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Bonilla DA, Orozco CA, Forero DA, Odriozola A. Techniques, procedures, and applications in host genetic analysis. ADVANCES IN GENETICS 2024; 111:1-79. [PMID: 38908897 DOI: 10.1016/bs.adgen.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/24/2024]
Abstract
This chapter overviews genetic techniques' fundamentals and methodological features, including different approaches, analyses, and applications that have contributed to advancing health and disease. The aim is to describe laboratory methodologies and analyses employed to understand the genetic landscape of different biological contexts, from conventional techniques to cutting-edge technologies. Besides describing detailed aspects of the polymerase chain reaction (PCR) and derived types as one of the principles for many novel techniques, we also discuss microarray analysis, next-generation sequencing, and genome editing technologies such as transcription activator-like effector nucleases (TALENs) and the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems. These techniques study several phenotypes, ranging from autoimmune disorders to viral diseases. The significance of integrating diverse genetic methodologies and tools to understand host genetics comprehensively and addressing the ethical, legal, and social implications (ELSI) associated with using genetic information is highlighted. Overall, the methods, procedures, and applications in host genetic analysis provided in this chapter furnish researchers and practitioners with a roadmap for navigating the dynamic landscape of host-genome interactions.
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Affiliation(s)
- Diego A Bonilla
- Hologenomiks Research Group, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain; Research Division, Dynamical Business & Science Society-DBSS International SAS, Bogotá, Colombia.
| | - Carlos A Orozco
- Grupo de Investigación en Biología del Cáncer, Instituto Nacional de Cancerología de Colombia, Bogotá, Colombia
| | - Diego A Forero
- School of Health and Sport Sciences, Fundación Universitaria del Área Andina, Bogotá, Colombia
| | - Adrián Odriozola
- Hologenomiks Research Group, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
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Yuen BPN, Wong KS, So YM, Kwok WH, Cheung HW, Wan TSM, Ho ENM, Wong WT. Gene Doping Control Analysis of Human Erythropoietin Transgene in Equine Plasma by PCR-Liquid Chromatography High-Resolution Tandem Mass Spectrometry. Anal Chem 2024; 96:5307-5314. [PMID: 38504497 DOI: 10.1021/acs.analchem.4c00247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Gene doping involves the misuse of genetic materials to alter an athlete's performance, which is banned at all times in both human and equine sports. Quantitative polymerase chain reaction (qPCR) assays have been used to control the misuse of transgenes in equine sports. Our laboratory recently developed and implemented duplex as well as multiplex qPCR assays for transgenes detection. To further advance gene doping control, we have developed for the first time a sensitive and definitive PCR-liquid chromatography high-resolution tandem mass spectrometry (PCR-LC-HRMS/MS) method for transgene detection with an estimated limit of detection of below 100 copies/mL for the human erythropoietin (hEPO) transgene in equine plasma. The method involved magnetic-glass-particle-based extraction of DNA from equine plasma prior to PCR amplification with 2'-deoxyuridine 5'-triphosphate (dUTP) followed by treatments with uracil DNA glycosylase and hot piperidine for selective cleavage to give small oligonucleotide fragments. The resulting DNA fragments were then analyzed by LC-HRMS/MS. The applicability of this method has been demonstrated by the successful detection of hEPO transgene in a blood sample collected from a gelding (castrated male horse) that had been administered the transgene. This novel approach not only serves as a complementary method for transgene detection but also paves the way for developing a generic PCR-LC-HRMS/MS method for the detection of multiple transgenes.
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Affiliation(s)
- Bruce Pui-Nam Yuen
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
- Racing Laboratory, The Hong Kong Jockey Club, Sha Tin Racecourse, Sha Tin N.T., Hong Kong, China
| | - Kin-Sing Wong
- Racing Laboratory, The Hong Kong Jockey Club, Sha Tin Racecourse, Sha Tin N.T., Hong Kong, China
| | - Yat-Ming So
- Racing Laboratory, The Hong Kong Jockey Club, Sha Tin Racecourse, Sha Tin N.T., Hong Kong, China
| | - Wai Him Kwok
- Racing Laboratory, The Hong Kong Jockey Club, Sha Tin Racecourse, Sha Tin N.T., Hong Kong, China
| | - Hiu Wing Cheung
- Racing Laboratory, The Hong Kong Jockey Club, Sha Tin Racecourse, Sha Tin N.T., Hong Kong, China
| | - Terence See Ming Wan
- Racing Laboratory, The Hong Kong Jockey Club, Sha Tin Racecourse, Sha Tin N.T., Hong Kong, China
| | - Emmie Ngai-Man Ho
- Racing Laboratory, The Hong Kong Jockey Club, Sha Tin Racecourse, Sha Tin N.T., Hong Kong, China
| | - Wing-Tak Wong
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China
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Xing Y, Wang Y, Li X, Pang S. Digital microfluidics methods for nucleic acid detection: A mini review. BIOMICROFLUIDICS 2024; 18:021501. [PMID: 38456173 PMCID: PMC10917463 DOI: 10.1063/5.0180125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 02/01/2024] [Indexed: 03/09/2024]
Abstract
Many serious infectious diseases have occurred throughout human history. Rapid and accurate detection as well as the isolation of infected individuals, through nucleic acid testing, are effective means of containing the spread of these viruses. However, traditional nucleic acid testing methods rely on complex machines and specialized personnel, making it difficult to achieve large-scale, high-throughput, and rapid detection. In recent years, digital microfluidics has emerged as a promising technology that integrates various fields, including electrokinetics, acoustics, optics, magnetism, and mechanics. By leveraging the advantages of these different technologies, digital microfluidic chips offer several benefits, such as high detection throughput, integration of multiple functions, low reagent consumption, and portability. This rapid and efficient testing is crucial in the timely detection and isolation of infected individuals to prevent the virus spread. Another advantage is the low reagent consumption of digital microfluidic chips. Compared to traditional methods, these chips require smaller volumes of reagents, resulting in cost savings and reduced waste. Furthermore, digital microfluidic chips are portable and can be easily integrated into point-of-care testing devices. This enables testing to be conducted in remote or resource-limited areas, where access to complex laboratory equipment may be limited. Onsite testing reduces the time and cost associated with sample transportation. In conclusion, bioassay technologies based on digital microfluidic principles have the potential to significantly improve infectious disease detection and control. By enabling rapid, high-throughput, and portable testing, these technologies enhance our ability to contain the spread of infectious diseases and effectively manage public health outbreaks.
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Affiliation(s)
- Youqiang Xing
- School of Mechanical Engineering, Southeast University, Nanjing 211189, Jiangsu Province, People’s Republic of China
| | - Yan Wang
- Clinical Laboratory, Yantai Yuhuangding Hospital, Yantai 264000, Shandong Province, People’s Republic of China
| | - Xiang Li
- Bio-manufacturing Engineering Laboratory, Tsinghua Shenzhen International Graduate School, Tsinghua University, Guangdong 518000, Shenzhen, People’s Republic of China
| | - Shangran Pang
- Jinzhong Normal Junior College, 189 Guang'an Street, Yuci District, Jinzhong 030600, Shanxi Province, People’s Republic of China
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Pessoa FMCDP, Viana VBDJ, de Oliveira MB, Nogueira BMD, Ribeiro RM, Oliveira DDS, Lopes GS, Vieira RPG, de Moraes Filho MO, de Moraes MEA, Khayat AS, Moreira FC, Moreira-Nunes CA. Validation of Endogenous Control Genes by Real-Time Quantitative Reverse Transcriptase Polymerase Chain Reaction for Acute Leukemia Gene Expression Studies. Genes (Basel) 2024; 15:151. [PMID: 38397141 PMCID: PMC10887733 DOI: 10.3390/genes15020151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/09/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
Reference genes are used as internal reaction controls for gene expression analysis, and for this reason, they are considered reliable and must meet several important criteria. In view of the absence of studies regarding the best reference gene for the analysis of acute leukemia patients, a panel of genes commonly used as endogenous controls was selected from the literature for stability analysis: Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), Abelson murine leukemia viral oncogene human homolog 1 (ABL), Hypoxanthine phosphoribosyl-transferase 1 (HPRT1), Ribosomal protein lateral stalk subunit P0 (RPLP0), β-actin (ACTB) and TATA box binding protein (TBP). The stability of candidate reference genes was analyzed according to three statistical methods of assessment, namely, NormFinder, GeNorm and R software (version 4.0.3). From this study's analysis, it was possible to identify that the endogenous set composed of ACTB, ABL, TBP and RPLP0 demonstrated good performances and stable expressions between the analyzed groups. In addition to that, the GAPDH and HPRT genes could not be classified as good reference genes, considering that they presented a high standard deviation and great variability between groups, indicating low stability. Given these findings, this study suggests the main endogenous gene set for use as a control/reference for the gene expression in peripheral blood and bone marrow samples from patients with acute leukemias is composed of the ACTB, ABL, TBP and RPLP0 genes. Researchers may choose two to three of these housekeeping genes to perform data normalization.
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Affiliation(s)
- Flávia Melo Cunha de Pinho Pessoa
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
| | - Vitória Beatriz de Jesus Viana
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
| | - Marcelo Braga de Oliveira
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
| | - Beatriz Maria Dias Nogueira
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
| | | | - Deivide de Sousa Oliveira
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
- Department of Hematology, Fortaleza General Hospital (HGF), Fortaleza 60150-160, CE, Brazil
| | - Germison Silva Lopes
- Department of Hematology, César Cals General Hospital, Fortaleza 60015-152, CE, Brazil;
| | | | - Manoel Odorico de Moraes Filho
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
| | - Maria Elisabete Amaral de Moraes
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
| | - André Salim Khayat
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
| | - Fabiano Cordeiro Moreira
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
| | - Caroline Aquino Moreira-Nunes
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
- Central Unity, Molecular Biology Laboratory, Clementino Fraga Group, Fortaleza 60115-170, CE, Brazil
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Dignan LM, Turiello R, Layne TR, O'Connell KC, Hickey J, Chapman J, Poulter MD, Landers JP. An ultrafast SARS-CoV-2 virus enrichment and extraction method compatible with multiple modalities for RNA detection. Anal Chim Acta 2021; 1180:338846. [PMID: 34538333 PMCID: PMC8277111 DOI: 10.1016/j.aca.2021.338846] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/10/2021] [Accepted: 07/06/2021] [Indexed: 01/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a zoonotic RNA virus characterized by high transmission rates and pathogenicity worldwide. Continued control of the COVID-19 pandemic requires the diversification of rapid, easy to use, sensitive, and portable methods for SARS-CoV-2 sample preparation and analysis. Here, we propose a method for SARS-CoV-2 viral enrichment and enzymatic extraction of RNA from clinically relevant matrices in under 10 min. This technique utilizes affinity-capture hydrogel particles to concentrate SARS-CoV-2 from solution, and leverages existing PDQeX technology for RNA isolation. Characterization of our method is accomplished with reverse transcription real-time polymerase chain reaction (RT-PCR) for relative, comparative RNA detection. In a double-blind study analyzing viral transport media (VTM) obtained from clinical nasopharyngeal swabs, our sample preparation method demonstrated both comparable results to a routinely used commercial extraction kit and 100% concordance with laboratory diagnoses. Compatibility of eluates with alternative forms of analysis was confirmed using microfluidic RT-PCR (μRT-PCR), recombinase polymerase amplification (RPA), and loop-mediated isothermal amplification (LAMP). The alternative methods explored here conveyed successful amplification from all RNA eluates originating from positive clinical samples. Finally, this method demonstrated high performance within a saliva matrix across a broad range of viral titers and dilutions up to 90% saliva matrix, and sets the stage for miniaturization to the microscale.
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Affiliation(s)
- Leah M. Dignan
- Departments of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Rachelle Turiello
- Departments of Chemistry, University of Virginia, Charlottesville, VA 22904, USA,Corresponding author
| | - Tiffany R. Layne
- Departments of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Killian C. O'Connell
- Departments of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Jeff Hickey
- MicroGEM International PLC., Charlottesville, VA 22904, USA
| | - Jeff Chapman
- MicroGEM International PLC., Charlottesville, VA 22904, USA
| | - Melinda D. Poulter
- Departments of Pathology, University of Virginia, Charlottesville, VA 22904, USA
| | - James P. Landers
- Departments of Chemistry, University of Virginia, Charlottesville, VA 22904, USA,MicroGEM International PLC., Charlottesville, VA 22904, USA,Departments of Pathology, University of Virginia, Charlottesville, VA 22904, USA,Departments of Clinical Microbiology, University of Virginia, Charlottesville, VA 22904, USA,Departments of Mechanical and Aerospace Engineering, University of Virginia, Charlottesville, VA 22904, USA
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Vazirzadeh A, Roosta H, Masoumi H, Farhadi A, Jeffs A. Long-term effects of three probiotics, singular or combined, on serum innate immune parameters and expressions of cytokine genes in rainbow trout during grow-out. FISH & SHELLFISH IMMUNOLOGY 2020; 98:748-757. [PMID: 31726098 DOI: 10.1016/j.fsi.2019.11.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 10/31/2019] [Accepted: 11/10/2019] [Indexed: 06/10/2023]
Abstract
The long-term effects of three dietary probiotics on rainbow trout during grow-out (mean body weight = 250 ± 50 g) were investigated by feeding for 130 days on eight diet treatments supplemented with Lactobacillus buchneri, L. fermentum and Saccharomyces cerevisiae at 107 CFU/g, singularly or in combination. Fish samples were taken for biochemical and immunological analysis in addition to growth performance indices at days 30 and 130 of the experiment. The expression levels of TNF-α and IL-1β genes were also measured at day 130. A positive effect on food conversion was observed in rainbow trout with dietary inclusion of S. cerevisiae (P < 0.05) over 130 days. Also, the total number of white blood cells and their differential count (blood neutrophils, lymphocytes and monocytes), as well as respiratory burst activity were all significantly affected by different treatments at 130 days (P < 0.05). Moreover, at 130 days there was a significant increase in the expression of TNF-α and IL-1β in yeast present treatment compared to the control group (P < 0.05), but no significant difference in the combined probiotic treatments from control group. Yeast and L. buchneri showed a contrary effect on the immune gene expression regulation. Serum cholesterol was significantly lower in all treatments receiving yeast as a dietary probiotic, either alone or in combination with other probiotics. However, none of the probiotic treatments had a significant effect on trout growth performance, or total protein, albumin, globulin, triglyceride and the red blood cell count after 30 or 130 days. Overall, the results suggest that inclusion of a single dietary probiotic, especially S. cerevisiae, in rainbow trout during grow-out has a greater positive effect than combinations of probiotics on the immune system.
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Affiliation(s)
- Arya Vazirzadeh
- Department of Natural Resources and Environmental Engineering, School of Agriculture, Shiraz University, Shiraz, 71441-65186, Iran.
| | - Hasan Roosta
- Department of Natural Resources and Environmental Engineering, School of Agriculture, Shiraz University, Shiraz, 71441-65186, Iran
| | - Hajar Masoumi
- Department of Natural Resources and Environmental Engineering, School of Agriculture, Shiraz University, Shiraz, 71441-65186, Iran
| | - Ahmad Farhadi
- Department of Natural Resources and Environmental Engineering, School of Agriculture, Shiraz University, Shiraz, 71441-65186, Iran.
| | - Andrew Jeffs
- School of Biological Sciences and Institute of Marine Science, The University of Auckland, Auckland, New Zealand
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Affiliation(s)
- Jennifer A. Armstrong
- W.M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges Claremont California
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Taverniti V, Guglielmetti S. Methodological issues in the study of intestinal microbiota in irritable bowel syndrome. World J Gastroenterol 2014; 20:8821-8836. [PMID: 25083056 PMCID: PMC4112874 DOI: 10.3748/wjg.v20.i27.8821] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 04/10/2014] [Accepted: 06/05/2014] [Indexed: 02/06/2023] Open
Abstract
Irritable bowel syndrome (IBS) is an intestinal functional disorder with the highest prevalence in the industrialized world. The intestinal microbiota (IM) plays a role in the pathogenesis of IBS and is not merely a consequence of this disorder. Previous research efforts have not revealed unequivocal microbiological signatures of IBS, and the experimental results are contradictory. The experimental methodologies adopted to investigate the complex intestinal ecosystem drastically impact the quality and significance of the results. Therefore, to consider the methodological aspects of the research on IM in IBS, we reviewed 29 relevant original research articles identified through a PubMed search using three combinations of keywords: “irritable bowel syndrome + microflora”, “irritable bowel syndrome + microbiota” and “irritable bowel syndrome + microbiome”. For each study, we reviewed the quality and significance of the scientific evidence obtained with respect to the experimental method adopted. The data obtained from each study were compared with all considered publications to identify potential inconsistencies and explain contradictory results. The analytical revision of the studies referenced in the present review has contributed to the identification of microbial groups whose relative abundance significantly alters IBS, suggesting that these microbial groups could be IM signatures for this syndrome. The identification of microbial biomarkers in the IM can be advantageous for the development of new diagnostic tools and novel therapeutic strategies for the treatment of different subtypes of IBS.
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Mazaika E, Homsy J. Digital Droplet PCR: CNV Analysis and Other Applications. CURRENT PROTOCOLS IN HUMAN GENETICS 2014; 82:7.24.1-7.24.13. [PMID: 25042719 PMCID: PMC4355013 DOI: 10.1002/0471142905.hg0724s82] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Digital droplet PCR (ddPCR) is an assay that combines state-of-the-art microfluidics technology with TaqMan-based PCR to achieve precise target DNA quantification at high levels of sensitivity and specificity. Because quantification is achieved without the need for standard assays in an easy to interpret, unambiguous digital readout, ddPCR is far simpler, faster, and less error prone than real-time qPCR. The basic protocol can be modified with minor adjustments to suit a wide range of applications, such as CNV analysis, rare variant detection, SNP genotyping, and transcript quantification. This unit describes the ddPCR workflow in detail for the Bio-Rad QX100 system, but the theory and data interpretation are generalizable to any ddPCR system.
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Affiliation(s)
- Erica Mazaika
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Jason Homsy
- Department of Genetics, Harvard Medical School, Boston, Massachusetts,Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts
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