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Souzeau E, Thompson JA, McLaren TL, De Roach JN, Barnett CP, Lamey TM, Craig JE. Maternal uniparental isodisomy of chromosome 6 unmasks a novel variant in TULP1 in a patient with early onset retinal dystrophy. Mol Vis 2018; 24:478-484. [PMID: 30090012 PMCID: PMC6066270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 07/19/2018] [Indexed: 10/26/2022] Open
Abstract
Purpose Inherited retinal dystrophies are a clinically and genetically heterogeneous group of disorders. Molecular diagnosis has proven utility for affected individuals. In this study, we report an individual enrolled in the Australian Inherited Retinal Disease Registry and DNA Bank diagnosed with clinical features overlapping between Leber congenital amaurosis and retinitis pigmentosa. Methods DNA from the proband was sequenced using a gene panel for inherited retinal disorders, and a single nucleotide polymorphism (SNP) array was conducted to detect the presence of deletions and uniparental disomy. Results We identified a novel homozygous variant (c.524dupC, p.(Pro176ThrfsTer7)) in TULP1 resulting from maternal uniparental isodisomy of chromosome 6. The patient had clinical features consistent with biallelic pathogenic variants in TULP1, including congenital nystagmus, night blindness, non-recordable electroretinogram, mild myopia, and mild peripheral pigmentary changes in the fundus. Conclusions This is the first report of uniparental disomy 6 and a homozygous variant in TULP1 associated with a rod-cone dystrophy. Molecular diagnosis of inherited retinal dystrophies is essential to inform the mode of transmission and clinical management, and to identify potential candidates for future gene-specific therapies.
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Affiliation(s)
- Emmanuelle Souzeau
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Adelaide, Australia
| | - Jennifer A. Thompson
- Australian Inherited Retinal Disease Registry & DNA Bank, Department of Medical Technology & Physics, Sir Charles Gairdner Hospital, Perth, Australia
| | - Terri L. McLaren
- Australian Inherited Retinal Disease Registry & DNA Bank, Department of Medical Technology & Physics, Sir Charles Gairdner Hospital, Perth, Australia
| | - John N. De Roach
- Australian Inherited Retinal Disease Registry & DNA Bank, Department of Medical Technology & Physics, Sir Charles Gairdner Hospital, Perth, Australia,Centre for Ophthalmology & Visual Science, The University of Western Australia, Perth, Australia
| | - Christopher P. Barnett
- Paediatric and Reproductive Genetics unit, Women’s and Children’s Hospital, Adelaide, Australia
| | - Tina M. Lamey
- Australian Inherited Retinal Disease Registry & DNA Bank, Department of Medical Technology & Physics, Sir Charles Gairdner Hospital, Perth, Australia,Centre for Ophthalmology & Visual Science, The University of Western Australia, Perth, Australia
| | - Jamie E. Craig
- Department of Ophthalmology, Flinders University, Flinders Medical Centre, Adelaide, Australia
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2
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Huang J, Zhao Y, Shiraigol W, Li B, Bai D, Ye W, Daidiikhuu D, Yang L, Jin B, Zhao Q, Gao Y, Wu J, Bao W, Li A, Zhang Y, Han H, Bai H, Bao Y, Zhao L, Zhai Z, Zhao W, Sun Z, Zhang Y, Meng H, Dugarjaviin M. Analysis of horse genomes provides insight into the diversification and adaptive evolution of karyotype. Sci Rep 2014; 4:4958. [PMID: 24828444 PMCID: PMC4021364 DOI: 10.1038/srep04958] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 04/22/2014] [Indexed: 12/22/2022] Open
Abstract
Karyotypic diversification is more prominent in Equus species than in other mammals. Here, using next generation sequencing technology, we generated and de novo assembled quality genomes sequences for a male wild horse (Przewalski's horse) and a male domestic horse (Mongolian horse), with about 93-fold and 91-fold coverage, respectively. Portion of Y chromosome from wild horse assemblies (3 M bp) and Mongolian horse (2 M bp) were also sequenced and de novo assembled. We confirmed a Robertsonian translocation event through the wild horse's chromosomes 23 and 24, which contained sequences that were highly homologous with those on the domestic horse's chromosome 5. The four main types of rearrangement, insertion of unknown origin, inserted duplication, inversion, and relocation, are not evenly distributed on all the chromosomes, and some chromosomes, such as the X chromosome, contain more rearrangements than others, and the number of inversions is far less than the number of insertions and relocations in the horse genome. Furthermore, we discovered the percentages of LINE_L1 and LTR_ERV1 are significantly increased in rearrangement regions. The analysis results of the two representative Equus species genomes improved our knowledge of Equus chromosome rearrangement and karyotype evolution.
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Affiliation(s)
- Jinlong Huang
- 1] College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China [2]
| | - Yiping Zhao
- 1] College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China [2]
| | - Wunierfu Shiraigol
- 1] College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China [2]
| | - Bei Li
- 1] College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China [2]
| | - Dongyi Bai
- 1] College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China [2]
| | - Weixing Ye
- 1] Shanghai Personal Biotechnology Limited Company, 777 Longwu Road, Shanghai 200236, P.R. China [2]
| | - Dorjsuren Daidiikhuu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Lihua Yang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Burenqiqige Jin
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Qinan Zhao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Yahan Gao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Jing Wu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Wuyundalai Bao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Anaer Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Yuhong Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Haige Han
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Haitang Bai
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Yanqing Bao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Lele Zhao
- School of Agriculture and Biology, Shanghai Jiaotong University; Shanghai Key Laboratory of Veterinary Biotechnology, 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Zhengxiao Zhai
- School of Agriculture and Biology, Shanghai Jiaotong University; Shanghai Key Laboratory of Veterinary Biotechnology, 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Wenjing Zhao
- School of Agriculture and Biology, Shanghai Jiaotong University; Shanghai Key Laboratory of Veterinary Biotechnology, 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Zikui Sun
- Shanghai Personal Biotechnology Limited Company, 777 Longwu Road, Shanghai 200236, P.R. China
| | - Yan Zhang
- Virginia Bioinformatics Institute, Virginia Tech, Washington Street, MC0477, Blacksburg, Virginia, 24061, USA
| | - He Meng
- School of Agriculture and Biology, Shanghai Jiaotong University; Shanghai Key Laboratory of Veterinary Biotechnology, 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Manglai Dugarjaviin
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
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Catarzi S, Giunti L, Papadia F, Gabrielli O, Guerrini R, Donati MA, Genuardi M, Morrone A. Morquio A syndrome due to maternal uniparental isodisomy of the telomeric end of chromosome 16. Mol Genet Metab 2012; 105:438-42. [PMID: 22178352 DOI: 10.1016/j.ymgme.2011.11.196] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Revised: 11/23/2011] [Accepted: 11/23/2011] [Indexed: 11/23/2022]
Abstract
Morquio A syndrome (MPS IVA) is a recessive lysosomal storage disorder (LSD) caused by mutations in the GALNS gene leading to the deficiency of lysosomal enzyme N-acetylgalactosamine-6-sulfate sulfatase (GALNS). Patients show a broad spectrum of phenotypes ranging from classical severe type to mild forms. Classical forms are characterized by severe bone dysplasia and usually normal intelligence. So far, more than 170 unique mutations have been identified in the GALNS gene of MPS IVA patients. We report on a Morquio A patient with a classical phenotype who was found to be homozygous for a missense mutation (c.236 G>A; p.Cys79Tyr) in the GALNS gene. This alteration affects the highly conserved p.Cys79 that is transformed into formylglycine, the catalytic residue of the active site. The mutation was present in the proband's mother, but not in the father, whose paternity was confirmed by microsatellite analysis. In order to test the hypothesis of maternal uniparental disomy (UPD), we investigated the segregation of sixteen microsatellite markers from chromosome 16. The results showed a condition of maternal UPD due to an error in meiosis I. Maternal isodisomy of the 16q24 region led to homozygosity for the GALNS mutant allele, causing the patient's disease. These findings allow to add for the first time the LSD Morquio A syndrome to the list of conditions that can be caused by UPD. The possibility of UPD is relevant when giving genetic counseling to couples since the recurrent risk in future pregnancies is dramatically reduced.
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Affiliation(s)
- S Catarzi
- Metabolic and Muscular Unit, Clinical of Paediatric Neurology, Meyer Children's Hospital, University of Florence, Florence, Italy
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4
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Eggermann T, Kotzot D. Uniparentale Disomien. MED GENET-BERLIN 2010. [DOI: 10.1007/s11825-010-0242-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Zusammenfassung
Der Begriff uniparentale Disomie (UPD) beschreibt eine Chromosomenaberration, bei der beide Homologen/beide Kopien eines Chromosomenabschnitts (Heterodisomie) bzw. 2 Kopien eines Homologen/eines Chromosomenabschnitts (Isodisomie) von nur einem Elternteil herrühren. Man kann UPDs ganzer Chromosomen von segmentalen und von komplexen UPDs unterscheiden. Mögliche mit einer UPD assoziierte Probleme sind Trisomiemosaike, Homozygotie autosomal-rezessiv vererbter Mutationen, Vater-Kind- und Mutter-Tochter-Übertragung X-chromosomal vererbter Mutationen und mit einem Genomic Imprinting assoziierte Erkrankungen. Letzteres beschreibt die von der elterlichen Herkunft abhängige monoallelische Expression bestimmter Gene. Bislang bekannte Imprintingerkrankungen sind ein transienter neonataler Diabetes mellitus, das Silver-Russell-Syndrom, das Beckwith-Wiedemann-Syndrom, die upd(14)mat (Temple-Syndrom), die upd(14)pat, das Prader-Willi-Syndrom und das Angelman-Syndrom. Als Entstehungsmechanismen kommen ein Trisomic oder Monosomic Rescue, eine Gametenkomplementation oder ein Postfertilisierungsfehler in Frage. Gesamtinzidenz und -prävalenz sind nicht bekannt, für einzelne mit einer Imprintingerkrankung assoziierte UPDs werden Häufigkeiten bis 1:3400 unter Geburten angegeben. Als Nachweismethoden kommen in der Routinediagnostik vor allem die Mikrosatellitenmarkeranalyse, methylierungsspezifische Polymerasekettenreaktion (PCR) und methylierungsspezifische MLPA („multiplex ligation-dependent probe amplification“) zum Einsatz.
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Affiliation(s)
- T. Eggermann
- Aff1_242 grid.412301.5 0000000086531507 Institut für Humangenetik Universitätsklinikum Aachen, RWTH Aachen Pauwelsstraße 30 52074 Aachen Deutschland
| | - D. Kotzot
- Aff2_242 grid.5361.1 0000000088532677 Department für Medizinische Genetik, Molekulare und Klinische Pharmakologie Medizinische Universität Innsbruck Innsbruck Österreich
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5
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Ross LF. Good ethics requires good science: why transplant programs should not disclose misattributed parentage. Am J Transplant 2010; 10:742-746. [PMID: 20132166 DOI: 10.1111/j.1600-6143.2009.03011.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
In 1996, I argued that the recommendation by the Institute of Medicine (IOM) to inform women when tests reveal misattributed paternity and not to disclose this information to the women's partners was morally wrong. I argued in favor of disclosure to both parties. It is a position that I still hold. But claims of misattributed paternity are not 'incidental findings' as it was called in the old genetics literature, but a rather serious indictment of biological infidelity. In this paper I argue that the tests used by transplant programs for living donor-recipient compatibility are inadequate to accurately determine misattributed paternity. Further I argue that it is not the responsibility of the transplant community to undertake such serious forensic evaluations. Genetic inconsistencies in ABO and HLA inheritance should be reported as variations. Families who want further clarification should be referred to a genetic professional.
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Affiliation(s)
- L F Ross
- Department of Pediatrics and the MacLean Center for Clinical Medical Ethics, University of Chicago, Chicago, IL
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Hamvas A, Nogee LM, Wegner DJ, Depass K, Christodoulou J, Bennetts B, McQuade LR, Gray PH, Deterding RR, Carroll TR, Kammesheidt A, Kasch LM, Kulkarni S, Cole FS. Inherited surfactant deficiency caused by uniparental disomy of rare mutations in the surfactant protein-B and ATP binding cassette, subfamily a, member 3 genes. J Pediatr 2009; 155:854-859.e1. [PMID: 19647838 PMCID: PMC2794197 DOI: 10.1016/j.jpeds.2009.06.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2008] [Revised: 05/01/2009] [Accepted: 06/03/2009] [Indexed: 11/26/2022]
Abstract
OBJECTIVE To characterize inheritance of homozygous, rare, recessive loss-of-function mutations in surfactant protein-B (SFTPB) or ATP binding cassette, subfamily A, member 3 (ABCA3) genes in newborns with lethal respiratory failure. STUDY DESIGN We resequenced genes from parents whose infants were homozygous for mutations in SFTPB or ABCA3. For infants with only 1 heterozygous parent, we performed microsatellite analysis for chromosomes 2 (SFTPB) and 16 (ABCA3). RESULTS We identified 1 infant homozygous for the g.1549C > GAA mutation (121ins2) in SFTPB for whom only the mother was heterozygous and 3 infants homozygous for mutations in ABCA3 (p.K914R, p.P147L, and c.806_7insGCT) for whom only the fathers were heterozygous. For the SP-B-deficient infant, microsatellite markers confirmed maternal heterodisomy with segmental isodisomy. Microsatellite analysis confirmed paternal isodisomy for the 3 ABCA3-deficient infants. Two ABCA3-deficient infants underwent lung transplantation at 3 and 5 months of age, respectively, and 2 infants died. None exhibited any nonpulmonary phenotype. CONCLUSIONS Uniparental disomy should be suspected in infants with rare homozygous mutations in SFTPB or ABCA3. Confirmation of parental carrier status is important to provide recurrence risk and to monitor expression of other phenotypes that may emerge through reduction to homozygosity of recessive alleles.
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Affiliation(s)
- Aaron Hamvas
- Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine and St. Louis Children's Hospital, St. Louis, MO 63110, USA.
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7
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Malvagia S, Papi L, Morrone A, Donati MA, Ciani F, Pasquini E, la Marca G, Scholte HR, Genuardi M, Zammarchi E. Fatal malonyl CoA decarboxylase deficiency due to maternal uniparental isodisomy of the telomeric end of chromosome 16. Ann Hum Genet 2007; 71:705-12. [PMID: 17535268 DOI: 10.1111/j.1469-1809.2007.00373.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Malonic aciduria is a rare autosomal recessive disorder caused by deficiency of malonyl-CoA decarboxylase, encoded by the MLYCD gene. We report on a patient with clinical presentation in the neonatal period. Metabolic investigations led to a diagnosis of malonyl-CoA decarboxylase deficiency, confirmed by decreased activity in cultured fibroblasts. High doses of carnitine and a diet low in lipids led to a reduction in malonic acid excretion, and to an improvement in his clinical conditions, but at the age of 4 months he died suddenly and unexpectedly. No autopsy was performed. Molecular analysis of the MLYCD gene performed on the proband's RNA and genomic DNA identified a previously undescribed mutation (c.772-775delACTG) which was homozygous. This mutation was present in his mother but not in his father; paternity was confirmed by microsatellite analysis. A hypothesis of maternal uniparental disomy (UPD) was investigated using fourteen microsatellite markers on chromosome 16, and the results confirmed maternal UPD. Maternal isodisomy of the 16q24 region led to homozygosity for the MLYCD mutant allele, causing the patient's disease. These findings are relevant for genetic counselling of couples with a previously affected child, since the recurrence risk in future pregnancies is dramatically reduced by the finding of UPD. In addition, since the patient had none of the clinical manifestations previously associated with maternal UPD 16, this case provides no support for the existence of maternally imprinted genes on chromosome 16 with a major effect on phenotype.
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Affiliation(s)
- S Malvagia
- Department of Pediatrics, Metabolic Unit, Meyer Children's Hospital, University of Florence, Florence, Italy
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8
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Fremeaux-Bacchi V, Sanlaville D, Menouer S, Blouin J, Dragon-Durey MA, Fischbach M, Vekemans M, Fridman WH. Unusual clinical severity of complement membrane cofactor protein-associated hemolytic-uremic syndrome and uniparental isodisomy. Am J Kidney Dis 2007; 49:323-9. [PMID: 17261436 DOI: 10.1053/j.ajkd.2006.10.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2006] [Accepted: 10/10/2006] [Indexed: 11/11/2022]
Abstract
Atypical hemolytic-uremic syndrome (aHUS; OMIM 235400) is genetically and clinically heterogeneous. Mutations in membrane cofactor protein (MCP; CD46), a widely expressed complement regulator, predispose to recurrent forms of the disease. Patients carrying MCP mutations have a favorable clinical outcome in comparison to those with factor H (CFH) or factor I (IF) mutations, which lead in most cases to end-stage renal failure. We identified 1 patient who presented at 1 year of age with a first episode of aHUS requiring dialysis therapy. After 2 recurrences of the disease, the patient developed end-stage renal failure. No mutation in the CFH and IF genes was found. A novel homozygous mutation (IVS10+2 T-->C) in the splice-donor of exon 10 encoding the transmembrane region of the MCP gene was associated with dramatically decreased cell-surface expression of MCP. Because the nucleotide substitution was inherited from the patient's father, but not her mother, a large deletion or uniparental disomy was suspected. Both karyotyping and cytogenetic analysis of chromosome 1q32 were performed, for which MCP maps showed no abnormalities. Subsequent genotype analysis using microsatellite markers spanning chromosome 1 showed that the affected child was homozygous for the entire series of markers tested and that all alleles originated from the father. Complete paternal uniparental isodisomy of chromosome 1 is a novel mechanism resulting in severe deficiency of MCP expression. The outcome of the disease reported here indicates that MCP mutation and complete paternal uniparental disomy of chromosome 1 could have an additive effect in determining the severity of the HUS phenotype.
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Affiliation(s)
- Veronique Fremeaux-Bacchi
- Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Service d'Immunologie Biologique, France.
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9
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Xiao P, Liu P, Weber JL, Papasian CJ, Recker RR, Deng HW. Paternal uniparental isodisomy of the entire chromosome 3 revealed in a person with no apparent phenotypic disorders. Hum Mutat 2006; 27:133-7. [PMID: 16429396 DOI: 10.1002/humu.20302] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Uniparental disomy (UPD) is a rare genetic abnormality. During a whole genome linkage study we identified a case of paternal uniparental isodisomy 3 serendipitously. This is the first ascertained human paternal UPD for chromosome 3 (UPD3pat). The finding of this paternal UPD case of the entire chromosome 3 with no apparent phenotypic disorders suggests that there are no paternal imprinted genes causing rare genetic disorders on chromosome 3.
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Affiliation(s)
- Peng Xiao
- Department of Biomedical Sciences, School of Medicine, Creighton University, Omaha, Nebraska, USA
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10
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Weber JL. Clinical applications of Genome Polymorphism Scans. Biol Direct 2006; 1:16. [PMID: 16756678 PMCID: PMC1524726 DOI: 10.1186/1745-6150-1-16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2006] [Accepted: 06/06/2006] [Indexed: 12/22/2022] Open
Abstract
Applications of Genome Polymorphism Scans range from the relatively simple such as gender determination and confirmation of biological relationships, to the relatively complex such as determination of autozygosity and propagation of genetic information throughout pedigrees. Unlike nearly all other clinical DNA tests, the Scan is a universal test--it covers all people and all genes. In balance, I argue that the Genome Polymorphism Scan is the most powerful, affordable clinical DNA test available today.
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Affiliation(s)
- James L Weber
- Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, WI, USA.
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Ting JC, Ye Y, Thomas GH, Ruczinski I, Pevsner J. Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan. BMC Bioinformatics 2006; 7:25. [PMID: 16420694 PMCID: PMC1382255 DOI: 10.1186/1471-2105-7-25] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2005] [Accepted: 01/18/2006] [Indexed: 11/25/2022] Open
Abstract
Background A variety of diseases are caused by chromosomal abnormalities such as aneuploidies (having an abnormal number of chromosomes), microdeletions, microduplications, and uniparental disomy. High density single nucleotide polymorphism (SNP) microarrays provide information on chromosomal copy number changes, as well as genotype (heterozygosity and homozygosity). SNP array studies generate multiple types of data for each SNP site, some with more than 100,000 SNPs represented on each array. The identification of different classes of anomalies within SNP data has been challenging. Results We have developed SNPscan, a web-accessible tool to analyze and visualize high density SNP data. It enables researchers (1) to visually and quantitatively assess the quality of user-generated SNP data relative to a benchmark data set derived from a control population, (2) to display SNP intensity and allelic call data in order to detect chromosomal copy number anomalies (duplications and deletions), (3) to display uniparental isodisomy based on loss of heterozygosity (LOH) across genomic regions, (4) to compare paired samples (e.g. tumor and normal), and (5) to generate a file type for viewing SNP data in the University of California, Santa Cruz (UCSC) Human Genome Browser. SNPscan accepts data exported from Affymetrix Copy Number Analysis Tool as its input. We validated SNPscan using data generated from patients with known deletions, duplications, and uniparental disomy. We also inspected previously generated SNP data from 90 apparently normal individuals from the Centre d'Étude du Polymorphisme Humain (CEPH) collection, and identified three cases of uniparental isodisomy, four females having an apparently mosaic X chromosome, two mislabelled SNP data sets, and one microdeletion on chromosome 2 with mosaicism from an apparently normal female. These previously unrecognized abnormalities were all detected using SNPscan. The microdeletion was independently confirmed by fluorescence in situ hybridization, and a region of homozygosity in a UPD case was confirmed by sequencing of genomic DNA. Conclusion SNPscan is useful to identify chromosomal abnormalities based on SNP intensity (such as chromosomal copy number changes) and heterozygosity data (including regions of LOH and some cases of UPD). The program and source code are available at the SNPscan website .
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Affiliation(s)
- Jason C Ting
- Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA
| | - Ying Ye
- Pathobiology Graduate Program, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
| | - George H Thomas
- Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
- Department of Genetics, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
| | - Jonathan Pevsner
- Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA
- Pathobiology Graduate Program, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
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12
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Tsukishiro S, Li QY, Tanemura M, Sugiura-Ogasawara M, Suzumori K, Sonta SI. Paternal uniparental disomy of chromosome 14 and unique exchange of chromosome 7 in cases of spontaneous abortion. J Hum Genet 2005; 50:112-117. [PMID: 15747166 DOI: 10.1007/s10038-005-0229-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2004] [Accepted: 12/20/2004] [Indexed: 01/21/2023]
Abstract
To investigate the involvement of uniparental disomies (UPDs) in spontaneous abortion, the polymorphic patterns of microsatellites on each chromosome were analyzed in 164 cases of abortion. Eighty-three of the 164 cases had chromosomal abnormalities. In 79 of the remaining 81 cases with normal karyotypes, the microsatellite analysis revealed that biparental patterns were present in the informative microsatellites in all chromosomes. In one of the remaining two cases, however, the polymorphic patterns of chromosome 14 appeared to be both of paternal origin. The patterns of the distal of the long arm were homozygous, and those of the remaining region were heterozygous. That is, this fetus had paternal UPD 14, originating from meiosis I nondisjunction. In the other case, the polymorphic patterns of the distal one third of the long arm of chromosome 7 were uniparental (maternal) in origin whereas those of the remaining region of this chromosome were biparental. These findings thus suggested that this chromosome might have originated from chromatid exchange between the long arms of paternal and maternal chromosome 7 at the first mitotic division. Microsatellite analysis, however, produced no evidence of duplication or deletion of any segments. The findings also suggest the possibility that some UPDs may cause spontaneous abortion.
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Affiliation(s)
- Sami Tsukishiro
- Department of Obstetrics and Gynecology, Nagoya City University Medical School, Nagoya, Japan
| | - Qing Ying Li
- Department of Obstetrics and Gynecology, Nagoya City University Medical School, Nagoya, Japan
| | - Mitsuyo Tanemura
- Department of Obstetrics and Gynecology, Nagoya City University Medical School, Nagoya, Japan
| | | | - Kaoru Suzumori
- Department of Obstetrics and Gynecology, Nagoya City University Medical School, Nagoya, Japan
| | - Shin-Ichi Sonta
- Department of Genetics, Institute for Developmental Research, Aichi Human Service Center, 713-8 Kamiya-cho, Kasugai, Aichi, 480-0392, Japan.
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Chu C, Schwartz S, McPherson E. Paternal uniparental isodisomy for chromosome 14 in a patient with a normal 46,XY karyotype. Am J Med Genet A 2005; 127A:167-71. [PMID: 15108205 DOI: 10.1002/ajmg.a.20618] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Chromosome 14 demonstrates imprinting with differing phenotypes for both maternal and paternal uniparental disomy (UPD). Although only 11 cases of paternal uniparental disomy 14 (patUPD14) have been reported, a distinct clinically recognizable syndrome has emerged. The major features are polyhydramnios, small thorax, mildly short limbs, abdominal wall defects, and characteristic face with short palpebral fissures, broad flat nasal bridge, prominent philtrum, and small ears. Radiographically, the chest is bell-shaped and the ribs are distinctive with caudal bowing anteriorly and cranial bowing posteriorly. Several affected infants have died from respiratory failure. The survivors have short stature and mental retardation. The initial cases were all recognized because of translocations involving chromosome 14. Subsequently, several patients with a similar phenotype and normal chromosomes have been reported, including two with mixed iso- and hetero-disomy as well as one with segmental UPD14. Our patient is the first with pure paternal isodisomy 14 in the absence of a translocation. We present additional clinical information, review the literature, and discuss mechanisms that may explain paternal isodisomy 14 in our chromosomally normal patient. Paternal UPD14 with normal karyotype may be more common than previously suspected and may be overlooked unless recognition of the clinical phenotype prompts investigation for UPD.
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Affiliation(s)
- Cathy Chu
- University of Pittsburgh, Pittsburgh, Pennsylvania
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14
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Spena S, Duga S, Asselta R, Peyvandi F, Mahasandana C, Malcovati M, Tenchini ML. Congenital afibrinogenaemia caused by uniparental isodisomy of chromosome 4 containing a novel 15-kb deletion involving fibrinogen Aα-chain gene. Eur J Hum Genet 2004; 12:891-8. [PMID: 15489905 DOI: 10.1038/sj.ejhg.5201207] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Among rare inherited deficiencies of coagulation factors, congenital afibrinogenaemia is characterised by the lack of fibrinogen in plasma. In the last few years, several genetic defects underlying afibrinogenaemia (mostly point mutations) have been described in the fibrinogen gene cluster. In this study, the molecular basis responsible for afibrinogenaemia in a Thai proband was defined. Point mutation screening was accomplished by directly sequencing the three fibrinogen genes. The impossibility to amplify fibrinogen Aalpha-chain gene (FGA) exons 5 and 6 suggested the presence of a homozygous deletion. A specific long-range PCR assay enabled the identification of a novel 15-kb deletion, representing the largest afibrinogenaemia-causing deletion described so far. Direct sequencing of the deletion junction allowed mapping of the breakpoints in FGA intron 4 and in the intergenic region between Aalpha- and Bbeta-chain genes. Since the mutation was inherited only from the mother and nonpaternity was ruled out, a maternal uniparental disomy (UPD) was hypothesised. UPD test, carried out with markers covering the whole chromosome 4, revealed that maternal isodisomy was responsible for homozygosity of the 15-kb deletion in the proband. The apparently normal phenotype of the proband, except for afibrinogenaemia, suggests that UPD for chromosome 4 is clinically silent. This represents the first case of a documented complete isodisomy of chromosome 4 causing the phenotypic expression of a recessive disorder. In silico analyses of the regions surrounding the breakpoints suggested that the 15-kb deletion might have originated from an inappropriate repair of a double-strand break by the nonhomologous end joining mechanism.
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Affiliation(s)
- Silvia Spena
- Department of Biology and Genetics for Medical Sciences, University of Milan, Italy
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15
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Kondo Y, Tsukishiro S, Tanemura M, Sugiura-Ogasawara M, Suzumori K, Sonta SI. Maternal uniparental disomy of chromosome 16 in a case of spontaneous abortion. J Hum Genet 2004; 49:177-181. [PMID: 14997362 DOI: 10.1007/s10038-004-0128-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2003] [Accepted: 01/07/2004] [Indexed: 11/28/2022]
Abstract
To investigate the involvement of uniparental disomies (UPDs) in spontaneous abortions, we analyzed in detail the polymorphism of microsatellites on each chromosome in cases of abortion. Of the 52 spontaneous abortions investigated, 25 had a normal karyotype. The polymorphic analysis of these cases revealed that, in the villi from 24 of the 25 cases, biparental patterns were present in informative microsatellites in all autosomes. In the remaining case with a 46,XX karyotype (case 18), however, the informative patterns of the microsatellites of chromosome 16 appeared to be both of maternal origin. The results also showed that the region from the distal end of the short arm to near the middle point of the long arm of chromosome 16 (pter to D16S3107) were heterozygous, and those of the remaining region of the long arm (D16S3018 to qter) were homozygous. That is, this fetus had maternal isodisomy and heterodisomy of chromosome 16, originating from a maternal, meiosis I non-disjunction of dyad 16 that accompanied a crossover at near the middle point of the long arm. The present finding suggests that some UPDs may become a cause for spontaneous abortions.
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Affiliation(s)
- Yuko Kondo
- Department of Obstetrics and Gynecology, Nagoya City University Medical School, Nagoya 467-8601, Japan
- Department of Obstetrics and Gynecology, Moriyama Municipal Hospital, Nagoya 463-8567, Japan
| | - Sami Tsukishiro
- Department of Obstetrics and Gynecology, Nagoya City University Medical School, Nagoya 467-8601, Japan
| | - Mitsuyo Tanemura
- Department of Obstetrics and Gynecology, Nagoya City University Medical School, Nagoya 467-8601, Japan
| | - Mayumi Sugiura-Ogasawara
- Department of Obstetrics and Gynecology, Nagoya City University Medical School, Nagoya 467-8601, Japan
| | - Kaoru Suzumori
- Department of Obstetrics and Gynecology, Nagoya City University Medical School, Nagoya 467-8601, Japan
| | - Shin-Ichi Sonta
- Department of Genetics, Institute for Developmental Research, Aichi Human Service Center, 713-8 Kamiya-cho, Kasugai, Aichi 480-0392, Japan.
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16
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Thompson DA, Gal A. Vitamin A metabolism in the retinal pigment epithelium: genes, mutations, and diseases. Prog Retin Eye Res 2003; 22:683-703. [PMID: 12892646 DOI: 10.1016/s1350-9462(03)00051-x] [Citation(s) in RCA: 138] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Mutations in the genes necessary for the metabolism of vitamin A (all-trans retinol) and cycling of retinoids between the photoreceptors and retinal pigment epithelium (RPE) (the visual cycle) have recently emerged as an important class of genetic defects responsible for retinal dystrophies and dysfunctions. Research into the causes and treatment of diseases resulting from defects in retinal vitamin A metabolism is currently the subject of intense interest, since disorders affecting the RPE are, in principle, more accessible to therapeutic intervention than those affecting the proteins of photoreceptor cells. This chapter presents an overview of the visual cycle, as well as the function of the RPE genes involved in the conversion of vitamin A to 11-cis retinal, the chromophore of the visual pigments. The identification of disease-causing mutations in this group of genes is described as well as the associated phenotypes that range from stationary night blindness to childhood-onset severe visual handicap. Consideration is also given to alternative genetic paradigms potentially relevant to defects in vitamin A metabolism, including a discussion of the relationship of this pathway to age-related macular degeneration, a non-Mendelian disease of late onset. Finally, progress and prospects for targeted therapeutic intervention in vitamin A metabolism are presented, including retinoid and gene replacement therapy. On the basis of early successes in animal models, and plans underway for Phase I/II clinical trials, it is hoped that the near future will bring effective therapies for many retinal dystrophy patients with defects in vitamin A metabolism.
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Affiliation(s)
- Debra A Thompson
- Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, MI 48105, USA.
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17
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Reddy KS, Wang S, Groh S, Gonatos J. SKY assessment of two karyotypes with 0-6 supernumerary marker/ring chromosomes and review of previously reported cases with two or more markers. Am J Med Genet A 2003; 118A:156-71. [PMID: 12655496 DOI: 10.1002/ajmg.a.10045] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A 7-month-old boy with developmental delay and congenital abnormalities and a 58-year-old man with mental retardation, impaired speech, and dysmorphic features were referred for cytogenetic studies. The peripheral blood chromosome studies of Patient 1 had a de novo mosaic karyotype with 2-6 supernumerary marker chromosomes. Patient 2 had a mosaic karyotype with 1-5 supernumerary marker chromosomes and normal cells. All markers appeared to have a centromere by C-banding and also by fluorescence in situ hybridization (FISH) using all centromere probe for Patient 1. The majority of the markers appeared like rings. Except for one marker in Patient 1 and 2-3 markers in Patient 2 with discernible >5 Mb euchromatin, the rest of the markers were minute and some appeared to have barely discernible euchromatin in C-banding or FISH. Spectral karyotyping (SKY) was attempted to determine the origin of the marker chromosomes. Because some markers had barely any euchromatin, their classification was not clear cut and they were identified as derived from more than one chromosome. The SKY classification of the markers in Patient 1 was 1, 3, 5, 7, 11, 15, and 22 and in Patient 2 was 1, 5, 6, or 7. Patient 2 was lost to further follow-up studies. To confirm the recurring SKY classifications in Patient 1, centromere probes for chromosomes 1, 3, 5, 7, 11, 15, and 22 were used. The markers were negative for 1, 3, and 11 but positive for 7, 15, and 22 and probably 5. Since 5 centromere probe cross hybridizes with 1 and 19, the weak signal on the marker/s in successive hybridization did not give a definitive answer. Also, the 5 paint probe was not conclusive because of the minute size of the marker. In some metaphases, two markers were derived from 5 or 22. For clinical considerations, the marker derived from 7, although variable in size, appeared to consistently have euchromatin, followed by 15, while 22 and 5 markers were mostly centromeric heterochromatin. The elastin gene probe that maps to 7q11.23, SNRPN gene that maps to 15q11.2, and TUPLE gene that maps to 22q11.2 did not give a signal on the markers. As expected for a majority of ring chromosomes, the pan telomere probe did not hybridize to any of the markers. This highly unusual karyotype was confirmed in the buccal epithelium using a mix of centromere 7 and 15 probes and the combination 14/22 probe. The ratio of additional FISH signals in the buccal mucosal cells was comparable to the ratios observed in the peripheral blood. In this study, we have attempted to consolidate the data on >/=2 marker cases to understand the analysis constraints, the range of clinical abnormalities, and the mechanisms involved. The literature was surveyed for multiple markers cases. A majority of the reported cases had two markers, either derived from the same chromosome or from two different chromosomes or two cell lines with different markers derived from the same chromosome. Cases with three or more markers were rare. The nature and extent of euchromatin content of the multiple markers appears to determine the phenotype. Frequently, multiple marker cases had small to minute markers. The clinical presentation varied from mild to severe. While two bisatellited markers may be associated with infertility, the phenotype in other cases ranged from borderline intelligence and mild dysmorphism to developmental delay, mental retardation, and congenital abnormalities.
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Affiliation(s)
- Kavita S Reddy
- Department of Cytogenetics, Quest Diagnostics, Inc., San Juan Capistrano, California, USA.
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18
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Spiekerkoetter U, Eeds A, Yue Z, Haines J, Strauss AW, Summar M. Uniparental disomy of chromosome 2 resulting in lethal trifunctional protein deficiency due to homozygous alpha-subunit mutations. Hum Mutat 2002; 20:447-51. [PMID: 12442268 DOI: 10.1002/humu.10142] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The mitochondrial trifunctional protein (TFP) is an enzyme complex of the fatty acid beta-oxidation cycle composed of an alpha- and a beta-subunit. The two encoding genes are located in the same region on chromosome 2 (2p23). TFP deficiency due to either alpha- or beta-subunit mutations is characterized by mutational and phenotypic heterogeneity with severe, early-onset, cardiac forms and milder, later-onset, myopathic phenotypes. In two unrelated patients with lethal TFP deficiency, we delineated apparently homozygous alpha-subunit mutations that were present in heterozygous form in both mothers, but not in either biological father. We performed a microsatellite repeat analysis of both patients and their parents using seven chromosome 2-specific polymorphic DNA markers and four nonchromosome 2 markers. In both patients, two chromosome 2-specific markers demonstrated maternal isodisomy of chromosome 2. The other five chromosome 2-specific markers were noninformative in each patient. Inheritance of alleles from chromosomes 4, 5, and 7 was consistent with paternity. These results explain the apparently anomalous pattern of transmission. Six of our 12 known TFP-deficient patients with alpha-subunit mutations have disease due to homozygous changes and two of them via the mechanism of uniparental disomy (UPD) (16.7%). For very rare autosomal recessive diseases, UPD may represent a common mechanism. This study emphasizes the need to confirm mutations in parents whenever possible. TFP deficiency is another disorder that has become manifest due to isodisomy of chromosome 2. This information will impact genetic counseling for these families, reducing greatly the 25% risk normally used for recessive disorders.
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Affiliation(s)
- Ute Spiekerkoetter
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA.
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19
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Kayashima T, Katahira M, Harada N, Miwa N, Ohta T, Yoshiura KI, Matsumoto N, Nakane Y, Nakamura Y, Kajii T, Niikawa N, Kishino T. Maternal isodisomy for 14q21-q24 in a man with diabetes mellitus. AMERICAN JOURNAL OF MEDICAL GENETICS 2002; 111:38-42. [PMID: 12124731 DOI: 10.1002/ajmg.10511] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We report a 20-year-old man with maternal uniparental disomy for chromosome 14 (UPD14) and maturity-onset diabetes mellitus (DM). He had pre- and postnatal growth retardation, developed DM at age 20 years without any autoimmune antibodies, and had a mosaic 45,XY,der(14;14)(q10;q10)[129]/46,XY,+14,der(14;14)(q10;q10)[1] karyotype. Allelotyping using microsatellite markers covering the entire 14q indicated segmental maternal isodisomy for 14q21-q24 and maternal heterodisomy of the remaining regions of the chromosome. It is thus tempting to speculate that the segmental isodisomy led to reduction to homozygosity for a mutant gene and thus caused his DM, although the possibility of coincidental occurrence of the two events cannot totally be ruled out. Fluorescence in situ hybridization (FISH) analysis using BAC clone probes revealed that the isodisomic segment did not overlap any known IDDM or NIDDM susceptibility loci on chromosome 14, suggesting a novel locus for a subset of DM at the isodisomic segment.
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20
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Thompson DA, McHenry CL, Li Y, Richards JE, Othman MI, Schwinger E, Vollrath D, Jacobson SG, Gal A. Retinal dystrophy due to paternal isodisomy for chromosome 1 or chromosome 2, with homoallelism for mutations in RPE65 or MERTK, respectively. Am J Hum Genet 2002; 70:224-9. [PMID: 11727200 PMCID: PMC384890 DOI: 10.1086/338455] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2001] [Accepted: 10/31/2001] [Indexed: 11/03/2022] Open
Abstract
Uniparental disomy (UPD) is a rare condition in which a diploid offspring carries a chromosomal pair from a single parent. We now report the first two cases of UPD resulting in retinal degeneration. We identified an apparently homozygous loss-of-function mutation of RPE65 (1p31) in one retinal dystrophy patient and an apparently homozygous loss-of-function mutation of MERTK (2q14.1) in a second retinal dystrophy patient. In both families, the gene defect was present in the patient's heterozygous father but not in the patient's mother. Analysis of haplotypes in each nuclear kindred, by use of DNA polymorphisms distributed along both chromosomal arms, indicated the absence of the maternal allele for all informative markers tested on chromosome 1 in the first patient and on chromosome 2 in the second patient. Our results suggest that retinal degeneration in these individuals is due to apparently complete paternal isodisomy involving reduction to homoallelism for RPE65 or MERTK loss-of-function alleles. Our findings provide evidence for the first time, in the case of chromosome 2, and confirm previous observations, in the case of chromosome 1, that there are no paternally imprinted genes on chromosomes 1 and 2 that have a major effect on phenotype.
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Affiliation(s)
- Debra A. Thompson
- Departments of Ophthalmology and Visual Sciences and Biological Chemistry, University of Michigan Medical School, Ann Arbor; Institut für Humangenetik, Universitätsklinikum Hamburg-Eppendorf, Hamburg; Institut für Humangenetik, Universitätsklinikum, Lübeck, Germany, Department of Genetics, Stanford University School of Medicine, Stanford; Scheie Eye Institute, Department of Ophthalmology, University of Pennsylvania Medical School, Philadelphia
| | - Christina L. McHenry
- Departments of Ophthalmology and Visual Sciences and Biological Chemistry, University of Michigan Medical School, Ann Arbor; Institut für Humangenetik, Universitätsklinikum Hamburg-Eppendorf, Hamburg; Institut für Humangenetik, Universitätsklinikum, Lübeck, Germany, Department of Genetics, Stanford University School of Medicine, Stanford; Scheie Eye Institute, Department of Ophthalmology, University of Pennsylvania Medical School, Philadelphia
| | - Yun Li
- Departments of Ophthalmology and Visual Sciences and Biological Chemistry, University of Michigan Medical School, Ann Arbor; Institut für Humangenetik, Universitätsklinikum Hamburg-Eppendorf, Hamburg; Institut für Humangenetik, Universitätsklinikum, Lübeck, Germany, Department of Genetics, Stanford University School of Medicine, Stanford; Scheie Eye Institute, Department of Ophthalmology, University of Pennsylvania Medical School, Philadelphia
| | - Julia E. Richards
- Departments of Ophthalmology and Visual Sciences and Biological Chemistry, University of Michigan Medical School, Ann Arbor; Institut für Humangenetik, Universitätsklinikum Hamburg-Eppendorf, Hamburg; Institut für Humangenetik, Universitätsklinikum, Lübeck, Germany, Department of Genetics, Stanford University School of Medicine, Stanford; Scheie Eye Institute, Department of Ophthalmology, University of Pennsylvania Medical School, Philadelphia
| | - Mohammad I. Othman
- Departments of Ophthalmology and Visual Sciences and Biological Chemistry, University of Michigan Medical School, Ann Arbor; Institut für Humangenetik, Universitätsklinikum Hamburg-Eppendorf, Hamburg; Institut für Humangenetik, Universitätsklinikum, Lübeck, Germany, Department of Genetics, Stanford University School of Medicine, Stanford; Scheie Eye Institute, Department of Ophthalmology, University of Pennsylvania Medical School, Philadelphia
| | - Eberhard Schwinger
- Departments of Ophthalmology and Visual Sciences and Biological Chemistry, University of Michigan Medical School, Ann Arbor; Institut für Humangenetik, Universitätsklinikum Hamburg-Eppendorf, Hamburg; Institut für Humangenetik, Universitätsklinikum, Lübeck, Germany, Department of Genetics, Stanford University School of Medicine, Stanford; Scheie Eye Institute, Department of Ophthalmology, University of Pennsylvania Medical School, Philadelphia
| | - Douglas Vollrath
- Departments of Ophthalmology and Visual Sciences and Biological Chemistry, University of Michigan Medical School, Ann Arbor; Institut für Humangenetik, Universitätsklinikum Hamburg-Eppendorf, Hamburg; Institut für Humangenetik, Universitätsklinikum, Lübeck, Germany, Department of Genetics, Stanford University School of Medicine, Stanford; Scheie Eye Institute, Department of Ophthalmology, University of Pennsylvania Medical School, Philadelphia
| | - Samuel G. Jacobson
- Departments of Ophthalmology and Visual Sciences and Biological Chemistry, University of Michigan Medical School, Ann Arbor; Institut für Humangenetik, Universitätsklinikum Hamburg-Eppendorf, Hamburg; Institut für Humangenetik, Universitätsklinikum, Lübeck, Germany, Department of Genetics, Stanford University School of Medicine, Stanford; Scheie Eye Institute, Department of Ophthalmology, University of Pennsylvania Medical School, Philadelphia
| | - Andreas Gal
- Departments of Ophthalmology and Visual Sciences and Biological Chemistry, University of Michigan Medical School, Ann Arbor; Institut für Humangenetik, Universitätsklinikum Hamburg-Eppendorf, Hamburg; Institut für Humangenetik, Universitätsklinikum, Lübeck, Germany, Department of Genetics, Stanford University School of Medicine, Stanford; Scheie Eye Institute, Department of Ophthalmology, University of Pennsylvania Medical School, Philadelphia
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21
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Hauschild R, Wollina U, Bruckner-Tuderman L. Junctional epidermolysis bullosa gravis (Herlitz): diagnostic and genetic aspects. J Eur Acad Dermatol Venereol 2001; 15:73-6. [PMID: 11451332 DOI: 10.1046/j.1468-3083.2001.00215.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report on a boy suffering from lethal junctional epidermolysis bullosa gravis (JEBH) (Herlitz-type) (OMIM 226700). Screening for mutations of LAMB3 gene with polymerase chain reaction (PCR) amplification of all exons from genomic DNA and subsequent heteroduplex analysis and dideoxynucleotide sequencing of heteroduplex forming PCR products disclosed two mutations: the recurrent maternal mutation R635X and the novel paternal mutation 1629insG, both in exon 14 of LAMB3. Both mutations lead to a premature termination code, non-sense mediated mRNA decay and to absence of the synthesis of the beta3 chain of laminin 5. During the mutation screening of the index patient a second pregnancy was ascertained. After amniocentesis (14 + 1 week of pregnancy), prenatal diagnosis from fetal cells was performed and compound heterozygosity for both mutations was evident. The consultants decided to have a termination of pregnancy shortly after the diagnosis. Remarkable skin fragility of the fetus was evident by clinical examination. Complete absence of laminin 5 could be demonstrated by immunofluorescence staining. By the third pregnancy of this couple so far screened for mutations by chorionic villus sampling for prenatal molecular diagnosis a healthy but heterozygous child is expected.
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Affiliation(s)
- R Hauschild
- Institute of Human Genetics and Anthropology, Friedrich-Schiller-University of Jena, Germany
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22
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Abstract
The expression of a few genes in the human genome depends on whether they are located on the maternal or on the paternal chromosome. This phenomenon is called genomic imprinting. Several of these genes have a role in normal embryonic and fetal growth, as indicated by an abnormal development associated with disturbed genomic imprinting. This has lead to the suggestion that the genomic imprinting has evolved as a mechanism to regulate embryonic and fetal growth.
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Affiliation(s)
- K Devriendt
- Center for Human Genetics, University Hospital Gasthuisberg, Herestraat 49, 3000, Leuven, Belgium.
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23
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Abstract
Steroid 5alpha-reductase 2 deficiency is an autosomal recessive form of male pseudohermaphroditism caused by mutations in the SRD5A2 gene. In this study, we performed DNA analyses in two unrelated subjects bearing the enzyme deficiency and found differences in the mode of transmission for the disease. The data showed that in both families the fathers were carriers for an E197D mutation, whereas the mothers were carriers for a P212R mutation. Patient 1 was identified as compound heterozygote because he had both alterations (E197D/P212R). On the contrary, patient 2 was found to be homozygous, but only for the paternal mutation. Because this finding could not be explained on the basis ofnonpaternity or a chromosomal abnormality, the presence of uniparental disomy was suggested. The reduction to homozygosity for the E197D mutation, as confirmed by restriction analysis, supported this view. The results of our study give evidence of the first case of 5alpha-reductase deficiency resulting from uniparental disomy and also disclose an alternate mechanism whereby this enzymatic disorder can derive from a single parent.
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Affiliation(s)
- B Chávez
- Department of Reproductive Biology, Instituto Nacional de la Nutrición Salvador Zubirán, México
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24
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Kalousek DK, Vekemans M. Confined placental mosaicism and genomic imprinting. Best Pract Res Clin Obstet Gynaecol 2000; 14:723-30. [PMID: 10985941 DOI: 10.1053/beog.2000.0107] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The concept of confined placental mosaicism and its relationship to genomic imprinting and uniparental disomy is explained in this chapter. Clinically significant imprinting syndromes, such as Prader-Willi syndrome, Angelman syndrome, Beckwith-Wiedemann syndrome, Silver-Russell syndrome and transient neonatal diabetes mellitus, potentially associated with confined placental mosaicism are described and referenced. Non-Mendelian inheritance of recessive mutations in uniparental disomy is illustrated. Both skewed X chromosome inactivation and isolated gonadal mosaicism are outlined as newly recognized consequences of post-zygotic chromosomal mutation and confined placental mosaicism. Clinical management of pregnancies with confined placental mosaicism is proposed as well as future research directions in the field of confined placental mosaicism and its consequences.
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Affiliation(s)
- D K Kalousek
- Cytogenetic Laboratory, B.C. Children's and Women's Hospital, Vancouver, B.C., Canada
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25
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Karanjawala ZE, Kääriäinen H, Ghosh S, Tannenbaum J, Martin C, Ally D, Tuomilehto J, Valle T, Collins FS. Complete maternal isodisomy of chromosome 8 in an individual with an early-onset ileal carcinoid tumor. AMERICAN JOURNAL OF MEDICAL GENETICS 2000; 93:207-10. [PMID: 10925383 DOI: 10.1002/1096-8628(20000731)93:3<207::aid-ajmg9>3.0.co;2-a] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Uniparental disomy (UPD) is a condition in which diploid individuals possess a chromosome pair from a single parent. In some instances, UPD causes an abnormal phenotype due to imprinting effects, reduction to homozygosity at recessive disease loci, or trisomy mosaicism. Here we report the first account of an individual with apparently nonmosaic complete maternal isodisomy of chromosome 8. This individual was identified during routine genotyping in a genomewide search for type 2 diabetes susceptibility genes, although he does not have diabetes. He is of normal appearance, stature, and intelligence, but there is an unusual history of early onset ileal carcinoid. The discovery of other maternal UPD 8 cases will be necessary to define whether this condition causes a distinct phenotype.
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Affiliation(s)
- Z E Karanjawala
- Positional Cloning Section, Genetics and Molecular Biology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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26
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Abstract
Uniparental disomy (UPD) refers to the situation in which both copies of a chromosome pair have originated from one parent. In humans, it can result in clinical conditions by producing either homozygosity for recessive mutations or aberrant patterns of imprinting. Furthermore, UPD is frequently found in conjunction with mosaicism for a chromosomally abnormal cell line, which can also contribute to phenotypic abnormalities. Investigations into the mechanisms by which UPD may arise have helped to expand our general awareness of the impact of chromosomal abnormalities and chromosomal mosaicism in normal human development. Specifically, it appears that errors in the transmission of a chromosome from parent to gamete and during early somatic cell divisions are remarkably common but that embryo and cell selection during early embryogenesis help to ensure the presence of a numerically balanced chromosome complement in the developing fetus. UPD is also likely to occur within a portion of cells in all individuals simply as a consequence of somatic recombination occurring during mitotic cell divisions. This can be an important step in cancer development as well as a contributing factor to other late onset diseases. This review summarizes mechanisms by which UPD may arise and their associated clinical consequences.
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Affiliation(s)
- W P Robinson
- Department of Medical Genetics, University of British Columbia, B.C. Research Institute for Children's & Women's Health, Vancouver, Canada.
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27
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Manzoni MF, Pramparo T, Stroppolo A, Chiaino F, Bosi E, Zuffardi O, Carrozzo R. A patient with maternal chromosome 14 UPD presenting with a mild phenotype and MODY. Clin Genet 2000; 57:406-8. [PMID: 10852378 DOI: 10.1034/j.1399-0004.2000.570514.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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28
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Mergenthaler S, Wollmann HA, Burger B, Eggermann K, Kaiser P, Ranke MB, Schwanitz G, Eggermann T. Formation of uniparental disomy 7 delineated from new cases and a UPD7 case after trisomy 7 rescue. Presentation of own results and review of the literature. ANNALES DE GENETIQUE 2000; 43:15-21. [PMID: 10818216 DOI: 10.1016/s0003-3995(00)00010-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Maternal uniparental disomy for the entire chromosome 7 (matUPD7) has been reported several times in Silver-Russell syndrome (SRS) and growth-restricted patients. Here we present our results from the analysis of an abortion with confined placental mosaicism (CPM) for trisomy 7 which showed a maternal meiotic origin of the trisomy in the placenta and rescue to maternal UPD7 in foetal membrane. Furthermore, two newly detected SRS cases with maternal UPD7 revealed isodisomy and partial heterodisomy, respectively. Summarising these results with those published previously on the origin of UPD7, similar numbers of isodisomy (n=11) and cases with complete or partial heterodisomy (n=12) have been reported. In respect to the different formation mechanisms of UPD, complete isodisomy should be the result of a post-zygotic mitotic segregation error, whereas heterodisomic UPDs should be caused by trisomic rescue after meiotic non-disjunction events. In maternal UPD7, 50% of cases seem to be caused by post-zygotic mitotic segregation errors, which is similar to the situation in trisomy 7. This result corresponds to the situation in trisomy 8 but is in contrast to observations in the frequent aneuploidies. Thus, the different findings in these aberrations reflect the presence of multiple factors that act to ensure normal segregation, varying in importance for each chromosome.
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Affiliation(s)
- S Mergenthaler
- Institute of Human Genetics, Technical University of Aachen, Pauwelsstrasse 30, 52074, Aachen, Germany
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Spiro RP, Christian SL, Ledbetter DH, New MI, Wilson RC, Roizen N, Rosenfield RL. Intrauterine growth retardation associated with maternal uniparental disomy for chromosome 6 unmasked by congenital adrenal hyperplasia. Pediatr Res 1999; 46:510-3. [PMID: 10541311 DOI: 10.1203/00006450-199911000-00004] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We report the first case of maternal uniparental disomy for chromosome 6 (UPD6mat) ascertained through congenital adrenal hyperplasia (CAH), which arose because of reduction to homozygosity of an autosomal recessive mutation. This case suggests that UPD6mat is associated with intrauterine growth retardation (IUGR). A case of paternal UPD (involving only the short arm of chromosome 6) ascertained as CAH has previously been reported, but was not stated to have IUGR. Our patient was born with IUGR followed by extraordinarily good catch-up growth. She had a history of a marked lag in motor development. She presented at 2.65 y of age with pubarche of 3 mo duration, clitoral enlargement, and an advanced bone age. Simple virilizing CAH was diagnosed by elevations of plasma 17-hydroxyprogesterone and testosterone. Mutation analysis showed that the CAH was due to homozygosity for the 1172N exon 4 mutation. When parental DNA was examined, the mother was found to be heterozygous for the uncommon exon 4 mutation, while the father had no detectable mutations. DNA microsatellite analysis was subsequently performed on the patient and parents using polymorphic markers spanning the entire chromosome 6. Seven markers were informative for inheritance of a single maternal allele and absence of paternal alleles in the proband. Analysis of microsatellite markers from other chromosomes confirmed biparental inheritance at these loci. This combination of findings is diagnostic of UPD6mat. The only other reported case of UPD6mat was discovered serendipitously when genotyped for renal transplantation; this patient had a history of IUGR. Since both cases of UPD6mat had IUGR, the phenotype appears to include IUGR as well as the potential to unmask an autosomal recessive trait.
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Affiliation(s)
- R P Spiro
- Department of Human Genetics, The University of Chicago, Pritzker School of Medicine, Illinois, USA
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Laan LA, v Haeringen A, Brouwer OF. Angelman syndrome: a review of clinical and genetic aspects. Clin Neurol Neurosurg 1999; 101:161-70. [PMID: 10536901 DOI: 10.1016/s0303-8467(99)00030-x] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
This paper reviews Angelman syndrome (AS) with regard to the clinical features in childhood and adulthood, epileptic seizures and EEG findings, neuroimaging studies and the present knowledge on the genetic mechanisms underlying this syndrome. Different clinical phenotypes and genotypes of AS are described, including chromosome 15q11-13 deletion, uniparental disomy, methylation imprinting abnormalities and mutations in the UBE3A gene.
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Affiliation(s)
- L A Laan
- Department of Neurology, Leiden University Medical Center, The Netherlands
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Sankaranarayanan K. Ionizing radiation and genetic risks. X. The potential "disease phenotypes" of radiation-induced genetic damage in humans: perspectives from human molecular biology and radiation genetics. Mutat Res 1999; 429:45-83. [PMID: 10434024 DOI: 10.1016/s0027-5107(99)00100-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Estimates of genetic risks of radiation exposure of humans are traditionally expressed as expected increases in the frequencies of genetic diseases (single-gene, chromosomal and multifactorial) over and above those of naturally-occurring ones in the population. An important assumption in expressing risks in this manner is that gonadal radiation exposures can cause an increase in the frequency of mutations and that this would result in an increase in the frequency of genetic diseases under study. However, despite compelling evidence for radiation-induced mutations in experimental systems, no increases in the frequencies of genetic diseases of concern or other adverse effects (i.e., those which are not formally classified as genetic diseases), have been found in human studies involving parents who have sustained radiation exposures. The known differences between spontaneous mutations that underlie naturally-occurring single-gene diseases and radiation-induced mutations studied in experimental systems now permit us to address and resolve these issues to some extent. The fact that spontaneous mutations (among which are point mutations and DNA deletions generally restricted to the gene) originate through a number of different mechanisms and that the latter are intimately related to the DNA organization of the genes, are now well-documented. Further, spontaneous mutations include those that cause diseases through loss of function as well as gain of function of genes. In contrast, most radiation-induced mutations studied in experimental systems (although identified through the phenotypes of the marker genes) are predominantly multigene deletions which cause loss of function; the recoverability of an induced deletion in a livebirth seems dependent on whether the gene and the genomic region in which it is located can tolerate heterozygosity for the deletion and yet be compatible with viability. In retrospect, the successful mutation test systems (such as the mouse specific locus test) used in radiation studies have involved genes which are non-essential for survival and are also located in genomic regions, likewise non-essential for survival. In contrast, most of the human genes at which induced mutations have been looked for, do not seem to have these attributes. The inference therefore is that the failure to find induced germline mutations in humans is not due to the resistance of human genes to induced mutations but due to the structural and functional constraints associated with their recoverability in livebirths. Since the risk of inducible genetic diseases in humans is estimated using rates of "recovered" mutations in mice, there is a need to introduce appropriate correction factors to bridge the gap between these rates and the rates at which mutations causing diseases are potentially recoverable in humans. Since the whole genome is the "target" for radiation-induced genetic damage, the failure to find increases in the frequencies of specific single-gene diseases of societal concern does not imply that there are no genetic risks of radiation exposures: the problem lies in delineating the phenotypes of recoverable genetic damage that are recognizable in livebirths. Data from studies of naturally-occurring microdeletion syndromes in humans and those from mouse radiation studies are instructive in this regard. They (i) support the view that growth retardation, mental retardation and multisystem developmental abnormalities are likely to be among the quantitatively more important adverse effects of radiation-induced genetic damage than mutations in a few selected genes and (ii) underscore the need to expand the focus in risk estimation from known genetic diseases (as has been the case thus far) to include these induced adverse developmental effects although most of these are not formally classified as "genetic diseases". (ABSTRACT TRUNCATED)
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Affiliation(s)
- K Sankaranarayanan
- MGC, Department of Radiation Genetics and Chemical Mutagenesis, Leiden University Medical Centre, Sylvius Laboratories, Wassenaarseweg 72, 2333 AL, Leiden, Netherlands.
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