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Rosenfeld JA, Fox JE, Descartes M, Brewer F, Stroud T, Gorski JL, Upton SJ, Moeschler JB, Monteleone B, Neill NJ, Lamb AN, Ballif BC, Shaffer LG, Ravnan JB. Clinical features associated with copy number variations of the 14q32 imprinted gene cluster. Am J Med Genet A 2014; 167A:345-53. [DOI: 10.1002/ajmg.a.36866] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Jill A. Rosenfeld
- Signature Genomic Laboratories; PerkinElmer; Inc.; Spokane Washington
| | - Joyce E. Fox
- Division of Medical Genetics; Steven and Alexandra Cohen Children's Medical Center of New York; New York
| | - Maria Descartes
- Department of Genetics; University of Alabama at Birmingham; Alabama
| | - Fallon Brewer
- Department of Genetics; University of Alabama at Birmingham; Alabama
| | - Tracy Stroud
- Division of Developmental Pediatrics; University of Missouri; Columbia Missouri
| | - Jerome L. Gorski
- Division of Medical Genetics; University of Missouri School of Medicine; Columbia Missouri
| | - Sheila J. Upton
- Children's Hospital at Dartmouth; Dartmouth-Hitchcock Medical Center; Lebanon New Hampshire
| | - John B. Moeschler
- Children's Hospital at Dartmouth; Dartmouth-Hitchcock Medical Center; Lebanon New Hampshire
| | | | - Nicholas J. Neill
- Signature Genomic Laboratories; PerkinElmer; Inc.; Spokane Washington
- Department of Molecular and Human Genetics; Baylor College of Medicine; Houston Texas
| | - Allen N. Lamb
- ARUP Laboratories; Department of Pathology; University of Utah; Salt Lake City Utah
| | - Blake C. Ballif
- Signature Genomic Laboratories; PerkinElmer; Inc.; Spokane Washington
- Paw Print Genetics; Genetic Veterinary Sciences; Inc.; Spokane Washington
| | - Lisa G. Shaffer
- Signature Genomic Laboratories; PerkinElmer; Inc.; Spokane Washington
- Paw Print Genetics; Genetic Veterinary Sciences; Inc.; Spokane Washington
| | - J. Britt Ravnan
- Signature Genomic Laboratories; PerkinElmer; Inc.; Spokane Washington
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Rosenfeld JA, Morton SA, Hummel C, Sulpizio SG, McDaniel LD, Schultz RA, Torchia BS, Ravnan JB, Ellison JW, Fisher AJ. Experience using a rapid assay for aneuploidy and microdeletion/microduplication detection in over 2,900 prenatal specimens. Fetal Diagn Ther 2014; 36:231-41. [PMID: 25115231 DOI: 10.1159/000360081] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 01/23/2014] [Indexed: 11/19/2022]
Abstract
BACKGROUND While microarray testing can identify chromosomal abnormalities missed by karyotyping, its prenatal use is often avoided in low-risk pregnancies due to the possible identification of variants of uncertain significance (VOUS). METHODS We tested 2,970 prenatal samples of all referral indications using a rapid BACs-on-Beads-based assay with probes for sex chromosomes, common autosomal aneuploidies, and 20 microdeletion/microduplication syndromes, designed as an alternative to microarray in low-risk pregnancies and an alternative to rapid aneuploidy testing in pregnancies also undergoing microarray analysis. RESULTS Interpretable results were obtained in 2,940 cases (99.0%), with 89% receiving results in 1 day. Aneuploidies were detected in 7.3% and partial chromosome abnormalities in 0.45% (n = 13), including 5 referred for maternal age, abnormal maternal serum screen, or isolated ultrasound markers. The added detection above karyotype was 1 in 745 in lower-risk cases with normal ultrasounds or isolated ultrasound markers/increased nuchal measurements and 1 in 165 for fetuses with structural/growth abnormalities. Neither false negatives nor false positives were found within test limitations. Female polyploidy could not be detected, while polyploidies with Y chromosomes were suspected and confirmed through additional analysis. CONCLUSION When combined with karyotyping, this assay provides increased interrogation of specific chromosomal regions, while limiting VOUS identification.
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Affiliation(s)
- Jill A Rosenfeld
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, Wash., USA
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Shuvarikov A, Campbell IM, Dittwald P, Neill NJ, Bialer MG, Moore C, Wheeler PG, Wallace SE, Hannibal MC, Murray MF, Giovanni MA, Terespolsky D, Sodhi S, Cassina M, Viskochil D, Moghaddam B, Herman K, Brown CW, Beck CR, Gambin A, Cheung SW, Patel A, Lamb AN, Shaffer LG, Ellison JW, Ravnan JB, Stankiewicz P, Rosenfeld JA. Recurrent HERV-H-mediated 3q13.2-q13.31 deletions cause a syndrome of hypotonia and motor, language, and cognitive delays. Hum Mutat 2013; 34:1415-23. [PMID: 23878096 DOI: 10.1002/humu.22384] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 07/11/2013] [Indexed: 11/09/2022]
Abstract
We describe the molecular and clinical characterization of nine individuals with recurrent, 3.4-Mb, de novo deletions of 3q13.2-q13.31 detected by chromosomal microarray analysis. All individuals have hypotonia and language and motor delays; they variably express mild to moderate cognitive delays (8/9), abnormal behavior (7/9), and autism spectrum disorders (3/9). Common facial features include downslanting palpebral fissures with epicanthal folds, a slightly bulbous nose, and relative macrocephaly. Twenty-eight genes map to the deleted region, including four strong candidate genes, DRD3, ZBTB20, GAP43, and BOC, with important roles in neural and/or muscular development. Analysis of the breakpoint regions based on array data revealed directly oriented human endogenous retrovirus (HERV-H) elements of ~5 kb in size and of >95% DNA sequence identity flanking the deletion. Subsequent DNA sequencing revealed different deletion breakpoints and suggested nonallelic homologous recombination (NAHR) between HERV-H elements as a mechanism of deletion formation, analogous to HERV-I-flanked and NAHR-mediated AZFa deletions. We propose that similar HERV elements may also mediate other recurrent deletion and duplication events on a genome-wide scale. Observation of rare recurrent chromosomal events such as these deletions helps to further the understanding of mechanisms behind naturally occurring variation in the human genome and its contribution to genetic disease.
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Affiliation(s)
- Andrey Shuvarikov
- Signature Genomic Laboratories, PerkinElmer, Inc, Spokane, Washington
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Ellison JW, Ravnan JB, Rosenfeld JA, Morton SA, Neill NJ, Williams MS, Lewis J, Torchia BS, Walker C, Traylor RN, Moles K, Miller E, Lantz J, Valentin C, Minier SL, Leiser K, Powell BR, Wilks TM, Shaffer LG. Clinical utility of chromosomal microarray analysis. Pediatrics 2012; 130:e1085-95. [PMID: 23071206 DOI: 10.1542/peds.2012-0568] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVE To test the hypothesis that chromosomal microarray analysis frequently diagnoses conditions that require specific medical follow-up and that referring physicians respond appropriately to abnormal test results. METHODS A total of 46,298 postnatal patients were tested by chromosomal microarray analysis for a variety of indications, most commonly intellectual disability/developmental delay, congenital anomalies, dysmorphic features, and neurobehavioral problems. The frequency of detection of abnormalities associated with actionable clinical features was tallied, and the rate of physician response to a subset of abnormal tests results was monitored. RESULTS A total of 2088 diagnoses were made of more than 100 different disorders that have specific clinical features that warrant follow-up. The detection rate for these conditions using high-resolution whole-genome microarrays was 5.4%, which translates to 35% of all clinically significant abnormal test results identified in our laboratory. In a subset of cases monitored for physician response, appropriate clinical action was taken more than 90% of the time as a direct result of the microarray finding. CONCLUSIONS The disorders diagnosed by chromosomal microarray analysis frequently have clinical features that need medical attention, and physicians respond to the diagnoses with specific clinical actions, thus arguing that microarray testing provides clinical utility for a significant number of patients tested.
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Affiliation(s)
- Jay W Ellison
- Signature Genomic Laboratories, PerkinElmer, Inc, Spokane, Washington 99207, USA.
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Shaffer LG, Rosenfeld JA, Dabell MP, Coppinger J, Bandholz AM, Ellison JW, Ravnan JB, Torchia BS, Ballif BC, Fisher AJ. Detection rates of clinically significant genomic alterations by microarray analysis for specific anomalies detected by ultrasound. Prenat Diagn 2012; 32:986-95. [PMID: 22847778 PMCID: PMC3509216 DOI: 10.1002/pd.3943] [Citation(s) in RCA: 178] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Revised: 06/01/2012] [Accepted: 06/26/2012] [Indexed: 12/18/2022]
Abstract
OBJECTIVE The aim of this study is to understand the diagnostic utility of comparative genomic hybridization (CGH)-based microarrays for pregnancies with abnormal ultrasound findings. METHODS We performed a retrospective analysis of 2858 pregnancies with abnormal ultrasounds and normal karyotypes (when performed) tested in our laboratory using CGH microarrays targeted to known chromosomal syndromes with later versions providing backbone coverage of the entire genome. Abnormalities were stratified according to organ system involvement. Detection rates for clinically significant findings among these categories were calculated. RESULTS Clinically significant genomic alterations were identified in cases with a single ultrasound anomaly (n = 99/1773, 5.6%), anomalies in two or more organ systems (n = 77/808, 9.5%), isolated growth abnormalities (n = 2/76, 2.6%), and soft markers (n = 2/77, 2.6%). The following anomalies in isolation or with additional anomalies had particularly high detection rates: holoprosencephaly (n = 9/85, 10.6%), posterior fossa defects (n = 21/144, 14.6%), skeletal anomalies (n = 15/140, 10.7%), ventricular septal defect (n = 14/132, 10.6%), hypoplastic left heart (n = 11/68, 16.2%), and cleft lip/palate (n = 14/136, 10.3%). CONCLUSIONS Microarray analysis identified clinically significant genomic alterations in 6.5% of cases with one or more abnormal ultrasound findings; the majority were below the resolution of karyotyping. Larger data sets such as this allow for sub-stratification by specific anomalies to determine risks for genomic alterations detectable by microarray analysis.
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Affiliation(s)
- Lisa G Shaffer
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, Washington, USA.
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Shaffer LG, Dabell MP, Fisher AJ, Coppinger J, Bandholz AM, Ellison JW, Ravnan JB, Torchia BS, Ballif BC, Rosenfeld JA. Experience with microarray-based comparative genomic hybridization for prenatal diagnosis in over 5000 pregnancies. Prenat Diagn 2012; 32:976-85. [PMID: 22865506 PMCID: PMC3491694 DOI: 10.1002/pd.3945] [Citation(s) in RCA: 152] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 06/11/2012] [Accepted: 07/01/2012] [Indexed: 01/12/2023]
Abstract
Objective To demonstrate the usefulness of microarray testing in prenatal diagnosis based on our laboratory experience. Methods Prenatal samples received from 2004 to 2011 for a variety of indications (n = 5003) were tested using comparative genomic hybridization-based microarrays targeted to known chromosomal syndromes with later versions of the microarrays providing backbone coverage of the entire genome. Results The overall detection rate of clinically significant copy number alterations (CNAs) among unbiased, nondemise cases was 5.3%. Detection rates were 6.5% and 8.2% for cases referred with abnormal ultrasounds and fetal demise, respectively. The overall rate of findings with unclear clinical significance was 4.2% but would reduce to 0.39% if only de novo CNAs were considered. In cases with known chromosomal rearrangements in the fetus or parent, 41.1% showed CNAs related to the rearrangements, whereas 1.3% showed clinically significant CNAs unrelated to the karyotype. Finally, 71% of the clinically significant CNAs found by microarray were below the resolution of conventional karyotyping of fetal chromosomes. Conclusions Microarray analysis has advantages over conventional cytogenetics, including the ability to more precisely characterize CNAs associated with abnormal karyotypes. Moreover, a significant proportion of cases studied by array will show a clinically significant CNA even with apparently normal karyotypes. © 2012 John Wiley & Sons, Ltd.
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Affiliation(s)
- Lisa G Shaffer
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA, USA.
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Meyertholen K, Ravnan JB, Matalon R. Identification of a Novel 14q13.3 Deletion Involving the SLC25A21 Gene Associated with Familial Synpolydactyly. Mol Syndromol 2012; 3:25-9. [PMID: 25759628 DOI: 10.1159/000339177] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/23/2012] [Indexed: 11/19/2022] Open
Abstract
Synpolydactyly is a relatively rare malformation. Recently, we came across a male infant with a familial synpolydactyly of the hands and feet. As most familial synpolydactyly syndromes have not been linked to any specific mutations, we felt further investigation was warranted. Using microarray and fluorescent in situ hybridization analysis, we identified a novel mutation of the SLC25A21 gene on chromosome 14.
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Affiliation(s)
- K Meyertholen
- School of Medicine, University of Texas Medical Branch, Galveston, Tex., USA
| | | | - R Matalon
- Division of Genetics, Department of Pediatrics, University of Texas Medical Branch, Galveston, Tex., USA
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Shaffer LG, Ravnan JB, Torchia BS, Ellison JW, Kashork CD, Deigan E, Herard P, Thomas SJ, Bauer S, Monroe J, Patel VD, Reilly SA, Coppinger J. 710: A targeted approach for the prenatal detection of common aneuploidies and 15 microdeletion syndromes. Am J Obstet Gynecol 2012. [DOI: 10.1016/j.ajog.2011.10.728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Ballif BC, Rosenfeld JA, Traylor R, Theisen A, Bader PI, Ladda RL, Sell SL, Steinraths M, Surti U, McGuire M, Williams S, Farrell SA, Filiano J, Schnur RE, Coffey LB, Tervo RC, Stroud T, Marble M, Netzloff M, Hanson K, Aylsworth AS, Bamforth JS, Babu D, Niyazov DM, Ravnan JB, Schultz RA, Lamb AN, Torchia BS, Bejjani BA, Shaffer LG. High-resolution array CGH defines critical regions and candidate genes for microcephaly, abnormalities of the corpus callosum, and seizure phenotypes in patients with microdeletions of 1q43q44. Hum Genet 2011; 131:145-56. [DOI: 10.1007/s00439-011-1073-y] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Accepted: 07/16/2011] [Indexed: 02/04/2023]
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Shaffer LG, Coppinger J, Morton SA, Alliman S, Burleson J, Traylor R, Walker C, Byerly S, Lamb AN, Schultz R, Ravnan JB, Kashork CD, Torchia BS, Sulpizio S, Sundin K, Schermer M, Adler K, Dallaire S, Ballif BC. The development of a rapid assay for prenatal testing of common aneuploidies and microdeletion syndromes. Prenat Diagn 2011; 31:778-87. [DOI: 10.1002/pd.2766] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Revised: 03/11/2011] [Accepted: 03/25/2011] [Indexed: 02/01/2023]
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Neill NJ, Ballif BC, Lamb AN, Parikh S, Ravnan JB, Schultz RA, Torchia BS, Rosenfeld JA, Shaffer LG. Recurrence, submicroscopic complexity, and potential clinical relevance of copy gains detected by array CGH that are shown to be unbalanced insertions by FISH. Genome Res 2011; 21:535-44. [PMID: 21383316 DOI: 10.1101/gr.114579.110] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Insertions occur when a segment of one chromosome is translocated and inserted into a new region of the same chromosome or a non-homologous chromosome. We report 71 cases with unbalanced insertions identified using array CGH and FISH in 4909 cases referred to our laboratory for array CGH and found to have copy-number abnormalities. Although the majority of insertions were non-recurrent, several recurrent unbalanced insertions were detected, including three der(Y)ins(Y;18)(q?11.2;p11.32p11.32)pat inherited from parents carrying an unbalanced insertion. The clinical significance of these recurrent rearrangements is unclear, although the small size, limited gene content, and inheritance pattern of each suggests that the phenotypic consequences may be benign. Cryptic, submicroscopic duplications were observed at or near the insertion sites in two patients, further confounding the clinical interpretation of these insertions. Using FISH, linear amplification, and array CGH, we identified a 126-kb duplicated region from 19p13.3 inserted into MECP2 at Xq28 in a patient with symptoms of Rett syndrome. Our results demonstrate that although the interpretation of most non-recurrent insertions is unclear without high-resolution insertion site characterization, the potential for an otherwise benign duplication to result in a clinically relevant outcome through the disruption of a gene necessitates the use of FISH to determine whether copy-number gains detected by array CGH represent tandem duplications or unbalanced insertions. Further follow-up testing using techniques such as linear amplification or sequencing should be used to determine gene involvement at the insertion site after FISH has identified the presence of an insertion.
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Giampietro PF, Babu D, Zabel CA, Silberman T, Zador I, DeBauche D, Ravnan JB, Dave BJ. Novel clinical features in a child with partial deletion of chromosome 11 [del(11)(q24.2)]: Further evidence for phenotypic heterogeneity. Am J Med Genet A 2006; 140:385-7. [PMID: 16411193 DOI: 10.1002/ajmg.a.31067] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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McClarren J, Donnenfeld AE, Ravnan JB. Prenatal diagnosis of an unexpected interstitial 22q11.2 deletion causing truncus arteriosus and thymic hypoplasia in a ring 22 chromosome derived from a maternally inherited paracentric inversion. Prenat Diagn 2006; 26:1212-5. [PMID: 17099929 DOI: 10.1002/pd.1590] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
OBJECTIVE To present the prenatal diagnosis of an interstitial 22q11.2 deletion involving a ring 22 chromosome associated with truncus arteriosus and a hypoplastic thymus. CASE Following the sonographic diagnosis of a cystic hygroma at 12 weeks of gestation, chromosome analysis revealed a ring 22 chromosome. RESULTS Ring chromosomes typically result in the deletion of genetic material from the distal long and short arms of the affected chromosome. The presence of an interstitial deletion in a ring chromosome is therefore unusual. FISH analysis revealed an unexpected deletion involving the TUPLE1 gene in the DiGeorge/Velocardiofacial syndrome region in 22q11.2. Maternal chromosome analysis revealed the cause of the apparent interstitial deletion, a paracentric inversion in the long arm of chromosome 22, resulting in the distal long arm of 22q being located adjacent to the centromere and the proximal end being located near the telomere. The fetus was subsequently diagnosed with truncus arteriosus and a hypoplastic thymus, consistent with DiGeorge syndrome. CONCLUSION The ring chromosome 22 found in the fetus appears to have been derived from a rearrangement of the mother's inverted 22, resulting in ring formation and loss of the end of the distal long arm of the inverted 22, including the TUPLE1 locus, causing DiGeorge syndrome in the fetus. The apparent interstitial deletion was actually a terminal deletion in a maternally inherited rearranged chromosome 22.
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MESH Headings
- Abnormalities, Multiple
- Abortion, Eugenic
- Adolescent
- Chorionic Villi Sampling
- Chromosome Aberrations
- Chromosome Deletion
- Chromosome Inversion
- Chromosomes, Human, Pair 22/genetics
- Fatal Outcome
- Female
- Humans
- In Situ Hybridization, Fluorescence
- Lymphangioma, Cystic/diagnostic imaging
- Lymphangioma, Cystic/embryology
- Pregnancy
- Pregnancy Complications
- Ring Chromosomes
- Spectral Karyotyping
- Thymus Hyperplasia/genetics
- Truncus Arteriosus, Persistent/genetics
- Truncus Arteriosus, Persistent/pathology
- Ultrasonography, Prenatal
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Ravnan JB, Tepperberg JH, Papenhausen P, Lamb AN, Hedrick J, Eash D, Ledbetter DH, Martin CL. Subtelomere FISH analysis of 11 688 cases: an evaluation of the frequency and pattern of subtelomere rearrangements in individuals with developmental disabilities. J Med Genet 2005; 43:478-89. [PMID: 16199540 PMCID: PMC2564531 DOI: 10.1136/jmg.2005.036350] [Citation(s) in RCA: 273] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Subtelomere fluorescence in situ hybridisation (FISH) analysis has increasingly been used as an adjunct to routine cytogenetic testing in order to detect small rearrangements. Previous reports have estimated an overall abnormality rate of 6%, with a range of 2-29% because of different inclusion criteria. METHODS This study presents data compiled from 11 688 cases referred for subtelomere FISH testing in three clinical cytogenetic laboratories. RESULTS In this study population, the detection rate for clinically significant subtelomere abnormalities was approximately 2.5%, with an additional 0.5% detection of presumed familial variants. Approximately half of the clinically significant abnormalities identified were terminal deletions, the majority of which were de novo. Most of the remaining cases were unbalanced translocations between two chromosomes or two arms of the same chromosome. Approximately 60% of the unbalanced translocations were inherited from a parent carrying a balanced form of the rearrangement. Other abnormalities identified included tandem duplications, apparently balanced translocations, partial deletions, and insertions. Interestingly, 9 cases (0.08%) were found to have interstitial deletions of non-telomeric control loci, either BCR on 22q or PML on 15q. The most common clinically significant imbalances found were deletions of 1p, 22q, 4p, 9q, 8p, 2q and 20p. The most common familial variants were a deletion or duplication of 10q, deletion of 4q, deletion of Yq, and duplication of X/Yp onto Xq. CONCLUSIONS This study of subtelomere rearrangements is a 20 fold increase in number over the previously reported largest study and represents an unbiased analysis of subtelomere rearrangements in a large, unselected patient population.
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Affiliation(s)
- J B Ravnan
- Genzyme Genetics, Santa Fe, New Mexico, USA
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Ravnan JB. Ascribe the simplest interpretation. Am J Med Genet 2001; 100:84. [PMID: 11337755 DOI: 10.1002/ajmg.1202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Abstract
Velocardiofacial syndrome (VCFS) and the DiGeorge sequence (DGS) are caused by 22q11.2 deletions. Fluorescence in situ hybridization (FISH) using the DiGeorge chromosome region (DGCR) probe (Oncor) was used to detect 31 deletions in 100 patients with possible VCFS. Retrospective FISH analysis of archived slides from 14 patients originally studied only by high-resolution G banding detected 6 patients with a DGCR deletion, and only 2 of these 6 had a microscopically visible chromosome deletion. The 4 familial deletions found exhibited a wide range of clinical presentations within each family. Comparison of clinical characteristics of patients with and without the DGCR deletion determined findings predictive of the deletion: abundant or unruly scalp hair; narrow palpebral fissures; a laterally "built-up" nose; velopharyngeal inadequacy; thymic hypoplasia; and congenital heart defects, specifically tetralogy of Fallot, ventriculoseptal defect, and interrupted aortic arch.
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Affiliation(s)
- J B Ravnan
- Department of Pediatrics, University of California, San Francisco, USA
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Ten Hagen KG, Ravnan JB, Cohen SN. Disparate replication properties of integrated and extrachromosomal forms of bovine papilloma virus in ID13 cells. J Mol Biol 1995; 254:119-29. [PMID: 7490737 DOI: 10.1006/jmbi.1995.0605] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Bovine papillomavirus (BPV) previously has been reported to exist in transformed rodent cell lines as both chromosomally integrated and extrachromosomal forms. In the BPV-transformed mouse cell line ID13, extrachromosomal BPV molecules replicate throughout S phase of the cell cycle in a random choice mode. We report here that these replication properties were altered for chromosomally integrated BPV DNA in five independent ID13 subclones. In all of the subclones, the integrated BPV sequences, which had no detectable deletions or mutations, existed in head-to-tail tandem arrays that replicated once per cell cycle, predominantly late in S phase. In contrast, extrachromosomal BPV molecules present in other subclones of the same cell line replicated in the random choice mode observed previously for non-integrated BPV. Our results indicate that the replication origin of integrated BPV either is inactivated as a consequence of chromosomal insertion, leading to the replication of BPV from origins in the flanking chromosomal DNA, or alternatively is reprogrammed to function in a once-per-cell cycle mode predominantly late in S phase.
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Affiliation(s)
- K G Ten Hagen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5120, USA
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Abstract
Rare cells that contain large amounts of bovine papilloma virus (BPV) DNA have been observed in populations of BPV-transformed mouse ID13 cells. The viral DNA molecules in these "jackpot cells" have been thought to have switched from the controlled replication typical of latent BPV infection to the uncontrolled "runaway" prelytic replication characteristic of terminal stage infection of bovine epidermal cells. By sequential subcloning of high-BPV derivatives of ID13, we isolated stable cell lines enriched more than 1000-fold for cells showing large amounts of BPV by fluorescence in situ hybridization analysis. High-BPV subclones contained a variant plasmid as well as wild-type BPV DNA; analysis of the BPV variants in two independently isolated subclones that showed the high-BPV phenotype in 50 to 80% of cells in the population indicated that both variants had undergone tandem duplication of the BPV long control region, which contains the viral origin of replication and transcription enhancer sequences. Transfer of the high-copy-number phenotype by transfection of DNA from high-BPV cells was accompanied by transfer of the variant plasmid. Density gradient analysis of BPV plasmid replication in high-BPV subclones showed the random-choice mode of replication observed in the parental ID13 population, rather than the rapid BPV replication found in epidermal cells destined for lysis and death. Our results indicate that high-BPV cells in actively dividing ID13 populations are not produced by uncontrolled replication of viral DNA and suggest that they may result instead from abnormal plasmid partitioning.
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Affiliation(s)
- J B Ravnan
- Department of Genetics, Stanford University School of Medicine, California 94305, USA
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Ravnan JB, Gilbert DM, Ten Hagen KG, Cohen SN. Random-choice replication of extrachromosomal bovine papillomavirus (BPV) molecules in heterogeneous, clonally derived BPV-infected cell lines. J Virol 1992; 66:6946-52. [PMID: 1331505 PMCID: PMC240326 DOI: 10.1128/jvi.66.12.6946-6952.1992] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Using fluorescence in situ hybridization and Southern blot analysis, we show that three clonally derived cell lines transformed with bovine papillomavirus (BPV), including ID13, the cell line commonly employed for BPV replication studies, are heterogeneous populations having extensive cell-to-cell variation in both the distribution and amount of BPV DNA. Different subclones of ID13 were found to differ in the form and amount of BPV DNA they contain. Most subclones showed no detectable BPV sequences; some contained either extrachromosomal BPV molecules distributed throughout the nucleus or BPV sequences integrated at discrete chromosomal sites, while others contained both integrated and plasmid forms. The results of density gradient analysis of BPV DNA from individual homogeneous subclones showed replication of the extrachromosomal BPV plasmids in a random-choice mode. In all cell lines studied, the presence after one round of chromosomal DNA replication of unreplicated BPV DNA and of BPV DNA having two postreplicative strands was independent of the presence of high-BPV-copy-number ("jackpot") cells. Our results substantiate the earlier conclusion that extrachromosomal BPV molecules replicate randomly and not according to a once-per-cell-cycle mechanism.
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Affiliation(s)
- J B Ravnan
- Department of Genetics, Stanford University School of Medicine, California 94305-5120
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