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Vervoort L, Vermeesch JR. The 22q11.2 Low Copy Repeats. Genes (Basel) 2022; 13:2101. [PMID: 36421776 PMCID: PMC9690962 DOI: 10.3390/genes13112101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/19/2022] [Accepted: 10/25/2022] [Indexed: 07/22/2023] Open
Abstract
LCR22s are among the most complex loci in the human genome and are susceptible to nonallelic homologous recombination. This can lead to a variety of genomic disorders, including deletions, duplications, and translocations, of which the 22q11.2 deletion syndrome is the most common in humans. Interrogating these phenomena is difficult due to the high complexity of the LCR22s and the inaccurate representation of the LCRs across different reference genomes. Optical mapping techniques, which provide long-range chromosomal maps, could be used to unravel the complex duplicon structure. These techniques have already uncovered the hypervariability of the LCR22-A haplotype in the human population. Although optical LCR22 mapping is a major step forward, long-read sequencing approaches will be essential to reach nucleotide resolution of the LCR22s and map the crossover sites. Accurate maps and sequences are needed to pinpoint potential predisposing alleles and, most importantly, allow for genotype-phenotype studies exploring the role of the LCR22s in health and disease. In addition, this research might provide a paradigm for the study of other rare genomic disorders.
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Vervoort L, Demaerel W, Rengifo LY, Odrzywolski A, Vergaelen E, Hestand MS, Breckpot J, Devriendt K, Swillen A, McDonald-McGinn DM, Fiksinski AM, Zinkstok JR, Morrow BE, Heung T, Vorstman JAS, Bassett AS, Chow EWC, Shashi V, Vermeesch JR. Atypical chromosome 22q11.2 deletions are complex rearrangements and have different mechanistic origins. Hum Mol Genet 2019; 28:3724-3733. [PMID: 31884517 PMCID: PMC6935389 DOI: 10.1093/hmg/ddz166] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/03/2019] [Accepted: 07/08/2019] [Indexed: 11/13/2022] Open
Abstract
The majority (99%) of individuals with 22q11.2 deletion syndrome (22q11.2DS) have a deletion that is caused by non-allelic homologous recombination between two of four low copy repeat clusters on chromosome 22q11.2 (LCR22s). However, in a small subset of patients, atypical deletions are observed with at least one deletion breakpoint within unique sequence between the LCR22s. The position of the chromosome breakpoints and the mechanisms driving those atypical deletions remain poorly studied. Our large-scale, whole genome sequencing study of >1500 subjects with 22q11.2DS identified six unrelated individuals with atypical deletions of different types. Using a combination of whole genome sequencing data and fiber-fluorescence in situ hybridization, we mapped the rearranged alleles in these subjects. In four of them, the distal breakpoints mapped within one of the LCR22s and we found that the deletions likely occurred by replication-based mechanisms. Interestingly, in two of them, an inversion probably preceded inter-chromosomal 'allelic' homologous recombination between differently oriented LCR22-D alleles. Inversion associated allelic homologous recombination (AHR) may well be a common mechanism driving (atypical) deletions on 22q11.2.
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Affiliation(s)
| | | | | | - Adrian Odrzywolski
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Lublin, Poland
| | - Elfi Vergaelen
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Matthew S Hestand
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | | | - Koen Devriendt
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Ann Swillen
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Donna M McDonald-McGinn
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ania M Fiksinski
- Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
- The Dalglish Family 22q Clinic and Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Janneke R Zinkstok
- Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bernice E Morrow
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Tracy Heung
- The Dalglish Family 22q Clinic and Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Jacob A S Vorstman
- Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
- The Dalglish Family 22q Clinic and Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Anne S Bassett
- The Dalglish Family 22q Clinic and Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Eva W C Chow
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
- Clinical Genetics Service, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Vandana Shashi
- Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA
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3
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Motahari Z, Moody SA, Maynard TM, LaMantia AS. In the line-up: deleted genes associated with DiGeorge/22q11.2 deletion syndrome: are they all suspects? J Neurodev Disord 2019; 11:7. [PMID: 31174463 PMCID: PMC6554986 DOI: 10.1186/s11689-019-9267-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 04/21/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND 22q11.2 deletion syndrome (22q11DS), a copy number variation (CNV) disorder, occurs in approximately 1:4000 live births due to a heterozygous microdeletion at position 11.2 (proximal) on the q arm of human chromosome 22 (hChr22) (McDonald-McGinn and Sullivan, Medicine 90:1-18, 2011). This disorder was known as DiGeorge syndrome, Velo-cardio-facial syndrome (VCFS) or conotruncal anomaly face syndrome (CTAF) based upon diagnostic cardiovascular, pharyngeal, and craniofacial anomalies (McDonald-McGinn and Sullivan, Medicine 90:1-18, 2011; Burn et al., J Med Genet 30:822-4, 1993) before this phenotypic spectrum was associated with 22q11.2 CNVs. Subsequently, 22q11.2 deletion emerged as a major genomic lesion associated with vulnerability for several clinically defined behavioral deficits common to a number of neurodevelopmental disorders (Fernandez et al., Principles of Developmental Genetics, 2015; Robin and Shprintzen, J Pediatr 147:90-6, 2005; Schneider et al., Am J Psychiatry 171:627-39, 2014). RESULTS The mechanistic relationships between heterozygously deleted 22q11.2 genes and 22q11DS phenotypes are still unknown. We assembled a comprehensive "line-up" of the 36 protein coding loci in the 1.5 Mb minimal critical deleted region on hChr22q11.2, plus 20 protein coding loci in the distal 1.5 Mb that defines the 3 Mb typical 22q11DS deletion. We categorized candidates based upon apparent primary cell biological functions. We analyzed 41 of these genes that encode known proteins to determine whether haploinsufficiency of any single 22q11.2 gene-a one gene to one phenotype correspondence due to heterozygous deletion restricted to that locus-versus complex multigenic interactions can account for single or multiple 22q11DS phenotypes. CONCLUSIONS Our 22q11.2 functional genomic assessment does not support current theories of single gene haploinsufficiency for one or all 22q11DS phenotypes. Shared molecular functions, convergence on fundamental cell biological processes, and related consequences of individual 22q11.2 genes point to a matrix of multigenic interactions due to diminished 22q11.2 gene dosage. These interactions target fundamental cellular mechanisms essential for development, maturation, or homeostasis at subsets of 22q11DS phenotypic sites.
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Affiliation(s)
- Zahra Motahari
- The Institute for Neuroscience, and Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, Washington DC, 20037 USA
| | - Sally Ann Moody
- The Institute for Neuroscience, and Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, Washington DC, 20037 USA
| | - Thomas Michael Maynard
- The Institute for Neuroscience, and Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, Washington DC, 20037 USA
| | - Anthony-Samuel LaMantia
- The Institute for Neuroscience, and Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, Washington DC, 20037 USA
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4
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Ittleman BR, Mckissick J, Bosanko KA, Ocal E, Golinko M, Zarate YA. Less common underlying genetic diagnoses found in a cohort of 139 individuals surgically corrected for craniosynostosis. Am J Med Genet A 2017; 176:487-491. [PMID: 29160013 DOI: 10.1002/ajmg.a.38532] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 10/09/2017] [Accepted: 10/15/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Benjamin R Ittleman
- Department of Pediatrics, Arkansas Children's Hospital, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Jasmine Mckissick
- University of Arkansas for Medical Sciences College of Medicine, Little Rock, Arkansas
| | - Katherine A Bosanko
- Section of Genetics and Metabolism, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Eylem Ocal
- Department of Neurosurgery, Arkansas Children's Hospital, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Michael Golinko
- Division of Plastic Surgery, Department of Surgery, Arkansas Children's Hospital, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Yuri A Zarate
- Section of Genetics and Metabolism, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas
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5
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Carvalho CMB, Lupski JR. Mechanisms underlying structural variant formation in genomic disorders. Nat Rev Genet 2016; 17:224-38. [PMID: 26924765 DOI: 10.1038/nrg.2015.25] [Citation(s) in RCA: 414] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
With the recent burst of technological developments in genomics, and the clinical implementation of genome-wide assays, our understanding of the molecular basis of genomic disorders, specifically the contribution of structural variation to disease burden, is evolving quickly. Ongoing studies have revealed a ubiquitous role for genome architecture in the formation of structural variants at a given locus, both in DNA recombination-based processes and in replication-based processes. These reports showcase the influence of repeat sequences on genomic stability and structural variant complexity and also highlight the tremendous plasticity and dynamic nature of our genome in evolution, health and disease susceptibility.
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Affiliation(s)
- Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Centro de Pesquisas René Rachou - FIOCRUZ, Belo Horizonte, MG 30190-002, Brazil
| | - 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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6
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Gollo Dantas A, Bortolai A, Moysés-Oliveira M, Takeno Herrero S, Azoubel Antunes A, Tavares Costa-Carvalho B, Ayres Meloni V, Melaragno MI. 22q11.2 Deletion Syndrome due to a Translocation t(6;22) in a Patient Conceived via in vitro Fertilization. Mol Syndromol 2015; 6:242-7. [PMID: 26997945 DOI: 10.1159/000441243] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2015] [Indexed: 11/19/2022] Open
Abstract
We report on a patient conceived via in vitro fertilization (IVF) with a 22q11.2 deletion due to an unusual unbalanced translocation involving chromosomes 6 and 22 in a karyotype with 45 chromosomes. Cytogenomic studies showed that the patient has a 3.3-Mb deletion of chromosome 22q and a 0.4-Mb deletion of chromosome 6p, which resulted in haploinsufficiency of the genes responsible for the 22q11.2 deletion syndrome and also of the IRF4 gene, a member of the interferon regulatory factor family of transcription factors, which is expressed in the immune system cells. The rearrangement could be due to the manipulation of the embryo or as a sporadic event unrelated to IVF. Translocation involving chromosome 22 in a karyotype with 45 chromosomes is a rare event, with no previous reports involving chromosomes 6p and 22q.
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Affiliation(s)
- Anelisa Gollo Dantas
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, Brazil
| | - Adriana Bortolai
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, Brazil; Cytogenetics Division, Hospital do Servidor Público do Estado de São Paulo, São Paulo, Brazil
| | - Mariana Moysés-Oliveira
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, Brazil
| | - Sylvia Takeno Herrero
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, Brazil
| | | | | | - Vera Ayres Meloni
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, Brazil
| | - Maria Isabel Melaragno
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, Brazil
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Poirsier C, Besseau-Ayasse J, Schluth-Bolard C, Toutain J, Missirian C, Le Caignec C, Bazin A, de Blois MC, Kuentz P, Catty M, Choiset A, Plessis G, Basinko A, Letard P, Flori E, Jimenez M, Valduga M, Landais E, Lallaoui H, Cartault F, Lespinasse J, Martin-Coignard D, Callier P, Pebrel-Richard C, Portnoi MF, Busa T, Receveur A, Amblard F, Yardin C, Harbuz R, Prieur F, Le Meur N, Pipiras E, Kleinfinger P, Vialard F, Doco-Fenzy M. A French multicenter study of over 700 patients with 22q11 deletions diagnosed using FISH or aCGH. Eur J Hum Genet 2015; 24:844-51. [PMID: 26508576 DOI: 10.1038/ejhg.2015.219] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 09/02/2015] [Accepted: 09/08/2015] [Indexed: 12/31/2022] Open
Abstract
Although 22q11.2 deletion syndrome (22q11.2DS) is the most recurrent human microdeletion syndrome associated with a highly variable phenotype, little is known about the condition's true incidence and the phenotype at diagnosis. We performed a multicenter, retrospective analysis of postnatally diagnosed patients recruited by members of the Association des Cytogénéticiens de Langue Française (the French-Speaking Cytogeneticists Association). Clinical and cytogenetic data on 749 cases diagnosed between 1995 and 2013 were collected by 31 French cytogenetics laboratories. The most frequent reasons for referral of postnatally diagnosed cases were a congenital heart defect (CHD, 48.6%), facial dysmorphism (49.7%) and developmental delay (40.7%). Since 2007 (the year in which array comparative genomic hybridization (aCGH) was introduced for the routine screening of patients with intellectual disability), almost all cases have been diagnosed using FISH (96.1%). Only 15 cases (all with an atypical phenotype) were diagnosed with aCGH; the deletion size ranged from 745 to 2904 kb. The deletion was inherited in 15.0% of cases and was of maternal origin in 85.5% of the latter. This is the largest yet documented cohort of patients with 22q11.2DS (the most commonly diagnosed microdeletion) from the same population. French cytogenetics laboratories diagnosed at least 108 affected patients (including fetuses) per year from among a national population of ∼66 million. As observed for prenatal diagnoses, CHDs were the most frequently detected malformation in postnatal diagnoses. The most common CHD in postnatal diagnoses was an isolated septal defect.
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Affiliation(s)
| | | | | | | | | | - Cédric Le Caignec
- CHU Nantes, Service de Génétique Médicale, Inserm UMR957, Faculté de Médecine, Nantes, France
| | - Anne Bazin
- Laboratoire de Cytogénétique Pasteur-Cerba, Saint-Ouen l'Aumône, France
| | - Marie Christine de Blois
- Service de Cytogénétique, CHU de Necker, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Paul Kuentz
- Service de Cytogénétique, CHU de Besançon, Besançon, France
| | - Marie Catty
- Service de Cytogénétique, Biolille, Lille, France
| | - Agnès Choiset
- Service de Cytogénétique, Hôpital Saint Vincent de Paul, Paris, France
| | - Ghislaine Plessis
- Laboratoire de Cytogénétique Postnatal, CHU Clemenceau, Caen, France
| | - Audrey Basinko
- Service de Cytogénétique et Biologie de la Reproduction, CHRU de Brest, Brest, France
| | | | - Elisabeth Flori
- Service de Cytogénétique, CHU de Strasbourg, Strasbourg, France
| | | | | | | | | | - François Cartault
- Service de Cytogénétique, Hôpital de Saint-Denis, Saint-Denis de la Réunion, France
| | | | | | | | - Céline Pebrel-Richard
- Univ Clermont 1, UFR Médecine, Histologie Embryologie Cytogénétique, Clermont-Ferrand, France.,CHU-Estaing Clermont-Ferrand, Cytogénétique Médicale, Clermont-Ferrand, France.,EA 4677 ERTICA, Univ Clermont 1, UFR Médecine, Clermont-Ferrand, France
| | | | - Tiffany Busa
- Departement de Genétique Medicale, Hopital de la Timone, CHU de Marseille, Marseille, France
| | | | | | | | - Radu Harbuz
- Service de Génétique, CHU de Poitiers, Poitiers, France
| | - Fabienne Prieur
- Service de Cytogénétique, CHU de Saint-Etienne, Saint-Etienne, France
| | - Nathalie Le Meur
- Service de Cytogénétique, Etablissement Français du Sang de Normandie, Rouen, France
| | - Eva Pipiras
- Hôpital Jean Verdier, UF de Cytogénétique, CHU Paris, Paris, France.,Université Paris 13, Sorbonne Paris Cité, INSERM 1141, Paris, France
| | - Pascale Kleinfinger
- Laboratoire de Cytogénétique Pasteur-Cerba, Saint-Ouen l'Aumône, France.,Association des Cytogénéticiens de Langue Française (French-Speaking Cytogeneticists Association), Paris, France
| | - François Vialard
- Service de Cytogénétique, Hôpital Poissy/Saint-Germain-en-Laye, Poissy, France.,Association des Cytogénéticiens de Langue Française (French-Speaking Cytogeneticists Association), Paris, France.,GIG, UVSQ, Versailles, Paris, France
| | - Martine Doco-Fenzy
- Département de Génétique, CHU de Reims, Reims, France.,Association des Cytogénéticiens de Langue Française (French-Speaking Cytogeneticists Association), Paris, France.,EA3801, SFR-CAP Santé, Reims, France
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8
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Burnside RD. 22q11.21 Deletion Syndromes: A Review of Proximal, Central, and Distal Deletions and Their Associated Features. Cytogenet Genome Res 2015; 146:89-99. [PMID: 26278718 DOI: 10.1159/000438708] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2015] [Indexed: 04/13/2024] Open
Abstract
Chromosome 22q11.21 contains a cluster of low-copy repeats (LCRs), referred to as LCR22A-H, that mediate meiotic non-allelic homologous recombination, resulting in either deletion or duplication of various intervals in the region. The deletion of the DiGeorge/velocardiofacial syndrome interval LCR22A-D is the most common recurrent microdeletion in humans, with an estimated incidence of ∼1:4,000 births. Deletion of other intervals in 22q11.21 have also been described, but the literature is often confusing, as the terms 'proximal', 'nested', 'distal', and 'atypical' have all been used to describe various of the other intervals. Individuals with deletions tend to have features with widely variable expressivity, even among families. This review concisely delineates each interval and classifies the reported literature accordingly.
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Affiliation(s)
- Rachel D Burnside
- Department of Cytogenetics, Laboratory Corporation of America Holdings, Center for Molecular Biology and Pathology, Research Triangle Park, N.C., USA
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9
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Goldmuntz E, Paluru P, Glessner J, Hakonarson H, Biegel JA, White PS, Gai X, Shaikh TH. Microdeletions and microduplications in patients with congenital heart disease and multiple congenital anomalies. CONGENIT HEART DIS 2011; 6:592-602. [PMID: 22010865 DOI: 10.1111/j.1747-0803.2011.00582.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
OBJECTIVE Multiple genetic syndromes are caused by recurrent chromosomal microdeletions or microduplications. The increasing use of high-resolution microarrays in clinical analysis has allowed the identification of previously undetectable submicroscopic copy number variants (CNVs) associated with genetic disorders. We hypothesized that patients with congenital heart disease and additional dysmorphic features or other anomalies would be likely to harbor previously undetected CNVs, which might identify new disease loci or disease-related genes for various cardiac defects. DESIGN Copy number analysis with single nucleotide polymorphism-based, oligonucleotide microarrays was performed on 58 patients with congenital heart disease and other dysmorphic features and/or other anomalies. The observed CNVs were validated using independent techniques and validated CNVs were further analyzed using computational algorithms and comparison with available control CNV datasets in order to assess their pathogenic potential. RESULTS Potentially pathogenic CNVs were detected in twelve of 58 patients (20.7%), ranging in size from 240 Kb to 9.6 Mb. These CNVs contained between 1 and 55 genes, including NRP1, NTRK3, MESP1, ADAM19, and HAND1, all of which are known to participate in cardiac development. CONCLUSIONS Genome-wide analysis in patients with congenital heart disease and additional phenotypes has identified potentially pathogenic CNVs affecting genes involved in cardiac development. The identified variant loci and the genes within them warrant further evaluation in similarly syndromic and nonsyndromic cardiac cohorts.
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Affiliation(s)
- Elizabeth Goldmuntz
- Divisions of Cardiology Human Genetics Oncology Center for Applied Genomics Center for Biomedical Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
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10
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Tan TY, Gordon CT, Amor DJ, Farlie PG. Developmental perspectives on copy number abnormalities of the 22q11.2 region. Clin Genet 2010; 78:201-18. [DOI: 10.1111/j.1399-0004.2010.01456.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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11
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Pacanaro ANX, Christofolini DM, Kulikowski LD, Belangero SIN, da Silva Bellucco FT, Varela MC, Koiffmann CP, Yoshimoto M, Squire JA, Schiavon AV, Heck B, Melaragno MI. A rare case of trisomy 15pter-q21.2 due to a de novo marker chromosome. Am J Med Genet A 2010; 152A:753-8. [DOI: 10.1002/ajmg.a.33308] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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12
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Sørensen KM, Agergaard P, Olesen C, Andersen PS, Larsen LA, Ostergaard JR, Schouten JP, Christiansen M. Detecting 22q11.2 deletions by use of multiplex ligation-dependent probe amplification on DNA from neonatal dried blood spot samples. J Mol Diagn 2010; 12:147-51. [PMID: 20075206 DOI: 10.2353/jmoldx.2010.090099] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The 22q11 deletion syndrome, which is caused by a 1.5- to 3.0-megabase hemizygous deletion in chromosome 22q11.2, has a prevalence of 1/2000 to 1/4000. However, the syndrome presents with highly variable phenotypes and thus may be underestimated among Danish newborns. To establish a true incidence of 22q11.2 deletions among certain manifestations, eg, congenital heart disease, on selected Danes, a multiplex ligation-dependant probe amplification (MLPA) analysis was designed. The analysis was planned to be performed on DNA extracted from dried blood spot samples (DBSS) obtained from Guthrie cards collected during neonatal screening programs. However, the DNA concentration necessary for a standard MLPA analysis (20 ng) could not be attained from DBSS, and a novel MLPA design was developed to permit for analysis on limited amounts of DNA (2 ng). A pilot study is reported here that validates the new MLPA design using nine patients diagnosed with the 22q11.2 deletion and 101 controls. All deletions were identified using DNA extracted from DBSS, and no copy number variations were detected in the controls, resulting in a specificity and sensitivity of 100%. It is thereby concluded that the novel MLPA probe design is successful and reliable using minimal amounts of DNA. This allows for use of DBSS samples in a retrospective study of 22q11.2 deletion among certain manifestations associated with DiGeorge Syndrome.
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Affiliation(s)
- Karina M Sørensen
- Department of Clinical Biochemistry and Immunology 85/232, Statens Serum Institut, Artillerivej 5, 2300 Kbh. S, Denmark.
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13
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A deletion and a duplication in distal 22q11.2 deletion syndrome region. Clinical implications and review. BMC MEDICAL GENETICS 2009; 10:48. [PMID: 19490635 PMCID: PMC2700091 DOI: 10.1186/1471-2350-10-48] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2008] [Accepted: 06/02/2009] [Indexed: 12/31/2022]
Abstract
Background Individuals affected with DiGeorge and Velocardiofacial syndromes present with both phenotypic diversity and variable expressivity. The most frequent clinical features include conotruncal congenital heart defects, velopharyngeal insufficiency, hypocalcemia and a characteristic craniofacial dysmorphism. The etiology in most patients is a 3 Mb recurrent deletion in region 22q11.2. However, cases of infrequent deletions and duplications with different sizes and locations have also been reported, generally with a milder, slightly different phenotype for duplications but with no clear genotype-phenotype correlation to date. Methods We present a 7 month-old male patient with surgically corrected ASD and multiple VSDs, and dysmorphic facial features not clearly suggestive of 22q11.2 deletion syndrome, and a newborn male infant with cleft lip and palate and upslanting palpebral fissures. Karyotype, FISH, MLPA, microsatellite markers segregation studies and SNP genotyping by array-CGH were performed in both patients and parents. Results Karyotype and FISH with probe N25 were normal for both patients. MLPA analysis detected a partial de novo 1.1 Mb deletion in one patient and a novel partial familial 0.4 Mb duplication in the other. Both of these alterations were located at a distal position within the commonly deleted region in 22q11.2. These rearrangements were confirmed and accurately characterized by microsatellite marker segregation studies and SNP array genotyping. Conclusion The phenotypic diversity found for deletions and duplications supports a lack of genotype-phenotype correlation in the vicinity of the LCRC-LCRD interval of the 22q11.2 chromosomal region, whereas the high presence of duplications in normal individuals supports their role as polymorphisms. We suggest that any hypothetical correlation between the clinical phenotype and the size and location of these alterations may be masked by other genetic and/or epigenetic modifying factors.
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Beaujard MP, Chantot S, Dubois M, Keren B, Carpentier W, Mabboux P, Whalen S, Vodovar M, Siffroi JP, Portnoï MF. Atypical deletion of 22q11.2: detection using the FISH TBX1 probe and molecular characterization with high-density SNP arrays. Eur J Med Genet 2009; 52:321-7. [PMID: 19467348 DOI: 10.1016/j.ejmg.2009.05.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Accepted: 05/09/2009] [Indexed: 12/24/2022]
Abstract
Despite the heterogeneous clinical presentations, the majority of patients with 22q11.2 deletion syndrome (22q11.2 DS) have either a common recurrent 3 Mb deletion or a less common, 1.5 Mb nested deletion, with breakpoint sites in flanking low-copy repeats (LCR) sequences. Only a small number of atypical deletions have been reported and precisely defined. Haploinsufficiency of the TBX1 gene was determined to be the likely cause of 22q11.2 DS. The diagnostic procedure usually used is FISH using commercially probes (N25 or TUPLE1). However, this test does not contain TBX1, and fails to detect deletions that are either proximal or distal to the FISH probes. Here, we report on two patients with clinical features suggestive of 22q11.2 DS, a male infant with facial dysmorphia, pulmonary atresia, ventricular septal defect, neonatal hypocalcemia, and his affected mother, with facial dysmorphia, learning disabilities, and hypernasal speech. They were tested negative for 22q11.2 DS using N25 or TUPLE1 probes, but were shown deleted for a probe containing TBX1. Delineation of the deletion was performed using high-density SNP arrays (Illumina, 370K). This atypical deletion was spanning 1.89 Mb. The distal breakpoint resided in LCR-D, sharing the same distal breakpoint with the 3 Mb common deletion. The proximal breakpoint was located 105 kb telomeric to TUPLE1, representing a new breakpoint variant that does not correspond to known LCRs of 22q11.2. We conclude that FISH with the TBX1 probe is an accurate diagnostic tool for 22q11.2 DS, with a higher sensitivity than FISH using standard probes, detecting all but the rarest deletions, greatly reducing the false negative rate.
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