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Atli EI, Atli E, Yalcintepe S, Demir S, Mail C, Eker D, Ozen Y, Gurkan H. Clinical Features of Aberrations Chromosome 22q: A Pilot Study. Glob Med Genet 2021; 9:42-50. [PMID: 35169783 PMCID: PMC8837404 DOI: 10.1055/s-0041-1739496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 09/29/2021] [Indexed: 11/12/2022] Open
Abstract
Objective
A significant number of genetic variations have been identified in chromosome 22, using molecular genetic techniques. Various genomic disorders on chromosome 22, including cat's eye syndrome caused by extra copies of the proximal region of the 22q chromosome, are now well-defined. Our aim in the study was to show phenotypic variability associated with rearrangements of the 22q chromosomal region.
Methods
We focused our study on clinical aspects of these disorders, including genetic testing, genotype-phenotype correlation, and potential treatments. A total of 998 patients were referred for genetic analysis (Karyotyping, MLPA, array-CGH) during January 2015 to February 2020 because of intellectual deficiency, behavior issues, and/or multiple congenital abnormalities in several genetics departments. Informed consent was obtained from all the patients and/or their parents.
Results
22q11.21 or 22q13.33 microdeletions and 22q11.22-q11.23 microduplication were identified in 31 patients out of referrals. The 22q aberrations were detected in 31/998 patients, giving a prevalence of 3.1%. In this study, 18 patients with 22q11.2 (LCR22A-H) deletion, three patients with 22q13.31 deletion, 9 patients with 22q11.2 duplication and one patient with 22q13.31 duplication were identified. We report on the clinical and molecular characterization of 31 individuals with distal deletions and duplications of chromosome 22q.
Conclusions
The current study demonstrated in the largest postnatal case series reporting the whole spectrum of atypical phenotypic and genotypic variations at 22q. We believe that when all the phenotypic differences are taken into account, various anomalies including developmental delay and intellectual disability might be considered as an indication to search for aberrations of 22q along with congenital heart diseases.
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Affiliation(s)
- Emine Ikbal Atli
- Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Engin Atli
- Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Sinem Yalcintepe
- Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Selma Demir
- Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Cisem Mail
- Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Damla Eker
- Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Yasemin Ozen
- Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Hakan Gurkan
- Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, Turkey
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2
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Mosley TJ, Johnston HR, Cutler DJ, Zwick ME, Mulle JG. Sex-specific recombination patterns predict parent of origin for recurrent genomic disorders. BMC Med Genomics 2021; 14:154. [PMID: 34107974 PMCID: PMC8190997 DOI: 10.1186/s12920-021-00999-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 06/02/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Structural rearrangements of the genome, which generally occur during meiosis and result in large-scale (> 1 kb) copy number variants (CNV; deletions or duplications ≥ 1 kb), underlie genomic disorders. Recurrent pathogenic CNVs harbor similar breakpoints in multiple unrelated individuals and are primarily formed via non-allelic homologous recombination (NAHR). Several pathogenic NAHR-mediated recurrent CNV loci demonstrate biases for parental origin of de novo CNVs. However, the mechanism underlying these biases is not well understood. METHODS We performed a systematic, comprehensive literature search to curate parent of origin data for multiple pathogenic CNV loci. Using a regression framework, we assessed the relationship between parental CNV origin and the male to female recombination rate ratio. RESULTS We demonstrate significant association between sex-specific differences in meiotic recombination and parental origin biases at these loci (p = 1.07 × 10-14). CONCLUSIONS Our results suggest that parental origin of CNVs is largely influenced by sex-specific recombination rates and highlight the need to consider these differences when investigating mechanisms that cause structural variation.
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Affiliation(s)
- Trenell J Mosley
- Graduate Program in Genetics and Molecular Biology, Laney Graduate School, Emory University, 201 Dowman Drive, Atlanta, GA, 30322, USA
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Whitehead Building Suite 300, Atlanta, GA, 30322, USA
| | - H Richard Johnston
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Whitehead Building Suite 300, Atlanta, GA, 30322, USA
- Emory Integrated Computational Core, Emory University, 101 Woodruff Circle, Atlanta, GA, 30322, USA
| | - David J Cutler
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Whitehead Building Suite 300, Atlanta, GA, 30322, USA
| | - Michael E Zwick
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Whitehead Building Suite 300, Atlanta, GA, 30322, USA
- Department of Pediatrics, Emory University School of Medicine, 2015 Uppergate Drive, Atlanta, GA, 30322, USA
| | - Jennifer G Mulle
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Whitehead Building Suite 300, Atlanta, GA, 30322, USA.
- Department of Epidemiology, Rollins School of Public Health, Emory University, 1518 Clifton Road NE, Atlanta, GA, 30322, USA.
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3
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Campbell IM, Sheppard SE, Crowley TB, McGinn DE, Bailey A, McGinn MJ, Unolt M, Homans JF, Chen EY, Salmons HI, Gaynor JW, Goldmuntz E, Jackson OA, Katz LE, Mascarenhas MR, Deeney VFX, Castelein RM, Zur KB, Elden L, Kallish S, Kolon TF, Hopkins SE, Chadehumbe MA, Lambert MP, Forbes BJ, Moldenhauer JS, Schindewolf EM, Solot CB, Moss EM, Gur RE, Sullivan KE, Emanuel BS, Zackai EH, McDonald-McGinn DM. What is new with 22q? An update from the 22q and You Center at the Children's Hospital of Philadelphia. Am J Med Genet A 2019; 176:2058-2069. [PMID: 30380191 DOI: 10.1002/ajmg.a.40637] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 08/23/2018] [Indexed: 12/26/2022]
Abstract
22q11.2 deletion syndrome (22q11.2DS) is a disorder caused by recurrent, chromosome-specific, low copy repeat (LCR)-mediated copy-number losses of chromosome 22q11. The Children's Hospital of Philadelphia has been involved in the clinical care of individuals with what is now known as 22q11.2DS since our initial report of the association with DiGeorge syndrome in 1982. We reviewed the medical records on our continuously growing longitudinal cohort of 1,421 patients with molecularly confirmed 22q11.2DS from 1992 to 2018. Most individuals are Caucasian and older than 8 years. The mean age at diagnosis was 3.9 years. The majority of patients (85%) had typical LCR22A-LCR22D deletions, and only 7% of these typical deletions were inherited from a parent harboring the deletion constitutionally. However, 6% of individuals harbored other nested deletions that would not be identified by traditional 22q11.2 FISH, thus requiring an orthogonal technology to diagnose. Major medical problems included immune dysfunction or allergies (77%), palatal abnormalities (67%), congenital heart disease (64%), gastrointestinal difficulties (65%), endocrine dysfunction (>50%), scoliosis (50%), renal anomalies (16%), and airway abnormalities. Median full-scale intelligence quotient was 76, with no significant difference between individuals with and without congenital heart disease or hypocalcemia. Characteristic dysmorphic facial features were present in most individuals, but dermatoglyphic patterns of our cohort are similar to normal controls. This is the largest longitudinal study of patients with 22q11.2DS, helping to further describe the condition and aid in diagnosis and management. Further surveillance will likely elucidate additional clinically relevant findings as they age.
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Affiliation(s)
- Ian M Campbell
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Sarah E Sheppard
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - T Blaine Crowley
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Daniel E McGinn
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Davidson College, Davidson, North Carolina
| | - Alice Bailey
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Michael J McGinn
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Marta Unolt
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Division of Cardiology, Bambino Gesu Hospital, Rome, Italy
| | - Jelle F Homans
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Orthopaedic Surgery, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Erin Y Chen
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Johns Hopkins University, Baltimore, Maryland
| | - Harold I Salmons
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - J William Gaynor
- Division of Cardiothoracic Surgery, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Surgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Elizabeth Goldmuntz
- Division of Cardiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Oksana A Jackson
- Department of Surgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.,Division of Plastic Surgery, Department of Pediatric Surgery, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Division of Plastic Surgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Lorraine E Katz
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.,Division of Endocrinology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Maria R Mascarenhas
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.,Division of Gastroenterology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Vincent F X Deeney
- Department of Surgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.,Division of Orthopaedics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - René M Castelein
- Department of Orthopaedic Surgery, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Karen B Zur
- Division of Otolaryngology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Lisa Elden
- Division of Otolaryngology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Staci Kallish
- Department of Medicine, Division of Translational Medicine and Human Genetics, The Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Thomas F Kolon
- Division of Pediatric Urology, Department of Pediatric Surgery, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Surgery (Urology), Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Sarah E Hopkins
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Madeline A Chadehumbe
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Michele P Lambert
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Brian J Forbes
- Division of Ophthalmology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Julie S Moldenhauer
- Department of Surgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.,Center for Fetal Diagnosis and Treatment at Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Erica M Schindewolf
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Center for Fetal Diagnosis and Treatment at Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Cynthia B Solot
- Center for Childhood Communication, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Edward M Moss
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Malamut and Moss, Bryn Mawr, Pennsylvania
| | - Raquel E Gur
- Department of Psychiatry, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kathleen E Sullivan
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.,Division of Allergy and Immunology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Beverly S Emanuel
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Elaine H Zackai
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Donna M McDonald-McGinn
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
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4
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Williams CL, Nelson KR, Grant JH, Mikhail FM, Robin NH. Cleft palate in a patient with the nested 22q11.2 LCR C to D deletion. Am J Med Genet A 2015; 170A:260-2. [PMID: 26419407 DOI: 10.1002/ajmg.a.37408] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 09/18/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Crescenda L Williams
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Katherine R Nelson
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - John H Grant
- Division of Plastic Surgery, Department of Surgery, University of Alabama at Birmingham, Birmingham, Alabama.,Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Nathaniel H Robin
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama.,Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama
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5
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DGCR6 at the proximal part of the DiGeorge critical region is involved in conotruncal heart defects. Hum Genome Var 2015; 2:15004. [PMID: 27081520 PMCID: PMC4785558 DOI: 10.1038/hgv.2015.4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 12/12/2014] [Accepted: 12/17/2014] [Indexed: 02/06/2023] Open
Abstract
Cardiac anomaly is one of the hallmarks of DiGeorge syndrome (DGS), observed in approximately 80% of patients. It often shows a characteristic morphology, termed as conotruncal heart defects. In many cases showing only the conotruncal heart defect, deletion of 22q11.2 region cannot be detected by fluorescence in situ hybridization (FISH), which is used to detect deletion in DGS. We investigated the presence of genomic aberrations in six patients with congenital conotruncal heart defects, who show no deletion at 22q11.2 in an initial screening by FISH. In these patients, no abnormalities were identified in the coding region of the TBX1 gene, one of the key genes responsible for the phenotype of DGS. However, when copy number alteration was analyzed by high-resolution array analysis, a small deletion or duplication in the proximal end of DiGeorge critical region was detected in two patients. The affected region contains the DGCR6 and PRODH genes. DGCR6 has been reported to affect the expression of the TBX1 gene. Our results suggest that altered dosage of gene(s) other than TBX1, possibly DGCR6, may also be responsible for the development of conotruncal heart defects observed in patients with DGS and, in particular, in those with stand-alone conotruncal heart defects.
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6
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Understanding the role of Tbx1 as a candidate gene for 22q11.2 deletion syndrome. Curr Allergy Asthma Rep 2014; 13:613-21. [PMID: 23996541 DOI: 10.1007/s11882-013-0384-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
22q11.2 deletion syndrome (22q11.2DS) is caused by a commonly occurring microdeletion on chromosome 22. Clinical findings include cardiac malformations, thymic and parathyroid hypoplasia, craniofacial dysmorphisms, and dental defects. These phenotypes are due mainly to abnormal development of the pharyngeal apparatus. Targeted deletion studies in mice and analysis of naturally occurring mutations in humans have implicated Tbx1 as a candidate gene for 22q11.2DS. Tbx1 belongs to an evolutionarily conserved T-box family of transcription factors, whose expression is precisely regulated during embryogenesis, and it appears to regulate the proliferation and differentiation of various progenitor cells during organogenesis. In this review, we discuss the mechanisms of Tbx1 during development of the heart, thymus and parathyroid glands, as well as during formation of the palate, teeth, and other craniofacial features.
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7
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de la Morena MT, Eitson JL, Dozmorov IM, Belkaya S, Hoover AR, Anguiano E, Pascual MV, van Oers NSC. Signature MicroRNA expression patterns identified in humans with 22q11.2 deletion/DiGeorge syndrome. Clin Immunol 2013; 147:11-22. [PMID: 23454892 DOI: 10.1016/j.clim.2013.01.011] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2012] [Revised: 01/16/2013] [Accepted: 01/18/2013] [Indexed: 11/19/2022]
Abstract
Patients with 22q11.2 deletion syndrome have heterogeneous clinical presentations including immunodeficiency, cardiac anomalies, and hypocalcemia. The syndrome arises from hemizygous deletions of up to 3Mb on chromosome 22q11.2, a region that contains 60 genes and 4 microRNAs. MicroRNAs are important post-transcriptional regulators of gene expression, with mutations in several microRNAs causal to specific human diseases. We characterized the microRNA expression patterns in the peripheral blood of patients with 22q11.2 deletion syndrome (n=31) compared to normal controls (n=22). Eighteen microRNAs had a statistically significant differential expression (p<0.05), with miR-185 expressed at 0.4× normal levels. The 22q11.2 deletion syndrome cohort exhibited microRNA expression hyper-variability and group dysregulation. Selected microRNAs distinguished patients with cardiac anomalies, hypocalcemia, and/or low circulating T cell counts. In summary, microRNA profiling of chromosome 22q11.2 deletion syndrome/DiGeorge patients revealed a signature microRNA expression pattern distinct from normal controls with clinical relevance.
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Affiliation(s)
- M Teresa de la Morena
- Department of Pediatrics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9063, USA.
| | - Jennifer L Eitson
- Department of Immunology, The University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390-9093, USA
| | - Igor M Dozmorov
- Department of Immunology, The University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390-9093, USA
| | - Serkan Belkaya
- Department of Immunology, The University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390-9093, USA
| | - Ashley R Hoover
- Department of Immunology, The University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390-9093, USA
| | | | | | - Nicolai S C van Oers
- Department of Pediatrics, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9063, USA; Department of Immunology, The University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390-9093, USA; Department of Microbiology, The University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390-9093, USA.
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8
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Bassett AS, McDonald-McGinn DM, Devriendt K, Digilio MC, Goldenberg P, Habel A, Marino B, Oskarsdottir S, Philip N, Sullivan K, Swillen A, Vorstman J. Practical guidelines for managing patients with 22q11.2 deletion syndrome. J Pediatr 2011; 159:332-9.e1. [PMID: 21570089 PMCID: PMC3197829 DOI: 10.1016/j.jpeds.2011.02.039] [Citation(s) in RCA: 362] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Revised: 01/24/2011] [Accepted: 02/25/2011] [Indexed: 10/18/2022]
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9
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McDonald-McGinn DM, Sullivan KE. Chromosome 22q11.2 deletion syndrome (DiGeorge syndrome/velocardiofacial syndrome). Medicine (Baltimore) 2011; 90:1-18. [PMID: 21200182 DOI: 10.1097/md.0b013e3182060469] [Citation(s) in RCA: 264] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Chromosome 22q11.2 deletion syndrome is a common syndrome also known as DiGeorge syndrome and velocardiofacial syndrome. It occurs in approximately 1:4000 births, and the incidence is increasing due to affected parents bearing their own affected children. The manifestations of this syndrome cross all medical specialties, and care of the children and adults can be complex. Many patients have a mild to moderate immune deficiency, and the majority of patients have a cardiac anomaly. Additional features include renal anomalies, eye anomalies, hypoparathyroidism, skeletal defects, and developmental delay. Each child's needs must be tailored to his or her specific medical problems, and as the child transitions to adulthood, additional issues will arise. A holistic approach, addressing medical and behavioral needs, can be very helpful.
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10
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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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11
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Bittel DC, Yu S, Newkirk H, Kibiryeva N, Holt A, Butler MG, Cooley LD. Refining the 22q11.2 deletion breakpoints in DiGeorge syndrome by aCGH. Cytogenet Genome Res 2009; 124:113-20. [PMID: 19420922 DOI: 10.1159/000207515] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2008] [Indexed: 01/08/2023] Open
Abstract
Hemizygous deletions of the chromosome 22q11.2 region result in the 22q11.2 deletion syndrome also referred to as DiGeorge, Velocardiofacial or Shprintzen syndromes. The phenotype is variable but commonly includes conotruncal cardiac defects, palatal abnormalities, learning and behavioral problems, immune deficiency, and facial anomalies. Four distinct highly homologous blocks of low copy number repeat sequences (LCRs) flank the deletion region. Mispairing of LCRs during meiosis with unequal meiotic exchange is assumed to cause the recurrent and consistent deletions. The proximal LCR is reportedly located at 22q11.2 from 17.037 to 17.083 Mb while the distal LCR is located from 19.835 to 19.880 Mb. Although the chromosome breakpoints are thought to localize to the LCRs, the positions of the breakpoints have been investigated in only a few individuals. Therefore, we used high resolution oligonucleotide-based 244K microarray comparative genomic hybridization (aCGH) to resolve the breakpoints in a cohort of 20 subjects with known 22q11.2 deletions. We also investigated copy number variation (CNV) in the rest of the genome. The 22q11.2 breaks occurred on either side of the LCR in our subjects, although more commonly on the distal side of the reported proximal LCR. The proximal breakpoints in our subjects spanned the region from 17.036 to 17.398 Mb. This region includes the genes DGCR6 (DiGeorge syndrome critical region protein 6) and PRODH (proline dehydrogenase 1), along with three open reading frames that may encode proteins of unknown function. The distal breakpoints spanned the region from 19.788 to 20.122 Mb. This region includes the genes GGT2 (gamma-glutamyltransferase-like protein 2), HIC2 (hypermethylated in cancer 2), and multiple transcripts of unknown function. The genes in these two breakpoint regions are variably hemizygous depending on the location of the breakpoints. Our 20 subjects had 254 CNVs throughout the genome, 94 duplications and 160 deletions, ranging in size from 1 kb to 2.4 Mb. The presence or absence of genes at the breakpoints depending on the size of the deletion plus variation in the rest of the genome due to CNVs likely contribute to the variable phenotype associated with the 22q11.2 deletion or DiGeorge syndrome.
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Affiliation(s)
- D C Bittel
- Children's Mercy Hospitals and Clinics, University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, USA.
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12
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Yeshaya J, Amir I, Rimon A, Freedman J, Shohat M, Avivi L. Microdeletion syndromes disclose replication timing alterations of genes unrelated to the missing DNA. Mol Cytogenet 2009; 2:11. [PMID: 19284877 PMCID: PMC2660353 DOI: 10.1186/1755-8166-2-11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2009] [Accepted: 03/14/2009] [Indexed: 11/26/2022] Open
Abstract
Background The temporal order of allelic replication is interrelated to the epigenomic profile. A significant epigenetic marker is the asynchronous replication of monoallelically-expressed genes versus the synchronous replication of biallelically-expressed genes. The present study sought to determine whether a microdeletion in the genome affects epigenetic profiles of genes unrelated to the missing segment. In order to test this hypothesis, we checked the replication patterns of two genes – SNRPN, a normally monoallelically expressed gene (assigned to 15q11.13), and the RB1, an archetypic biallelically expressed gene (assigned to 13.q14) in the genomes of patients carrying the 22q11.2 deletion (DiGeorge/Velocardiofacial syndrome) and those carrying the 7q11.23 deletion (Williams syndrome). Results The allelic replication timing was determined by fluorescence in situ hybridization (FISH) technology performed on peripheral blood cells. As expected, in the cells of normal subjects the frequency of cells showing asynchronous replication for SNRPN was significantly (P < 10-12) higher than the corresponding value for RB1. In contrast, cells of the deletion-carrying patients exhibited a reversal in this replication pattern: there was a significantly lower frequency of cells engaging in asynchronous replication for SNRPN than for RB1 (P < 10-4 and P < 10-3 for DiGeorge/Velocardiofacial and Williams syndromes, respectively). Accordingly, the significantly lower frequency of cells showing asynchronous replication for SNRPN than for RB1 is a new epigenetic marker distinguishing these deletion syndrome genotypes from normal ones. Conclusion In cell samples of each deletion-carrying individual, an aberrant, reversed pattern of replication is delineated, namely, where a monoallelic gene replicates more synchronously than a biallelic gene. This inverted pattern, which appears to be non-deletion-specific, clearly distinguishes cells of deletion-carriers from normal ones. As such, it offers a potential epigenetic marker for suspecting a hidden microdeletion that is too small to be detected by conventional karyotyping methods.
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Affiliation(s)
- Josepha Yeshaya
- Raphael Recanati Genetic Institute, Rabin Medical Center Beilinson Campus, Petah-Tikva, Israel
| | - Itay Amir
- Raphael Recanati Genetic Institute, Rabin Medical Center Beilinson Campus, Petah-Tikva, Israel.,Department of Human Molecular Genetics & Biochemistry, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Ayelet Rimon
- Raphael Recanati Genetic Institute, Rabin Medical Center Beilinson Campus, Petah-Tikva, Israel
| | - Jane Freedman
- Raphael Recanati Genetic Institute, Rabin Medical Center Beilinson Campus, Petah-Tikva, Israel
| | - Mordechai Shohat
- Raphael Recanati Genetic Institute, Rabin Medical Center Beilinson Campus, Petah-Tikva, Israel.,Department of Human Molecular Genetics & Biochemistry, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Department of Pediatrics C, Schneider Children's Medical Center of Israel, Petah Tikva, Israel
| | - Lydia Avivi
- Department of Human Molecular Genetics & Biochemistry, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
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Emanuel BS. Molecular mechanisms and diagnosis of chromosome 22q11.2 rearrangements. ACTA ACUST UNITED AC 2008; 14:11-8. [PMID: 18636632 DOI: 10.1002/ddrr.3] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Several recurrent, constitutional genomic disorders are present on chromosome 22q. These include the translocations and deletions associated with DiGeorge and velocardiofacial syndrome and the translocations that give rise to the recurrent t(11;22) supernumerary der(22) syndrome (Emanuel syndrome). The rearrangement breakpoints on 22q cluster around the chromosome-specific segmental duplications of proximal 22q11, which are involved in the etiology of these disorders. While the deletions are the result of nonallelic homologous recombination (NAHR) between low copy repeats or segmental duplications within 22q11, the t(11;22) is the result of rearrangement between palindromic AT-rich repeats on 11q and 22q. Here we describe the mechanisms responsible for these recurrent rearrangements, discuss the recurrent deletion endpoints that are the result of NAHR between chromosome 22q specific low copy repeats as well as present current diagnostic approaches to deletion detection.
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Affiliation(s)
- Beverly S Emanuel
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104-4318, USA.
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14
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Abstract
Velocardiofacial syndrome, DiGeorge syndrome, and some other clinical syndromes have in common a high frequency of hemizygous deletions of chromosome 22q11.2. This deletion syndrome is very common, affecting nearly one in 3000 children. Here, we focus on recent advances in cardiac assessment, speech, immunology, and pathophysiology of velocardiofacial syndrome. The complex medical care of patients needs a multidisciplinary approach, and every patient has his own unique clinical features that need a tailored approach. Patients with chromosome 22q11.2 deletion syndrome might have high level of functioning, but most often need interventions to improve the function of many organ systems.
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Affiliation(s)
- Lisa J Kobrynski
- Department of Pediatrics, Allergy and Immunology Section, Emory University School of Medicine, Atlanta, GA, USA
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15
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Torres-Juan L, Rosell J, Sánchez-de-la-Torre M, Fibla J, Heine-Suñer D. Analysis of meiotic recombination in 22q11.2, a region that frequently undergoes deletions and duplications. BMC MEDICAL GENETICS 2007; 8:14. [PMID: 17397557 PMCID: PMC1855045 DOI: 10.1186/1471-2350-8-14] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2006] [Accepted: 04/02/2007] [Indexed: 01/26/2023]
Abstract
Background The 22q11.2 deletion syndrome is the most frequent genomic disorder with an estimated frequency of 1/4000 live births. The majority of patients (90%) have the same deletion of 3 Mb (Typically Deleted Region, TDR) that results from aberrant recombination at meiosis between region specific low-copy repeats (LCRs). Methods As a first step towards the characterization of recombination rates and breakpoints within the 22q11.2 region we have constructed a high resolution recombination breakpoint map based on pedigree analysis and a population-based historical recombination map based on LD analysis. Results Our pedigree map allows the location of recombination breakpoints with a high resolution (potential recombination hotspots), and this approach has led to the identification of 5 breakpoint segments of 50 kb or less (8.6 kb the smallest), that coincide with historical hotspots. It has been suggested that aberrant recombination leading to deletion (and duplication) is caused by low rates of Allelic Homologous Recombination (AHR) within the affected region. However, recombination rate estimates for 22q11.2 region show that neither average recombination rates in the 22q11.2 region or within LCR22-2 (the LCR implicated in most deletions and duplications), are significantly below chromosome 22 averages. Furthermore, LCR22-2, the repeat most frequently implicated in rearrangements, is also the LCR22 with the highest levels of AHR. In addition, we find recombination events in the 22q11.2 region to cluster within families. Within this context, the same chromosome recombines twice in one family; first by AHR and in the next generation by NAHR resulting in an individual affected with the del22q11.2 syndrome. Conclusion We show in the context of a first high resolution pedigree map of the 22q11.2 region that NAHR within LCR22 leading to duplications and deletions cannot be explained exclusively under a hypothesis of low AHR rates. In addition, we find that AHR recombination events cluster within families. If normal and aberrant recombination are mechanistically related, the fact that LCR22s undergo frequent AHR and that we find familial differences in recombination rates within the 22q11.2 region would have obvious health-related implications.
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Affiliation(s)
- Laura Torres-Juan
- Secció de Genètica, Hospital Universitari Son Dureta, Andrea Doria 55, Palma de Mallorca 07014, Balears, Spain
| | - Jordi Rosell
- Secció de Genètica, Hospital Universitari Son Dureta, Andrea Doria 55, Palma de Mallorca 07014, Balears, Spain
| | | | - Joan Fibla
- Departament de Ciències Mèdiques Bàsiques, Irblleida, Universitat de Lleida, Lleida, Spain
| | - Damià Heine-Suñer
- Secció de Genètica, Hospital Universitari Son Dureta, Andrea Doria 55, Palma de Mallorca 07014, Balears, Spain
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Thomas NS, Durkie M, Potts G, Sandford R, Van Zyl B, Youings S, Dennis NR, Jacobs PA. Parental and chromosomal origins of microdeletion and duplication syndromes involving 7q11.23, 15q11-q13 and 22q11. Eur J Hum Genet 2006; 14:831-7. [PMID: 16617304 DOI: 10.1038/sj.ejhg.5201617] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Non-allelic homologous recombination between chromosome-specific LCRs is the most common mechanism leading to recurrent microdeletions and duplications. To look for locus-specific differences, we have used microsatellites to determine the parental and chromosomal origins of a large series of patients with de novo deletions of chromosome 7q11.23 (Williams syndrome), 15q11-q13 (Angelman syndrome, Prader-Willi syndrome) and 22q11 (Di George syndrome) and duplications of 15q11-q13. Overall the majority of rearrangements were interchromosomal, so arising from unequal meiotic exchange, and there were approximately equal numbers of maternal and paternal deletions. Duplications and deletions of 15q11-q13 appear to be reciprocal products that arise by the same mechanisms. The proportion arising from interchromosomal exchanges varied among deletions with 22q11 the highest and 15q11-q13 the lowest. However, parental and chromosomal origins were not always independent. For 15q11-q13, maternal deletions tended to be interchromosomal while paternal deletions tended to be intrachromosomal; for 22q11 there was a possible excess of maternal cases among intrachromosomal deletions. Several factors are likely to be involved in the formation of recurrent rearrangements and the relative importance of these appear to be locus-specific.
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Affiliation(s)
- N Simon Thomas
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, UK.
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Fernández L, Lapunzina P, Pajares IL, Criado GR, García-Guereta L, Pérez J, Quero J, Delicado A. Higher frequency of uncommon 1.5-2 Mb deletions found in familial cases of 22q11.2 deletion syndrome. Am J Med Genet A 2005; 136:71-5. [PMID: 15889418 DOI: 10.1002/ajmg.a.30756] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Familial 22q11.2 deletions have been reported as a 6%-28% of the total affected cases of 22q11.2 microdeletion syndrome (del22q11.2). Different deletion genotypes have been described for this disorder, with a predominant 3 Mb deletion present in 90% of the cases, a less common 1.5-2 Mb deletion in 8%, and atypical smaller deletions in 2%. We have studied 15 cases of del22q11.2 from 6 families (two of them three-generation families) that were previously diagnosed through FISH. We have sized the deleted region by allele genotyping of 12-16 polymorphic markers in all cases, and we have found three families affected with the 1.5-2 Mb deletion, two affected with the 3 Mb deletion, and one in which the deletion size could not be determined. This predominance of the smaller 1.5-2 Mb deletions in our familial cases differs from the minor frequency observed in sporadic cases of del22q11.2. This finding suggests that small deletions are more linked to familial inheritance than large ones, possibly due to psychosocial or biological factors associated with differences in the phenotype. Deletion sizing on routine diagnosis may help characterizing the inheritability of 22q11.2 microdeletion syndrome.
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Affiliation(s)
- Luis Fernández
- Servicio de Genética Médica, Hospital Universitario La Paz, Madrid, Spain
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