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Zürcher JF, Kleefeldt AA, Funke LFH, Birnbaum J, Fredens J, Grazioli S, Liu KC, Spinck M, Petris G, Murat P, Rehm FBH, Sale JE, Chin JW. Continuous synthesis of E. coli genome sections and Mb-scale human DNA assembly. Nature 2023; 619:555-562. [PMID: 37380776 PMCID: PMC7614783 DOI: 10.1038/s41586-023-06268-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 05/26/2023] [Indexed: 06/30/2023]
Abstract
Whole-genome synthesis provides a powerful approach for understanding and expanding organism function1-3. To build large genomes rapidly, scalably and in parallel, we need (1) methods for assembling megabases of DNA from shorter precursors and (2) strategies for rapidly and scalably replacing the genomic DNA of organisms with synthetic DNA. Here we develop bacterial artificial chromosome (BAC) stepwise insertion synthesis (BASIS)-a method for megabase-scale assembly of DNA in Escherichia coli episomes. We used BASIS to assemble 1.1 Mb of human DNA containing numerous exons, introns, repetitive sequences, G-quadruplexes, and long and short interspersed nuclear elements (LINEs and SINEs). BASIS provides a powerful platform for building synthetic genomes for diverse organisms. We also developed continuous genome synthesis (CGS)-a method for continuously replacing sequential 100 kb stretches of the E. coli genome with synthetic DNA; CGS minimizes crossovers1,4 between the synthetic DNA and the genome such that the output for each 100 kb replacement provides, without sequencing, the input for the next 100 kb replacement. Using CGS, we synthesized a 0.5 Mb section of the E. coli genome-a key intermediate in its total synthesis1-from five episomes in 10 days. By parallelizing CGS and combining it with rapid oligonucleotide synthesis and episome assembly5,6, along with rapid methods for compiling a single genome from strains bearing distinct synthetic genome sections1,7,8, we anticipate that it will be possible to synthesize entire E. coli genomes from functional designs in less than 2 months.
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Affiliation(s)
- Jérôme F Zürcher
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Askar A Kleefeldt
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Louise F H Funke
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore
| | - Jakob Birnbaum
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Julius Fredens
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Synthetic Biology for Clinical and Technological Innovation, Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Simona Grazioli
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Kim C Liu
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Martin Spinck
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Gianluca Petris
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Pierre Murat
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Fabian B H Rehm
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Julian E Sale
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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2
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Improved protocols for BAC insert DNA isolation, BAC end sequencing and FISH for construction of BAC based physical map of genes on the chromosomes. Mol Biol Rep 2020; 47:2405-2413. [PMID: 32020430 DOI: 10.1007/s11033-020-05283-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/27/2020] [Indexed: 10/25/2022]
Abstract
Bacterial artificial chromosome (BAC) library is an important genomic resource useful in targeted marker development, positional cloning, physical mapping and a substrate for genome sequencing for better understanding the genome organization of a species. The present manuscript elucidates the improvement in protocols for economical and efficient BAC insert DNA isolation, BAC end sequencing and FISH for physical localization on the metaphase chromosome complements. BAC clones of Clarias magur, maintained in 384-well plate format in our laboratory, were used in this study. The protocols gave consistent and efficient results. We use routinely these protocols for BAC insert DNA extraction, generating end sequence data of the clone and constructing DNA probes to hybridize on the metaphase spreads of C. magur using FISH for physical their localization.
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3
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Osoegawa K, Iovannisci DM, Lin B, Parodi C, Schultz K, Shaw GM, Lammer EJ. Identification of novel candidate gene loci and increased sex chromosome aneuploidy among infants with conotruncal heart defects. Am J Med Genet A 2013; 164A:397-406. [PMID: 24127225 DOI: 10.1002/ajmg.a.36291] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 09/10/2013] [Indexed: 12/17/2022]
Abstract
Congenital heart defects (CHDs) are common malformations, affecting four to eight per 1,000 total births. Conotruncal defects are an important pathogenetic subset of CHDs, comprising nearly 20% of the total. Although both environmental and genetic factors are known to contribute to the occurrence of conotruncal defects, the causes remain unknown for most. To identify novel candidate genes/loci, we used array comparative genomic hybridization to detect chromosomal microdeletions/duplications. From a population base of 974,579 total births born during 1999-2004, we screened 389 California infants born with tetralogy of Fallot or d-transposition of the great arteries. We found that 1.7% (5/288) of males with a conotruncal defect had sex chromosome aneuploidy, a sevenfold increased frequency (relative risk = 7.0; 95% confidence interval 2.9-16.9). We identified eight chromosomal microdeletions/duplications for conotruncal defects. From these duplications and deletions, we found five high priority candidate genes (GATA4, CRKL, BMPR1A, SNAI2, and ZFHX4). This is the initial report that sex chromosome aneuploidy is associated with conotruncal defects among boys. These chromosomal microduplications/deletions provide evidence that GATA4, SNAI2, and CRKL are highly dosage sensitive genes involved in outflow tract development. Genome wide screening for copy number variation can be productive for identifying novel genes/loci contributing to non-syndromic common malformations.
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Affiliation(s)
- Kazutoyo Osoegawa
- Center for Genetics, Children's Hospital Oakland Research Institute, Children's Hospital Research Center Oakland, Oakland, California
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4
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Chatterjee PK, Shakes LA, Wolf HM, Mujalled MA, Zhou C, Hatcher C, Norford DC. Identifying Distal cis-acting Gene-Regulatory Sequences by Expressing BACs Functionalized with loxP-Tn10 Transposons in Zebrafish. RSC Adv 2013; 3:8604-8617. [PMID: 24772295 DOI: 10.1039/c3ra40332g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Bacterial Artificial Chromosomes (BACs) are large pieces of DNA from the chromosomes of organisms propagated faithfully in bacteria as large extra-chromosomal plasmids. Expression of genes contained in BACs can be monitored after functionalizing the BAC DNA with reporter genes and other sequences that allow stable maintenance and propagation of the DNA in the new host organism. The DNA in BACs can be altered within its bacterial host in several ways. Here we discuss one such approach, using Tn10 mini-transposons, to introduce exogenous sequences into BACs for a variety of purposes. The largely random insertions of Tn10 transposons carrying lox sites have been used to position mammalian cell-selectable antibiotic resistance genes, enhancer-traps and inverted repeat ends of the vertebrate transposon Tol2 precisely at the ends of the genomic DNA insert in BACs. These modified BACs are suitable for expression in zebrafish or mouse, and have been used to functionally identify important long-range gene regulatory sequences in both species. Enhancer-trapping using BACs should prove uniquely useful in analyzing multiple discontinuous DNA domains that act in concert to regulate expression of a gene, and is not limited by genome accessibility issues of traditional enhancer-trapping methods.
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Affiliation(s)
- Pradeep K Chatterjee
- Julius L. Chambers Biomedical/ Biotechnology Research Institute & Department of Chemistry, North Carolina Central University, 1801 Fayetteville Street, Durham, NC 27707, USA
| | - Leighcraft A Shakes
- Julius L. Chambers Biomedical/ Biotechnology Research Institute & Department of Chemistry, North Carolina Central University, 1801 Fayetteville Street, Durham, NC 27707, USA
| | - Hope M Wolf
- Julius L. Chambers Biomedical/ Biotechnology Research Institute & Department of Chemistry, North Carolina Central University, 1801 Fayetteville Street, Durham, NC 27707, USA
| | - Mohammad A Mujalled
- Julius L. Chambers Biomedical/ Biotechnology Research Institute & Department of Chemistry, North Carolina Central University, 1801 Fayetteville Street, Durham, NC 27707, USA
| | - Constance Zhou
- Julius L. Chambers Biomedical/ Biotechnology Research Institute & Department of Chemistry, North Carolina Central University, 1801 Fayetteville Street, Durham, NC 27707, USA
| | - Charles Hatcher
- Julius L. Chambers Biomedical/ Biotechnology Research Institute & Department of Chemistry, North Carolina Central University, 1801 Fayetteville Street, Durham, NC 27707, USA
| | - Derek C Norford
- Julius L. Chambers Biomedical/ Biotechnology Research Institute & Department of Chemistry, North Carolina Central University, 1801 Fayetteville Street, Durham, NC 27707, USA
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5
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Schoenmakers EFPM, Bunt J, Hermers L, Schepens M, Merkx G, Janssen B, Kersten M, Huys E, Pauwels P, Debiec-Rychter M, van Kessel AG. Identification of CUX1 as the recurrent chromosomal band 7q22 target gene in human uterine leiomyoma. Genes Chromosomes Cancer 2012; 52:11-23. [PMID: 22965931 DOI: 10.1002/gcc.22001] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Accepted: 08/01/2012] [Indexed: 11/12/2022] Open
Abstract
Uterine leiomyomas are benign solid tumors of mesenchymal origin which occur with an estimated incidence of up to 77% of all women of reproductive age. The majority of these tumors remains symptomless, but in about a quarter of cases they cause leiomyoma-associated symptoms including chronic pelvic pain, menorrhagia-induced anemia, and impaired fertility. As a consequence, they are the most common indication for pre-menopausal hysterectomy in the USA and Japan and annually translate into a multibillion dollar healthcare problem. Approximately 40% of these neoplasms present with recurring structural cytogenetic anomalies, including del(7)(q22), t(12;14)(q15;q24), t(1;2)(p36;p24), and anomalies affecting 6p21 and/or 10q22. Using positional cloning strategies, we and others previously identified HMGA1, HMGA2, RAD51L1, MORF, and, more recently, NCOA1 as primary target (fusion) genes associated with tumor initiation in four of these distinct cytogenetic subgroups. Despite the fact that the del(7)(q22) subgroup is the largest among leiomyomas, and was first described more than twenty years ago, the 7q22 leiomyoma target gene still awaits unequivocal identification. We here describe a positional cloning effort from two independent uterine leiomyomas, containing respectively a pericentric and a paracentric chromosomal inversion, both affecting band 7q22. We found that both chromosomal inversions target the cut-like homeobox 1 (CUX1) gene on chromosomal band 7q22.1 in a way which is functionally equivalent to the more frequently observed del(7q) cases, and which is compatible with a mono-allelic knock-out scenario, similar as was previously described for the cytogenetic subgroup showing chromosome 14q involvement.
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Affiliation(s)
- Eric F P M Schoenmakers
- Department of Human Genetics, Radboud University Nijmegen Medical Centre and Nijmegen Centre for Molecular Life Sciences, Nijmegen, The Netherlands.
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6
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Capozzi O, Carbone L, Stanyon RR, Marra A, Yang F, Whelan CW, de Jong PJ, Rocchi M, Archidiacono N. A comprehensive molecular cytogenetic analysis of chromosome rearrangements in gibbons. Genome Res 2012; 22:2520-8. [PMID: 22892276 PMCID: PMC3514681 DOI: 10.1101/gr.138651.112] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Chromosome rearrangements in small apes are up to 20 times more frequent than in most mammals. Because of their complexity, the full extent of chromosome evolution in these hominoids is not yet fully documented. However, previous work with array painting, BAC-FISH, and selective sequencing in two of the four karyomorphs has shown that high-resolution methods can precisely define chromosome breakpoints and map the complex flow of evolutionary chromosome rearrangements. Here we use these tools to precisely define the rearrangements that have occurred in the remaining two karyomorphs, genera Symphalangus (2n = 50) and Hoolock (2n = 38). This research provides the most comprehensive insight into the evolutionary origins of chromosome rearrangements involved in transforming small apes genome. Bioinformatics analyses of the human–gibbon synteny breakpoints revealed association with transposable elements and segmental duplications, providing some insight into the mechanisms that might have promoted rearrangements in small apes. In the near future, the comparison of gibbon genome sequences will provide novel insights to test hypotheses concerning the mechanisms of chromosome evolution. The precise definition of synteny block boundaries and orientation, chromosomal fusions, and centromere repositioning events presented here will facilitate genome sequence assembly for these close relatives of humans.
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Affiliation(s)
- Oronzo Capozzi
- Department of Genetics and Microbiology, University of Bari, 70126 Bari, Italy
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7
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Raish M, Khurshid M, Ansari MA, Chaturvedi PK, Bae SM, Kim JH, Park EK, Park DC, Ahn WS. Analysis of molecular cytogenetic alterations in uterine leiomyosarcoma by array-based comparative genomic hybridization. J Cancer Res Clin Oncol 2012; 138:1173-86. [DOI: 10.1007/s00432-012-1182-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 02/20/2012] [Indexed: 10/28/2022]
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8
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Duplication 8q12: confirmation of a novel recognizable phenotype with duane retraction syndrome and developmental delay. Eur J Hum Genet 2012; 20:580-3. [PMID: 22258531 DOI: 10.1038/ejhg.2011.243] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Duane retraction syndrome (DRS) is a rare congenital strabismus condition with genetic heterogeneity. DRS associated with intellectual disability or developmental delay is observed in several genetic diseases: syndromes such as Goldenhar or Wildervanck syndrome and chromosomal anomalies such as 12q12 deletion. We report on the case of a patient with DRS, developmental delay and particular facial features (horizontal and flared eyebrows, long and smooth philtrum, thin upper lip, full lower lip and full cheeks). We identified a duplication of the long arm of chromosome 8 (8q12) with SNP-array. This is the third case of a patient with common clinical features and 8q12 duplication described in the literature. The minimal critical region is 1.2 Mb and encompasses four genes: CA8, RAB2, RLBP1L1 and CHD7. To our knowledge, no information is available in the literature regarding pathological effects caused by to overexpression of these genes. However, loss of function of the CHD7 gene leads to CHARGE syndrome, suggesting a possible role of the overexpression of this gene in the phenotype observed in 8q12 duplication patients. We have observed that patients with 8q12 duplication share a common recognizable phenotype characterized by DRS, developmental delay and facial features. Such data combined to the literature strongly suggest that this entity may define a novel syndrome. We hypothesize that CHD7 duplication is responsible for a part of the features observed in 8q12.2 duplication.
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Holcomb IN, Trask BJ. Comparative genomic hybridization to detect variation in the copy number of large DNA segments. Cold Spring Harb Protoc 2011; 2011:1323-1333. [PMID: 22046040 DOI: 10.1101/pdb.top066589] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Array comparative genomic hybridization (CGH) is an excellent tool to scan the genome for copy number variations (CNVs) when used conscientiously. This article is intended to provide an understanding of the basic principles of array CGH and the different options available to the user to design their array CGH experiments. Specifically, the six subsections discuss the different array platforms available, test and reference DNA preparation, reference DNA choice, the basics of hybridization, data processing, and our current understanding of CNVs in the human genome.
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Stacher E, Boldt V, Leibl S, Halbwedl I, Popper HH, Ullmann R, Tavassoli FA, Moinfar F. Chromosomal aberrations as detected by array comparative genomic hybridization in early low-grade intraepithelial neoplasias of the breast. Histopathology 2011; 59:549-55. [DOI: 10.1111/j.1365-2559.2011.03918.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Genome-wide copy number variation analysis in attention-deficit/hyperactivity disorder: association with neuropeptide Y gene dosage in an extended pedigree. Mol Psychiatry 2011; 16:491-503. [PMID: 20308990 DOI: 10.1038/mp.2010.29] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Attention-deficit/hyperactivity disorder (ADHD) is a common, highly heritable neurodevelopmental syndrome characterized by hyperactivity, inattention and increased impulsivity. To detect micro-deletions and micro-duplications that may have a role in the pathogenesis of ADHD, we carried out a genome-wide screen for copy number variations (CNVs) in a cohort of 99 children and adolescents with severe ADHD. Using high-resolution array comparative genomic hybridization (aCGH), a total of 17 potentially syndrome-associated CNVs were identified. The aberrations comprise 4 deletions and 13 duplications with approximate sizes ranging from 110 kb to 3 Mb. Two CNVs occurred de novo and nine were inherited from a parent with ADHD, whereas five are transmitted by an unaffected parent. Candidates include genes expressing acetylcholine-metabolizing butyrylcholinesterase (BCHE), contained in a de novo chromosome 3q26.1 deletion, and a brain-specific pleckstrin homology domain-containing protein (PLEKHB1), with an established function in primary sensory neurons, in two siblings carrying a 11q13.4 duplication inherited from their affected mother. Other genes potentially influencing ADHD-related psychopathology and involved in aberrations inherited from affected parents are the genes for the mitochondrial NADH dehydrogenase 1 α subcomplex assembly factor 2 (NDUFAF2), the brain-specific phosphodiesterase 4D isoform 6 (PDE4D6) and the neuronal glucose transporter 3 (SLC2A3). The gene encoding neuropeptide Y (NPY) was included in a ∼3 Mb duplication on chromosome 7p15.2-15.3, and investigation of additional family members showed a nominally significant association of this 7p15 duplication with increased NPY plasma concentrations (empirical family-based association test, P=0.023). Lower activation of the left ventral striatum and left posterior insula during anticipation of large rewards or losses elicited by functional magnetic resonance imaging links gene dose-dependent increases in NPY to reward and emotion processing in duplication carriers. These findings implicate CNVs of behaviour-related genes in the pathogenesis of ADHD and are consistent with the notion that both frequent and rare variants influence the development of this common multifactorial syndrome.
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Muradyan A, Gilbertz K, Stabentheiner S, Klause S, Madle H, Meineke V, Ullmann R, Scherthan H. Acute high-dose X-radiation-induced genomic changes in A549 cells. Radiat Res 2011; 175:700-7. [PMID: 21361782 DOI: 10.1667/rr2341.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Accidents with ionizing radiation often involve single, acute high-dose exposures that can lead to acute radiation syndrome and late effects such as carcinogenesis. To study such effects at the cellular level, we investigated acute ionizing radiation-induced chromosomal aberrations in A549 adenocarcinoma cells at the genome-wide level by exposing the cells to an acute dose of 6 Gy 240 kV X rays. One sham-irradiated clone and four surviving irradiated clones were recovered by minimal dilution and further expanded and analyzed by chromosome painting and tiling-path array CGH, with the nonirradiated clone 0 serving as the control. Acute X-ray exposure induced specific translocations and changes in modal chromosome number in the four irradiated clones. Array CGH disclosed unique and recurrent genomic changes, predominantly losses, and revealed that the fragile sites FRA3B and FRA16D were preferential regions of genomic alterations in all irradiated clones, which is likely related to radioresistant S-phase progression and genomic stress. Furthermore, clone 4 displayed an increased radiosensitivity at doses >5 Gy. Pairwise comparisons of the gene expression patterns of all irradiated clones to the sham-irradiated clone 0 revealed an enrichment of the Gene Ontology term "M Phase" (P = 6.2 × 10(-7)) in the set of differentially expressed genes of clone 4 but not in those of clones 1-3. Ionizing radiation-induced genomic changes and fragile site expression highlight the capacity of a single acute radiation exposure to affect the genome of exposed cells by inflicting genomic stress.
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Affiliation(s)
- A Muradyan
- a Max-Planck-Inst. für Molekulare Genetik, D-14195 Berlin, Germany
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Fullston T, Gabb B, Callen D, Ullmann R, Woollatt E, Bain S, Ropers HH, Cooper M, Chandler D, Carter K, Jablensky A, Kalaydjieva L, Gecz J. Inherited balanced translocation t(9;17)(q33.2;q25.3) concomitant with a 16p13.1 duplication in a patient with schizophrenia. Am J Med Genet B Neuropsychiatr Genet 2011; 156:204-14. [PMID: 21302349 DOI: 10.1002/ajmg.b.31157] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Accepted: 11/30/2010] [Indexed: 11/08/2022]
Abstract
We report two rare genetic aberrations in a schizophrenia patient that may act together to confer disease susceptibility. A previously unreported balanced t(9;17)(q33.2;q25.3) translocation was observed in two schizophrenia-affected members of a small family with diverse psychiatric disorders. The proband also carried a 1.5 Mbp microduplication at 16p13.1 that could not be investigated in other family members. The duplication has been reported to predispose to schizophrenia, autism and mental retardation, with incomplete penetrance and variable expressivity. The t(9;17) (q33.2;q25.3) translocation breakpoint occurs within the open reading frames of KIAA1618 on 17q25.3, and TTLL11 (tyrosine tubulin ligase like 11) on 9q33.2, causing no change in the expression level of KIAA1618 but leading to loss of expression of one TTLL11 allele. TTLL11 belongs to a family of enzymes catalyzing polyglutamylation, an unusual neuron-specific post-translational modification of microtubule proteins, which modulates microtubule development and dynamics. The 16p13.1 duplication resulted in increased expression of NDE1, encoding a DISC1 protein partner mediating DISC1 functions in microtubule dynamics. We hypothesize that concomitant TTLL11-NDE1 deregulation may increase mutation load, among others, also on the DISC1 pathway, which could contribute to disease pathogenesis through multiple effects on neuronal development, synaptic plasticity, and neurotransmission. Our data illustrate the difficulties in interpreting the contribution of multiple potentially pathogenic changes likely to emerge in future next-generation sequencing studies, where access to extended families will be increasingly important.
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Affiliation(s)
- Tod Fullston
- SA Pathology, Women's and Children's Hospital, Adelaide, South Australia 5006, Australia
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Heron SE, Scheffer IE, Grinton BE, Eyre H, Oliver KL, Bain S, Berkovic SF, Mulley JC. Familial neonatal seizures with intellectual disability caused by a microduplication of chromosome 2q24.3. Epilepsia 2010; 51:1865-9. [PMID: 20384724 DOI: 10.1111/j.1528-1167.2010.02558.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A family with dominantly inherited neonatal seizures and intellectual disability was atypical for neonatal and infantile seizure syndromes associated with potassium (KCNQ2 and KCNQ3) and sodium (SCN2A) channel mutations. Microsatellite markers linked to KCNQ2, KCNQ3, and SCN2A were examined to exclude candidate locations, but instead revealed a duplication detected by observation of three alleles for two markers flanking SCN2A. Characterization revealed a 1.57 Mb duplication at 2q24.3 containing eight genes including SCN2A, SCN3A, and the 3¢ end of SCN1A. The duplication was partially inverted and inserted within or near SCN1A, probably affecting the expression levels of associated genes, including sodium channels. Rare or unique microchromosomal copy number mutations might underlie familial epilepsies that do not fit within the clinical criteria for the established syndromes.
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Affiliation(s)
- Sarah E Heron
- SA Pathology at Women's and Children's Hospital, Adelaide, South Australia, Australia.
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15
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Bolton KL, Tyrer J, Song H, Ramus SJ, Notaridou M, Jones C, Sher T, Gentry-Maharaj A, Wozniak E, Tsai YY, Weidhaas J, Paik D, Van Den Berg DJ, Stram DO, Pearce CL, Wu AH, Brewster W, Anton-Culver H, Ziogas A, Narod SA, Levine DA, Kaye SB, Brown R, Paul J, Flanagan J, Sieh W, McGuire V, Whittemore AS, Campbell I, Gore ME, Lissowska J, Yang H, Medrek K, Gronwald J, Lubinski J, Jakubowska A, Le ND, Cook LS, Kelemen LE, Brooks-Wilson A, Massuger LF, Kiemeney LA, Aben KK, van Altena AM, Houlston R, Tomlinson I, Palmieri RT, Moorman PG, Schildkraut J, Iversen ES, Phelan C, Vierkant RA, Cunningham JM, Goode EL, Fridley BL, Kruger-Kjaer S, Blaeker J, Hogdall E, Hogdall C, Gross J, Karlan BY, Ness RB, Edwards RP, Odunsi K, Moyisch KB, Baker JA, Modugno F, Heikkinenen T, Butzow R, Nevanlinna H, Leminen A, Bogdanova N, Antonenkova N, Doerk T, Hillemanns P, Dürst M, Runnebaum I, Thompson PJ, Carney ME, Goodman MT, Lurie G, Wang-Gohrke S, Hein R, Chang-Claude J, Rossing MA, Cushing-Haugen KL, Doherty J, Chen C, Rafnar T, Besenbacher S, Sulem P, Stefansson K, Birrer MJ, Terry KL, Hernandez D, Cramer DW, Vergote I, Amant F, Lambrechts D, Despierre E, Fasching PA, Beckmann MW, Thiel FC, Ekici AB, Chen X, Johnatty SE, Webb PM, Beesley J, Chanock S, Garcia-Closas M, Sellers T, Easton DF, Berchuck A, Chenevix-Trench G, Pharoah PD, Gayther SA, Gayther SA. Common variants at 19p13 are associated with susceptibility to ovarian cancer. Nat Genet 2010; 42:880-4. [PMID: 20852633 PMCID: PMC3125495 DOI: 10.1038/ng.666] [Citation(s) in RCA: 217] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2010] [Accepted: 07/30/2010] [Indexed: 02/02/2023]
Abstract
Epithelial ovarian cancer (EOC) is the leading cause of death from gynecological malignancy in the developed world, accounting for 4% of the deaths from cancer in women. We performed a three-phase genome-wide association study of EOC survival in 8,951 individuals with EOC (cases) with available survival time data and a parallel association analysis of EOC susceptibility. Two SNPs at 19p13.11, rs8170 and rs2363956, showed evidence of association with survival (overall P = 5 × 10⁻⁴ and P = 6 × 10⁻⁴, respectively), but they did not replicate in phase 3. However, the same two SNPs demonstrated genome-wide significance for risk of serous EOC (P = 3 × 10⁻⁹ and P = 4 × 10⁻¹¹, respectively). Expression analysis of candidate genes at this locus in ovarian tumors supported a role for the BRCA1-interacting gene C19orf62, also known as MERIT40, which contains rs8170, in EOC development.
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Affiliation(s)
- Kelly L. Bolton
- Department of Oncology, University of Cambridge, Cambridge, UK,Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, USA
| | - Jonathan Tyrer
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - Honglin Song
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - Susan J. Ramus
- Department of Gynaecological Oncology, University College London, EGA Institute for Women’s Health, London, UK
| | - Maria Notaridou
- Department of Gynaecological Oncology, University College London, EGA Institute for Women’s Health, London, UK
| | - Chris Jones
- Department of Gynaecological Oncology, University College London, EGA Institute for Women’s Health, London, UK
| | - Tanya Sher
- Department of Gynaecological Oncology, University College London, EGA Institute for Women’s Health, London, UK
| | - Aleksandra Gentry-Maharaj
- Department of Gynaecological Oncology, University College London, EGA Institute for Women’s Health, London, UK
| | - Eva Wozniak
- Department of Gynaecological Oncology, University College London, EGA Institute for Women’s Health, London, UK
| | - Ya-Yu Tsai
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Joanne Weidhaas
- Department of Therapeutic Radiology, Yale University, New Haven, Connecticut, USA
| | - Daniel Paik
- Department of Obstetrics and Gynecology, Yale University, New Haven, Connecticut, USA
| | - David J. Van Den Berg
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Daniel O. Stram
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Celeste Leigh Pearce
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Anna H. Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Wendy Brewster
- Department of Epidemiology, School of Medicine, University of California, Irvine, California, USA
| | - Hoda Anton-Culver
- Department of Epidemiology, School of Medicine, University of California, Irvine, California, USA
| | - Argyrios Ziogas
- Department of Epidemiology, School of Medicine, University of California, Irvine, California, USA
| | | | - Douglas A. Levine
- Gynecology Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Stanley B. Kaye
- Section of Medicine, Institute of Cancer Research, Sutton, UK
| | - Robert Brown
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Jim Paul
- Cancer Research UK Clinical Trials Unit, Glasgow University, Glasgow, UK
| | - James Flanagan
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Weiva Sieh
- Department of Health Research and Policy, Stanford University School of Medicine, Standford, California, USA
| | - Valerie McGuire
- Department of Health Research and Policy, Stanford University School of Medicine, Standford, California, USA
| | - Alice S. Whittemore
- Department of Health Research and Policy, Stanford University School of Medicine, Standford, California, USA
| | - Ian Campbell
- Peter MacCallum Cancer Institute, Melbourne, Australia
| | - Martin E. Gore
- The Royal Marsden Hospital, Gynecological Oncology Unit, London, UK
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, M Sklodowska-Curie Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Hannah Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, USA
| | - Krzysztof Medrek
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Jacek Gronwald
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Jan Lubinski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Anna Jakubowska
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Nhu D. Le
- Cancer Control Research, BC Cancer Agency, Vancouver, BC, Canada
| | - Linda S. Cook
- Division of Epidemiology and Biostatistics, University of New Mexico, Albuquerque, New Mexico, USA,Alberta Health Services-Cancer Care, Calgary, AB, Canada
| | | | - Angela Brooks-Wilson
- Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada,Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
| | - Leon F.A.G. Massuger
- Department of Gynaecology, Radboud University, Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Lambertus A. Kiemeney
- Department of Gynaecology, Radboud University, Nijmegen Medical Centre, Nijmegen, The Netherlands
| | | | - Anne M. van Altena
- Department of Gynaecology, Radboud University, Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Richard Houlston
- Section of Cancer Genetics, Institute of Cancer Research, Sutton, UK
| | - Ian Tomlinson
- Population and Functional Genetics Lab, Wellcome Trust Centre for Human Genetics, Oxford, UK
| | - Rachel T. Palmieri
- Department of Community and Family Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Patricia G. Moorman
- Department of Community and Family Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Joellen Schildkraut
- Department of Community and Family Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Edwin S. Iversen
- Department of Statistics, Duke University, Durham, North Carolina, USA
| | - Catherine Phelan
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Robert A. Vierkant
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
| | - Julie M. Cunningham
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
| | - Ellen L. Goode
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
| | - Brooke L. Fridley
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
| | - Susan Kruger-Kjaer
- Department of Virus, Hormones and Cancer Institute of Cancer Epidemiology, Danish Cancer Society, Copenhagen, Denmark
| | - Jan Blaeker
- Aarhus University Hospital, Skejby, Aarhus, Denmark
| | - Estrid Hogdall
- Department of Virus, Hormones and Cancer Institute of Cancer Epidemiology, Danish Cancer Society, Copenhagen, Denmark
| | - Claus Hogdall
- The Gynaecologic Clinic, The Juliane Marie Centre, Rigshospitalet, Copenhagen, Denmark
| | - Jenny Gross
- Women's Cancer Research Institute at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Beth Y. Karlan
- Women's Cancer Research Institute at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Roberta B. Ness
- University of Texas School of Public Health, Houston, Texas, USA
| | | | - Kunle Odunsi
- Department of Gynecological Oncology, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Kirsten B. Moyisch
- Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Julie A. Baker
- Department of Obstetrics and Gynecology, Brown University, Providence, Rhode Island, USA
| | - Francesmary Modugno
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Tuomas Heikkinenen
- Department of Obstetrics and Gynaecology, Helsinki University Central Hospital, Helsinki, Finland
| | - Ralf Butzow
- Department of Obstetrics and Gynaecology, Helsinki University Central Hospital, Helsinki, Finland
| | - Heli Nevanlinna
- Department of Obstetrics and Gynaecology, Helsinki University Central Hospital, Helsinki, Finland
| | - Arto Leminen
- Department of Obstetrics and Gynaecology, Helsinki University Central Hospital, Helsinki, Finland
| | - Natalia Bogdanova
- Byelorussian Institute for Oncology and Medical Radiology Aleksandrov N.N., Minsk, Belarus
| | - Natalia Antonenkova
- Byelorussian Institute for Oncology and Medical Radiology Aleksandrov N.N., Minsk, Belarus
| | - Thilo Doerk
- Clinics of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | - Peter Hillemanns
- Clinics of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | - Matthias Dürst
- Clinics of Obstetrics and Gynaecology, Friedrich Schiller University, Jena, Germany
| | - Ingo Runnebaum
- Clinics of Obstetrics and Gynaecology, Friedrich Schiller University, Jena, Germany
| | - Pamela J. Thompson
- Cancer Research Center of Hawaii, University of Hawaii, Honolulu, Hawaii, USA
| | - Michael E. Carney
- Cancer Research Center of Hawaii, University of Hawaii, Honolulu, Hawaii, USA
| | - Marc T. Goodman
- Cancer Research Center of Hawaii, University of Hawaii, Honolulu, Hawaii, USA
| | - Galina Lurie
- Cancer Research Center of Hawaii, University of Hawaii, Honolulu, Hawaii, USA
| | - Shan Wang-Gohrke
- Department of Obstetrics and Gynecology, University of Ulm, Ulm, Germany
| | - Rebecca Hein
- Unit of Genetic Epidemiology, Division of Cancer Epidemiology, Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Jenny Chang-Claude
- Unit of Genetic Epidemiology, Division of Cancer Epidemiology, Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Mary Anne Rossing
- Program in Epidemiology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Kara L. Cushing-Haugen
- Program in Epidemiology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Jennifer Doherty
- Program in Epidemiology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Chu Chen
- Program in Epidemiology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | | | | | | | - Michael J. Birrer
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Kathryn L. Terry
- Obstetrics and Gynecology Epidemology Center, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Dena Hernandez
- National Institute of Aging, National Institutues of Health, Bethesda, Maryland, USA
| | - Daniel W. Cramer
- Obstetrics and Gynecology Epidemology Center, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Ignace Vergote
- Department of Gynaecologic Oncology, University Hospitals Leuven, Belgium
| | - Frederic Amant
- Department of Gynaecologic Oncology, University Hospitals Leuven, Belgium
| | | | - Evelyn Despierre
- Department of Gynaecologic Oncology, University Hospitals Leuven, Belgium
| | - Peter A. Fasching
- Division of Hematology and Oncology, Department of Medicine, David Geffen School of Medicine, Los Angeles, California, USA
| | - Matthias W. Beckmann
- Department of Cancer Epidemiology and Prevention, The M.Sklodowska-Curie Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Falk C. Thiel
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Erlangen, Germany
| | - Arif B. Ekici
- Institute of Human Genetics, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Xiaoqing Chen
- The Queensland Institute of Medical Research, Post Office Royal Brisbane Hospital, Australia
| | | | | | | | - Sharon E. Johnatty
- The Queensland Institute of Medical Research, Post Office Royal Brisbane Hospital, Australia
| | - Penelope M. Webb
- The Queensland Institute of Medical Research, Post Office Royal Brisbane Hospital, Australia
| | - Jonathan Beesley
- The Queensland Institute of Medical Research, Post Office Royal Brisbane Hospital, Australia
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, USA
| | - Montserrat Garcia-Closas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, USA
| | - Tom Sellers
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | | | - Andrew Berchuck
- Department of Community and Family Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Georgia Chenevix-Trench
- The Queensland Institute of Medical Research, Post Office Royal Brisbane Hospital, Australia
| | | | - Simon A. Gayther
- Department of Gynaecological Oncology, University College London, EGA Institute for Women’s Health, London, UK
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Cheung KJJ, Delaney A, Ben-Neriah S, Schein J, Lee T, Shah SP, Cheung D, Johnson NA, Mungall AJ, Telenius A, Lai B, Boyle M, Connors JM, Gascoyne RD, Marra MA, Horsman DE. High resolution analysis of follicular lymphoma genomes reveals somatic recurrent sites of copy-neutral loss of heterozygosity and copy number alterations that target single genes. Genes Chromosomes Cancer 2010; 49:669-81. [PMID: 20544841 DOI: 10.1002/gcc.20780] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
A multiplatform approach, including conventional cytogenetic techniques, BAC array comparative genomic hybridization, and Affymetrix 500K SNP arrays, was applied to the study of the tumor genomes of 25 follicular lymphoma biopsy samples with paired normal DNA samples to characterize balanced translocations, copy number imbalances, and copy-neutral loss of heterozygosity (cnLOH). In addition to the t(14;18), eight unique balanced translocations were found. Commonly reported FL-associated copy number regions were revealed including losses of 1p32-36, 6q, and 10q, and gains of 1q, 6p, 7, 12, 18, and X. The most frequent regions affected by copy-neutral loss of heterozygosity were 1p36.33 (28%), 6p21.3 (20%), 12q21.2-q24.33 (16%), and 16p13.3 (24%). We also identified by SNP analysis, 45 aberrant regions that each affected one gene, including CDKN2A, CDKN2B, FHIT, KIT, PEX14, and PTPRD, which were associated with canonical pathways involved in tumor development. This study illustrates the power of using complementary high-resolution platforms on paired tumor/normal specimens and computational analysis to provide potential insights into the significance of single-gene somatic aberrations in FL tumorigenesis.
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Affiliation(s)
- K-John J Cheung
- Center for Lymphoid Cancer, British Columbia Cancer Agency, Vancouver, BC, Canada.
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17
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Xiao Y, Ye Y, Zou X, Jones S, Yearsley K, Shetuni B, Tellez J, Barsky SH. The lymphovascular embolus of inflammatory breast cancer exhibits a Notch 3 addiction. Oncogene 2010; 30:287-300. [PMID: 20838375 DOI: 10.1038/onc.2010.405] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Inflammatory breast carcinoma (IBC) is characterized by exaggerated lymphovascular invasion (LVI), recapitulated in our human xenograft, MARY-X. This model exhibited lymphovascular emboli in vivo and corresponding spheroids in vitro. Owing to the morphological and gene profile resemblance of these spheroids to embryonal blastocysts, we wondered whether they might exhibit embryonic stem cell signaling. Specifically we investigated Notch and observed selective Notch 3 activation by expression profiling, reverse transcriptase- and real-time PCR, western blot and immunofluorescence in vitro, and immunohistochemistry in vivo. Notch 3 intracellular domain (N3icd) and six target genes, HES-5, HEY-1, c-Myc, Deltex-1, NRARP and PBX1, markedly increased in MARY-X. In addition, a significant percentage of MARY-X cells expressed aldehyde dehydrogenase (ALDH), a stem cell marker. Only the ALDH(+) cells were capable of secondary spheroidgenesis, tumorigenicity and self-renewal. Inhibiting Notch 3 activation in vitro with γ-secretase inhibitors (GSIs) or small interfering RNA resulted in a downregulation of Notch target genes, including CD133, and an induction of caspase 3-mediated apoptosis. Transfection of N3icd but not Notch 1 intracellular domain into normal human mammary epithelial cells resulted in increased expression of Notch target genes and induction of spheroidgenesis. GSI in vivo resulted in inhibitory but diffusion-limited effects on Notch 3 signaling, resulting in xenograft growth reduction. The lymphovascular emboli of human IBC exhibited dual N3icd and ALDH1 immunoreactivities independently of molecular subtype. This Notch 3 addiction of lymphovascular emboli might be exploited in future therapeutic strategies.
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Affiliation(s)
- Y Xiao
- Department of Pathology, The Ohio State University College of Medicine, Columbus, OH, USA
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18
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Thorwarth A, Mueller I, Biebermann H, Ropers HH, Grueters A, Krude H, Ullmann R. Screening chromosomal aberrations by array comparative genomic hybridization in 80 patients with congenital hypothyroidism and thyroid dysgenesis. J Clin Endocrinol Metab 2010; 95:3446-52. [PMID: 20427504 DOI: 10.1210/jc.2009-2195] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
OBJECTIVE Congenital hypothyroidism occurs in 1:3500 live births and is therefore the most common congenital endocrine disorder. A spectrum of defective thyroid morphology, termed thyroid dysgenesis (TD), represents 80% of permanent congenital hypothyroidism cases. Although several candidate genes have been implicated in thyroid development, comprehensive screens failed to detect mutation carriers in a significant number of patients with nonsyndromic TD. Due to the sporadic occurrence of TD, de novo chromosomal rearrangements are conceivably representing one of the molecular mechanisms participating in its etiology. METHODS The introduction of array comparative genomic hybridization (CGH) has provided the ability to map DNA copy number variations (CNVs) genome wide with high resolution. We performed an array CGH screen of 80 TD patients to determine the role of CNVs in the etiology of the disease. RESULTS We identified novel CNVs that have not been described as frequent variations in the healthy population in 8.75% of all patients. These CNVs exclusively affected patients with athyreosis or thyroid hypoplasia and were nonrecurrent, and the regions flanking the CNVs were not enriched for segmental duplications. CONCLUSIONS The high rate of chromosomal changes in TD argues for an involvement of CNVs in the etiology of this disease. Yet the lack of recurrent aberrations suggests that the genetic causes of TD are heterogenous and not restricted to specific genomic hot spots. Thus, future studies may have to shift the focus from singling out specific genes to the identification of deregulated pathways as the underlying cause of the disease.
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Affiliation(s)
- A Thorwarth
- Charité University Medicine Berlin, Institute for Experimental Pediatric Endocrinology, Augustenburger Platz 1, 13353 Berlin, Germany
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Semerci CN, Cinbis M, Ullmann R, Steininger A, Bahce M, Yagci B, Ozden S, Sabir N, Gumus D, Tepeli E, Arteaga J, Mutchinick OM. Subtelomeric 6p monosomy and 12q trisomy in a patient with a 46,XX,der(6)t(6;12)(p25.3;q24.31) karyotype: Phenotypic overlap with Mutchinick syndrome. Am J Med Genet A 2010; 152A:1724-9. [DOI: 10.1002/ajmg.a.33383] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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20
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Boldt V, Stacher E, Halbwedl I, Popper H, Hultschig C, Moinfar F, Ullmann R, Tavassoli FA. Positioning of necrotic lobular intraepithelial neoplasias (LIN, grade 3) within the sequence of breast carcinoma progression. Genes Chromosomes Cancer 2010; 49:463-70. [DOI: 10.1002/gcc.20756] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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21
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Nordgren A, Corcoran M, Sääf A, Bremer A, Kluin-Nelemans HC, Schoumans J, Grandér D. Characterisation of hairy cell leukaemia by tiling resolution array-based comparative Genome hybridisation: a series of 13 cases and review of the literature. Eur J Haematol 2010; 84:17-25. [DOI: 10.1111/j.1600-0609.2009.01334.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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22
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Shoichet SA, Waibel S, Endruhn S, Sperfeld AD, Vorwerk B, Müller I, Erdogan F, Ludolph AC, Ropers HH, Ullmann R. Identification of candidate genes for sporadic amyotrophic lateral sclerosis by array comparative genomic hybridization. ACTA ACUST UNITED AC 2009; 10:162-9. [PMID: 18985462 DOI: 10.1080/17482960802535001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating disorder of the central nervous system that leads to progressive loss of upper and lower motor neurons. Most cases are sporadic and of unknown aetiology. In this study, we screened 72 patients with sporadic ALS for the presence of DNA copy number variations, in order to identify novel candidate disease genes. We have used sub-megabase resolution BAC array comparative genomic hybridization to detect genomic imbalances in our ALS patient cohort. Aberrations with potential relevance for disease aetiology were verified by oligo array CGH. In 72 patients with sporadic ALS, we identified a total of six duplications and five deletions that scored above our threshold. Nine of these 11 variations were smaller than 1Mb, and five were observed exclusively in ALS patients. In conclusion, non-polymorphic sub-microscopic duplications and deletions observable by array CGH are frequent in patients with sporadic ALS. Analysis of such aberrations serves as a starting point in deciphering the aetiology of this complex disease, given that affected genes can be considered candidates for influencing disease susceptibility.
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Carbone L, Harris RA, Vessere GM, Mootnick AR, Humphray S, Rogers J, Kim SK, Wall JD, Martin D, Jurka J, Milosavljevic A, de Jong PJ. Evolutionary breakpoints in the gibbon suggest association between cytosine methylation and karyotype evolution. PLoS Genet 2009; 5:e1000538. [PMID: 19557196 PMCID: PMC2695003 DOI: 10.1371/journal.pgen.1000538] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2009] [Accepted: 05/26/2009] [Indexed: 01/30/2023] Open
Abstract
Gibbon species have accumulated an unusually high number of chromosomal changes since diverging from the common hominoid ancestor 15-18 million years ago. The cause of this increased rate of chromosomal rearrangements is not known, nor is it known if genome architecture has a role. To address this question, we analyzed sequences spanning 57 breaks of synteny between northern white-cheeked gibbons (Nomascus l. leucogenys) and humans. We find that the breakpoint regions are enriched in segmental duplications and repeats, with Alu elements being the most abundant. Alus located near the gibbon breakpoints (<150 bp) have a higher CpG content than other Alus. Bisulphite allelic sequencing reveals that these gibbon Alus have a lower average density of methylated cytosine that their human orthologues. The finding of higher CpG content and lower average CpG methylation suggests that the gibbon Alu elements are epigenetically distinct from their human orthologues. The association between undermethylation and chromosomal rearrangement in gibbons suggests a correlation between epigenetic state and structural genome variation in evolution.
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Affiliation(s)
- Lucia Carbone
- Children's Hospital and Research Center Oakland, Oakland, California, United States of America.
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24
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Indistinguishable genomic profiles and shared prognostic markers in undifferentiated pleomorphic sarcoma and leiomyosarcoma: different sides of a single coin? J Transl Med 2009; 89:668-75. [PMID: 19290004 DOI: 10.1038/labinvest.2009.18] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Soft tissue sarcoma (STS) diagnostics and prognostics are challenging, particularly in highly malignant and pleomorphic subtypes such as undifferentiated pleomorphic sarcoma (UPS) and leiomyosarcoma (LMS). We applied 32K BAC arrays and gene expression profiling to 18 extremity soft tissue LMS and 31 extremity soft tissue UPS with the aim of identifying molecular subtype signatures and genomic prognostic markers. Both the gains/losses and gene expression signatures revealed striking similarities between UPS and LMS, which were indistinguishable using unsupervised hierarchical cluster analysis and significance analysis for microarrays. Gene expression analysis revealed just nine genes, among them tropomyosin beta, which were differentially expressed. Loss of 4q31 (encompassing the SMAD1 locus), loss of 18q22, and tumor necrosis were identified as independent predictors of metastasis in multivariate stepwise Cox regression analysis. Combined analysis applying loss of 4q31 and 18q22 and the presence of necrosis improved the area under receiver operating characteristic curve for metastasis prediction from 0.64 to 0.86. The extensive genetic similarities between extremity soft tissue UPS and LMS suggest a shared lineage of these STS subtypes and the new and independent genetic prognosticators identified hold promise for refined prognostic determination in high-grade, genetically complex STS.
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Veerla S, Lindgren D, Kvist A, Frigyesi A, Staaf J, Persson H, Liedberg F, Chebil G, Gudjonsson S, Borg A, Månsson W, Rovira C, Höglund M. MiRNA expression in urothelial carcinomas: important roles of miR-10a, miR-222, miR-125b, miR-7 and miR-452 for tumor stage and metastasis, and frequent homozygous losses of miR-31. Int J Cancer 2009; 124:2236-42. [PMID: 19127597 DOI: 10.1002/ijc.24183] [Citation(s) in RCA: 184] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We analyzed 34 cases of urothelial carcinomas by miRNA, mRNA and genomic profiling. Unsupervised hierarchical clustering using expression information for 300 miRNAs produced 3 major clusters of tumors corresponding to Ta, T1 and T2-T3 tumors, respectively. A subsequent SAM analysis identified 51 miRNAs that discriminated the 3 pathological subtypes. A score based on the expression levels of the 51 miRNAs, identified muscle invasive tumors with high precision and sensitivity. MiRNAs showing high expression in muscle invasive tumors included miR-222 and miR-125b and in Ta tumors miR-10a. A miRNA signature for FGFR3 mutated cases was also identified with miR-7 as an important member. MiR-31, located in 9p21, was found to be homozygously deleted in 3 cases and miR-452 and miR-452* were shown to be over expressed in node positive tumors. In addition, these latter miRNAs were shown to be excellent prognostic markers for death by disease as outcome. The presented data shows that pathological subtypes of urothelial carcinoma show distinct miRNA gene expression signatures.
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Affiliation(s)
- Srinivas Veerla
- Department of Clinical Genetics, Lund University Hospital, Lund, Sweden
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26
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Koolen DA, Pfundt R, de Leeuw N, Hehir-Kwa JY, Nillesen WM, Neefs I, Scheltinga I, Sistermans E, Smeets D, Brunner HG, van Kessel AG, Veltman JA, de Vries BB. Genomic microarrays in mental retardation: A practical workflow for diagnostic applications. Hum Mutat 2009; 30:283-92. [DOI: 10.1002/humu.20883] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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27
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Ratnakumar A, Barris W, McWilliam S, Brauning R, McEwan JC, Snelling WM, Dalrymple BP. A multiway analysis for identifying high integrity bovine BACs. BMC Genomics 2009; 10:46. [PMID: 19166603 PMCID: PMC2660975 DOI: 10.1186/1471-2164-10-46] [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: 06/10/2008] [Accepted: 01/23/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In large genomics projects involving many different types of analyses of bacterial artificial chromosomes (BACs), such as fingerprinting, end sequencing (BES) and full BAC sequencing there are many opportunities for the identities of BACs to become confused. However, by comparing the results from the different analyses, inconsistencies can be identified and a set of high integrity BACs preferred for future research can be defined. RESULTS The location of each bovine BAC in the BAC fingerprint-based genome map and in the genome assembly were compared based on the reported BESs, and for a smaller number of BACs the full sequence. BACs with consistent positions in all three datasets, or if the full sequence was not available, for both the fingerprint map and BES-based alignments, were deemed to be correctly positioned. BACs with consistent BES-based and fingerprint-based locations, but with conflicting locations based on the fully sequenced BAC, appeared to have been misidentified during sequencing, and included a number of apparently swapped BACs. Inconsistencies between BES-based and fingerprint map positions identified thirty one plates from the CHORI-240 library that appear to have suffered substantial systematic problems during the end-sequencing of the BACs. No systematic problems were identified in the fingerprinting of the BACs. Analysis of BACs overlapping in the assembly identified a small overrepresentation of clones with substantial overlap in the library and a substantial enrichment of highly overlapping BACs on the same plate in the CHORI-240 library. More than half of these BACs appear to have been present as duplicates on the original BAC-library plates and thus should be avoided in subsequent projects. CONCLUSION Our analysis shows that approximately 95% of the bovine CHORI-240 library clones with both a BAC fingerprint and two BESs mapping to the genome in the expected orientations (approximately 27% of all BACs) have consistent locations in the BAC fingerprint map and the genome assembly. We have developed a broadly applicable methodology for checking the integrity of BAC-based datasets even where only incomplete and partially assembled genomic sequence is available.
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Affiliation(s)
- Abhirami Ratnakumar
- CSIRO Livestock Industries, 306 Carmody Road, St. Lucia, QLD 4067, Australia.
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Array-Based Comparative Genomic Hybridization as a Tool for Analyzing the Leukemia Genome. Methods Mol Biol 2009; 538:151-77. [DOI: 10.1007/978-1-59745-418-6_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Woldringh G, Janssen I, Hehir-Kwa J, van den Elzen C, Kremer J, de Boer P, Schoenmakers E. Constitutional DNA copy number changes in ICSI children. Hum Reprod 2008; 24:233-40. [DOI: 10.1093/humrep/den323] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Cooke SL, Pole JCM, Chin SF, Ellis IO, Caldas C, Edwards PAW. High-resolution array CGH clarifies events occurring on 8p in carcinogenesis. BMC Cancer 2008; 8:288. [PMID: 18840272 PMCID: PMC2576333 DOI: 10.1186/1471-2407-8-288] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2008] [Accepted: 10/07/2008] [Indexed: 01/29/2023] Open
Abstract
Background Rearrangement of the short arm of chromosome 8 (8p) is very common in epithelial cancers such as breast cancer. Usually there is an unbalanced translocation breakpoint in 8p12 (29.7 Mb – 38.5 Mb) with loss of distal 8p, sometimes with proximal amplification of 8p11-12. Rearrangements in 8p11-12 have been investigated using high-resolution array CGH, but the first 30 Mb of 8p are less well characterised, although this region contains several proposed tumour suppressor genes. Methods We analysed the whole of 8p by array CGH at tiling-path BAC resolution in 32 breast and six pancreatic cancer cell lines. Regions of recurrent rearrangement distal to 8p12 were further characterised, using regional fosmid arrays. FISH, and quantitative RT-PCR on over 60 breast tumours validated the existence of similar events in primary material. Results We confirmed that 8p is usually lost up to at least 30 Mb, but a few lines showed focal loss or copy number steps within this region. Three regions showed rearrangements common to at least two cases: two regions of recurrent loss and one region of amplification. Loss within 8p23.3 (0 Mb – 2.2 Mb) was found in six cell lines. Of the genes always affected, ARHGEF10 showed a point mutation of the remaining normal copies in the DU4475 cell line. Deletions within 12.7 Mb – 19.1 Mb in 8p22, in two cases, affected TUSC3. A novel amplicon was found within 8p21.3 (19.1 Mb – 23.4 Mb) in two lines and one of 98 tumours. Conclusion The pattern of rearrangements seen on 8p may be a consequence of the high density of potential targets on this chromosome arm, and ARHGEF10 may be a new candidate tumour suppressor gene.
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Affiliation(s)
- Susanna L Cooke
- Department of Pathology and Hutchison/MRC Research Centre, University of Cambridge, Cambridge, UK.
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Miller DT, Shen Y, Wu BL. Oligonucleotide microarrays for clinical diagnosis of copy number variation. ACTA ACUST UNITED AC 2008; Chapter 8:Unit 8.12. [PMID: 18633976 DOI: 10.1002/0471142905.hg0812s58] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Detection of genomic copy number variation is now considered the standard of care in the evaluation of children with developmental delay, and is used for other clinical indications such as multiple congenital anomalies and autism spectrum disorders. Fluorescence in situ hybridization (FISH) was the first molecular method for detection of submicroscopic genomic copy number variation, but microarray based comparative genomic hybridization (array CGH) offers several advantages as an adjunct to traditional cytogenetic methods such as karyotype and FISH. This unit focuses on oligonucleotide arrays, but includes background information on basic differences between oligonucleotide arrays and bacterial artificial chromosome (BAC) arrays. Array sensitivity is influenced by probe coverage or density, probe location, and choice of oligo array formats (i.e., targeted versus whole genome). Array platform influences the likelihood of detecting variants of unknown significance. Clinical interpretation of such variants is discussed.
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Affiliation(s)
- David T Miller
- Department of Laboratory Medicine, Children's Hospital Boston, Boston, Massachusetts, USA
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Enhanced detection of clinically relevant genomic imbalances using a targeted plus whole genome oligonucleotide microarray. Genet Med 2008; 10:415-29. [PMID: 18496225 DOI: 10.1097/gim.0b013e318177015c] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
PURPOSE Array comparative genomic hybridization is rapidly becoming an integral part of cytogenetic diagnostics. We report the design, validation, and clinical utility of an oligonucleotide array which combines genome-wide coverage with targeted enhancement at known clinically relevant regions. METHODS Probes were placed every 75 kb across the entire euchromatic genome to establish a chromosomal "backbone" with a resolution of approximately 500 kb, which is increased to approximately 50 kb in targeted regions. RESULTS For validation, 30 samples showed 100% concordance with previous G-banding and/or fluorescence in situ hybridization results. Prospective array analysis of 211 clinical samples identified 33 (15.6%) cases with clinically significant abnormalities. Of these, 23 (10.9%) were detected by the "targeted" coverage and 10 (4.7%) by the genome-wide coverage (average size of 3.7 Mb). All abnormalities were verified by fluorescence in situ hybridization, using commercially available or homebrew probes using the 32K bacterial artificial chromosome set. Four (1.9%) cases had previously reported imbalances of uncertain clinical significance. Five (2.4%) cases required parental studies for interpretation and all were benign familial variants. CONCLUSIONS Our results highlight the enhanced diagnostic utility of a genome-wide plus targeted array design, as the use of only a targeted array would have failed to detect 4.7% of the clinically relevant imbalances.
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Klopocki E, Graul-Neumann LM, Grieben U, Tönnies H, Ropers HH, Horn D, Mundlos S, Ullmann R. A further case of the recurrent 15q24 microdeletion syndrome, detected by array CGH. Eur J Pediatr 2008; 167:903-8. [PMID: 17932688 PMCID: PMC2757600 DOI: 10.1007/s00431-007-0616-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2007] [Accepted: 09/19/2007] [Indexed: 11/24/2022]
Abstract
We report on a 10-year-old patient with developmental delay, craniofacial dysmorphism, digital and genital abnormalities. In addition, muscular hypotonia, strabism, and splenomegaly were observed; inguinal and umbilical hernias were surgically corrected. Mucopolysaccharidoses and CDG syndromes could not be found. Chromosome analysis revealed a normal male karyotype (46,XY). A more detailed investigation of the patient's genomic DNA by microarray-based comparative genomic hybridization (array CGH) detected an interstitial 3.7 Mb deletion ranging from 15q24.1 to 15q24.3 which was shown to be de novo. Interstitial deletions involving 15q24 are rare. Sharp et al. (Hum Mol Genet 16:567-572, 2007) recently characterized a recurrent 15q24 microdeletion syndrome with breakpoints in regions of segmental duplications. The de novo microdeletion described here colocalizes with the minimal deletion region of the 15q24 microdeletion syndrome. The distinct clinical phenotype associated with this novel microdeletion syndrome is similar to the phenotype of our patient with respect to specific facial features, developmental delay, microcephaly, digital abnormalities, and genital abnormalities in males. We present a genotype-phenotype correlation and comparison with patients from the literature.
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Affiliation(s)
- Eva Klopocki
- Institute of Medical Genetics, Charité Universitätsmedizin Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353, Berlin, Germany.
| | - Luitgard M. Graul-Neumann
- Institute of Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Ulrike Grieben
- Department of Neuropaediatrics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Holger Tönnies
- Institute of Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Hans-Hilger Ropers
- Max-Planck Institute for Molecular Genetics, Ihnestrasse 63, Berlin, Germany
| | - Denise Horn
- Institute of Medical Genetics, Charité Universitätsmedizin Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Stefan Mundlos
- Institute of Medical Genetics, Charité Universitätsmedizin Berlin, Campus Virchow Klinikum, Augustenburger Platz 1, 13353 Berlin, Germany ,Max-Planck Institute for Molecular Genetics, Ihnestrasse 63, Berlin, Germany
| | - Reinhard Ullmann
- Max-Planck Institute for Molecular Genetics, Ihnestrasse 63, Berlin, Germany
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Steichen-Gersdorf E, Gassner I, Superti-Furga A, Ullmann R, Stricker S, Klopocki E, Mundlos S. Triangular tibia with fibular aplasia associated with a microdeletion on 2q11.2 encompassing LAF4. Clin Genet 2008; 74:560-5. [PMID: 18616733 DOI: 10.1111/j.1399-0004.2008.01050.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nievergelt syndrome (NS) is an autosomal dominant mesomelic dysplasia characterized by specific deformities of the radius, ulna, fibula and a rhomboid shape of the tibia. Phenotypically overlapping conditions such as mesomelic dysplasia, Savarirayan-type (MIM 605274), have been described, but their pathogenesis also remains unknown. We report on a girl with fibular agenesis, severely abnormal, triangular tibiae, urogenital tract malformations, failure to thrive, convulsions and recurrent apnoeas leading to respiratory arrest at the age of 4 months. Her skeletal findings correspond to those of the mesomelic dysplasia, Savarirayan-type recently described in two patients. In addition to the skeletal findings, our patient had central nervous system manifestations and developmental anomalies of the urogenital tract. In the patient described in this study, array comparative genomic hybridization (CGH) analysis revealed a de novo interstitial microdeletion of 500 kb on chromosome 2q11.1 containing the LAF4/AFF3 (lymphoid-nuclear-protein-related AF4) gene. In situ hybridization analysis of Laf4 in mouse embryos revealed expression in the developing brain, in the limb buds and in the zeugopod corresponding to the limb phenotype. Haploinsufficiency for LAF4/AFF3 is associated with limb, brain and urogenital malformations and specific changes of the tibia that are part of the NS spectrum.
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Affiliation(s)
- E Steichen-Gersdorf
- Department of Pediatrics, Medical University of Innsbruck, Innsbruck, Austria.
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Mathewson CA, Schein JE, Marra MA. Large-scale BAC clone restriction digest fingerprinting. ACTA ACUST UNITED AC 2008; Chapter 5:Unit 5.19. [PMID: 18428413 DOI: 10.1002/0471142905.hg0519s53] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Restriction digest fingerprinting is a common method for characterizing large insert genomic clones, e.g., bacterial artificial chromosome (BAC), P1 artificial chromosome (PAC) and Fosmid clones. This clone fingerprinting method has been widely applied in the construction of clone-based physical maps, which have been used as positional cloning resources as well as to support directed and genome-wide sequencing efforts. This unit describes a robust, large-scale procedure for generation of agarose gel-based clone fingerprints from BAC clones.
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Affiliation(s)
- Carrie A Mathewson
- Canada's Michael Smith Genome Sciences Center Vancouver, British Columbia, Canada
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Howarth KD, Blood KA, Ng BL, Beavis JC, Chua Y, Cooke SL, Raby S, Ichimura K, Collins VP, Carter NP, Edwards PAW. Array painting reveals a high frequency of balanced translocations in breast cancer cell lines that break in cancer-relevant genes. Oncogene 2008; 27:3345-59. [PMID: 18084325 PMCID: PMC2423006 DOI: 10.1038/sj.onc.1210993] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2007] [Revised: 11/13/2007] [Accepted: 11/15/2007] [Indexed: 12/21/2022]
Abstract
Chromosome translocations in the common epithelial cancers are abundant, yet little is known about them. They have been thought to be almost all unbalanced and therefore dismissed as mostly mediating tumour suppressor loss. We present a comprehensive analysis by array painting of the chromosome translocations of breast cancer cell lines HCC1806, HCC1187 and ZR-75-30. In array painting, chromosomes are isolated by flow cytometry, amplified and hybridized to DNA microarrays. A total of 200 breakpoints were identified and all were mapped to 1 Mb resolution on bacterial artificial chromosome (BAC) arrays, then 40 selected breakpoints, including all balanced breakpoints, were further mapped on tiling-path BAC arrays or to around 2 kb resolution using oligonucleotide arrays. Many more of the translocations were balanced at 1 Mb resolution than expected, either reciprocal (eight in total) or balanced for at least one participating chromosome (19 paired breakpoints). Second, many of the breakpoints were at genes that are plausible targets of oncogenic translocation, including balanced breaks at CTCF, EP300/p300 and FOXP4. Two gene fusions were demonstrated, TAX1BP1-AHCY and RIF1-PKD1L1. Our results support the idea that chromosome rearrangements may play an important role in common epithelial cancers such as breast cancer.
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Affiliation(s)
- KD Howarth
- Hutchison-MRC Research Centre, Department of Pathology, University of Cambridge, Hills Road, Cambridge CB2 0XZ, U.K
| | - KA Blood
- Hutchison-MRC Research Centre, Department of Pathology, University of Cambridge, Hills Road, Cambridge CB2 0XZ, U.K
| | - BL Ng
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, U.K
| | - JC Beavis
- Hutchison-MRC Research Centre, Department of Pathology, University of Cambridge, Hills Road, Cambridge CB2 0XZ, U.K
| | - Y Chua
- Hutchison-MRC Research Centre, Department of Pathology, University of Cambridge, Hills Road, Cambridge CB2 0XZ, U.K
| | - SL Cooke
- Hutchison-MRC Research Centre, Department of Pathology, University of Cambridge, Hills Road, Cambridge CB2 0XZ, U.K
| | - S Raby
- Hutchison-MRC Research Centre, Department of Pathology, University of Cambridge, Hills Road, Cambridge CB2 0XZ, U.K
| | - K Ichimura
- Division of Molecular Histopathology, Department of Pathology, University of Cambridge, Box 231 Addenbrookes Hospital, Hills Road, Cambridge, U.K
| | - VP Collins
- Division of Molecular Histopathology, Department of Pathology, University of Cambridge, Box 231 Addenbrookes Hospital, Hills Road, Cambridge, U.K
| | - NP Carter
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, U.K
| | - PAW Edwards
- Hutchison-MRC Research Centre, Department of Pathology, University of Cambridge, Hills Road, Cambridge CB2 0XZ, U.K
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Krzywinski M, Bosdet I, Mathewson C, Wye N, Brebner J, Chiu R, Corbett R, Field M, Lee D, Pugh T, Volik S, Siddiqui A, Jones S, Schein J, Collins C, Marra M. A BAC clone fingerprinting approach to the detection of human genome rearrangements. Genome Biol 2008; 8:R224. [PMID: 17953769 PMCID: PMC2246298 DOI: 10.1186/gb-2007-8-10-r224] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2007] [Revised: 08/28/2007] [Accepted: 10/22/2007] [Indexed: 11/10/2022] Open
Abstract
Fingerprint Profiling (FPP) is a new method which uses restriction digest fingerprints of bacterial artificial chromosome (BAC) clones for detecting and classifying rearrangements in the human genome. We present a method, called fingerprint profiling (FPP), that uses restriction digest fingerprints of bacterial artificial chromosome clones to detect and classify rearrangements in the human genome. The approach uses alignment of experimental fingerprint patterns to in silico digests of the sequence assembly and is capable of detecting micro-deletions (1-5 kb) and balanced rearrangements. Our method has compelling potential for use as a whole-genome method for the identification and characterization of human genome rearrangements.
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Affiliation(s)
- Martin Krzywinski
- BC Cancer Agency Genome Sciences Centre, West 7th Avenue, Vancouver, British Columbia, Canada V5Z 4S6.
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Morozova O, Marra MA. From cytogenetics to next-generation sequencing technologies: advances in the detection of genome rearrangements in tumorsThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB — Systems and Chemical Biology, and has undergone the Journal's usual peer review process. Biochem Cell Biol 2008; 86:81-91. [PMID: 18443621 DOI: 10.1139/o08-003] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Genome rearrangements have long been recognized as hallmarks of human tumors and have been used to diagnose cancer. Techniques used to detect genome rearrangements have evolved from microscopic examinations of chromosomes to the more recent microarray-based approaches. The availability of next-generation sequencing technologies may provide a means for scrutinizing entire cancer genomes and transcriptomes at unparalleled resolution. Here we review the methods that have been used to detect genome rearrangements and discuss the scope and limitations of each approach. We end with a discussion of the potential that next-generation sequencing technologies may offer to the field.
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Affiliation(s)
- Olena Morozova
- BC Cancer Agency Genome Sciences Centre, Suite 100-570 West 7th Avenue, Vancouver, BC V5Z 4S6, Canada
| | - Marco A. Marra
- BC Cancer Agency Genome Sciences Centre, Suite 100-570 West 7th Avenue, Vancouver, BC V5Z 4S6, Canada
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Raphael BJ, Volik S, Yu P, Wu C, Huang G, Linardopoulou EV, Trask BJ, Waldman F, Costello J, Pienta KJ, Mills GB, Bajsarowicz K, Kobayashi Y, Sridharan S, Paris PL, Tao Q, Aerni SJ, Brown RP, Bashir A, Gray JW, Cheng JF, de Jong P, Nefedov M, Ried T, Padilla-Nash HM, Collins CC. A sequence-based survey of the complex structural organization of tumor genomes. Genome Biol 2008; 9:R59. [PMID: 18364049 PMCID: PMC2397511 DOI: 10.1186/gb-2008-9-3-r59] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2007] [Revised: 02/20/2008] [Accepted: 03/25/2008] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND The genomes of many epithelial tumors exhibit extensive chromosomal rearrangements. All classes of genome rearrangements can be identified using end sequencing profiling, which relies on paired-end sequencing of cloned tumor genomes. RESULTS In the present study brain, breast, ovary, and prostate tumors, along with three breast cancer cell lines, were surveyed using end sequencing profiling, yielding the largest available collection of sequence-ready tumor genome breakpoints and providing evidence that some rearrangements may be recurrent. Sequencing and fluorescence in situ hybridization confirmed translocations and complex tumor genome structures that include co-amplification and packaging of disparate genomic loci with associated molecular heterogeneity. Comparison of the tumor genomes suggests recurrent rearrangements. Some are likely to be novel structural polymorphisms, whereas others may be bona fide somatic rearrangements. A recurrent fusion transcript in breast tumors and a constitutional fusion transcript resulting from a segmental duplication were identified. Analysis of end sequences for single nucleotide polymorphisms revealed candidate somatic mutations and an elevated rate of novel single nucleotide polymorphisms in an ovarian tumor. CONCLUSION These results suggest that the genomes of many epithelial tumors may be far more dynamic and complex than was previously appreciated and that genomic fusions, including fusion transcripts and proteins, may be common, possibly yielding tumor-specific biomarkers and therapeutic targets.
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Affiliation(s)
- Benjamin J Raphael
- Department of Computer Science & Center for Computational Molecular Biology, Brown University, Waterman Street, Providence, RI 02912-1910, USA.
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40
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Gajduskova P, Snijders AM, Kwek S, Roydasgupta R, Fridlyand J, Tokuyasu T, Pinkel D, Albertson DG. Genome position and gene amplification. Genome Biol 2008; 8:R120. [PMID: 17584934 PMCID: PMC2394771 DOI: 10.1186/gb-2007-8-6-r120] [Citation(s) in RCA: 21] [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: 11/06/2006] [Revised: 05/15/2007] [Accepted: 06/21/2007] [Indexed: 01/05/2023] Open
Abstract
Genomic analyses of human cells expressing dihydrofolate reductase provide insight into the effects of genome position on the propensity for a drug-resistance gene to amplify in human cells.
Background Amplifications, regions of focal high-level copy number change, lead to overexpression of oncogenes or drug resistance genes in tumors. Their presence is often associated with poor prognosis; however, the use of amplification as a mechanism for overexpression of a particular gene in tumors varies. To investigate the influence of genome position on propensity to amplify, we integrated a mutant form of the gene encoding dihydrofolate reductase into different positions in the human genome, challenged cells with methotrexate and then studied the genomic alterations arising in drug resistant cells. Results We observed site-specific differences in methotrexate sensitivity, amplicon organization and amplification frequency. One site was uniquely associated with a significantly enhanced propensity to amplify and recurrent amplicon boundaries, possibly implicating a rare folate-sensitive fragile site in initiating amplification. Hierarchical clustering of gene expression patterns and subsequent gene enrichment analysis revealed two clusters differing significantly in expression of MYC target genes independent of integration site. Conclusion These studies suggest that genome context together with the particular challenges to genome stability experienced during the progression to cancer contribute to the propensity to amplify a specific oncogene or drug resistance gene, whereas the overall functional response to drug (or other) challenge may be independent of the genomic location of an oncogene.
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Affiliation(s)
- Pavla Gajduskova
- Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143-0808, USA
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská, Brno, 612 65, Czech Republic
| | - Antoine M Snijders
- Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Serena Kwek
- Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Ritu Roydasgupta
- Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Jane Fridlyand
- Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143-0808, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Taku Tokuyasu
- Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Daniel Pinkel
- Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143-0808, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Donna G Albertson
- Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143-0808, USA
- Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143-0808, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143-0808, USA
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Detection of submicroscopic constitutional chromosome aberrations in clinical diagnostics: a validation of the practical performance of different array platforms. Eur J Hum Genet 2008; 16:786-92. [DOI: 10.1038/ejhg.2008.14] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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Heidenblad M, Lindgren D, Jonson T, Liedberg F, Veerla S, Chebil G, Gudjonsson S, Borg Å, Månsson W, Höglund M. Tiling resolution array CGH and high density expression profiling of urothelial carcinomas delineate genomic amplicons and candidate target genes specific for advanced tumors. BMC Med Genomics 2008; 1:3. [PMID: 18237450 PMCID: PMC2227947 DOI: 10.1186/1755-8794-1-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2007] [Accepted: 01/31/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Urothelial carcinoma (UC) is characterized by nonrandom chromosomal aberrations, varying from one or a few changes in early-stage and low-grade tumors, to highly rearranged karyotypes in muscle-invasive lesions. Recent array-CGH analyses have shed further light on the genomic changes underlying the neoplastic development of UC, and have facilitated the molecular delineation amplified and deleted regions to the level of specific candidate genes. In the present investigation we combine detailed genomic information with expression information to identify putative target genes for genomic amplifications. METHODS We analyzed 38 urothelial carcinomas by whole-genome tiling resolution array-CGH and high density expression profiling to identify putative target genes in common genomic amplifications. When necessary expression profiling was complemented with Q-PCR of individual genes. RESULTS Three genomic segments were frequently and exclusively amplified in high grade tumors; 1q23, 6p22 and 8q22, respectively. Detailed mapping of the 1q23 segment showed a heterogeneous amplification pattern and no obvious commonly amplified region. The 6p22 amplicon was defined by a 1.8 Mb core region present in all amplifications, flanked both distally and proximally by segments amplified to a lesser extent. By combining genomic profiles with expression profiles we could show that amplification of E2F3, CDKAL1, SOX4, and MBOAT1 as well as NUP153, AOF1, FAM8A1 and DEK in 6p22 was associated with increased gene expression. Amplification of the 8q22 segment was primarily associated with YWHAZ (14-3-3-zeta) and POLR2K over expression. The possible importance of the YWHA genes in the development of urothelial carcinomas was supported by another recurrent amplicon paralogous to 8q22, in 2p25, where increased copy numbers lead to enhanced expression of YWHAQ (14-3-3-theta). Homozygous deletions were identified at 10 different genomic locations, most frequently affecting CDKN2A/CDKN2B in 9p21 (32%). Notably, the latter occurred mutually exclusive with 6p22 amplifications. CONCLUSION The presented data indicates 6p22 as a composite amplicon with more than one possible target gene. The data also suggests that amplification of 6p22 and homozygous deletions of 9p21 may have complementary roles. Furthermore, the analysis of paralogous regions that showed genomic amplification indicated altered expression of YWHA (14-3-3) genes as important events in the development of UC.
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Affiliation(s)
- Markus Heidenblad
- Department of Clinical Genetics, Lund University Hospital, SE-221 85 Lund, Sweden
| | - David Lindgren
- Department of Clinical Genetics, Lund University Hospital, SE-221 85 Lund, Sweden
| | - Tord Jonson
- Department of Clinical Genetics, Lund University Hospital, SE-221 85 Lund, Sweden
| | - Fredrik Liedberg
- Department of Urology, Lund University Hospital, SE-221 85 Lund, Sweden
| | - Srinivas Veerla
- Department of Clinical Genetics, Lund University Hospital, SE-221 85 Lund, Sweden
| | - Gunilla Chebil
- Department of Pathology and Cytology, Helsingborg Hospital AB, SE-251 87 Helsingborg, Sweden
| | | | - Åke Borg
- Department of Oncology, Lund University Hospital, SE-221 85 Lund, Sweden
| | - Wiking Månsson
- Department of Urology, Lund University Hospital, SE-221 85 Lund, Sweden
| | - Mattias Höglund
- Department of Clinical Genetics, Lund University Hospital, SE-221 85 Lund, Sweden
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So J, Müller I, Kunath M, Herrmann S, Ullmann R, Schweiger S. Diagnosis of a terminal deletion of 4p with duplication of Xp22.31 in a patient with findings of Opitz G/BBB syndrome and Wolf-Hirschhorn syndrome. Am J Med Genet A 2008; 146A:103-9. [PMID: 18074389 DOI: 10.1002/ajmg.a.32055] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Opitz G/BBB syndrome (OS) is a congenital midline malformation syndrome characterized by hypertelorism, hypospadias, cleft lip/palate, laryngotracheoesophageal abnormalities, imperforate anus, developmental delay and cardiac defects. The X-linked form is caused by mutations in the MID1 gene, while no gene has yet been identified for the autosomal dominant form. Here, we report on a 15-year-old boy who was referred for MID1 mutation analysis with findings typical of OS, including apparent hypertelorism, hypospadias, a history of feeding difficulties, dysphagia secondary to esophageal arteria lusoria, growth retardation and developmental delay. No MID1 mutation was found, but subsequent sub-megabase resolution array CGH unexpectedly documented a 2.34 Mb terminal 4p deletion, suggesting a diagnosis of WHS, and a duplication in Xp22.31. Wolf-Hirschhorn syndrome (WHS) is a contiguous gene deletion syndrome involving terminal chromosome 4p deletions, in particular 4p16.3. WHS is characterized by typical facial appearance ("Greek helmet facies"), mental retardation, congenital hypotonia, and growth retardation. While the severity of developmental delay in this patient supports the diagnosis of WHS rather than OS, this case illustrates the striking similarities of clinical findings in seemingly unrelated syndromes, suggesting common or interacting pathways at the molecular and pathogenetic level. This is the first report of arteria lusoria (esophageal vascular ring) in a patient with WHS.
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Affiliation(s)
- Joyce So
- Max Planck Institute for Molecular Genetics, Berlin, Germany
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44
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Feenstra I, Vissers LELM, Orsel M, van Kessel AG, Brunner HG, Veltman JA, van Ravenswaaij-Arts CMA. Genotype-phenotype mapping of chromosome 18q deletions by high-resolution array CGH: an update of the phenotypic map. Am J Med Genet A 2007; 143A:1858-67. [PMID: 17632778 DOI: 10.1002/ajmg.a.31850] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Partial deletions of the long arm of chromosome 18 lead to variable phenotypes. Common clinical features include a characteristic face, short stature, congenital aural atresia (CAA), abnormalities of the feet, and mental retardation (MR). The presence or absence of these clinical features may depend on the size and position of the deleted region. Conversely, it is also known that patients whose breakpoints are localized within the same chromosome band may exhibit distinct phenotypes. New molecular techniques such as array CGH allow for a more precise determination of breakpoints in cytogenetic syndromes, thus leading to better-defined genotype-phenotype correlations. In order to update the phenotypic map for chromosome 18q deletions, we applied a tiling resolution chromosome 18 array to determine the exact breakpoints in 29 patients with such deletions. Subsequently, we linked the genotype to the patient's phenotype and integrated our results with those previously published. Using this approach, we were able to refine the critical regions for microcephaly (18q21.33), short stature (18q12.1-q12.3, 18q21.1-q21.33, and 18q22.3-q23), white matter disorders and delayed myelination (18q22.3-q23), growth hormone insufficiency (18q22.3-q23), and CAA (18q22.3). Additionally, the overall level of MR appeared to be mild in patients with deletions distal to 18q21.33 and severe in patients with deletions proximal to 18q21.31. The critical region for the 'typical' 18q-phenotype is a region of 4.3 Mb located within 18q22.3-q23. Molecular characterization of more patients will ultimately lead to a further delineation of the critical regions and thus to the identification of candidate genes for these specific traits.
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Affiliation(s)
- Ilse Feenstra
- Department of Human Genetics, University Medical Centre Nijmegen, Nijmegen, The Netherlands
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45
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NIELÄNDER INGA, BUG STEFANIE, RICHTER JULIA, GIEFING MACIEJ, IGNACIO MARTÍN-SUBERO JOSÉ, SIEBERT REINER. Combining array-based approaches for the identification of candidate tumor suppressor loci in mature lymphoid neoplasms. APMIS 2007; 115:1107-34. [DOI: 10.1111/j.1600-0463.2007.apm_883.xml.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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46
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Shen Y, Irons M, Miller DT, Cheung SW, Lip V, Sheng X, Tomaszewicz K, Shao H, Fang H, Tang HS, Irons M, Walsh CA, Platt O, Gusella JF, Wu BL. Development of a focused oligonucleotide-array comparative genomic hybridization chip for clinical diagnosis of genomic imbalance. Clin Chem 2007; 53:2051-9. [PMID: 17901113 DOI: 10.1373/clinchem.2007.090290] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Submicroscopic genomic imbalance underlies well-defined microdeletion and microduplication syndromes and contributes to general developmental disorders such as mental retardation and autism. Array comparative genomic hybridization (CGH) complements routine cytogenetic methods such as karyotyping and fluorescence in situ hybridization (FISH) for the detection of genomic imbalance. Oligonucleotide arrays in particular offer advantages in ease of manufacturing, but standard arrays for single-nucleotide polymorphism genotyping or linkage analysis offer variable coverage in clinically relevant regions. We report the design and validation of a focused oligonucleotide-array CGH assay for clinical laboratory diagnosis of genomic imbalance. METHODS We selected >10 000 60-mer oligonucleotide features from Agilent's eArray probe library to interrogate all subtelomeric and pericentromeric regions and 95 additional clinically relevant regions for a total of 179 loci. Sensitivity and specificity were measured for 105 patient samples, including 51 with known genomic-imbalance events, as detected by bacterial artificial chromosome-based array CGH, FISH, or multiplex ligation-dependent probe amplification. RESULTS Focused array CGH detected all known regions of genomic imbalance in 51 validation samples with 100% concordance and an excellent signal-to-noise ratio. The mean SD among log(2) ratios of all noncontrol features without copy number alteration was 0.062 (median, 0.055). Clinical testing of another 211 samples from individuals with developmental delay, unexplained mental retardation, dysmorphic features, or multiple congenital anomalies revealed genomic imbalance in 25 samples (11.9%). CONCLUSIONS This focused oligonucleotide-array CGH assay, a flexible, robust method for clinically diagnosing genetic disorders associated with genomic imbalance, offers appreciable advantages over currently available platforms.
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Affiliation(s)
- Yiping Shen
- Department of Laboratory Medicine, Children's Hospital Boston, Boston, MA 02115, USA
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47
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Lundin C, Heidenblad M, Strombeck B, Borg A, Hovland R, Heim S, Johansson B. Tiling resolution array CGH of dic(7;9)(p11∼13;p11∼13) in B-cell precursor acute lymphoblastic leukemia reveals clustered breakpoints at 7p11.2∼12.1 and 9p13.1. Cytogenet Genome Res 2007; 118:13-8. [PMID: 17901695 DOI: 10.1159/000106436] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2007] [Accepted: 03/26/2007] [Indexed: 11/19/2022] Open
Abstract
The dic(7;9)(p11 approximately 13;p11 approximately 13) is a recurrent chromosomal abnormality in acute lymphoblastic leukemia (ALL), mainly of B-lineage. Although more than 20 dic(7;9)-positive ALLs have been reported to date, the molecular genetic consequences of this aberration are unknown. We performed tiling resolution (32K) genome-wide array-based comparative genomic hybridization (array CGH) analysis of three cases with dic(7;9) in order to characterize the breakpoints on 7p and 9p. The analysis showed a clustering of breakpoints within 9p13.1 in all three cases and within 7p11.2 in two cases; the array CGH revealed two different breakpoints - 7p12.1 and 7p14.1 - in the remaining case. Based on these findings the abnormality should hence be designated dic(7;9)(p11.2 approximately 12.1;p13.1). Locus-specific fluorescence in situhybridization analysis of one of the cases narrowed down the 7p11.2 breakpoint to a <500-kb segment in this sub-band, a region containing three known genes. Unfortunately, lack of material precluded further molecular genetic studies, and it thus remains unknown whether the pathogenetically important outcome of the dic(7;9) is formation of a chimeric gene or loss of 7p and/or 9p material.
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Affiliation(s)
- C Lundin
- Department of Clinical Genetics, Lund University Hospital, Lund, Sweden.
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48
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Osoegawa K, Vessere GM, Utami KH, Mansilla MA, Johnson MK, Riley BM, L'Heureux J, Pfundt R, Staaf J, van der Vliet WA, Lidral AC, Schoenmakers EFPM, Borg A, Schutte BC, Lammer EJ, Murray JC, de Jong PJ. Identification of novel candidate genes associated with cleft lip and palate using array comparative genomic hybridisation. J Med Genet 2007; 45:81-6. [PMID: 17873121 PMCID: PMC3732463 DOI: 10.1136/jmg.2007.052191] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
AIM AND METHOD We analysed DNA samples isolated from individuals born with cleft lip and cleft palate to identify deletions and duplications of candidate gene loci using array comparative genomic hybridisation (array-CGH). RESULTS Of 83 syndromic cases analysed we identified one subject with a previously unknown 2.7 Mb deletion at 22q11.21 coinciding with the DiGeorge syndrome region. Eighteen of the syndromic cases had clinical features of Van der Woude syndrome and deletions were identified in five of these, all of which encompassed the interferon regulatory factor 6 (IRF6) gene. In a series of 104 non-syndromic cases we found one subject with a 3.2 Mb deletion at chromosome 6q25.1-25.2 and another with a 2.2 Mb deletion at 10q26.11-26.13. Analyses of parental DNA demonstrated that the two deletion cases at 22q11.21 and 6q25.1-25.2 were de novo, while the deletion of 10q26.11-26.13 was inherited from the mother, who also has a cleft lip. These deletions appear likely to be causally associated with the phenotypes of the subjects. Estrogen receptor 1 (ESR1) and fibroblast growth factor receptor 2 (FGFR2) genes from the 6q25.1-25.2 and 10q26.11-26.13, respectively, were identified as likely causative genes using a gene prioritization software. CONCLUSION We have shown that array-CGH analysis of DNA samples derived from cleft lip and palate subjects is an efficient and productive method for identifying candidate chromosomal loci and genes, complementing traditional genetic mapping strategies.
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Affiliation(s)
- K Osoegawa
- Center for Genetics, Children's Hospital Oakland Research Institute (CHORI), 5700 Martin Luther King Jr. Way Oakland, CA 94609, USA.
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Zahir F, Friedman JM. The impact of array genomic hybridization on mental retardation research: a review of current technologies and their clinical utility. Clin Genet 2007; 72:271-87. [PMID: 17850622 DOI: 10.1111/j.1399-0004.2007.00847.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Our understanding of the causes of mental retardation is benefiting greatly from whole-genome scans to detect submicroscopic pathogenic copy number variants (CNVs) that are undetectable by conventional cytogenetic analysis. The current method of choice for performing whole-genome scans for CNVs is array genomic hybridization (AGH). Several platforms are available for AGH, each with its own strengths and limitations. This review discusses considerations that are relevant to the clinical use of whole-genome AGH platforms for the diagnosis of pathogenic CNVs in children with mental retardation. Whole-genome AGH studies are a maturing technology, but their high diagnostic utility assures their increasing use in clinical genetics.
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Affiliation(s)
- F Zahir
- Department of Medical Genetics, University of British Columbia Children's and Women's Hospital, 4500 Oak Street, Vancouver, BC, Canada.
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50
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Choi YW, Bae SM, Kim YW, Lee HN, Kim YW, Park TC, Ro DY, Shin JC, Shin SJ, Seo JS, Ahn WS. Gene expression profiles in squamous cell cervical carcinoma using array-based comparative genomic hybridization analysis. Int J Gynecol Cancer 2007; 17:687-96. [PMID: 17504382 DOI: 10.1111/j.1525-1438.2007.00834.x] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Our aim was to identify novel genomic regions of interest and provide highly dynamic range information on correlation between squamous cell cervical carcinoma and its related gene expression patterns by a genome-wide array-based comparative genomic hybridization (array-CGH). We analyzed 15 cases of cervical cancer from KangNam St Mary's Hospital of the Catholic University of Korea. Microdissection assay was performed to obtain DNA samples from paraffin-embedded cervical tissues of cancer as well as of the adjacent normal tissues. The bacterial artificial chromosome (BAC) array used in this study consisted of 1440 human BACs and the space among the clones was 2.08 Mb. All the 15 cases of cervical cancer showed the differential changes of the cervical cancer-associated genetic alterations. The analysis limit of average gains and losses was 53%. A significant positive correlation was found in 8q24.3, 1p36.32, 3q27.1, 7p21.1, 11q13.1, and 3p14.2 changes through the cervical carcinogenesis. The regions of high level of gain were 1p36.33-1p36.32, 8q24.3, 16p13.3, 1p36.33, 3q27.1, and 7p21.1. And the regions of homozygous loss were 2q12.1, 22q11.21, 3p14.2, 6q24.3, 7p15.2, and 11q25. In the high level of gain regions, GSDMDC1, RECQL4, TP73, ABCF3, ALG3, HDAC9, ESRRA, and RPS6KA4 were significantly correlated with cervical cancer. The genes encoded by frequently lost clones were PTPRG, GRM7, ZDHHC3, EXOSC7, LRP1B, and NR3C2. Therefore, array-CGH analyses showed that specific genomic alterations were maintained in cervical cancer that were critical to the malignant phenotype and may give a chance to find out possible target genes present in the gained or lost clones.
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Affiliation(s)
- Y-W Choi
- Department of Anesthesiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
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