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Shuga J, Zeng Y, Novak R, Lan Q, Tang X, Rothman N, Vermeulen R, Li L, Hubbard A, Zhang L, Mathies RA, Smith MT. Single molecule quantitation and sequencing of rare translocations using microfluidic nested digital PCR. Nucleic Acids Res 2013; 41:e159. [PMID: 23873959 PMCID: PMC3763562 DOI: 10.1093/nar/gkt613] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Cancers are heterogeneous and genetically unstable. New methods are needed that provide the sensitivity and specificity to query single cells at the genetic loci that drive cancer progression, thereby enabling researchers to study the progression of individual tumors. Here, we report the development and application of a bead-based hemi-nested microfluidic droplet digital PCR (dPCR) technology to achieve ‘quantitative’ measurement and single-molecule sequencing of somatically acquired carcinogenic translocations at extremely low levels (<10−6) in healthy subjects. We use this technique in our healthy study population to determine the overall concentration of the t(14;18) translocation, which is strongly associated with follicular lymphoma. The nested dPCR approach improves the detection limit to 1 × 10−7 or lower while maintaining the analysis efficiency and specificity. Further, the bead-based dPCR enabled us to isolate and quantify the relative amounts of the various clonal forms of t(14;18) translocation in these subjects, and the single-molecule sensitivity and resolution of dPCR led to the discovery of new clonal forms of t(14;18) that were otherwise masked by the conventional quantitative PCR measurements. In this manner, we created a quantitative map for this carcinogenic mutation in this healthy population and identified the positions on chromosomes 14 and 18 where the vast majority of these t(14;18) events occur.
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Affiliation(s)
- Joe Shuga
- School of Public Health, University of California, Berkeley, CA 94720, USA, Department of Chemistry, University of California, Berkeley, CA 94720, USA, Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA, UC San Francisco/UC Berkeley Graduate Program in Bioengineering, University of California, Berkeley, CA 94720, USA, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Department of Health and Human Services, Bethesda, MD 20852, USA, Guangdong Poison Control Center, Guangzhou 510300, China and Environmental Epidemiology Division, Institute for Risk Assessment Sciences, Utrecht University, Utrecht, NL-3508, The Netherlands
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Bibliography. Lymphoma. Current world literature. Curr Opin Oncol 2011; 23:537-41. [PMID: 21836468 DOI: 10.1097/cco.0b013e32834b18ec] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Abstract
Histological transformation of follicular lymphoma (FL) to a more aggressive non-Hodgkin's lymphomas is a pivotal event in the natural history of FL and is associated with poor outcome. While commonly observed in clinical practice and despite multiple studies designed to address its pathogenesis, the biology of this process represents an enigma. In this chapter we present a state of the art review summarizing the definition of histologic transformation, its incidence, pathogenesis, clinical manifestations, treatment and outcome. Furthermore, we specifically emphasize gaps in our knowledge that should be addressed in future studies.
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MESH Headings
- Biomarkers, Tumor/analysis
- Biomarkers, Tumor/biosynthesis
- Biopsy
- Burkitt Lymphoma/etiology
- Burkitt Lymphoma/genetics
- Burkitt Lymphoma/mortality
- Burkitt Lymphoma/pathology
- Burkitt Lymphoma/therapy
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/pathology
- Chromosome Aberrations
- Disease Progression
- Disease-Free Survival
- Humans
- Lymphoma, Follicular/complications
- Lymphoma, Follicular/genetics
- Lymphoma, Follicular/mortality
- Lymphoma, Follicular/pathology
- Lymphoma, Follicular/therapy
- Lymphoma, Large B-Cell, Diffuse/etiology
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/mortality
- Lymphoma, Large B-Cell, Diffuse/pathology
- Lymphoma, Large B-Cell, Diffuse/therapy
- Mutation
- Prognosis
- Salvage Therapy
- Stem Cell Transplantation
- Transplantation, Autologous
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Affiliation(s)
- Izidore S Lossos
- Department of Medicine & Division of Hematology/Oncology, Sylvester Comprehensive Cancer Center, University of Miami, 1475NW 12th Ave, D8-4, Miami, FL 33136, USA.
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