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Ogiwara Y, Kobori Y, Suzuki E, Hattori A, Tanase-Nakao K, Osaka A, Iwahata T, Okada H, Kuroki Y, Fukami M. Isodicentric Y Chromosome with Multiple Breakpoints in the Pseudoautosomal Region 1. Cytogenet Genome Res 2024:1-6. [PMID: 39074465 DOI: 10.1159/000540634] [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: 02/29/2024] [Accepted: 07/26/2024] [Indexed: 07/31/2024] Open
Abstract
INTRODUCTION Isodicentric Y chromosomes are relatively common structural variants of the human genome. The underlying mechanism of isodicentric Y chromosomes with short arm breakpoints [idic(Yq)] remains to be clarified. CASE PRESENTATION We encountered a Japanese man with azoospermia and mild short stature. G-banding and array-based comparative genomic hybridization indicated that his karyotype was 45,X/46,X,idic(Y)(qter→p11.32::p11.32→qter) with a ∼1.8 Mb terminal deletion. Whole-genome sequencing suggested that the Y chromosome had four breakpoints in a ∼7 kb region of the pseudoautosomal region 1 (PAR1). CONCLUSION This case was assumed to have an idic(Yq) resulting from multiple DNA double-strand breaks in PAR1. This rearrangement may have been facilitated by the PAR1-specific chromatin architecture. The clinical features of the patient can be ascribed to SHOX haploinsufficiency and the presence of a 45,X cell line, although copy-number gains of some Yq genes and the size reduction of PAR1 may also contribute to his spermatogenic failure.
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Affiliation(s)
- Yasuko Ogiwara
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of Advanced Pediatric Medicine, Tohoku University School of Medicine, Tokyo, Japan
| | - Yoshitomo Kobori
- International Center for Reproductive Medicine, Dokkyo Medical University Saitama Medical Center, Koshigaya, Japan
| | - Erina Suzuki
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Atsushi Hattori
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
- Division of Diversity Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kanako Tanase-Nakao
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Akiyoshi Osaka
- International Center for Reproductive Medicine, Dokkyo Medical University Saitama Medical Center, Koshigaya, Japan
| | - Toshiyuki Iwahata
- International Center for Reproductive Medicine, Dokkyo Medical University Saitama Medical Center, Koshigaya, Japan
| | - Hiroshi Okada
- International Center for Reproductive Medicine, Dokkyo Medical University Saitama Medical Center, Koshigaya, Japan
| | - Yoko Kuroki
- Division of Diversity Research, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of Genome Medicine, National Research Institute for Child Health and Development, Tokyo, Japan
- Division of Collaborative Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
- Division of Diversity Research, National Research Institute for Child Health and Development, Tokyo, Japan
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2
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Zemet R, Du H, Gambin T, Lupski JR, Liu P, Stankiewicz P. SNV/indel hypermutator phenotype in biallelic RAD51C variant: Fanconi anemia. Hum Genet 2023; 142:721-733. [PMID: 37031326 PMCID: PMC10996436 DOI: 10.1007/s00439-023-02550-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 03/24/2023] [Indexed: 04/10/2023]
Abstract
We previously reported a fetus with Fanconi anemia (FA), complementation group O due to compound heterozygous variants involving RAD51C. Interestingly, the trio exome sequencing analysis also detected eight apparent de novo mosaic variants with variant allele fraction (VAF) ranging between 11.5 and 37%. Here, using whole genome sequencing and a 'home-brew' variant filtering pipeline and DeepMosaic module, we investigated the number and signature of de novo heterozygous and mosaic variants and the hypothesis of a rare phenomenon of hypermutation. Eight-hundred-thirty apparent de novo SNVs and 21 de novo indels had VAFs below 37.41% and were considered postzygotic somatic mosaic variants. The VAFs showed a bimodal distribution, with one component having an average VAF of 25% (range: 18.7-37.41%) (n = 446), representing potential postzygotic first mitotic events, and the other component with an average VAF of 12.5% (range 9.55-18.69%) (n = 384), describing potential second mitotic events. No increased rate of CNV formation was observed. The mutational pattern analysis for somatic single base substitution showed SBS40, SBS5, and SBS3 as the top recognized signatures. SBS3 is a known signature associated with homologous recombination-based DNA damage repair error. Our data demonstrate that biallelic RAD51C variants show evidence for defective genomic DNA damage repair and thereby result in a hypermutator phenotype with the accumulation of postzygotic de novo mutations, at least in the prenatal period. This 'genome hypermutator phenomenon' might contribute to the observed hematological manifestations and the predisposition to tumors in patients with FA. We propose that other FA groups should be investigated for genome-wide de novo variants.
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Affiliation(s)
- Roni Zemet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Tomasz Gambin
- Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Baylor Genetics, Houston, TX, USA.
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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3
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Zemet R, Du H, Gambin T, Lupski JR, Liu P, Stankiewicz P. SNV/indel hypermutator phenotype in biallelic RAD51C variant - Fanconi anemia. RESEARCH SQUARE 2023:rs.3.rs-2628288. [PMID: 36909564 PMCID: PMC10002829 DOI: 10.21203/rs.3.rs-2628288/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
We previously reported a fetus with Fanconi anemia (FA), complementation group O due to compound heterozygous variants involving RAD51C . Interestingly, the trio exome sequencing analysis also detected eight apparent de novo mosaic variants with variant allele fraction (VAF) ranging between 11.5%-37%. Here, using whole genome sequencing and a 'home-brew' variant filtering pipeline and DeepMosaic module, we investigated the number and signature of de novo heterozygous and mosaic variants and the rare phenomenon of hypermutation. Eight-hundred-thirty apparent dnSNVs and 21 de novo indels had VAFs below 37.41% and were considered postzygotic somatic mosaic variants. The VAFs showed a bimodal distribution, with one component with an average VAF of 25% (range: 18.7-37.41%) (n=446), representing potential postzygotic first mitotic events, and the other component with an average VAF of 12.5% (range: 9.55-18.69%) (n=384), describing potential second mitotic events. No increased rate of CNV formation was observed. The mutational pattern analysis for somatic single base substitution showed SBS40, SBS5, and SBS3 as the top recognized signatures. SBS3 is a known signature associated with homologous recombination-based DNA damage repair error. Our data demonstrate that biallelic RAD51C variants show evidence for defective genomic DNA damage repair and thereby result in a hypermutator phenotype with the accumulation of postzygotic de novo mutations, at least in the prenatal period. This 'genome hypermutator phenomenon' might contribute to the observed hematological manifestations and the predisposition to tumors in patients with FA, and pregnancy loss in general. We propose that other FA groups should be investigated for genome-wide de novo variants.
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Affiliation(s)
- Roni Zemet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Tomasz Gambin
- Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Baylor Genetics, Houston, TX
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
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4
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Balachandran P, Walawalkar IA, Flores JI, Dayton JN, Audano PA, Beck CR. Transposable element-mediated rearrangements are prevalent in human genomes. Nat Commun 2022; 13:7115. [PMID: 36402840 PMCID: PMC9675761 DOI: 10.1038/s41467-022-34810-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 11/08/2022] [Indexed: 11/21/2022] Open
Abstract
Transposable elements constitute about half of human genomes, and their role in generating human variation through retrotransposition is broadly studied and appreciated. Structural variants mediated by transposons, which we call transposable element-mediated rearrangements (TEMRs), are less well studied, and the mechanisms leading to their formation as well as their broader impact on human diversity are poorly understood. Here, we identify 493 unique TEMRs across the genomes of three individuals. While homology directed repair is the dominant driver of TEMRs, our sequence-resolved TEMR resource allows us to identify complex inversion breakpoints, triplications or other high copy number polymorphisms, and additional complexities. TEMRs are enriched in genic loci and can create potentially important risk alleles such as a deletion in TRIM65, a known cancer biomarker and therapeutic target. These findings expand our understanding of this important class of structural variation, the mechanisms responsible for their formation, and establish them as an important driver of human diversity.
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Affiliation(s)
| | | | - Jacob I Flores
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Jacob N Dayton
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Peter A Audano
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Christine R Beck
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA.
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA.
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5
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Du H, Jolly A, Grochowski CM, Yuan B, Dawood M, Jhangiani SN, Li H, Muzny D, Fatih JM, Coban-Akdemir Z, Carlin ME, Scheuerle AE, Witzl K, Posey JE, Pendleton M, Harrington E, Juul S, Hastings PJ, Bi W, Gibbs RA, Sedlazeck FJ, Lupski JR, Carvalho CMB, Liu P. The multiple de novo copy number variant (MdnCNV) phenomenon presents with peri-zygotic DNA mutational signatures and multilocus pathogenic variation. Genome Med 2022; 14:122. [PMID: 36303224 PMCID: PMC9609164 DOI: 10.1186/s13073-022-01123-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 10/10/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The multiple de novo copy number variant (MdnCNV) phenotype is described by having four or more constitutional de novo CNVs (dnCNVs) arising independently throughout the human genome within one generation. It is a rare peri-zygotic mutational event, previously reported to be seen once in every 12,000 individuals referred for genome-wide chromosomal microarray analysis due to congenital abnormalities. These rare families provide a unique opportunity to understand the genetic factors of peri-zygotic genome instability and the impact of dnCNV on human diseases. METHODS Chromosomal microarray analysis (CMA), array-based comparative genomic hybridization, short- and long-read genome sequencing (GS) were performed on the newly identified MdnCNV family to identify de novo mutations including dnCNVs, de novo single-nucleotide variants (dnSNVs), and indels. Short-read GS was performed on four previously published MdnCNV families for dnSNV analysis. Trio-based rare variant analysis was performed on the newly identified individual and four previously published MdnCNV families to identify potential genetic etiologies contributing to the peri-zygotic genomic instability. Lin semantic similarity scores informed quantitative human phenotype ontology analysis on three MdnCNV families to identify gene(s) driving or contributing to the clinical phenotype. RESULTS In the newly identified MdnCNV case, we revealed eight de novo tandem duplications, each ~ 1 Mb, with microhomology at 6/8 breakpoint junctions. Enrichment of de novo single-nucleotide variants (SNV; 6/79) and de novo indels (1/12) was found within 4 Mb of the dnCNV genomic regions. An elevated post-zygotic SNV mutation rate was observed in MdnCNV families. Maternal rare variant analyses identified three genes in distinct families that may contribute to the MdnCNV phenomenon. Phenotype analysis suggests that gene(s) within dnCNV regions contribute to the observed proband phenotype in 3/3 cases. CNVs in two cases, a contiguous gene duplication encompassing PMP22 and RAI1 and another duplication affecting NSD1 and SMARCC2, contribute to the clinically observed phenotypic manifestations. CONCLUSIONS Characteristic features of dnCNVs reported here are consistent with a microhomology-mediated break-induced replication (MMBIR)-driven mechanism during the peri-zygotic period. Maternal genetic variants in DNA repair genes potentially contribute to peri-zygotic genomic instability. Variable phenotypic features were observed across a cohort of three MdnCNV probands, and computational quantitative phenotyping revealed that two out of three had evidence for the contribution of more than one genetic locus to the proband's phenotype supporting the hypothesis of de novo multilocus pathogenic variation (MPV) in those families.
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Affiliation(s)
- Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Christopher M Grochowski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Baylor Genetics Laboratory, Houston, TX, 77021, USA
- Seattle Children's Hospital, Seattle, WA, 98105, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Moez Dawood
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA
- Human Genome Sequencing Center, 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, One Baylor Plaza, Houston, TX, 77030, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, 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
| | - Mary Esther Carlin
- Division of Genetics and Metabolism, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Angela E Scheuerle
- Division of Genetics and Metabolism, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Division of Genetics Diagnostics, Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Karin Witzl
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, 1000, Ljubljana, Slovenia
- Medical Faculty, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | | | | | - Sissel Juul
- Oxford Nanopore Technologies Inc, New York, NY, 10013, USA
| | - P J Hastings
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, BCM, Houston, TX, 77030, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Baylor Genetics Laboratory, Houston, TX, 77021, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Fritz J Sedlazeck
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Texas Children's Hospital, Houston, TX, 77030, USA.
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
- Pacific Northwest Research Institute, 720 Broadway, Seattle, WA, 98122, USA.
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
- Baylor Genetics Laboratory, Houston, TX, 77021, USA.
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6
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Bae T, Fasching L, Wang Y, Shin JH, Suvakov M, Jang Y, Norton S, Dias C, Mariani J, Jourdon A, Wu F, Panda A, Pattni R, Chahine Y, Yeh R, Roberts RC, Huttner A, Kleinman JE, Hyde TM, Straub RE, Walsh CA, Urban AE, Leckman JF, Weinberger DR, Vaccarino FM, Abyzov A. Analysis of somatic mutations in 131 human brains reveals aging-associated hypermutability. Science 2022; 377:511-517. [PMID: 35901164 PMCID: PMC9420557 DOI: 10.1126/science.abm6222] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We analyzed 131 human brains (44 neurotypical, 19 with Tourette syndrome, 9 with schizophrenia, and 59 with autism) for somatic mutations after whole genome sequencing to a depth of more than 200×. Typically, brains had 20 to 60 detectable single-nucleotide mutations, but ~6% of brains harbored hundreds of somatic mutations. Hypermutability was associated with age and damaging mutations in genes implicated in cancers and, in some brains, reflected in vivo clonal expansions. Somatic duplications, likely arising during development, were found in ~5% of normal and diseased brains, reflecting background mutagenesis. Brains with autism were associated with mutations creating putative transcription factor binding motifs in enhancer-like regions in the developing brain. The top-ranked affected motifs corresponded to MEIS (myeloid ectopic viral integration site) transcription factors, suggesting a potential link between their involvement in gene regulation and autism.
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Affiliation(s)
- Taejeong Bae
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905
| | - Liana Fasching
- Child Study Center, Yale University, New Haven, CT 06520
| | - Yifan Wang
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905
| | - Joo Heon Shin
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Milovan Suvakov
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905
| | - Yeongjun Jang
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905
| | - Scott Norton
- Child Study Center, Yale University, New Haven, CT 06520
| | - Caroline Dias
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, USA
- Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA
| | | | | | - Feinan Wu
- Child Study Center, Yale University, New Haven, CT 06520
| | - Arijit Panda
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905
| | - Reenal Pattni
- Department of Psychiatry and Behavioral Sciences, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | - Yasmine Chahine
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, USA
- Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA
| | - Rebecca Yeh
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, USA
- Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA
| | - Rosalinda C. Roberts
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham Al, 35294
| | - Anita Huttner
- Department of Pathology, Yale University, New Haven, CT 06520
| | - Joel E. Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD
| | - Thomas M. Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD
| | - Richard E. Straub
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD
| | - Christopher A. Walsh
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, USA
- Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA
| | | | - Alexander E. Urban
- Department of Psychiatry and Behavioral Sciences, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | | | - Daniel R. Weinberger
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD
| | - Flora M. Vaccarino
- Child Study Center, Yale University, New Haven, CT 06520
- Department of Neuroscience, Yale University, New Haven, CT 06520
| | - Alexej Abyzov
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905
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7
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Lupski JR. Biology in balance: human diploid genome integrity, gene dosage, and genomic medicine. Trends Genet 2022; 38:554-571. [PMID: 35450748 PMCID: PMC9222541 DOI: 10.1016/j.tig.2022.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 01/01/2023]
Abstract
The path to completion of the functional annotation of the haploid human genome reference build, exploration of the clan genomics hypothesis, understanding human gene and genome functional biology, and gene genome and organismal evolution, is in reach.
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Affiliation(s)
- James R Lupski
- Genetics & Genomics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX 77030, USA.
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8
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Liu P, Vossaert L. Emerging technologies for prenatal diagnosis: The application of whole genome and RNA sequencing. Prenat Diagn 2022; 42:686-696. [PMID: 35416301 PMCID: PMC10014115 DOI: 10.1002/pd.6146] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 11/10/2022]
Abstract
DNA sequencing technologies for clinical genetic testing have been rapidly evolving in recent years, and steadily become more important within the field of prenatal diagnostics. This review aims to give an overview of recent developments and to describe how they have the potential to fill the gaps of the currently clinically implemented methods for prenatal diagnosis of various genetic disorders. It has been shown for postnatal testing that whole genome sequencing provides a set of added benefits compared to exome sequencing, and it is to be expected that this will be the case for prenatal testing as well. RNA-sequencing, already used postnatally, can provide valuable complementary data to DNA-based testing, and aid in variant interpretation. While not ready for clinical implementation, emerging technologies such as long-read and Hi-C sequencing analyses might add to the toolbox for interpreting the expanding genetic data sets generated by genome-wide sequencing. Lastly, we also discuss some more practical implications of introducing these emerging technologies, which generate larger and larger genomic data sets, in the prenatal field.
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Affiliation(s)
- Pengfei Liu
- Baylor College of Medicine and Baylor Genetics, Houston, Texas, USA
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9
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Kaplanis J, Ide B, Sanghvi R, Neville M, Danecek P, Coorens T, Prigmore E, Short P, Gallone G, McRae J, Carmichael J, Barnicoat A, Firth H, O'Brien P, Rahbari R, Hurles M. Genetic and chemotherapeutic influences on germline hypermutation. Nature 2022; 605:503-508. [PMID: 35545669 PMCID: PMC9117138 DOI: 10.1038/s41586-022-04712-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 03/31/2022] [Indexed: 01/06/2023]
Abstract
Mutations in the germline generates all evolutionary genetic variation and is a cause of genetic disease. Parental age is the primary determinant of the number of new germline mutations in an individual's genome1,2. Here we analysed the genome-wide sequences of 21,879 families with rare genetic diseases and identified 12 individuals with a hypermutated genome with between two and seven times more de novo single-nucleotide variants than expected. In most families (9 out of 12), the excess mutations came from the father. Two families had genetic drivers of germline hypermutation, with fathers carrying damaging genetic variation in DNA-repair genes. For five of the families, paternal exposure to chemotherapeutic agents before conception was probably a key driver of hypermutation. Our results suggest that the germline is well protected from mutagenic effects, hypermutation is rare, the number of excess mutations is relatively modest and most individuals with a hypermutated genome will not have a genetic disease.
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Affiliation(s)
- Joanna Kaplanis
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Benjamin Ide
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Rashesh Sanghvi
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Matthew Neville
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Petr Danecek
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Tim Coorens
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Elena Prigmore
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Patrick Short
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Jeremy McRae
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Jenny Carmichael
- East Anglian Medical Genetics Service, Cambridge University Hospitals, Cambridge, UK
| | - Angela Barnicoat
- North East Thames Regional Genetics Service, Great Ormond Street Hospital, London, UK
| | - Helen Firth
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- East Anglian Medical Genetics Service, Cambridge University Hospitals, Cambridge, UK
| | - Patrick O'Brien
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Raheleh Rahbari
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Matthew Hurles
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
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10
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Zhang CZ, Pellman D. Cancer Genomic Rearrangements and Copy Number Alterations from Errors in Cell Division. ANNUAL REVIEW OF CANCER BIOLOGY 2022. [DOI: 10.1146/annurev-cancerbio-070620-094029] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Analysis of cancer genomes has shown that a large fraction of chromosomal changes originate from catastrophic events including whole-genome duplication, chromothripsis, breakage-fusion-bridge cycles, and chromoplexy. Through sophisticated computational analysis of cancer genomes and experimental recapitulation of these catastrophic alterations, we have gained significant insights into the origin, mechanism, and evolutionary dynamics of cancer genome complexity. In this review, we summarize this progress and survey the major unresolved questions, with particular emphasis on the relative contributions of chromosome fragmentation and DNA replication errors to complex chromosomal alterations.
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Affiliation(s)
- Cheng-Zhong Zhang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Biomedical Informatics, Blavatnik Institute of Harvard Medical School, Boston, Massachusetts, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - David Pellman
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Cell Biology, Blavatnik Institute of Harvard Medical School, Boston, Massachusetts, USA
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11
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Lupski JR. Clan genomics: From OMIM phenotypic traits to genes and biology. Am J Med Genet A 2021; 185:3294-3313. [PMID: 34405553 PMCID: PMC8530976 DOI: 10.1002/ajmg.a.62434] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/29/2021] [Accepted: 07/04/2021] [Indexed: 12/20/2022]
Abstract
Clinical characterization of a patient phenotype has been the quintessential approach for elucidating a differential diagnosis and a hypothesis to explore a potential clinical diagnosis. This has resulted in a language of medicine and a semantic ontology, with both specialty- and subspecialty-specific lexicons, that can be challenging to translate and interpret. There is no 'Rosetta Stone' of clinical medicine such as the genetic code that can assist translation and interpretation of the language of genetics. Nevertheless, the information content embodied within a clinical diagnosis can guide management, therapeutic intervention, and potentially prognostic outlook of disease enabling anticipatory guidance for patients and families. Clinical genomics is now established firmly in medical practice. The granularity and informative content of a personal genome is immense. Yet, we are limited in our utility of much of that personal genome information by the lack of functional characterization of the overwhelming majority of computationally annotated genes in the haploid human reference genome sequence. Whereas DNA and the genetic code have provided a 'Rosetta Stone' to translate genetic variant information, clinical medicine, and clinical genomics provide the context to understand human biology and disease. A path forward will integrate deep phenotyping, such as available in a clinical synopsis in the Online Mendelian Inheritance in Man (OMIM) entries, with personal genome analyses.
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Affiliation(s)
- James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
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12
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Osia B, Alsulaiman T, Jackson T, Kramara J, Oliveira S, Malkova A. Cancer cells are highly susceptible to accumulation of templated insertions linked to MMBIR. Nucleic Acids Res 2021; 49:8714-8731. [PMID: 34379776 PMCID: PMC8421209 DOI: 10.1093/nar/gkab685] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 07/25/2021] [Accepted: 07/29/2021] [Indexed: 01/23/2023] Open
Abstract
Microhomology-mediated break-induced replication (MMBIR) is a DNA repair pathway initiated by polymerase template switching at microhomology, which can produce templated insertions that initiate chromosomal rearrangements leading to neurological and metabolic diseases, and promote complex genomic rearrangements (CGRs) found in cancer. Yet, how often templated insertions accumulate from processes like MMBIR in genomes is poorly understood due to difficulty in directly identifying these events by whole genome sequencing (WGS). Here, by using our newly developed MMBSearch software, we directly detect such templated insertions (MMB-TIs) in human genomes and report substantial differences in frequency and complexity of MMB-TI events between normal and cancer cells. Through analysis of 71 cancer genomes from The Cancer Genome Atlas (TCGA), we observed that MMB-TIs readily accumulate de novo across several cancer types, with particularly high accumulation in some breast and lung cancers. By contrast, MMB-TIs appear only as germline variants in normal human fibroblast cells, and do not accumulate as de novo somatic mutations. Finally, we performed WGS on a lung adenocarcinoma patient case and confirmed MMB-TI-initiated chromosome fusions that disrupted potential tumor suppressors and induced chromothripsis-like CGRs. Based on our findings we propose that MMB-TIs represent a trigger for widespread genomic instability and tumor evolution.
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Affiliation(s)
- Beth Osia
- Department of Biology, University of Iowa, Iowa City, IA 52245, USA
| | - Thamer Alsulaiman
- Department of Computer Science, University of Iowa, Iowa City, IA 52245, USA
| | - Tyler Jackson
- Department of Biology, University of Iowa, Iowa City, IA 52245, USA
| | - Juraj Kramara
- Department of Biology, University of Iowa, Iowa City, IA 52245, USA
| | - Suely Oliveira
- Department of Computer Science, University of Iowa, Iowa City, IA 52245, USA
| | - Anna Malkova
- Department of Biology, University of Iowa, Iowa City, IA 52245, USA
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13
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Munisha M, Schimenti JC. Genome maintenance during embryogenesis. DNA Repair (Amst) 2021; 106:103195. [PMID: 34358805 DOI: 10.1016/j.dnarep.2021.103195] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 12/25/2022]
Abstract
Genome maintenance during embryogenesis is critical, because defects during this period can be perpetuated and thus have a long-term impact on individual's health and longevity. Nevertheless, genome instability is normal during certain aspects of embryonic development, indicating that there is a balance between the exigencies of timely cell proliferation and mutation prevention. In particular, early embryos possess unique cellular and molecular features that underscore the challenge of having an appropriate balance. Here, we discuss genome instability during embryonic development, the mechanisms used in various cell compartments to manage genomic stress and address outstanding questions regarding the balance between genome maintenance mechanisms in key cell types that are important for adulthood and progeny.
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Affiliation(s)
- Mumingjiang Munisha
- Dept. of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY 14853, United States
| | - John C Schimenti
- Dept. of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY 14853, United States.
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14
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Ma JY, Feng X, Xie FY, Li S, Chen LN, Luo SM, Yin S, Ou XH. Double-strand breaks induce short-scale DNA replication and damage amplification in the fully grown mouse oocytes. Genetics 2021; 218:iyab054. [PMID: 33792683 PMCID: PMC8225347 DOI: 10.1093/genetics/iyab054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/26/2021] [Indexed: 12/20/2022] Open
Abstract
Break-induced replication (BIR) is essential for the repair of DNA double-strand breaks (DSBs) with single ends. DSBs-induced microhomology-mediated BIR (mmBIR) and template-switching can increase the risk of complex genome rearrangement. In addition, DSBs can also induce the multi-invasion-mediated DSB amplification. The mmBIR-induced genomic rearrangement has been identified in cancer cells and patients with rare diseases. However, when and how mmBIR is initiated have not been fully and deeply studied. Furthermore, it is not well understood about the conditions for initiation of multi-invasion-mediated DSB amplification. In the G2 phase oocyte of mouse, we identified a type of short-scale BIR (ssBIR) using the DNA replication indicator 5-ethynyl-2'-deoxyuridine (EdU). These ssBIRs could only be induced in the fully grown oocytes but not the growing oocytes. If the DSB oocytes were treated with Rad51 or Chek1/2 inhibitors, both EdU signals and DSB marker γH2A.X foci would decrease. In addition, the DNA polymerase inhibitor Aphidicolin could inhibit the ssBIR and another inhibitor ddATP could reduce the number of γH2A.X foci in the DSB oocytes. In conclusion, our results showed that DNA DSBs in the fully grown oocytes can initiate ssBIR and be amplified by Rad51 or DNA replication.
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Affiliation(s)
- Jun-Yu Ma
- Fertility Preservation Lab, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou 510317, China
| | - Xie Feng
- Fertility Preservation Lab, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou 510317, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
| | - Feng-Yun Xie
- Fertility Preservation Lab, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou 510317, China
| | - Sen Li
- Fertility Preservation Lab, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou 510317, China
| | - Lei-Ning Chen
- Fertility Preservation Lab, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou 510317, China
| | - Shi-Ming Luo
- Fertility Preservation Lab, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou 510317, China
| | - Shen Yin
- College of Life Sciences, Institute of Reproductive Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Xiang-Hong Ou
- Fertility Preservation Lab, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou 510317, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510320, China
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15
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Maury EA, Walsh CA. Somatic copy number variants in neuropsychiatric disorders. Curr Opin Genet Dev 2021; 68:9-17. [PMID: 33444936 PMCID: PMC8205940 DOI: 10.1016/j.gde.2020.12.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/19/2020] [Accepted: 12/22/2020] [Indexed: 01/11/2023]
Abstract
Copy number variants (CNVs) have been implicated in neuropsychiatric disorders, with rare-inherited and de novo CNVs (dnCNVs) having large effects on disease liability. Recent studies started exploring a class of dnCNVs that occur post-zygotically, and are therefore present in some but not all cells of the body. Analogous to conditional mutations in animal models, the presence of risk mutations in a fraction of cells has the potential to enlighten how damaging mutations affect cell-type/cell-circuit specific pathologies leading to neuropsychiatric manifestations. Although mosaic CNVs appear to contribute to a modest fraction of risk (0.3-0.5%), expanding our insights about them with more sensitive experimental and statistical methods, has the potential to help clarify mechanisms of neuropsychiatric disease.
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Affiliation(s)
- Eduardo A Maury
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA; Bioinformatics & Integrative Genomics Program and Harvard/MIT MD-PHD Program, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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16
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Shukla V, Høffding MK, Hoffmann ER. Genome diversity and instability in human germ cells and preimplantation embryos. Semin Cell Dev Biol 2021; 113:132-147. [PMID: 33500205 PMCID: PMC8097364 DOI: 10.1016/j.semcdb.2020.12.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 12/18/2020] [Indexed: 12/26/2022]
Abstract
Genome diversity is essential for evolution and is of fundamental importance to human health. Generating genome diversity requires phases of DNA damage and repair that can cause genome instability. Humans have a high incidence of de novo congenital disorders compared to other organisms. Recent access to eggs, sperm and preimplantation embryos is revealing unprecedented rates of genome instability that may result in infertility and de novo mutations that cause genomic imbalance in at least 70% of conceptions. The error type and incidence of de novo mutations differ during developmental stages and are influenced by differences in male and female meiosis. In females, DNA repair is a critical factor that determines fertility and reproductive lifespan. In males, aberrant meiotic recombination causes infertility, embryonic failure and pregnancy loss. Evidence suggest germ cells are remarkably diverse in the type of genome instability that they display and the DNA damage responses they deploy. Additionally, the initial embryonic cell cycles are characterized by a high degree of genome instability that cause congenital disorders and may limit the use of CRISPR-Cas9 for heritable genome editing.
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Affiliation(s)
- Vallari Shukla
- DNRF Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Miya Kudo Høffding
- DNRF Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Eva R Hoffmann
- DNRF Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.
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17
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Kockler ZW, Osia B, Lee R, Musmaker K, Malkova A. Repair of DNA Breaks by Break-Induced Replication. Annu Rev Biochem 2021; 90:165-191. [PMID: 33792375 DOI: 10.1146/annurev-biochem-081420-095551] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Double-strand DNA breaks (DSBs) are the most lethal type of DNA damage, making DSB repair critical for cell survival. However, some DSB repair pathways are mutagenic and promote genome rearrangements, leading to genome destabilization. One such pathway is break-induced replication (BIR), which repairs primarily one-ended DSBs, similar to those formed by collapsed replication forks or telomere erosion. BIR is initiated by the invasion of a broken DNA end into a homologous template, synthesizes new DNA within the context of a migrating bubble, and is associated with conservative inheritance of new genetic material. This mode of synthesis is responsible for a high level of genetic instability associated with BIR. Eukaryotic BIR was initially investigated in yeast, but now it is also actively studied in mammalian systems. Additionally, a significant breakthrough has been made regarding the role of microhomology-mediated BIR in the formation of complex genomic rearrangements that underly various human pathologies.
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Affiliation(s)
- Z W Kockler
- Department of Biology, University of Iowa, Iowa City, Iowa 52242, USA;
| | - B Osia
- Department of Biology, University of Iowa, Iowa City, Iowa 52242, USA;
| | - R Lee
- Department of Biology, University of Iowa, Iowa City, Iowa 52242, USA;
| | - K Musmaker
- Department of Biology, University of Iowa, Iowa City, Iowa 52242, USA;
| | - A Malkova
- Department of Biology, University of Iowa, Iowa City, Iowa 52242, USA;
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18
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Del Gobbo GF, Yuan V, Robinson WP. Confined placental mosaicism involving multiple de novo copy number variants associated with fetal growth restriction: A case report. Am J Med Genet A 2021; 185:1908-1912. [PMID: 33750025 PMCID: PMC8251599 DOI: 10.1002/ajmg.a.62183] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/01/2021] [Accepted: 03/06/2021] [Indexed: 12/28/2022]
Abstract
The presence of multiple large (>1 Mb) copy number variants (CNVs) in non‐malignant tissue is rare in human genetics. We present a liveborn male with a birth weight below the first percentile associated with placental mosaicism involving eight 2.4–3.9 Mb de novo duplications. We found that the duplications likely co‐localized to the same cells, were mosaic in the placenta, and impacted maternal and paternal chromosomes. In addition, 27.4 Mb and 240 genes were duplicated in affected cells, including candidate placental genes KISS1 and REN. We ruled out involvement of homologous recombination‐based mechanisms or an altered epigenome in generating the CNVs. This case highlights the diversity of genetic abnormalities in the human placenta and the gaps in our knowledge of how such errors arise.
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Affiliation(s)
- Giulia F Del Gobbo
- BC Children's Hospital Research Institute, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Victor Yuan
- BC Children's Hospital Research Institute, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Wendy P Robinson
- BC Children's Hospital Research Institute, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
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19
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Pellestor F, Gaillard JB, Schneider A, Puechberty J, Gatinois V. Chromoanagenesis, the mechanisms of a genomic chaos. Semin Cell Dev Biol 2021; 123:90-99. [PMID: 33608210 DOI: 10.1016/j.semcdb.2021.01.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 01/22/2021] [Indexed: 02/07/2023]
Abstract
Designated under the name of chromoanagenesis, the phenomena of chromothripsis, chromanasynthesis and chromoplexy constitute new types of complex rearrangements, including many genomic alterations localized on a few chromosomal regions, and whose discovery over the last decade has changed our perception about the formation of chromosomal abnormalities and their etiology. Although exhibiting specific features, these new catastrophic mechanisms generally occur within a single cell cycle and their emergence is closely linked to genomic instability. Various non-exclusive exogenous or cellular mechanisms capable of generating chromoanagenesis have been evoked. However, recent experimental data shed light on 2 major processes, which following a defect in the mitotic segregation of chromosomes, can generate a cascade of cellular events leading to chromoanagenesis. These mechanisms are the formation of micronuclei integrating isolated chromosomal material, and the occurrence of chromatin bridges around chromosomal material resulting from telomeric fusions. In both cases, the cellular and molecular mechanisms of fragmentation, repair and transmission of damaged chromosomal material are consistent with the features of chromoanagenesis-related complex chromosomal rearrangements. In this review, we introduce each type of chromoanagenesis, and describe the experimental models that have allowed to validate the existence of chromoanagenesis events and to better understand their cellular mechanisms of formation and transmission, as well as their impact on the stability and the plasticity of the genome.
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Affiliation(s)
- F Pellestor
- Unit of Chromosomal Genetics and Research Plateform Chromostem, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHU, 371 avenue du Doyen Gaston Giraud, Montpellier Cedex 5 34295, France; INSERM 1183 Unit "Genome and Stem Cell Plasticity in Development and Aging" Institute of Regenerative Medecine and Biotherapies, St Eloi Hospital, Montpellier, France.
| | - J B Gaillard
- Unit of Chromosomal Genetics and Research Plateform Chromostem, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHU, 371 avenue du Doyen Gaston Giraud, Montpellier Cedex 5 34295, France
| | - A Schneider
- Unit of Chromosomal Genetics and Research Plateform Chromostem, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHU, 371 avenue du Doyen Gaston Giraud, Montpellier Cedex 5 34295, France
| | - J Puechberty
- Unit of Chromosomal Genetics and Research Plateform Chromostem, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHU, 371 avenue du Doyen Gaston Giraud, Montpellier Cedex 5 34295, France
| | - V Gatinois
- Unit of Chromosomal Genetics and Research Plateform Chromostem, Department of Medical Genetics, Arnaud de Villeneuve Hospital, Montpellier CHU, 371 avenue du Doyen Gaston Giraud, Montpellier Cedex 5 34295, France; INSERM 1183 Unit "Genome and Stem Cell Plasticity in Development and Aging" Institute of Regenerative Medecine and Biotherapies, St Eloi Hospital, Montpellier, France
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20
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Uchiyama Y, Yamaguchi D, Iwama K, Miyatake S, Hamanaka K, Tsuchida N, Aoi H, Azuma Y, Itai T, Saida K, Fukuda H, Sekiguchi F, Sakaguchi T, Lei M, Ohori S, Sakamoto M, Kato M, Koike T, Takahashi Y, Tanda K, Hyodo Y, Honjo RS, Bertola DR, Kim CA, Goto M, Okazaki T, Yamada H, Maegaki Y, Osaka H, Ngu LH, Siew CG, Teik KW, Akasaka M, Doi H, Tanaka F, Goto T, Guo L, Ikegawa S, Haginoya K, Haniffa M, Hiraishi N, Hiraki Y, Ikemoto S, Daida A, Hamano SI, Miura M, Ishiyama A, Kawano O, Kondo A, Matsumoto H, Okamoto N, Okanishi T, Oyoshi Y, Takeshita E, Suzuki T, Ogawa Y, Handa H, Miyazono Y, Koshimizu E, Fujita A, Takata A, Miyake N, Mizuguchi T, Matsumoto N. Efficient detection of copy-number variations using exome data: Batch- and sex-based analyses. Hum Mutat 2020; 42:50-65. [PMID: 33131168 DOI: 10.1002/humu.24129] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 09/29/2020] [Accepted: 10/15/2020] [Indexed: 12/16/2022]
Abstract
Many algorithms to detect copy number variations (CNVs) using exome sequencing (ES) data have been reported and evaluated on their sensitivity and specificity, reproducibility, and precision. However, operational optimization of such algorithms for a better performance has not been fully addressed. ES of 1199 samples including 763 patients with different disease profiles was performed. ES data were analyzed to detect CNVs by both the eXome Hidden Markov Model (XHMM) and modified Nord's method. To efficiently detect rare CNVs, we aimed to decrease sequencing biases by analyzing, at the same time, the data of all unrelated samples sequenced in the same flow cell as a batch, and to eliminate sex effects of X-linked CNVs by analyzing female and male sequences separately. We also applied several filtering steps for more efficient CNV selection. The average number of CNVs detected in one sample was <5. This optimization together with targeted CNV analysis by Nord's method identified pathogenic/likely pathogenic CNVs in 34 patients (4.5%, 34/763). In particular, among 142 patients with epilepsy, the current protocol detected clinically relevant CNVs in 19 (13.4%) patients, whereas the previous protocol identified them in only 14 (9.9%) patients. Thus, this batch-based XHMM analysis efficiently selected rare pathogenic CNVs in genetic diseases.
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Affiliation(s)
- Yuri Uchiyama
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan.,Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | | | - Kazuhiro Iwama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Pediatrics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Clinical Genetics Department, Yokohama City University Hospital, Yokohama, Japan
| | - Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Naomi Tsuchida
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan.,Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Hiromi Aoi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Obstetrics and Gynecology, Faculty of Medicine Juntendo University, Tokyo, Japan
| | - Yoshiteru Azuma
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Toshiyuki Itai
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Ken Saida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Hiromi Fukuda
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Futoshi Sekiguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Tomohiro Sakaguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Ming Lei
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Sachiko Ohori
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Masamune Sakamoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Pediatrics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Tokyo, Japan
| | - Takayoshi Koike
- National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, Shizuoka, Japan
| | - Yukitoshi Takahashi
- National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, Shizuoka, Japan
| | - Koichi Tanda
- Department of Pediatrics, Japanese Red Cross Kyoto Daiichi Hospital, Kyoto, Japan
| | - Yuki Hyodo
- Department of Child Neurology, Okayama University Hospital, Okayama, Japan
| | - Rachel S Honjo
- Unidade de Genetica do Instituto da Crianca do Hospital das Clinicas da Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Debora Romeo Bertola
- Unidade de Genetica do Instituto da Crianca do Hospital das Clinicas da Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Chong Ae Kim
- Unidade de Genetica do Instituto da Crianca do Hospital das Clinicas da Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Masahide Goto
- Department of Pediatrics, Jichi Medical University, Shimotsuke, Japan
| | - Tetsuya Okazaki
- Department of Brain and Neurosciences, Division of Child Neurology, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Hiroyuki Yamada
- Department of Brain and Neurosciences, Division of Child Neurology, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Yoshihiro Maegaki
- Department of Brain and Neurosciences, Division of Child Neurology, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Hitoshi Osaka
- Department of Pediatrics, Jichi Medical University, Shimotsuke, Japan
| | - Lock-Hock Ngu
- Department of Genetics, Kuala Lumpur Hospital, Kuala Lumpur, Malaysia
| | - Ch'ng G Siew
- Department of Genetics, Kuala Lumpur Hospital, Kuala Lumpur, Malaysia
| | - Keng W Teik
- Department of Genetics, Kuala Lumpur Hospital, Kuala Lumpur, Malaysia
| | - Manami Akasaka
- Department of Pediatrics, Iwate Medical University School of Medicine, Morioka, Japan
| | - Hiroshi Doi
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Fumiaki Tanaka
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Tomohide Goto
- Division of Neurology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Long Guo
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Shiro Ikegawa
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Kazuhiro Haginoya
- Department of Pediatric Neurology, Miyagi Children's Hospital, Sendai, Japan
| | - Muzhirah Haniffa
- Department of Genetics, Kuala Lumpur Hospital, Kuala Lumpur, Malaysia
| | - Nozomi Hiraishi
- Department of Pediatrics, Yokohama City University Medical Center, Yokohama, Japan
| | - Yoko Hiraki
- Hiroshima Municipal Center for Child Health and Development, Hiroshima, Japan
| | - Satoru Ikemoto
- Division of Neurology, Saitama Children's Medical Center, Saitama, Japan
| | - Atsuro Daida
- Division of Neurology, Saitama Children's Medical Center, Saitama, Japan
| | - Shin-Ichiro Hamano
- Division of Neurology, Saitama Children's Medical Center, Saitama, Japan
| | - Masaki Miura
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan.,Department of Pediatrics, Nagaoka Red Cross Hospital, Nagaoka, Japan
| | - Akihiko Ishiyama
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Osamu Kawano
- Department of Pediatrics, Hokkaido University Hospital, Sapporo, Japan
| | - Akane Kondo
- Clinical Genetics Center, Shikoku Medical Center for Children and Adults, National Hospital Organization, Kagawa, Japan
| | - Hiroshi Matsumoto
- Department of Pediatrics, National Defense Medical College, Saitama, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Tohru Okanishi
- Department of Brain and Neurosciences, Division of Child Neurology, Faculty of Medicine, Tottori University, Yonago, Japan.,Department of Child Neurology, Comprehensive Epilepsy Center, Seirei Hamamatsu General Hospital, Hamamatsu, Japan
| | - Yukimi Oyoshi
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Eri Takeshita
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Toshifumi Suzuki
- Department of Obstetrics and Gynecology, Faculty of Medicine Juntendo University, Tokyo, Japan
| | - Yoshiyuki Ogawa
- Department of Hematology, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Hiroshi Handa
- Department of Hematology, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Yayoi Miyazono
- Department of Child Health, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Atsushi Takata
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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21
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Abstract
Conventional models of genome evolution are centered around the principle that mutations form independently of each other and build up slowly over time. We characterized the occurrence of bursts of genome-wide loss-of-heterozygosity (LOH) in Saccharomyces cerevisiae, providing support for an additional nonindependent and faster mode of mutation accumulation. We initially characterized a yeast clone isolated for carrying an LOH event at a specific chromosome site, and surprisingly found that it also carried multiple unselected rearrangements elsewhere in its genome. Whole-genome analysis of over 100 additional clones selected for carrying primary LOH tracts revealed that they too contained unselected structural alterations more often than control clones obtained without any selection. We also measured the rates of coincident LOH at two different chromosomes and found that double LOH formed at rates 14- to 150-fold higher than expected if the two underlying single LOH events occurred independently of each other. These results were consistent across different strain backgrounds and in mutants incapable of entering meiosis. Our results indicate that a subset of mitotic cells within a population can experience discrete episodes of systemic genomic instability, when the entire genome becomes vulnerable and multiple chromosomal alterations can form over a narrow time window. They are reminiscent of early reports from the classic yeast genetics literature, as well as recent studies in humans, both in cancer and genomic disorder contexts. The experimental model we describe provides a system to further dissect the fundamental biological processes responsible for punctuated bursts of structural genomic variation.
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22
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Singh SM, Castellani CA, Hill KA. Postzygotic Somatic Mutations in the Human Brain Expand the Threshold-Liability Model of Schizophrenia. Front Psychiatry 2020; 11:587162. [PMID: 33192734 PMCID: PMC7642466 DOI: 10.3389/fpsyt.2020.587162] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 09/22/2020] [Indexed: 12/11/2022] Open
Abstract
The search for what causes schizophrenia has been onerous. This research has included extensive assessment of a variety of genetic and environmental factors using ever emerging high-resolution technologies and traditional understanding of the biology of the brain. These efforts have identified a large number of schizophrenia-associated genes, some of which are altered by mutational and epi-mutational mechanisms in a threshold liability model of schizophrenia development. The results, however, have limited predictability and the actual cause of the disease remains unknown. This current state asks for conceptualizing the problem differently in light of novel insights into the nature of mutations, the biology of the brain and the fine precision and resolution of emerging technologies. There is mounting evidence that mutations acquired during postzygotic development are more common than germline mutations. Also, the postzygotic somatic mutations including epimutations (PZMs), which often lead to somatic mosaicism, are relatively common in the mammalian brain in comparison to most other tissues and PZMs are more common in patients with neurodevelopmental mental disorders, including schizophrenia. Further, previously inaccessible, detection of PZMs is becoming feasible with the advent of novel technologies that include single-cell genomics and epigenomics and the use of exquisite experimental designs including use of monozygotic twins discordant for the disease. These developments allow us to propose a working hypothesis and expand the threshold liability model of schizophrenia that already encompasses familial genetic, epigenetic and environmental factors to include somatic de novo PZMs. Further, we offer a test for this expanded model using currently available genome sequences and methylome data on monozygotic twins discordant for schizophrenia (MZD) and their parents. The results of this analysis argue that PZMs play a significant role in the development of schizophrenia and explain extensive heterogeneity seen across patients. It also offers the potential to convincingly link PZMs to both nervous system health and disease, an area that has remained challenging to study and relatively under explored.
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Affiliation(s)
- Shiva M. Singh
- Molecular Genetics Unit, Department of Biology, The University of Western Ontario, London, ON, Canada
| | | | - Kathleen A. Hill
- Molecular Genetics Unit, Department of Biology, The University of Western Ontario, London, ON, Canada
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23
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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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24
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Prenatal Diagnosis of a De Novo Partial Trisomy 6q and Partial Monosomy 18p Associated with Cephalocele: A Case Report. Balkan J Med Genet 2020; 23:99-102. [PMID: 32953417 PMCID: PMC7474219 DOI: 10.2478/bjmg-2020-0014] [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] [Indexed: 11/20/2022] Open
Abstract
A 28-year-old woman underwent amniocentesis at 18 weeks’ gestation upon detection of increased fetal nuchal fold and parietal cephalocele on the second trimester ultrasound examination. Prenatal microarray showed a de novo unbalanced translocation resulting in a gain in 6q and loss in 18p. A female infant was delivered at 38 weeks’ gestation. At birth, cephalocele and webbed neck were noted as major dysmorphic features. The case presented here shows how a combination of different genetic studies is used to accurately elucidate a chromosomal anomaly in a prenatal setting.
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25
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Brás A, Rodrigues AS, Rueff J. Copy number variations and constitutional chromothripsis (Review). Biomed Rep 2020; 13:11. [PMID: 32765850 PMCID: PMC7391299 DOI: 10.3892/br.2020.1318] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 02/13/2020] [Indexed: 02/07/2023] Open
Abstract
Both copy number variations (CNVs) and chromothripsis are phenomena that involve complex genomic rearrangements. Chromothripsis results in CNVs and other structural changes. CNVs are frequently observed in the human genome. Studies on CNVs have been increasing exponentially; the Database of Genomic Variants shows an increase in the number of data published on structural variations added to the database in the last 15 years. CNVs may be a result of replicative and non-replicative mechanisms, and are hypothesized to serve important roles in human health and disease. Chromothripsis is a phenomena of chromosomal rearrangement following chromosomal breaks at multiple locations and involves impaired DNA repair. In 2011, Stephens et al coined the term chromothripsis for this type of fragmenting event. Several proposed mechanisms have been suggested to underlie chromothripsis, such as p53 inactivation, micronuclei formation, abortive apoptosis and telomere fusions in telomere crisis. Chromothripsis gives rise to normal or abnormal phenotypes. In this review, constitutional chromothripsis, which may coexist with multiple de novo CNVs are described and discussed. This reviews aims to summarize recent advances in our understanding of CNVs and chromothripsis, and describe the effects of these phenomena on human health and birth defects.
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Affiliation(s)
- Aldina Brás
- Centre for Toxicogenomics and Human Health (ToxOmics), Genetics, Oncology and Human Toxicology, NOVA Medical School, Faculty of Medical Sciences, NOVA University of Lisbon, Lisbon 1169-056, Portugal
| | - António Sebastião Rodrigues
- Centre for Toxicogenomics and Human Health (ToxOmics), Genetics, Oncology and Human Toxicology, NOVA Medical School, Faculty of Medical Sciences, NOVA University of Lisbon, Lisbon 1169-056, Portugal
| | - José Rueff
- Centre for Toxicogenomics and Human Health (ToxOmics), Genetics, Oncology and Human Toxicology, NOVA Medical School, Faculty of Medical Sciences, NOVA University of Lisbon, Lisbon 1169-056, Portugal
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26
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Hattori A, Fukami M. Established and Novel Mechanisms Leading to de novo Genomic Rearrangements in the Human Germline. Cytogenet Genome Res 2020; 160:167-176. [DOI: 10.1159/000507837] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 03/31/2020] [Indexed: 01/05/2023] Open
Abstract
During gametogenesis, the human genome can acquire various de novo rearrangements. Most constitutional genomic rearrangements are created through 1 of the 4 well-known mechanisms, i.e., nonallelic homologous recombination, erroneous repair after double-strand DNA breaks, replication errors, and retrotransposition. However, recent studies have identified 2 types of extremely complex rearrangements that cannot be simply explained by these mechanisms. The first type consists of chaotic structural changes in 1 or a few chromosomes that result from “chromoanagenesis (an umbrella term that covers chromothripsis, chromoanasynthesis, and chromoplexy).” The other type is large independent rearrangements in multiple chromosomes indicative of “transient multifocal genomic crisis.” Germline chromoanagenesis (chromothripsis) likely occurs predominantly during spermatogenesis or postzygotic embryogenesis, while multifocal genomic crisis appears to be limited to a specific time window during oogenesis and early embryogenesis or during spermatogenesis. This review article introduces the current understanding of the molecular basis of de novo rearrangements in the germline.
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27
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Albertini DF. Novel insights into the genetics of early human development: PGT as a catalyst for reform. J Assist Reprod Genet 2020; 37:495-496. [PMID: 32219599 PMCID: PMC7100432 DOI: 10.1007/s10815-020-01759-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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28
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Karolak JA, Gambin T, Honey EM, Slavik T, Popek E, Stankiewicz P. A de novo 2.2 Mb recurrent 17q23.1q23.2 deletion unmasks novel putative regulatory non-coding SNVs associated with lethal lung hypoplasia and pulmonary hypertension: a case report. BMC Med Genomics 2020; 13:34. [PMID: 32143628 PMCID: PMC7060516 DOI: 10.1186/s12920-020-0701-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 02/27/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Application of whole genome sequencing (WGS) enables identification of non-coding variants that play a phenotype-modifying role and are undetectable by exome sequencing. Recently, non-coding regulatory single nucleotide variants (SNVs) have been reported in patients with lethal lung developmental disorders (LLDDs) or congenital scoliosis with recurrent copy-number variant (CNV) deletions at 17q23.1q23.2 or 16p11.2, respectively. CASE PRESENTATION Here, we report a deceased newborn with pulmonary hypertension and pulmonary interstitial emphysema with features suggestive of pulmonary hypoplasia, resulting in respiratory failure and neonatal death soon after birth. Using the array comparative genomic hybridization and WGS, two heterozygous recurrent CNV deletions: ~ 2.2 Mb on 17q23.1q23.2, involving TBX4, and ~ 600 kb on 16p11.2, involving TBX6, that both arose de novo on maternal chromosomes were identified. In the predicted lung-specific enhancer upstream to TBX4, we have detected seven novel putative regulatory non-coding SNVs that were absent in 13 control individuals with the overlapping deletions but without any structural lung anomalies. CONCLUSIONS Our findings further support a recently reported model of complex compound inheritance of LLDD in which both non-coding and coding heterozygous TBX4 variants contribute to the lung phenotype. In addition, this is the first report of a patient with combined de novo heterozygous recurrent 17q23.1q23.2 and 16p11.2 CNV deletions.
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Affiliation(s)
- Justyna A Karolak
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, 60-781, Poznan, Poland
| | - Tomasz Gambin
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Institute of Computer Science, Warsaw University of Technology, 00-665, Warsaw, Poland
| | - Engela M Honey
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Science, University of Pretoria, Pretoria, South Africa
| | - Tomas Slavik
- Ampath Pathology Laboratories, and Department of Anatomical Pathology, University of Pretoria, Pretoria, South Africa
| | - Edwina Popek
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Paweł Stankiewicz
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
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29
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Poot M. Genomic Earthquakes in the Human Germline and Their Ramifications. Mol Syndromol 2020; 10:291-293. [PMID: 32021602 DOI: 10.1159/000503366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2019] [Indexed: 02/05/2023] Open
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30
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Li Y, Roberts ND, Wala JA, Shapira O, Schumacher SE, Kumar K, Khurana E, Waszak S, Korbel JO, Haber JE, Imielinski M, Weischenfeldt J, Beroukhim R, Campbell PJ. Patterns of somatic structural variation in human cancer genomes. Nature 2020; 578:112-121. [PMID: 32025012 PMCID: PMC7025897 DOI: 10.1038/s41586-019-1913-9] [Citation(s) in RCA: 450] [Impact Index Per Article: 112.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 11/18/2019] [Indexed: 01/28/2023]
Abstract
A key mutational process in cancer is structural variation, in which rearrangements delete, amplify or reorder genomic segments that range in size from kilobases to whole chromosomes1-7. Here we develop methods to group, classify and describe somatic structural variants, using data from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), which aggregated whole-genome sequencing data from 2,658 cancers across 38 tumour types8. Sixteen signatures of structural variation emerged. Deletions have a multimodal size distribution, assort unevenly across tumour types and patients, are enriched in late-replicating regions and correlate with inversions. Tandem duplications also have a multimodal size distribution, but are enriched in early-replicating regions-as are unbalanced translocations. Replication-based mechanisms of rearrangement generate varied chromosomal structures with low-level copy-number gains and frequent inverted rearrangements. One prominent structure consists of 2-7 templates copied from distinct regions of the genome strung together within one locus. Such cycles of templated insertions correlate with tandem duplications, and-in liver cancer-frequently activate the telomerase gene TERT. A wide variety of rearrangement processes are active in cancer, which generate complex configurations of the genome upon which selection can act.
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Affiliation(s)
- Yilong Li
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Totient Inc, Cambridge, MA, USA
| | - Nicola D Roberts
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Jeremiah A Wala
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Bioinformatics and Integrative Genomics, Harvard University, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ofer Shapira
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Bioinformatics and Integrative Genomics, Harvard University, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Steven E Schumacher
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Bioinformatics and Integrative Genomics, Harvard University, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kiran Kumar
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Bioinformatics and Integrative Genomics, Harvard University, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ekta Khurana
- Weill Cornell Medical College, New York, NY, USA
| | - Sebastian Waszak
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Jan O Korbel
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - James E Haber
- Department of Molecular Biology, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA, USA
| | | | - Joachim Weischenfeldt
- Biotech Research & Innovation Centre (BRIC), The Finsen Laboratory, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.
| | - Rameen Beroukhim
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Bioinformatics and Integrative Genomics, Harvard University, Cambridge, MA, USA.
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Peter J Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
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31
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Perez-Rodriguez D, Kalyva M, Leija-Salazar M, Lashley T, Tarabichi M, Chelban V, Gentleman S, Schottlaender L, Franklin H, Vasmatzis G, Houlden H, Schapira AHV, Warner TT, Holton JL, Jaunmuktane Z, Proukakis C. Investigation of somatic CNVs in brains of synucleinopathy cases using targeted SNCA analysis and single cell sequencing. Acta Neuropathol Commun 2019; 7:219. [PMID: 31870437 PMCID: PMC6929293 DOI: 10.1186/s40478-019-0873-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 12/17/2019] [Indexed: 12/17/2022] Open
Abstract
Synucleinopathies are mostly sporadic neurodegenerative disorders of partly unexplained aetiology, and include Parkinson's disease (PD) and multiple system atrophy (MSA). We have further investigated our recent finding of somatic SNCA (α-synuclein) copy number variants (CNVs, specifically gains) in synucleinopathies, using Fluorescent in-situ Hybridisation for SNCA, and single-cell whole genome sequencing for the first time in a synucleinopathy. In the cingulate cortex, mosaicism levels for SNCA gains were higher in MSA and PD than controls in neurons (> 2% in both diseases), and for MSA also in non-neurons. In MSA substantia nigra (SN), we noted SNCA gains in > 3% of dopaminergic (DA) neurons (identified by neuromelanin) and neuromelanin-negative cells, including olig2-positive oligodendroglia. Cells with CNVs were more likely to have α-synuclein inclusions, in a pattern corresponding to cell categories mostly relevant to the disease: DA neurons in Lewy-body cases, and other cells in the striatonigral degeneration-dominant MSA variant (MSA-SND). Higher mosaicism levels in SN neuromelanin-negative cells may correlate with younger onset in typical MSA-SND, and in cingulate neurons with younger death in PD. Larger sample sizes will, however, be required to confirm these putative findings. We obtained genome-wide somatic CNV profiles from 169 cells from the substantia nigra of two MSA cases, and pons and putamen of one. These showed somatic CNVs in ~ 30% of cells, with clonality and origins in segmental duplications for some. CNVs had distinct profiles based on cell type, with neurons having a mix of gains and losses, and other cells having almost exclusively gains, although control data sets will be required to determine possible disease relevance. We propose that somatic SNCA CNVs may contribute to the aetiology and pathogenesis of synucleinopathies, and that genome-wide somatic CNVs in MSA brain merit further study.
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Affiliation(s)
- Diego Perez-Rodriguez
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Maria Kalyva
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Melissa Leija-Salazar
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Tammaryn Lashley
- Queen Square Brain Bank for Neurological disorders, UCL Queen Square Institute of Neurology, 1 Wakefield street, London, WC1N 1PJ, UK
| | - Maxime Tarabichi
- The Francis Crick Institute, Midland Road 1, London, NW1 1AT, UK
| | - Viorica Chelban
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | | | - Lucia Schottlaender
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - Hannah Franklin
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - George Vasmatzis
- Center for Individualized Medicine, Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - Anthony H V Schapira
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Thomas T Warner
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- Queen Square Brain Bank for Neurological disorders, UCL Queen Square Institute of Neurology, 1 Wakefield street, London, WC1N 1PJ, UK
- National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - Janice L Holton
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- Queen Square Brain Bank for Neurological disorders, UCL Queen Square Institute of Neurology, 1 Wakefield street, London, WC1N 1PJ, UK
| | - Zane Jaunmuktane
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- Queen Square Brain Bank for Neurological disorders, UCL Queen Square Institute of Neurology, 1 Wakefield street, London, WC1N 1PJ, UK
- National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - Christos Proukakis
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK.
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32
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Distinct patterns of complex rearrangements and a mutational signature of microhomeology are frequently observed in PLP1 copy number gain structural variants. Genome Med 2019; 11:80. [PMID: 31818324 PMCID: PMC6902434 DOI: 10.1186/s13073-019-0676-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 10/10/2019] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND We investigated the features of the genomic rearrangements in a cohort of 50 male individuals with proteolipid protein 1 (PLP1) copy number gain events who were ascertained with Pelizaeus-Merzbacher disease (PMD; MIM: 312080). We then compared our new data to previous structural variant mutagenesis studies involving the Xq22 region of the human genome. The aggregate data from 159 sequenced join-points (discontinuous sequences in the reference genome that are joined during the rearrangement process) were studied. Analysis of these data from 150 individuals enabled the spectrum and relative distribution of the underlying genomic mutational signatures to be delineated. METHODS Genomic rearrangements in PMD individuals with PLP1 copy number gain events were investigated by high-density customized array or clinical chromosomal microarray analysis and breakpoint junction sequence analysis. RESULTS High-density customized array showed that the majority of cases (33/50; ~ 66%) present with single duplications, although complex genomic rearrangements (CGRs) are also frequent (17/50; ~ 34%). Breakpoint mapping to nucleotide resolution revealed further previously unknown structural and sequence complexities, even in single duplications. Meta-analysis of all studied rearrangements that occur at the PLP1 locus showed that single duplications were found in ~ 54% of individuals and that, among all CGR cases, triplication flanked by duplications is the most frequent CGR array CGH pattern observed. Importantly, in ~ 32% of join-points, there is evidence for a mutational signature of microhomeology (highly similar yet imperfect sequence matches). CONCLUSIONS These data reveal a high frequency of CGRs at the PLP1 locus and support the assertion that replication-based mechanisms are prominent contributors to the formation of CGRs at Xq22. We propose that microhomeology can facilitate template switching, by stabilizing strand annealing of the primer using W-C base complementarity, and is a mutational signature for replicative repair.
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Hijazi H, Coelho FS, Gonzaga-Jauregui C, Bernardini L, Mar SS, Manning MA, Hanson-Kahn A, Naidu S, Srivastava S, Lee JA, Jones JR, Friez MJ, Alberico T, Torres B, Fang P, Cheung SW, Song X, Davis-Williams A, Jornlin C, Wight PA, Patyal P, Taube J, Poretti A, Inoue K, Zhang F, Pehlivan D, Carvalho CMB, Hobson GM, Lupski JR. Xq22 deletions and correlation with distinct neurological disease traits in females: Further evidence for a contiguous gene syndrome. Hum Mutat 2019; 41:150-168. [PMID: 31448840 DOI: 10.1002/humu.23902] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 08/14/2019] [Accepted: 08/22/2019] [Indexed: 01/24/2023]
Abstract
Xq22 deletions that encompass PLP1 (Xq22-PLP1-DEL) are notable for variable expressivity of neurological disease traits in females ranging from a mild late-onset form of spastic paraplegia type 2 (MIM# 312920), sometimes associated with skewed X-inactivation, to an early-onset neurological disease trait (EONDT) of severe developmental delay, intellectual disability, and behavioral abnormalities. Size and gene content of Xq22-PLP1-DEL vary and were proposed as potential molecular etiologies underlying variable expressivity in carrier females where two smallest regions of overlap (SROs) were suggested to influence disease. We ascertained a cohort of eight unrelated patients harboring Xq22-PLP1-DEL and performed high-density array comparative genomic hybridization and breakpoint-junction sequencing. Molecular characterization of Xq22-PLP1-DEL from 17 cases (eight herein and nine published) revealed an overrepresentation of breakpoints that reside within repeats (11/17, ~65%) and the clustering of ~47% of proximal breakpoints in a genomic instability hotspot with characteristic non-B DNA density. These findings implicate a potential role for genomic architecture in stimulating the formation of Xq22-PLP1-DEL. The correlation of Xq22-PLP1-DEL gene content with neurological disease trait in female cases enabled refinement of the associated SROs to a single genomic interval containing six genes. Our data support the hypothesis that genes contiguous to PLP1 contribute to EONDT.
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Affiliation(s)
- Hadia Hijazi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Fernanda S Coelho
- Programa de Pós-Graduação em Genética Departmento de Biologia Geral, UFMG, Belo Horizonte, Minas Gerais, Brazil.,Instituto René Rachou, FIOCRUZ, Belo Horizonte, Minas Gerais, Brazil
| | | | - Laura Bernardini
- Medical Genetics Division, IRCCS "Casa Sollievo della Sofferenza" Foundation, San Giovanni Rotondo (FG), Italy
| | - Soe S Mar
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri
| | - Melanie A Manning
- Division of Medical Genetics, Department of Pediatrics, Stanford University School of Medicine, Palo Alto, California.,Department of Pathology, Stanford University School of Medicine, Palo Alto, California
| | - Andrea Hanson-Kahn
- Division of Medical Genetics, Department of Pediatrics, Stanford University School of Medicine, Palo Alto, California.,Department of Genetics, Stanford University School of Medicine, Palo Alto, California
| | - SakkuBai Naidu
- Departments of Neurology and Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, Maryland
| | | | - Jennifer A Lee
- Molecular Diagnostic Laboratory, Greenwood Genetic Center, Greenwood, South Carolina
| | - Julie R Jones
- Molecular Diagnostic Laboratory, Greenwood Genetic Center, Greenwood, South Carolina
| | - Michael J Friez
- Molecular Diagnostic Laboratory, Greenwood Genetic Center, Greenwood, South Carolina
| | - Thomas Alberico
- Nemours Biomedical Research, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - Barbara Torres
- Medical Genetics Division, IRCCS "Casa Sollievo della Sofferenza" Foundation, San Giovanni Rotondo (FG), Italy
| | - Ping Fang
- Clinical Genomics, WuXi NextCODE, Cambridge, Massachusetts
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Xiaofei Song
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Angelique Davis-Williams
- Nemours Biomedical Research, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - Carly Jornlin
- Nemours Biomedical Research, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - Patricia A Wight
- Department of Physiology and Biophysics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Pankaj Patyal
- Department of Physiology and Biophysics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Jennifer Taube
- Nemours Biomedical Research, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - Andrea Poretti
- Departments of Neurology and Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ken Inoue
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Feng Zhang
- State Key Laboratory of Genetic Engineering at School of Life Sciences, Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Section of Neurology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Grace M Hobson
- Nemours Biomedical Research, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas.,Texas Children's Hospital, Houston, Texas
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Lindstrand A, Eisfeldt J, Pettersson M, Carvalho CMB, Kvarnung M, Grigelioniene G, Anderlid BM, Bjerin O, Gustavsson P, Hammarsjö A, Georgii-Hemming P, Iwarsson E, Johansson-Soller M, Lagerstedt-Robinson K, Lieden A, Magnusson M, Martin M, Malmgren H, Nordenskjöld M, Norling A, Sahlin E, Stranneheim H, Tham E, Wincent J, Ygberg S, Wedell A, Wirta V, Nordgren A, Lundin J, Nilsson D. From cytogenetics to cytogenomics: whole-genome sequencing as a first-line test comprehensively captures the diverse spectrum of disease-causing genetic variation underlying intellectual disability. Genome Med 2019; 11:68. [PMID: 31694722 PMCID: PMC6836550 DOI: 10.1186/s13073-019-0675-1] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 10/09/2019] [Indexed: 12/30/2022] Open
Abstract
Background Since different types of genetic variants, from single nucleotide variants (SNVs) to large chromosomal rearrangements, underlie intellectual disability, we evaluated the use of whole-genome sequencing (WGS) rather than chromosomal microarray analysis (CMA) as a first-line genetic diagnostic test. Methods We analyzed three cohorts with short-read WGS: (i) a retrospective cohort with validated copy number variants (CNVs) (cohort 1, n = 68), (ii) individuals referred for monogenic multi-gene panels (cohort 2, n = 156), and (iii) 100 prospective, consecutive cases referred to our center for CMA (cohort 3). Bioinformatic tools developed include FindSV, SVDB, Rhocall, Rhoviz, and vcf2cytosure. Results First, we validated our structural variant (SV)-calling pipeline on cohort 1, consisting of three trisomies and 79 deletions and duplications with a median size of 850 kb (min 500 bp, max 155 Mb). All variants were detected. Second, we utilized the same pipeline in cohort 2 and analyzed with monogenic WGS panels, increasing the diagnostic yield to 8%. Next, cohort 3 was analyzed by both CMA and WGS. The WGS data was processed for large (> 10 kb) SVs genome-wide and for exonic SVs and SNVs in a panel of 887 genes linked to intellectual disability as well as genes matched to patient-specific Human Phenotype Ontology (HPO) phenotypes. This yielded a total of 25 pathogenic variants (SNVs or SVs), of which 12 were detected by CMA as well. We also applied short tandem repeat (STR) expansion detection and discovered one pathologic expansion in ATXN7. Finally, a case of Prader-Willi syndrome with uniparental disomy (UPD) was validated in the WGS data. Important positional information was obtained in all cohorts. Remarkably, 7% of the analyzed cases harbored complex structural variants, as exemplified by a ring chromosome and two duplications found to be an insertional translocation and part of a cryptic unbalanced translocation, respectively. Conclusion The overall diagnostic rate of 27% was more than doubled compared to clinical microarray (12%). Using WGS, we detected a wide range of SVs with high accuracy. Since the WGS data also allowed for analysis of SNVs, UPD, and STRs, it represents a powerful comprehensive genetic test in a clinical diagnostic laboratory setting.
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Affiliation(s)
- Anna Lindstrand
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden. .,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden. .,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.
| | - Jesper Eisfeldt
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Maria Pettersson
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Malin Kvarnung
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Giedre Grigelioniene
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Britt-Marie Anderlid
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Olof Bjerin
- The Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Peter Gustavsson
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Anna Hammarsjö
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Erik Iwarsson
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Maria Johansson-Soller
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Kristina Lagerstedt-Robinson
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Agne Lieden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Måns Magnusson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden.,Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Marcel Martin
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Helena Malmgren
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Magnus Nordenskjöld
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ameli Norling
- The Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Ellika Sahlin
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Henrik Stranneheim
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Emma Tham
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Josephine Wincent
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Sofia Ygberg
- The Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.,Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Wedell
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Valtteri Wirta
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden.,Science for Life Laboratory, Department of Microbiology, Tumor and Cell biology, Karolinska Institutet, Stockholm, Sweden
| | - Ann Nordgren
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Johanna Lundin
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Daniel Nilsson
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
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35
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In vitro fertilization does not increase the incidence of de novo copy number alterations in fetal and placental lineages. Nat Med 2019; 25:1699-1705. [PMID: 31686035 DOI: 10.1038/s41591-019-0620-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 09/20/2019] [Indexed: 01/21/2023]
Abstract
Although chromosomal instability (CIN) is a common phenomenon in cleavage-stage embryogenesis following in vitro fertilization (IVF)1-3, its rate in naturally conceived human embryos is unknown. CIN leads to mosaic embryos that contain a combination of genetically normal and abnormal cells, and is significantly higher in in vitro-produced preimplantation embryos as compared to in vivo-conceived preimplantation embryos4. Even though embryos with CIN-derived complex aneuploidies may arrest between the cleavage and blastocyst stages of embryogenesis5,6, a high number of embryos containing abnormal cells can pass this strong selection barrier7,8. However, neither the prevalence nor extent of CIN during prenatal development and at birth, following IVF treatment, is well understood. Here we profiled the genomic landscape of fetal and placental tissues postpartum from both IVF and naturally conceived children, to investigate the prevalence and persistence of large genetic aberrations that probably arose from IVF-related CIN. We demonstrate that CIN is not preserved at later stages of prenatal development, and that de novo numerical aberrations or large structural DNA imbalances occur at similar rates in IVF and naturally conceived live-born neonates. Our findings affirm that human IVF treatment has no detrimental effect on the chromosomal constitution of fetal and placental lineages.
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Kaplanis J, Akawi N, Gallone G, McRae JF, Prigmore E, Wright CF, Fitzpatrick DR, Firth HV, Barrett JC, Hurles ME. Exome-wide assessment of the functional impact and pathogenicity of multinucleotide mutations. Genome Res 2019; 29:1047-1056. [PMID: 31227601 PMCID: PMC6633265 DOI: 10.1101/gr.239756.118] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 05/24/2019] [Indexed: 01/25/2023]
Abstract
Approximately 2% of de novo single-nucleotide variants (SNVs) appear as part of clustered mutations that create multinucleotide variants (MNVs). MNVs are an important source of genomic variability as they are more likely to alter an encoded protein than a SNV, which has important implications in disease as well as evolution. Previous studies of MNVs have focused on their mutational origins and have not systematically evaluated their functional impact and contribution to disease. We identified 69,940 MNVs and 91 de novo MNVs in 6688 exome-sequenced parent–offspring trios from the Deciphering Developmental Disorders Study comprising families with severe developmental disorders. We replicated the previously described MNV mutational signatures associated with DNA polymerase zeta, an error-prone translesion polymerase, and the APOBEC family of DNA deaminases. We estimate the simultaneous MNV germline mutation rate to be 1.78 × 10−10 mutations per base pair per generation. We found that most MNVs within a single codon create a missense change that could not have been created by a SNV. MNV-induced missense changes were, on average, more physicochemically divergent, were more depleted in highly constrained genes (pLI ≥ 0.9), and were under stronger purifying selection compared with SNV-induced missense changes. We found that de novo MNVs were significantly enriched in genes previously associated with developmental disorders in affected children. This shows that MNVs can be more damaging than SNVs even when both induce missense changes, and are an important variant type to consider in relation to human disease.
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Affiliation(s)
- Joanna Kaplanis
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, United Kingdom
| | - Nadia Akawi
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DU, United Kingdom
| | - Giuseppe Gallone
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, United Kingdom
| | - Jeremy F McRae
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, United Kingdom
| | - Elena Prigmore
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, United Kingdom
| | - Caroline F Wright
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, EX2 5DW, United Kingdom
| | - David R Fitzpatrick
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
| | - Helen V Firth
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, United Kingdom.,Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, United Kingdom
| | - Jeffrey C Barrett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, United Kingdom
| | - Matthew E Hurles
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, United Kingdom
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Beal MA, Meier MJ, Williams A, Rowan-Carroll A, Gagné R, Lindsay SJ, Fitzgerald T, Hurles ME, Marchetti F, Yauk CL. Paternal exposure to benzo(a)pyrene induces genome-wide mutations in mouse offspring. Commun Biol 2019; 2:228. [PMID: 31240266 PMCID: PMC6586636 DOI: 10.1038/s42003-019-0476-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 05/23/2019] [Indexed: 01/14/2023] Open
Abstract
Understanding the effects of environmental exposures on germline mutation rates has been a decades-long pursuit in genetics. We used next-generation sequencing and comparative genomic hybridization arrays to investigate genome-wide mutations in the offspring of male mice exposed to benzo(a)pyrene (BaP), a common environmental pollutant. We demonstrate that offspring developing from sperm exposed during the mitotic or post-mitotic phases of spermatogenesis have significantly more de novo single nucleotide variants (1.8-fold; P < 0.01) than controls. Both phases of spermatogenesis are susceptible to the induction of heritable mutations, although mutations arising from post-fertilization events are more common after post-mitotic exposure. In addition, the mutation spectra in sperm and offspring of BaP-exposed males are consistent. Finally, we report a significant increase in transmitted copy number duplications (P = 0.001) in BaP-exposed sires. Our study demonstrates that germ cell mutagen exposures induce genome-wide mutations in the offspring that may be associated with adverse health outcomes.
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Affiliation(s)
- Marc A. Beal
- Carleton University, Ottawa, Ontario K1S 5B6 Canada
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario K1A 0K9 Canada
| | - Matthew J. Meier
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario K1A 0K9 Canada
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario K1A 0K9 Canada
| | - Andrea Rowan-Carroll
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario K1A 0K9 Canada
| | - Rémi Gagné
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario K1A 0K9 Canada
| | - Sarah J. Lindsay
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Tomas Fitzgerald
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Matthew E. Hurles
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Francesco Marchetti
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario K1A 0K9 Canada
| | - Carole L. Yauk
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario K1A 0K9 Canada
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2017 Roadmap for Innovation-ACC Health Policy Statement on Healthcare Transformation in the Era of Digital Health, Big Data, and Precision Health: A Report of the American College of Cardiology Task Force on Health Policy Statements and Systems of Care. J Am Coll Cardiol 2019; 70:2696-2718. [PMID: 29169478 DOI: 10.1016/j.jacc.2017.10.018] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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39
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Hattori A, Okamura K, Terada Y, Tanaka R, Katoh-Fukui Y, Matsubara Y, Matsubara K, Kagami M, Horikawa R, Fukami M. Transient multifocal genomic crisis creating chromothriptic and non-chromothriptic rearrangements in prezygotic testicular germ cells. BMC Med Genomics 2019; 12:77. [PMID: 31138192 PMCID: PMC6540402 DOI: 10.1186/s12920-019-0526-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 05/10/2019] [Indexed: 12/15/2022] Open
Abstract
Background The co-occurrence of multiple de novo copy number variations (CNVs) is a rare phenomenon in the human genome. Recently, an “organismal CNV mutator phenotype” has been reported to result in transient genomic instability introducing multiple de novo CNVs in primary oocytes and early-stage zygotes. These findings opened a new area of human genome research. Methods We performed genome-wide copy number analysis for ~ 2100 individuals with various congenital defects. Furthermore, extensive molecular analyses, including synthetic long-read whole-genome sequencing and haplotype-phasing, were carried out for an individual with multiple de novo CNVs. Results A boy was found to have de novo rearrangements on five chromosomes. The rearrangements comprised simple duplication and inversion as well as chaotic changes, all of which affected paternally derived chromosomes. Postzygotic genomic instability was ruled out. The duplicated regions on 6q and 13q contained both diallelic and triallelic loci, indicating that the genomic rearrangements were initially created during premeiotic mitosis and subsequently modified by physiological cross-over during meiosis I. Breakpoints of the rearrangements were indicative of non-homologous end joining, replication-based errors, and/or chromothripsis. The mutagenic event was independent of specific local DNA motifs or de novo point mutations, but may be driven by spermatogenesis-specific factors. Conclusions These results indicate that during spermatogenesis, a transient multifocal genomic crisis can introduce several chromothriptic and non-chromothriptic changes into the genome. These findings broaden the concept of the “organismal CNV mutator phenotype”. This study provides insights into mechanisms for altering the global chromosomal architecture of human embryos. Electronic supplementary material The online version of this article (10.1186/s12920-019-0526-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Atsushi Hattori
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan.,Department of Advanced Pediatric Medicine, Tohoku University School of Medicine, Tokyo, 157-8535, Japan
| | - Kohji Okamura
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Yumiko Terada
- Division of Endocrinology and Metabolism, National Medical Center for Children and Mothers, Tokyo, 157-8535, Japan
| | - Rika Tanaka
- Department of Neonatology, Aiiku Hospital, Tokyo, 105-8321, Japan
| | - Yuko Katoh-Fukui
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Yoichi Matsubara
- National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Keiko Matsubara
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Masayo Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Reiko Horikawa
- Division of Endocrinology and Metabolism, National Medical Center for Children and Mothers, Tokyo, 157-8535, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan.
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40
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Kermi C, Aze A, Maiorano D. Preserving Genome Integrity During the Early Embryonic DNA Replication Cycles. Genes (Basel) 2019; 10:genes10050398. [PMID: 31137726 PMCID: PMC6563053 DOI: 10.3390/genes10050398] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 05/15/2019] [Indexed: 02/06/2023] Open
Abstract
During the very early stages of embryonic development chromosome replication occurs under rather challenging conditions, including a very short cell cycle, absence of transcription, a relaxed DNA damage response and, in certain animal species, a highly contracted S-phase. This raises the puzzling question of how the genome can be faithfully replicated in such a peculiar metabolic context. Recent studies have provided new insights into this issue, and unveiled that embryos are prone to accumulate genetic and genomic alterations, most likely due to restricted cellular functions, in particular reduced DNA synthesis quality control. These findings may explain the low rate of successful development in mammals and the occurrence of diseases, such as abnormal developmental features and cancer. In this review, we will discuss recent findings in this field and put forward perspectives to further study this fascinating question.
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Affiliation(s)
- Chames Kermi
- Laboratoire Surveillance et Stabilité du Génome, Institut de Génétique Humaine, UMR9002, CNRS, Université de Montpellier, 34090 Montpellier, France.
- Department of Chemical and Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, CA 94305-5441, USA.
| | - Antoine Aze
- Laboratoire Surveillance et Stabilité du Génome, Institut de Génétique Humaine, UMR9002, CNRS, Université de Montpellier, 34090 Montpellier, France.
| | - Domenico Maiorano
- Laboratoire Surveillance et Stabilité du Génome, Institut de Génétique Humaine, UMR9002, CNRS, Université de Montpellier, 34090 Montpellier, France.
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Iourov IY, Vorsanova SG, Yurov YB, Kutsev SI. Ontogenetic and Pathogenetic Views on Somatic Chromosomal Mosaicism. Genes (Basel) 2019; 10:E379. [PMID: 31109140 PMCID: PMC6562967 DOI: 10.3390/genes10050379] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/14/2019] [Accepted: 05/15/2019] [Indexed: 12/27/2022] Open
Abstract
Intercellular karyotypic variability has been a focus of genetic research for more than 50 years. It has been repeatedly shown that chromosome heterogeneity manifesting as chromosomal mosaicism is associated with a variety of human diseases. Due to the ability of changing dynamically throughout the ontogeny, chromosomal mosaicism may mediate genome/chromosome instability and intercellular diversity in health and disease in a bottleneck fashion. However, the ubiquity of negligibly small populations of cells with abnormal karyotypes results in difficulties of the interpretation and detection, which may be nonetheless solved by post-genomic cytogenomic technologies. In the post-genomic era, it has become possible to uncover molecular and cellular pathways to genome/chromosome instability (chromosomal mosaicism or heterogeneity) using advanced whole-genome scanning technologies and bioinformatic tools. Furthermore, the opportunities to determine the effect of chromosomal abnormalities on the cellular phenotype seem to be useful for uncovering the intrinsic consequences of chromosomal mosaicism. Accordingly, a post-genomic review of chromosomal mosaicism in the ontogenetic and pathogenetic contexts appears to be required. Here, we review chromosomal mosaicism in its widest sense and discuss further directions of cyto(post)genomic research dedicated to chromosomal heterogeneity.
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Affiliation(s)
- Ivan Y Iourov
- Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, 117152 Moscow, Russia.
- Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, 125412 Moscow, Russia.
| | - Svetlana G Vorsanova
- Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, 117152 Moscow, Russia.
- Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, 125412 Moscow, Russia.
| | - Yuri B Yurov
- Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, 117152 Moscow, Russia.
- Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, 125412 Moscow, Russia.
| | - Sergei I Kutsev
- Research Centre for Medical Genetics, 115522 Moscow, Russia.
- Molecular & Cell Genetics Department, Pirogov Russian National Research Medical University, 117997 Moscow, Russia.
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42
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Carvalho CMB, Coban-Akdemir Z, Hijazi H, Yuan B, Pendleton M, Harrington E, Beaulaurier J, Juul S, Turner DJ, Kanchi RS, Jhangiani SN, Muzny DM, Gibbs RA, Stankiewicz P, Belmont JW, Shaw CA, Cheung SW, Hanchard NA, Sutton VR, Bader PI, Lupski JR. Interchromosomal template-switching as a novel molecular mechanism for imprinting perturbations associated with Temple syndrome. Genome Med 2019; 11:25. [PMID: 31014393 PMCID: PMC6480824 DOI: 10.1186/s13073-019-0633-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 04/02/2019] [Indexed: 12/13/2022] Open
Abstract
Background Intrachromosomal triplications (TRP) can contribute to disease etiology via gene dosage effects, gene disruption, position effects, or fusion gene formation. Recently, post-zygotic de novo triplications adjacent to copy-number neutral genomic intervals with runs of homozygosity (ROH) have been shown to result in uniparental isodisomy (UPD). The genomic structure of these complex genomic rearrangements (CGRs) shows a consistent pattern of an inverted triplication flanked by duplications (DUP-TRP/INV-DUP) formed by an iterative DNA replisome template-switching mechanism during replicative repair of a single-ended, double-stranded DNA (seDNA), the ROH results from an interhomolog or nonsister chromatid template switch. It has been postulated that these CGRs may lead to genetic abnormalities in carriers due to dosage-sensitive genes mapping within the copy-number variant regions, homozygosity for alleles at a locus causing an autosomal recessive (AR) disease trait within the ROH region, or imprinting-associated diseases. Methods Here, we report a family wherein the affected subject carries a de novo 2.2-Mb TRP followed by 42.2 Mb of ROH and manifests clinical features overlapping with those observed in association with chromosome 14 maternal UPD (UPD(14)mat). UPD(14)mat can cause clinical phenotypic features enabling a diagnosis of Temple syndrome. This CGR was then molecularly characterized by high-density custom aCGH, genome-wide single-nucleotide polymorphism (SNP) and methylation arrays, exome sequencing (ES), and the Oxford Nanopore long-read sequencing technology. Results We confirmed the postulated DUP-TRP/INV-DUP structure by multiple orthogonal genomic technologies in the proband. The methylation status of known differentially methylated regions (DMRs) on chromosome 14 revealed that the subject shows the typical methylation pattern of UPD(14)mat. Consistent with these molecular findings, the clinical features overlap with those observed in Temple syndrome, including speech delay. Conclusions These data provide experimental evidence that, in humans, triplication can lead to segmental UPD and imprinting disease. Importantly, genotype/phenotype analyses further reveal how a post-zygotically generated complex structural variant, resulting from a replication-based mutational mechanism, contributes to expanding the clinical phenotype of known genetic syndromes. Mechanistically, such events can distort transmission genetics resulting in homozygosity at a locus for which only one parent is a carrier as well as cause imprinting diseases. Electronic supplementary material The online version of this article (10.1186/s13073-019-0633-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, TX, 77030-3498, USA.
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, TX, 77030-3498, USA
| | - Hadia Hijazi
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, TX, 77030-3498, USA
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, TX, 77030-3498, USA
| | | | | | | | - Sissel Juul
- Oxford Nanopore Technologies Inc, New York, NY, USA.,Oxford Nanopore Technologies Inc, San Francisco, CA, USA
| | | | | | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, TX, 77030-3498, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, TX, 77030-3498, USA
| | - John W Belmont
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, TX, 77030-3498, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, TX, 77030-3498, USA
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, TX, 77030-3498, USA
| | - Neil A Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, TX, 77030-3498, USA
| | - V Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, TX, 77030-3498, USA.,Texas Children's Hospital, Houston, TX, USA
| | | | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Room 604B, Houston, TX, 77030-3498, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.,Texas Children's Hospital, Houston, TX, USA
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43
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Ly P, Brunner SF, Shoshani O, Kim DH, Lan W, Pyntikova T, Flanagan AM, Behjati S, Page DC, Campbell PJ, Cleveland DW. Chromosome segregation errors generate a diverse spectrum of simple and complex genomic rearrangements. Nat Genet 2019; 51:705-715. [PMID: 30833795 PMCID: PMC6441390 DOI: 10.1038/s41588-019-0360-8] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 01/23/2019] [Indexed: 01/05/2023]
Abstract
Cancer genomes are frequently characterized by numerical and structural chromosomal abnormalities. Here we integrated a centromere-specific inactivation approach with selection for a conditionally essential gene, a strategy termed CEN-SELECT, to systematically interrogate the structural landscape of mis-segregated chromosomes. We show that single-chromosome mis-segregation into a micronucleus can directly trigger a broad spectrum of genomic rearrangement types. Cytogenetic profiling revealed that mis-segregated chromosomes exhibit 120-fold-higher susceptibility to developing seven major categories of structural aberrations, including translocations, insertions, deletions, and complex reassembly through chromothripsis coupled to classical non-homologous end joining. Whole-genome sequencing of clonally propagated rearrangements identified random patterns of clustered breakpoints with copy-number alterations resulting in interspersed gene deletions and extrachromosomal DNA amplification events. We conclude that individual chromosome segregation errors during mitotic cell division are sufficient to drive extensive structural variations that recapitulate genomic features commonly associated with human disease.
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Affiliation(s)
- Peter Ly
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA.
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | | | - Ofer Shoshani
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Dong Hyun Kim
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Weijie Lan
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA
| | | | - Adrienne M Flanagan
- University College London Cancer Institute, London, UK
- Department of Histopathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, UK
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - David C Page
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Don W Cleveland
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA.
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44
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Beck CR, Carvalho CMB, Akdemir ZC, Sedlazeck FJ, Song X, Meng Q, Hu J, Doddapaneni H, Chong Z, Chen ES, Thornton PC, Liu P, Yuan B, Withers M, Jhangiani SN, Kalra D, Walker K, English AC, Han Y, Chen K, Muzny DM, Ira G, Shaw CA, Gibbs RA, Hastings PJ, Lupski JR. Megabase Length Hypermutation Accompanies Human Structural Variation at 17p11.2. Cell 2019; 176:1310-1324.e10. [PMID: 30827684 PMCID: PMC6438178 DOI: 10.1016/j.cell.2019.01.045] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 11/06/2018] [Accepted: 01/25/2019] [Indexed: 01/16/2023]
Abstract
DNA rearrangements resulting in human genome structural variants (SVs) are caused by diverse mutational mechanisms. We used long- and short-read sequencing technologies to investigate end products of de novo chromosome 17p11.2 rearrangements and query the molecular mechanisms underlying both recurrent and non-recurrent events. Evidence for an increased rate of clustered single-nucleotide variant (SNV) mutation in cis with non-recurrent rearrangements was found. Indel and SNV formation are associated with both copy-number gains and losses of 17p11.2, occur up to ∼1 Mb away from the breakpoint junctions, and favor C > G transversion substitutions; results suggest that single-stranded DNA is formed during the genesis of the SV and provide compelling support for a microhomology-mediated break-induced replication (MMBIR) mechanism for SV formation. Our data show an additional mutational burden of MMBIR consisting of hypermutation confined to the locus and manifesting as SNVs and indels predominantly within genes.
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Affiliation(s)
- Christine R Beck
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | | | - Zeynep C Akdemir
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | | | - Xiaofei Song
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Qingchang Meng
- Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | - Jianhong Hu
- Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | | | - Zechen Chong
- Department of Genetics and the Informatics Institute, the University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Edward S Chen
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Philip C Thornton
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Bo Yuan
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Marjorie Withers
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | | | - Divya Kalra
- Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | | | - Adam C English
- Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | - Yi Han
- Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | - Grzegorz Ira
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | - P J Hastings
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, BCM, Houston, TX 77030, USA.
| | - James R Lupski
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Human Genome Sequencing Center, BCM, Houston, TX 77030, USA; Department of Pediatrics, BCM, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, BCM, Houston, TX 77030, USA.
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45
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Lupski JR. 2018 Victor A. McKusick Leadership Award: Molecular Mechanisms for Genomic and Chromosomal Rearrangements. Am J Hum Genet 2019; 104:391-406. [PMID: 30849326 PMCID: PMC6407437 DOI: 10.1016/j.ajhg.2018.12.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, and Texas Children's Hospital, Houston, TX 77030, USA.
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46
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Bazrgar M, Gourabi H, Karimpour-Fard A, Boroujeni PB, Anisi K, Movaghar B, Valojerdi MR. Origins of Intraindividual Genetic Variation in Human Fetuses. Reprod Sci 2018; 26:1139-1145. [PMID: 30453833 DOI: 10.1177/1933719118808919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Intraindividual copy number variation (CNV) origin is largely unknown. They might be due to aging and/or common genome instability at the preimplantation stage while contribution of preimplantation in human intraindividual CNVs occurrence is unknown. To address this question, we investigated mosaicism and its origin in the fetuses of natural conception. METHODS We studied normal fetuses following therapeutic abortion due to maternal indications. We analyzed the genome of 22 tissues of each fetus by array comparative genomic hybridization for intraindividual CNVs. Each tissue was studied in 2 microarray experiments; the reciprocal aberrations larger than 40 Kb, identified by comparing tissues of each fetus, were subsequently validated using quantitative polymerase chain reaction. RESULTS Through intraindividual comparison, frequency of reciprocal events varied from 2 to 9. According to the distribution pattern of the frequent CNV in derivatives of different germ layers, we found that its origin is early development including preimplantation, whereas CNVs with low frequency have occurred in later stages. Shared CNVs in both fetuses were belonged to thymus and related to the functional role of genes located in these CNVs. CONCLUSIONS The origin of some of fetal CNVs is preimplantation stage. Each organ might inherit CNVs with an unpredictable pattern due to the extensive cell mixing/migration in embryonic development.
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Affiliation(s)
- Masood Bazrgar
- 1 Department of Genetics, Reproductive Biomedicine Research Centre, Royan Institute for Reproductive Biomedicine, Tehran, Iran
- authors share the first authorship for this article
| | - Hamid Gourabi
- 1 Department of Genetics, Reproductive Biomedicine Research Centre, Royan Institute for Reproductive Biomedicine, Tehran, Iran
- authors share the first authorship for this article
| | - Anis Karimpour-Fard
- 2 Department of Pharmacology, University of Colorado, Anschutz Medical Campus, Aurora, Colorado
| | - Parnaz Borjian Boroujeni
- 1 Department of Genetics, Reproductive Biomedicine Research Centre, Royan Institute for Reproductive Biomedicine, Tehran, Iran
| | - Khadije Anisi
- 1 Department of Genetics, Reproductive Biomedicine Research Centre, Royan Institute for Reproductive Biomedicine, Tehran, Iran
| | - Bahar Movaghar
- 3 Department of Embryology, Reproductive Biomedicine Research Centre, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Mojtaba Rezazadeh Valojerdi
- 3 Department of Embryology, Reproductive Biomedicine Research Centre, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
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48
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Song X, Beck CR, Du R, Campbell IM, Coban-Akdemir Z, Gu S, Breman AM, Stankiewicz P, Ira G, Shaw CA, Lupski JR. Predicting human genes susceptible to genomic instability associated with Alu/ Alu-mediated rearrangements. Genome Res 2018; 28:1228-1242. [PMID: 29907612 PMCID: PMC6071635 DOI: 10.1101/gr.229401.117] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 06/06/2018] [Indexed: 12/14/2022]
Abstract
Alu elements, the short interspersed element numbering more than 1 million copies per human genome, can mediate the formation of copy number variants (CNVs) between substrate pairs. These Alu/Alu-mediated rearrangements (AAMRs) can result in pathogenic variants that cause diseases. To investigate the impact of AAMR on gene variation and human health, we first characterized Alus that are involved in mediating CNVs (CNV-Alus) and observed that these Alus tend to be evolutionarily younger. We then computationally generated, with the assistance of a supercomputer, a test data set consisting of 78 million Alu pairs and predicted ∼18% of them are potentially susceptible to AAMR. We further determined the relative risk of AAMR in 12,074 OMIM genes using the count of predicted CNV-Alu pairs and experimentally validated the predictions with 89 samples selected by correlating predicted hotspots with a database of CNVs identified by clinical chromosomal microarrays (CMAs) on the genomes of approximately 54,000 subjects. We fine-mapped 47 duplications, 40 deletions, and two complex rearrangements and examined a total of 52 breakpoint junctions of simple CNVs. Overall, 94% of the candidate breakpoints were at least partially Alu mediated. We successfully predicted all (100%) of Alu pairs that mediated deletions (n = 21) and achieved an 87% positive predictive value overall when including AAMR-generated deletions and duplications. We provided a tool, AluAluCNVpredictor, for assessing AAMR hotspots and their role in human disease. These results demonstrate the utility of our predictive model and provide insights into the genomic features and molecular mechanisms underlying AAMR.
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Affiliation(s)
- Xiaofei Song
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Christine R Beck
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Renqian Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Ian M Campbell
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Shen Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Amy M Breman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Baylor Genetics, Houston, Texas 77021, USA
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Baylor Genetics, Houston, Texas 77021, USA
| | - Grzegorz Ira
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Baylor Genetics, Houston, Texas 77021, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
- Texas Children's Hospital, Houston, Texas 77030, USA
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Grochowski CM, Gu S, Yuan B, Tcw J, Brennand KJ, Sebat J, Malhotra D, McCarthy S, Rudolph U, Lindstrand A, Chong Z, Levy DL, Lupski JR, Carvalho CMB. Marker chromosome genomic structure and temporal origin implicate a chromoanasynthesis event in a family with pleiotropic psychiatric phenotypes. Hum Mutat 2018; 39:939-946. [PMID: 29696747 PMCID: PMC5995661 DOI: 10.1002/humu.23537] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 04/11/2018] [Accepted: 04/16/2018] [Indexed: 12/13/2022]
Abstract
Small supernumerary marker chromosomes (sSMC) are chromosomal fragments difficult to characterize genomically. Here, we detail a proband with schizoaffective disorder and a mother with bipolar disorder with psychotic features who present with a marker chromosome that segregates with disease. We explored the architecture of this marker and investigated its temporal origin. Array comparative genomic hybridization (aCGH) analysis revealed three duplications and three triplications that spanned the short arm of chromosome 9, suggestive of a chromoanasynthesis-like event. Segregation of marker genotypes, phased using sSMC mosaicism in the mother, provided evidence that it was generated during a germline-level event in the proband's maternal grandmother. Whole-genome sequencing (WGS) was performed to resolve the structure and junctions of the chromosomal fragments, revealing further complexities. While structural variations have been previously associated with neuropsychiatric disorders and marker chromosomes, here we detail the precise architecture, human life-cycle genesis, and propose a DNA replicative/repair mechanism underlying formation.
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Affiliation(s)
| | - Shen Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Julia Tcw
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Kristen J Brennand
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jonathan Sebat
- Beyster Center for Psychiatric Genomics, Department of Psychiatry, University of California at San Diego, San Diego, California
| | | | - Shane McCarthy
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | - Uwe Rudolph
- Laboratory of Genetic Neuropharmacology, McLean Hospital, Belmont, Massachusetts
- Department of Psychiatry, Harvard Medical School, Boston, Massachusetts
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Zechen Chong
- Department of Genetics and the Informatics Institute, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Deborah L Levy
- Department of Psychiatry, Harvard Medical School, Boston, Massachusetts
- Psychology Research Laboratory, McLean Hospital, Belmont, Massachusetts
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- Texas Children's Hospital, Houston, Texas
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
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Integrating CNVs into meta-QTL identified GBP4 as positional candidate for adult cattle stature. Funct Integr Genomics 2018; 18:559-567. [PMID: 29737453 DOI: 10.1007/s10142-018-0613-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 04/21/2018] [Accepted: 04/24/2018] [Indexed: 02/03/2023]
Abstract
Copy number variation (CNV) of DNA sequences, functionally significant but yet fully ascertained, is believed to confer considerable increments in unexplained heritability of quantitative traits. Identification of phenotype-associated CNVs (paCNVs) therefore is a pressing need in CNV studies to speed up their exploitation in cattle breeding programs. Here, we provided a new avenue to achieve this goal that is to project the published CNV data onto meta-quantitative trait loci (meta-QTL) map which connects causal genes with phenotypes. Any CNVs overlapping meta-QTL therefore will be potential paCNVs. This study reported potential paCNVs in Bos taurus autosome 3 (BTA3). Notably, overview indexes and CNVs both highlighted a narrower region (BTA3 54,500,000-55,000,000 bp, named BTA3_INQTL_6) within one constructed meta-QTL. Then, we ascertained guanylate-binding protein 4 (GBP4) among the nine positional candidate genes was significantly associated with adult cattle stature, including body weight (BW, P < 0.05) and withers height (WHT, P < 0.05), fitting GBP4 CNV either with three levels or with six levels in the model. Although higher copy number downregulated the mRNA levels of GBP2 (P < 0.05) and GBP4 (P < 0.05) in 1-Mb window (54.0-55.0 Mb) in muscle and adipose, additional analyses will be needed to clarify the causality behind the ascertained association.
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