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Rickard BP, Overchuk M, Chappell VA, Kemal Ruhi M, Sinawang PD, Nguyen Hoang TT, Akin D, Demirci U, Franco W, Fenton SE, Santos JH, Rizvi I. Methods to Evaluate Changes in Mitochondrial Structure and Function in Cancer. Cancers (Basel) 2023; 15:2564. [PMID: 37174030 PMCID: PMC10177605 DOI: 10.3390/cancers15092564] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
Mitochondria are regulators of key cellular processes, including energy production and redox homeostasis. Mitochondrial dysfunction is associated with various human diseases, including cancer. Importantly, both structural and functional changes can alter mitochondrial function. Morphologic and quantifiable changes in mitochondria can affect their function and contribute to disease. Structural mitochondrial changes include alterations in cristae morphology, mitochondrial DNA integrity and quantity, and dynamics, such as fission and fusion. Functional parameters related to mitochondrial biology include the production of reactive oxygen species, bioenergetic capacity, calcium retention, and membrane potential. Although these parameters can occur independently of one another, changes in mitochondrial structure and function are often interrelated. Thus, evaluating changes in both mitochondrial structure and function is crucial to understanding the molecular events involved in disease onset and progression. This review focuses on the relationship between alterations in mitochondrial structure and function and cancer, with a particular emphasis on gynecologic malignancies. Selecting methods with tractable parameters may be critical to identifying and targeting mitochondria-related therapeutic options. Methods to measure changes in mitochondrial structure and function, with the associated benefits and limitations, are summarized.
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Affiliation(s)
- Brittany P. Rickard
- Curriculum in Toxicology & Environmental Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Marta Overchuk
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, and North Carolina State University, Raleigh, NC 27695, USA
| | - Vesna A. Chappell
- Mechanistic Toxicology Branch, Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Mustafa Kemal Ruhi
- Institute of Biomedical Engineering, Boğaziçi University, Istanbul 34684, Turkey
| | - Prima Dewi Sinawang
- Canary Center at Stanford for Cancer Early Detection, Department of Radiology, School of Medicine, Palo Alto, CA 94304, USA
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Tina Thuy Nguyen Hoang
- Department of Biomedical Engineering, University of Massachusetts Lowell, Lowell, MA 01854, USA
| | - Demir Akin
- Canary Center at Stanford for Cancer Early Detection, Department of Radiology, School of Medicine, Palo Alto, CA 94304, USA
- Center for Cancer Nanotechnology Excellence for Translational Diagnostics (CCNE-TD), School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Utkan Demirci
- Canary Center at Stanford for Cancer Early Detection, Department of Radiology, School of Medicine, Palo Alto, CA 94304, USA
| | - Walfre Franco
- Department of Biomedical Engineering, University of Massachusetts Lowell, Lowell, MA 01854, USA
| | - Suzanne E. Fenton
- Mechanistic Toxicology Branch, Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Janine H. Santos
- Mechanistic Toxicology Branch, Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Imran Rizvi
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, and North Carolina State University, Raleigh, NC 27695, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
- Center for Environmental Health and Susceptibility, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Shekhawat DS, Sharma C, Singh K, Singh P, Bhardwaj A, Patwa P. Critical appraisal of droplet digital polymerase chain reaction application for noninvasive prenatal testing. Congenit Anom (Kyoto) 2022; 62:188-197. [PMID: 35662261 DOI: 10.1111/cga.12481] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/13/2022] [Accepted: 04/21/2022] [Indexed: 11/29/2022]
Abstract
Maternal-fetal medicine (FM) is currently a highly demanding branch and is gaining importance as increasing number of genetic disorders rise in incidence. Prenatal testing helps to detect such abnormalities that could affect the health status of the developing fetus like birth defects or genetic disorders. Considering the rising trend of genetic disorders, there is a need for a highly sensitive way of noninvasive prenatal testing (NIPT) that may reduce the incidence of unnecessary invasive procedures and iatrogenic fetal loss. The concept of NIPT for screening of genetic disorders is continuously evolving over the last two decades and multiple techniques have come up to utilize this in the field of FM. The crucial factor which decides the accuracy of NIPS is cell free fetal DNA (cffDNA) that is present in extremely low fraction (10%-15%) in the maternal plasma. Among the available methods, the next generation sequencing (NGS) is considered as the gold standard. However, the higher cost diminishes its utility in low-resource settings. Droplet digital Polymerase chain reaction (ddPCR), a type of digital PCR is a novel technique that is frugal, equally sensitive, less labor intensive, less time-consuming and plain algorithm dependent method for detecting cffDNA fraction. Considering these impressive attributes of ddPCR, we decided to critically review the existing literature on ddPCR for NIPT whilst highlighting the clinical utility, challenges and its advantages over NGS.
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Affiliation(s)
| | - Charu Sharma
- Department of Obstetrics & Gynecology, AIIMS, Jodhpur, India
| | | | - Pratibha Singh
- Department of Obstetrics & Gynecology, AIIMS, Jodhpur, India
| | - Abhishek Bhardwaj
- Department of Dermatology, Venereology and Leprology, AIIMS, Jodhpur, India
| | - Payal Patwa
- Department of Obstetrics & Gynecology, AIIMS, Jodhpur, India
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Porath‐Krause A, Strauss AT, Henning JA, Seabloom EW, Borer ET. Pitfalls and pointers: An accessible guide to marker gene amplicon sequencing in ecological applications. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13764] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Anita Porath‐Krause
- Department of Ecology, Evolution, and Behavior University of Minnesota St. Paul MN USA
| | - Alexander T. Strauss
- Department of Ecology, Evolution, and Behavior University of Minnesota St. Paul MN USA
| | - Jeremiah A. Henning
- Department of Ecology, Evolution, and Behavior University of Minnesota St. Paul MN USA
| | - Eric W. Seabloom
- Department of Ecology, Evolution, and Behavior University of Minnesota St. Paul MN USA
| | - Elizabeth T. Borer
- Department of Ecology, Evolution, and Behavior University of Minnesota St. Paul MN USA
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Dass SA, Tan KL, Selva Rajan R, Mokhtar NF, Mohd Adzmi ER, Wan Abdul Rahman WF, Tengku Din TADAA, Balakrishnan V. Triple Negative Breast Cancer: A Review of Present and Future Diagnostic Modalities. MEDICINA (KAUNAS, LITHUANIA) 2021; 57:62. [PMID: 33445543 PMCID: PMC7826673 DOI: 10.3390/medicina57010062] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/15/2020] [Accepted: 12/15/2020] [Indexed: 12/12/2022]
Abstract
Triple-negative breast cancer (TNBC) is an aggressive breast type of cancer with no expression of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor-2 (HER2). It is a highly metastasized, heterogeneous disease that accounts for 10-15% of total breast cancer cases with a poor prognosis and high relapse rate within five years after treatment compared to non-TNBC cases. The diagnostic and subtyping of TNBC tumors are essential to determine the treatment alternatives and establish personalized, targeted medications for every TNBC individual. Currently, TNBC is diagnosed via a two-step procedure of imaging and immunohistochemistry (IHC), which are operator-dependent and potentially time-consuming. Therefore, there is a crucial need for the development of rapid and advanced technologies to enhance the diagnostic efficiency of TNBC. This review discusses the overview of breast cancer with emphasis on TNBC subtypes and the current diagnostic approaches of TNBC along with its challenges. Most importantly, we have presented several promising strategies that can be utilized as future TNBC diagnostic modalities and simultaneously enhance the efficacy of TNBC diagnostic.
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Affiliation(s)
- Sylvia Annabel Dass
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, USM, Penang 11800, Malaysia; (S.A.D.); (K.L.T.); (R.S.R.)
| | - Kim Liu Tan
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, USM, Penang 11800, Malaysia; (S.A.D.); (K.L.T.); (R.S.R.)
| | - Rehasri Selva Rajan
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, USM, Penang 11800, Malaysia; (S.A.D.); (K.L.T.); (R.S.R.)
| | - Noor Fatmawati Mokhtar
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Kubang Kerian, Kelantan 16150, Malaysia; (N.F.M.); (E.R.M.A.)
| | - Elis Rosliza Mohd Adzmi
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Kubang Kerian, Kelantan 16150, Malaysia; (N.F.M.); (E.R.M.A.)
| | - Wan Faiziah Wan Abdul Rahman
- Department of Pathology, School of Medical Sciences, Health Campus, Kubang Kerian, Kelantan 16150, Malaysia;
- Breast Cancer Awareness & Research Unit, Hospital Universiti Sains Malaysia, Kubang Kerian, Kelantan 16150, Malaysia;
| | - Tengku Ahmad Damitri Al-Astani Tengku Din
- Breast Cancer Awareness & Research Unit, Hospital Universiti Sains Malaysia, Kubang Kerian, Kelantan 16150, Malaysia;
- Chemical Pathology Department, School of Medical Sciences, Health Campus, Kubang Kerian, Kelantan 16150, Malaysia
| | - Venugopal Balakrishnan
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, USM, Penang 11800, Malaysia; (S.A.D.); (K.L.T.); (R.S.R.)
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Hess J, Kohl T, Kotrová M, Rönsch K, Paprotka T, Mohr V, Hutzenlaub T, Brüggemann M, Zengerle R, Niemann S, Paust N. Library preparation for next generation sequencing: A review of automation strategies. Biotechnol Adv 2020; 41:107537. [DOI: 10.1016/j.biotechadv.2020.107537] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 02/27/2020] [Accepted: 03/16/2020] [Indexed: 01/08/2023]
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Zhao S, Zhang C, Mu J, Zhang H, Yao W, Ding X, Ding J, Chang Y. All-in-one sequencing: an improved library preparation method for cost-effective and high-throughput next-generation sequencing. PLANT METHODS 2020; 16:74. [PMID: 32489396 PMCID: PMC7247233 DOI: 10.1186/s13007-020-00615-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/14/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND Next generation sequencing (NGS) has been widely used in biological research, due to its rapid decrease in cost and increasing ability to generate data. However, while the sequence generation step has seen many improvements over time, the library preparation step has not, resulting in low-efficiency library preparation methods, especially for the most time-consuming and labor-intensive steps: size-selection and quantification. Consequently, there can be bottlenecks in projects with large sample cohorts. RESULTS We have described the all-in-one sequencing (AIO-seq) method, where instead of performing size-selection and quantification for samples individually, one sample one tube, up to 116 samples are pooled and analyzed in a single tube, 'All-In-One'. The AIO-seq method pools libraries based on the samples' expected data yields and the calculated concentrations of the size selected regions (target region), which can easily be obtained with the Agilent 2100 Bioanalyzer and Qubit Fluorometer. AIO-seq was applied to whole genome sequencing and RNA-seq libraries successfully, and it is envisaged that it could be applied to any type of NGS library, such as chromatin immunoprecipitation coupled with massively parallel sequencing, assays for transposase-accessible chromatin with high-throughput sequencing, and high-throughput chromosome conformation capture. We also demonstrated that for genetic population samples with low coverage sequences, like recombinant inbred lines (RIL), AIO-seq could be further simplified, by mixing the libraries immediately after PCR, without calculating the target region concentrations. CONCLUSIONS The AIO-seq method is thus labor saving and cost effective, and suitable for projects with large sample cohorts, like those used in plant breeding or population genetics research.
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Affiliation(s)
- Sheng Zhao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
| | - Cuicui Zhang
- College of Life Science and Technology, Guangxi University, Nanning, 530004 China
| | - Jianqiang Mu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
| | - Hui Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
| | - Wen Yao
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002 China
| | - Xinhua Ding
- State Key Laboratory of Crop Biology, College of Plant Protection, Shandong Agricultural University, Taian, 271018 China
| | - Junqiang Ding
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002 China
| | - Yuxiao Chang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
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Lee J, Lim H, Jang H, Hwang B, Lee JH, Cho J, Lee JH, Bang D. CRISPR-Cap: multiplexed double-stranded DNA enrichment based on the CRISPR system. Nucleic Acids Res 2019; 47:e1. [PMID: 30215766 PMCID: PMC6326800 DOI: 10.1093/nar/gky820] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 09/04/2018] [Indexed: 12/26/2022] Open
Abstract
Existing methods to enrich target regions of genomic DNA based on PCR, hybridization capture, or molecular inversion probes have various drawbacks, including long experiment times and low throughput and/or enrichment quality. We developed CRISPR-Cap, a simple and scalable CRISPR-based method to enrich target regions of dsDNA, requiring only two short experimental procedures that can be completed within two hours. We used CRISPR-Cap to enrich 10 target genes 355.7-fold on average from Escherichia coli genomic DNA with a maximum on-target ratio of 81% and high enrichment uniformity. We also used CRISPR-Cap to measure gene copy numbers and detect rare alleles with frequencies as low as 1%. Finally, we enriched coding sequence regions of 20 genes from the human genome. We envision that CRISPR-Cap can be used as an alternative to other widely used target-enrichment methods, which will broaden the scope of CRISPR applications to the field of target enrichment field.
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Affiliation(s)
- Jeewon Lee
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Hyeonseob Lim
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Hoon Jang
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Byungjin Hwang
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Joon Ho Lee
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Junhyuk Cho
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Ji Hyun Lee
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea.,Department of Biomedical Science and Technology, Kyung Hee Medical Science Research Institute, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Duhee Bang
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
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8
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Coulter SJ. Mitigation of the effect of variability in digital PCR assays through use of duplexed reference assays for normalization. Biotechniques 2019; 65:86-91. [PMID: 30091389 DOI: 10.2144/btn-2018-0058] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Digital PCR has been promoted as a technique for obtaining absolute measures of the amount of nucleic acid target sequence in a sample, but still lacks standardization in data reporting. The initial method of representing data as copies per microliter produced inconsistent results and made inter-assay comparisons difficult. Normalizing copies to amount of nucleic acid gives more uniform results, but factors influencing the effective concentration of nucleic acid in the final digital PCR assay must be considered. Using droplet digital PCR and previously validated reference genes duplexed with target genes, a method of normalization was developed to estimate the amount of input nucleic acid in individual assays, subsequently reporting the number of copies of target gene relative to this amount. Correcting for the actual amount of amplifiable nucleic acid present demonstrated a higher correlation between various dilutions of sample mRNA and allowed more accurate comparisons of digital PCR results.
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Affiliation(s)
- Sherry J Coulter
- National Cancer Institute at the National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
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Krumbholz M, Goerlitz K, Albert C, Lawlor J, Suttorp M, Metzler M. Large amplicon droplet digital PCR for DNA-based monitoring of pediatric chronic myeloid leukaemia. J Cell Mol Med 2019; 23:4955-4961. [PMID: 31199062 PMCID: PMC6653534 DOI: 10.1111/jcmm.14321] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 02/27/2019] [Accepted: 03/25/2019] [Indexed: 12/16/2022] Open
Abstract
Quantification of tumour‐specific molecular markers at the RNA and DNA level for treatment response monitoring is crucial for risk‐adapted stratification and guidance of individualized therapy in leukaemia and other malignancies. Most pediatric leukaemias and solid tumours of mesenchymal origin are characterized by a relatively low mutation burden at the single nucleotide level and the presence of recurrent chromosomal translocations. The genomic fusion sites resulting from translocations are stable molecular tumour markers; however, repeat‐rich DNA sequences flanking intronic breakpoints limit the design of high sensitivity PCR assays for minimal residual disease (MRD) monitoring. Here, we quantitatively evaluated the impact of repeat elements on assay selection and the feasibility of using extended amplicons (≤1330 bp) amplified by droplet digital PCR to monitor pediatric chronic myeloid leukaemia (CML). Molecular characterization of 178 genomic BCR‐ABL1 fusion sites showed that 64% were located within sequence repeat elements, impeding optimal primer/probe design. Comparative quantification of DNA and RNA BCR‐ABL1 copy numbers in 687 specimens from 55 pediatric patients revealed that their levels were highly correlated. The combination of droplet digital PCR, double quenched probes and extended amplicons represents a valuable tool for sensitive MRD assessment in CML and may be adapted to other translocation‐positive tumours.
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Affiliation(s)
- Manuela Krumbholz
- Department of Pediatrics, University Hospital Erlangen, Erlangen, Germany
| | - Katharina Goerlitz
- Department of Pediatrics, University Hospital Erlangen, Erlangen, Germany
| | - Christian Albert
- Department of Pediatrics, University Hospital Erlangen, Erlangen, Germany
| | - Jennifer Lawlor
- Department of Pediatrics, University Hospital Erlangen, Erlangen, Germany.,Department of Biology, Division of Genetics, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Meinolf Suttorp
- Medical Faculty, Pediatric Hemato-Oncology, Technical University, Dresden, Germany
| | - Markus Metzler
- Department of Pediatrics, University Hospital Erlangen, Erlangen, Germany
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Affiliation(s)
- Marilynn Ransom Fairfax
- Department of Pathology, Wayne State University School of Medicine, 540 East Canfield Street, Detroit, MI 48201, USA; Clinical Microbiology Laboratories, DMC University Laboratories, 4201 St. Antoine Street, Detroit, MI 48201, USA.
| | - Martin H Bluth
- Department of Pathology, Wayne State University School of Medicine, 540 East Canfield Street, Detroit, MI 48201, USA; Pathology Laboratories, Michigan Surgical Hospital, 21230 Dequindre Road, Warren, MI 48091, USA
| | - Hossein Salimnia
- Department of Pathology, Wayne State University School of Medicine, 540 East Canfield Street, Detroit, MI 48201, USA; Clinical Microbiology Laboratories, DMC University Laboratories, 4201 St. Antoine Street, Detroit, MI 48201, USA
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Fernando MR, Jiang C, Krzyzanowski GD, Ryan WL. Analysis of human blood plasma cell-free DNA fragment size distribution using EvaGreen chemistry based droplet digital PCR assays. Clin Chim Acta 2018; 483:39-47. [PMID: 29655637 DOI: 10.1016/j.cca.2018.04.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 04/02/2018] [Accepted: 04/11/2018] [Indexed: 12/27/2022]
Abstract
BACKGROUND Plasma cell-free DNA (cfDNA) fragment size distribution provides important information required for diagnostic assay development. We have developed and optimized droplet digital PCR (ddPCR) assays that quantify short and long DNA fragments. These assays were used to analyze plasma cfDNA fragment size distribution in human blood. METHODS Assays were designed to amplify 76,135, 490 and 905 base pair fragments of human β-actin gene. These assays were used for fragment size analysis of plasma cell-free, exosome and apoptotic body DNA obtained from normal and pregnant donors. RESULTS The relative percentages for 76, 135, 490 and 905 bp fragments from non-pregnant plasma and exosome DNA were 100%, 39%, 18%, 5.6% and 100%, 40%, 18%,3.3%, respectively. The relative percentages for pregnant plasma and exosome DNA were 100%, 34%, 14%, 23%, and 100%, 30%, 12%, 18%, respectively. The relative percentages for non-pregnant plasma pellet (obtained after 2nd centrifugation step) were 100%, 100%, 87% and 83%, respectively. CONCLUSION Non-pregnant Plasma cell-free and exosome DNA share a unique fragment distribution pattern which is different from pregnant donor plasma and exosome DNA fragment distribution indicating the effect of physiological status on cfDNA fragment size distribution. Fragment distribution pattern for plasma pellet that includes apoptotic bodies and nuclear DNA was greatly different from plasma cell-free and exosome DNA.
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Affiliation(s)
- M Rohan Fernando
- Department of Obstetrics and Gynecology, University of Nebraska Medical Center, Omaha, NE, USA; Department of Research and Development, CFGenome, Omaha, NE, USA.
| | - Chao Jiang
- Department of Obstetrics and Gynecology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Gary D Krzyzanowski
- Department of Obstetrics and Gynecology, University of Nebraska Medical Center, Omaha, NE, USA; Department of Research and Development, CFGenome, Omaha, NE, USA
| | - Wayne L Ryan
- Department of Research and Development, CFGenome, Omaha, NE, USA
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12
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Pinheiro LB, O'Brien H, Druce J, Do H, Kay P, Daniels M, You J, Burke D, Griffiths K, Emslie KR. Interlaboratory Reproducibility of Droplet Digital Polymerase Chain Reaction Using a New DNA Reference Material Format. Anal Chem 2017; 89:11243-11251. [PMID: 28968098 DOI: 10.1021/acs.analchem.6b05032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Use of droplet digital PCR technology (ddPCR) is expanding rapidly in the diversity of applications and number of users around the world. Access to relatively simple and affordable commercial ddPCR technology has attracted wide interest in use of this technology as a molecular diagnostic tool. For ddPCR to effectively transition to a molecular diagnostic setting requires processes for method validation and verification and demonstration of reproducible instrument performance. In this study, we describe the development and characterization of a DNA reference material (NMI NA008 High GC reference material) comprising a challenging methylated GC-rich DNA template under a novel 96-well microplate format. A scalable process using high precision acoustic dispensing technology was validated to produce the DNA reference material with a certified reference value expressed in amount of DNA molecules per well. An interlaboratory study, conducted using blinded NA008 High GC reference material to assess reproducibility among seven independent laboratories demonstrated less than 4.5% reproducibility relative standard deviation. With the exclusion of one laboratory, laboratories had appropriate technical competency, fully functional instrumentation, and suitable reagents to perform accurate ddPCR based DNA quantification measurements at the time of the study. The study results confirmed that NA008 High GC reference material is fit for the purpose of being used for quality control of ddPCR systems, consumables, instrumentation, and workflow.
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Affiliation(s)
- Leonardo B Pinheiro
- National Measurement Institute (NMI) , Lindfield, Sydney, New South Wales 2070, Australia
| | - Helen O'Brien
- Research and Development, Australian Red Cross Blood Service , Kelvin Grove, Queensland 4059, Australia
| | - Julian Druce
- Victorian Infectious Diseases Reference Laboratory , Melbourne, Victoria 3000, Australia
| | - Hongdo Do
- Olivia Newton-John Cancer Research Institute , Translation Genomics and Epigenomics Laboratory, Heidelberg, Victoria 3084, Australia
| | - Pippa Kay
- Agri-Bio Molecular Genetics, Biosciences Research Division, Bundoora, Victoria 3083, Australia
| | - Marissa Daniels
- The Prince Charles Hospital University of Queensland , Thoracic Research Centre, Chermside, Queensland 4032, Australia
| | - Jingjing You
- Save Sight Institute, Sydney Eye Hospital, Sydney Medical School, University of Sydney , Sydney, New South Wales 2000, Australia
| | - Daniel Burke
- National Measurement Institute (NMI) , Lindfield, Sydney, New South Wales 2070, Australia
| | - Kate Griffiths
- National Measurement Institute (NMI) , Lindfield, Sydney, New South Wales 2070, Australia
| | - Kerry R Emslie
- National Measurement Institute (NMI) , Lindfield, Sydney, New South Wales 2070, Australia
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An exploratory study of predisposing genetic factors for DiGeorge/velocardiofacial syndrome. Sci Rep 2017; 7:40031. [PMID: 28059126 PMCID: PMC5216377 DOI: 10.1038/srep40031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 12/01/2016] [Indexed: 12/13/2022] Open
Abstract
DiGeorge/velocardiofacial syndrome (DGS/VCFS) is a disorder caused by a 22q11.2 deletion mediated by non-allelic homologous recombination (NAHR) between low-copy repeats (LCRs). We have evaluated the role of LCR22 genomic architecture and PRDM9 variants as DGS/VCFS predisposing factors. We applied FISH using fosmid probes on chromatin fibers to analyze the number of tandem repeat blocks in LCR22 in two DGS/VCFS fathers-of-origin with proven 22q11.2 NAHR susceptibility. Results revealed copy number variations (CNVs) of L9 and K3 fosmids in these individuals compared to controls. The total number of L9 and K3 copies was also characterized using droplet digital PCR (ddPCR). Although we were unable to confirm variations, we detected an additional L9 amplicon corresponding to a pseudogene. Moreover, none of the eight DGS/VCFS parents-of-origin was heterozygote for the inv(22)(q11.2) haplotype. PRDM9 sequencing showed equivalent allelic distributions between DGS/VCFS parents-of-origin and controls, although a new PRDM9 allele (L50) was identified in one case. Our results support the hypothesis that LCR22s variations influences 22q11.2 NAHR events, however further studies are needed to confirm this association and clarify the contribution of pseudogenes and rare PDRM9 alleles to NAHR susceptibility.
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14
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Witte AK, Mester P, Fister S, Witte M, Schoder D, Rossmanith P. A Systematic Investigation of Parameters Influencing Droplet Rain in the Listeria monocytogenes prfA Assay - Reduction of Ambiguous Results in ddPCR. PLoS One 2016; 11:e0168179. [PMID: 27992475 PMCID: PMC5167268 DOI: 10.1371/journal.pone.0168179] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 11/25/2016] [Indexed: 11/18/2022] Open
Abstract
The droplet digital polymerase chain reaction (ddPCR) determines DNA amounts based upon the pattern of positive and negative droplets, according to Poisson distribution, without the use of external standards. However, division into positive and negative droplets is often not clear because a part of the droplets has intermediate fluorescence values, appearing as “rain” in the plot. Despite the droplet rain, absolute quantification with ddPCR is possible, as shown previously for the prfA assay in quantifying Listeria monocytogenes. Nevertheless, reducing the rain, and thus ambiguous results, promotes the accuracy and credibility of ddPCR. In this study, we extensively investigated chemical and physical parameters for optimizing the prfA assay for ddPCR. While differences in the concentration of all chemicals and the dye, quencher and supplier of the probe did not alter the droplet pattern, changes in the PCR cycling program, such as prolonged times and increased cycle numbers, improved the assay.
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Affiliation(s)
- Anna Kristina Witte
- Christian Doppler Laboratory for Monitoring of Microbial Contaminants, Institute of Milk Hygiene, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Patrick Mester
- Christian Doppler Laboratory for Monitoring of Microbial Contaminants, Institute of Milk Hygiene, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Susanne Fister
- Christian Doppler Laboratory for Monitoring of Microbial Contaminants, Institute of Milk Hygiene, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Matthias Witte
- Department of Psychology, University of Graz, Graz, Austria
| | - Dagmar Schoder
- Christian Doppler Laboratory for Monitoring of Microbial Contaminants, Institute of Milk Hygiene, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
- Institute of Milk Hygiene, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Peter Rossmanith
- Christian Doppler Laboratory for Monitoring of Microbial Contaminants, Institute of Milk Hygiene, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
- Institute of Milk Hygiene, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
- * E-mail:
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15
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Buschmann D, Haberberger A, Kirchner B, Spornraft M, Riedmaier I, Schelling G, Pfaffl MW. Toward reliable biomarker signatures in the age of liquid biopsies - how to standardize the small RNA-Seq workflow. Nucleic Acids Res 2016; 44:5995-6018. [PMID: 27317696 PMCID: PMC5291277 DOI: 10.1093/nar/gkw545] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 06/03/2016] [Indexed: 12/21/2022] Open
Abstract
Small RNA-Seq has emerged as a powerful tool in transcriptomics, gene expression profiling and biomarker discovery. Sequencing cell-free nucleic acids, particularly microRNA (miRNA), from liquid biopsies additionally provides exciting possibilities for molecular diagnostics, and might help establish disease-specific biomarker signatures. The complexity of the small RNA-Seq workflow, however, bears challenges and biases that researchers need to be aware of in order to generate high-quality data. Rigorous standardization and extensive validation are required to guarantee reliability, reproducibility and comparability of research findings. Hypotheses based on flawed experimental conditions can be inconsistent and even misleading. Comparable to the well-established MIQE guidelines for qPCR experiments, this work aims at establishing guidelines for experimental design and pre-analytical sample processing, standardization of library preparation and sequencing reactions, as well as facilitating data analysis. We highlight bottlenecks in small RNA-Seq experiments, point out the importance of stringent quality control and validation, and provide a primer for differential expression analysis and biomarker discovery. Following our recommendations will encourage better sequencing practice, increase experimental transparency and lead to more reproducible small RNA-Seq results. This will ultimately enhance the validity of biomarker signatures, and allow reliable and robust clinical predictions.
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Affiliation(s)
- Dominik Buschmann
- Department of Animal Physiology and Immunology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University Munich, Goethestraße 29, 80336 München, Germany
| | - Anna Haberberger
- Department of Animal Physiology and Immunology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Benedikt Kirchner
- Department of Animal Physiology and Immunology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Melanie Spornraft
- Department of Animal Physiology and Immunology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Irmgard Riedmaier
- Eurofins Medigenomix Forensik GmbH, Anzinger Straße 7a, 85560 Ebersberg, Germany Department of Anesthesiology, University Hospital, Ludwig-Maximilians-University Munich, Marchioninistraße 15, 81377 München, Germany
| | - Gustav Schelling
- Department of Physiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany
| | - Michael W Pfaffl
- Department of Animal Physiology and Immunology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany
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16
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Aigrain L, Gu Y, Quail MA. Quantitation of next generation sequencing library preparation protocol efficiencies using droplet digital PCR assays - a systematic comparison of DNA library preparation kits for Illumina sequencing. BMC Genomics 2016; 17:458. [PMID: 27297323 PMCID: PMC4906846 DOI: 10.1186/s12864-016-2757-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 05/19/2016] [Indexed: 02/03/2023] Open
Abstract
Background The emergence of next-generation sequencing (NGS) technologies in the past decade has allowed the democratization of DNA sequencing both in terms of price per sequenced bases and ease to produce DNA libraries. When it comes to preparing DNA sequencing libraries for Illumina, the current market leader, a plethora of kits are available and it can be difficult for the users to determine which kit is the most appropriate and efficient for their applications; the main concerns being not only cost but also minimal bias, yield and time efficiency. Results We compared 9 commercially available library preparation kits in a systematic manner using the same DNA sample by probing the amount of DNA remaining after each protocol steps using a new droplet digital PCR (ddPCR) assay. This method allows the precise quantification of fragments bearing either adaptors or P5/P7 sequences on both ends just after ligation or PCR enrichment. We also investigated the potential influence of DNA input and DNA fragment size on the final library preparation efficiency. The overall library preparations efficiencies of the libraries show important variations between the different kits with the ones combining several steps into a single one exhibiting some final yields 4 to 7 times higher than the other kits. Detailed ddPCR data also reveal that the adaptor ligation yield itself varies by more than a factor of 10 between kits, certain ligation efficiencies being so low that it could impair the original library complexity and impoverish the sequencing results. When a PCR enrichment step is necessary, lower adaptor-ligated DNA inputs leads to greater amplification yields, hiding the latent disparity between kits. Conclusion We describe a ddPCR assay that allows us to probe the efficiency of the most critical step in the library preparation, ligation, and to draw conclusion on which kits is more likely to preserve the sample heterogeneity and reduce the need of amplification. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2757-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Louise Aigrain
- Wellcome Trust Sanger Institute, Wellcome Trust Campus, Hinxton, Cambs, CB10 1SA, UK.
| | - Yong Gu
- Wellcome Trust Sanger Institute, Wellcome Trust Campus, Hinxton, Cambs, CB10 1SA, UK
| | - Michael A Quail
- Wellcome Trust Sanger Institute, Wellcome Trust Campus, Hinxton, Cambs, CB10 1SA, UK
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17
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Bhat S, Emslie KR. Digital polymerase chain reaction for characterisation of DNA reference materials. BIOMOLECULAR DETECTION AND QUANTIFICATION 2016; 10:47-49. [PMID: 27990349 PMCID: PMC5154631 DOI: 10.1016/j.bdq.2016.04.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 03/30/2016] [Accepted: 04/01/2016] [Indexed: 12/26/2022]
Abstract
Accurate, reliable and reproducible quantification of nucleic acids (DNA/RNA) is important for many diagnostic applications and in routine laboratory testing, for example, for pathogen detection and detection of genetically modified organisms in food. To ensure reliable nucleic acid measurement, reference materials (RM) that are accurately characterised for quantity of target nucleic acid sequences (in copy number or copy number concentration) with a known measurement uncertainty are needed. Recently developed digital polymerase chain reaction (dPCR) technology allows absolute and accurate quantification of nucleic acid target sequences without need for a reference standard. Due to these properties, this technique has the potential to not only improve routine quantitative nucleic acid analysis, but also to be used as a reference method for certification of nucleic acid RM. The article focuses on the use and application of both dPCR and RMs for accurate quantification.
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Affiliation(s)
- Somanath Bhat
- National Measurement Institute, Lindfield, NSW 2070, Australia
| | - Kerry R Emslie
- National Measurement Institute, Lindfield, NSW 2070, Australia
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18
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Comparison of DNA Quantification Methods for Next Generation Sequencing. Sci Rep 2016; 6:24067. [PMID: 27048884 PMCID: PMC4822169 DOI: 10.1038/srep24067] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 03/21/2016] [Indexed: 12/18/2022] Open
Abstract
Next Generation Sequencing (NGS) is a powerful tool that depends on loading a precise amount of DNA onto a flowcell. NGS strategies have expanded our ability to investigate genomic phenomena by referencing mutations in cancer and diseases through large-scale genotyping, developing methods to map rare chromatin interactions (4C; 5C and Hi-C) and identifying chromatin features associated with regulatory elements (ChIP-seq, Bis-Seq, ChiA-PET). While many methods are available for DNA library quantification, there is no unambiguous gold standard. Most techniques use PCR to amplify DNA libraries to obtain sufficient quantities for optical density measurement. However, increased PCR cycles can distort the library’s heterogeneity and prevent the detection of rare variants. In this analysis, we compared new digital PCR technologies (droplet digital PCR; ddPCR, ddPCR-Tail) with standard methods for the titration of NGS libraries. DdPCR-Tail is comparable to qPCR and fluorometry (QuBit) and allows sensitive quantification by analysis of barcode repartition after sequencing of multiplexed samples. This study provides a direct comparison between quantification methods throughout a complete sequencing experiment and provides the impetus to use ddPCR-based quantification for improvement of NGS quality.
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19
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Gregory MT, Bertout JA, Ericson NG, Taylor SD, Mukherjee R, Robins HS, Drescher CW, Bielas JH. Targeted single molecule mutation detection with massively parallel sequencing. Nucleic Acids Res 2015; 44:e22. [PMID: 26384417 PMCID: PMC4756847 DOI: 10.1093/nar/gkv915] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 09/02/2015] [Indexed: 11/14/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have transformed genomic research and have the potential to revolutionize clinical medicine. However, the background error rates of sequencing instruments and limitations in targeted read coverage have precluded the detection of rare DNA sequence variants by NGS. Here we describe a method, termed CypherSeq, which combines double-stranded barcoding error correction and rolling circle amplification (RCA)-based target enrichment to vastly improve NGS-based rare variant detection. The CypherSeq methodology involves the ligation of sample DNA into circular vectors, which contain double-stranded barcodes for computational error correction and adapters for library preparation and sequencing. CypherSeq is capable of detecting rare mutations genome-wide as well as those within specific target genes via RCA-based enrichment. We demonstrate that CypherSeq is capable of correcting errors incurred during library preparation and sequencing to reproducibly detect mutations down to a frequency of 2.4 × 10−7 per base pair, and report the frequency and spectra of spontaneous and ethyl methanesulfonate-induced mutations across the Saccharomycescerevisiae genome.
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Affiliation(s)
- Mark T Gregory
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jessica A Bertout
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Nolan G Ericson
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Sean D Taylor
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Rithun Mukherjee
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Harlan S Robins
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Charles W Drescher
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jason H Bielas
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA Department of Pathology, University of Washington, Seattle, WA 98195, USA
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20
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Kim TG, Jeong SY, Cho KS. Development of droplet digital PCR assays for methanogenic taxa and examination of methanogen communities in full-scale anaerobic digesters. Appl Microbiol Biotechnol 2014; 99:445-58. [DOI: 10.1007/s00253-014-6007-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 07/30/2014] [Accepted: 07/31/2014] [Indexed: 01/14/2023]
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21
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Miotke L, Lau BT, Rumma RT, Ji HP. High sensitivity detection and quantitation of DNA copy number and single nucleotide variants with single color droplet digital PCR. Anal Chem 2014; 86:2618-24. [PMID: 24483992 PMCID: PMC3982983 DOI: 10.1021/ac403843j] [Citation(s) in RCA: 158] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
![]()
In
this study, we present a highly customizable method for quantifying
copy number and point mutations utilizing a single-color, droplet
digital PCR platform. Droplet digital polymerase chain reaction (ddPCR)
is rapidly replacing real-time quantitative PCR (qRT-PCR) as an efficient
method of independent DNA quantification. Compared to quantative PCR,
ddPCR eliminates the needs for traditional standards; instead, it
measures target and reference DNA within the same well. The applications
for ddPCR are widespread including targeted quantitation of genetic
aberrations, which is commonly achieved with a two-color fluorescent
oligonucleotide probe (TaqMan) design. However, the overall cost and
need for optimization can be greatly reduced with an alternative method
of distinguishing between target and reference products using the
nonspecific DNA binding properties of EvaGreen (EG) dye. By manipulating
the length of the target and reference amplicons, we can distinguish
between their fluorescent signals and quantify each independently.
We demonstrate the effectiveness of this method by examining copy
number in the proto-oncogene FLT3 and the common
V600E point mutation in BRAF. Using a series of well-characterized
control samples and cancer cell lines, we confirmed the accuracy of
our method in quantifying mutation percentage and integer value copy
number changes. As another novel feature, our assay was able to detect
a mutation comprising less than 1% of an otherwise wild-type sample,
as well as copy number changes from cancers even in the context of
significant dilution with normal DNA. This flexible and cost-effective
method of independent DNA quantification proves to be a robust alternative
to the commercialized TaqMan assay.
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Affiliation(s)
- Laura Miotke
- Division of Oncology, Department of Medicine, Stanford University School of Medicine , CCSR 1115, 269 Campus Drive, Stanford, California, 94305 United States
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22
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Lian DS, Zhao SJ. Capillary electrophoresis based on the nucleic acid detection in the application of cancer diagnosis and therapy. Analyst 2014; 139:3492-506. [DOI: 10.1039/c4an00400k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
This review focuses on capillary electrophoresis-based nucleic acid detection as it is applied to cancer diagnosis and therapy, and provides an introduction to the drawbacks and future developments of analysis with CE.
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Affiliation(s)
- Dong-Sheng Lian
- School of Bioscience and Bioengineering
- South China University of Technology
- Guangzhou 510006, China
| | - Shu-Jin Zhao
- School of Bioscience and Bioengineering
- South China University of Technology
- Guangzhou 510006, China
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23
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McDermott GP, Do D, Litterst CM, Maar D, Hindson CM, Steenblock ER, Legler TC, Jouvenot Y, Marrs SH, Bemis A, Shah P, Wong J, Wang S, Sally D, Javier L, Dinio T, Han C, Brackbill TP, Hodges SP, Ling Y, Klitgord N, Carman GJ, Berman JR, Koehler RT, Hiddessen AL, Walse P, Bousse L, Tzonev S, Hefner E, Hindson BJ, Cauly TH, Hamby K, Patel VP, Regan JF, Wyatt PW, Karlin-Neumann GA, Stumbo DP, Lowe AJ. Multiplexed Target Detection Using DNA-Binding Dye Chemistry in Droplet Digital PCR. Anal Chem 2013; 85:11619-27. [PMID: 24180464 DOI: 10.1021/ac403061n] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Geoffrey P. McDermott
- The
Digital Biology Center, Bio-Rad Laboratories, Inc., 5731 West Las Positas
Boulevard, Pleasanton, California 94566, United States
| | - Duc Do
- The
Digital Biology Center, Bio-Rad Laboratories, Inc., 5731 West Las Positas
Boulevard, Pleasanton, California 94566, United States
| | - Claudia M. Litterst
- The
Digital Biology Center, Bio-Rad Laboratories, Inc., 5731 West Las Positas
Boulevard, Pleasanton, California 94566, United States
| | - Dianna Maar
- The
Digital Biology Center, Bio-Rad Laboratories, Inc., 5731 West Las Positas
Boulevard, Pleasanton, California 94566, United States
| | | | - Erin R. Steenblock
- The
Digital Biology Center, Bio-Rad Laboratories, Inc., 5731 West Las Positas
Boulevard, Pleasanton, California 94566, United States
| | - Tina C. Legler
- The
Digital Biology Center, Bio-Rad Laboratories, Inc., 5731 West Las Positas
Boulevard, Pleasanton, California 94566, United States
| | - Yann Jouvenot
- The
Digital Biology Center, Bio-Rad Laboratories, Inc., 5731 West Las Positas
Boulevard, Pleasanton, California 94566, United States
| | - Samuel H. Marrs
- The
Digital Biology Center, Bio-Rad Laboratories, Inc., 5731 West Las Positas
Boulevard, Pleasanton, California 94566, United States
| | - Adam Bemis
- The
Digital Biology Center, Bio-Rad Laboratories, Inc., 5731 West Las Positas
Boulevard, Pleasanton, California 94566, United States
| | - Pallavi Shah
- The
Digital Biology Center, Bio-Rad Laboratories, Inc., 5731 West Las Positas
Boulevard, Pleasanton, California 94566, United States
| | - Josephine Wong
- The
Digital Biology Center, Bio-Rad Laboratories, Inc., 5731 West Las Positas
Boulevard, Pleasanton, California 94566, United States
| | - Shenglong Wang
- The
Digital Biology Center, Bio-Rad Laboratories, Inc., 5731 West Las Positas
Boulevard, Pleasanton, California 94566, United States
| | - David Sally
- The
Digital Biology Center, Bio-Rad Laboratories, Inc., 5731 West Las Positas
Boulevard, Pleasanton, California 94566, United States
| | - Leanne Javier
- The
Digital Biology Center, Bio-Rad Laboratories, Inc., 5731 West Las Positas
Boulevard, Pleasanton, California 94566, United States
| | - Theresa Dinio
- The
Digital Biology Center, Bio-Rad Laboratories, Inc., 5731 West Las Positas
Boulevard, Pleasanton, California 94566, United States
| | - Chunxiao Han
- The
Digital Biology Center, Bio-Rad Laboratories, Inc., 5731 West Las Positas
Boulevard, Pleasanton, California 94566, United States
| | - Timothy P. Brackbill
- The
Digital Biology Center, Bio-Rad Laboratories, Inc., 5731 West Las Positas
Boulevard, Pleasanton, California 94566, United States
| | - Shawn P. Hodges
- The
Digital Biology Center, Bio-Rad Laboratories, Inc., 5731 West Las Positas
Boulevard, Pleasanton, California 94566, United States
| | - Yunfeng Ling
- The
Digital Biology Center, Bio-Rad Laboratories, Inc., 5731 West Las Positas
Boulevard, Pleasanton, California 94566, United States
| | - Niels Klitgord
- The
Digital Biology Center, Bio-Rad Laboratories, Inc., 5731 West Las Positas
Boulevard, Pleasanton, California 94566, United States
| | - George J. Carman
- The
Digital Biology Center, Bio-Rad Laboratories, Inc., 5731 West Las Positas
Boulevard, Pleasanton, California 94566, United States
| | - Jennifer R. Berman
- The
Digital Biology Center, Bio-Rad Laboratories, Inc., 5731 West Las Positas
Boulevard, Pleasanton, California 94566, United States
| | - Ryan T. Koehler
- VerdAscend Sciences, West Linn, Oregon, 97068, United States
| | - Amy L. Hiddessen
- Purigen Biosystems, Inc., Alviso, California 95002, United States
| | - Pramod Walse
- The
Digital Biology Center, Bio-Rad Laboratories, Inc., 5731 West Las Positas
Boulevard, Pleasanton, California 94566, United States
| | - Luc Bousse
- The
Digital Biology Center, Bio-Rad Laboratories, Inc., 5731 West Las Positas
Boulevard, Pleasanton, California 94566, United States
| | - Svilen Tzonev
- The
Digital Biology Center, Bio-Rad Laboratories, Inc., 5731 West Las Positas
Boulevard, Pleasanton, California 94566, United States
| | - Eli Hefner
- The
Digital Biology Center, Bio-Rad Laboratories, Inc., 5731 West Las Positas
Boulevard, Pleasanton, California 94566, United States
| | | | - Thomas H. Cauly
- The
Digital Biology Center, Bio-Rad Laboratories, Inc., 5731 West Las Positas
Boulevard, Pleasanton, California 94566, United States
| | - Keith Hamby
- The
Digital Biology Center, Bio-Rad Laboratories, Inc., 5731 West Las Positas
Boulevard, Pleasanton, California 94566, United States
| | - Viresh P. Patel
- The
Digital Biology Center, Bio-Rad Laboratories, Inc., 5731 West Las Positas
Boulevard, Pleasanton, California 94566, United States
| | - John F. Regan
- The
Digital Biology Center, Bio-Rad Laboratories, Inc., 5731 West Las Positas
Boulevard, Pleasanton, California 94566, United States
| | - Paul W. Wyatt
- The
Digital Biology Center, Bio-Rad Laboratories, Inc., 5731 West Las Positas
Boulevard, Pleasanton, California 94566, United States
| | - George A. Karlin-Neumann
- The
Digital Biology Center, Bio-Rad Laboratories, Inc., 5731 West Las Positas
Boulevard, Pleasanton, California 94566, United States
| | | | - Adam J. Lowe
- The
Digital Biology Center, Bio-Rad Laboratories, Inc., 5731 West Las Positas
Boulevard, Pleasanton, California 94566, United States
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