potentially devastating eye condition characterized by small eyes with relatively normal anatomy, a high hyperopic refractive error, and frequent association with angle closure glaucoma and vision loss. The condition constitutes the extreme of hyperopia or farsightedness, a common refractive error that is associated with strabismus and amblyopia in children. NNO1 was the first mapped nanophthalmos locus. We used combined pooled exome sequencing and strong linkage data in the large family used to map this locus to identify a canonical splice site alteration upstream of the last exon of the gene encoding myelin regulatory factor (MYRF c.3376-1G>A), a membrane bound transcription factor that undergoes autoproteolytic cleavage for nuclear localization. This variant produced a stable RNA transcript, leading to a frameshift mutation p.Gly1126Valfs*31 in the C-terminus of the protein. In addition, we identified an early truncating MYRF frameshift mutation, c.769dupC (p.S264QfsX74), in a patient with extreme axial hyperopia and syndromic features. Myrf conditional knockout mice (CKO) developed depigmentation of the retinal pigment epithelium (RPE) and retinal degeneration supporting a role of this gene in retinal and RPE development. Furthermore, we demonstrated the reduced expression of Tmem98, another known nanophthalmos gene, in Myrf CKO mice, and the physical interaction of MYRF with TMEM98. Our study establishes MYRF as a nanophthalmos gene and uncovers a new pathway for eye growth and development.
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Affiliation(s)
- Sarah J. Garnai
- Department of Ophthalmology and Visual Sciences, W.K. Kellogg Eye Center, University of Michigan, Ann Arbor, MI, United States of America
- Harvard Medical School, Boston, MA, United States of America
| | - Michelle L. Brinkmeier
- Department of Ophthalmology and Visual Sciences, W.K. Kellogg Eye Center, University of Michigan, Ann Arbor, MI, United States of America
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, United States of America
| | - Ben Emery
- Jungers Center for Neurosciences Research, Department of Neurology, Oregon Health & Science University, Portland, OR, United States of America
| | - Tomas S. Aleman
- The Children’s Hospital of Philadelphia, Philadelphia, PA, United States of America
- Scheie Eye Institute, Department of Ophthalmology, Philadelphia, PA, United States of America
| | - Louise C. Pyle
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States of America
| | - Biliana Veleva-Rotse
- Jungers Center for Neurosciences Research, Department of Neurology, Oregon Health & Science University, Portland, OR, United States of America
| | - Robert A. Sisk
- Cincinnati Eye Institute, Cincinnati, Ohio, United States of America
| | - Frank W. Rozsa
- Department of Ophthalmology and Visual Sciences, W.K. Kellogg Eye Center, University of Michigan, Ann Arbor, MI, United States of America
- Molecular and Behavior Neuroscience Institute, University of Michigan, Ann Arbor, MI, United States of America
| | - Ayse Bilge Ozel
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, United States of America
| | - Jun Z. Li
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, United States of America
| | - Sayoko E. Moroi
- Department of Ophthalmology and Visual Sciences, W.K. Kellogg Eye Center, University of Michigan, Ann Arbor, MI, United States of America
| | - Steven M. Archer
- Department of Ophthalmology and Visual Sciences, W.K. Kellogg Eye Center, University of Michigan, Ann Arbor, MI, United States of America
| | - Cheng-mao Lin
- Department of Ophthalmology and Visual Sciences, W.K. Kellogg Eye Center, University of Michigan, Ann Arbor, MI, United States of America
| | - Sarah Sheskey
- Department of Ophthalmology and Visual Sciences, W.K. Kellogg Eye Center, University of Michigan, Ann Arbor, MI, United States of America
| | - Laurel Wiinikka-Buesser
- Department of Ophthalmology and Visual Sciences, W.K. Kellogg Eye Center, University of Michigan, Ann Arbor, MI, United States of America
| | - James Eadie
- Department of Ophthalmology and Visual Sciences, W.K. Kellogg Eye Center, University of Michigan, Ann Arbor, MI, United States of America
| | - Jill E. Urquhart
- Manchester Centre for Genomic Medicine, Manchester Academic Health Sciences Centre, Manchester University NHS Foundation Trust, St Mary’s Hospital, Manchester, United Kingdom
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Graeme C.M. Black
- Manchester Centre for Genomic Medicine, Manchester Academic Health Sciences Centre, Manchester University NHS Foundation Trust, St Mary’s Hospital, Manchester, United Kingdom
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Mohammad I. Othman
- Department of Ophthalmology and Visual Sciences, W.K. Kellogg Eye Center, University of Michigan, Ann Arbor, MI, United States of America
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, United States of America
| | - Scot A. Sullivan
- Dean McGee Eye Institute, Department of Ophthalmology, University of Oklahoma, Oklahoma City, OK
| | - Gregory L. Skuta
- Dean McGee Eye Institute, Department of Ophthalmology, University of Oklahoma, Oklahoma City, OK
| | - Hemant S. Pawar
- Department of Ophthalmology and Visual Sciences, W.K. Kellogg Eye Center, University of Michigan, Ann Arbor, MI, United States of America
| | - Alexander E. Katz
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - Laryssa A. Huryn
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, United States of America
| | - Robert B. Hufnagel
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, United States of America
| | | | - Sally A. Camper
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, United States of America
| | - Julia E. Richards
- Department of Ophthalmology and Visual Sciences, W.K. Kellogg Eye Center, University of Michigan, Ann Arbor, MI, United States of America
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, United States of America
| | - Lev Prasov
- Department of Ophthalmology and Visual Sciences, W.K. Kellogg Eye Center, University of Michigan, Ann Arbor, MI, United States of America
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, United States of America
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10
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Hong S, Wang L, Zhao D, Zhang Y, Chen Y, Tan J, Liang L, Zhu T. Clinical utility in infants with suspected monogenic conditions through next-generation sequencing. Mol Genet Genomic Med 2019; 7:e684. [PMID: 30968598 PMCID: PMC6565546 DOI: 10.1002/mgg3.684] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 02/06/2019] [Accepted: 03/04/2019] [Indexed: 12/14/2022] Open
Abstract
Background Rare diseases are complex disorders with huge variability in clinical manifestations. Decreasing cost of next‐generation sequencing (NGS) tests in recent years made it affordable. We witnessed the diagnostic yield and clinical use of different NGS strategies on a myriad of monogenic disorders in a pediatric setting. Methods Next‐generation sequencing tests are performed for 98 unrelated Chinese patients within their first year of life, who were admitted to Xin Hua Hospital, affiliated with Shanghai Jiao Tong University School of Medicine, during a 2‐year period. Results Clinical indications for NGS tests included a range of medical concerns. The mean age was 4.4 ± 4.2 months of age for infants undergoing targeting specific (known) disease‐causing genes (TRS) analysis, and 4.4 ± 4.3 months of age for whole‐exome sequencing (WES) (p > 0.05). A molecular diagnosis is done in 72 infants (73.47%), which finds a relatively high yield with phenotypes of metabolism/homeostasis abnormality (HP: 0001939) (odds ratio, 1.83; 95% CI, 0.56–6.04; p = 0.32) and a significantly low yield with atypical symptoms (without a definite HPO term) (odds ratio, 0.08; 95% CI, 0.01–0.73; p = 0.03). TRS analysis provides molecular yields higher than WES (p = 0.01). Ninety‐eight different mutations are discovered in 72 patients. Twenty‐seven of them have not been reported previously. Nearly half (43.06%, 31/72) of the patients are found to carry 11 common disorders, mostly being inborn errors of metabolism (IEM) and neurogenetic disorders and all of them are observed through TRS analysis. Eight positive cases are identified through WES, and all of them are sporadic, of highly variable phenotypes and severity. There are 26 patients with negative findings in this study. Conclusion This study provides evidence that NGS can yield high success rates in a tertiary pediatric setting, but suggests that the scope of known Mendelian conditions may be considerably broader than currently recognized.
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Affiliation(s)
- Sha Hong
- Department of Neonatal Medicine, Xin-Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li Wang
- Department of Neonatal Medicine, Xin-Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dongying Zhao
- Department of Neonatal Medicine, Xin-Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yonghong Zhang
- Department of Neonatal Medicine, Xin-Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yan Chen
- Department of Neonatal Medicine, Xin-Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jintong Tan
- Department of Neonatal Medicine, Xin-Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lili Liang
- Department of Endocrinology and Genetic Metabolism, Xin-Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tianwen Zhu
- Department of Neonatal Medicine, Xin-Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
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11
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Hellwege J, Keaton J, Giri A, Gao X, Velez Edwards DR, Edwards TL. Population Stratification in Genetic Association Studies. CURRENT PROTOCOLS IN HUMAN GENETICS 2017; 95:1.22.1-1.22.23. [PMID: 29044472 PMCID: PMC6007879 DOI: 10.1002/cphg.48] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Population stratification (PS) is a primary consideration in studies of genetic determinants of human traits. Failure to control for PS may lead to confounding, causing a study to fail for lack of significant results, or resources to be wasted following false-positive signals. Here, historical and current approaches for addressing PS when performing genetic association studies in human populations are reviewed. Methods for detecting the presence of PS, including global and local ancestry methods, are described. Also described are approaches for accounting for PS when calculating association statistics, such that measures of association are not confounded. Many traits are being examined for the first time in minority populations, which may inherently feature PS. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Jacklyn Hellwege
- Vanderbilt Genetics Institute, Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center,
Nashville, TN 37203, USA
| | - Jacob Keaton
- Vanderbilt Genetics Institute, Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center,
Nashville, TN 37203, USA
| | - Ayush Giri
- Vanderbilt Genetics Institute, Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center,
Nashville, TN 37203, USA
| | - Xiaoyi Gao
- Department of Ophthalmology and Preventive Medicine, Keck School of Medicine, University of Southern California, Los
Angeles, CA 90033, USA
| | - Digna R. Velez Edwards
- Vanderbilt Genetics Institute, Department of Obstetrics and Gynecology, Vanderbilt University Medical Center,
Nashville, TN 37203, USA
| | - Todd L. Edwards
- Vanderbilt Genetics Institute, Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center,
Nashville, TN 37203, USA
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12
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Genome-wide linkage and association analysis of cardiometabolic phenotypes in Hispanic Americans. J Hum Genet 2016; 62:175-184. [PMID: 27535031 PMCID: PMC5266668 DOI: 10.1038/jhg.2016.103] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 07/01/2016] [Accepted: 07/11/2016] [Indexed: 01/01/2023]
Abstract
Linkage studies of complex genetic diseases have been largely replaced by genome-wide association studies, due in part to limited success in complex trait discovery. However, recent interest in rare and low-frequency variants motivates re-examination of family-based methods. In this study, we investigated the performance of two-point linkage analysis for over 1.6 million single-nucleotide polymorphisms (SNPs) combined with single variant association analysis to identify high impact variants, which are both strongly linked and associated with cardiometabolic traits in up to 1414 Hispanics from the Insulin Resistance Atherosclerosis Family Study (IRASFS). Evaluation of all 50 phenotypes yielded 83 557 000 LOD (logarithm of the odds) scores, with 9214 LOD scores ⩾3.0, 845 ⩾4.0 and 89 ⩾5.0, with a maximal LOD score of 6.49 (rs12956744 in the LAMA1 gene for tumor necrosis factor-α (TNFα) receptor 2). Twenty-seven variants were associated with P<0.005 as well as having an LOD score >4, including variants in the NFIB gene under a linkage peak with TNFα receptor 2 levels on chromosome 9. Linkage regions of interest included a broad peak (31 Mb) on chromosome 1q with acute insulin response (max LOD=5.37). This region was previously documented with type 2 diabetes in family-based studies, providing support for the validity of these results. Overall, we have demonstrated the utility of two-point linkage and association in comprehensive genome-wide array-based SNP genotypes.
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13
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Cunha MLR, Meijers JCM, Middeldorp S. Introduction to the analysis of next generation sequencing data and its application to venous thromboembolism. Thromb Haemost 2015; 114:920-32. [PMID: 26446408 DOI: 10.1160/th15-05-0411] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 08/26/2015] [Indexed: 12/13/2022]
Abstract
Despite knowledge of various inherited risk factors associated with venous thromboembolism (VTE), no definite cause can be found in about 50% of patients. The application of data-driven searches such as GWAS has not been able to identify genetic variants with implications for clinical care, and unexplained heritability remains. In the past years, the development of several so-called next generation sequencing (NGS) platforms is offering the possibility of generating fast, inexpensive and accurate genomic information. However, so far their application to VTE has been very limited. Here we review basic concepts of NGS data analysis and explore the application of NGS technology to VTE. We provide both computational and biological viewpoints to discuss potentials and challenges of NGS-based studies.
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Affiliation(s)
- Marisa L R Cunha
- Marisa L. R. Cunha, Department of Experimental Vascular Medicine, Academic Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands, Tel.: +31 20 5662824, Fax: +31 20 6968833, E-mail:
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