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Rush DM, Luthra R, Hu P, Bueso-Ramos C, Nimmakayalu M, Tang Z, Patel K, Lucas FS, Ozenci J, Puthooran S, Medeiros LJ, Barkoh B, Raju S, Ahmed N, Kanagal-Shamanna R. 49. Clinical validation of Infinium CytoSNP-850K SNP-Array for routine copy number profiling of hematological malignancies. Cancer Genet 2022. [DOI: 10.1016/j.cancergen.2021.05.063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Yang H, Garcia-Manero G, Sasaki K, Montalban-Bravo G, Tang Z, Wei Y, Kadia T, Chien K, Rush D, Nguyen H, Kalia A, Nimmakayalu M, Bueso-Ramos C, Kantarjian H, Medeiros LJ, Luthra R, Kanagal-Shamanna R. High-resolution structural variant profiling of myelodysplastic syndromes by optical genome mapping uncovers cryptic aberrations of prognostic and therapeutic significance. Leukemia 2022; 36:2306-2316. [PMID: 35915143 PMCID: PMC9417987 DOI: 10.1038/s41375-022-01652-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 12/17/2022]
Abstract
Chromosome banding analysis (CBA) remains the standard-of-care for structural variant (SV) assessment in MDS. Optical genome mapping (OGM) is a novel, non-sequencing-based technique for high-resolution genome-wide SV profiling (SVP). We explored the clinical value of SVP by OGM in 101 consecutive, newly diagnosed MDS patients from a single-center, who underwent standard-of-care cytogenetic and targeted NGS studies. OGM detected 383 clinically significant, recurrent and novel SVs. Of these, 224 (51%) SVs, seen across 34% of patients, were cryptic by CBA (included rearrangements involving MECOM, NUP98::PRRX2, KMT2A partial tandem duplications among others). SVP decreased the proportion of normal karyotype by 16%, identified complex genomes (17%), chromothripsis (6%) and generated informative results in both patients with insufficient metaphases. Precise gene/exon-level mapping allowed assessment of clinically relevant biomarkers (TP53 allele status, KMT2A-PTD) without additional testing. SV data was complementary to NGS. When applied in retrospect, OGM results changed the comprehensive cytogenetic scoring system (CCSS) and R-IPSS risk-groups in 21% and 17% patients respectively with an improved prediction of prognosis. By multivariate analysis, CCSS by OGM only (not CBA), TP53 mutation and BM blasts independently predicted survival. This is the first and largest study reporting the value of combined SVP and NGS for MDS prognostication.
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Affiliation(s)
- Hui Yang
- grid.240145.60000 0001 2291 4776Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - Guillermo Garcia-Manero
- grid.240145.60000 0001 2291 4776Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - Koji Sasaki
- grid.240145.60000 0001 2291 4776Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - Guillermo Montalban-Bravo
- grid.240145.60000 0001 2291 4776Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - Zhenya Tang
- grid.240145.60000 0001 2291 4776Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - Yue Wei
- grid.240145.60000 0001 2291 4776Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - Tapan Kadia
- grid.240145.60000 0001 2291 4776Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - Kelly Chien
- grid.240145.60000 0001 2291 4776Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - Diana Rush
- grid.240145.60000 0001 2291 4776School of Health Professions, The University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - Ha Nguyen
- grid.240145.60000 0001 2291 4776School of Health Professions, The University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - Awdesh Kalia
- grid.240145.60000 0001 2291 4776School of Health Professions, The University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - Manjunath Nimmakayalu
- grid.240145.60000 0001 2291 4776School of Health Professions, The University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - Carlos Bueso-Ramos
- grid.240145.60000 0001 2291 4776Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - Hagop Kantarjian
- grid.240145.60000 0001 2291 4776Department of Leukemia, The University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - L. Jeffrey Medeiros
- grid.240145.60000 0001 2291 4776Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - Rajyalakshmi Luthra
- grid.240145.60000 0001 2291 4776Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA.
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Song J, Yu A, Munoz D, Han S, Nimmakayalu M, Hu PC, Dong J. Impact of Using Median vs. Mean in Calculating ERBB2 FISH Results in Breast Cancer. Cancer Med J 2021; 4:87-96. [PMID: 34095900 PMCID: PMC8171267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
INTRODUCTION Erb-b2 receptor tyrosine kinase 2 (ERBB2) testing is used to measure the status of ERBB2 gene expression and DNA amplification. Test results have been reported with a discrepancy as high as 20%. The purpose of this study was to improve ERBB2 fluorescence in situ hybridization (FISH) sensitivity by evaluating results generated by median as well as mean calculations. METHODS We retrospectively identified breast cancer cases at our institution in which ERBB2 FISH testing was performed in-house from June 2018 to May 2020. FISH results were classified using the 2018 American Society of Clinical Oncology/College of American Pathologists guidelines: groups 1 and 5 are FISH positive and negative, respectively, and groups 2-4 are equivocal requiring additional work-up. FISH counting sheets were collected and regrouped by median ERBB2 copy number counts and median ERBB2/CEP17 ratio and compared with the mean ERBB2 and mean ERBB2/CEP17 ratio. Intra-tumor genetic heterogeneity and CEP17 copy number gain (CEP17 ≥3) were assessed to see if they affect the discrepancy between median and mean groups. RESULTS Seventy-two breast cancer cases were collected and evaluated. Eleven cases (11 of 72 [15%]) had discrepant grouping by mean and median calculations. A significant number of discrepancies were found for CEP17 copy number gain (p = 0.027) but not for ERBB2 (p = 0.411), the ERBB2/CEP17 ratio (p = 0.445), FISH results (p = 0.194), or genetic heterogeneity (p = 0.465). Among the four cases regrouped to median group 1, 2 were from mean group 3 and underwent anti-ERBB2 targeted therapy and 2 were from mean groups 4 and 5 may have benefitted from targeted therapy with more than 30% amplified cells. The median may be better to reflect the monosomy subclone within tumor tissues for the case 387 moved from mean group 5 to median group 2. The 6 cases moved from mean group 5 to median group 4 with CEP17 copy number gain may have had a poor prognosis based on other study result. CONCLUSION Including the median calculation may increase ERBB2 sensitivity and identification of CEP17 copy number gain. Further clinical studies are necessary to examine the outcome of including median in calculating ERBB2/CEP17 values.
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Affiliation(s)
- Jie Song
- Program in Diagnostic Genetics and Genomics, School of Health Professions, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Alexander Yu
- School of Medicine, The University of Texas Medical Branch, Galveston, Texas, USA
| | - Diana Munoz
- Health Information Management, Houston Methodist, Houston, Texas, USA
| | - Song Han
- Department of Pathology, The University of Texas Medical Branch, Galveston, Texas, USA
| | - Manjunath Nimmakayalu
- Program in Diagnostic Genetics and Genomics, School of Health Professions, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Peter C Hu
- Program in Diagnostic Genetics and Genomics, School of Health Professions, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jianli Dong
- Department of Pathology, The University of Texas Medical Branch, Galveston, Texas, USA
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Abou Khouzam R, Rao SP, Venkatesh GH, Zeinelabdin NA, Buart S, Meylan M, Nimmakayalu M, Terry S, Chouaib S. An Eight-Gene Hypoxia Signature Predicts Survival in Pancreatic Cancer and Is Associated With an Immunosuppressed Tumor Microenvironment. Front Immunol 2021; 12:680435. [PMID: 34093582 PMCID: PMC8173254 DOI: 10.3389/fimmu.2021.680435] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 05/04/2021] [Indexed: 12/18/2022] Open
Abstract
Intratumoral hypoxia is a widely established element of the pancreatic tumor microenvironment (TME) promoting immune escape, tumor invasion, and progression, while contributing to treatment resistance and poor survival. Despite this critical role, hypoxia is underrepresented in molecular signatures of pancreatic ductal adenocarcinoma (PDA) and concurrent investigations into the hypoxia-immune status are lacking. In this work a literature-based approach was applied to derive an eight-gene hypoxia signature that was validated in fourteen cancer cell lines and in a cohort of PDA. The eight-gene hypoxia signature was significantly associated with overall survival in two distinct PDA datasets and showed independent prognostic value in multivariate analysis. Comparative analysis of tumors according to their hypoxia score (high versus low) determined that tumors with high hypoxia were significantly less enriched in cytotoxic T-cells, and cytolytic activity. In addition, they had lower expression of cytokines and tumor inflammatory markers, pointing to the signature’s ability to discern an immune “cold”, hypoxic TME. Combining the signature with an immune metric highlighted a worse survival probability in patients with high hypoxia and low immune reactivity, indicating that this approach could further refine survival estimates. Hypoxia as determined by our signature, was significantly associated with certain immune checkpoint inhibitors (ICI) biomarkers, suggesting that the signature reflects an aspect of the TME that is worth pursuing in future clinical trials. This is the first work of its kind in PDA, and our findings on the hypoxia-immune tumor contexture are not only relevant for ICI but could also guide combinatorial hypoxia-mediated therapeutic strategies in this cancer type.
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Affiliation(s)
- Raefa Abou Khouzam
- Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman, United Arab Emirates
| | - Shyama Prasad Rao
- Bioinformatics Division, Yenepoya Research Center, Yenepoya University, Mangalore, India
| | - Goutham Hassan Venkatesh
- Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman, United Arab Emirates
| | - Nagwa Ahmed Zeinelabdin
- Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman, United Arab Emirates
| | - Stephanie Buart
- INSERM UMR 1186, Integrative Tumor Immunology and Cancer Immunotherapy, Gustave Roussy, EPHE, Faculty De médecine Univ. Paris-Sud, University Paris-Saclay, Villejuif, France
| | - Maxime Meylan
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris, F-75006, Paris, France
| | - Manjunath Nimmakayalu
- Graduate Program in Diagnostic Genetics and Genomics, School of Health Professions, MD Anderson Cancer Center, The University of Texas, Houston, TX, United States
| | - Stéphane Terry
- INSERM UMR 1186, Integrative Tumor Immunology and Cancer Immunotherapy, Gustave Roussy, EPHE, Faculty De médecine Univ. Paris-Sud, University Paris-Saclay, Villejuif, France
| | - Salem Chouaib
- Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman, United Arab Emirates.,INSERM UMR 1186, Integrative Tumor Immunology and Cancer Immunotherapy, Gustave Roussy, EPHE, Faculty De médecine Univ. Paris-Sud, University Paris-Saclay, Villejuif, France
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Akdemir KC, Le VT, Kim JM, Killcoyne S, King DA, Lin YP, Tian Y, Inoue A, Amin SB, Robinson FS, Nimmakayalu M, Herrera RE, Lynn EJ, Chan K, Seth S, Klimczak LJ, Gerstung M, Gordenin DA, O'Brien J, Li L, Deribe YL, Verhaak RG, Campbell PJ, Fitzgerald R, Morrison AJ, Dixon JR, Andrew Futreal P. Somatic mutation distributions in cancer genomes vary with three-dimensional chromatin structure. Nat Genet 2020; 52:1178-1188. [PMID: 33020667 PMCID: PMC8350746 DOI: 10.1038/s41588-020-0708-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 09/01/2020] [Indexed: 12/31/2022]
Abstract
Somatic mutations in driver genes may ultimately lead to the development of cancer. Understanding how somatic mutations accumulate in cancer genomes and the underlying factors that generate somatic mutations is therefore crucial for developing novel therapeutic strategies. To understand the interplay between spatial genome organization and specific mutational processes, we studied 3,000 tumor-normal-pair whole-genome datasets from 42 different human cancer types. Our analyses reveal that the change in somatic mutational load in cancer genomes is co-localized with topologically-associating-domain boundaries. Domain boundaries constitute a better proxy to track mutational load change than replication timing measurements. We show that different mutational processes lead to distinct somatic mutation distributions where certain processes generate mutations in active domains, and others generate mutations in inactive domains. Overall, the interplay between three-dimensional genome organization and active mutational processes has a substantial influence on the large-scale mutation-rate variations observed in human cancers.
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Affiliation(s)
- Kadir C Akdemir
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Victoria T Le
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Justin M Kim
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Division of Biology and Medicine, Brown University, Providence, RI, USA
| | - Sarah Killcoyne
- MRC Cancer Unit, Hutchison/MRC Research Center, University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Devin A King
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Ya-Ping Lin
- Department of Ophthalmology and Visual Sciences, McGovern Medical School, The University of Texas Health Sciences Center at Houston, Houston, TX, USA
| | - Yanyan Tian
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Akira Inoue
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Frederick S Robinson
- Translational Research to Advance Therapeutics and Innovation in Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Manjunath Nimmakayalu
- Graduate Program in Diagnostic Genetics and Genomics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Erica J Lynn
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kin Chan
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Durham, NC, USA
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Sahil Seth
- Translational Research to Advance Therapeutics and Innovation in Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- UT Health Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Leszek J Klimczak
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, US National Institutes of Health, Durham, NC, USA
| | - Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Dmitry A Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Durham, NC, USA
| | - John O'Brien
- Department of Ophthalmology and Visual Sciences, McGovern Medical School, The University of Texas Health Sciences Center at Houston, Houston, TX, USA
| | - Lei Li
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Life Science Institute, Zhejiiang University, Hangzhou, China
| | - Yonathan Lissanu Deribe
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Cardiovascular and Thoracic Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Roel G Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Rebecca Fitzgerald
- MRC Cancer Unit, Hutchison/MRC Research Center, University of Cambridge, Cambridge, UK
| | | | - Jesse R Dixon
- Salk Institute for Biological Studies, La Jolla, CA, USA.
| | - P Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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6
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Nimmakayalu M, Horton VK, Darbro B, Patil SR, Alsayouf H, Keppler-Noreuil K, Shchelochkov OA. Apparent germline mosaicism for a novel 19p13.13 deletion disrupting NFIX and CACNA1A. Am J Med Genet A 2013; 161A:1105-9. [PMID: 23495138 DOI: 10.1002/ajmg.a.35790] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 10/30/2012] [Indexed: 11/05/2022]
Abstract
We report on a case of apparent germline mosaicism in a family of two sisters carrying a novel 19p13.13 deletion. The 11-year-old proposita was referred for evaluation of macrocephaly, moderate intellectual disability (ID), and episodic ataxia. Array comparative genomic hybridization (CGH) detected a 399 kb microdeletion with breakpoints within genes NFIX and CACNA1A. A similar deletion was also seen in the elder sibling who presented with macrocephaly, ID, and strabismus. The deletions were confirmed to be de novo after the parental aCGH analysis suggesting that this is an example of germinal mosaicism. This study contributes additional information for the newly identified 19p13 deletion syndrome and clarifies the clinical roles of genes in the involved region. This case of apparent germline mosaicism represents the only known family in the cohort of 1,800 patients analyzed by our group.
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Affiliation(s)
- Manjunath Nimmakayalu
- Division of Medical Genetics, Department of Pediatrics, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA
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7
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Nimmakayalu M, Noble N, Horton VK, Willing M, Copeland S, Sheffield V, Nagy PL, Wassink T, Patil S, Shchelochkov OA. 2q24 deletions: Further characterization of clinical findings and their relation to the SCN cluster. Am J Med Genet A 2012; 158A:2767-74. [DOI: 10.1002/ajmg.a.35362] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Accepted: 02/06/2012] [Indexed: 12/31/2022]
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Cyr AB, Nimmakayalu M, Longmuir SQ, Patil SR, Keppler-Noreuil KM, Shchelochkov OA. A novel 4p16.3 microduplication distal to WHSC1 and WHSC2 characterized by oligonucleotide array with new phenotypic features. Am J Med Genet A 2011; 155A:2224-8. [PMID: 21815251 DOI: 10.1002/ajmg.a.34120] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Accepted: 04/27/2011] [Indexed: 01/19/2023]
Abstract
Larger imbalances on chromosome 4p in the form of deletions associated with Wolf-Hirschhorn syndrome (WHS) and duplications of chromosome 4p have a defined clinical phenotype. The critical region for both these clinical disorders has been narrowed based on the genotype-phenotype correlations. However, cryptic rearrangements in this region have been reported infrequently. We report on a male patient with a microduplication of chromosome 4p, who presents with findings of macrocephaly, irregular iris pigmentation-heterochromia, and preserved linear growth in addition to overlapping features of trisomy 4p such as seizures, delayed psychomotor development, and dysmorphic features including prominent glabella, low-set ears, and short neck. Using a high-density oligonucleotide microarray, we have identified a novel submicroscopic duplication involving dosage sensitive genes TACC3, FGFR3, and LETM1. The microduplication did not involve WHSC1 and WHSC2 which are considered in the critical region for WHS and trisomy 4p. This patient's presentation and genomic findings help further delineate clinical significance of re-arrangements in the 4p16 region without the involvement of WHS critical region.
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Affiliation(s)
- Andrew B Cyr
- Division of Medical Genetics, Department of Pediatrics, University of Iowa Hospitals and Clinics, Iowa City, Iowa, USA
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9
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Nimmakayalu M, Major H, Sheffield V, Solomon DH, Smith RJ, Patil SR, Shchelochkov OA. Microdeletion of 17q22q23.2 encompassing TBX2 and TBX4 in a patient with congenital microcephaly, thyroid duct cyst, sensorineural hearing loss, and pulmonary hypertension. Am J Med Genet A 2011; 155A:418-23. [DOI: 10.1002/ajmg.a.33827] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Accepted: 10/27/2010] [Indexed: 11/08/2022]
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10
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Shaikh TH, O’Connor RJ, Pierpont ME, McGrath J, Hacker AM, Nimmakayalu M, Geiger E, Emanuel BS, Saitta SC. Low copy repeats mediate distal chromosome 22q11.2 deletions: sequence analysis predicts breakpoint mechanisms. Genome Res 2007; 17:482-91. [PMID: 17351135 PMCID: PMC1832095 DOI: 10.1101/gr.5986507] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Genomic disorders contribute significantly to genetic disease and, as detection methods improve, greater numbers are being defined. Paralogous low copy repeats (LCRs) mediate many of the chromosomal rearrangements that underlie these disorders, predisposing chromosomes to recombination errors. Deletions of proximal 22q11.2 comprise the most frequently occurring microdeletion syndrome, DiGeorge/Velocardiofacial syndrome (DGS/VCFS), in which most breakpoints have been localized to a 3 Mb region containing four large LCRs. Immediately distal to this region, there are another four related but smaller LCRs that have not been characterized extensively. We used paralog-specific primers and long-range PCR to clone, sequence, and examine the distal deletion breakpoints from two patients with de novo deletions mapping to these distal LCRs. Our results present definitive evidence of the direct involvement of LCRs in 22q11 deletions and map both breakpoints to the BCRL module, common to most 22q11 LCRs, suggesting a potential region for LCR-mediated rearrangement both in the distal LCRs and in the DGS interval. These are the first reported cases of distal 22q11 deletions in which breakpoints have been characterized at the nucleotide level within LCRs, confirming that distal 22q11 LCRs can and do mediate rearrangements leading to genomic disorders.
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Affiliation(s)
- Tamim H. Shaikh
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Ronald J. O’Connor
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Mary Ella Pierpont
- Children’s Hospital of Minnesota and University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - James McGrath
- Departments of Comparative Medicine, Genetics and Pediatrics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - April M. Hacker
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Manjunath Nimmakayalu
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Elizabeth Geiger
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Beverly S. Emanuel
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Sulagna C. Saitta
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
- Corresponding author.E-mail ; fax (215) 590-3764
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Li P, Zhang HZ, Huff S, Nimmakayalu M, Qumsiyeh M, Yu J, Szekely A, Xu T, Pober BR. Karyotype-phenotype insights from 11q14.1-q23.2 interstitial deletions: FZD4 haploinsufficiency and exudative vitreoretinopathy in a patient with a complex chromosome rearrangement. Am J Med Genet A 2007; 140:2721-9. [PMID: 17103440 DOI: 10.1002/ajmg.a.31498] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We detected a unique de novo complex chromosome rearrangement (CCR) in a patient with multiple abnormalities including growth retardation, facial anomalies, exudative vitreoretinopathy (EVR), cleft palate, and minor digital anomalies. Cytogenetic analysis, fluorescent in situ hybridization, and microsatellite genotyping showed a reciprocal translocation between chromosomes 5 and 8, and a complex translocation-deletion-inversion process in the formation of derivative chromosomes 11 and 16. High-density whole-genome oligonucleotide array comparative genomic hybridization (oaCGH) defined a 35-megabase interstitial deletion of 11q14.1-q23.2 and a 1 megabase deletion of 16q22.3-q23.1. The Frizzled-4 (FZD4) gene is located within this 11q deletion. Parental studies and sequencing analysis confirmed that the patient was hemizygous for FZD4 due to the loss of a paternal allele on the derivative chromosome 11. Mutations in FZD4 are known to cause autosomal dominant exudative vitreoretinopathy (EVR1). Our patient's findings suggest that haploinsufficiency of the FZD4 gene product can also be a disease-causing mechanism for EVR1. We reviewed the clinical manifestations of 23 cases with 11q14-q23 interstitial deletions, with particular scrutiny of the present case and four reported cases characterized by molecular cytogenetics. These findings were used to construct a regional deletion map consisting of a haplosufficient segment at 11q14.3, a flanking centromeric segment at 11q14.1-q14.2, and a flanking telomeric segment at 11q21-q23.3. We propose that deletions of the FZD4 gene located within the centromeric segment cause retinal dysgenesis, while deletions within the telomeric segment account for dysmorphic craniofacial features, growth and mental retardation, and mild digital anomalies. These results provide insight into karyotype-phenotype correlations and prompt a rational analytic approach to cases with interstitial deletions of the 11q14-q23 region.
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Affiliation(s)
- Peining Li
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA.
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Ming JE, Geiger E, James AC, Ciprero KL, Nimmakayalu M, Zhang Y, Huang A, Vaddi M, Rappaport E, Zackai EH, Shaikh TH. Rapid detection of submicroscopic chromosomal rearrangements in children with multiple congenital anomalies using high density oligonucleotide arrays. Hum Mutat 2006; 27:467-73. [PMID: 16619270 DOI: 10.1002/humu.20322] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chromosomal rearrangements such as microdeletions and interstitial duplications are the underlying cause of many human genetic disorders. These disorders can manifest in the form of multiple congenital anomalies (MCA), which are a significant cause of morbidity and mortality in children. The major limitations of cytogenetic tests currently used for the detection of such chromosomal rearrangements are low resolution and limited coverage of the genome. Thus, it is likely that children with MCA may have submicroscopic chromosomal rearrangements that are not detectable by current techniques. We report the use of a commercially available, oligonucleotide-based microarray for genome-wide analysis of copy number alterations. First, we validated the microarray in patients with known chromosomal rearrangements. Next, we identified previously undetected, de novo chromosomal deletions in patients with MCA who have had a normal high-resolution karyotype and subtelomeric fluorescence in situ hybridization (FISH) analysis. These findings indicate that high-density, oligonucleotide-based microarrays can be successfully used as tools for the detection of chromosomal rearrangement in clinical samples. Their higher resolution and commercial availability make this type of microarray highly desirable for application in the diagnosis of patients with multiple congenital defects.
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Affiliation(s)
- Jeffrey E Ming
- Division of Human Genetics, Stokes Research Institute, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
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13
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Zhang HZ, Li P, Wang D, Huff S, Nimmakayalu M, Qumsiyeh M, Pober BR. FOXC1 gene deletion is associated with eye anomalies in ring chromosome 6. Am J Med Genet A 2004; 124A:280-7. [PMID: 14708101 DOI: 10.1002/ajmg.a.20413] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We report a case of ring chromosome 6 presenting with growth and mental retardation, cerebral dysgenesis, eye malformations, mixed hearing loss, and abnormal physical features. Fluorescent in situ hybridization (FISH) and microsatellite genotyping demonstrated segmental deletions of less than 6 Mb on 6p and 1-2 Mb on 6q. The primary karyotype is designated as 46,XY,r(6)(p25q27).ish r(6)(p25.1q27)(D6S344-, FOXC1-, D6S1574+, D6S281-, D6S297+). Secondary structural and numerical variants of the ring 6 were observed in 16% of the cells analyzed. Intragenic genotyping revealed deletion of the paternal FOXC1 gene, haploinsufficiency of which has been reported to cause eye anterior chamber developmental defects. Accordingly, we propose that our patient's ophthalmologic abnormalities result from haploinsufficiency of the transcription factor FOXC1. We present clinical and cytogenetic summaries on 23 reported cases of ring 6 and categorize them into mild, moderate, and severely affected groups. Further phenotype comparisons between cases with ring 6 and cases with only 6p or 6q terminal deletions suggest that genes important for hearing, vision, and central nervous system development remain to be identified in chromosome 6 terminal regions. Molecular definition of the fusion points and tissue mosaicism studies are necessary to better understand the genotype-phenotype correlation of ring 6. We recommend ophthalmology, audiology, cardiology, and central nervous system examinations be part of the routine evaluation for children with a ring chromosome 6.
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Affiliation(s)
- Hui Z Zhang
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA
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Hui P, Howe JG, Crouch J, Nimmakayalu M, Qumsiyeh MB, Tallini G, Flynn SD, Smith BR. Real-time quantitative RT-PCR of cyclin D1 mRNA in mantle cell lymphoma: comparison with FISH and immunohistochemistry. Leuk Lymphoma 2003; 44:1385-94. [PMID: 12952233 DOI: 10.1080/1042819031000079168] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Presence of the balanced translocation t(11;14)(q13;q32) and the consequent overexpression of cyclin D1 found in mantle cell lymphoma (MCL) has been shown to be of important diagnostic value. Although many molecular and immunohistochemical approaches have been applied to analyze cyclin D1 status, correlative studies to compare different methods for the diagnosis of MCL are lacking. In this study, we examined 39 archived paraffin specimens from patients diagnosed with a variety of lymphoproliferative diseases including nine cases meeting morphologic and immunophenotypic criteria for MCL by: (1) real-time quantitative RT-PCR to evaluate cyclin D1 mRNA expression; (2) dual fluorescence in situ hybridization (FISH) to evaluate the t(11;14) translocation in interphase nuclei; and (3) tissue array immunohistochemistry to evaluate the cyclin D1 protein level. Among the nine cases of possible MCL, seven cases showed overexpression of cyclin D1 mRNA (cyclin D1 positive MCL) and two cases showed no cyclin D1 mRNA increase (cyclin D1 negative "MCL-like"). In six of seven cyclin D1 positive cases, the t(11;14) translocation was demonstrated by FISH analysis; in one case FISH was unsuccessful. Six of the seven cyclin D1 mRNA overexpressing cases showed increased cyclin D1 protein on tissue array immunohistochemistry; one was technically suboptimal. Among the two cyclin D1 negative MCL-like cases, FISH confirmed the absence of the t(11;14) translocation in both cases. All other lymphoproliferative diseases studied were found to have low or no cyclin D1 mRNA expression and were easily distinguishable from the cyclin D1 overexpressing MCLs by all three techniques. In addition, to confirming the need to assess cyclin D1 status, as well as, morphology and immunophenotyping to establish the diagnosis of MCL, this study demonstrates good correlation and comparability between measure of cyclin D1 mRNA, the 11;14 translocation and cyclin D1 protein.
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Affiliation(s)
- Pei Hui
- Department of Laboratory Medicine, Yale University School of Medicine, 333 Cedar Street, P.O. Box 208035, New Haven, CT 06520-8035, USA
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15
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Kone J, Arroyo J, Savinelli T, Lin S, Boyd K, Wu Y, Nimmakayalu M, Copeland NG, Jenkins NA, Qumsiyeh M, Hu P, Prescott A, Wu H, Yang L, Roe B, Perkins AS. F-MuLV acceleration of myelomonocytic tumorigenesis in SV40 large T antigen transgenic mice is accompanied by retroviral insertion at Fli1 and a novel locus, Fim4. Leukemia 2002; 16:1827-34. [PMID: 12200699 DOI: 10.1038/sj.leu.2402598] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2001] [Accepted: 02/12/2002] [Indexed: 11/09/2022]
Abstract
We describe here the development of a murine system for the identification of genes involved in myelomonocytic neoplasms. Transgenic C57BL/6J mice expressing SV40 early region under a myelomonocytic promoter develop histiocytic sarcomas with a latency of 167 days. We used retroviral proviral tagging to accelerate tumorigenesis and to uncover genetic changes that contribute to tumor development. Infection of transgenic mice with Friend murine leukemia virus (F-MuLV) shortened the latency of morbidity to 103 days (P< 0.001); this was associated with clonal proviral integrations in tumor DNA. As expected for F-MuLV, proviral insertions occurred at Fli1 in both transgenic and nontransgenic tumors. Four insertions were found at a novel locus, termed Fim4, on chromosome 6. This region is syntenic to human 7q32, a region that is commonly deleted in human myelodysplastic syndrome and acute myeloid leukemia. A murine BAC containing Fim4 was sequenced and analyzed, and while there was significant human-mouse homology in the area of the insertions, no candidate gene has been identified. Thus we have established a system to identify genes involved in myelomonocytic tumors, and have used it to identify Fim4, a new common site of proviral insertion. Study of this locus may provide insight into genes involved in AML-associated 7q32 deletions in humans.
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MESH Headings
- Animals
- Antigens, Polyomavirus Transforming/genetics
- Antigens, Polyomavirus Transforming/metabolism
- Blotting, Southern
- Chromosome Mapping
- Chromosomes, Artificial, Bacterial
- Cloning, Molecular
- DNA Primers/chemistry
- DNA-Binding Proteins/genetics
- Friend murine leukemia virus/genetics
- Humans
- In Situ Hybridization, Fluorescence
- Leukemia, Experimental/genetics
- Leukemia, Experimental/metabolism
- Leukemia, Experimental/virology
- Leukemia, Myelomonocytic, Acute/genetics
- Leukemia, Myelomonocytic, Acute/metabolism
- Leukemia, Myelomonocytic, Acute/virology
- Mice
- Mice, Inbred C3H
- Mice, Inbred C57BL
- Mice, Transgenic
- Polymerase Chain Reaction
- Proto-Oncogene Protein c-fli-1
- Proto-Oncogene Proteins
- Proviruses/genetics
- Retroviridae Infections/genetics
- Retroviridae Infections/virology
- Trans-Activators/genetics
- Tumor Virus Infections/genetics
- Tumor Virus Infections/metabolism
- Tumor Virus Infections/virology
- Virus Integration
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Affiliation(s)
- J Kone
- Department of Pathology, Yale University, New Haven, CT, USA
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Stankiewicz P, Rujner J, Löffler C, Krüger A, Nimmakayalu M, Piłacik B, Krajewska-Walasek M, Gutkowska A, Hansmann I, Giannakudis I. Alagille syndrome associated with a paracentric inversion 20p12.2p13 disrupting the JAG1 gene. Am J Med Genet 2001; 103:166-71. [PMID: 11568926 DOI: 10.1002/ajmg.1531] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Mutations in the human gene Jagged1 (JAG1) localized in 20p12 have been recently identified as causal for the anomalies found in patients with Alagille syndrome (AGS). This gene encodes a ligand for the Notch1 transmembrane receptor, which plays a key role in cell-to-cell signaling during differentiation and is conserved from C. elegans to human. We report a paracentric inversion (PAI) of chromosome 20p12.2p13 in an individual with AGS who also had alpha-1-antitrypsin deficiency. To our knowledge, this is the first published case of PAI involving the short arm of chromosome 20. Using FISH, fiberFISH, and molecular studies with a approximately 40 kb cosmid clone encompassing the entire 36 kb JAG1 gene, we demonstrate that the gene was disrupted by the inversion breakpoint between exons 5 and 6. An unusual association between two most common causes of chronic liver disease in childhood, AGS and alpha-1-antitrypsin deficiency, as well as their influence on the proband's abnormal phenotype are discussed.
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Affiliation(s)
- P Stankiewicz
- Institute of Human Genetics and Medical Biology, University Halle-Wittenberg, Halle/S, Germany.
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Abstract
It has been shown in animal models that hepatocytes and cholangiocytes can derive from bone marrow cells. We have investigated whether such a process occurs in humans. Archival autopsy and biopsy liver specimens were obtained from 2 female recipients of therapeutic bone marrow transplantations with male donors and from 4 male recipients of orthotopic liver transplantations from female donors. Immunohistochemical staining with monoclonal antibody CAM5.2, specific for cytokeratins 8, 18, and 19, gave typical strong staining of hepatocytes, cholangiocytes, and ductular reactions in all tissues, to the exclusion of all nonepithelial cells. Slides were systematically photographed and then restained by fluorescence in situ hybridization (FISH) for X and Y chromosomes. Using morphologic criteria, field-by-field comparison of the fluorescent images with the prior photomicrographs, and persistence of the diaminiobenzidene (DAB) stain through the FISH protease digestion, Y-positive hepatocytes and cholangiocytes could be identified in male control liver tissue and in all study specimens. Cell counts were adjusted based on the number of Y-positive cells in the male control liver to correct for partial sampling of nuclei in the 3-micron thin tissue sections. Adjusted Y-positive hepatocyte and cholangiocyte engraftment ranged from 4% to 43% and from 4% to 38%, respectively, in study specimens, with the peak values being found in a case of fibrosing cholestatic recurrent hepatitis C in one of the liver transplant recipients. We therefore show that in humans, hepatocytes and cholangiocytes can be derived from extrahepatic circulating stem cells, probably of bone marrow origin, and such "transdifferentiation can replenish large numbers of hepatic parenchymal cells.
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Affiliation(s)
- N D Theise
- Department of Pathology, New York University, School of Medicine, New York, NY 10016, USA.
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Cremona O, Nimmakayalu M, Haffner C, Bray-Ward P, Ward DC, De Camilli P. Assignment of SYNJ1 to human chromosome 21q22.2 and Synj12 to the murine homologous region on chromosome 16C3-4 by in situ hybridization. Cytogenet Cell Genet 2000; 88:89-90. [PMID: 10773674 DOI: 10.1159/000015493] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- O Cremona
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA
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Abstract
Many projects, such as multiplex-fluorescence in situ hybridization (M-FISH) karyotyping, require the use of relatively large amounts of multiple fluor- or hapten-labeled nucleotides for the preparation of DNA probes. Such a requirement makes these experimental approaches prohibitively expensive for many researchers. The cost of such nucleotides can be reduced approximately 99% by purchasing the chemical precursors, fluor or hapten succinimidyl esters and 5-(3-aminoallyl)-2'-deoxyuridine 5' triphosphate (AA-dUTP), and performing the simple coupling/purification described here. It is possible to finish four to ten different fluor/hapten dUTP preparations of 2.5 microM scale within a 24 h period. The reagent cost for each preparation ranges from $33-$237 per microM, depending on the fluor/hapten. This laboratory uses such nucleotide preparations to prepare FISH probes by nick translation or PCR amplification.
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Affiliation(s)
- M Nimmakayalu
- Yale University School of Medicine, New Haven, CT 06510, USA
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