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Kang H, Chen Y, Wang L, Gao C, Li X, Hu Y. Pathogenic recurrent copy number variants in 7,078 pregnancies via chromosomal microarray analysis. J Perinat Med 2024; 52:171-180. [PMID: 38081620 DOI: 10.1515/jpm-2022-0580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 09/30/2023] [Indexed: 02/09/2024]
Abstract
OBJECTIVES To investigate the incidence of pathogenic recurrent CNVs in fetuses with different referral indications and review the intrauterine phenotypic features of each CNV. METHODS A total of 7,078 amniotic fluid samples were collected for chromosome microarray analysis (CMA) and cases carrying pathogenic recurrent CNVs were further studied. RESULTS The highest incidence of pathogenic recurrent CNVs was 2.25 % in fetal ultrasound anomalies (FUA) group. Moreover, regardless of other indications, pregnant women with advanced maternal age have a lower incidence compared with whom less than 35 years old (p<0.05). In total 1.17 % (83/7,078) samples carried pathogenic recurrent CNVs: 20 cases with 22q11.2 recurrent region (12 microdeletion and eight microduplication), 11 with 1q21.1 (five microdeletion and six microduplication) and 16p13.11 (four microdeletion and seven microduplication), 10 with 15q11.2 recurrent microdeletion, seven with Xp22.31 recurrent microdeletion and 16p11.2 (three microdeletion and four microduplication), four with 7q11.23 (two microdeletion and two microduplication), three with 17p11.2 (three microdeletion), 17p12 (two microdeletion and one microduplication) and 17q12 (two microdeletion and one microduplication). The rest ones were rare in this study. CONCLUSIONS Pathogenic recurrent CNVs are more likely to be identified in FUA group. Pregnant women with advanced maternal age have a lower incidence of pathogenic recurrent CNVs. The profile of pathogenic recurrent CNVs between prenatal and postnatal is different, especially in 22q11.2, 1q21.1, 15q13.3 recurrent region and 15q11.2 deletion.
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Affiliation(s)
- Han Kang
- Prenatal Diagnosis Department, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, P.R. China
| | - Yifei Chen
- Prenatal Diagnosis Department, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, P.R. China
| | - Lingxi Wang
- Prenatal Diagnosis Department, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, P.R. China
| | - Chonglan Gao
- Prenatal Diagnosis Department, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, P.R. China
| | - Xingyu Li
- Prenatal Diagnosis Department, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, P.R. China
| | - Yu Hu
- Prenatal Diagnosis Department, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, P.R. China
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2
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Array Comparative Genomic Hybridisation and Droplet Digital PCR Uncover Recurrent Copy Number Variation of the TTN Segmental Duplication Region. Genes (Basel) 2022; 13:genes13050905. [PMID: 35627290 PMCID: PMC9142044 DOI: 10.3390/genes13050905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/13/2022] [Accepted: 05/17/2022] [Indexed: 02/04/2023] Open
Abstract
Intragenic segmental duplication regions are potential hotspots for recurrent copy number variation and possible pathogenic aberrations. Two large sarcomeric genes, nebulin and titin, both contain such segmental duplication regions. Using our custom Comparative Genomic Hybridisation array, we have previously shown that a gain or loss of more than one copy of the repeated block of the nebulin triplicate region constitutes a recessive pathogenic mutation. Using targeted array-CGH, similar copy number variants can be detected in the segmental duplication region of titin. Due to the limitations of the array-CGH methodology and the repetitiveness of the region, the exact copy numbers of the blocks could not be determined. Therefore, we developed complementary custom Droplet Digital PCR assays for the titin segmental duplication region to confirm true variation. Our combined methods show that the titin segmental duplication region is subject to recurrent copy number variation. Gains and losses were detected in samples from healthy individuals as well as in samples from patients with different muscle disorders. The copy number variation observed in our cohort is likely benign, but pathogenic copy number variants in the segmental duplication region of titin cannot be excluded. Further investigations are needed, however, this region should no longer be neglected in genetic analyses.
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Zhang Y, Liu X, Gao H, He R, Chu G, Zhao Y. Copy number variations of chromosome 17p11.2 region in children with development delay and in fetuses with abnormal imaging findings. BMC Med Genomics 2021; 14:215. [PMID: 34470638 PMCID: PMC8411507 DOI: 10.1186/s12920-021-01065-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/20/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Deletion and duplication of the 3.7 Mb region in 17p11.2 result in two syndromes, Smith-Magenis syndrome and Potocki-Lupski syndrome, which are well-known development disorders. The purpose of this study was to determine the prevalence, genetic characteristics and clinical phenotypes of 17p11.2 deletion/duplication in Chinese children with development delay and in fetuses with potential congenital defects. METHODS 7077 children with development delay and/or intellectual disability were screened by multiplex ligation-dependent probe amplification P245 assay. 7319 fetuses with potential congenital defects were tested using next generation sequencing technique. RESULTS 417 of 7077 pediatric patients were determined to carry chromosome imbalance. 28 (28/7077, 0.4%) cases had imbalance at chromosome 17p11.2. Among them, 12 cases (42.9%) had heterozygous deletions and 16 cases (57.1%) had heterozygous duplications. The clinical phenotypes were variable, including neurobehavioral disorders, craniofacial/skeletal anomalies, immunologic defects, ocular problems and organ malformations. 263 of 7319 fetuses were recognized to have genomic copy number variations. Only 2 of them were found to harbor 17p11.2 imbalance. The fetus with deletion presented with ventricular septal defect and the fetus with duplication had cerebral ventricle dilation. CONCLUSION Our study highlights the phenotypic variability associated with 17p11.2 variations in China. The results further expand the phenotypic spectrum of SMS/PTLS and increase awareness of these disruptive mutations among clinicians.
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Affiliation(s)
- Yuanyuan Zhang
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiaoliang Liu
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Haiming Gao
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Rong He
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Guoming Chu
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yanyan Zhao
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, China.
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4
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Mosley TJ, Johnston HR, Cutler DJ, Zwick ME, Mulle JG. Sex-specific recombination patterns predict parent of origin for recurrent genomic disorders. BMC Med Genomics 2021; 14:154. [PMID: 34107974 PMCID: PMC8190997 DOI: 10.1186/s12920-021-00999-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 06/02/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Structural rearrangements of the genome, which generally occur during meiosis and result in large-scale (> 1 kb) copy number variants (CNV; deletions or duplications ≥ 1 kb), underlie genomic disorders. Recurrent pathogenic CNVs harbor similar breakpoints in multiple unrelated individuals and are primarily formed via non-allelic homologous recombination (NAHR). Several pathogenic NAHR-mediated recurrent CNV loci demonstrate biases for parental origin of de novo CNVs. However, the mechanism underlying these biases is not well understood. METHODS We performed a systematic, comprehensive literature search to curate parent of origin data for multiple pathogenic CNV loci. Using a regression framework, we assessed the relationship between parental CNV origin and the male to female recombination rate ratio. RESULTS We demonstrate significant association between sex-specific differences in meiotic recombination and parental origin biases at these loci (p = 1.07 × 10-14). CONCLUSIONS Our results suggest that parental origin of CNVs is largely influenced by sex-specific recombination rates and highlight the need to consider these differences when investigating mechanisms that cause structural variation.
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Affiliation(s)
- Trenell J Mosley
- Graduate Program in Genetics and Molecular Biology, Laney Graduate School, Emory University, 201 Dowman Drive, Atlanta, GA, 30322, USA
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Whitehead Building Suite 300, Atlanta, GA, 30322, USA
| | - H Richard Johnston
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Whitehead Building Suite 300, Atlanta, GA, 30322, USA
- Emory Integrated Computational Core, Emory University, 101 Woodruff Circle, Atlanta, GA, 30322, USA
| | - David J Cutler
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Whitehead Building Suite 300, Atlanta, GA, 30322, USA
| | - Michael E Zwick
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Whitehead Building Suite 300, Atlanta, GA, 30322, USA
- Department of Pediatrics, Emory University School of Medicine, 2015 Uppergate Drive, Atlanta, GA, 30322, USA
| | - Jennifer G Mulle
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Whitehead Building Suite 300, Atlanta, GA, 30322, USA.
- Department of Epidemiology, Rollins School of Public Health, Emory University, 1518 Clifton Road NE, Atlanta, GA, 30322, USA.
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5
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Koczkodaj D, Muzyka-Kasietczuk J, Chocholska S, Podhorecka M. Prognostic significance of isochromosome 17q in hematologic malignancies. Oncotarget 2021; 12:708-718. [PMID: 33868591 PMCID: PMC8021031 DOI: 10.18632/oncotarget.27914] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 02/19/2021] [Indexed: 11/29/2022] Open
Abstract
Isochromosome 17q [i(17q)] with its two identical long arms is formed by duplication of the q arm and loss of the short p arm. The breakpoint in chromosome 17 that allows the formation of this isochromosome is located at 17p11.2, and the ~240 kb region with its large, palindromic, low-copy repeat sequences are present here. The region is highly unstable and susceptible to a variety of genomic alterations which may be induced by or without toxic agents. One molecular consequence of i(17q) development is the obligatory loss of a single TP53 allele of the tumor suppressor P53 protein located at 17p13.1. Isochromosome 17q is involved in cancer development and progression. It occurs in combination with other chromosomal defects (complex cytogenetics), and rarely as a single mutation. The i(17q) rearrangement has been described as the most common chromosomal aberration in primitive neuroectodermal tumors and medulloblastomas. This isochromosome is also detected in different hematological disorders. In this article, we analyze literature data on the presence of i(17q) in proliferative disorders of the hematopoietic system in the context of its role as a prognostic factor of disease progression. The case reports are added to support the presented data. Currently, there are no indications for the use of specific treatment regimens in the subjects with a presence of the isochromosome 17q. Thus, it is of importance to continue studies on the prognostic role of this abnormality and even single cases should be reported as they may be used for further statistical analyses or meta-analyses.
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Affiliation(s)
- Dorota Koczkodaj
- Department of Cancer Genetics with the Cytogenetic Laboratory, Medical University of Lublin, Lublin, Poland
| | - Justyna Muzyka-Kasietczuk
- Department of Hematooncology and Bone Marrow Transplantation, Medical University of Lublin, Lublin, Poland
| | - Sylwia Chocholska
- Department of Hematooncology and Bone Marrow Transplantation, Medical University of Lublin, Lublin, Poland
| | - Monika Podhorecka
- Department of Hematooncology and Bone Marrow Transplantation, Medical University of Lublin, Lublin, Poland
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6
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Prenatal diagnosis and neonatal phenotype of a de novo microdeletion of 17p11.2p12 associated with Smith‒Magenis syndrome and external genital defects. J Genet 2020. [DOI: 10.1007/s12041-020-01213-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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7
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Beck CR, Carvalho CMB, Akdemir ZC, Sedlazeck FJ, Song X, Meng Q, Hu J, Doddapaneni H, Chong Z, Chen ES, Thornton PC, Liu P, Yuan B, Withers M, Jhangiani SN, Kalra D, Walker K, English AC, Han Y, Chen K, Muzny DM, Ira G, Shaw CA, Gibbs RA, Hastings PJ, Lupski JR. Megabase Length Hypermutation Accompanies Human Structural Variation at 17p11.2. Cell 2019; 176:1310-1324.e10. [PMID: 30827684 PMCID: PMC6438178 DOI: 10.1016/j.cell.2019.01.045] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 11/06/2018] [Accepted: 01/25/2019] [Indexed: 01/16/2023]
Abstract
DNA rearrangements resulting in human genome structural variants (SVs) are caused by diverse mutational mechanisms. We used long- and short-read sequencing technologies to investigate end products of de novo chromosome 17p11.2 rearrangements and query the molecular mechanisms underlying both recurrent and non-recurrent events. Evidence for an increased rate of clustered single-nucleotide variant (SNV) mutation in cis with non-recurrent rearrangements was found. Indel and SNV formation are associated with both copy-number gains and losses of 17p11.2, occur up to ∼1 Mb away from the breakpoint junctions, and favor C > G transversion substitutions; results suggest that single-stranded DNA is formed during the genesis of the SV and provide compelling support for a microhomology-mediated break-induced replication (MMBIR) mechanism for SV formation. Our data show an additional mutational burden of MMBIR consisting of hypermutation confined to the locus and manifesting as SNVs and indels predominantly within genes.
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Affiliation(s)
- Christine R Beck
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | | | - Zeynep C Akdemir
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | | | - Xiaofei Song
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Qingchang Meng
- Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | - Jianhong Hu
- Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | | | - Zechen Chong
- Department of Genetics and the Informatics Institute, the University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Edward S Chen
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Philip C Thornton
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Bo Yuan
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Marjorie Withers
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | | | - Divya Kalra
- Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | | | - Adam C English
- Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | - Yi Han
- Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | - Grzegorz Ira
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | - P J Hastings
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, BCM, Houston, TX 77030, USA.
| | - James R Lupski
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Human Genome Sequencing Center, BCM, Houston, TX 77030, USA; Department of Pediatrics, BCM, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, BCM, Houston, TX 77030, USA.
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8
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Identification of 15 novel partial SHOX deletions and 13 partial duplications, and a review of the literature reveals intron 3 to be a hotspot region. J Hum Genet 2016; 62:229-234. [PMID: 27604558 DOI: 10.1038/jhg.2016.113] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 07/29/2016] [Accepted: 08/02/2016] [Indexed: 12/31/2022]
Abstract
Short stature homeobox gene (SHOX) is located in the pseudoautosomal region 1 of the sex chromosomes. It encodes a transcription factor implicated in the skeletal growth. Point mutations, deletions or duplications of SHOX or its transcriptional regulatory elements are associated with two skeletal dysplasias, Léri-Weill dyschondrosteosis (LWD) and Langer mesomelic dysplasia (LMD), as well as in a small proportion of idiopathic short stature (ISS) individuals. We have identified a total of 15 partial SHOX deletions and 13 partial SHOX duplications in LWD, LMD and ISS patients referred for routine SHOX diagnostics during a 10 year period (2004-2014). Subsequently, we characterized these alterations using MLPA (multiplex ligation-dependent probe amplification assay), fine-tiling array CGH (comparative genomic hybridation) and breakpoint PCR. Nearly half of the alterations have a distal or proximal breakpoint in intron 3. Evaluation of our data and that in the literature reveals that although partial deletions and duplications only account for a small fraction of SHOX alterations, intron 3 appears to be a breakpoint hotspot, with alterations arising by non-allelic homologous recombination, non-homologous end joining or other complex mechanisms.
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9
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Kurtovic-Kozaric A, Mehinovic L, Stomornjak-Vukadin M, Kurtovic-Basic I, Catibusic F, Kozaric M, Mesihovic-Dinarevic S, Hasanhodzic M, Glamuzina D. Diagnostics of common microdeletion syndromes using fluorescence in situ hybridization: single center experience in a developing country. Bosn J Basic Med Sci 2016; 16:121-5. [PMID: 26937776 PMCID: PMC4852993 DOI: 10.17305/bjbms.2016.994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 01/23/2016] [Accepted: 01/25/2016] [Indexed: 12/14/2022] Open
Abstract
Microdeletion syndromes are caused by chromosomal deletions of less than 5 megabases which can be detected by fluorescence in situ hybridization (FISH). We evaluated the most commonly detected microdeletions for the period from June 01, 2008 to June 01, 2015 in the Federation of Bosnia and Herzegovina, including DiGeorge, Prader-Willi/Angelman, Wolf-Hirschhorn, and Williams syndromes. We report 4 patients with DiGeorge syndromes, 4 patients with Prader-Willi/Angelman, 4 patients with Wolf-Hirschhorn syndrome, and 3 patients with Williams syndrome in the analyzed 7 year period. Based on the positive FISH results for each syndrome, the incidence was calculated for the Federation of Bosnia and Herzegovina. These are the first reported frequencies of the microdeletion syndromes in the Federation of Bosnia and Herzegovina.
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10
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Termolino P, Cremona G, Consiglio MF, Conicella C. Insights into epigenetic landscape of recombination-free regions. Chromosoma 2016; 125:301-8. [PMID: 26801812 PMCID: PMC4830869 DOI: 10.1007/s00412-016-0574-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 01/10/2016] [Accepted: 01/12/2016] [Indexed: 11/29/2022]
Abstract
Genome architecture is shaped by gene-rich and repeat-rich regions also known as euchromatin and heterochromatin, respectively. Under normal conditions, the repeat-containing regions undergo little or no meiotic crossover (CO) recombination. COs within repeats are risky for the genome integrity. Indeed, they can promote non-allelic homologous recombination (NAHR) resulting in deleterious genomic rearrangements associated with diseases in humans. The assembly of heterochromatin is driven by the combinatorial action of many factors including histones, their modifications, and DNA methylation. In this review, we discuss current knowledge dealing with the epigenetic signatures of the major repeat regions where COs are suppressed. Then we describe mutants for epiregulators of heterochromatin in different organisms to find out how chromatin structure influences the CO rate and distribution.
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Affiliation(s)
- Pasquale Termolino
- CNR, National Research Council of Italy, Institute of Biosciences and Bioresources, Research Division Portici, Via Università 133, 80055, Portici, Italy
| | - Gaetana Cremona
- CNR, National Research Council of Italy, Institute of Biosciences and Bioresources, Research Division Portici, Via Università 133, 80055, Portici, Italy
| | - Maria Federica Consiglio
- CNR, National Research Council of Italy, Institute of Biosciences and Bioresources, Research Division Portici, Via Università 133, 80055, Portici, Italy
| | - Clara Conicella
- CNR, National Research Council of Italy, Institute of Biosciences and Bioresources, Research Division Portici, Via Università 133, 80055, Portici, Italy.
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11
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Poisson A, Nicolas A, Cochat P, Sanlaville D, Rigard C, de Leersnyder H, Franco P, Des Portes V, Edery P, Demily C. Behavioral disturbance and treatment strategies in Smith-Magenis syndrome. Orphanet J Rare Dis 2015; 10:111. [PMID: 26336863 PMCID: PMC4559928 DOI: 10.1186/s13023-015-0330-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 08/27/2015] [Indexed: 11/10/2022] Open
Abstract
Background Smith-Magenis syndrome is a complex neurodevelopmental disorder that includes intellectual deficiency, speech delay, behavioral disturbance and typical sleep disorders. Ninety percent of the cases are due to a 17p11.2 deletion encompassing the RAI1 gene; other cases are linked to mutations of the same gene. Behavioral disorders often include outbursts, attention deficit/hyperactivity disorders, self-injury with onychotillomania and polyembolokoilamania (insertion of objects into body orifices), etc. Interestingly, the stronger the speech delay and sleep disorders, the more severe the behavioral issues. Sleep disturbances associate excessive daytime sleepiness with nighttime agitation. They are underpinned by an inversion of the melatonin secretion cycle. However, the combined intake of beta-blockers in the morning and melatonin in the evening may radically alleviate the circadian rhythm problems. Discussion Once sleep disorders are treated, the next challenge is finding an effective treatment for the remaining behavioral problems. Unfortunately, there is a lack of objective guidelines. A comprehensive evaluation of such disorders should include sleep disorders, potential causes of pain, neurocognitive level and environment (i.e. family and school). In any case, efforts should focus on improving communication skills, identifying and treating attention deficit/hyperactivity, aggressiveness and anxiety. Summary Treatment of Smith-Magenis syndrome is complex and requires a multidisciplinary team including, among others, geneticists, psychiatrists, neuropediatricians/neurologists, somnologists, developmental and behavioral pediatricians, and speech and language therapists.
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Affiliation(s)
- Alice Poisson
- Center for Screening and Treatment of Psychiatric Disorders of Genetic Origin, Vinatier Hospital, 95 Bd Pinel, 69678, Lyon, France. .,Cognitive Neuroscience Center, UMR 5229, French National Research Center (CNRS), Bron, France. .,Lyon 1 University, Lyon, France.
| | - Alain Nicolas
- Center for Screening and Treatment of Psychiatric Disorders of Genetic Origin, Vinatier Hospital, 95 Bd Pinel, 69678, Lyon, France.,Michel Jouvet Unite (sleep Medicine), Vinatier Hospital, Human chronobiology team INSERM 846, Bron, France
| | - Pierre Cochat
- Lyon 1 University, Lyon, France.,Pediatric Nephrology and Rhumatology Ward, Reference Center for Rare Kidney Diseases, Civil Hospices of Lyon, INSERM U820, Bron, France
| | - Damien Sanlaville
- Lyon 1 University, Lyon, France.,Department of Genetics, Reference Center for Developmental Anomalies and Malformation Syndromes, Civil Hospices of Lyon, Bron, France
| | - Caroline Rigard
- Center for Screening and Treatment of Psychiatric Disorders of Genetic Origin, Vinatier Hospital, 95 Bd Pinel, 69678, Lyon, France.,Cognitive Neuroscience Center, UMR 5229, French National Research Center (CNRS), Bron, France
| | | | - Patricia Franco
- Lyon 1 University, Lyon, France.,Hypnology Unit, Neuropediatric Ward, Civil Hospices of Lyon and INSERM U628, Lyon, France
| | - Vincent Des Portes
- Lyon 1 University, Lyon, France.,Pediatric Neurology Ward, Reference Center "Intellectual Deficiencies with Rare Causes", Civil Hospices of Lyon, Bron, France. CNRS UMR 5304, L2C2, Institute of Cognitive Sciences, 69675, Bron, France
| | - Patrick Edery
- Lyon 1 University, Lyon, France.,Department of Genetics, Reference Center for Developmental Anomalies and Malformation Syndromes, Civil Hospices of Lyon, Bron, France.,Neuroscience Research Center of Lyon, Inserm U1028, CNRS UMR 5292, UCBL, TIGER Team, Bron, France
| | - Caroline Demily
- Center for Screening and Treatment of Psychiatric Disorders of Genetic Origin, Vinatier Hospital, 95 Bd Pinel, 69678, Lyon, France.,Cognitive Neuroscience Center, UMR 5229, French National Research Center (CNRS), Bron, France.,Lyon 1 University, Lyon, France
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12
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Poisson A, Nicolas A, Sanlaville D, Cochat P, De Leersnyder H, Rigard C, Franco P, des Portes V, Edery P, Demily C. [Smith-Magenis syndrome is an association of behavioral and sleep/wake circadian rhythm disorders]. Arch Pediatr 2015; 22:638-45. [PMID: 25934608 DOI: 10.1016/j.arcped.2015.03.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 12/21/2014] [Accepted: 03/21/2015] [Indexed: 12/12/2022]
Abstract
Smith-Magenis syndrome (SMS) is a genetic disorder characterized by the association of facial dysmorphism, oral speech delay, as well as behavioral and sleep/wake circadian rhythm disorders. Most SMS cases (90%) are due to a 17p11.2 deletion encompassing the RAI1 gene; other cases stem from mutations of the RAI1 gene. Behavioral issues may include frequent outbursts, attention deficit/hyperactivity disorders, self-injuries with onychotillomania and polyembolokoilamania (insertion of objects into bodily orifices), etc. It is noteworthy that the longer the speech delay and the more severe the sleep disorders, the more severe the behavioral issues are. Typical sleep/wake circadian rhythm disorders associate excessive daytime sleepiness with nocturnal agitation. They are related to an inversion of the physiological melatonin secretion cycle. Yet, with an adapted therapeutic strategy, circadian rhythm disorders can radically improve. Usually an association of beta-blockers in the morning (stops daily melatonin secretion) and melatonin in the evening (mimics the evening deficient peak) is used. Once the sleep disorders are controlled, effective treatment of the remaining psychiatric features is needed. Unfortunately, as for many orphan diseases, objective guidelines have not been drawn up. However, efforts should be focused on improving communication skills. In the same vein, attention deficit/hyperactivity disorders, aggressiveness, and anxiety should be identified and specifically treated. This whole appropriate medical management is underpinned by the diagnosis of SMS. Diagnostic strategies include fluorescent in situ hybridization (FISH) or array comparative genomic hybridization (array CGH) when a microdeletion is sought and Sanger sequencing when a point mutation is suspected. Thus, the diagnosis of SMS can be made from a simple blood sample and should be questioned in subjects of any age presenting with an association of facial dysmorphism, speech delay with behavioral and sleep/wake circadian rhythm disorders, and other anomalies including short stature and mild dysmorphic features.
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Affiliation(s)
- A Poisson
- UDEIP, centre de dépistage et de prise en charge des troubles psychiatriques d'origine génétique, centre hospitalier le Vinatier, 95, boulevard Pinel, 69678 Bron cedex, France; Centre de neurosciences cognitives, UMR 5229 CNRS, 69500 Bron, France; Université Lyon 1, 69500 Lyon, France.
| | - A Nicolas
- UDEIP, centre de dépistage et de prise en charge des troubles psychiatriques d'origine génétique, centre hospitalier le Vinatier, 95, boulevard Pinel, 69678 Bron cedex, France; Université Lyon 1, 69500 Lyon, France
| | - D Sanlaville
- Université Lyon 1, 69500 Lyon, France; Service de génétique, centre des anomalies du développement, laboratoire de cytogénétique, hospices civils de Lyon, 69500 Bron, France
| | - P Cochat
- Université Lyon 1, 69500 Lyon, France; Service de néphrologie et rhumatologie pédiatrique, centre de référence des maladies rénales rares, Inserm U820, hospices civils de Lyon, 69500 Bron, France
| | - H De Leersnyder
- Centre de recherche en neurosciences de Lyon, Inserm U1028, CNRS UMR 5292, UCBL, équipe TIGER, 69500 Bron, France
| | - C Rigard
- UDEIP, centre de dépistage et de prise en charge des troubles psychiatriques d'origine génétique, centre hospitalier le Vinatier, 95, boulevard Pinel, 69678 Bron cedex, France; Centre de neurosciences cognitives, UMR 5229 CNRS, 69500 Bron, France
| | - P Franco
- Université Lyon 1, 69500 Lyon, France; Unité d'hypnologie, service de neuropédiatrie, Inserm U 628, hospices civils de Lyon, 69500 Bron, France
| | - V des Portes
- Université Lyon 1, 69500 Lyon, France; Centre de référence X fragile et autres déficiences intellectuelles de causes rares, hospices civils de Lyon, 69500 Bron, France
| | - P Edery
- Service de génétique, centre de référence des anomalies du développement et des syndromes malformatifs, hospices civils de Lyon, 69500 Bron, France; Université Lyon 1, 69500 Lyon, France; Centre de référence X fragile et autres déficiences intellectuelles de causes rares, hospices civils de Lyon, 69500 Bron, France
| | - C Demily
- UDEIP, centre de dépistage et de prise en charge des troubles psychiatriques d'origine génétique, centre hospitalier le Vinatier, 95, boulevard Pinel, 69678 Bron cedex, France; Centre de neurosciences cognitives, UMR 5229 CNRS, 69500 Bron, France; Université Lyon 1, 69500 Lyon, France
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13
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Lee CG, Park SJ, Yim SY, Sohn YB. Clinical and cytogenetic features of a Potocki-Lupski syndrome with the shortest 0.25Mb microduplication in 17p11.2 including RAI1. Brain Dev 2013; 35:681-5. [PMID: 23078968 DOI: 10.1016/j.braindev.2012.09.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Revised: 09/19/2012] [Accepted: 09/20/2012] [Indexed: 10/27/2022]
Abstract
Potocki-Lupski syndrome (PTLS [MIM 610883]) is a recently recognized microduplication syndrome associated with 17p11.2. It is characterized by mild facial dysmorphic features, hypermetropia, infantile hypotonia, failure to thrive, mental retardation, autistic spectrum disorders, behavioral abnormalities, sleep apnea, and cardiovascular anomalies. In several studies, the critical PTLS region was deduced to be 1.3Mb in length, and included RAI1 and 17 other genes. We report a 3-year-old Korean boy with the smallest duplication in 17p11.2 and a milder phenotype. He had no family history of neurologic disease or developmental delay and no history of seizure, autistic features, or behavior problems. He showed subtle facial dysmorphic features (dolichocephaly and a mildly asymmetric smile) and flat feet. All laboratory tests were normal and he had no evidence of internal organ anomalies. He was found to have mild intellectual disabilities (full scale IQ 65 on K-WPPSI) and language developmental delay (age of 2.2year-old on PRESS). Array comparative genomic hybridization (CGH) showed about a 0.25Mb microduplication on chromosome 17p11.2 containing four Refseq (NCBI reference sequence) genes, including RAI1 [arr 17p11.2(17,575,978-17,824,623)×3]. When compared with previously reported cases, the milder phenotype of our patient may be associated with the smallest duplication in 17p11.2, 0.25Mb in length.
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Affiliation(s)
- Cha Gon Lee
- Department of Medical Genetics, Ajou University School of Medicine, Suwon, South Korea
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14
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Lee CG, Park SJ, Yun JN, Yim SY, Sohn YB. Reciprocal deletion and duplication of 17p11.2-11.2: Korean patients with Smith-Magenis syndrome and Potocki-Lupski syndrome. J Korean Med Sci 2012; 27:1586-90. [PMID: 23255863 PMCID: PMC3524443 DOI: 10.3346/jkms.2012.27.12.1586] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Accepted: 08/14/2012] [Indexed: 11/24/2022] Open
Abstract
Deletion and duplication of the -3.7-Mb region in 17p11.2 result in two reciprocal syndrome, Smith-Magenis syndrome and Potocki-Lupski syndrome. Smith-Magenis syndrome is a well-known developmental disorder. Potocki-Lupski syndrome has recently been recognized as a microduplication syndrome that is a reciprocal disease of Smith-Magenis syndrome. In this paper, we report on the clinical and cytogenetic features of two Korean patients with Smith-Magenis syndrome and Potocki-Lupski syndrome. Patient 1 (Smith-Magenis syndrome) was a 2.9-yr-old boy who showed mild dysmorphic features, aggressive behavioral problems, and developmental delay. Patient 2 (Potocki-Lupski syndrome), a 17-yr-old boy, had only intellectual disabilities and language developmental delay. We used array comparative genomic hybridization (array CGH) and found a 2.6 Mb-sized deletion and a reciprocal 2.1 Mb-sized duplication involving the 17p11.2. These regions overlapped in a 2.1 Mb size containing 11 common genes, including RAI1 and SREBF.
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Affiliation(s)
- Cha Gon Lee
- Department of Pediatrics, Eulji General Hospital, Seoul, Korea
| | | | - Jun-No Yun
- Department of Medical Genetics, Ajou University School of Medicine, Suwon, Korea
| | - Shin-Young Yim
- Department of Physical Medicine and Rehabilitation, Ajou University School of Medicine, Suwon, Korea
| | - Young Bae Sohn
- Department of Medical Genetics, Ajou University School of Medicine, Suwon, Korea
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15
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Zhao L, Triche EW, Walsh KM, Bracken MB, Saftlas AF, Hoh J, Dewan AT. Genome-wide association study identifies a maternal copy-number deletion in PSG11 enriched among preeclampsia patients. BMC Pregnancy Childbirth 2012; 12:61. [PMID: 22748001 PMCID: PMC3476390 DOI: 10.1186/1471-2393-12-61] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Accepted: 06/20/2012] [Indexed: 12/02/2022] Open
Abstract
Background Specific genetic contributions for preeclampsia (PE) are currently unknown. This genome-wide association study (GWAS) aims to identify maternal single nucleotide polymorphisms (SNPs) and copy-number variants (CNVs) involved in the etiology of PE. Methods A genome-wide scan was performed on 177 PE cases (diagnosed according to National Heart, Lung and Blood Institute guidelines) and 116 normotensive controls. White female study subjects from Iowa were genotyped on Affymetrix SNP 6.0 microarrays. CNV calls made using a combination of four detection algorithms (Birdseye, Canary, PennCNV, and QuantiSNP) were merged using CNVision and screened with stringent prioritization criteria. Due to limited DNA quantities and the deleterious nature of copy-number deletions, it was decided a priori that only deletions would be selected for assay on the entire case-control dataset using quantitative real-time PCR. Results The top four SNP candidates had an allelic or genotypic p-value between 10-5 and 10-6, however, none surpassed the Bonferroni-corrected significance threshold. Three recurrent rare deletions meeting prioritization criteria detected in multiple cases were selected for targeted genotyping. A locus of particular interest was found showing an enrichment of case deletions in 19q13.31 (5/169 cases and 1/114 controls), which encompasses the PSG11 gene contiguous to a highly plastic genomic region. All algorithm calls for these regions were assay confirmed. Conclusions CNVs may confer risk for PE and represent interesting regions that warrant further investigation. Top SNP candidates identified from the GWAS, although not genome-wide significant, may be useful to inform future studies in PE genetics.
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Affiliation(s)
- Linlu Zhao
- Center for Perinatal, Pediatric and Environmental Epidemiology, Yale School of Public Health, New Haven, CT 06520, USA
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16
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Liu P, Lacaria M, Zhang F, Withers M, Hastings P, Lupski J. Frequency of nonallelic homologous recombination is correlated with length of homology: evidence that ectopic synapsis precedes ectopic crossing-over. Am J Hum Genet 2011; 89:580-8. [PMID: 21981782 DOI: 10.1016/j.ajhg.2011.09.009] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Revised: 09/14/2011] [Accepted: 09/15/2011] [Indexed: 10/16/2022] Open
Abstract
Genomic disorders constitute a class of diseases that are associated with DNA rearrangements resulting from region-specific genome instability, that is, genome architecture incites genome instability. Nonallelic homologous recombination (NAHR) or crossing-over in meiosis between sequences that are not in allelic positions (i.e., paralogous sequences) can result in recurrent deletions or duplications causing genomic disorders. Previous studies of NAHR have focused on description of the phenomenon, but it remains unclear how NAHR occurs during meiosis and what factors determine its frequency. Here we assembled two patient cohorts with reciprocal genomic disorders; deletion associated Smith-Magenis syndrome and duplication associated Potocki-Lupski syndrome. By assessing the full spectrum of rearrangement types from the two cohorts, we find that complex rearrangements (those with more than one breakpoint) are more prevalent in copy-number gains (17.7%) than in copy-number losses (2.3%); an observation that supports a role for replicative mechanisms in complex rearrangement formation. Interestingly, for NAHR-mediated recurrent rearrangements, we show that crossover frequency is positively associated with the flanking low-copy repeat (LCR) length and inversely influenced by the inter-LCR distance. To explain this, we propose that the probability of ectopic chromosome synapsis increases with increased LCR length, and that ectopic synapsis is a necessary precursor to ectopic crossing-over.
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17
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Boone PM, Reiter RJ, Glaze DG, Tan DX, Lupski JR, Potocki L. Abnormal circadian rhythm of melatonin in Smith-Magenis syndrome patients with RAI1 point mutations. Am J Med Genet A 2011; 155A:2024-7. [PMID: 21739587 DOI: 10.1002/ajmg.a.34098] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Accepted: 04/13/2011] [Indexed: 12/15/2022]
Affiliation(s)
- Philip M Boone
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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18
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Smith–Magenis syndrome: haploinsufficiency of RAI1 results in altered gene regulation in neurological and metabolic pathways. Expert Rev Mol Med 2011; 13:e14. [DOI: 10.1017/s1462399411001827] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Smith–Magenis syndrome (SMS) is a complex neurobehavioural disorder characterised by intellectual disability, self-injurious behaviours, sleep disturbance, obesity, and craniofacial and skeletal anomalies. Diagnostic strategies are focused towards identification of a 17p11.2 microdeletion encompassing the gene RAI1 (retinoic acid induced 1) or a mutation of RAI1. Molecular evidence shows that most SMS features are due to RAI1 haploinsufficiency, whereas variability and severity are modified by other genes in the 17p11.2 region for 17p11.2 deletion cases. The functional role of RAI1 is not completely understood, but it is probably a transcription factor acting in several different biological pathways that are dysregulated in SMS. Functional studies based on the hypothesis that RAI1 acts through phenotype-specific pathways involving several downstream genes have shown that RAI1 gene dosage is crucial for normal regulation of circadian rhythm, lipid metabolism and neurotransmitter function. Here, we review the clinical and molecular features of SMS and explore more recent studies supporting possible therapeutic strategies for behavioural management.
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Yusupov R, Roberts AE, Lacro RV, Sandstrom M, Ligon AH. Potocki-Lupski syndrome: An inherited dup(17)(p11.2p11.2) with hypoplastic left heart. Am J Med Genet A 2011; 155A:367-71. [DOI: 10.1002/ajmg.a.33845] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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20
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van Bon BWM, Balciuniene J, Fruhman G, Nagamani SCS, Broome DL, Cameron E, Martinet D, Roulet E, Jacquemont S, Beckmann JS, Irons M, Potocki L, Lee B, Cheung SW, Patel A, Bellini M, Selicorni A, Ciccone R, Silengo M, Vetro A, Knoers NV, de Leeuw N, Pfundt R, Wolf B, Jira P, Aradhya S, Stankiewicz P, Brunner HG, Zuffardi O, Selleck SB, Lupski JR, de Vries BBA. The phenotype of recurrent 10q22q23 deletions and duplications. Eur J Hum Genet 2011; 19:400-8. [PMID: 21248748 DOI: 10.1038/ejhg.2010.211] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The genomic architecture of the 10q22q23 region is characterised by two low-copy repeats (LCRs3 and 4), and deletions in this region appear to be rare. We report the clinical and molecular characterisation of eight novel deletions and six duplications within the 10q22.3q23.3 region. Five deletions and three duplications occur between LCRs3 and 4, whereas three deletions and three duplications have unique breakpoints. Most of the individuals with the LCR3-4 deletion had developmental delay, mainly affecting speech. In addition, macrocephaly, mild facial dysmorphisms, cerebellar anomalies, cardiac defects and congenital breast aplasia were observed. For congenital breast aplasia, the NRG3 gene, known to be involved in early mammary gland development in mice, is a putative candidate gene. For cardiac defects, BMPR1A and GRID1 are putative candidate genes because of their association with cardiac structure and function. Duplications between LCRs3 and 4 are associated with variable phenotypic penetrance. Probands had speech and/or motor delays and dysmorphisms including a broad forehead, deep-set eyes, upslanting palpebral fissures, a smooth philtrum and a thin upper lip. In conclusion, duplications between LCRs3 and 4 on 10q22.3q23.2 may lead to a distinct facial appearance and delays in speech and motor development. However, the phenotypic spectrum is broad, and duplications have also been found in healthy family members of a proband. Reciprocal deletions lead to speech and language delay, mild facial dysmorphisms and, in some individuals, to cerebellar, breast developmental and cardiac defects.
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Affiliation(s)
- Bregje W M van Bon
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.
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22
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Evolution in health and medicine Sackler colloquium: Genomic disorders: a window into human gene and genome evolution. Proc Natl Acad Sci U S A 2010; 107 Suppl 1:1765-71. [PMID: 20080665 DOI: 10.1073/pnas.0906222107] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Gene duplications alter the genetic constitution of organisms and can be a driving force of molecular evolution in humans and the great apes. In this context, the study of genomic disorders has uncovered the essential role played by the genomic architecture, especially low copy repeats (LCRs) or segmental duplications (SDs). In fact, regardless of the mechanism, LCRs can mediate or stimulate rearrangements, inciting genomic instability and generating dynamic and unstable regions prone to rapid molecular evolution. In humans, copy-number variation (CNV) has been implicated in common traits such as neuropathy, hypertension, color blindness, infertility, and behavioral traits including autism and schizophrenia, as well as disease susceptibility to HIV, lupus nephritis, and psoriasis among many other clinical phenotypes. The same mechanisms implicated in the origin of genomic disorders may also play a role in the emergence of segmental duplications and the evolution of new genes by means of genomic and gene duplication and triplication, exon shuffling, exon accretion, and fusion/fission events.
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23
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High-resolution SNP arrays in mental retardation diagnostics: how much do we gain? Eur J Hum Genet 2009; 18:178-85. [PMID: 19809473 DOI: 10.1038/ejhg.2009.154] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We used Affymetrix 6.0 GeneChip SNP arrays to characterize copy number variations (CNVs) in a cohort of 70 patients previously characterized on lower-density oligonucleotide arrays affected by idiopathic mental retardation and dysmorphic features. The SNP array platform includes approximately 900,000 SNP probes and 900,000 non-SNP oligonucleotide probes at an average distance of 0.7 Kb, which facilitates coverage of the whole genome, including coding and noncoding regions. The high density of probes is critical for detecting small CNVs, but it can lead to data interpretation problems. To reduce the number of false positives, parameters were set to consider only imbalances >75 Kb encompassing at least 80 probe sets. The higher resolution of the SNP array platform confirmed the increased ability to detect small CNVs, although more than 80% of these CNVs overlapped to copy number 'neutral' polymorphism regions and 4.4% of them did not contain known genes. In our cohort of 70 patients, of the 51 previously evaluated as 'normal' on the Agilent 44K array, the SNP array platform disclosed six additional CNV changes, including three in three patients, which may be pathogenic. This suggests that about 6% of individuals classified as 'normal' using the lower-density oligonucleotide array could be found to be affected by a genomic disorder when evaluated with the higher-density microarray platforms.
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Tian X, Pascal G, Monget P. Evolution and functional divergence of NLRP genes in mammalian reproductive systems. BMC Evol Biol 2009; 9:202. [PMID: 19682372 PMCID: PMC2735741 DOI: 10.1186/1471-2148-9-202] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2009] [Accepted: 08/14/2009] [Indexed: 12/31/2022] Open
Abstract
Background NLRPs (Nucleotide-binding oligomerization domain, Leucine rich Repeat and Pyrin domain containing Proteins) are members of NLR (Nod-like receptors) protein family. Recent researches have shown that NLRP genes play important roles in both mammalian innate immune system and reproductive system. Several of NLRP genes were shown to be specifically expressed in the oocyte in mammals. The aim of the present work was to study how these genes evolved and diverged after their duplication, as well as whether natural selection played a role during their evolution. Results By using in silico methods, we have evaluated the evolution and functional divergence of NLRP genes, in particular of mouse reproduction-related Nlrp genes. We found that (1) major NLRP genes have been duplicated before the divergence of mammals, with certain lineage-specific duplications in primates (NLRP7 and 11) and in rodents (Nlrp1, 4 and 9 duplicates); (2) tandem duplication events gave rise to a mammalian reproduction-related NLRP cluster including NLRP2, 4, 5, 7, 8, 9, 11, 13 and 14 genes; (3) the function of mammalian oocyte-specific NLRP genes (NLRP4, 5, 9 and 14) might have diverged during gene evolution; (4) recent segmental duplications concerning Nlrp4 copies and vomeronasal 1 receptor encoding genes (V1r) have been undertaken in the mouse; and (5) duplicates of Nlrp4 and 9 in the mouse might have been subjected to adaptive evolution. Conclusion In conclusion, this study brings us novel information on the evolution of mammalian reproduction-related NLRPs. On the one hand, NLRP genes duplicated and functionally diversified in mammalian reproductive systems (such as NLRP4, 5, 9 and 14). On the other hand, during evolution, different lineages adapted to develop their own NLRP genes, particularly in reproductive function (such as the specific expansion of Nlrp4 and Nlrp9 in the mouse).
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Affiliation(s)
- Xin Tian
- Physiologie de la Reproduction et des Comportements, UMR 6175 INRA-CNRS-Université François Rabelais de Tours-Haras Nationaux, 37380 Nouzilly, France.
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25
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Abstract
It is now becoming generally accepted that a significant amount of human genetic variation is due to structural changes of the genome rather than to base-pair changes in the DNA. As for base-pair changes, knowledge of gene and genome function has been informed by structural alterations that convey clinical phenotypes. Genomic disorders are a class of human conditions that result from structural changes of the human genome that convey traits or susceptibility to traits. The path to the delineation of genomic disorders is intertwined with the evolving technologies that have enabled the resolution of human genome analyses to continue increasing. Similarly, the ability to perform high-resolution human genome analysis has fueled the current and future clinical implementation of such discoveries in the evolving field of genome medicine.
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Affiliation(s)
- James R Lupski
- Departments of Molecular and Human Genetics, and Pediatrics, Baylor College of Medicine, and Texas Children's Hospital, Houston, TX 77030, USA.
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26
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Kogan JM, Miller E, Ware SM. High resolution SNP based microarray mapping of mosaic supernumerary marker chromosomes 13 and 17: Delineating novel loci for apraxia. Am J Med Genet A 2009; 149A:887-93. [DOI: 10.1002/ajmg.a.32750] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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27
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Gu W, Zhang F, Lupski JR. Mechanisms for human genomic rearrangements. PATHOGENETICS 2008; 1:4. [PMID: 19014668 PMCID: PMC2583991 DOI: 10.1186/1755-8417-1-4] [Citation(s) in RCA: 427] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2008] [Accepted: 11/03/2008] [Indexed: 02/08/2023]
Abstract
Genomic rearrangements describe gross DNA changes of the size ranging from a couple of hundred base pairs, the size of an average exon, to megabases (Mb). When greater than 3 to 5 Mb, such changes are usually visible microscopically by chromosome studies. Human diseases that result from genomic rearrangements have been called genomic disorders. Three major mechanisms have been proposed for genomic rearrangements in the human genome. Non-allelic homologous recombination (NAHR) is mostly mediated by low-copy repeats (LCRs) with recombination hotspots, gene conversion and apparent minimal efficient processing segments. NAHR accounts for most of the recurrent rearrangements: those that share a common size, show clustering of breakpoints, and recur in multiple individuals. Non-recurrent rearrangements are of different sizes in each patient, but may share a smallest region of overlap whose change in copy number may result in shared clinical features among different patients. LCRs do not mediate, but may stimulate non-recurrent events. Some rare NAHRs can also be mediated by highly homologous repetitive sequences (for example, Alu, LINE); these NAHRs account for some of the non-recurrent rearrangements. Other non-recurrent rearrangements can be explained by non-homologous end-joining (NHEJ) and the Fork Stalling and Template Switching (FoSTeS) models. These mechanisms occur both in germ cells, where the rearrangements can be associated with genomic disorders, and in somatic cells in which such genomic rearrangements can cause disorders such as cancer. NAHR, NHEJ and FoSTeS probably account for the majority of genomic rearrangements in our genome and the frequency distribution of the three at a given locus may partially reflect the genomic architecture in proximity to that locus. We provide a review of the current understanding of these three models.
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Affiliation(s)
- Wenli Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
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28
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Carvalho CMB, Lupski JR. Copy number variation at the breakpoint region of isochromosome 17q. Genome Res 2008; 18:1724-32. [PMID: 18714090 DOI: 10.1101/gr.080697.108] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Isochromosome 17q, or i(17q), is one of the most frequent nonrandom changes occurring in human neoplasia. Most of the i(17q) breakpoints cluster within a approximately 240-kb interval located in the Smith-Magenis syndrome common deletion region in 17p11.2. The breakpoint cluster region is characterized by a complex architecture with large ( approximately 38-49 kb), inverted and directly oriented, low-copy repeats (LCRs), known as REPA and REPB that apparently lead to genomic instability and facilitate somatic genetic rearrangements. Through the analysis of bacterial artificial chromosome (BAC) clones, pulsed-field gel electrophoresis (PFGE), and public array comparative genomic hybridization (array CGH) data, we show that the REPA/B structure is also susceptible to frequent meiotic rearrangements. It is a highly dynamic genomic region undergoing deletions, inversions, and duplications likely produced by non-allelic homologous recombination (NAHR) mediated by the highly identical SNORD3@, also known as U3, gene cluster present therein. We detected at least seven different REPA/B structures in samples from 29 individuals of which six represented potentially novel structures. Two polymorphic copy-number variation (CNV) variants, detected in 20% of samples, could be structurally described along with the likely underlying molecular mechanism for formation. Our data show the high susceptibility to rearrangements at the i(17q) breakpoint cluster region in the general population and exemplifies how large genomic regions laden with LCRs still represent a technical challenge for both determining specific structure and assaying population variation. The variant REPA/B structures identified may have different susceptibilities for inducing i(17q), thus potentially representing important risk alleles for tumor progression.
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Affiliation(s)
- Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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29
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Doco-Fenzy M, Holder-Espinasse M, Bieth E, Magdelaine C, Vincent MC, Khoury M, Andrieux J, Zhang F, Lupski JR, Klink R, Schneider A, Goze-Martineau O, Cuisset JM, Vallee L, Manouvrier-Hanu S, Gaillard D, de Martinville B. The clinical spectrum associated with a chromosome 17 short arm proximal duplication (dup 17p11.2) in three patients. Am J Med Genet A 2008; 146A:917-24. [PMID: 18327785 DOI: 10.1002/ajmg.a.32195] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The p11.2-p12 region of human chromosome 17 is gene rich and composed of at least two genomically unstable domains: the Smith-Magenis syndrome region (17p11.2) and the Charcot-Marie-Tooth region (17p12), both of which are flanked by several low-copy repeat sequences. Homologous recombination between these flanking repeats results in either deletion- or duplication-associated phenotypes caused by a gene dosage effect. We report on the clinical phenotype of three patients presenting with either a 17p11.2 or 17p11.2p12 duplication, revealed by chromosome analysis and confirmed by fluorescent in situ hybridization analysis, high resolution genomic analysis of the 17p region using oligonucleotide array comparative genomic hybridization, and molecular studies with microsatellite markers. Two patients carry the 17p11.2 duplication, while the third one shows a larger duplication including the 17p12 region. The facial features observed in our patients include triangular face, full cheeks, smooth philtrum, thin upper lip, dental malocclusion, irregular eyebrows, and sparse hair, all of which are consistent with the pure proximal dup 17p phenotype. The patients' other clinical features are compared with previously published cases.
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Affiliation(s)
- Martine Doco-Fenzy
- Service de Génétique, Hôpital Maison-Blanche, CHRU, UFR de Médecine, Reims, France.
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30
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Abstract
There is growing appreciation that the human genome contains significant numbers of structural rearrangements, such as insertions, deletions, inversions, and large tandem repeats. Recent studies have defined approximately 5% of the human genome as structurally variant in the normal population, involving more than 800 independent genes. We present a detailed review of the various structural rearrangements identified to date in humans, with particular reference to their influence on human phenotypic variation. Our current knowledge of the extent of human structural variation shows that the human genome is a highly dynamic structure that shows significant large-scale variation from the currently published genome reference sequence.
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Affiliation(s)
- Andrew J Sharp
- Department of Genome Sciences, University of Washington, Howard Hughes Medical Institute, Seattle, Washington 98195, USA
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31
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Abstract
Smith-Magenis syndrome (SMS) is a complex neurobehavioral disorder caused by haploinsufficiency of the retinoic acid-induced 1 (RAI1) gene on chromosome 17p11.2. Diagnostic strategies include molecular identification of a 17p11.2 microdeletion encompassing RAI1 or a mutation in RAI1. G-banding and fluorescent in situ hybridization (FISH) are the classical methods used to detect the SMS deletions, while multiplex ligation-dependent probe amplification (MLPA) and real-time quantitative PCR are the newer, cost-effective, and high-throughput technologies. Most SMS features are due to RAI1 haploinsufficiency, while the variability and severity of the disorder are modified by other genes in the 17p11.2 region. The functional role for RAI1 is not completely understood, but it is likely involved in transcription, based on homology and preliminary studies. Management of SMS is primarily a multidisciplinary approach and involves treatment for sleep disturbance, speech and occupational therapies, minor medical interventions, and management of behaviors.
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Toward accurate high-throughput SNP genotyping in the presence of inherited copy number variation. BMC Genomics 2007; 8:211. [PMID: 17608949 PMCID: PMC1934372 DOI: 10.1186/1471-2164-8-211] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2007] [Accepted: 07/03/2007] [Indexed: 11/29/2022] Open
Abstract
Background The recent discovery of widespread copy number variation in humans has forced a shift away from the assumption of two copies per locus per cell throughout the autosomal genome. In particular, a SNP site can no longer always be accurately assigned one of three genotypes in an individual. In the presence of copy number variability, the individual may theoretically harbor any number of copies of each of the two SNP alleles. Results To address this issue, we have developed a method to infer a "generalized genotype" from raw SNP microarray data. Here we apply our approach to data from 48 individuals and uncover thousands of aberrant SNPs, most in regions that were previously unreported as copy number variants. We show that our allele-specific copy numbers follow Mendelian inheritance patterns that would be obscured in the absence of SNP allele information. The interplay between duplication and point mutation in our data shed light on the relative frequencies of these events in human history, showing that at least some of the duplication events were recurrent. Conclusion This new multi-allelic view of SNPs has a complicated role in disease association studies, and further work will be necessary in order to accurately assess its importance. Software to perform generalized genotyping from SNP array data is freely available online [1].
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Vissers LELM, Stankiewicz P, Yatsenko SA, Crawford E, Creswick H, Proud VK, de Vries BBA, Pfundt R, Marcelis CLM, Zackowski J, Bi W, van Kessel AG, Lupski JR, Veltman JA. Complex chromosome 17p rearrangements associated with low-copy repeats in two patients with congenital anomalies. Hum Genet 2007; 121:697-709. [PMID: 17457615 PMCID: PMC1914245 DOI: 10.1007/s00439-007-0359-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2006] [Accepted: 03/19/2007] [Indexed: 01/01/2023]
Abstract
Recent molecular cytogenetic data have shown that the constitution of complex chromosome rearrangements (CCRs) may be more complicated than previously thought. The complicated nature of these rearrangements challenges the accurate delineation of the chromosomal breakpoints and mechanisms involved. Here, we report a molecular cytogenetic analysis of two patients with congenital anomalies and unbalanced de novo CCRs involving chromosome 17p using high-resolution array-based comparative genomic hybridization (array CGH) and fluorescent in situ hybridization (FISH). In the first patient, a 4-month-old boy with developmental delay, hypotonia, growth retardation, coronal synostosis, mild hypertelorism, and bilateral club feet, we found a duplication of the Charcot-Marie-Tooth disease type 1A and Smith-Magenis syndrome (SMS) chromosome regions, inverted insertion of the Miller-Dieker lissencephaly syndrome region into the SMS region, and two microdeletions including a terminal deletion of 17p. The latter, together with a duplication of 21q22.3-qter detected by array CGH, are likely the unbalanced product of a translocation t(17;21)(p13.3;q22.3). In the second patient, an 8-year-old girl with mental retardation, short stature, microcephaly and mild dysmorphic features, we identified four submicroscopic interspersed 17p duplications. All 17 breakpoints were examined in detail by FISH analysis. We found that four of the breakpoints mapped within known low-copy repeats (LCRs), including LCR17pA, middle SMS-REP/LCR17pB block, and LCR17pC. Our findings suggest that the LCR burden in proximal 17p may have stimulated the formation of these CCRs and, thus, that genome architectural features such as LCRs may have been instrumental in the generation of these CCRs.
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Affiliation(s)
- L. E. L. M. Vissers
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - P. Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - S. A. Yatsenko
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - E. Crawford
- Sentara Hospital Laboratories, Norfolk, VA USA
| | - H. Creswick
- Children’s Hospital of the King’s Daughters, Norfolk, VA USA
| | - V. K. Proud
- Children’s Hospital of the King’s Daughters, Norfolk, VA USA
| | - B. B. A. de Vries
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - R. Pfundt
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - C. L. M. Marcelis
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - J. Zackowski
- Children’s Hospital of the King’s Daughters, Norfolk, VA USA
| | - W. Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - A. Geurts van Kessel
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - J. R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX USA
- Texas Children’s Hospital, Houston, TX USA
| | - J. A. Veltman
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
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34
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Lam KWG, Jeffreys AJ. Processes of de novo duplication of human alpha-globin genes. Proc Natl Acad Sci U S A 2007; 104:10950-5. [PMID: 17573529 PMCID: PMC1904127 DOI: 10.1073/pnas.0703856104] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2007] [Indexed: 12/27/2022] Open
Abstract
Ectopic recombination between repeated but nonallelic DNA sequences plays a major role in genome evolution, creating gene families and generating copy number variation and pathological rearrangements in human chromosomes. Previous studies on the alpha2- and alpha1-globin genes have shown that de novo deletions common in alpha(+)-thalassemics can be directly accessed in human DNA and provide an informative system for studying deletion dynamics and processes. However, nothing is known about the reciprocal products of ectopic recombination, namely gene duplications. We now show that molecules carrying three alpha-globin genes can be detected in human DNA by using physical enrichment plus an inverse PCR strategy. These de novo duplications are common in blood and sperm and appear to arise by two distinct mechanisms: meiotic exchanges between homologous chromosomes that generate a minority of sperm duplications, plus mitotic ectopic exchanges that occur in the soma and germ line and can show erratic fluctuations in frequency most likely caused by mutational mosaicism. The dynamics and processes of duplication are very similar to those of deletion, particularly for meiotic exchanges. This result suggests rearrangement pathways dominated by fully reciprocal ectopic exchange, with nonreciprocal pathways such as intramolecular recombination and single-strand annealing playing at best only a minor role in the generation of deletions. Finally, the high level of instability at the alpha-globin locus contrasts with the rarity in most populations of chromosomes carrying duplications or deletions, pointing to strong selective constraints that maintain alpha-globin gene copy number in human populations.
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Affiliation(s)
- Kwan-Wood G. Lam
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - Alec J. Jeffreys
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom
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35
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Potocki L, Bi W, Treadwell-Deering D, Carvalho CMB, Eifert A, Friedman EM, Glaze D, Krull K, Lee JA, Lewis RA, Mendoza-Londono R, Robbins-Furman P, Shaw C, Shi X, Weissenberger G, Withers M, Yatsenko SA, Zackai EH, Stankiewicz P, Lupski JR. Characterization of Potocki-Lupski syndrome (dup(17)(p11.2p11.2)) and delineation of a dosage-sensitive critical interval that can convey an autism phenotype. Am J Hum Genet 2007; 80:633-49. [PMID: 17357070 PMCID: PMC1852712 DOI: 10.1086/512864] [Citation(s) in RCA: 281] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2006] [Accepted: 01/17/2007] [Indexed: 12/26/2022] Open
Abstract
The duplication 17p11.2 syndrome, associated with dup(17)(p11.2p11.2), is a recently recognized syndrome of multiple congenital anomalies and mental retardation and is the first predicted reciprocal microduplication syndrome described--the homologous recombination reciprocal of the Smith-Magenis syndrome (SMS) microdeletion (del(17)(p11.2p11.2)). We previously described seven subjects with dup(17)(p11.2p11.2) and noted their relatively mild phenotype compared with that of individuals with SMS. Here, we molecularly analyzed 28 additional patients, using multiple independent assays, and also report the phenotypic characteristics obtained from extensive multidisciplinary clinical study of a subset of these patients. Whereas the majority of subjects (22 of 35) harbor the homologous recombination reciprocal product of the common SMS microdeletion (~3.7 Mb), 13 subjects (~37%) have nonrecurrent duplications ranging in size from 1.3 to 15.2 Mb. Molecular studies suggest potential mechanistic differences between nonrecurrent duplications and nonrecurrent genomic deletions. Clinical features observed in patients with the common dup(17)(p11.2p11.2) are distinct from those seen with SMS and include infantile hypotonia, failure to thrive, mental retardation, autistic features, sleep apnea, and structural cardiovascular anomalies. We narrow the critical region to a 1.3-Mb genomic interval that contains the dosage-sensitive RAI1 gene. Our results refine the critical region for Potocki-Lupski syndrome, provide information to assist in clinical diagnosis and management, and lend further support for the concept that genomic architecture incites genomic instability.
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Affiliation(s)
- Lorraine Potocki
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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36
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Mikhail FM, McIlvried D, Holt RL, Messiaen L, Descartes MD, Carroll AJ. Complete trisomy 17p syndrome in a girl with der(14)t(14;17)(p11.2;p11.2). Am J Med Genet A 2007; 140:1647-54. [PMID: 16835929 DOI: 10.1002/ajmg.a.31330] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We report on an 8-year-old girl with near-complete trisomy 17p syndrome due to a de novo unbalanced t(14;17)(p11.2;p11.2). She has features consistent with the previously described cases with complete trisomy 17p, including pre- and post-natal growth retardation, motor and mental retardation, skeletal anomalies, clinodactyly of the 5th finger, hypertrichosis, as well as facial characteristics including microcephaly, receding forehead, ptosis, low-set malformed ears, smooth philtrum, high-arched palate, and a short broad neck. Fluorescence in situ hybridization showed that the breakpoints were p11.2 for both chromosome 14 and 17. Microsatellite analysis showed that the duplicated 17p was of paternal origin, and indicated that the breakpoint involving 17p11.2 is most likely located within the approximately 1-Mb segment from the centromere, and not involving the proximal Smith-Magenis syndrome (SMS) low copy repeat. We compare the clinical features of our patient with those previously reported to further delineate the phenotype of complete trisomy 17p syndrome.
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Affiliation(s)
- Fady M Mikhail
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
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37
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de Ravel TJL, Balikova I, Thienpont B, Hannes F, Maas N, Fryns JP, Devriendt K, Vermeesch JR. Molecular karyotyping of patients with MCA/MR: the blurred boundary between normal and pathogenic variation. Cytogenet Genome Res 2006; 115:225-30. [PMID: 17124404 DOI: 10.1159/000095918] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2006] [Accepted: 05/02/2006] [Indexed: 11/19/2022] Open
Abstract
Molecular karyotyping has revealed that microdeletions/duplications in the human genome are a major cause of multiple congenital anomalies associated with mental retardation (MCA/MR). The identification of a de novo chromosomal imbalance in a patient with MCA/MR is usually considered causal for the phenotype while a chromosomal imbalance inherited from a phenotypically normal parent is considered as a benign variation and not related to the disorder. Around 40% of imbalances in patients with MCA/MR in this series is inherited from a healthy parent and the majority of these appear to be (extremely) rare variants. As some of these contain known disease-causing genes and have also been found to be de novo in MCA/MR patients, this challenges the general view that such familial variants are innocent and of no major phenotypic consequence. Rather, we argue, that human genomes can be tolerant of genomic copy number variations depending on the genetic and environmental background and that different mechanisms play a role in determining whether these chromosomal imbalances manifest themselves.
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Affiliation(s)
- T J L de Ravel
- Centre for Human Genetics, UZ Gasthuisberg, Leuven, Belgium
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38
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Lee JA, Lupski JR. Genomic rearrangements and gene copy-number alterations as a cause of nervous system disorders. Neuron 2006; 52:103-21. [PMID: 17015230 DOI: 10.1016/j.neuron.2006.09.027] [Citation(s) in RCA: 199] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Genomic disorders are a group of human genetic diseases caused by genomic rearrangements resulting in copy-number variation (CNV) affecting a dosage-sensitive gene or genes critical for normal development or maintenance. These disorders represent a wide range of clinically distinct entities but include many diseases affecting nervous system function. Herein, we review selected neurodevelopmental, neurodegenerative, and psychiatric disorders either known or suggested to be caused by genomic rearrangement and CNV. Further, we emphasize the cause-and-effect relationship between gene CNV and complex disease traits. We also discuss the prevalence and heritability of CNV, the correlation between CNV and higher-order genome architecture, and the heritability of personality, behavioral, and psychiatric traits. We speculate that CNV could underlie a significant proportion of normal human variation including differences in cognitive, behavioral, and psychological features.
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Affiliation(s)
- Jennifer A Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
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39
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Girirajan S, Vlangos CN, Szomju BB, Edelman E, Trevors CD, Dupuis L, Nezarati M, Bunyan DJ, Elsea SH. Genotype–phenotype correlation in Smith-Magenis syndrome: Evidence that multiple genes in 17p11.2 contribute to the clinical spectrum. Genet Med 2006; 8:417-27. [PMID: 16845274 DOI: 10.1097/01.gim.0000228215.32110.89] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
PURPOSE Smith-Magenis syndrome (SMS) is a complex disorder that includes mental retardation, craniofacial and skeletal anomalies, and behavioral abnormalities. We report the molecular and genotype-phenotype analyses of 31 patients with SMS who carry 17p11.2 deletions or mutations in the RAI1 gene. METHODS Patients with SMS were evaluated by fluorescence in situ hybridization and/or sequencing of RAI1 to identify 17p11.2 deletions or intragenic mutations, respectively, and were compared for 30 characteristic features of this disorder by the Fisher exact test. RESULTS In our cohort, 8 of 31 individuals carried a common 3.5 Mb deletion, whereas 10 of 31 individuals carried smaller deletions, two individuals carried larger deletions, and one individual carried an atypical 17p11.2 deletion. Ten patients with nondeletion harbored a heterozygous mutation in RAI1. Phenotypic comparison between patients with deletions and patients with RAI1 mutations show that 21 of 30 SMS features are the result of haploinsufficiency of RAI1, whereas cardiac anomalies, speech and motor delay, hypotonia, short stature, and hearing loss are associated with 17p11.2 deletions rather than RAI1 mutations (P<.05). Further, patients with smaller deletions show features similar to those with RAI1 mutations. CONCLUSION Although RAI1 is the primary gene responsible for most features of SMS, other genes within 17p11.2 contribute to the variable features and overall severity of the syndrome.
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Affiliation(s)
- Santhosh Girirajan
- Department of Human Genetics, Medical College of Virginia Campus, Virginia Commonwealth University, Richmond, Virginia 23298, USA
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40
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Saugier-Veber P, Goldenberg A, Drouin-Garraud V, de La Rochebrochard C, Layet V, Drouot N, Le Meur N, Gilbert-Du-Ssardier B, Joly-Hélas G, Moirot H, Rossi A, Tosi M, Frébourg T. Simple detection of genomic microdeletions and microduplications using QMPSF in patients with idiopathic mental retardation. Eur J Hum Genet 2006; 14:1009-17. [PMID: 16773131 DOI: 10.1038/sj.ejhg.5201661] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022] Open
Abstract
In contrast to the numerous well-known microdeletion syndromes, only a few microduplications have been described, and this discrepancy may be due in part to methodological bias. In order to facilitate the detection of genomic microdeletions and microduplications, we developed a new assay based on QMPSF (Quantitative Multiplex PCR of Short fluorescent Fragments) able to explore simultaneously 12 candidate loci involved in mental retardation (MR) and known to be the target of genomic rearrangements. We first screened 153 patients with MR and facial dysmorphism associated with malformations, or growth anomalies, or familial history, with cytogenetically normal chromosomes, and the absence of FRAXA mutation and subtelomeric rearrangements. In this series, we found a 5q35 deletion removing the NSD1 gene in a patient with severe epilepsy, profound MR and, retrospectively, craniofacial features of Sotos syndrome. In a second series, we screened 140 patients with MR and behaviour disturbance who did not fulfil the de Vries criteria for subtelomeric rearrangements and who had a normal karyotype and no detectable FRAXA mutation. We detected a 22q11 deletion in a patient with moderate MR, obesity, and facial dysmorphism and a 4 Mb 17p11 duplication in a patient with moderate MR, behaviour disturbance, strabismus, and aspecific facial features. This new QMPSF assay can be gradually upgraded to include additional loci involved in newly recognised microduplication/microdeletion syndromes, and should facilitate wide screenings of patients with idiopathic MR and provide better estimates of the microduplication frequency in the MR population.
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41
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Abstract
Rearrangements of our genome can be responsible for inherited as well as sporadic traits. The analyses of chromosome breakpoints in the proximal short arm of Chromosome 17 (17p) reveal nonallelic homologous recombination (NAHR) as a major mechanism for recurrent rearrangements whereas nonhomologous end-joining (NHEJ) can be responsible for many of the nonrecurrent rearrangements. Genome architectural features consisting of low-copy repeats (LCRs), or segmental duplications, can stimulate and mediate NAHR, and there are hotspots for the crossovers within the LCRs. Rearrangements introduce variation into our genome for selection to act upon and as such serve an evolutionary function analogous to base pair changes. Genomic rearrangements may cause Mendelian diseases, produce complex traits such as behaviors, or represent benign polymorphic changes. The mechanisms by which rearrangements convey phenotypes are diverse and include gene dosage, gene interruption, generation of a fusion gene, position effects, unmasking of recessive coding region mutations (single nucleotide polymorphisms, SNPs, in coding DNA) or other functional SNPs, and perhaps by effects on transvection.
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Affiliation(s)
- James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, and at the Texas Children's Hospital, Houston, Texas, United States of America.
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42
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Thomas NS, Durkie M, Potts G, Sandford R, Van Zyl B, Youings S, Dennis NR, Jacobs PA. Parental and chromosomal origins of microdeletion and duplication syndromes involving 7q11.23, 15q11-q13 and 22q11. Eur J Hum Genet 2006; 14:831-7. [PMID: 16617304 DOI: 10.1038/sj.ejhg.5201617] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Non-allelic homologous recombination between chromosome-specific LCRs is the most common mechanism leading to recurrent microdeletions and duplications. To look for locus-specific differences, we have used microsatellites to determine the parental and chromosomal origins of a large series of patients with de novo deletions of chromosome 7q11.23 (Williams syndrome), 15q11-q13 (Angelman syndrome, Prader-Willi syndrome) and 22q11 (Di George syndrome) and duplications of 15q11-q13. Overall the majority of rearrangements were interchromosomal, so arising from unequal meiotic exchange, and there were approximately equal numbers of maternal and paternal deletions. Duplications and deletions of 15q11-q13 appear to be reciprocal products that arise by the same mechanisms. The proportion arising from interchromosomal exchanges varied among deletions with 22q11 the highest and 15q11-q13 the lowest. However, parental and chromosomal origins were not always independent. For 15q11-q13, maternal deletions tended to be interchromosomal while paternal deletions tended to be intrachromosomal; for 22q11 there was a possible excess of maternal cases among intrachromosomal deletions. Several factors are likely to be involved in the formation of recurrent rearrangements and the relative importance of these appear to be locus-specific.
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Affiliation(s)
- N Simon Thomas
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, UK.
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43
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Goldman AM, Potocki L, Walz K, Lynch JK, Glaze DG, Lupski JR, Noebels JL. Epilepsy and chromosomal rearrangements in Smith-Magenis Syndrome [del(17)(p11.2p11.2)]. J Child Neurol 2006; 21:93-8. [PMID: 16566870 DOI: 10.1177/08830738060210021201] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Smith-Magenis syndrome is a multiple congenital anomalies/mental retardation syndrome associated with a heterozygous deletion of chromosome 17p11.2. Seizures have not been formally studied in this population. Our objectives were to estimate the prevalence of seizures and electroencephalographic (EEG) epileptiform abnormalities in patients with Smith-Magenis syndrome with defined chromosomal rearrangements and to describe the spectrum of abnormal EEG patterns. Prolonged video-EEGs were obtained in 60 patients. Eighteen percent of patients reported a seizure history; however, abnormal EEGs were identified in 31 of the 60 subjects and 27 of 31 were epileptiform. Generalized epileptiform patterns were the most common (73%). Most patients with either small or large deletions had an abnormal EEG (83%; 75%) in contrast to those with a common deletion (49%). Our results indicate that epileptiform EEG abnormalities are frequent in patients with Smith-Magenis syndrome. Considering that close to one third of individuals with Smith-Magenis syndrome with epileptiform abnormalities also had a history of clinical seizures, cortical hyperexcitability and epilepsy should be considered an important component of the Smith-Magenis syndrome clinical phenotype.
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Affiliation(s)
- Alica M Goldman
- Department of Neurology, Baylor College of Medicine, Texas Children's Hospital, Houston, TX 77030, USA.
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44
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Kriek M, White SJ, Szuhai K, Knijnenburg J, van Ommen GJB, den Dunnen JT, Breuning MH. Copy number variation in regions flanked (or unflanked) by duplicons among patients with developmental delay and/or congenital malformations; detection of reciprocal and partial Williams-Beuren duplications. Eur J Hum Genet 2005; 14:180-9. [PMID: 16391556 DOI: 10.1038/sj.ejhg.5201540] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Duplicons, that is, DNA sequences with minimum length 10 kb and a high sequence similarity, are known to cause unequal homologous recombination, leading to deletions and the reciprocal duplications. In this study, we designed a Multiplex Amplifiable Probe Hybridisation (MAPH) assay containing 63 exon-specific single-copy sequences from within a selection of the 169 regions flanked by duplicons that were identified, at a first pass, in 2001. Subsequently, we determined the frequency of chromosomal rearrangements among patients with developmental delay (DD) and/or congenital malformations (CM). In addition, we tried to identify new regions involved in DD/CM using the same assay. In 105 patients, six imbalances (5.8%) were detected and verified. Three of these were located in microdeletion-related regions, two alterations were polymorphic duplications and the effect of the last alteration is currently unknown. The same study population was tested for rearrangements in regions with no known duplicons nearby, using a set of probes derived from 58 function-selected genes. The latter screening revealed two alterations. As expected, the alteration frequency per unit of DNA is much higher in regions flanked by duplicons (fraction of the genome tested: 5.2%) compared to regions without known duplicons nearby (fraction of the genome tested: 24.5-90.2%). We were able to detect three novel rearrangements, including the previously undescribed reciprocal duplication of the Williams Beuren critical region, a subduplicon alteration within this region and a duplication on chromosome band 16p13.11. Our results support the hypothesis that regions flanked by duplicons are enriched for copy number variations.
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Affiliation(s)
- Marjolein Kriek
- Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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45
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Sharp AJ, Locke DP, McGrath SD, Cheng Z, Bailey JA, Vallente RU, Pertz LM, Clark RA, Schwartz S, Segraves R, Oseroff VV, Albertson DG, Pinkel D, Eichler EE. Segmental duplications and copy-number variation in the human genome. Am J Hum Genet 2005; 77:78-88. [PMID: 15918152 PMCID: PMC1226196 DOI: 10.1086/431652] [Citation(s) in RCA: 682] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2005] [Accepted: 05/04/2005] [Indexed: 01/15/2023] Open
Abstract
The human genome contains numerous blocks of highly homologous duplicated sequence. This higher-order architecture provides a substrate for recombination and recurrent chromosomal rearrangement associated with genomic disease. However, an assessment of the role of segmental duplications in normal variation has not yet been made. On the basis of the duplication architecture of the human genome, we defined a set of 130 potential rearrangement hotspots and constructed a targeted bacterial artificial chromosome (BAC) microarray (with 2,194 BACs) to assess copy-number variation in these regions by array comparative genomic hybridization. Using our segmental duplication BAC microarray, we screened a panel of 47 normal individuals, who represented populations from four continents, and we identified 119 regions of copy-number polymorphism (CNP), 73 of which were previously unreported. We observed an equal frequency of duplications and deletions, as well as a 4-fold enrichment of CNPs within hotspot regions, compared with control BACs (P < .000001), which suggests that segmental duplications are a major catalyst of large-scale variation in the human genome. Importantly, segmental duplications themselves were also significantly enriched >4-fold within regions of CNP. Almost without exception, CNPs were not confined to a single population, suggesting that these either are recurrent events, having occurred independently in multiple founders, or were present in early human populations. Our study demonstrates that segmental duplications define hotspots of chromosomal rearrangement, likely acting as mediators of normal variation as well as genomic disease, and it suggests that the consideration of genomic architecture can significantly improve the ascertainment of large-scale rearrangements. Our specialized segmental duplication BAC microarray and associated database of structural polymorphisms will provide an important resource for the future characterization of human genomic disorders.
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Affiliation(s)
- Andrew J Sharp
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
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Bi W, Ohyama T, Nakamura H, Yan J, Visvanathan J, Justice MJ, Lupski JR. Inactivation of Rai1 in mice recapitulates phenotypes observed in chromosome engineered mouse models for Smith–Magenis syndrome. Hum Mol Genet 2005; 14:983-95. [PMID: 15746153 DOI: 10.1093/hmg/ddi085] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Retinoic acid induced 1 (RAI1) is among the 20 genes identified in the critical region of Smith-Magenis syndrome (SMS), a genomic disorder with multiple congenital anomalies associated with a 3.7 Mb heterozygous deletion of 17p11.2. Heterozygous premature termination mutations in RAI1 have been identified recently in SMS patients without detectable deletions. To investigate Rai1 function, we generated a null allele in mice by gene targeting and simultaneously inserted a lacZ reporter gene into the Rai1 locus. X-gal staining of the Rai1(+/-) mice recapitulated the endogenous expression pattern of Rai1. The gene was predominantly expressed in the epithelial cells involved in organogenesis. Obesity and craniofacial abnormalities, which have been reported in SMS mouse models containing a heterozygous deletion of the syntenic SMS critical region, were observed in Rai1(+/-) mice. Thus, haploinsufficiency of Rai1 causes obesity and craniofacial abnormalities in mice. Interestingly, the penetrance of craniofacial anomalies is further reduced in Rai1(+/-) mice. Most homozygous mice died during gastrulation and organogenesis. The surviving Rai1(-/-) mice were growth retarded and displayed malformations in both the craniofacial and the axial skeleton. Using green fluorescence protein and GAL4 DNA binding domain fusions to Rai1, we showed that Rai1 is translocated to the nucleus and it has transactivation activity. Our data are consistent with Rai1 functioning as a transcriptional regulator, document that Rai1 haploinsufficiency is responsible for obesity and craniofacial phenotypes in mice with SMS deletions, and indicate Rai1 is important for embryonic and postnatal developments.
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Affiliation(s)
- Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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Stankiewicz P, Shaw CJ, Withers M, Inoue K, Lupski JR. Serial segmental duplications during primate evolution result in complex human genome architecture. Genome Res 2005; 14:2209-20. [PMID: 15520286 PMCID: PMC525679 DOI: 10.1101/gr.2746604] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The human genome is particularly rich in low-copy repeats (LCRs) or segmental duplications (5%-10%), and this characteristic likely distinguishes us from lower mammals such as rodents. How and why the complex human genome architecture consisting of multiple LCRs has evolved remains an open question. Using molecular and computational analyses of human and primate genomic regions, we analyzed the structure and evolution of LCRs that resulted in complex architectural features of the human genome in proximal 17p. We found that multiple LCRs of different origins are situated adjacent to one another, whereas each LCR changed at different time points between >25 to 3-7 million years ago (Mya) during primate evolution. Evolutionary studies in primates suggested communication between the LCRs by gene conversion. The DNA transposable element MER1-Charlie3 and retroviral ERVL elements were identified at the breakpoint of the t(4;19) chromosome translocation in Gorilla gorilla, suggesting a potential role for transpositions in evolution of the primate genome. Thus, a series of consecutive segmental duplication events during primate evolution resulted in complex genome architecture in proximal 17p. Some of the more recent events led to the formation of novel genes that in human are expressed primarily in the brain. Our observations support the contention that serial segmental duplication events might have orchestrated primate evolution by the generation of novel fusion/fission genes as well as potentially by genomic inversions associated with decreased recombination rates facilitating gene divergence.
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Affiliation(s)
- Pawełl Stankiewicz
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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48
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Abstract
The finding, during the last decade, that several common, clinically delineated syndromes are caused by submicroscopic deletions or, more rarely, by duplications, has provided a powerful tool in the annotation of the human genome. Since most microdeletion/microduplication syndromes are defined by a common deleted/duplicated region, abnormal dosage of genes located within these regions can explain the phenotypic similarities among individuals with a specific syndrome. As such, they provide a unique resource towards the genetic dissection of complex phenotypes such as congenital heart defects, mental and growth retardation and abnormal behaviour. In addition, the study of phenotypic differences in individuals with the same microdeletion syndrome may also become a treasury for the identification of modifying factors for complex phenotypes. The molecular analysis of these chromosomal anomalies has led to a growing understanding of their mechanisms of origin. Novel tools to uncover additional submicroscopic chromosomal anomalies at a higher resolution and higher speed, as well as the novel tools at hand for deciphering the modifying factors and epistatic interactors, are 'on the doorstep' and will, besides their obvious diagnostic role, play a pivotal role in the genetic dissection of complex phenotypes.
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Affiliation(s)
- Koen Devriendt
- Center for Human Genetics, University Hospital Leuven, Herestraat 49, B-3000 Leuven, Belgium
| | - Joris R Vermeesch
- Center for Human Genetics, University Hospital Leuven, Herestraat 49, B-3000 Leuven, Belgium
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Kotzot D, Haberlandt E, Fauth C, Baumgartner S, Scholl-Bürgi S, Utermann G. Del(18)(q12.2q21.1) caused by a paternal sister chromatid rearrangement in a developmentally delayed girl. Am J Med Genet A 2005; 135:304-7. [PMID: 15887269 DOI: 10.1002/ajmg.a.30727] [Citation(s) in RCA: 10] [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
Monosomy of 18q12.3 has been reported in only 16 cases, in one as a mosaic with a normal cell line. Abnormal behaviour, developmental delay, normal measurements, and minor facial anomalies including ptosis, bilateral epicanthus, strabismus, short and slightly down-slanting palpebral fissures, and full cheeks are characteristic manifestations. We report on a 26-month-old girl with del(18)(q12.2q21.1) and typical phenotype. Microsatellite mediated haplotype analysis showed approximately 12 Mb deletion and demonstrated that the deletion was most likely formed during paternal meiosis by a rearrangement between the grandpaternal sister chromatids.
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Affiliation(s)
- Dieter Kotzot
- Institute of Medical Biology and Human Genetics, Medical University of Innsbruck, Innsbruck, Austria.
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Yatsenko SA, Treadwell-Deering D, Krull K, Lewis RA, Glaze D, Stankiewicz P, Lupski JR, Potocki L. Trisomy 17p10-p12 due to mosaic supernumerary marker chromosome: Delineation of molecular breakpoints and clinical phenotype, and comparison to other proximal 17p segmental duplications. Am J Med Genet A 2005; 138A:175-80. [PMID: 16152635 DOI: 10.1002/ajmg.a.30948] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The unstable, gene-rich chromosome region 17p11.2-p12 is associated with various structural aberrations including supernumerary marker chromosomes (SMCs). In some cases, SMC(17)s utilize the same substrates for recombination as the common recurrent 17p11.2 and 17p12 rearrangements. We report on a 9-year-old girl with a de novo mosaic SMC(17). The der(17) encompasses genetic material from 17p10-p11.2 and is present in 97% of peripheral blood lymphocytes and in 79% of buccal cells. The patient has few features similar to individuals with duplication 17p11.2 including mental retardation, language impairment, and sleep disturbances but has normal growth, and no structural abnormalities of the heart, kidneys, or brain. She has no substantial behavioral abnormalities or dysmorphic features. Molecular analyses determined that the der(17) contains RAI1 but not PMP22. We found one chromosome breakpoint within the centromere and the second breakpoint within the distal Smith-Magenis syndrome low-copy repeat (distal SMS-REP). Recently we characterized the breakpoints of three other marker chromosomes originating from the proximal short arm of chromosome 17. In all four cases, one breakpoint maps within the centromere and in three cases the second breakpoint maps within a low-copy repeat. We thus propose that genome architecture may play a significant role in the formation of marker chromosomes. We present the cytogenetic, molecular, and clinical data of this patient and compare our results with those of patients with dup(17)(p11.2p11.2) syndrome and other patients with SMC(17).
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Affiliation(s)
- Svetlana A Yatsenko
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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