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Waldvogel SM, Posey JE, Goodell MA. Human embryonic genetic mosaicism and its effects on development and disease. Nat Rev Genet 2024:10.1038/s41576-024-00715-z. [PMID: 38605218 DOI: 10.1038/s41576-024-00715-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2024] [Indexed: 04/13/2024]
Abstract
Nearly every mammalian cell division is accompanied by a mutational event that becomes fixed in a daughter cell. When carried forward to additional cell progeny, a clone of variant cells can emerge. As a result, mammals are complex mosaics of clones that are genetically distinct from one another. Recent high-throughput sequencing studies have revealed that mosaicism is common, clone sizes often increase with age and specific variants can affect tissue function and disease development. Variants that are acquired during early embryogenesis are shared by multiple cell types and can affect numerous tissues. Within tissues, variant clones compete, which can result in their expansion or elimination. Embryonic mosaicism has clinical implications for genetic disease severity and transmission but is likely an under-recognized phenomenon. To better understand its implications for mosaic individuals, it is essential to leverage research tools that can elucidate the mechanisms by which expanded embryonic variants influence development and disease.
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Affiliation(s)
- Sarah M Waldvogel
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
- Graduate Program in Cancer and Cell Biology, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Margaret A Goodell
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
- Graduate Program in Cancer and Cell Biology, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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2
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Du H, Dardas Z, Jolly A, Grochowski CM, Jhangiani SN, Li H, Muzny D, Fatih JM, Yesil G, Elçioglu NH, Gezdirici A, Marafi D, Pehlivan D, Calame DG, Carvalho CMB, Posey JE, Gambin T, Coban-Akdemir Z, Lupski JR. HMZDupFinder: a robust computational approach for detecting intragenic homozygous duplications from exome sequencing data. Nucleic Acids Res 2024; 52:e18. [PMID: 38153174 PMCID: PMC10899794 DOI: 10.1093/nar/gkad1223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 11/18/2023] [Accepted: 12/13/2023] [Indexed: 12/29/2023] Open
Abstract
Homozygous duplications contribute to genetic disease by altering gene dosage or disrupting gene regulation and can be more deleterious to organismal biology than heterozygous duplications. Intragenic exonic duplications can result in loss-of-function (LoF) or gain-of-function (GoF) alleles that when homozygosed, i.e. brought to homozygous state at a locus by identity by descent or state, could potentially result in autosomal recessive (AR) rare disease traits. However, the detection and functional interpretation of homozygous duplications from exome sequencing data remains a challenge. We developed a framework algorithm, HMZDupFinder, that is designed to detect exonic homozygous duplications from exome sequencing (ES) data. The HMZDupFinder algorithm can efficiently process large datasets and accurately identifies small intragenic duplications, including those associated with rare disease traits. HMZDupFinder called 965 homozygous duplications with three or less exons from 8,707 ES with a recall rate of 70.9% and a precision of 16.1%. We experimentally confirmed 8/10 rare homozygous duplications. Pathogenicity assessment of these copy number variant alleles allowed clinical genomics contextualization for three homozygous duplications alleles, including two affecting known OMIM disease genes EDAR (MIM# 224900), TNNT1(MIM# 605355), and one variant in a novel candidate disease gene: PAAF1.
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Affiliation(s)
- Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zain Dardas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - He Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gozde Yesil
- Department of Medical Genetics, Istanbul Medical Faculty, Istanbul 34093, Turkey
| | - Nursel H Elçioglu
- Department of Pediatric Genetics, Marmara University Medical Faculty, Istanbul and Eastern Mediterranean University Faculty of Medicine, Mersin 10, Turkey
| | - Alper Gezdirici
- Department of Medical Genetics, University of Health Sciences, Basaksehir Cam and Sakura City Hospital, 34480 Istanbul, Turkey
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pediatrics, Faculty of Medicine, Kuwait University, Kuwait
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX 77030, USA
| | - Daniel G Calame
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX 77030, USA
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Pacific Northwest Research Institute, Seattle, WA 98122, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tomasz Gambin
- Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children's Hospital, Houston, TX 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
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3
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Laufer VA, Glover TW, Wilson TE. Applications of advanced technologies for detecting genomic structural variation. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2023; 792:108475. [PMID: 37931775 PMCID: PMC10792551 DOI: 10.1016/j.mrrev.2023.108475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/07/2023] [Accepted: 11/02/2023] [Indexed: 11/08/2023]
Abstract
Chromosomal structural variation (SV) encompasses a heterogenous class of genetic variants that exerts strong influences on human health and disease. Despite their importance, many structural variants (SVs) have remained poorly characterized at even a basic level, a discrepancy predicated upon the technical limitations of prior genomic assays. However, recent advances in genomic technology can identify and localize SVs accurately, opening new questions regarding SV risk factors and their impacts in humans. Here, we first define and classify human SVs and their generative mechanisms, highlighting characteristics leveraged by various SV assays. We next examine the first-ever gapless assembly of the human genome and the technical process of assembling it, which required third-generation sequencing technologies to resolve structurally complex loci. The new portions of that "telomere-to-telomere" and subsequent pangenome assemblies highlight aspects of SV biology likely to develop in the near-term. We consider the strengths and limitations of the most promising new SV technologies and when they or longstanding approaches are best suited to meeting salient goals in the study of human SV in population-scale genomics research, clinical, and public health contexts. It is a watershed time in our understanding of human SV when new approaches are expected to fundamentally change genomic applications.
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Affiliation(s)
- Vincent A Laufer
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Thomas W Glover
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Thomas E Wilson
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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4
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Strang‐Karlsson S, Keigwin S, Anttonen A, Baker D, Bean K, Jakkula E. Multi-exon COL5A1 deletion in a child with classical Ehlers-Danlos syndrome: A case report expanding the allelic spectrum and showing evidence of parental gonosomal mosaicism. Clin Case Rep 2022; 10:e6455. [PMID: 36245460 PMCID: PMC9552984 DOI: 10.1002/ccr3.6455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/25/2022] [Accepted: 09/20/2022] [Indexed: 11/10/2022] Open
Abstract
Classical Ehlers-Danlos syndrome (cEDS) is a rare inherited autosomal dominant connective tissue disorder with core clinical features including skin hyperextensibility, abnormal scarring, and generalized joint hypermobility. Classical EDS is predominantly caused by small pathogenic variants in the genes COL5A1 and COL5A2 and occasionally by a COL1A1 point mutation p.(Arg312Cys), while gross deletions or duplications are uncommon. Gonosomal mosaicism is thought to be exceedingly rare with only two cases reported in the literature. We report a child with cEDS due to a rare gross deletion of exons 2-65 in the COL5A1 gene, inherited from an unaffected mosaic father. The level of mosaicism in the father was approximately 43% in leucocyte cells and 30% in DNA extracted from skin. Our results expand the allelic spectrum of cEDS variants and suggest that parental mosaicism needs to be considered in patients with suspected cEDS, given its implication for genetic counseling.
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Affiliation(s)
- Sonja Strang‐Karlsson
- Department of Clinical Genetics, HUS Diagnostic CenterUniversity of Helsinki and Helsinki University HospitalHelsinkiFinland
| | - Sylvia Keigwin
- Sheffield Diagnostic Genetics ServiceSheffield Children's NHS Foundation TrustSheffieldUK
| | - Anna‐Kaisa Anttonen
- Department of Clinical Genetics, HUS Diagnostic CenterUniversity of Helsinki and Helsinki University HospitalHelsinkiFinland
| | - Duncan Baker
- Sheffield Diagnostic Genetics ServiceSheffield Children's NHS Foundation TrustSheffieldUK
| | - Kerry Bean
- Sheffield Diagnostic Genetics ServiceSheffield Children's NHS Foundation TrustSheffieldUK
| | - Eveliina Jakkula
- Department of Clinical Genetics, HUS Diagnostic CenterUniversity of Helsinki and Helsinki University HospitalHelsinkiFinland,Department of Medical and Clinical GeneticsUniversity of HelsinkiHelsinkiFinland
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Fragile X Syndrome Caused by Maternal Somatic Mosaicism of FMR1 Gene: Case Report and Literature Review. Genes (Basel) 2022; 13:genes13091609. [PMID: 36140775 PMCID: PMC9498456 DOI: 10.3390/genes13091609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 11/28/2022] Open
Abstract
Fragile X syndrome (FXS) is caused by an abnormal expansion of the number of trinucleotide CGG repeats located in the 5′ UTR in the first exon of the FMR1 gene. Size and methylation mosaicisms are commonly observed in FXS patients. Both types of mosaicisms might be associated with less severe phenotypes depending on the number of cells expressing FMRP. Although this dynamic mutation is the main underlying cause of FXS, other mechanisms, including point mutations or deletions, can lead to FXS. Several reports have demonstrated that de novo deletions including the entire or a portion of the FMR1 gene end up with the absence of FMRP and, thus, can lead to the typical clinical features of FXS. However, very little is known about the clinical manifestations associated with FMR1 gene deletions in mosaicism. Here, we report an FXS case caused by an entire hemizygous deletion of the FMR1 gene caused by maternal mosaicism. This manuscript reports this case and a literature review of the clinical manifestations presented by carriers of FMR1 gene deletions in mosaicism.
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Frisk S, Wachtmeister A, Laurell T, Lindstrand A, Jäntti N, Malmgren H, Lagerstedt-Robinson K, Tesi B, Taylan F, Nordgren A. Detection of germline mosaicism in fathers of children with intellectual disability syndromes caused by de novo variants. Mol Genet Genomic Med 2022; 10:e1880. [PMID: 35118825 PMCID: PMC9000944 DOI: 10.1002/mgg3.1880] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/21/2021] [Accepted: 01/14/2022] [Indexed: 12/03/2022] Open
Abstract
Background De novo variants are a common cause to rare intellectual disability syndromes, associated with low recurrence risk. However, when such variants occur pre‐zygotically in parental germ cells, the recurrence risk might be higher. Still, the recurrence risk estimates are mainly based on empirical data and the prevalence of germline mosaicism is often unknown. Methods To establish the prevalence of mosaicism in parents of children with intellectual disability syndromes caused by de novo variants, we performed droplet digital PCR on DNA extracted from blood (43 trios), and sperm (31 fathers). Results We detected low‐level mosaicism in sperm‐derived DNA but not in blood in the father of a child with Kleefstra syndrome caused by an EHMT1 variant. Additionally, we found a higher level of paternal mosaicism in sperm compared to blood in the father of a child with Gillespie syndrome caused by an ITPR1 variant. Conclusion By employing droplet digital PCR, we detected paternal germline mosaicism in two intellectual disability syndromes. In both cases, the mosaicism level was higher in sperm than blood, indicating that analysis of blood alone may underestimate germline mosaicism. Therefore, sperm analysis can be clinically useful to establish the recurrence risk for parents and improve genetic counselling.
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Affiliation(s)
- Sofia Frisk
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Alexandra Wachtmeister
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Tobias Laurell
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Hand Surgery, Södersjukhuset, Stockholm, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Nina Jäntti
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Helena Malmgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Kristina Lagerstedt-Robinson
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Bianca Tesi
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Fulya Taylan
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
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7
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Oliveira Netto AB, Brusius-Facchin AC, Leistner-Segal S, Kubaski F, Josahkian J, Giugliani R. Detection of Mosaic Variants in Mothers of MPS II Patients by Next Generation Sequencing. Front Mol Biosci 2021; 8:789350. [PMID: 34805285 PMCID: PMC8602069 DOI: 10.3389/fmolb.2021.789350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 10/22/2021] [Indexed: 11/13/2022] Open
Abstract
Mucopolysaccharidosis type II is an X-linked lysosomal storage disorder caused by mutations in the IDS gene that encodes the iduronate-2-sulfatase enzyme. The IDS gene is located on the long arm of the X-chromosome, comprising 9 exons, spanning approximately 24 kb. The analysis of carriers, in addition to detecting mutations in patients, is essential for genetic counseling, since the risk of recurrence for male children is 50%. Mosaicism is a well-known phenomenon described in many genetic disorders caused by a variety of mechanisms that occur when a mutation arises in the early development of an embryo. Sanger sequencing is limited in detecting somatic mosaicism and sequence change levels of less than 20% may be missed. The Next Generation Sequencing (NGS) has been increasingly used in diagnosis. It is a sensitive and fast method for the detection of somatic mosaicism. Compared to Sanger sequencing, which represents a cumulative signal, NGS technology analyzes the sequence of each DNA read in a sample. NGS might therefore facilitate the detection of mosaicism in mothers of MPS II patients. The aim of this study was to reanalyze, by NGS, all MPS II mothers that showed to be non-carriers by Sanger analysis. Twelve non-carriers were selected for the reanalysis on the Ion PGM and Ion Torrent S5 platform, using a custom panel that includes the IDS gene. Results were visualized in the Integrative Genomics Viewer (IGV). We were able to detected the presence of the variant previously found in the index case in three of the mothers, with frequencies ranging between 13 and 49% of the reads. These results suggest the possibility of mosaicism in the mothers. The use of a more sensitive technology for detecting low-level mosaic mutations is essential for accurate recurrence-risk estimates. In our study, the NGS analysis showed to be an effective methodology to detect the mosaic event.
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Affiliation(s)
- Alice Brinckmann Oliveira Netto
- Laboratory of Molecular Genetics, Medical Genetics Service, HCPA, Porto Alegre, Brazil.,Postgraduate Program in Genetics and Molecular Biology, UFRGS, Porto Alegre, Brazil
| | - Ana Carolina Brusius-Facchin
- Laboratory of Molecular Genetics, Medical Genetics Service, HCPA, Porto Alegre, Brazil.,National Institute on Population Medical Genetics, INAGEMP, Porto Alegre, Brazil.,BioDiscovery Laboratory, Experimental Research Center, HCPA, Porto Alegre, Brazil
| | - Sandra Leistner-Segal
- Laboratory of Molecular Genetics, Medical Genetics Service, HCPA, Porto Alegre, Brazil
| | - Francyne Kubaski
- Laboratory of Molecular Genetics, Medical Genetics Service, HCPA, Porto Alegre, Brazil.,Postgraduate Program in Genetics and Molecular Biology, UFRGS, Porto Alegre, Brazil.,National Institute on Population Medical Genetics, INAGEMP, Porto Alegre, Brazil.,BioDiscovery Laboratory, Experimental Research Center, HCPA, Porto Alegre, Brazil
| | - Juliana Josahkian
- Postgraduate Program in Genetics and Molecular Biology, UFRGS, Porto Alegre, Brazil.,Department of Clinical Medicine, Hospital Universitario de Santa Maria (HUSM), Santa Maria, Brazil
| | - Roberto Giugliani
- Laboratory of Molecular Genetics, Medical Genetics Service, HCPA, Porto Alegre, Brazil.,National Institute on Population Medical Genetics, INAGEMP, Porto Alegre, Brazil.,BioDiscovery Laboratory, Experimental Research Center, HCPA, Porto Alegre, Brazil.,Department of Genetics, UFRGS, Porto Alegre, Brazil
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Competitiveness of Quantitative Polymerase Chain Reaction (qPCR) and Droplet Digital Polymerase Chain Reaction (ddPCR) Technologies, with a Particular Focus on Detection of Antibiotic Resistance Genes (ARGs). Appl Microbiol 2021. [DOI: 10.3390/applmicrobiol1030028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
With fast-growing polymerase chain reaction (PCR) technologies and various application methods, the technique has benefited science and medical fields. While having strengths and limitations on each technology, there are not many studies comparing the efficiency and specificity of PCR technologies. The objective of this review is to summarize a large amount of scattered information on PCR technologies focused on the two majorly used technologies: qPCR (quantitative polymerase chain reaction) and ddPCR (droplet-digital polymerase chain reaction). Here we analyze and compare the two methods for (1) efficiency, (2) range of detection and limitations under different disciplines and gene targets, (3) optimization, and (4) status on antibiotic resistance genes (ARGs) analysis. It has been identified that the range of detection and quantification limit varies depending on the PCR method and the type of sample. Careful optimization of target gene analysis is essential for building robust analysis for both qPCR and ddPCR. In our era where mutation of genes may lead to a pandemic of viral infectious disease or antibiotic resistance-induced health threats, this study hopes to set guidelines for meticulous detection, quantification, and analysis to help future prevention and protection of global health, the economy, and ecosystems.
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9
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Mary L, Loget P, Odent S, Aussel D, Le Bouar G, Launay E, Henry C, Belaud-Rotureau MA, Jaillard S. Multicolor-FISH Characterization of a Prenatal Mosaicism for a Chromosomal Rearrangement Undetected by Molecular Cytogenetics. Cytogenet Genome Res 2021; 161:143-152. [PMID: 33827072 DOI: 10.1159/000514592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/19/2021] [Indexed: 11/19/2022] Open
Abstract
Fetal mosaicism for chromosomal rearrangements remains a challenge to diagnose, even in the era of whole-genome sequencing. We present here a case of fetal mosaicism for a chromosomal rearrangement explored in amniocytes and fetal muscle, consisting of a major cell population (95%) with partial monosomy 4q and a minor population (5%) with additional material replacing the 4qter deleted segment. Molecular techniques (MLPA, array-CGH) failed to assess the origin of this material. Only multicolor-FISH identified the additional segment on chromosome 4 as derived from chromosome 17. Due to the poor prognosis, the couple chose to terminate the pregnancy. Because of low-level mosaicism, chromosomal microarray analysis (CMA), now considered as first-tier prenatal genetic analysis, did not allow the identification of the minor cell line. In case of large CNVs (>5 Mb) detected by CMA, karyotyping may be considered to elucidate the mechanism of the underlying rearrangement and eliminate mosaicism.
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Affiliation(s)
- Laura Mary
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France.,INSERM, EHESP, IRSET - UMR_S 1085, Université Rennes 1, Rennes, France
| | - Philippe Loget
- Service d'Anatomie et Cytologie Pathologiques, CHU Rennes, Rennes, France
| | - Sylvie Odent
- Service de Génétique Clinique, CHU Rennes, CLAD Ouest, Rennes, France
| | - Dominique Aussel
- Service de Gynécologie-Obstétrique, Clinique de La Sagesse, Rennes, France
| | - Gwenaelle Le Bouar
- Unité de Médecine fœtale, Service de Gynécologie-Obstétrique, CHU Rennes, Rennes, France
| | - Erika Launay
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France
| | - Catherine Henry
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France
| | - Marc-Antoine Belaud-Rotureau
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France.,INSERM, EHESP, IRSET - UMR_S 1085, Université Rennes 1, Rennes, France
| | - Sylvie Jaillard
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France.,INSERM, EHESP, IRSET - UMR_S 1085, Université Rennes 1, Rennes, France
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10
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Glessner JT, Chang X, Liu Y, Li J, Khan M, Wei Z, Sleiman PMA, Hakonarson H. MONTAGE: a new tool for high-throughput detection of mosaic copy number variation. BMC Genomics 2021; 22:133. [PMID: 33627065 PMCID: PMC7905641 DOI: 10.1186/s12864-021-07395-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 01/19/2021] [Indexed: 01/21/2023] Open
Abstract
Background Not all cells in a given individual are identical in their genomic makeup. Mosaicism describes such a phenomenon where a mixture of genotypic states in certain genomic segments exists within the same individual. Mosaicism is a prevalent and impactful class of non-integer state copy number variation (CNV). Mosaicism implies that certain cell types or subset of cells contain a CNV in a segment of the genome while other cells in the same individual do not. Several studies have investigated the impact of mosaicism in single patients or small cohorts but no comprehensive scan of mosaic CNVs has been undertaken to accurately detect such variants and interpret their impact on human health and disease. Results We developed a tool called Montage to improve the accuracy of detection of mosaic copy number variants in a high throughput fashion. Montage directly interfaces with ParseCNV2 algorithm to establish disease phenotype genome-wide association and determine which genomic ranges had more or less than expected frequency of mosaic events. We screened for mosaic events in over 350,000 samples using 1% allele frequency as the detection limit. Additionally, we uncovered disease associations of multiple phenotypes with mosaic CNVs at several genomic loci. We additionally investigated the allele imbalance observations genome-wide to define non-diploid and non-integer copy number states. Conclusions Our novel algorithm presents an efficient tool with fast computational runtime and high levels of accuracy of mosaic CNV detection. A curated mosaic CNV callset of 3716 events in 2269 samples is presented with comparability to previous reports and disease phenotype associations. The new algorithm can be freely accessed via: https://github.com/CAG-CNV/MONTAGE. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07395-7.
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Affiliation(s)
- Joseph T Glessner
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA. .,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA.
| | - Xiao Chang
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Yichuan Liu
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Jin Li
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Munir Khan
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Zhi Wei
- New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Patrick M A Sleiman
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Hakon Hakonarson
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA
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11
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Iourov IY, Vorsanova SG, Yurov YB. Systems Cytogenomics: Are We Ready Yet? Curr Genomics 2021; 22:75-78. [PMID: 34220294 PMCID: PMC8188578 DOI: 10.2174/1389202922666210219112419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/01/2020] [Accepted: 12/01/2020] [Indexed: 11/26/2022] Open
Abstract
With the introduction of systems theory to genetics, numerous opportunities for genomic research have been identified. Consequences of DNA sequence variations are systematically evaluated using the network- or pathway-based analysis, a technological basis of systems biology or, more precisely, systems genomics. Despite comprehensive descriptions of advantages offered by systems genomic approaches, pathway-based analysis is uncommon in cytogenetic (cytogenomic) studies, i.e. genome analysis at the chromosomal level. Here, we would like to express our opinion that current cytogenomics benefits from the application of systems biology methodology. Accordingly, systems cytogenomics appears to be a biomedical area requiring more attention than it actually receives.
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Affiliation(s)
- Ivan Y Iourov
- Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, 117152, Russia.,Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Moscow, 125412, Russia.,Department of Medical Biological Disciplines, Belgorod State University, 308015, Belgorod, Russia
| | - Svetlana G Vorsanova
- Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, 117152, Russia.,Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Moscow, 125412, Russia
| | - Yuri B Yurov
- Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, 117152, Russia.,Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Moscow, 125412, Russia
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12
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Innella G, Greco D, Carli D, Magini P, Giorgio E, Galesi O, Ferrero GB, Romano C, Brusco A, Graziano C. Clinical spectrum and follow-up in six individuals with Lamb-Shaffer syndrome (SOX5). Am J Med Genet A 2020; 185:608-613. [PMID: 33296143 DOI: 10.1002/ajmg.a.62001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/19/2020] [Accepted: 11/14/2020] [Indexed: 11/05/2022]
Affiliation(s)
- Giovanni Innella
- Medical Genetics Unit, Policlinico di S. Orsola, University of Bologna, Bologna, Italy
| | | | - Diana Carli
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Pamela Magini
- Medical Genetics Unit, Policlinico di S. Orsola, University of Bologna, Bologna, Italy
| | - Elisa Giorgio
- Department of Medical Sciences, University of Turin, Turin, Italy
| | | | | | | | - Alfredo Brusco
- Department of Medical Sciences, University of Turin, Turin, Italy.,Unit of Medical Genetics, "Città della Salute e della Scienza" University Hospital, Turin, Italy
| | - Claudio Graziano
- Medical Genetics Unit, Policlinico di S. Orsola, University of Bologna, Bologna, Italy
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13
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Liu X, Tao T, Zhao L, Li G, Yang L. Molecular diagnosis based on comprehensive genetic testing in 800 Chinese families with non-syndromic inherited retinal dystrophies. Clin Exp Ophthalmol 2020; 49:46-59. [PMID: 33090715 DOI: 10.1111/ceo.13875] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 09/23/2020] [Accepted: 10/05/2020] [Indexed: 12/16/2022]
Abstract
IMPORTANCE Inherited retinal dystrophies (IRDs) are a group of monogenic diseases, one of the leading causes of blindness. BACKGROUND Introducing a comprehensive genetic testing strategy by combining single gene Sanger sequencing, next-generation sequencing (NGS) including whole exome sequencing (WES), and a specific hereditary eye disease enrichment panel (HEDEP) sequencing, to identify the disease-causing variants of 800 Chinese probands affected with non-syndromic IRDs. DESIGN Retrospective analysis. PARTICIPANTS Eight hundred Chinese non-syndromic IRDs probands and their families. METHODS A total of 149 patients were subjected to Sanger sequencing. Of the 651 patients subjected to NGS, 86 patients underwent WES and 565 underwent HEDEP. Patients that likely carried copy number variations (CNVs) detected by HEDEP were further validated by multiplex ligation-dependent probe amplification (MLPA) or quantitative fluorescence PCR (QF-PCR). MAIN OUTCOME MEASURES The diagnostic rate. RESULTS (Likely) pathogenic variants were determined in 481 cases (60.13% detection rate). The detection rates of single gene Sanger sequencing, WES and HEDEP were 86.58%, 31.40% and 56.99%, respectively. Approximately 11.64% of 481 cases carried autosomal dominant variants, 72.97% carried AR variants and 15.39% were found to be X-linked. CNVs were confirmed by MLPA or QF-PCR in 17 families. Fourteen genes that each caused disease in 1% or more of the cohort were detected, and these genes were collectively responsible for disease in almost one half (46.38%) of the families. CONCLUSIONS AND RELEVANCE Sanger sequencing is ideal to detect pathogenic variants of clinical homogeneous diseases, whereas NGS is more appropriate for patients without an explicit clinical diagnosis.
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Affiliation(s)
- Xiaozhen Liu
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China.,Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
| | - Tianchang Tao
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Lin Zhao
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China.,Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
| | - Genlin Li
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Liping Yang
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China.,Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
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14
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Lupski JR, Liu P, Stankiewicz P, Carvalho CMB, Posey JE. Clinical genomics and contextualizing genome variation in the diagnostic laboratory. Expert Rev Mol Diagn 2020; 20:995-1002. [PMID: 32954863 DOI: 10.1080/14737159.2020.1826312] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
INTRODUCTION The human genome contains the instructions for the development and biological homeostasis of the human organism and the genetic transmission of traits. Genome variation in human populations is the basis of evolution; individual or personal genomes vary tremendously, making each of us truly unique. AREAS COVERED Assaying this individual variation using genomic technologies has many applications in clinical medicine, from elucidating the biology of disease to designing strategies to ameliorate perturbations from homeostasis. Detecting pathogenic rare variation in a genome may provide a molecular diagnosis that can be informative for patient management and family healthcare. EXPERT OPINION Despite the increasing clinical use of unbiased genomic testing, including chromosome microarray analysis (CMA) with array comparative genomic hybridization (aCGH) or SNP arrays, clinical exome sequencing (cES), and whole-genome sequencing (WGS), to survey genome-wide for molecular aberrations, clinical acumen paired with an understanding of the limitations of each testing type will be needed to achieve molecular diagnoses. Potential opportunities for improving case solved rates, functionally annotating the majority of genes in the human genome, and further understanding genetic contributions to disease will empower clinical genomics and the precision medicine initiative.
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Affiliation(s)
- James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine , Houston, TX, USA.,Department of Pediatrics, Baylor College of Medicine , Houston, TX, USA.,Human Genome Sequencing Center, Baylor College of Medicine , Houston, TX, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine , Houston, TX, USA.,Baylor Genetics, Baylor College of Medicine , Houston, TX, USA
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine , Houston, TX, USA
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine , Houston, TX, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine , Houston, TX, USA
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15
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Gambin T, Liu Q, Karolak JA, Grochowski CM, Xie NG, Wu LR, Yan YH, Cao Y, Coban Akdemir ZH, Wilson TA, Jhangiani SN, Chen E, Eng CM, Muzny D, Posey JE, Yang Y, Zhang DY, Shaw C, Liu P, Lupski JR, Stankiewicz P. Low-level parental somatic mosaic SNVs in exomes from a large cohort of trios with diverse suspected Mendelian conditions. Genet Med 2020; 22:1768-1776. [PMID: 32655138 PMCID: PMC7606563 DOI: 10.1038/s41436-020-0897-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 06/25/2020] [Accepted: 06/25/2020] [Indexed: 02/06/2023] Open
Abstract
Purpose: The goal of this study was to assess the scale of low-level parental mosaicism in exome sequencing (ES) databases. Methods: We analyzed approximately 2000 family trio ES datasets from the Baylor-Hopkins Center for Mendelian Genomics (BHCMG) and Baylor Genetics (BG). Among apparent de novo single nucleotide variants (SNVs) identified in the affected probands, we selected rare unique variants with variant allele fraction (VAF) between 30-70% in the probands and lower than 10% in one of the parents. Results: Out of 102 candidate mosaic variants validated using amplicon-based NGS, droplet digital PCR, or blocker displacement amplification, 27 (26.4%) were confirmed to be low- (VAF between 1-10%) or very low- (VAF <1%) level mosaic. Detection precision in parental samples with two or more alternate reads was 63.6% (BHCMG) and 43.6% (BG). In nine investigated individuals, we observed variability of mosaic ratios among blood, saliva, fibroblast, buccal, hair, and urine samples. Conclusion: Our computational pipeline enables robust discrimination between true and false positive candidate mosaic variants and efficient detection of low-level mosaicism in ES samples. We confirm that the presence of two or more alternate reads in the parental sample is a reliable predictor of low-level parental somatic mosaicism.
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Affiliation(s)
- Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland.,Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Qian Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Justyna A Karolak
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | | | - Nina G Xie
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Lucia R Wu
- Department of Bioengineering, Rice University, Houston, TX, USA
| | | | - Ye Cao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA.,Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zeynep H Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Theresa A Wilson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Ed Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - David Y Zhang
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Chad Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA.,Department of Statistics, Rice University, Houston, TX, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics, Houston, TX, USA.,Texas Children's Hospital, Houston, TX, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. .,Baylor Genetics, Houston, TX, USA.
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