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Szafranski P, Kośmider E, Liu Q, Karolak JA, Currie L, Parkash S, Kahler SG, Roeder E, Littlejohn RO, DeNapoli TS, Shardonofsky FR, Henderson C, Powers G, Poisson V, Bérubé D, Oligny L, Michaud JL, Janssens S, De Coen K, Van Dorpe J, Dheedene A, Harting MT, Weaver MD, Khan AM, Tatevian N, Wambach J, Gibbs KA, Popek E, Gambin A, Stankiewicz P. LINE- and Alu-containing genomic instability hotspot at 16q24.1 associated with recurrent and nonrecurrent CNV deletions causative for ACDMPV. Hum Mutat 2018; 39:1916-1925. [PMID: 30084155 DOI: 10.1002/humu.23608] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 08/01/2018] [Accepted: 08/02/2018] [Indexed: 01/20/2023]
Abstract
Transposable elements modify human genome by inserting into new loci or by mediating homology-, microhomology-, or homeology-driven DNA recombination or repair, resulting in genomic structural variation. Alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV) is a rare lethal neonatal developmental lung disorder caused by point mutations or copy-number variant (CNV) deletions of FOXF1 or its distant tissue-specific enhancer. Eighty-five percent of 45 ACDMPV-causative CNV deletions, of which junctions have been sequenced, had at least one of their two breakpoints located in a retrotransposon, with more than half of them being Alu elements. We describe a novel ∼35 kb-large genomic instability hotspot at 16q24.1, involving two evolutionarily young LINE-1 (L1) elements, L1PA2 and L1PA3, flanking AluY, two AluSx, AluSx1, and AluJr elements. The occurrence of L1s at this location coincided with the branching out of the Homo-Pan-Gorilla clade, and was preceded by the insertion of AluSx, AluSx1, and AluJr. Our data show that, in addition to mediating recurrent CNVs, L1 and Alu retrotransposons can predispose the human genome to formation of variably sized CNVs, both of clinical and evolutionary relevance. Nonetheless, epigenetic or other genomic features of this locus might also contribute to its increased instability.
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Affiliation(s)
- Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Ewelina Kośmider
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
| | - Qian Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Justyna A Karolak
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | - Lauren Currie
- Maritime Medical Genetics Service, IWK Health Centre, Halifax, Canada
| | - Sandhya Parkash
- Maritime Medical Genetics Service, IWK Health Centre, Halifax, Canada
| | - Stephen G Kahler
- Section of Genetics and Metabolism, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Elizabeth Roeder
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Department of Pediatrics, Baylor College of Medicine, San Antonio, Texas
| | | | - Thomas S DeNapoli
- Department of Pathology, Children's Hospital of San Antonio, San Antonio, Texas
| | - Felix R Shardonofsky
- Pediatric Pulmonary Center, Children's Hospital of San Antonio, San Antonio, Texas
| | - Cody Henderson
- Department of Pediatrics, Baylor College of Medicine, San Antonio, Texas.,Neonatal-Perinatal Medicine, Children's Hospital of San Antonio, San Antonio, Texas
| | - George Powers
- Department of Pediatrics, Baylor College of Medicine, San Antonio, Texas.,Neonatal-Perinatal Medicine, Children's Hospital of San Antonio, San Antonio, Texas
| | | | | | | | | | - Sandra Janssens
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Kris De Coen
- Department of Neonatal Intensive Care, Ghent University, Ghent, Belgium
| | - Jo Van Dorpe
- Department of Pathology, Ghent University, Ghent, Belgium
| | | | | | | | - Amir M Khan
- McGovern Medical School at UTHealth, Houston, Texas
| | | | - Jennifer Wambach
- Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Kathleen A Gibbs
- Children's Hospital of Philadelphia, and University of Pennsylvania, Philadelphia, Pennsylvania
| | - Edwina Popek
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
| | - Anna Gambin
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
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Glessner JT, Bick AG, Ito K, Homsy J, Rodriguez-Murillo L, Fromer M, Mazaika E, Vardarajan B, Italia M, Leipzig J, DePalma SR, Golhar R, Sanders SJ, Yamrom B, Ronemus M, Iossifov I, Willsey AJ, State MW, Kaltman JR, White PS, Shen Y, Warburton D, Brueckner M, Seidman C, Goldmuntz E, Gelb BD, Lifton R, Seidman J, Hakonarson H, Chung WK. Increased frequency of de novo copy number variants in congenital heart disease by integrative analysis of single nucleotide polymorphism array and exome sequence data. Circ Res 2014; 115:884-896. [PMID: 25205790 DOI: 10.1161/circresaha.115.304458] [Citation(s) in RCA: 175] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
RATIONALE Congenital heart disease (CHD) is among the most common birth defects. Most cases are of unknown pathogenesis. OBJECTIVE To determine the contribution of de novo copy number variants (CNVs) in the pathogenesis of sporadic CHD. METHODS AND RESULTS We studied 538 CHD trios using genome-wide dense single nucleotide polymorphism arrays and whole exome sequencing. Results were experimentally validated using digital droplet polymerase chain reaction. We compared validated CNVs in CHD cases with CNVs in 1301 healthy control trios. The 2 complementary high-resolution technologies identified 63 validated de novo CNVs in 51 CHD cases. A significant increase in CNV burden was observed when comparing CHD trios with healthy trios, using either single nucleotide polymorphism array (P=7×10(-5); odds ratio, 4.6) or whole exome sequencing data (P=6×10(-4); odds ratio, 3.5) and remained after removing 16% of de novo CNV loci previously reported as pathogenic (P=0.02; odds ratio, 2.7). We observed recurrent de novo CNVs on 15q11.2 encompassing CYFIP1, NIPA1, and NIPA2 and single de novo CNVs encompassing DUSP1, JUN, JUP, MED15, MED9, PTPRE SREBF1, TOP2A, and ZEB2, genes that interact with established CHD proteins NKX2-5 and GATA4. Integrating de novo variants in whole exome sequencing and CNV data suggests that ETS1 is the pathogenic gene altered by 11q24.2-q25 deletions in Jacobsen syndrome and that CTBP2 is the pathogenic gene in 10q subtelomeric deletions. CONCLUSIONS We demonstrate a significantly increased frequency of rare de novo CNVs in CHD patients compared with healthy controls and suggest several novel genetic loci for CHD.
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Affiliation(s)
- Joseph T Glessner
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | | | - Kaoru Ito
- Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Jason Homsy
- Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Laura Rodriguez-Murillo
- Mindich Child Health and Development Institute, Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Menachem Fromer
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Psychiatric Genomics in the Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Erica Mazaika
- Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Badri Vardarajan
- Systems Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Michael Italia
- Center for Biomedical Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jeremy Leipzig
- Center for Biomedical Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | | | - Ryan Golhar
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Stephan J Sanders
- Genetics, Yale University, New Haven, CT 06520, USA.,Psychiatry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Boris Yamrom
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Michael Ronemus
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Ivan Iossifov
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - A Jeremy Willsey
- Genetics, Yale University, New Haven, CT 06520, USA.,Psychiatry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Matthew W State
- Genetics, Yale University, New Haven, CT 06520, USA.,Psychiatry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jonathan R Kaltman
- Cardiovascular Sciences, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, MD 20892, USA
| | - Peter S White
- Center for Biomedical Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yufeng Shen
- Systems Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Dorothy Warburton
- Genetics and Development (in Medicine), Columbia University Medical Center, New York, NY 10032, USA
| | | | | | - Elizabeth Goldmuntz
- Cardiology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Bruce D Gelb
- Mindich Child Health and Development Institute, Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Richard Lifton
- Genetics, Yale University, New Haven, CT 06520, USA.,Medicine, Yale University, New Haven, CT 06520, USA
| | | | - Hakon Hakonarson
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Wendy K Chung
- Pediatrics and Medicine, Columbia University Medical Center, New York, NY 10032, USA
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3
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Verkerk AJMH, Schot R, van Waterschoot L, Douben H, Poddighe PJ, Lequin MH, de Vries LS, Terhal P, Hahnemann JMD, de Coo IFM, de Wit MCY, Wafelman LS, Garavelli L, Dobyns WB, Van der Spek PJ, de Klein A, Mancini GMS. Unbalanced der(5)t(5;20) translocation associated with megalencephaly, perisylvian polymicrogyria, polydactyly and hydrocephalus. Am J Med Genet A 2010; 152A:1488-97. [PMID: 20503325 DOI: 10.1002/ajmg.a.33408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The combination of megalencephaly, perisylvian polymicrogyria, polydactyly and hydrocephalus (MPPH) is a rare syndrome of unknown cause. We observed two first cousins affected by an MPPH-like phenotype with a submicroscopic chromosome 5q35 deletion as a result of an unbalanced der(5)t(5;20)(q35.2;q13.3) translocation, including the NSD1 Sotos syndrome locus. We describe the phenotype and the deletion breakpoints of the two MPPH-like patients and compare these with five unrelated MPPH and Sotos patients harboring a 5q35 microdeletion. Mapping of the breakpoints in the two cousins was performed by MLPA, FISH, high density SNP-arrays and Q-PCR for the 5q35 deletion and 20q13 duplication. The 5q35 deletion area of the two cousins almost completely overlaps with earlier described patients with an atypical Sotos microdeletion, except for the DRD1 gene. The five unrelated MPPH patients neither showed submicroscopic chromosomal aberrations nor DRD1 mutations. We reviewed the brain MRI of 10 Sotos patients and did not detect polymicrogyria in any of them. In our two cousins, the MPPH-like phenotype is probably caused by the contribution of genes on both chromosome 5q35 and 20q13. Some patients with MPPH may harbor a submicroscopic chromosomal aberration and therefore high-resolution array analysis should be part of the diagnostic workup.
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