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Fry TJ, Aplan PD. A robust in vivo model for B cell precursor acute lymphoblastic leukemia. J Clin Invest 2015; 125:3427-9. [PMID: 26301807 DOI: 10.1172/jci83799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
B cell precursor acute lymphoblastic leukemia (BCP ALL) is the most common malignancy in children. While treatments have improved remarkably over the past four decades, resistant disease and late effects that result from cytotoxic chemotherapy remain serious problems for individuals with BCP ALL. Improved genetic tools have led to the discovery of numerous somatic mutations associated with BCP ALL, leading to a framework for the genetic classification of BCP ALL. In this issue of the JCI, Duque-Afonso et al. develop an accurate in vivo model for BCP ALL that recapitulates the key features of human disease, including acquired mutations in genes encoding PAX5 and components of the JAK/STAT pathway. The authors further show, as proof of principle, that this model can be used to evaluate the efficacy of drugs designed to target specific acquired mutations in patients with BCP ALL.
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Tirado CA, Shabsovich D, Kim Y, Traum P, Pullarkat S, Kallen M, Rao N. A case of B-cell acute lymphoblastic leukemia in a child with Down syndrome bearing a t(2;12)(p12;p13) involving ETV6 and biallelic IGH@ rearrangements. Biomark Res 2015. [PMID: 26203356 PMCID: PMC4509750 DOI: 10.1186/s40364-015-0036-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background Rearrangements involving ETV6 (12p13) are among the most common structural abnormalities in pediatric B-cell acute lymphoblastic leukemia (B-ALL) and involve numerous partner genes. Additionally, the t(8;14)(q11.2;q32), which can result in the placement of CEBPD (8q11.2) near the regulatory regions of IGH@ (14q32) and consequent overexpression of CEPBD, occurs at a higher frequency in individuals with Down syndrome-associated ALL (DS-ALL) compared to both the general and pediatric population. The coexistence of cytogenetically detectable ETV6 abnormalities and t(8;14)(q11.2;q32) is a rare occurrence in B-ALL and has only been reported in a single case in the literature. Findings Herein, we present a case of B-ALL in a 9-year old male with Down syndrome in which conventional cytogenetic analysis revealed two reciprocal translocations: a t(8;14)(q11.2;q32) and a t(2;12)(p12;p13). Interphase and metaphase fluorescence in situ hybridization (FISH) analysis using break apart probes confirmed the involvement of IGH@ and ETV6 in these translocations, respectively. Additionally, interphase FISH revealed a clonal subpopulation bearing biallelic IGH@ rearrangements not observed by conventional cytogenetic analysis. Conclusions To the best of our knowledge, this is the first reported case of B-ALL bearing an ETV6 translocation with a partner gene on the short arm of chromosome 2 confirmed by FISH. Additionally, it is the second reported case of t(8;14)(q11.2;q32)-ALL bearing a concomitant, cytogenetically detectable abnormality involving ETV6. This case provides insight into a novel translocation involving ETV6 as well as potentially unique and understudied mechanisms of clonal evolution in pediatric B-ALL.
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Affiliation(s)
- Carlos A Tirado
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA USA
| | - David Shabsovich
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA USA
| | - Yeun Kim
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA USA
| | - Peter Traum
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA USA
| | - Sheeja Pullarkat
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA USA
| | - Michael Kallen
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA USA
| | - Nagesh Rao
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA USA
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3
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Xiang DB, Wei B, Abraham SC, Huo L, Albarracin CT, Zhang H, Babiera G, Caudle AS, Akay CL, Rao P, Zhao YJ, Lu X, Wu Y. Molecular cytogenetic characterization of mammary neuroendocrine carcinoma. Hum Pathol 2014; 45:1951-6. [PMID: 25074542 DOI: 10.1016/j.humpath.2014.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 06/01/2014] [Accepted: 06/04/2014] [Indexed: 02/05/2023]
Abstract
Primary mammary neuroendocrine carcinoma (NEC) is an uncommon entity that accounts for 2% to 5% of breast carcinomas. Recent reports have shown that NEC of the breast is an aggressive subtype of mammary carcinoma that is distinct from invasive ductal carcinoma, not otherwise specified, and have suggested that these tumors have a poorer prognosis than invasive ductal carcinoma, not otherwise specified. In this study, we provide the first cytogenetic characterization of mammary NEC using both conventional G-banding and spectral karyotype on a group of 7 tumors. We identified clonal chromosomal aberrations in 5 (71.4%) cases, with 4 of them showing complex karyotypes. Of these, recurrent numerical aberrations included gain of chromosome 7 (n = 2) and loss of chromosome 15 (n = 2). Recurrent clonal structural chromosomal aberrations involved chromosomes 1 (n = 3), 3 (n = 2), 6q (n = 3), and 17q (n = 3). Of the 4 (57.1%) cases with complex karyotypes, 2 showed evidence of chromothripsis, a phenomenon in which tens to hundreds of genomic rearrangements occur in a one-off cellular crisis. One of these had evidence of chromothripsis involving chromosomes 1, 6, 8, and 15. The other also had evidence of chromosome 8 chromothripsis, making this a recurrent finding shared by both cases. We also found that mammary NEC shared some cytogenetic abnormalities--such as trisomy 7 and 12--with other neuroendocrine tumors in the lung and gastrointestinal tract, suggesting trisomy 7 and 12 as potential common molecular aberrations in neuroendocrine tumors. To our knowledge, this is the first report on molecular cytogenetic characterization of mammary NEC.
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Affiliation(s)
- De-Bing Xiang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030; Cancer Center, Jiangjin Central Hospital, Chongqing, China 402260
| | - Bing Wei
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030; Department of Pathology, West China Hospital, Sichuan University, Chengdu, China 610041
| | - Susan C Abraham
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Lei Huo
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Constance T Albarracin
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Hong Zhang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Gildy Babiera
- Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Abigail S Caudle
- Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Catherine L Akay
- Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Pulivarthi Rao
- Department of Pediatrics, Molecular and Cytogenetics Laboratory, Texas Children's Hospital, Houston, TX 77030
| | - Yi-Jue Zhao
- Department of Pediatrics, Molecular and Cytogenetics Laboratory, Texas Children's Hospital, Houston, TX 77030
| | - Xinyan Lu
- Department of Pediatrics, Molecular and Cytogenetics Laboratory, Texas Children's Hospital, Houston, TX 77030; Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Yun Wu
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030.
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4
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Guo B, Han X, Wu Z, Da W, Zhu H. Spectral karyotyping: an unique technique for the detection of complex genomic rearrangements in leukemia. Transl Pediatr 2014; 3:135-9. [PMID: 26835331 PMCID: PMC4729104 DOI: 10.3978/j.issn.2224-4336.2014.01.02] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Spectral karyotyping (SKY) is a novel cytogenetic technique, has been developed to unambiguously display and identify all 24 humans chromosomes at one time without a priori knowledge of any abnormalities involved. SKY can discern the aberrations that can't be detected very well by conventional banding technique and Fluorescent in situ hybridization (FISH). So SKY is hyper accurate, hypersensitive, and hyper intuitionist. We will review the elements and application of SKY in leukemia.
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Affiliation(s)
- Bo Guo
- 1 Department of Hematology, 2 Department of Hematology, General Hospital of PLA, Beijing 100853, China ; 3 Western Sydney Genomic Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, NSW, Australia
| | - Xiaoping Han
- 1 Department of Hematology, 2 Department of Hematology, General Hospital of PLA, Beijing 100853, China ; 3 Western Sydney Genomic Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, NSW, Australia
| | - Zhanhe Wu
- 1 Department of Hematology, 2 Department of Hematology, General Hospital of PLA, Beijing 100853, China ; 3 Western Sydney Genomic Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, NSW, Australia
| | - Wanming Da
- 1 Department of Hematology, 2 Department of Hematology, General Hospital of PLA, Beijing 100853, China ; 3 Western Sydney Genomic Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, NSW, Australia
| | - Hongli Zhu
- 1 Department of Hematology, 2 Department of Hematology, General Hospital of PLA, Beijing 100853, China ; 3 Western Sydney Genomic Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, NSW, Australia
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5
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Warren M, Weindel M, Ringrose J, Venable C, Reyes A, Terashima K, Rao P, Chintagumpala M, Hicks MJ, Lopez-Terrada D, Lu XY. Integrated multimodal genetic testing of Ewing sarcoma—a single-institution experience. Hum Pathol 2013; 44:2010-9. [DOI: 10.1016/j.humpath.2013.03.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 03/02/2013] [Accepted: 03/14/2013] [Indexed: 10/26/2022]
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6
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Vallespín E, Palomares Bralo M, Mori MÁ, Martín R, García-Miñaúr S, Fernández L, de Torres ML, García-Santiago F, Mansilla E, Santos F, M-Montaño VE, Crespo MC, Martín S, Martínez-Glez V, Delicado A, Lapunzina P, Nevado J. Customized high resolution CGH-array for clinical diagnosis reveals additional genomic imbalances in previous well-defined pathological samples. Am J Med Genet A 2013; 161A:1950-60. [DOI: 10.1002/ajmg.a.35960] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Accepted: 03/03/2013] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Victoria E. M-Montaño
- Section of Functional and Structural Genomics of Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ; Hospital Universitario La Paz; Madrid; Spain
| | - M. Carmen Crespo
- Section of Functional and Structural Genomics of Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ; Hospital Universitario La Paz; Madrid; Spain
| | - Sol Martín
- Section of Functional and Structural Genomics of Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ; Hospital Universitario La Paz; Madrid; Spain
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7
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De Braekeleer E, Douet-Guilbert N, Morel F, Le Bris MJ, Basinko A, De Braekeleer M. ETV6 fusion genes in hematological malignancies: a review. Leuk Res 2012; 36:945-61. [PMID: 22578774 DOI: 10.1016/j.leukres.2012.04.010] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Revised: 03/13/2012] [Accepted: 04/16/2012] [Indexed: 01/01/2023]
Abstract
Translocations involving band 12p13 are one of the most commonly observed chromosomal abnormalities in human leukemia and myelodysplastic syndrome. Their frequently result in rearrangements of the ETV6 gene. At present, 48 chromosomal bands have been identified to be involved in ETV6 translocations, insertions or inversions and 30 ETV6 partner genes have been molecularly characterized. The ETV6 protein contains two major domains, the HLH (helix-loop-helix) domain, encoded by exons 3 and 4, and the ETS domain, encoded by exons 6 through 8, with in between the internal domain encoded by exon 5. ETV6 is a strong transcriptional repressor, acting through its HLH and internal domains. Five potential mechanisms of ETV6-mediated leukemogenesis have been identified: constitutive activation of the kinase activity of the partner protein, modification of the original functions of a transcription factor, loss of function of the fusion gene, affecting ETV6 and the partner gene, activation of a proto-oncogene in the vicinity of a chromosomal translocation and dominant negative effect of the fusion protein over transcriptional repression mediated by wild-type ETV6. It is likely that ETV6 is frequently involved in leukemogenesis because of the large number of partners with which it can rearrange and the several pathogenic mechanisms by which it can lead to cell transformation.
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Affiliation(s)
- Etienne De Braekeleer
- Laboratoire d'Histologie, Embryologie et Cytogénétique, Université de Brest, Brest, France
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8
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Stanchescu R, Betts DR, Rechavi G, Amariglio N, Trakhtenbrot L. Involvement of der(12)t(12;21)(p13;q22) and as well as additional rearrangements of chromosome 12 homolog in ETV6/RUNX1-positive acute lymphoblastic leukemia. ACTA ACUST UNITED AC 2009; 190:26-32. [PMID: 19264230 DOI: 10.1016/j.cancergencyto.2008.12.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2008] [Accepted: 11/20/2008] [Indexed: 12/18/2022]
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9
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Clinical features and outcome of MLL gene rearranged acute lymphoblastic leukemia in infants with additional chromosomal abnormalities other than 11q23 translocation. Leuk Res 2008; 32:1523-9. [DOI: 10.1016/j.leukres.2008.03.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2008] [Revised: 03/03/2008] [Accepted: 03/19/2008] [Indexed: 11/23/2022]
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10
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Betts DR, Stanchescu R, Niggli FK, Cohen N, Rechavi G, Amariglio N, Trakhtenbrot L. SKY reveals a high frequency of unbalanced translocations involving chromosome 6 in t(12;21)-positive acute lymphoblastic leukemia. Leuk Res 2008; 32:39-43. [PMID: 17418891 DOI: 10.1016/j.leukres.2007.03.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2007] [Revised: 01/17/2007] [Accepted: 03/02/2007] [Indexed: 11/21/2022]
Abstract
The G-band cryptic t(12;21)(p13;q22) is the most common chromosomal rearrangement in childhood acute lymphoblastic leukemia (ALL). To investigate the nature of additional chromosomal events in this group of patients spectral karyotyping (SKY) following G-banding analysis was performed in 14 cases. From these cases six showed structural aberrations of chromosome 6, including both simple deletions and unbalanced translocations, and involved both q (n=4) and p (n=3) arms. The results show that rearrangements of 6p are also non-random events t(12;21)-positive ALL. This study illustrates the value of a combined SKY and G-banding approach in identifying novel karyotypic events in childhood ALL.
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Affiliation(s)
- David R Betts
- Department of Oncology, University Children's Hospital, Steinwiesstrasse 75, CH-8032 Zurich, Switzerland.
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11
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Lilljebjörn H, Heidenblad M, Nilsson B, Lassen C, Horvat A, Heldrup J, Behrendtz M, Johansson B, Andersson A, Fioretos T. Combined high-resolution array-based comparative genomic hybridization and expression profiling of ETV6/RUNX1-positive acute lymphoblastic leukemias reveal a high incidence of cryptic Xq duplications and identify several putative target genes within the commonly gained region. Leukemia 2007; 21:2137-44. [PMID: 17690704 DOI: 10.1038/sj.leu.2404879] [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] [Received: 03/13/2007] [Revised: 06/08/2007] [Accepted: 06/28/2007] [Indexed: 11/08/2022]
Abstract
Seventeen ETV6/RUNX1-positive pediatric acute lymphoblastic leukemias were investigated by high-resolution array-based comparative genomic hybridization (array CGH), gene expression profiling and fluorescence in situ hybridization. Comparing the array CGH and gene expression patterns revealed that genomic imbalances conferred a great impact on the expression of genes in the affected regions. The array CGH analyses identified a high frequency of cytogenetically cryptic genetic changes, for example, del(9p) and del(12p). Interestingly, a duplication of Xq material, varying between 30 and 60 Mb in size, was found in 6 of 11 males (55%), but not in females. Genes on Xq were found to have a high expression level in cases with dup(Xq); a similar overexpression was confirmed in t(12;21)-positive cases in an external gene expression data set. By studying the expression profile and the proposed function of genes in the minimally gained region, several candidate target genes (SPANXB, HMGB3, FAM50A, HTATSF1 and RAP2C) were identified. Among them, the testis-specific SPANXB gene was the only one showing a high and uniform overexpression, irrespective of gender and presence of Xq duplication, suggesting that this gene plays an important pathogenetic role in t(12;21)-positive leukemia.
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Affiliation(s)
- H Lilljebjörn
- Department of Clinical Genetics, Lund University Hospital, Lund, Sweden.
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12
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Lu X, Shaw CA, Patel A, Li J, Cooper ML, Wells WR, Sullivan CM, Sahoo T, Yatsenko SA, Bacino CA, Stankiewicz P, Ou Z, Chinault AC, Beaudet AL, Lupski JR, Cheung SW, Ward PA. Clinical implementation of chromosomal microarray analysis: summary of 2513 postnatal cases. PLoS One 2007; 2:e327. [PMID: 17389918 PMCID: PMC1828620 DOI: 10.1371/journal.pone.0000327] [Citation(s) in RCA: 178] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2006] [Accepted: 03/05/2007] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Array Comparative Genomic Hybridization (a-CGH) is a powerful molecular cytogenetic tool to detect genomic imbalances and study disease mechanism and pathogenesis. We report our experience with the clinical implementation of this high resolution human genome analysis, referred to as Chromosomal Microarray Analysis (CMA). METHODS AND FINDINGS CMA was performed clinically on 2513 postnatal samples from patients referred with a variety of clinical phenotypes. The initial 775 samples were studied using CMA array version 4 and the remaining 1738 samples were analyzed with CMA version 5 containing expanded genomic coverage. Overall, CMA identified clinically relevant genomic imbalances in 8.5% of patients: 7.6% using V4 and 8.9% using V5. Among 117 cases referred for additional investigation of a known cytogenetically detectable rearrangement, CMA identified the majority (92.5%) of the genomic imbalances. Importantly, abnormal CMA findings were observed in 5.2% of patients (98/1872) with normal karyotypes/FISH results, and V5, with expanded genomic coverage, enabled a higher detection rate in this category than V4. For cases without cytogenetic results available, 8.0% (42/524) abnormal CMA results were detected; again, V5 demonstrated an increased ability to detect abnormality. Improved diagnostic potential of CMA is illustrated by 90 cases identified with 51 cryptic microdeletions and 39 predicted apparent reciprocal microduplications in 13 specific chromosomal regions associated with 11 known genomic disorders. In addition, CMA identified copy number variations (CNVs) of uncertain significance in 262 probands; however, parental studies usually facilitated clinical interpretation. Of these, 217 were interpreted as familial variants and 11 were determined to be de novo; the remaining 34 await parental studies to resolve the clinical significance. CONCLUSIONS This large set of clinical results demonstrates the significantly improved sensitivity of CMA for the detection of clinically relevant genomic imbalances and highlights the need for comprehensive genetic counseling to facilitate accurate clinical correlation and interpretation.
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Affiliation(s)
- Xinyan Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Chad A. Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jiangzhen Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - M. Lance Cooper
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - William R. Wells
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Cathy M. Sullivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Trilochan Sahoo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Svetlana A. Yatsenko
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Carlos A. Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Zhishu Ou
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - A. Craig Chinault
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Arthur L. Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sau W. Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Patricia A. Ward
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
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13
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Schrock E, Zschieschang P, O'Brien P, Helmrich A, Hardt T, Matthaei A, Stout-Weider K. Spectral karyotyping of human, mouse, rat and ape chromosomes--applications for genetic diagnostics and research. Cytogenet Genome Res 2006; 114:199-221. [PMID: 16954656 DOI: 10.1159/000094203] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2006] [Accepted: 05/19/2006] [Indexed: 01/30/2023] Open
Abstract
Spectral karyotyping (SKY) is a widely used methodology to identify genetic aberrations. Multicolor fluorescence in situ hybridization using chromosome painting probes in individual colors for all metaphase chromosomes at once is combined with a unique spectral measurement and analysis system to automatically classify normal and aberrant chromosomes. Based on countless studies and investigations in many laboratories worldwide, numerous new chromosome translocations and other aberrations have been identified in clinical and tumor cytogenetics. Thus, gene identification studies have been facilitated resulting in the dissection of tumor development and progression. For example, different translocation partners of the TEL/ETV6 transcription factor that is specially required for hematopoiesis within the bone marrow were identified. Also, the correct classification of complex karyotypes of solid tumors supports the prognostication of cancer patients. Important accomplishments for patients with genetic diseases, leukemias and lymphomas, mesenchymal tumors and solid cancers are summarized and exemplified. Furthermore, studies of disease mechanisms such as centromeric DNA breakage, DNA double strand break repair, telomere shortening and radiation-induced neoplastic transformation have been accompanied by SKY analyses. Besides the hybridization of human chromosomes, mouse karyotyping has also contributed to the comprehensive characterization of mouse models of human disease and for gene therapy studies.
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Affiliation(s)
- E Schrock
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
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14
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Preiss BS, Kerndrup GB, Pedersen RK, Hasle H, Pallisgaard N. Contribution of multiparameter genetic analysis to the detection of genetic alterations in hematologic neoplasia. An evaluation of combining G-band analysis, spectral karyotyping, and multiplex reverse-transcription polymerase chain reaction (multiplex RT-PCR). ACTA ACUST UNITED AC 2006; 165:1-8. [PMID: 16490591 DOI: 10.1016/j.cancergencyto.2005.07.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2005] [Revised: 07/20/2005] [Accepted: 07/26/2005] [Indexed: 01/25/2023]
Abstract
We investigated 150 acute myeloid leukemia (AML) patients and 48 acute lymphoblastic leukemia (ALL) patients by multiplex RT-PCR to 7evaluate the adjuvant diagnostic effect, vis-à-vis G-banding and spectral karyotyping (SKY), and the potentials of this method for providing means for monitoring residual disease by real-time quantitative RT-PCR. An abnormal G-banded karyotype was found in 57% of AML and 68% of ALL cases. Ninety-six patients were investigated by SKY in parallel which extended or confirmed the G-banding finding in 94/96 cases. In patients with an abnormal G-banded karyotype, classification of chromosomes involved in structural aberrations by SKY was possible in 98% of the cases and SKY extended the G-banded karyotype in 34% of cases. In 32 cases, an mRNA hybrid was detected by PCR. These cases constitute 16% of the cases investigated at diagnosis (AML: 11% and ALL: 31%). In 13 of these cases, we detected an mRNA hybrid the equivalent of which was not found by G-banding or SKY (AML: 4% and ALL: 13%). By including multiplex RT-PCR, we were able to detect abnormalities in 62% of the investigated patients as opposed to 59% by G-banding. Genetic techniques complement each other and selection of relevant and targeted primer kits for the multiplex RT-PCR assay is recommended.
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Affiliation(s)
- Birgitte S Preiss
- Institute of Pathology-Laboratory of Molecular Pathology and Chromosome Laboratory, Odense University Hospital, Odense C. DK-5000, Denmark
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15
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Abstract
This review will focus on the molecular biology of lymphoproliferative disorders with emphasis on lymphomas. The spectrum of known recurrent gene rearrangements found in lymphomas will be outlined and their relevance to diagnosis and subclassification of disease will be discussed. Finally, a survey of the current trends in gene expression profiling of lymphomas by microarray technology will be presented with reference to implications for diagnosis, classification, prognosis and treatment.
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Affiliation(s)
- Alberto Catalano
- Institute of Haematology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia.
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16
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MacKinnon RN, Zordan A, Campbell LJ. Recurrent duplication of Xq27∼qter in hematological malignancies revealed by multicolor fluorescence in situ hybridization and multicolor banding. ACTA ACUST UNITED AC 2005; 161:125-9. [PMID: 16102582 DOI: 10.1016/j.cancergencyto.2005.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2004] [Revised: 01/28/2005] [Accepted: 02/07/2005] [Indexed: 01/18/2023]
Abstract
Multicolor fluorescence in situ hybridization (M-FISH) experiments were performed to determine the composition of abnormal complex karyotypes in 15 cases of hematological malignancy. Four cases were found to have unsuspected unbalanced X chromosome translocations, which resulted in the presence of extra X chromosome material. We determined the identity of the duplicated chromosome regions using the multicolor banding (mBAND) technique. Xq27-qter was duplicated in three of the four male cases with an X chromosome abnormality (i.e., in one third of male cases and one fifth of all cases). These preliminary results may point to the existence of a recurrent chromosome abnormality, either translocation at a specific Xq27 locus or duplication of Xq27-qter.
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Affiliation(s)
- Ruth N MacKinnon
- University of Melbourne Department of Medicine, St Vincent's Hospital, Melbourne, Victoria, Australia.
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Kearney L, Horsley SW. Molecular cytogenetics in haematological malignancy: current technology and future prospects. Chromosoma 2005; 114:286-94. [PMID: 16003502 DOI: 10.1007/s00412-005-0002-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2005] [Revised: 04/25/2005] [Accepted: 04/25/2005] [Indexed: 01/22/2023]
Abstract
Cytogenetics has played a pivotal role in haematological malignancy, both as an aid to diagnosis and in identifying recurrent chromosomal rearrangements, an essential prerequisite to identifying genes involved in leukaemia and lymphoma pathogenesis. In the late 1980s, a series of technologies based around fluorescence in situ hybridisation (FISH) revolutionised the field. Interphase FISH, multiplex-FISH (M-FISH, SKY) and comparative genomic hybridisation (CGH) have emerged as the most significant of these. More recently, microarray technologies have come to prominence. In the acute leukaemias, the finding of characteristic gene expression signatures corresponding to biological subgroups has heralded gene expression profiling as a possible future alternative to current cytogenetic and morphological methods for diagnosis. In the lymphomas, high-resolution array CGH has successfully identified new regions of deletion and amplification, providing the prospect of disease-specific arrays.
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Affiliation(s)
- Lyndal Kearney
- Section of Haemato-Oncology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK.
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Martineau M, Jalali GR, Barber KE, Broadfield ZJ, Cheung KL, Lilleyman J, Moorman AV, Richards S, Robinson HM, Ross F, Harrison CJ. ETV6/RUNX1 fusion at diagnosis and relapse: some prognostic indications. Genes Chromosomes Cancer 2005; 43:54-71. [PMID: 15704129 DOI: 10.1002/gcc.20158] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
This study was undertaken in order to compare the interphase and metaphase cytogenetics of 28 patients with ETV6/RUNX1 positive acute lymphoblastic leukemia, at diagnosis and relapse. The median time to relapse was 26 months. The significant fusion positive population heterogeneity revealed at interphase by a commercial probe for ETV6/RUNX1 fusion has not been described before. Six diagnostic samples had a single abnormal population; others had up to five each, which differed in the numbers of RUNX1 signals, and in the retention or loss of the second ETV6 signal. In contrast, the number of fusion signals was more constant. At relapse, there were fewer populations; the largest or unique clone was sometimes a re-emergence of a minor, diagnostic one, with a retained copy of ETV6 and the most RUNX1 signals. Abnormal, fusion negative clones were identified in bone marrow samples at extra-medullary relapse. Variant three or four-way translocations, which involved chromosomes 12 and 21, were prominent among the complex rearrangements revealed by metaphase FISH. The frequency of their occurrence at diagnosis and reappearance at relapse, sometimes accompanied by minor clonal evolution, was another new observation. Other recurrent cytogenetic features included a second copy of the fusion signal in six cases, partial duplication of the long arm of the X chromosome in two cases, and trisomy 10 in three cases. In comparing our data with previously reported cases, a picture is beginning to emerge of certain diagnostic features, which may provide circumstantial evidence of an increased risk of relapse.
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Affiliation(s)
- Mary Martineau
- LRF Cytogenetics Group, Cancer Sciences Division, University of Southampton, United Kingdom.
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Paulsson K, Mörse H, Fioretos T, Behrendtz M, Strömbeck B, Johansson B. Evidence for a single-step mechanism in the origin of hyperdiploid childhood acute lymphoblastic leukemia. Genes Chromosomes Cancer 2005; 44:113-22. [PMID: 15942938 DOI: 10.1002/gcc.20222] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
High hyperdiploidy (>50 chromosomes) in childhood acute lymphoblastic leukemia (ALL) is characterized by nonrandom multiple trisomies and tetrasomies involving in particular chromosomes X, 4, 6, 8, 10, 14, 17, 18, and 21. This characteristic karyotypic pattern, the most common in pediatric ALL, may arise via a tetraploid state with subsequent loss of chromosomes, by sequential gains of chromosomes in consecutive cell divisions, or by simultaneous gain of chromosomes in a single mitosis. These alternatives may be distinguished by investigation of the allelic ratios of loci on the tetrasomic and disomic chromosomes. Previous studies of tetrasomy 21 and of the occurrence of uniparental disomies (UPDs) have suggested that the most likely mechanism is simultaneous gain. However, the other pathways have not been definitely excluded because complete analyses of all disomies and tetrasomies have never been performed. In the present study, we investigated 27 hyperdiploid ALLs by using 58 polymorphic microsatellite markers mapped to 23 of the 24 human chromosomes. Twenty-six tetrasomies were analyzed (involving chromosomes X, 8, 10, 14, 18, and 21), and the frequency of UPDs was determined in 10 cases. In total, 200 chromosomes were studied. Equal allele dosage was observed in 24 of 26 tetrasomies, and only 7 UPDs were found. These data strongly suggest that hyperdiploidy in childhood ALL generally arises by a simultaneous gain of all additional chromosomes in a single abnormal mitosis.
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Affiliation(s)
- Kajsa Paulsson
- Department of Clinical Genetics, Lund University Hospital, Lund, Sweden.
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Abstract
Cytogenetic analyses in acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL) have revealed a great number of non-random chromosome abnormalities. In many instances, molecular studies of these abnormalities identified specific genes implicated in the process of leukemogenesis. The more common chromosome aberrations have been associated with specific laboratory and clinical characteristics, and are now being used as diagnostic and prognostic markers guiding the clinician in selecting the most effective therapies. Specific chromosome aberrations and their molecular counterparts have been included in the World Health Organization classification of hematologic malignancies, and together with morphology, immunophenotype and clinical features are used to define distinct disease entities. However, the prognostic importance of less frequent recurrent aberrations in AML and ALL, both primary and secondary, is still to be determined. This review summarizes current views on clinical relevance of major cytogenetic findings in adult AML and ALL.
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Affiliation(s)
- Krzysztof Mrózek
- Division of Hematology and Oncology, The Comprehensive Cancer Center, The Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Room 1248B, The Ohio State University, Columbus, OH 43210-1228, USA.
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Huth U, Wieschollek A, Garini Y, Schubert R, Peschka-Süss R. Fourier transformed spectral bio-imaging for studying the intracellular fate of liposomes. Cytometry A 2004; 57:10-21. [PMID: 14699601 DOI: 10.1002/cyto.a.10105] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
BACKGROUND To improve the efficiency of liposomal drug targeting systems, it is necessary to understand the mechanism of liposome uptake by the cell and to follow the intracellular fate of internalized liposomes and their contents. METHODS We applied multiple-color fluorescence imaging spectroscopy, using a combination of five fluorescent dyes with a significant spectral overlap. pH-sensitive liposomes were labeled with the hydrophilic dye fluorescein isothiocyanate-dextran (FITC-dextran) or the lipophilic membrane marker rhodamine-B-phosphoethanolamine (Rh-PE) and incubated with COS-7 cells. Further, the cells were stained with specific markers: the cell membrane was fluorescently labeled with Vybrant DiO, lysosomes were stained with LysoTracker Red, and 4',6 diamidino-2-phenylindole dihydrochloride was used for counterstaining the nucleus. RESULTS All five dyes were used simultaneously and were spectrally distinguished by the system. FITC-dextran-labeled liposomes showed a distribution pattern different from identically composed liposomes labeled with Rh-PE: the highly lipophilic Rh-PE was colocalized with the lysosomotropic dye LysoTracker Red, whereas liposomal FITC-dextran was not accompanied by LysoTracker Red in all cases. CONCLUSIONS (a) Spectral (bio-) imaging is a powerful method for studying the intracellular fate of liposomal compounds. (b) We assume that the liposome membrane marker Rh-PE influences the uptake of particles due to its surface-modifying properties. We propose that this head-group-labeled phospholipid acts as a ligand for cellular receptors and triggers receptor-mediated (clathrin-dependent) endocytosis.
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Affiliation(s)
- Ulrich Huth
- Department of Pharmaceutical Technology, Albert-Ludwigs University, Freiburg, Germany.
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Cowell JK, Matsui SI, Wang YD, LaDuca J, Conroy J, McQuaid D, Nowak NJ. Application of bacterial artificial chromosome array-based comparative genomic hybridization and spectral karyotyping to the analysis of glioblastoma multiforme. ACTA ACUST UNITED AC 2004; 151:36-51. [PMID: 15120909 DOI: 10.1016/j.cancergencyto.2003.09.012] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2003] [Accepted: 09/10/2003] [Indexed: 01/08/2023]
Abstract
Identification of genetic losses and gains is valuable in analysis of brain tumors. Locus-by-locus analyses have revealed correlations between prognosis and response to chemotherapy and loss or gain of specific genes and loci. These approaches are labor intensive and do not provide a global view of the genetic changes within the tumor cells. Bacterial artificial chromosome (BAC) arrays, which cover the genome with an average resolution of less than 1 MbP, allow defining the sum total of these genetic changes in a single comparative genomic hybridization (CGH) experiment. These changes are directly overlaid on the human genome sequence, thus providing the extent of the amplification or deletion, reflected by a megabase position, and gene content of the abnormal region. Although this array-based CGH approach (CGHa) seems to detect the extent of the genetic changes in tumors reliably, it has not been robustly tested. We compared genetic changes in four newly derived, early-passage glioma cell lines, using spectral karyotyping (SKY) and CGHa. Chromosome changes seen in cell lines under SKY analysis were also detected with CGHa. In addition, CGHa detected cryptic genetic gains and losses and resolved the nature of subtle marker chromosomes that could not be resolved with SKY, thus providing distinct advantages over previous technologies. There was remarkable general concordance between the CGHa results comparing the cell lines to the original tumor, except that the magnitude of the changes seen in the tumor sample was generally suppressed compared with the cell lines, a consequence of normal cells contaminating the tumor sample. CGHa revealed changes in cell lines that were not present in the original tumors and vice versa, even when analyzed at the earliest passage possible, which highlights the adaptation of the cells to in vitro culture. CGHa proved to be highly accurate and efficient for identifying genetic changes in tumor cells. This approach can accurately identify subtle, novel genetic abnormalities in tumors directly linked to the human genome sequence. CGHa far surpasses the resolution and information provided by conventional metaphase CGH, without relying on in vitro culture of tumors for metaphase spreads.
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Affiliation(s)
- John K Cowell
- Department of Cancer Genetics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263 USA.
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Abstract
Robertsonian translocations are the most common constitutional structural abnormalities but are rarely reported as acquired aberrations in hematologic malignancies. The nonhomologous acrocentric rearrangements are designated as Robertsonian translocations, whereas the homologous acrocentric rearrangements are referred to as isochromosomes. Robertsonian rearrangements have the highest mutation rates of structural chromosome rearrangements based on surveys of newborns and spontaneous abortions. It would be expected that Robertsonian recombinations would be more common than suggested by the literature. A survey of the cytogenetics database from a single institution found 17 patients with acquired Robertsonian rearrangement and hematologic malignancies. This is combined with data from the literature for a total of 237 patients. All of the possible types of Robertsonian rearrangements have been reported in hematologic malignancies, with the i(13q), i(14q), and i(21q) accounting for nearly 60%. Complex karyotypic changes are seen in the majority of cases, corresponding with disease evolution. These karyotypes consistently show loss of chromosomes 5 and/or 7 in the myelocytic disorders, nonacrocentric isochromosomes, and centromeric breakage and reunion. However, nearly 25% of the acquired rearrangements were found as the sole abnormality or in addition to an established cytogenetic aberration. Most of these were the i(14q) with the myelodysplasia subtypes refractory anemia and chronic myelomonocytic leukemia.
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Affiliation(s)
- Jeanna Welborn
- Department of Internal Medicine and Pathology, University of California at Davis Medical Center Cancer Center, Room 3017, 4501 X Street, Sacramento, CA 95817 USA.
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