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da Costa SS, Fishman V, Pinheiro M, Rodrigueiro A, Sanseverino MT, Zielinsky P, Carvalho CMB, Rosenberg C, Krepischi ACV. A germline chimeric KANK1-DMRT1 transcript derived from a complex structural variant is associated with a congenital heart defect segregating across five generations. Chromosome Res 2024; 32:6. [PMID: 38504027 DOI: 10.1007/s10577-024-09750-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/27/2024] [Accepted: 03/08/2024] [Indexed: 03/21/2024]
Abstract
Structural variants (SVs) pose a challenge to detect and interpret, but their study provides novel biological insights and molecular diagnosis underlying rare diseases. The aim of this study was to resolve a 9p24 rearrangement segregating in a family through five generations with a congenital heart defect (congenital pulmonary and aortic valvular stenosis and pulmonary artery stenosis), by applying a combined genomic analysis. The analysis involved multiple techniques, including karyotype, chromosomal microarray analysis (CMA), FISH, genome sequencing (GS), RNA-seq, and optical genome mapping (OGM). A complex 9p24 SV was hinted at by CMA results, showing three interspersed duplicated segments. Combined GS and OGM analyses revealed that the 9p24 duplications constitute a complex SV, on which a set of breakpoints matches the boundaries of the CMA duplicated sequences. The proposed structure for this complex rearrangement implies three duplications associated with an inversion of ~ 2 Mb region on chromosome 9 and a SINE element insertion at the more distal breakpoint. Interestingly, this genomic structure of rearrangement forms a chimeric transcript of the KANK1/DMRT1 loci, which was confirmed by both RNA-seq and Sanger sequencing on blood samples from 9p24 rearrangement carriers. Altogether with breakpoint amplification and FISH analysis, this combined approach allowed a deep characterization of this complex rearrangement. Although the genotype-phenotype correlation remains elusive from the molecular mechanism point of view, this study identified a large genomic rearrangement at 9p24 segregating with a familial congenital heart defect, revealing a genetic biomarker that was successfully applied for embryo selection, changing the reproductive perspective of affected individuals.
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Affiliation(s)
- Silvia Souza da Costa
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Veniamin Fishman
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Mara Pinheiro
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | | | - Maria Teresa Sanseverino
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- School of Medicine, Pontifícia Universidade Catolica do Rio Grande Do Sul, Porto Alegre, Brazil
| | - Paulo Zielinsky
- Department of Pediatrics and Childcare, Federal University of the Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Carla Rosenberg
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Ana Cristina Victorino Krepischi
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil.
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Mazzonetto PC, Villela D, da Costa SS, Krepischi ACV, Milanezi F, Migliavacca MP, Pierry PM, Bonaldi A, Almeida LGD, De Souza CA, Kroll JE, Paula MG, Guarischi-Sousa R, Scapulatempo-Neto C, Rosenberg C. Low-pass whole genome sequencing is a reliable and cost-effective approach for copy number variant analysis in the clinical setting. Ann Hum Genet 2024; 88:113-125. [PMID: 37807935 DOI: 10.1111/ahg.12532] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/10/2023]
Abstract
INTRODUCTION Next generation sequencing technology has greatly reduced the cost and time required for sequencing a genome. An approach that is rapidly being adopted as an alternative method for CNV analysis is the low-pass whole genome sequencing (LP-WGS). Here, we evaluated the performance of LP-WGS to detect copy number variants (CNVs) in clinical cytogenetics. MATERIALS AND METHODS DNA samples with known CNVs detected by chromosomal microarray analyses (CMA) were selected for comparison and used as positive controls; our panel included 44 DNA samples (12 prenatal and 32 postnatal), comprising a total of 55 chromosome imbalances. The selected cases were chosen to provide a wide range of clinically relevant CNVs, the vast majority being associated with intellectual disability or recognizable syndromes. The chromosome imbalances ranged in size from 75 kb to 90.3 Mb, including aneuploidies and two cases of mosaicism. RESULTS All CNVs were successfully detected by LP-WGS, showing a high level of consistency and robust performance of the sequencing method. Notably, the size of chromosome imbalances detected by CMA and LP-WGS were compatible between the two different platforms, which indicates that the resolution and sensitivity of the LP-WGS approach are at least similar to those provided by CMA. DISCUSSION Our data show the potential use of LP-WGS to detect CNVs in clinical diagnosis and confirm the method as an alternative for chromosome imbalances detection. The diagnostic effectiveness and feasibility of LP-WGS, in this technical validation study, were evidenced by a clinically representative dataset of CNVs that allowed a systematic assessment of the detection power and the accuracy of the sequencing approach. Further, since the software used in this study is commercially available, the method can easily be tested and implemented in a routine diagnostic setting.
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Affiliation(s)
- Patricia C Mazzonetto
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
| | | | - Silvia Souza da Costa
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Ana C V Krepischi
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | | | | | | | | | | | | | | | | | | | | | - Carla Rosenberg
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
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Tolezano GC, Bastos GC, da Costa SS, Freire BL, Homma TK, Honjo RS, Yamamoto GL, Passos-Bueno MR, Koiffmann CP, Kim CA, Vianna-Morgante AM, de Lima Jorge AA, Bertola DR, Rosenberg C, Krepischi ACV. Burden of Rare Copy Number Variants in Microcephaly: A Brazilian Cohort of 185 Microcephalic Patients and Review of the Literature. J Autism Dev Disord 2024; 54:1181-1212. [PMID: 36502452 DOI: 10.1007/s10803-022-05853-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2022] [Indexed: 12/14/2022]
Abstract
Microcephaly presents heterogeneous genetic etiology linked to several neurodevelopmental disorders (NDD). Copy number variants (CNVs) are a causal mechanism of microcephaly whose investigation is a crucial step for unraveling its molecular basis. Our purpose was to investigate the burden of rare CNVs in microcephalic individuals and to review genes and CNV syndromes associated with microcephaly. We performed chromosomal microarray analysis (CMA) in 185 Brazilian patients with microcephaly and evaluated microcephalic patients carrying < 200 kb CNVs documented in the DECIPHER database. Additionally, we reviewed known genes and CNV syndromes causally linked to microcephaly through the PubMed, OMIM, DECIPHER, and ClinGen databases. Rare clinically relevant CNVs were detected in 39 out of the 185 Brazilian patients investigated by CMA (21%). In 31 among the 60 DECIPHER patients carrying < 200 kb CNVs, at least one known microcephaly gene was observed. Overall, four gene sets implicated in microcephaly were disclosed: known microcephaly genes; genes with supporting evidence of association with microcephaly; known macrocephaly genes; and novel candidates, including OTUD7A, BBC3, CNTN6, and NAA15. In the review, we compiled 957 known microcephaly genes and 58 genomic CNV loci, comprising 13 duplications and 50 deletions, which have already been associated with clinical findings including microcephaly. We reviewed genes and CNV syndromes previously associated with microcephaly, reinforced the high CMA diagnostic yield for this condition, pinpointed novel candidate loci linked to microcephaly deserving further evaluation, and provided a useful resource for future research on the field of neurodevelopment.
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Affiliation(s)
- Giovanna Cantini Tolezano
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Giovanna Civitate Bastos
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Silvia Souza da Costa
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Bruna Lucheze Freire
- Unidade de Endocrinologia Genética (LIM25), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 455 Avenida Doutor Arnaldo, São Paulo, SP, 01246-903, Brazil
| | - Thais Kataoka Homma
- Unidade de Endocrinologia Genética (LIM25), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 455 Avenida Doutor Arnaldo, São Paulo, SP, 01246-903, Brazil
| | - Rachel Sayuri Honjo
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 647 Avenida Doutor Enéas Carvalho de Aguiar, São Paulo, SP, 05403-900, Brazil
| | - Guilherme Lopes Yamamoto
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 647 Avenida Doutor Enéas Carvalho de Aguiar, São Paulo, SP, 05403-900, Brazil
| | - Maria Rita Passos-Bueno
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Celia Priszkulnik Koiffmann
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Chong Ae Kim
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 647 Avenida Doutor Enéas Carvalho de Aguiar, São Paulo, SP, 05403-900, Brazil
| | - Angela Maria Vianna-Morgante
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Alexander Augusto de Lima Jorge
- Unidade de Endocrinologia Genética (LIM25), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 455 Avenida Doutor Arnaldo, São Paulo, SP, 01246-903, Brazil
| | - Débora Romeo Bertola
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 647 Avenida Doutor Enéas Carvalho de Aguiar, São Paulo, SP, 05403-900, Brazil
| | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Ana Cristina Victorino Krepischi
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil.
- Institute of Biosciences, University of São Paulo, 277 Rua do Matão, São Paulo, SP, 05508-090, Brazil.
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Costa SS, Fishman V, Pinheiro M, Rodrigueiro A, Sanseverino MT, Zielinsky P, Carvalho CMB, Rosenberg C, Krepischi ACV. A germline chimeric KANK1-DMRT1 transcript derived from a complex structural variant is associated with a congenital heart defect segregating across five generations. RESEARCH SQUARE 2023:rs.3.rs-3740005. [PMID: 38168413 PMCID: PMC10760254 DOI: 10.21203/rs.3.rs-3740005/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Structural variants (SVs) pose a challenge to detect and interpret, but their study provides novel biological insights and molecular diagnosis underlying rare diseases. The aim of this study was to resolve a 9p24 rearrangement segregating in a family through five generations with a congenital heart defect (congenital pulmonary and aortic valvular stenosis, and pulmonary artery stenosis), by applying a combined genomic analysis. The analysis involved multiple techniques, including karyotype, chromosomal microarray analysis (CMA), FISH, whole-genome sequencing (WGS), RNA-seq and optical genome mapping (OGM). A complex 9p24 SV was hinted at by CMA results, showing three interspersed duplicated segments. Combined WGS and OGM analyses revealed that the 9p24 duplications constitute a complex SV, on which a set of breakpoints match the boundaries of the CMA duplicated sequences. The proposed structure for this complex rearrangement implies three duplications associated with an inversion of ~ 2Mb region on chromosome 9 with a SINE element insertion at the more distal breakpoint. Interestingly, this hypothesized genomic structure of rearrangement forms a chimeric transcript of the KANK1/DMRT1 loci, which was confirmed by RNA-seq on blood from 9p24 rearrangement carriers. Altogether with breakpoint amplification and FISH analysis, this combined approach allowed a deep characterization of this complex rearrangement. Although the genotype-phenotype correlation remains elusive from the molecular mechanism point of view, this study identified a large genomic rearrangement at 9p segregating with a familial congenital clinical trait, revealing a genetic biomarker that was successfully applied for embryo selection, changing the reproductive perspective of affected individuals.
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5
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Copy number variation profiling in pharmacogenes using panel-based exome resequencing and correlation to human liver expression. Hum Genet 2019; 139:137-149. [PMID: 31786673 DOI: 10.1007/s00439-019-02093-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 11/23/2019] [Indexed: 12/13/2022]
Abstract
Structural variants including copy number variations (CNV) have gained widespread attention, especially in pharmacogenomics but for several genes functional relevance and clinical evidence are still lacking. Detection of CNVs in next-generation sequencing data is challenging but offers widespread applications. We developed a cohort-based CNV detection workflow to extract CNVs from read counts of targeted NGS of 340 genes involved in absorption, distribution, metabolism and excretion (ADME) of drugs. We applied our method to 150 human liver tissue samples and correlated identified CNVs to mRNA expression levels. In total, we identified 445 deletions (73%) and 167 duplications (27%) in 36 pharmacogenes including all well-known CNVs of CYPs, GSTs, SULTs, UGTs, numerous described rare CNVs of CYP2E1, SLC16A3 or UGT2B15 as well as novel observations, e.g., for SLC22A12, SLC22A17 and GPS2 (G Protein Pathway Suppressor 2). We were able to fine-map complex CNVs of CYP2A6 and CYP2D6 with exon resolution. Correlation analysis confirmed known expression patterns for common CNVs and suggested an influence on expression variability for some rare CNVs. Our straightforward CNV detection workflow can be easily applied to any NGS coverage data and helped to analyze CNVs in an ADME-NGS panel of 340 pharmacogenes to improve genotype-phenotype correlations.
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Villela D, Costa SS, Vianna-Morgante AM, Krepischi AC, Rosenberg C. Efficient detection of chromosome imbalances and single nucleotide variants using targeted sequencing in the clinical setting. Eur J Med Genet 2017; 60:667-674. [DOI: 10.1016/j.ejmg.2017.08.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/30/2017] [Accepted: 08/31/2017] [Indexed: 11/29/2022]
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7
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Maini I, Ivanovski I, Iodice A, Rosato S, Pollazzon M, Mussini M, Belligni EF, Coutton C, Marinelli M, Barbieri V, Napoli M, Pascarella R, Sartori C, Madia F, Fusco C, Franchi F, Street ME, Garavelli L. Endocrinological Abnormalities Are a Main Feature of 17p13.1 Microduplication Syndrome: A New Case and Literature Review. Mol Syndromol 2016; 7:337-343. [PMID: 27920637 DOI: 10.1159/000450718] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2016] [Indexed: 11/19/2022] Open
Abstract
To date, 5 cases of 17p13.1 microduplications have been described in the literature. Intellectual disability was reported as the core feature, together with minor facial dysmorphisms and obesity, but a characteristic phenotype for 17p13.1 microduplication has not been delineated. Here, we describe a patient with a 1.56-Mb de novo duplication in 17p13.1, affected by mild intellectual disability, facial dysmorphisms, obesity, and diabetes. By comparing the different phenotypes of currently described cases, we delineated the main clinical features of 17p13.1 microduplication syndrome. All patients described to date had variable facial dysmorphisms; therefore, it was difficult to define a common facial gestalt. Furthermore, we stress endocrinological abnormalities as important features and the need to monitor these over time.
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Affiliation(s)
- Ilenia Maini
- Clinical Genetics Unit, Università degli Studi di Parma, Parma, Italy; Scuola di Specializzazione in Neuropsichiatria Infantile, Università degli Studi di Parma, Parma, Italy
| | - Ivan Ivanovski
- Clinical Genetics Unit, Università degli Studi di Parma, Parma, Italy; Department of Surgical, Medical, Dental and Morphological Sciences with interest in Transplant, Oncology and Regenerative Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | - Alessandro Iodice
- Paediatric Neuropsychiatry Unit, Università degli Studi di Parma, Parma, Italy
| | - Simonetta Rosato
- Clinical Genetics Unit, Università degli Studi di Parma, Parma, Italy
| | - Marzia Pollazzon
- Clinical Genetics Unit, Università degli Studi di Parma, Parma, Italy
| | - Manuela Mussini
- Clinical Genetics Unit, Università degli Studi di Parma, Parma, Italy
| | - Elga F Belligni
- Department of Paediatrics, University of Turin, Turin, Italy
| | - Charles Coutton
- Laboratoire de Génétique Chromosomique, Département de Génétique et Procréation, Hôpital Couple Enfant, Grenoble, France
| | - Maria Marinelli
- Medical Genetics Laboratory, Department of Obstetrics and Paediatrics, Università degli Studi di Parma, Parma, Italy
| | - Veronica Barbieri
- Medical Genetics Laboratory, Department of Obstetrics and Paediatrics, Università degli Studi di Parma, Parma, Italy
| | - Manuela Napoli
- Neuroradiology Unit, Department of Diagnostic Imaging, Università degli Studi di Parma, Parma, Italy
| | - Rosario Pascarella
- Neuroradiology Unit, Department of Diagnostic Imaging, Università degli Studi di Parma, Parma, Italy
| | - Chiara Sartori
- Division of Paediatric Endocrinology and Diabetology, Department of Obstetrics and Paediatrics, Arcispedale Santa Maria Nuova-IRCCS, Reggio Emilia, Università degli Studi di Parma, Parma, Italy
| | - Francesca Madia
- Laboratory of Neurogenetics and Neuroscience, Department of Neuroscience, Istituto 'G. Gaslini', Genova, Italy
| | - Carlo Fusco
- Medical Genetics Laboratory, Department of Obstetrics and Paediatrics, Università degli Studi di Parma, Parma, Italy
| | - Fabrizia Franchi
- Medical Genetics Laboratory, Department of Obstetrics and Paediatrics, Università degli Studi di Parma, Parma, Italy
| | - Maria E Street
- Division of Paediatric Endocrinology and Diabetology, Department of Obstetrics and Paediatrics, Arcispedale Santa Maria Nuova-IRCCS, Reggio Emilia, Università degli Studi di Parma, Parma, Italy
| | - Livia Garavelli
- Clinical Genetics Unit, Università degli Studi di Parma, Parma, Italy
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Giordano L, Palestra F, Giuffrida MG, Molinaro A, Iodice A, Bernardini L, La Boria P, Accorsi P, Novelli A. 17p13.1 microdeletion: genetic and clinical findings in a new patient with epilepsy and comparison with literature. Am J Med Genet A 2015; 164A:225-30. [PMID: 24501763 DOI: 10.1002/ajmg.a.36225] [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] [Indexed: 11/05/2022]
Abstract
Array comparative genomic hybridization is now a powerful tool to investigate patients with multiple congenital abnormalities and intellectual/motor impairment, and genomic imbalances are identified in a growing number of children with intellectual disability. Deletions in the 17p13.1 region have been reported in patients with dysmorphic features and developmental delay but a consistent phenotype has yet to emerge. Here, we report on the diagnosis of a 17p13.1 microdeletion of 829 kb in an 8-year-old girl presenting with profound cognitive disability, psychomotor delay, facial dysmorphisms, and refractory epilepsy. This deletion comprises 44 genes, including 8 OMIM morbid genes. We discuss genetic, clinical, and epileptic features comparing our patient with those previously reported in the literature.
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Dosage changes of a segment at 17p13.1 lead to intellectual disability and microcephaly as a result of complex genetic interaction of multiple genes. Am J Hum Genet 2014; 95:565-78. [PMID: 25439725 DOI: 10.1016/j.ajhg.2014.10.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 10/03/2014] [Indexed: 11/24/2022] Open
Abstract
The 17p13.1 microdeletion syndrome is a recently described genomic disorder with a core clinical phenotype of intellectual disability, poor to absent speech, dysmorphic features, and a constellation of more variable clinical features, most prominently microcephaly. We identified five subjects with copy-number variants (CNVs) on 17p13.1 for whom we performed detailed clinical and molecular studies. Breakpoint mapping and retrospective analysis of published cases refined the smallest region of overlap (SRO) for microcephaly to a genomic interval containing nine genes. Dissection of this phenotype in zebrafish embryos revealed a complex genetic architecture: dosage perturbation of four genes (ASGR1, ACADVL, DVL2, and GABARAP) impeded neurodevelopment and decreased dosage of the same loci caused a reduced mitotic index in vitro. Moreover, epistatic analyses in vivo showed that dosage perturbations of discrete gene pairings induce microcephaly. Taken together, these studies support a model in which concomitant dosage perturbation of multiple genes within the CNV drive the microcephaly and possibly other neurodevelopmental phenotypes associated with rearrangements in the 17p13.1 SRO.
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Mooneyham KA, Holden KR, Cathey S, Dwivedi A, Dupont BR, Lyons MJ. Neurodevelopmental delays and macrocephaly in 17p13.1 microduplication syndrome. Am J Med Genet A 2014; 164A:2887-91. [PMID: 25123844 DOI: 10.1002/ajmg.a.36708] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Accepted: 06/23/2014] [Indexed: 11/07/2022]
Abstract
Microduplication of chromosome 17p13.1 is a rarely reported chromosome abnormality associated with neurodevelopmental delays. We describe two unrelated patients with overlapping microduplications of chromosome 17p13.1. The first patient is a 2-year-old male who presented with neurodevelopmental delays and macrocephaly. He was found to have a de novo 788 kb copy gain of 17p13.2p13.1 and a de novo 134 kb copy gain of 17p13.1. These duplications include multiple candidate genes, including EFNB3, NLGN2, DLG4, GABARAP, and DULLARD, which may be responsible for neurodevelopmental delays in affected individuals. The second patient is a 29-year-old female with mild intellectual disability and relative macrocephaly. She was found to have a 62.5 kb copy gain of chromosome 17p13.1 that includes the DLG4, GABARAP, and DULLARD genes. The DLG4, GABARAP, and DULLARD genes included in the microduplications of both our patients appear to be candidate genes for neurodevelopmental delays and macrocephaly in individuals with 17p13.1 microduplication syndrome.
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11
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Sun Y, Overvad K, Olsen J. Cancer risks in children with congenital malformations in the nervous and circulatory system—A population based cohort study. Cancer Epidemiol 2014; 38:393-400. [DOI: 10.1016/j.canep.2014.04.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Revised: 03/05/2014] [Accepted: 04/08/2014] [Indexed: 11/17/2022]
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12
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Xie L, Chen JL, Zhang WZ, Wang SZ, Zhao TL, Huang C, Wang J, Yang JF, Yang YF, Tan ZP. Rare de novo copy number variants in patients with congenital pulmonary atresia. PLoS One 2014; 9:e96471. [PMID: 24826987 PMCID: PMC4020819 DOI: 10.1371/journal.pone.0096471] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Accepted: 04/08/2014] [Indexed: 11/18/2022] Open
Abstract
Background Ongoing studies using genomic microarrays and next-generation sequencing have demonstrated that the genetic contributions to cardiovascular diseases have been significantly ignored in the past. The aim of this study was to identify rare copy number variants in individuals with congenital pulmonary atresia (PA). Methods and Results Based on the hypothesis that rare structural variants encompassing key genes play an important role in heart development in PA patients, we performed high-resolution genome-wide microarrays for copy number variations (CNVs) in 82 PA patient-parent trios and 189 controls with an Illumina SNP array platform. CNVs were identified in 17/82 patients (20.7%), and eight of these CNVs (9.8%) are considered potentially pathogenic. Five de novo CNVs occurred at two known congenital heart disease (CHD) loci (16p13.1 and 22q11.2). Two de novo CNVs that may affect folate and vitamin B12 metabolism were identified for the first time. A de novo 1-Mb deletion at 17p13.2 may represent a rare genomic disorder that involves mild intellectual disability and associated facial features. Conclusions Rare CNVs contribute to the pathogenesis of PA (9.8%), suggesting that the causes of PA are heterogeneous and pleiotropic. Together with previous data from animal models, our results might help identify a link between CHD and folate-mediated one-carbon metabolism (FOCM). With the accumulation of high-resolution SNP array data, these previously undescribed rare CNVs may help reveal critical gene(s) in CHD and may provide novel insights about CHD pathogenesis.
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MESH Headings
- Adolescent
- Case-Control Studies
- Child
- Child, Preschool
- Chromosome Aberrations
- Chromosomes, Human, Pair 16
- Chromosomes, Human, Pair 17
- Chromosomes, Human, Pair 22
- DNA Copy Number Variations
- Female
- Folic Acid/metabolism
- Genetic Loci
- Genome-Wide Association Study
- Heart Defects, Congenital/diagnostic imaging
- Heart Defects, Congenital/genetics
- Heart Defects, Congenital/pathology
- Heart Defects, Congenital/surgery
- Humans
- Infant
- Infant, Newborn
- Male
- Oligonucleotide Array Sequence Analysis
- Pulmonary Atresia/diagnostic imaging
- Pulmonary Atresia/genetics
- Pulmonary Atresia/pathology
- Pulmonary Atresia/surgery
- Ultrasonography
- Vitamin B 12/metabolism
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Affiliation(s)
- Li Xie
- Department of Cardiothoracic Surgery, the Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Jin-Lan Chen
- Department of Cardiothoracic Surgery, the Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Wei-Zhi Zhang
- Department of Cardiothoracic Surgery, the Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Shou-Zheng Wang
- Department of Cardiothoracic Surgery, the Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Tian-Li Zhao
- Department of Cardiothoracic Surgery, the Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Can Huang
- Department of Cardiothoracic Surgery, the Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Jian Wang
- Department of Cardiothoracic Surgery, the Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
- The Clinical Center for Gene Diagnosis and Therapy of the State Key Laboratory of Medical Genetics, the Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Jin-Fu Yang
- Department of Cardiothoracic Surgery, the Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
- The Clinical Center for Gene Diagnosis and Therapy of the State Key Laboratory of Medical Genetics, the Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Yi-Feng Yang
- Department of Cardiothoracic Surgery, the Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
- The Clinical Center for Gene Diagnosis and Therapy of the State Key Laboratory of Medical Genetics, the Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
- * E-mail: (ZPT); (YFY)
| | - Zhi-Ping Tan
- Department of Cardiothoracic Surgery, the Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
- The Clinical Center for Gene Diagnosis and Therapy of the State Key Laboratory of Medical Genetics, the Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
- * E-mail: (ZPT); (YFY)
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Kuroda Y, Ohashi I, Tominaga M, Saito T, Nagai JI, Ida K, Naruto T, Masuno M, Kurosawa K. De novo duplication of 17p13.1-p13.2 in a patient with intellectual disability and obesity. Am J Med Genet A 2014; 164A:1550-4. [PMID: 24668897 DOI: 10.1002/ajmg.a.36477] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 01/08/2014] [Indexed: 12/31/2022]
Abstract
17p13.1 Deletion encompassing TP53 has been described as a syndrome characterized by intellectual disability and dysmorphic features. Only one case with a 17p13.1 duplication encompassing TP53 has been reported in a patient with intellectual disability, seizures, obesity, and diabetes mellitus. Here, we present a patient with a 17p13.1 duplication who exhibited obesity and intellectual disability, similar to the previous report. The 9-year-old proposita was referred for the evaluation of intellectual disability and obesity. She also exhibited insulin resistance and liver dysfunction. She had wide palpebral fissures, upturned nostrils, a long mandible, short and slender fingers, and skin hyperpigmentation. Array comparative genomic hybridization (array CGH) detected a 3.2 Mb duplication of 17p13.1-p13.2 encompassing TP53, FXR2, NLGN2, and SLC2A4, which encodes the insulin-responsive glucose transporter 4 (GLUT4) associated with insulin-stimulated glucose uptake in adipocytes and muscle. We suggest that 17p13.1 duplication may represent a clinically recognizable condition characterized partially by a characteristic facial phenotype, developmental delay, and obesity.
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Affiliation(s)
- Yukiko Kuroda
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
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14
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Poultney C, Goldberg A, Drapeau E, Kou Y, Harony-Nicolas H, Kajiwara Y, De Rubeis S, Durand S, Stevens C, Rehnström K, Palotie A, Daly M, Ma’ayan A, Fromer M, Buxbaum J. Identification of small exonic CNV from whole-exome sequence data and application to autism spectrum disorder. Am J Hum Genet 2013; 93:607-19. [PMID: 24094742 DOI: 10.1016/j.ajhg.2013.09.001] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 08/29/2013] [Accepted: 09/03/2013] [Indexed: 12/13/2022] Open
Abstract
Copy number variation (CNV) is an important determinant of human diversity and plays important roles in susceptibility to disease. Most studies of CNV carried out to date have made use of chromosome microarray and have had a lower size limit for detection of about 30 kilobases (kb). With the emergence of whole-exome sequencing studies, we asked whether such data could be used to reliably call rare exonic CNV in the size range of 1-30 kilobases (kb), making use of the eXome Hidden Markov Model (XHMM) program. By using both transmission information and validation by molecular methods, we confirmed that small CNV encompassing as few as three exons can be reliably called from whole-exome data. We applied this approach to an autism case-control sample (n = 811, mean per-target read depth = 161) and observed a significant increase in the burden of rare (MAF ≤1%) 1-30 kb CNV, 1-30 kb deletions, and 1-10 kb deletions in ASD. CNV in the 1-30 kb range frequently hit just a single gene, and we were therefore able to carry out enrichment and pathway analyses, where we observed enrichment for disruption of genes in cytoskeletal and autophagy pathways in ASD. In summary, our results showed that XHMM provided an effective means to assess small exonic CNV from whole-exome data, indicated that rare 1-30 kb exonic deletions could contribute to risk in up to 7% of individuals with ASD, and implicated a candidate pathway in developmental delay syndromes.
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15
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Li Y, Zhou B, Dai J, Liu R, Han ZG. Aberrant upregulation of LRRC1 contributes to human hepatocellular carcinoma. Mol Biol Rep 2013; 40:4543-51. [PMID: 23645086 DOI: 10.1007/s11033-013-2549-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 04/29/2013] [Indexed: 10/26/2022]
Abstract
Loss of apico-basal polarity often results in a malignant phenotype in epithelial tissues. Aberrant expression of polarity mediator proteins is closely associated with this process. LRRC1/LANO, a putative cell polarity regulator, was previously screened from our gene expression profiling in which its expression was significantly upregulated in hepatocellular carcinoma (HCC). In the present study, we provide evidences that LRRC1 plays a potential oncogenic function in HCC. Consistent with the microarray data, quantitative real-time PCR results showed LRRC1 was aberrantly upregulated in 37/56 (66.1 %, more than twofolds) of HCC specimens compared with adjacent non-cancerous livers. Furthermore, the cellular expression of LRRC1 in all HCC cell lines examined exhibited much higher level than that in normal adult liver tissue. Functional analyses revealed that overexpression of LRRC1 promoted, while knockdown of LRRC1 by RNA interference inhibited the growth and colony formation of HCC cells. Importantly, enhanced expression of LRRC1 conferred NIH3T3 cells the ability of cell transformation. In a xenograft tumor model, we found LRRC1 overexpression increased the tumorigenicity of HCC cells. Thus, our collective findings suggest that LRRC1 contributes to HCC development, and may be a potential target for therapeutic intervention in this disease.
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Affiliation(s)
- Yandong Li
- Key Laboratory of Systems Biomedicine (Ministry of Education) of Rui-Jin Hospital, Shanghai Jiaotong University School of Medicine, 197 Rui-Jin II Road, Shanghai, 200025, China
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17
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Coutton C, Devillard F, Vieville G, Amblard F, Lopez G, Jouk PS, Satre V. 17p13.1 microduplication in a boy with Silver-Russell syndrome features and intellectual disability. Am J Med Genet A 2012; 158A:2564-70. [PMID: 22903743 DOI: 10.1002/ajmg.a.35553] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Accepted: 06/07/2012] [Indexed: 01/14/2023]
Abstract
Many deletions of chromosome 17p13.1 have been described, but very few 17p13.1 duplications have been reported yet. Here, we describe the genotype and phenotype of a boy with a duplication of this region. The main clinical features are mild intellectual deficiency, growth retardation, and a typical Silver-Russell syndrome (SRS) appearance with small triangular face, prominent forehead, micrognathia, low-set ears, and clinodactyly. Array-CGH revealed a 586 kb duplication containing many genes with a high neuronal expression. Interestingly, this region covers the minimal critical region including all candidate genes suggested to explain the 17p13.1 microdeletion syndrome. In the neighboring region 17p13.3, deletions and duplications of the same region are each responsible of a specific phenotype. Future case descriptions will show if a similar mechanism applies to the region 17p13.1. The 17p13.1 region contains interesting putative candidate genes that might be involved in the SRS etiology. Additional data are needed to verify the significance of this aberration.
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Affiliation(s)
- Charles Coutton
- Laboratoire de Génétique Chromosomique, Département de Génétique et Procréation, Hôpital Couple Enfant, CHU Grenoble, France.
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18
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Zeesman S, Kjaergaard S, Hove HD, Kirchhoff M, Stevens JM, Nowaczyk MJM. Microdeletion in distal 17p13.1: a recognizable phenotype with microcephaly, distinctive facial features, and intellectual disability. Am J Med Genet A 2012; 158A:1832-6. [PMID: 22753084 DOI: 10.1002/ajmg.a.35508] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 05/06/2012] [Indexed: 12/24/2022]
Abstract
Array comparative genomic hybridization has led to the identification of new syndromes by identifying genomic imbalances not detectable by standard karyotyping methods and by allowing correlations with physical findings. Deletions in the 17p13.1 region have been reported in patients with dysmorphic features and developmental delay but a consistent phenotype has yet to emerge. This report describes two unrelated patients with a characteristic phenotype associated with overlapping de novo deletions in the distal region of 17p13.1 detected with array comparative genomic hybridization and confirmed by real-time PCR. These patients share remarkably similar clinical features including microcephaly, mild developmental delay, generalized joint laxity, and a body posture with knee and elbow flexion and hands held in midline. They have distinctive facial features which include long midface with retrognathia with overbite, and protruding ears. The deletions in both patients are the smallest ever reported in this region (approximately 252 and 219 kb). The overlapping region contains 18 genes. Various isolated deletions of the 17p13.1 region have been reported previously without delineation of a consistent phenotype. We propose that the described microdeletions in the distal portion of 17p13.1 represent a novel microdeletion syndrome.
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Affiliation(s)
- Susan Zeesman
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
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19
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Palka Bayard de Volo C, Alfonsi M, Gatta V, Novelli A, Bernardini L, Fantasia D, Antonucci I, Angelucci D, Zori R, Stuppia L, Chiarelli F, Calabrese G. 16q22.1 microdeletion detected by array-CGH in a family with mental retardation and lobular breast cancer. Gene 2012; 498:328-31. [DOI: 10.1016/j.gene.2012.01.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 01/19/2012] [Indexed: 02/02/2023]
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Rostasy K, Fauth C, Gautsch K, Laimer I, Krabichler B, Wimmer K, Frühmesser A, Kotzot D, Moshir S. Modification of risk for cancer as a coincidental finding in DNA array investigation. Clin Genet 2012; 83:284-7. [PMID: 22428932 DOI: 10.1111/j.1399-0004.2012.01881.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The high resolution of modern DNA arrays has the implification of unintended coincidental detection of gene deletions predisposing to late-onset neurological and oncological disorders. Here, we report the case of an 18-year-old girl with mild intellectual disability, facial dysmorphisms, and a microdeletion of approximately 6.3 Mb on 22q12.1q12.3 including NF2, the gene for neurofibromatosis type 2, and CHEK2, a modifier gene for breast cancer. Subsequent magnetic resonance imaging of the brain showed she had already developed bilateral vestibular schwannomas. The challenge of DNA arrays and the consequences for genetic counselling and informed consent will be discussed in the light of this unique case with a microdeletion including both a high risk and a moderate risk cancer predisposition gene.
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Affiliation(s)
- K Rostasy
- Clinical Department of Pediatrics IV, Innsbruck Medical University, Innsbruck, Austria
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21
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Krepischi AC, Achatz MIW, Santos EM, Costa SS, Lisboa BC, Brentani H, Santos TM, Gonçalves A, Nóbrega AF, Pearson PL, Vianna-Morgante AM, Carraro DM, Brentani RR, Rosenberg C. Germline DNA copy number variation in familial and early-onset breast cancer. Breast Cancer Res 2012; 14:R24. [PMID: 22314128 PMCID: PMC3496142 DOI: 10.1186/bcr3109] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Revised: 01/20/2012] [Accepted: 02/07/2012] [Indexed: 11/10/2022] Open
Abstract
Introduction Genetic factors predisposing individuals to cancer remain elusive in the majority of patients with a familial or clinical history suggestive of hereditary breast cancer. Germline DNA copy number variation (CNV) has recently been implicated in predisposition to cancers such as neuroblastomas as well as prostate and colorectal cancer. We evaluated the role of germline CNVs in breast cancer susceptibility, in particular those with low population frequencies (rare CNVs), which are more likely to cause disease." Methods Using whole-genome comparative genomic hybridization on microarrays, we screened a cohort of women fulfilling criteria for hereditary breast cancer who did not carry BRCA1/BRCA2 mutations. Results The median numbers of total and rare CNVs per genome were not different between controls and patients. A total of 26 rare germline CNVs were identified in 68 cancer patients, however, a proportion that was significantly different (P = 0.0311) from the control group (23 rare CNVs in 100 individuals). Several of the genes affected by CNV in patients and controls had already been implicated in cancer. Conclusions This study is the first to explore the contribution of germline CNVs to BRCA1/2-negative familial and early-onset breast cancer. The data suggest that rare CNVs may contribute to cancer predisposition in this small cohort of patients, and this trend needs to be confirmed in larger population samples.
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Affiliation(s)
- Ana Cv Krepischi
- National Institute of Science and Technology in Oncogenomics, AC Camargo Hospital, Rua Taguá 440, 01508-010, São Paulo, Brazil.
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22
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Chen D, Zheng X, Kang D, Yan B, Liu X, Gao Y, Zhang K. Apoptosis and expression of the Bcl-2 family of proteins and P53 in human pancreatic ductal adenocarcinoma. Med Princ Pract 2012; 21:68-73. [PMID: 22024503 DOI: 10.1159/000332423] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Accepted: 06/12/2011] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE The purpose of this study was to clarify the association between P53 and the Bcl-2 family (Bcl-2, Bax, Bcl-xL, Bcl-xS) expression and apoptosis in pancreatic ductal adenocarcinoma (PDAC). SUBJECTS AND METHODS A total of 70 patients with PDAC were studied. The expression of P53 protein in PDAC was assessed using the immunohistochemical method, which categorized the PDAC patients into two groups: group 1: 36 cases with immunonegative P53(-), and group 2: 34 cases with immunopositive P53(+). The expression of Bcl-2, Bax, Bcl-xL, and Bcl-xS in the 70 PDAC cases was detected by immunohistochemical and Western blotting methods. The apoptotic index (AI) was also measured in these samples by the terminal deoxynucleotidyl transferase-mediated dUTP-biotin nick end labeling (TUNEL) method. The relation between P53 and the Bcl-2 protein family and apoptosis was then evaluated. RESULTS Bcl-2 and Bcl-xS expression was significantly associated with P53 (p < 0.05). No clear associations were found among P53, Bax and Bcl-xL expression (p > 0.05). The AI of groups 1 and 2 was 12.1 ± 2.47 and 8.1 ± 1.48, respectively (p = 0.023). There was no relationship between AI and Bcl-2, Bax, Bcl-xL and Bcl-xS expression (p > 0.05, respectively). Bcl-2/Bax ratio was significantly associated with AI (p < 0.01). CONCLUSION Bcl-2 and Bcl-xS represent significant anti- and proapoptotic proteins, respectively, modulated through a P53-dependent pathway in PDAC, and P53 modulated apoptosis mainly through Bcl-2/Bax ratio.
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Affiliation(s)
- Dong Chen
- Department of General Surgery, Affiliated Hospital of Medical College, QingDao University, QingDao, ShanDong Province, People’s Republic of China
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23
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Haploinsufficiency of ANKRD11 causes mild cognitive impairment, short stature and minor dysmorphisms. Eur J Hum Genet 2011; 20:131-3. [PMID: 21654729 DOI: 10.1038/ejhg.2011.105] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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24
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Shlien A, Baskin B, Achatz MIW, Stavropoulos DJ, Nichols KE, Hudgins L, Morel CF, Adam MP, Zhukova N, Rotin L, Novokmet A, Druker H, Shago M, Ray PN, Hainaut P, Malkin D. A common molecular mechanism underlies two phenotypically distinct 17p13.1 microdeletion syndromes. Am J Hum Genet 2010; 87:631-42. [PMID: 21056402 DOI: 10.1016/j.ajhg.2010.10.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Revised: 09/24/2010] [Accepted: 10/12/2010] [Indexed: 12/16/2022] Open
Abstract
DNA copy-number variations (CNVs) underlie many neuropsychiatric conditions, but they have been less studied in cancer. We report the association of a 17p13.1 CNV, childhood-onset developmental delay (DD), and cancer. Through a screen of over 4000 patients with diverse diagnoses, we identified eight probands harboring microdeletions at TP53 (17p13.1). We used a purpose-built high-resolution array with 93.75% breakpoint accuracy to fine map these microdeletions. Four patients were found to have a common phenotype including DD, hypotonia, and hand and foot abnormalities, constituting a unique syndrome. Notably, these patients were not affected with cancer. Moreover, none of the TP53-deletion patients affected with cancer (n = 4) had neurocognitive impairments. DD patients have larger deletions, which encompass but do not disrupt TP53, whereas cancer-affected patients harbor CNVs with at least one breakpoint within TP53. Most 17p13.1 deletions arise by Alu-mediated nonallelic homologous recombination. Furthermore, we identify a critical genomic region associated with DD and containing six underexpressed genes. We conclude that, although they overlap, 17p13.1 CNVs are associated with distinct phenotypes depending on the position of the breakpoint with respect to TP53. Further, detailed characterization of breakpoints revealed a common formation signature. Future studies should consider whether other loci in the genome also give rise to phenotypically distinct disorders by means of a common mechanism, resulting in a similar formation signature.
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25
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Fraga AM, Sukoyan M, Rajan P, Braga DPDAF, Iaconelli A, Franco JG, Borges E, Pereira LV. Establishment of a Brazilian line of human embryonic stem cells in defined medium: implications for cell therapy in an ethnically diverse population. Cell Transplant 2010; 20:431-40. [PMID: 20719082 DOI: 10.3727/096368910x522261] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Pluripotent human embryonic stem (hES) cells are an important experimental tool for basic and applied research, and a potential source of different tissues for transplantation. However, one important challenge for the clinical use of these cells is the issue of immunocompatibility, which may be dealt with by the establishment of hES cell banks to attend different populations. Here we describe the derivation and characterization of a line of hES cells from the Brazilian population, named BR-1, in commercial defined medium. In contrast to the other hES cell lines established in defined medium, BR-1 maintained a stable normal karyotype as determined by genomic array analysis after 6 months in continuous culture (passage 29). To our knowledge, this is the first reported line of hES cells derived in South America. We have determined its genomic ancestry and compared the HLA-profile of BR-1 and another 22 hES cell lines established elsewhere with those of the Brazilian population, finding they would match only 0.011% of those individuals. Our results highlight the challenges involved in hES cell banking for populations with a high degree of ethnic admixture.
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Affiliation(s)
- Ana M Fraga
- Laboratório de Genética Molecular, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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26
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Schluth-Bolard C, Sanlaville D, Labalme A, Till M, Morin I, Touraine R, Edery P. 17p13.1 microdeletion involving the TP53 gene in a boy presenting with mental retardation but no tumor. Am J Med Genet A 2010; 152A:1278-82. [PMID: 20425836 DOI: 10.1002/ajmg.a.33316] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We report on the diagnosis of a 17p13.1 deletion in a 10-year-old boy. The patient presented with mild developmental delay, facial dysmorphism, joint hyperlaxity, pes planus, hypermetropia, hearing loss, and achromic patches following the Blaschko's lines on the right part of the thorax. Chromosome R-banding was normal. Array CGH using a 244 K oligonucleotide array showed a homogeneous de novo 17p13.1 microdeletion of 400 kb involving TP53 and 25 other genes, including genes involved in brain function (EFNB3, FXR2). To our knowledge, six patients presenting with a constitutional 17p13.1 microdeletion involving the TP53 gene have been reported. We discuss the phenotype of this microdeletion and the genetic counseling issues, especially regarding the risk of cancer associated with the deletion of the TP53 gene.
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Komoike Y, Shimojima K, Liang JS, Fujii H, Maegaki Y, Osawa M, Fujii S, Higashinakagawa T, Yamamoto T. A functional analysis of GABARAP on 17p13.1 by knockdown zebrafish. J Hum Genet 2010; 55:155-62. [PMID: 20111057 DOI: 10.1038/jhg.2010.1] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Array-based comparative genomic hybridization identified a 2.3-Mb microdeletion of 17p13.2p13.1 in a boy presenting with moderate mental retardation, intractable epilepsy and dysmorphic features. This deletion region was overlapped with the previously proposed shortest region overlapped for microdeletion of 17p13.1 in patients with mental retardation, microcephaly, microretrognathia and abnormal magnetic resonance imaging (MRI) findings of cerebral white matter, in which at least 17 known genes are included. Among them, DLG4/PSD95, GPS2, GABARAP and KCTD11 have a function in neuronal development. Because of the functional importance, we paid attention to DLG4/PSD95 and GABARAP, and analyzed zebrafish in which the zebrafish homolog of human DLG4/PSD95 and GABARAP was knocked down and found that gabarap knockdown resulted in small head and hypoplastic mandible. This finding would be similar to the common findings of the patients with 17p13.1 deletions. Although there were no pathogenic mutations in DLG4/PSD95 or GABARAP in a cohort study with 142 patients with idiopathic developmental delay with/without epilepsy, further studies would be required for genes included in this region.
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Affiliation(s)
- Yuta Komoike
- International Research and Educational Institute for Integrated Medical Sciences (IREIIMS), Tokyo Women's Medical University, Tokyo, Japan
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