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Huang S, Xia Y, Ding H, Wang Y, Wu Y, Chen S, Zhuang J, Li P. A Case of a Derivative Chromosome: der(Y)t(Y;18)Pat with Congenital Abnormalities. Fetal Pediatr Pathol 2021; 40:256-261. [PMID: 31805817 DOI: 10.1080/15513815.2019.1695297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
BACKGROUND Chromosome reciprocal translocations are frequently occurring structural rearrangements observed in humans. Although individuals with balanced reciprocal translocations tend to be clinically normal, they have an increased risk of reproductive failure, miscarriage and abnormal phenotype.Casereport: A 14 days old neonate was found to have a 46,X,der(Y)t(Y;18)(q12;q11)pat karyotype causing multiple dysmorphisms and death within one month. The proband inherited from his father(carrier) an abnormal Y chromosome with Yq deletion of regions (q12-qter) and an 18q duplication of regions (q11-qter), resulting in a severe clinical phenotype similar to Edwards syndrome (Trisomy 18 syndrome). CONCLUSION These findings expand our current knowledge of the mutation spectrum of Y-autosomal translocations associated with dysmorphosis.
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Affiliation(s)
- Shufang Huang
- Prenatal Diagnosis Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Department of Obstetrics and Gynecology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yu Xia
- Department of Cardiovascular Surgery of Guangdong Provincial Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Hong Ding
- Prenatal Diagnosis Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Department of Obstetrics and Gynecology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yonghua Wang
- Prenatal Diagnosis Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Department of Obstetrics and Gynecology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yueheng Wu
- Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Research Department of Medical Sciences, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Shaoxian Chen
- Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Research Department of Medical Sciences, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Jian Zhuang
- Department of Cardiovascular Surgery of Guangdong Provincial Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of South China Structural Heart Disease, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Ping Li
- Prenatal Diagnosis Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Department of Obstetrics and Gynecology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
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Toraman B, Bilginer SÇ, Hesapçıoğlu ST, Göker Z, Soykam HO, Ergüner B, Dinçer T, Yıldız G, Ünsal S, Kasap BK, Kandil S, Kalay E. Finding underlying genetic mechanisms of two patients with autism spectrum disorder carrying familial apparently balanced chromosomal translocations. J Gene Med 2021; 23:e3322. [PMID: 33591602 DOI: 10.1002/jgm.3322] [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: 11/11/2020] [Revised: 01/26/2021] [Accepted: 02/14/2021] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Genetic etiologies of autism spectrum disorders (ASD) are complex, and the genetic factors identified so far are very diverse. In complex genetic diseases such as ASD, de novo or inherited chromosomal abnormalities are valuable findings for researchers with respect to identifying the underlying genetic risk factors. With gene mapping studies on these chromosomal abnormalities, dozens of genes have been associated with ASD and other neurodevelopmental genetic diseases. In the present study, we aimed to idenitfy the causative genetic factors in patients with ASD who have an apparently balanced chromosomal translocation in their karyotypes. METHODS For mapping the broken genes as a result of chromosomal translocations, we performed whole genome DNA sequencing. Chromosomal breakpoints and large DNA copy number variations (CNV) were determined after genome alignment. Identified CNVs and single nucleotide variations (SNV) were evaluated with VCF-BED intersect and Gemini tools, respectively. A targeted resequencing approach was performed on the JMJD1C gene in all of the ASD cohorts (220 patients). For molecular modeling, we used a homology modeling approach via the SWISS-MODEL. RESULTS We found that there was no contribution of the broken genes or regulator DNA sequences to ASD, whereas the SNVs on the JMJD1C, CNKSR2 and DDX11 genes were the most convincing genetic risk factors for underlying ASD phenotypes. CONCLUSIONS Genetic etiologies of ASD should be analyzed comprehensively by taking into account of the all chromosomal structural abnormalities and de novo or inherited CNV/SNVs with all possible inheritance patterns.
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Affiliation(s)
- Bayram Toraman
- Faculty of Medicine Department of Medical Biology, Karadeniz Technical University, Trabzon, Turkey
| | - Samiye Çilem Bilginer
- Faculty of Medicine Child and Adolescent Psychiatry Department, Karadeniz Technical University, Trabzon, Turkey
| | - Selma Tural Hesapçıoğlu
- Child and Adolescent Psychiatry Department, Yildirim Beyazit University Faculty of Medicine, Ankara, Turkey
| | - Zeynep Göker
- Ministry of Health Ankara City Hospital, Child-Adolescent and Mental Health, Cankaya, Ankara, Turkey
| | - Hüseyin Okan Soykam
- Department of Biostatistics and Bioinformatics, Acibadem Mehmet Ali Aydinlar University, Institute of Health Sciences, İstanbul, Turkey
| | - Bekir Ergüner
- Sabanci University Faculty of Engineering and Natural Sciences, Molecular Biology, Genetics and Bio engineering, Istanbul, Turkey
| | - Tuba Dinçer
- Faculty of Medicine Department of Medical Biology, Karadeniz Technical University, Trabzon, Turkey
| | - Gökhan Yıldız
- Faculty of Medicine Department of Medical Biology, Karadeniz Technical University, Trabzon, Turkey
| | - Serbülent Ünsal
- Graduate School of Health Science, Biostatistics and Medical Informatics Department, PhD Candidate, Karadeniz Technical University, Trabzon, Turkey
| | - Burak Kaan Kasap
- Graduate School of Health Science, Medical Biology Department, PhD Candidate, Karadeniz Technical University, Trabzon, Turkey
| | - Sema Kandil
- Faculty of Medicine Child and Adolescent Psychiatry Department, Karadeniz Technical University, Trabzon, Turkey
| | - Ersan Kalay
- Faculty of Medicine Department of Medical Biology, Karadeniz Technical University, Trabzon, Turkey
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Levy B, Wapner R. Prenatal diagnosis by chromosomal microarray analysis. Fertil Steril 2018; 109:201-212. [PMID: 29447663 DOI: 10.1016/j.fertnstert.2018.01.005] [Citation(s) in RCA: 162] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 01/05/2018] [Indexed: 02/07/2023]
Abstract
Chromosomal microarray analysis (CMA) is performed either by array comparative genomic hybridization or by using a single nucleotide polymorphism array. In the prenatal setting, CMA is on par with traditional karyotyping for detection of major chromosomal imbalances such as aneuploidy and unbalanced rearrangements. CMA offers additional diagnostic benefits by revealing sub-microscopic imbalances or copy number variations that are too small to be seen on a standard G-banded chromosome preparation. These submicroscopic imbalances are also referred to as microdeletions and microduplications, particularly when they include specific genomic regions that are associated with clinical sequelae. Not all microdeletions/duplications are associated with adverse clinical phenotypes and in many cases, their presence is benign. In other cases, they are associated with a spectrum of clinical phenotypes that may range from benign to severe, while in some situations, the clinical significance may simply be unknown. These scenarios present a challenge for prenatal diagnosis, and genetic counseling prior to prenatal CMA greatly facilitates delivery of complex results. In prenatal diagnostic samples with a normal karyotype, chromosomal microarray will diagnose a clinically significant subchromosomal deletion or duplication in approximately 1% of structurally normal pregnancies and 6% with a structural anomaly. Pre-test counseling is also necessary to distinguish the primary differences between the benefits, limitations and diagnostic scope of CMA versus the powerful but limited screening nature of non-invasive prenatal diagnosis using cell-free fetal DNA.
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Affiliation(s)
- Brynn Levy
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York.
| | - Ronald Wapner
- Department of Obstetrics & Gynecology, Columbia University Medical Center, New York, New York
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4
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Di Gregorio E, Gai G, Botta G, Calcia A, Pappi P, Talarico F, Savin E, Ribotta M, Zonta A, Mancini C, Giorgio E, Cavalieri S, Restagno G, Ferrero GB, Viora E, Pasini B, Grosso E, Brusco A, Brussino A. Array-Comparative Genomic Hybridization Analysis in Fetuses with Major Congenital Malformations Reveals that 24% of Cases Have Pathogenic Deletions/Duplications. Cytogenet Genome Res 2015; 147:10-6. [PMID: 26658296 DOI: 10.1159/000442308] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2015] [Indexed: 11/19/2022] Open
Abstract
Karyotyping and aCGH are routinely used to identify genetic determinants of major congenital malformations (MCMs) in fetal deaths or terminations of pregnancy after prenatal diagnosis. Pathogenic rearrangements are found with a variable rate of 9-39% for aCGH. We collected 33 fetuses, 9 with a single MCM and 24 with MCMs involving 2-4 organ systems. aCGH revealed copy number variants in 14 out of 33 cases (42%). Eight were classified as pathogenic which account for a detection rate of 24% (8/33) considering fetuses with 1 or more MCMs and 33% (8/24) taking into account fetuses with multiple malformations only. Three of the pathogenic variants were known microdeletion syndromes (22q11.21 deletion, central chromosome 22q11.21 deletion, and TAR syndrome) and 5 were large rearrangements, adding up to >11 Mb per subject and comprising strong phenotype-related genes. One of those was a de novo complex rearrangement, and the remaining 4 duplications and 2 deletions were 130-900 kb in size, containing 1-7 genes, and were classified as variants of unknown clinical significance. Our study confirms aCGH as a powerful technique to ascertain the genetic etiology of fetal major congenital malformations.
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South ST. Chromosomal Structural Rearrangements: Detection and Elucidation of Mechanisms Using Cytogenomic Technologies. Clin Lab Med 2011; 31:513-24, vii. [DOI: 10.1016/j.cll.2011.08.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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6
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Treff NR, Tao X, Schillings WJ, Bergh PA, Scott RT, Levy B. Use of single nucleotide polymorphism microarrays to distinguish between balanced and normal chromosomes in embryos from a translocation carrier. Fertil Steril 2011; 96:e58-65. [PMID: 21575938 DOI: 10.1016/j.fertnstert.2011.04.038] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Revised: 04/12/2011] [Accepted: 04/13/2011] [Indexed: 10/18/2022]
Abstract
OBJECTIVE To prove the ability to distinguish between balanced and normal chromosomes in embryos from a translocation carrier. DESIGN Case report. SETTING Academic center for reproductive medicine. PATIENT(S) Woman with a balanced translocation causing Alagille syndrome seeking preimplantation genetic diagnosis (PGD). INTERVENTION(S) Blastocyst biopsy for PGD. MAIN OUTCOME MEASURE(S) Consistency of 3 methods of embryo genetic analysis (real-time polymerase chain reaction, single nucleotide polymorphism [SNP] microarray, and fluorescence in situ hybridization [FISH]) and normalcy in the newborn derived from PGD. RESULT(S) PGD was applied to 48 embryos. Real-time polymerase chain reaction, SNP microarray, and FISH demonstrated 100% consistency, although FISH failed to detect aneuploidies observed by comprehensive SNP microarray-based analyses. Two blastocysts were identified to be normal for all 3 factors using SNP microarray technology alone. The 2 normal embryos were transferred back to the patient, resulting in the delivery of a healthy boy with a normal karyotype. CONCLUSION(S) This is the first report of validation and successful clinical application of microarray-based PGD to distinguish between balanced and normal chromosomes in embryos from a translocation carrier.
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Affiliation(s)
- Nathan R Treff
- Reproductive Medicine Associates of New Jersey Research, 111 Madison Avenue, Suite 100, Morristown, NJ 07960, USA.
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7
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Single nucleotide polymorphism microarray–based concurrent screening of 24-chromosome aneuploidy and unbalanced translocations in preimplantation human embryos. Fertil Steril 2011; 95:1606-12.e1-2. [DOI: 10.1016/j.fertnstert.2010.11.004] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Revised: 11/02/2010] [Accepted: 11/02/2010] [Indexed: 11/22/2022]
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8
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South ST, Rector L, Aston E, Rowe L, Yang SP. Large clinically consequential imbalances detected at the breakpoints of apparently balanced and inherited chromosome rearrangements. J Mol Diagn 2010; 12:725-9. [PMID: 20595628 DOI: 10.2353/jmoldx.2010.090234] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
When a chromosome abnormality is identified in a child with a developmental delay and/or multiple congenital anomalies and the chromosome rearrangement appears balanced, follow-up studies often examine both parents for this rearrangement. If either clinically unaffected parent has a chromosome abnormality with a banding pattern identical to the affected child's study, then it is assumed that the chromosome rearrangement is balanced and directly inherited from the normal carrier parent. It is therefore unlikely that the chromosome rearrangement is responsible for the child's clinical presentation. We present two unrelated cases in which an identical and apparently balanced abnormal chromosome banding pattern was identified in both an affected child and an unaffected parent of that child. Despite the identical banding patterns, molecular characterization through genomic microarray and fluorescence in situ hybridization showed the parent to be balanced whereas the affected child was significantly unbalanced. These two cases emphasize the utility of genomic microarray for further characterization of apparently balanced inherited chromosome rearrangements and caution against the assumption that identical banding patterns between a child and parent represent identical genomic rearrangements.
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Affiliation(s)
- Sarah T South
- Institute for Clinical and Experimental Pathology, University of Utah, Salt Lake City, Utah, USA.
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9
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Gimelli S, Chrast J, Baban A, Henrichsen CN, Lerone M, Zuffardi O, Gimelli G, Reymond A. A t(7;12) balanced translocation with breakpoints overlapping those of the Williams-Beuren and 12q14 microdeletion syndromes. Am J Med Genet A 2010; 152A:1285-94. [PMID: 20425838 DOI: 10.1002/ajmg.a.33365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The molecular characterization of balanced chromosomal rearrangements have always been of advantage in identifying disease-causing genes. Here, we describe the breakpoint mapping of a de novo balanced translocation t(7;12)(q11.22;q14.2) in a patient presenting with a failure to thrive associated with moderate mental retardation, facial anomalies, and chronic constipation. The localization of the breakpoints and the co-occurrence of Williams-Beuren syndrome and 12q14 microdeletion syndrome phenotypes suggested that the expression of some of the dosage-sensitive genes of these two segmental aneuploidies were modified in cells of the proposita. However, we were unable to identify chromosomes 7 and/or 12-mapping genes that showed disturbed expression in the lymphoblastoids of the proposita. This case showed that position-effect might operate in some tissues, but not in others. It also illustrates the overlap of phenotypes presented by patients with the recently described 12q14 structural rearrangements.
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Affiliation(s)
- Stefania Gimelli
- Biologia Generale e Genetica Medica, Universita' di Pavia and IRCCS C. Mondino, Pavia, Italy.
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10
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Gruchy N, Barreau M, Kessler K, Gourdier D, Leporrier N. A paternally transmitted complex chromosomal rearrangement (CCR) involving chromosomes 2, 6, and 18 includes eight breakpoints and five insertional translocations (ITs) through three generations. Am J Med Genet A 2010; 152A:185-90. [PMID: 20034065 DOI: 10.1002/ajmg.a.33154] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Complex chromosomal rearrangements (CCRs) are uncommon and mainly occur de novo. We report here on a familial CCR involving chromosomes 2, 6, and 18. The propositus is a boy first referred because of growth delays, hypotonia, and facial anomalies, suggestive of deletion 18q syndrome. However, a cytogenetic family study disclosed a balanced CCR in three generations, which was detailed by FISH using BAC clones, and consisted of eight breakpoints with five insertional translocations (ITs). The propositus had a cryptic 18q deletion and a 6p duplication. Paternal transmission of this CCR was observed through three generations without meiotic recombination. Our investigation allowed us to provide porosities counseling and management of prenatal diagnosis for propositus cousin who carries this particular CCR.
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Affiliation(s)
- Nicolas Gruchy
- Laboratoire de cytogénétique prénatale niveau 3, Centre Hospitalier Universitaire de Caen, Avenue Côte de Nacre, 14033 Caen Cedex, France.
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11
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Cryptic genomic imbalances in de novo and inherited apparently balanced chromosomal rearrangements: Array CGH study of 47 unrelated cases. Eur J Med Genet 2009; 52:291-6. [DOI: 10.1016/j.ejmg.2009.05.011] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2008] [Accepted: 05/30/2009] [Indexed: 02/04/2023]
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12
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Ballarati L, Recalcati MP, Bedeschi MF, Lalatta F, Valtorta C, Bellini M, Finelli P, Larizza L, Giardino D. Cytogenetic, FISH and array-CGH characterization of a complex chromosomal rearrangement carried by a mentally and language impaired patient. Eur J Med Genet 2009; 52:218-23. [DOI: 10.1016/j.ejmg.2009.02.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2008] [Accepted: 02/12/2009] [Indexed: 10/21/2022]
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13
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Brown KK, Alkuraya FS, Matos M, Robertson RL, Kimonis VE, Morton CC. NR2F1 deletion in a patient with a de novo paracentric inversion, inv(5)(q15q33.2), and syndromic deafness. Am J Med Genet A 2009; 149A:931-8. [PMID: 19353646 DOI: 10.1002/ajmg.a.32764] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In an effort to discover genes important for human development, we have ascertained patients with congenital anomalies and cytogenetically balanced chromosomal rearrangements. Herein, we report a 4-year-old girl with profound deafness, a history of feeding difficulties, dysmorphism, strabismus, developmental delay, and an apparently balanced de novo paracentric chromosome 5 inversion, inv(5)(q15q33.2). Molecular cytogenetic analysis of the inversion revealed the presence of microdeletions of approximately 400-500 kb at or near both breakpoints. The 5q15 microdeletion completely removes the nuclear receptor NR2F1 (COUP-TFI) from the inverted chromosome 5. We propose haploinsufficiency of NR2F1 to be the cause of the patient's deafness and many of the other associated anomalies based on striking similarity with the Nr2f1 null mouse. Additionally, this study further highlights the need for high resolution analysis of clinical samples with chromosomal rearrangements as associated deletions may be primarily responsible for the clinical features of these patients.
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Affiliation(s)
- Kerry K Brown
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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Edelmann L, Hirschhorn K. Clinical Utility of Array CGH for the Detection of Chromosomal Imbalances Associated with Mental Retardation and Multiple Congenital Anomalies. Ann N Y Acad Sci 2008; 1151:157-66. [DOI: 10.1111/j.1749-6632.2008.03610.x] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Karadeniz N, Mrasek K, Weise A. Further delineation of complex chromosomal rearrangements in fertile male using multicolor banding. Mol Cytogenet 2008; 1:17. [PMID: 18687140 PMCID: PMC2531127 DOI: 10.1186/1755-8166-1-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2008] [Accepted: 08/07/2008] [Indexed: 11/20/2022] Open
Abstract
Background Complex chromosomal rearrangements (CCRs) are defined as structural chromosomal rearrangements with at least three breakpoints and exchange of genetic material between two or more chromosomes. Complex chromosomal translocations are rarely seen in the general population but the frequency of occurrence is anticipated to be much higher due balanced states with no phenotypic presentation. Here, we report a severely mentally retarded fertile male patient in whom further delineation of CCR involving chromosomes 1, 4 and 2 was carried out by using high resolution multicolor banding (MCB) technique. As a FISH based novel chromosome banding approach, high resolution MCB allows for the differentiation of chromosome region specific areas at band and subband levels. Results Cytogenetic studies using high resolution banding of the proband necessitated further delineation of the breakpoints because of their uncertainty: 46,XY,t(1;4;2)(p21~31;q31.3;q31). After using high resolution MCB based on microdissection derived region-specific libraries, the exact nature of chromosomal rearrangements for chromosomes 1, 2 and 4 were revealed and these breakpoints were located on 1p31.1, 1q24.3 and 4q31.3 giving rise to a balanced situation. Conclusion Further delineations are certainly required to provide detailed information about the relationship between balanced CCRs and their phenotypes in order to offer proper counseling to the families concerned. Carriers must be investigated with high resolution banding and molecular cytogenetic techniques to determine the exact locations of the breakpoints. High resolution MCB is an alternative and an efficient method to other FISH based chromosome banding techniques and can serve in clarifying the nature of CCR.
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Affiliation(s)
- Nilüfer Karadeniz
- Ankara Zübeyde Haným Maternity Hospital, Genetic Section, Ankara, Turkey.
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Fantes JA, Boland E, Ramsay J, Donnai D, Splitt M, Goodship JA, Stewart H, Whiteford M, Gautier P, Harewood L, Holloway S, Sharkey F, Maher E, van Heyningen V, Clayton-Smith J, Fitzpatrick DR, Black GCM. FISH mapping of de novo apparently balanced chromosome rearrangements identifies characteristics associated with phenotypic abnormality. Am J Hum Genet 2008; 82:916-26. [PMID: 18374296 PMCID: PMC2491339 DOI: 10.1016/j.ajhg.2008.02.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2007] [Revised: 02/03/2008] [Accepted: 02/05/2008] [Indexed: 11/16/2022] Open
Abstract
We report fluorescence in situ hybridization (FISH) mapping of 152, mostly de novo, apparently balanced chromosomal rearrangement (ABCR) breakpoints in 76 individuals, 30 of whom had no obvious phenotypic abnormality (control group) and 46 of whom had an associated disease (case group). The aim of this study was to identify breakpoint characteristics that could discriminate between these groups and which might be of predictive value in de novo ABCR (DN-ABCR) cases detected antenatally. We found no difference in the proportion of breakpoints that interrupted a gene, although in three cases, direct interruption or deletion of known autosomal-dominant or X-linked recessive Mendelian disease genes was diagnostic. The only significant predictor of phenotypic abnormality in the group as a whole was the localization of one or both breakpoints to an R-positive (G-negative) band with estimated predictive values of 0.69 (95% CL 0.54-0.81) and 0.90 (95% CL 0.60-0.98), respectively. R-positive bands are known to contain more genes and have a higher guanine-cytosine (GC) content than do G-positive (R-negative) bands; however, whether a gene was interrupted by the breakpoint or the GC content in the 200 kB around the breakpoint had no discriminant ability. Our results suggest that the large-scale genomic context of the breakpoint has prognostic utility and that the pathological mechanism of mapping to an R-band cannot be accounted for by direct gene inactivation.
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Affiliation(s)
- J A Fantes
- Medical and Developmental Genetics Section, Medical Research Council (MRC), Human Genetics Unit, Edinburgh EH4 2XU, Scotland, UK
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17
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Baptista J, Mercer C, Prigmore E, Gribble SM, Carter NP, Maloney V, Thomas NS, Jacobs PA, Crolla JA. Breakpoint mapping and array CGH in translocations: comparison of a phenotypically normal and an abnormal cohort. Am J Hum Genet 2008; 82:927-36. [PMID: 18371933 DOI: 10.1016/j.ajhg.2008.02.012] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2007] [Revised: 02/13/2008] [Accepted: 02/19/2008] [Indexed: 01/22/2023] Open
Abstract
We report the analyses of breakpoints in 31 phenotypically normal and 14 abnormal carriers of balanced translocations. Our study assesses the differences between balanced translocations in normal carriers and those in abnormal carriers, focusing on the presence of genomic imbalances at the breakpoints or elsewhere in the genome, presence of cryptic chromosome rearrangements, and gene disruption. Our hypothesis is that all four features will be associated with phenotypic abnormalities and absent or much less frequent in a normal population. In the normal cohort, we identified neither genomic imbalances at the breakpoints or elsewhere in the genome nor cryptic chromosome rearrangements. In contrast, we identified candidate disease-causing imbalances in 4/14 abnormal patients. These were three breakpoint associated deletions and three deletions unrelated to the breakpoints. All six de novo deletions originated on the paternally inherited chromosome. Additional complexity was also present in one of these cases. Gene disruption by the breakpoints was present in 16/31 phenotypically normal individuals and in 5/14 phenotypically abnormal patients. Our results show that translocations in phenotypically abnormal patients are molecularly distinct from those in normal individuals: the former are more likely to be associated with genomic imbalances at the breakpoints or elsewhere and with chromosomal complexity, whereas the frequency of gene disruption is similar in both normal and abnormal translocation carriers.
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18
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Higgins AW, Alkuraya FS, Bosco AF, Brown KK, Bruns GA, Donovan DJ, Eisenman R, Fan Y, Farra CG, Ferguson HL, Gusella JF, Harris DJ, Herrick SR, Kelly C, Kim HG, Kishikawa S, Korf BR, Kulkarni S, Lally E, Leach NT, Lemyre E, Lewis J, Ligon AH, Lu W, Maas RL, MacDonald ME, Moore SD, Peters RE, Quade BJ, Quintero-Rivera F, Saadi I, Shen Y, Shendure J, Williamson RE, Morton CC. Characterization of apparently balanced chromosomal rearrangements from the developmental genome anatomy project. Am J Hum Genet 2008; 82:712-22. [PMID: 18319076 DOI: 10.1016/j.ajhg.2008.01.011] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2007] [Revised: 12/17/2007] [Accepted: 01/04/2008] [Indexed: 12/27/2022] Open
Abstract
Apparently balanced chromosomal rearrangements in individuals with major congenital anomalies represent natural experiments of gene disruption and dysregulation. These individuals can be studied to identify novel genes critical in human development and to annotate further the function of known genes. Identification and characterization of these genes is the goal of the Developmental Genome Anatomy Project (DGAP). DGAP is a multidisciplinary effort that leverages the recent advances resulting from the Human Genome Project to increase our understanding of birth defects and the process of human development. Clinically significant phenotypes of individuals enrolled in DGAP are varied and, in most cases, involve multiple organ systems. Study of these individuals' chromosomal rearrangements has resulted in the mapping of 77 breakpoints from 40 chromosomal rearrangements by FISH with BACs and fosmids, array CGH, Southern-blot hybridization, MLPA, RT-PCR, and suppression PCR. Eighteen chromosomal breakpoints have been cloned and sequenced. Unsuspected genomic imbalances and cryptic rearrangements were detected, but less frequently than has been reported previously. Chromosomal rearrangements, both balanced and unbalanced, in individuals with multiple congenital anomalies continue to be a valuable resource for gene discovery and annotation.
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Shetty S, Boycott KM, Gillan TL, Bowser K, Parboosingh JS, McInnes B, Chernos JE, Bernier FP. Cytogenetic and molecular characterization of a de-novo cryptic deletion of 7p21 associated with an apparently balanced translocation and complex craniosynostosis. Clin Dysmorphol 2007; 16:253-6. [PMID: 17786117 DOI: 10.1097/mcd.0b013e3281e668eb] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We describe a female infant with complex craniosynostosis, significant craniofacial dysmorphism and developmental delay in which a de-novo apparently balanced translocation between chromosomes 7 and 18 [46,XX,t(7;18)(p15.3;q11.2)] was identified. Additional cytogenetic and molecular investigations identified a cryptic interstitial 7.6-10.6-Mb deletion of the region between bands 7p21.2 and 7p21.3 on the derivative chromosome 18. The deletion was of paternal origin and contained the TWIST1 gene, although her features were not completely characteristic of Saethre-Chotzen syndrome. The phenotype of this patient is likely further complicated by loss of other genes within the deleted region and/or disruption of a critical gene(s) at the sites of the breakpoints on chromosomes 7 and 18. This case illustrates the need for a systematic molecular study of breakpoints and the surrounding chromosomal regions in patients with apparently balanced rearrangements and phenotypic abnormalities.
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Affiliation(s)
- Shashirekha Shetty
- Department of Medical Genetics, Alberta Children's Hospital, Calgary, Alberta, Canada
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20
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Simovich MJ, Yatsenko SA, Kang SHL, Cheung SW, Dudek ME, Pursley A, Ward PA, Patel A, Lupski JR. Prenatal diagnosis of a 9q34.3 microdeletion by array-CGH in a fetus with an apparently balanced translocation. Prenat Diagn 2007; 27:1112-7. [PMID: 17849500 DOI: 10.1002/pd.1841] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
OBJECTIVES Use high-resolution genome analysis to clarify the genomic integrity in a fetus with a cytogenetically balanced translocation t(2;9)(q11.2;q34.3). METHODS High resolution molecular cytogenetic analyses including G-banded chromosome analysis, fluorescence in situ hybridization (FISH), and array-comparative genomic hybridization (CGH) were performed on cultured cells, and DNA extracted from chorionic villus sample (CVS), amniotic fluid cells and fetal tissue. In addition, a custom fosmid-based tiling path 9q34.3 microarray with a resolution of 35-40 kb was used for array-CGH. RESULTS GTG-banding analysis showed an apparently balanced de novo translocation between the long arms of chromosomes 2 and 9; t(2;9)(q11.2;q34.3). Array-CGH using a targeted chromosomal microarray analysis (CMA) uncovered a submicroscopic deletion of the subtelomeric region of 9q34.3 revealing the unbalanced nature of the rearrangement. These results were confirmed independently by FISH. The deletion was delimited to 2.7 Mb in size using the 9q34.3 fosmid-based tiling path array-CGH. CONCLUSION Array-CGH is a powerful tool for rapid detection of genomic imbalances associated with microdeletion/duplication syndromes and for the evaluation of de novo apparently balanced translocation to enable high-resolution genomic analysis at the breakpoints. Prenatal diagnosis of chromosomal rearrangements involving dosage-sensitive genomic regions is an important adjuvant to prenatal care and provides more accurate information for counseling and informed decision making.
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Affiliation(s)
- Marcia J Simovich
- Departments of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
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21
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Callier P, Faivre L, Marle N, Thauvin-Robinet C, Mosca AL, Masurel-Paulet A, Borgnon J, Falcon-Eicher S, Danino A, Malka G, Le Merrer M, Huet F, Mugneret F. Untreated growth hormone deficiency with extremely short stature, bone dysplasia, cleft lip--palate and severe mental retardation in a 26-year-old man with a de novo unbalanced translocation t(1;12)(q24;q24). Eur J Med Genet 2007; 50:455-64. [PMID: 17720646 DOI: 10.1016/j.ejmg.2007.06.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2007] [Accepted: 06/26/2007] [Indexed: 10/23/2022]
Abstract
We report on a 26-year-old patient presenting with extremely short stature (height 72cm, weight 6.5kg, OFC 42.5cm), facial dysmorphism, cleft lip--palate, severe mental retardation and de novo 1q24.2--q25.2 and 12q24.31 interstitial deletion. He was the only child of non-consanguineous parents and his birth length was 43cm. He had severe feeding difficulties and required enteral nutrition until the age of 3 years. Standard cytogenetic analysis showed an apparently balanced de novo translocation t(1;12)(q24;q24). Endocrine studies at 11 years of age for severe growth retardation revealed multiple pituitary hormone deficiency with severe growth hormone deficiency, but the child was untreated because of associated mental retardation. At 26 years of age, he could not walk or speak and had no signs of puberty. Investigations revealed spondylo-epi-metaphyseal dysplasia with severe osteoporosis, enlarged aorta when compared to the patient's size and apparently normal pituitary development. High resolution karyotype showed a 1q24-q25 deletion, and comparative genomic hybridization studies confirmed the 1q interstitial deletion. FISH studies of both breakpoints using PACs and BACs enabled us to further characterize the 1q interstitial deletion (1q24.2-1q25.2) and also revealed a 12q24.31 interstitial microdeletion. This case is compared with previously reported patients with similar deletions, but the untreated pituitary deficiency could also be responsible in part for the severity of the growth deficiency. This observation is of interest for two reasons. First, these deletions could be a clue in the search for a gene responsible for growth hormone deficiency/midline defects. Second, it shows the importance of molecular cytogenetics in the study of de novo apparently balanced translocation with abnormal phenotype.
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Affiliation(s)
- P Callier
- Laboratoire de Cytogénétique, Département de Génétique, CHU Le Bocage, 2 Bd Maréchal de Lattre de Tassigny, 21034 Dijon cédex, France.
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22
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Delahaye A, Pipiras E, Kanafani S, Touboul C, Vergnaud A, Encha-Razavi F, Sinico M, Benkhalifa M, Kasakyan S, Serero S, Wolf JP, Gérard-Blanluet M, Benzacken B. De novo Subtelomeric Deletion Additional to an Inherited Apparently Balanced Reciprocal Translocation. Fetal Diagn Ther 2007; 22:306-12. [PMID: 17361086 DOI: 10.1159/000100797] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2006] [Accepted: 07/12/2006] [Indexed: 11/19/2022]
Abstract
OBJECTIVE We describe the analysis of an apparently balanced inherited reciprocal translocation in a fetus presenting with multiple congenital abnormalities, characterize the structural chromosome rearrangement, and report an unexpected additional imbalance to the inherited rearrangement. METHODS DNA microarray was used to screen for genomic imbalance in subtelomeric and interstitial critical regions. High-resolution comparative genomic hybridization was used to screen for genomic imbalance at a genome-wide level. Fluorescence in situ hybridization using whole-chromosome painting and specific probes was used to characterize the inherited translocation, and the size of the de novoadditional deletion. RESULTS An unexpected additional deletion was found in 7qter on derivative 10 of the inherited maternal reciprocal translocation t(7;10)(q11.23; p14). CONCLUSIONS We show the usefulness of genome-wide and specific molecular cytogenetic techniques to explore apparently balanced rearrangements.
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MESH Headings
- Abnormalities, Multiple/diagnosis
- Abnormalities, Multiple/genetics
- Abnormalities, Multiple/pathology
- Abortion, Induced
- Adult
- Allelic Imbalance
- Brain/abnormalities
- Brain/pathology
- Chromosome Painting
- Cranial Fossa, Posterior/abnormalities
- Cranial Fossa, Posterior/pathology
- Cytogenetic Analysis
- Female
- Gene Deletion
- Heart Defects, Congenital/diagnosis
- Heart Defects, Congenital/genetics
- Heart Defects, Congenital/pathology
- Humans
- Karyotyping
- Oligonucleotide Array Sequence Analysis
- Pregnancy
- Prenatal Diagnosis/methods
- Telomere
- Translocation, Genetic
- Ultrasonography, Prenatal
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Affiliation(s)
- A Delahaye
- Service d'Histologie Embryologie Cytogénétique BDR, Hôpital Jean Verdier, AP-HP, Bondy, France
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23
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Complex balanced translocation t(1;5;7)(p32.1;q14.3;p21.3) and two microdeletions del(1)(p31.1p31.1) and del(7)(p14.1p14.1) in a patient with features of Greig cephalopolysyndactyly and mental retardation. Am J Med Genet A 2007; 143A:2738-43. [DOI: 10.1002/ajmg.a.32017] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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24
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Kanafani S, Aboura A, Pipiras E, Carbillon L, Tabet AC, Largillière C, Garel C, Gressens P, Bucourt M, Cedrin-Durnerin I, Lachassinne E, Roumegoux C, Uzan M, Hugues JN, Wolf JP, Benzacken B. Semilobar holoprosencephaly prenatal diagnosis: an unexpected complex rearrangement in ade novo apparently balanced reciprocal translocation on karyotype. Prenat Diagn 2007; 27:279-84. [PMID: 17269127 DOI: 10.1002/pd.1639] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We report a semilobar holoprosencephaly (HPE) in a post-intracytoplasmic-sperm-injection pregnancy. It was suggested by ultrasonography (US), documented on karyotype, identified with magnetic resonance imaging (MRI), established after birth and confirmed on post-mortem autopsy. An amniocentesis revealed a de novo apparently balanced reciprocal translocation 46,XY, t(7;8) (q31.3;q12). Fluorescence in situ hybridization (FISH) identified a deletion in the region of the Sonic Hedgehog gene (SHH) on der(8); nevertheless, the subtelomeric regions for chromosomes 7 and 8 were present. The parents decided to continue the pregnancy; a boy was born and survived for 3 days. The brain autopsy confirmed the semilobar HPE previously noted on US and MRI. Further, band-specific FISH revealed, in addition to SHH deletion, the presence of an inversion in the 7q translocated material on der(8). The parents' karyotypes were normal. An unexpected complex rearrangement was present in a de novo apparently balanced reciprocal translocation in a semilobar HPE.
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Affiliation(s)
- S Kanafani
- Service d'Histologie-Embryologie et Cytogénétique, Biologie de la Reproduction, Hôpital Jean Verdier, AP-HP, Bondy, France
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25
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Bisgaard AM, Kirchhoff M, Tümer Z, Jepsen B, Brøndum-Nielsen K, Cohen M, Hamborg-Petersen B, Bryndorf T, Tommerup N, Skovby F. Additional chromosomal abnormalities in patients with a previously detected abnormal karyotype, mental retardation, and dysmorphic features. Am J Med Genet A 2006; 140:2180-7. [PMID: 16955412 DOI: 10.1002/ajmg.a.31425] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The detection of chromosomal abnormalities in patients with mental retardation (MR) and dysmorphic features increases with improvements of molecular cytogenetic methods. We report on six patients referred for detailed characterization of chromosomal abnormalities (four translocations, one inversion, one deletion) detected by conventional cytogenetics, in whom metaphase CGH revealed imbalances not involved in the initially detected rearrangements. The detected abnormalities were validated by real-time PCR. Parents were investigated by CGH in four cases. The genomic screening revealed interstitial deletions of 2q33.2-q34, 3p21, 4q12-q13.1, 6q25, 13q22.2-q31.1, and 14q12. The estimated minimum sizes of the deletions ranged from 2.65 to 9.27 Mb. The CGH assay did not reveal imbalances that colocalized with the breakpoints of the inversion or the translocations. The deletion of 6q included ESR1, in which polymorphisms are associated with variation of adult height. FOXG1B, known to be involved in cortical development, was located in the 14q deletion. The results illustrate that whole-genome molecular cytogenetic analysis of phenotypically affected patients with abnormal conventional karyotypes may detect inapparent molecular cytogenetic abnormalities in patients with microscopic chromosomal abnormalities and that these data provide additional information of clinical importance.
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26
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Gajecka M, Glotzbach CD, Jarmuz M, Ballif BC, Shaffer LG. Identification of cryptic imbalance in phenotypically normal and abnormal translocation carriers. Eur J Hum Genet 2006; 14:1255-62. [PMID: 16941016 DOI: 10.1038/sj.ejhg.5201710] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Approximately one in 500 individuals carries a reciprocal translocation. Of the 121 monosomy 1p36 subjects ascertained by our laboratory, three independent cases involved unbalanced translocations of 1p and 9q, all of which were designated t(1;9)(p36.3;q34). These derivative chromosomes were inherited from balanced translocation carrier parents. To understand better the causes and consequences of chromosome breakage and rearrangement in the human genome, we characterized each derivative chromosome at the DNA sequence level and identified the junctions between 1p36 and 9q34. The breakpoint regions were unique in all individuals. Insertions and duplications were identified in two balanced translocation carrier parents and their unbalanced offspring. Sequence analyses revealed that the translocation breakpoints disrupted genes. This study demonstrates that apparently balanced reciprocal translocations in phenotypically normal carriers may have cryptic imbalance at the breakpoints. Because disrupted genes were identified in the phenotypically normal translocation carriers, caution should be exercised when interpreting data on phenotypically abnormal carriers with apparently balanced rearrangements that disrupt putative candidate genes.
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Affiliation(s)
- Marzena Gajecka
- Health Research and Education Center, Washington State University Spokane, Spokane, WA 99210, USA
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27
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Gribble SM, Prigmore E, Burford DC, Porter KM, Ng BL, Douglas EJ, Fiegler H, Carr P, Kalaitzopoulos D, Clegg S, Sandstrom R, Temple IK, Youings SA, Thomas NS, Dennis NR, Jacobs PA, Crolla JA, Carter NP. The complex nature of constitutional de novo apparently balanced translocations in patients presenting with abnormal phenotypes. J Med Genet 2006; 42:8-16. [PMID: 15635069 PMCID: PMC1735914 DOI: 10.1136/jmg.2004.024141] [Citation(s) in RCA: 168] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
OBJECTIVE To describe the systematic analysis of constitutional de novo apparently balanced translocations in patients presenting with abnormal phenotypes, characterise the structural chromosome rearrangements, map the translocation breakpoints, and report detectable genomic imbalances. METHODS DNA microarrays were used with a resolution of 1 Mb for the detailed genome-wide analysis of the patients. Array CGH was used to screen for genomic imbalance and array painting to map chromosome breakpoints rapidly. These two methods facilitate rapid analysis of translocation breakpoints and screening for cryptic chromosome imbalance. Breakpoints of rearrangements were further refined (to the level of spanning clones) using fluorescence in situ hybridisation where appropriate. RESULTS Unexpected additional complexity or genome imbalance was found in six of 10 patients studied. The patients could be grouped according to the general nature of the karyotype rearrangement as follows: (A) three cases with complex multiple rearrangements including deletions, inversions, and insertions at or near one or both breakpoints; (B) three cases in which, while the translocations appeared to be balanced, microarray analysis identified previously unrecognised imbalance on chromosomes unrelated to the translocation; (C) four cases in which the translocation breakpoints appeared simple and balanced at the resolution used. CONCLUSIONS This high level of unexpected rearrangement complexity, if generally confirmed in the study of further patients, will have an impact on current diagnostic investigations of this type and provides an argument for the more widespread adoption of microarray analysis or other high resolution genome-wide screens for chromosome imbalance and rearrangement.
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Affiliation(s)
- S M Gribble
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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28
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Baptista J, Prigmore E, Gribble SM, Jacobs PA, Carter NP, Crolla JA. Molecular cytogenetic analyses of breakpoints in apparently balanced reciprocal translocations carried by phenotypically normal individuals. Eur J Hum Genet 2006; 13:1205-12. [PMID: 16118644 DOI: 10.1038/sj.ejhg.5201488] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
To test the hypothesis that translocation breakpoints in normal individuals are simple and do not disrupt genes, we characterised the breakpoints in 13 phenotypically normal individuals incidentally ascertained with an apparently balanced reciprocal translocation. Cases were karyotyped, and the breakpoints were refined by fluorescence in situ hybridisation until breakpoint-spanning clones were identified. 1 Mb array-CGH was performed as a whole genome analysis tool to detect any imbalances in chromatin not directly involved in the breakpoints. Breakpoint-associated imbalances were not found in any of the patients analysed in this study. However, breakpoints which disrupted known genes were identified in two patients, with RYR2 disrupted in one patient and COL13A1 in the other. In a further eight patients, Ensembl mapping data suggested that a gene might be disrupted by a breakpoint. In one further patient, the translocation was shown to be nonreciprocal. This study shows that apparently balanced reciprocal translocations in phenotypically normal patients do not have imbalances at the breakpoints, in contrast to phenotypically abnormal patients where the translocation breakpoints are often associated with cryptic imbalances. However, phenotypically normal individuals, and phenotypically abnormal individuals may have genes disrupted and therefore inactivated by one of the breakpoints. The significance of these disruptions remains to be determined.
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Affiliation(s)
- Julia Baptista
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, Wiltshire, UK.
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29
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Sanlaville D, Lapierre JM, Turleau C, Coquin A, Borck G, Colleaux L, Vekemans M, Romana SP. Molecular karyotyping in human constitutional cytogenetics. Eur J Med Genet 2005; 48:214-31. [PMID: 16179218 DOI: 10.1016/j.ejmg.2005.04.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2005] [Accepted: 04/08/2005] [Indexed: 01/22/2023]
Abstract
Using array CGH it is possible to detect very small genetic imbalances anywhere in the genome. Its usefulness has been well documented in cancer and more recently in constitutional disorders. In particular it has been used to detect interstitial and subtelomeric submicroscopic imbalances, to characterize their size at the molecular level and to define the breakpoints of chromosomal translocation. Here, we review the various applications of array CGH in constitutional cytogenetics. This technology remains expensive and the existence of numerous sequence polymorphisms makes its interpretation difficult. The challenge today is to transfer this technology in the clinical setting.
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Affiliation(s)
- Damien Sanlaville
- Service de cytogénétique, laboratoire de cytogénétique, hôpital Necker-Enfants Malades, 149, rue de Sèvres, 75015 Paris, France.
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30
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Borg K, Stankiewicz P, Bocian E, Kruczek A, Obersztyn E, Lupski JR, Mazurczak T. Molecular analysis of a constitutional complex genome rearrangement with 11 breakpoints involving chromosomes 3, 11, 12, and 21 and a ∼0.5-Mb submicroscopic deletion in a patient with mild mental retardation. Hum Genet 2005; 118:267-75. [PMID: 16160854 DOI: 10.1007/s00439-005-0021-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2005] [Accepted: 06/03/2005] [Indexed: 02/02/2023]
Abstract
Complex chromosome rearrangements (CCRs) are extremely rare but often associated with mental retardation, congenital anomalies, or recurrent spontaneous abortions. We report a de novo apparently balanced CCR involving chromosomes 3 and 12 and a two-way translocation between chromosomes 11 and 21 in a woman with mild intellectual disability, obesity, coarse facies, and apparent synophrys without other distinctive dysmorphia or congenital anomalies. Molecular analysis of breakpoints using fluorescence in situ hybridization (FISH) with region-specific BAC clones revealed a more complex character for the CCR. The rearrangement is a result of nine breaks and involves reciprocal translocation of terminal chromosome fragments 3p24.1-->pter and 12q23.1-->qter, insertion of four fragments of the long arm of chromosome 12: q14.1-->q21?, q21?-->q22, q22-->q23.1, and q23.1-->q23.1 and a region 3p22.3-->p24.1 into chromosome 3q26.31. In addition, we detected a approximately 0.5-Mb submicroscopic deletion at 3q26.31. The deletion involves the chromosome region that has been previously associated with Cornelia de Lange syndrome (CdLS) in which a novel gene NAALADL2 has been mapped recently. Other potential genes responsible for intellectual deficiency disrupted as a result of patient's chromosomal rearrangement map at 12q14.1 (TAFA2), 12q23.1 (METAP2), and 11p14.1 (BDNF).
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Affiliation(s)
- Katarzyna Borg
- Department of Medical Genetics, Institute of Mother and Child, Kasprzaka 17A, 01-211, Warsaw, Poland
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31
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Albano F, Specchia G, Anelli L, Liso A, Zagaria A, Santoro A, Mirto S, Liso V, Rocchi M. Submicroscopic deletions in an acute myeloid leukemia case with a four-way t(8;11;16;21). Leuk Res 2005; 29:855-8. [PMID: 15927680 DOI: 10.1016/j.leukres.2004.12.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2004] [Accepted: 12/23/2004] [Indexed: 10/25/2022]
Abstract
The t(8;21)(q22;q22) rearrangement is observed in about 15% of acute myelocitic leukemia (AML) cases, while variant t(8;21) translocations are detected in 6-10% of AML patients positive for the 5'RUNX1/3'CBFA2T1 fusion gene. We report a detailed molecular cytogenetic analysis of a four-way variant t(8;11;16;21)(q22;q14;q12;q22) performed by fluorescence in situ hybridization with specific BAC and PAC clones. The study demonstrated the loss of several megabases belonging to chromosomes 11 and 16 whereas no deletion was detected on der(21). These findings suggest that a precise breakpoint characterization could identify submicroscopic genomic deletions whose meaning remains to be defined.
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MESH Headings
- Acute Disease
- Bone Marrow Cells/pathology
- Chromosomes, Human, Pair 11/genetics
- Chromosomes, Human, Pair 16/genetics
- Chromosomes, Human, Pair 21/genetics
- Chromosomes, Human, Pair 8/genetics
- Humans
- In Situ Hybridization, Fluorescence
- Leukemia, Myeloid/genetics
- Leukemia, Myeloid/pathology
- Sequence Deletion
- Translocation, Genetic
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Affiliation(s)
- Francesco Albano
- Department of Hematology, University of Bari, Policlinico, Piazza G. Cesare 11, 70124 Bari, Italy
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32
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Adeyinka A, Adams SA, Lorentz CP, Van Dyke DL, Jalal SM. Subtelomere deletions and translocations are frequently familial. Am J Med Genet A 2005; 135:28-35. [PMID: 15810004 DOI: 10.1002/ajmg.a.30675] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In recent years, strategies have been developed to investigate the possible role of chromosomal subtelomere regions in genetic disorders. The present study was to determine the incidence of familial subtelomeric abnormalities among individuals with developmental delay, idiopathic mental retardation, or non-specific congenital abnormalities. A review was conducted for patients and their relatives on whom subtelomeric DNA fluorescence in situ hybridization (telo-FISH) studies were performed. Patients were identified through a search of the Mayo Genetics System (MGS) database. Of 2,170 consecutive telo-FISH index case studies completed in our laboratory between January 2002 and December 2003, 121 or 5.6% had abnormalities of the subtelomere region. The present report includes 18 other abnormal index cases seen prior to 2002 to yield a total of 139 abnormal index cases. This represents 71 index patients with deletions, 53 index patients with derivative chromosomes, and 15 index patients with balanced rearrangements. A familial abnormality was identified in 29 (51.8%) of 56 families in whom parents and/or sibs were available for testing. Among 28 patients with deletions, 9 (32%) had an inherited deletion, whereas 19 (68%) were de novo. Family members of 20 index patients with derivative chromosomes were tested. Of these, 13 (65%) patients inherited the abnormality from a parent (12 from a parent who had a balanced translocation and 1 from a parent with the same abnormality), while 7 (35%) apparently arose de novo. Seven (88%) of 8 with balanced translocations inherited the translocation from one parent. The most common familial abnormalities involved 8pter deletion or rearrangement. The incidence of familial subtelomeric abnormalities is significantly high making parental telo-FISH studies an essential part of the investigation of patients with subtelomeric chromosome abnormalities.
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Affiliation(s)
- Adewale Adeyinka
- Cytogenetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
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33
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Harvard C, Malenfant P, Koochek M, Creighton S, Mickelson ECR, Holden JJA, Lewis MES, Rajcan-Separovic E. A variant Cri du Chat phenotype and autism spectrum disorder in a subject with de novo cryptic microdeletions involving 5p15.2 and 3p24.3-25 detected using whole genomic array CGH. Clin Genet 2005; 67:341-51. [PMID: 15733271 DOI: 10.1111/j.1399-0004.2005.00406.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Cri du Chat syndrome (CdCs) is a well-defined clinical entity, with an incidence of 1/15,000 to 1/50,000. The critical region for CdCs has been mapped to 5p15, with the hallmark cat-like cry sublocalized to 5p15.3 and the remaining clinical features to 5p15.2. We report findings in a subject with a de novo t(5;7)(p15.2;p12.2) and an inv(3)(p24q24), who was found to have a cryptic microdeletion in the critical region for CdCs detected using a 1-Mb genomic microarray. In addition to 5p deletion, the proband had a de novo single clone loss at the 3p breakpoint of inv(3)(p24q24) and a familial single clone deletion at 18q12. Deletions were confirmed using microsatellite analysis and fluorescence in situ hybridization. The 5p deletion encompasses approximately 3 Mb, mapping to the border between bands 5p15.2 and 5p15.31. The single clone deletion on chromosome 3 maps to 3p24.3-3p25, for which there is no known phenotype. The clinical features of our proband differ from the characteristic CdC phenotype, which may reflect the combined effect of the two de novo microdeletions and/or may further refine the critical region for CdCs. Typical features of CdCs that are present in the proband include moderate intellectual disability, speech, and motor delay as well as dysmorphic features (e.g. broad and high nasal root, hypertelorism, and coarse facies). Expected CdCs features that are not present are growth delay, microcephaly, round facies, micrognathia, epicanthal folds, and the signature high-pitched cry. Behavioral traits in this subject included autism spectrum disorder, attention-deficit hyperactivity disorder, and unmanageable behavior including aggression, tantrums, irritability, and self-destructive behavior. Several of these behaviors have been previously reported in patients with 5p deletion syndrome. Although most agree on the cat-cry critical region (5p15.3), there is discrepancy in the precise location and size of the region associated with the more severe manifestations of CdCs. The clinical description of this proband and the characterization of his 5p deletion may help to further refine the phenotype-genotype associations in CdCs and autism spectrum disorder.
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Affiliation(s)
- C Harvard
- Department of Pathology, University of British Columbia, Vancouver, British Columbia, Canada
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