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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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Goh SK, Cox DRA, Wong BKL, Musafer A, Witkowski T, Do H, Muralidharan V, Dobrovic A. A Synthetic DNA Construct to Evaluate the Recovery Efficiency of Cell-Free DNA Extraction and Bisulfite Modification. Clin Chem 2021; 67:1201-1209. [PMID: 34151944 DOI: 10.1093/clinchem/hvab095] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 04/20/2021] [Indexed: 12/18/2022]
Abstract
BACKGROUND Despite improvements in the genetic and epigenetic analysis of cell-free DNA (cfDNA), there has been limited focus on assessing the preanalytical variables of recovery efficiency following cfDNA extraction and bisulfite modification. Quantification of recovery efficiency after these steps can facilitate quality assurance and improve reliability when comparing serial samples. METHODS We developed an exogenous DNA Construct to Evaluate the Recovery Efficiency of cfDNA extraction and BISulfite modification (CEREBIS) after cfDNA extraction and/or subsequent bisulfite modification from plasma. The strategic placement of cytosine bases in the 180 bp CEREBIS enabled PCR amplification of the construct by a single primer set both after plasma DNA extraction and following subsequent bisulfite modification. RESULTS Plasma samples derived from 8 organ transplant donors and 6 serial plasma samples derived from a liver transplant recipient were spiked with a known number of copies of CEREBIS. Recovery of CEREBIS after cfDNA extraction and bisulfite modification was quantified with high analytical accuracy by droplet digital PCR. The use of CEREBIS and quantification of its recovery was useful in identifying problematic extractions. Furthermore, its use was shown to be invaluable towards improving the reliability of the analysis of serial samples. CONCLUSIONS CEREBIS can be used as a spike-in control to address the preanalytical variable of recovery efficiency both after cfDNA extraction from plasma and following bisulfite modification. Our approach can be readily implemented and its application may have significant benefits, especially in settings where longitudinal quantification of cfDNA for disease monitoring is necessary.
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Affiliation(s)
- Su Kah Goh
- Department of Surgery-Austin Precinct, The University of Melbourne, Melbourne, Victoria, Australia.,Department of Surgery, Austin Hospital, HPB & Transplant Unit, Melbourne, Victoria, Australia.,Department of Surgery-Austin Precinct, Translational Genomics and Epigenomics Laboratory, The University of Melbourne, Melbourne, Victoria, Australia
| | - Daniel R A Cox
- Department of Surgery-Austin Precinct, The University of Melbourne, Melbourne, Victoria, Australia.,Department of Surgery, Austin Hospital, HPB & Transplant Unit, Melbourne, Victoria, Australia.,Department of Surgery-Austin Precinct, Translational Genomics and Epigenomics Laboratory, The University of Melbourne, Melbourne, Victoria, Australia
| | - Boris Ka Leong Wong
- Department of Surgery-Austin Precinct, Translational Genomics and Epigenomics Laboratory, The University of Melbourne, Melbourne, Victoria, Australia.,School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia.,Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
| | - Ashan Musafer
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
| | - Tom Witkowski
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
| | - Hongdo Do
- School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia.,The University of Melbourne, Parkville Precinct, Victoria, Australia.,Pathology Department, St Vincent's Hospital Melbourne, Fitzroy, Victoria, Australia
| | - Vijayaragavan Muralidharan
- Department of Surgery-Austin Precinct, The University of Melbourne, Melbourne, Victoria, Australia.,Department of Surgery, Austin Hospital, HPB & Transplant Unit, Melbourne, Victoria, Australia
| | - Alexander Dobrovic
- Department of Surgery-Austin Precinct, The University of Melbourne, Melbourne, Victoria, Australia.,Department of Surgery-Austin Precinct, Translational Genomics and Epigenomics Laboratory, The University of Melbourne, Melbourne, Victoria, Australia.,School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia.,Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
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Koebley SR, Mikheikin A, Leslie K, Guest D, McConnell-Wells W, Lehman JH, Al Juhaishi T, Zhang X, Roberts CH, Picco L, Toor A, Chesney A, Reed J. Digital Polymerase Chain Reaction Paired with High-Speed Atomic Force Microscopy for Quantitation and Length Analysis of DNA Length Polymorphisms. ACS NANO 2020; 14:15385-15393. [PMID: 33169971 DOI: 10.1021/acsnano.0c05897] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
DNA length polymorphisms are found in many serious diseases, and assessment of their length and abundance is often critical for accurate diagnosis. However, measuring their length and frequency in a mostly wild-type background, as occurs in many situations, remains challenging due to their variable and repetitive nature. To overcome these hurdles, we combined two powerful techniques, digital polymerase chain reaction (dPCR) and high-speed atomic force microscopy (HSAFM), to create a simple, rapid, and flexible method for quantifying both the size and proportion of DNA length polymorphisms. In our approach, individual amplicons from each dPCR partition are imaged and sized directly. We focused on internal tandem duplications (ITDs) located within the FLT3 gene, which are associated with acute myeloid leukemia and often indicative of a poor prognosis. In an analysis of over 1.5 million HSAFM-imaged amplicons from cell line and clinical samples containing FLT3-ITDs, dPCR-HSAFM returned the expected variant length and variant allele frequency, down to 5% variant samples. As a high-throughput method with single-molecule resolution, dPCR-HSAFM thus represents an advance in HSAFM analysis and a powerful tool for the diagnosis of length polymorphisms.
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Affiliation(s)
- Sean R Koebley
- Physics Department, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Andrey Mikheikin
- Physics Department, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Kevin Leslie
- Physics Department, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Daniel Guest
- Physics Department, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Wendy McConnell-Wells
- Physics Department, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Joshua H Lehman
- Physics Department, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Taha Al Juhaishi
- Department of Internal Medicine, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Xiaojie Zhang
- Department of Internal Medicine, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Catherine H Roberts
- Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Loren Picco
- Physics Department, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Amir Toor
- Department of Internal Medicine, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Alden Chesney
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Jason Reed
- Physics Department, Virginia Commonwealth University, Richmond, Virginia 23284, United States
- Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, United States
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Goh SK, Do H, Testro A, Pavlovic J, Vago A, Lokan J, Jones RM, Christophi C, Dobrovic A, Muralidharan V. The Measurement of Donor-Specific Cell-Free DNA Identifies Recipients With Biopsy-Proven Acute Rejection Requiring Treatment After Liver Transplantation. Transplant Direct 2019; 5:e462. [PMID: 31334336 PMCID: PMC6616138 DOI: 10.1097/txd.0000000000000902] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 03/15/2019] [Accepted: 03/28/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Assessment of donor-specific cell-free DNA (dscfDNA) in the recipient is emerging as a noninvasive biomarker of organ rejection after transplantation. We previously developed a digital polymerase chain reaction (PCR)-based approach that readily measures dscfDNA within clinically relevant turnaround times. Using this approach, we characterized the dynamics and evaluated the clinical utility of dscfDNA after liver transplantation (LT). METHODS Deletion/insertion polymorphisms were used to distinguish donor-specific DNA from recipient-specific DNA. Posttransplant dscfDNA was measured in the plasma of the recipients. In the longitudinal cohort, dscfDNA was serially measured at days 3, 7, 14, 28, and 42 in 20 recipients. In the cross-sectional cohort, dscfDNA was measured in 4 clinically stable recipients (>1-y posttransplant) and 16 recipients (>1-mo posttransplant) who were undergoing liver biopsies. RESULTS Recipients who underwent LT without complications demonstrated an exponential decline in dscfDNA. Median levels at days 3, 7, 14, 28, and 42 were 1936, 1015, 247, 90, and 66 copies/mL, respectively. dscfDNA was higher in recipients with treated biopsy-proven acute rejection (tBPAR) when compared to those without. The area under the receiver operator characteristic curve of dscfDNA was higher than that of routine liver function tests for tBPAR (dscfDNA: 98.8% with 95% confidence interval, 95.8%-100%; alanine aminotransferase: 85.7%; alkaline phosphatase: 66.4%; gamma-glutamyl transferase: 80.1%; and bilirubin: 35.4%). CONCLUSIONS dscfDNA as measured by probe-free droplet digital PCR methodology was reflective of organ health after LT. Our findings demonstrate the potential utility of dscfDNA as a diagnostic tool of tBPAR.
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Affiliation(s)
- Su Kah Goh
- Department of Surgery, The University of Melbourne, Austin Health, Heidelberg, VIC, Australia
- Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, Australia
| | - Hongdo Do
- Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, Australia
- School of Cancer Medicine, La Trobe University, Heidelberg, VIC, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, Australia
| | - Adam Testro
- Liver Transplant Unit, Austin Health, Heidelberg, VIC, Australia
- Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, VIC, Australia
| | - Julie Pavlovic
- Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, Australia
| | - Angela Vago
- Liver Transplant Unit, Austin Health, Heidelberg, VIC, Australia
| | - Julie Lokan
- Department of Anatomical Pathology, Austin Health, Heidelberg, VIC, Australia
| | - Robert M. Jones
- Department of Surgery, The University of Melbourne, Austin Health, Heidelberg, VIC, Australia
- Liver Transplant Unit, Austin Health, Heidelberg, VIC, Australia
- Hepato-Pancreato-Biliary & Transplant Surgery Unit, Austin Health, Heidelberg, VIC, Australia
| | - Christopher Christophi
- Department of Surgery, The University of Melbourne, Austin Health, Heidelberg, VIC, Australia
- Liver Transplant Unit, Austin Health, Heidelberg, VIC, Australia
- Hepato-Pancreato-Biliary & Transplant Surgery Unit, Austin Health, Heidelberg, VIC, Australia
| | - Alexander Dobrovic
- Department of Surgery, The University of Melbourne, Austin Health, Heidelberg, VIC, Australia
- Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, Australia
- School of Cancer Medicine, La Trobe University, Heidelberg, VIC, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, Australia
| | - Vijayaragavan Muralidharan
- Department of Surgery, The University of Melbourne, Austin Health, Heidelberg, VIC, Australia
- Liver Transplant Unit, Austin Health, Heidelberg, VIC, Australia
- Hepato-Pancreato-Biliary & Transplant Surgery Unit, Austin Health, Heidelberg, VIC, Australia
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Roles of Methylated DNA Biomarkers in Patients with Colorectal Cancer. DISEASE MARKERS 2019; 2019:2673543. [PMID: 30944663 PMCID: PMC6421784 DOI: 10.1155/2019/2673543] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 11/22/2018] [Indexed: 12/25/2022]
Abstract
Colorectal cancer (CRC) is a leading cancer globally; therefore, early diagnosis and surveillance of this cancer are of paramount importance. Current methods of CRC diagnosis rely heavily on endoscopy or radiological imaging. Noninvasive tests including serum detection of the carcinoembryonic antigen (CEA) and faecal occult blood testing (FOBT) are associated with low sensitivity and specificity, especially at early stages. DNA methylation biomarkers have recently been found to have higher accuracy in CRC detection and enhanced prediction of prognosis and chemotherapy response. The most widely studied biomarker in CRC is methylated septin 9 (SEPT9), which is the only FDA-approved methylation-based biomarker for CRC. Apart from SEPT9, other methylated biomarkers including tachykinin-1 (TAC1), somatostatin (SST), and runt-related transcription factor 3 (RUNX3) have been shown to effectively detect CRC in a multitude of sample types. This review will discuss the performances of various methylated biomarkers used for CRC diagnosis and monitoring, when used alone or in combination.
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Yuan EF, Xia W, Huang JT, Hu L, Liao X, Dai X, Liu SM. A sensitive and convenient method for clinical detection of non-syndromic hearing loss-associated common mutations. Gene 2017; 628:322-328. [PMID: 28734895 DOI: 10.1016/j.gene.2017.07.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 06/21/2017] [Accepted: 07/13/2017] [Indexed: 12/25/2022]
Abstract
BACKGROUND The majority of non-syndromic hearing loss (NSHL) patients result from causative mutations in GJB2, SLC26A4 and mitochondrial 12S rRNA genes. Accurate detection of these genetic mutations is increasingly recognized for its clinical significance to reduce incidence and guide individual treatment of NSHL. Current methods for clinical practice are labor intensive, expensive or of low sensitivity. METHODS Genomic DNA from 7 newborns not passing the hearing screening and 94 newborns passing the hearing screening were analyzed for the common mutations using high resolution melting analysis (HRMA) and Sanger sequencing. RESULTS Our newly developed HRMA allowed the hot-spot mutations of GJB2 c.176_191del16 and c.235delC, SLC26A4 IVS7-2A>G and mitochondrial 12S rRNA 1494C>T and 1555A>G to be detected by melting profiles based on small amplicons. HRMA can distinguish different content mutant DNA from wildtype DNA, with a detection limit of 5%. Moreover, the results were highly concordant between HRMA and Sanger sequencing. CONCLUSIONS These results indicate that HRMA could be used as a routine clinical method for prenatal diagnosis and newborn genetic screening due to its accuracy, sensitivity, and rapid, low-cost and less laborious workflows.
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Affiliation(s)
- Er-Feng Yuan
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Donghu Road 169#, Wuhan 430071, China
| | - Wei Xia
- Department of Clinical Laboratory, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430016, China
| | - Jing-Tao Huang
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Donghu Road 169#, Wuhan 430071, China
| | - Ling Hu
- Department of Neurology, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430016, China
| | - Xing Liao
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Donghu Road 169#, Wuhan 430071, China
| | - Xiang Dai
- Laboratory of Reproductive Medicine, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430016, China
| | - Song-Mei Liu
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Donghu Road 169#, Wuhan 430071, China.
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Goh SK, Muralidharan V, Christophi C, Do H, Dobrovic A. Probe-Free Digital PCR Quantitative Methodology to Measure Donor-Specific Cell-Free DNA after Solid-Organ Transplantation. Clin Chem 2017; 63:742-750. [PMID: 28100495 DOI: 10.1373/clinchem.2016.264838] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 10/21/2016] [Indexed: 01/08/2023]
Abstract
BACKGROUND Donor-specific cell-free DNA (dscfDNA) is increasingly being considered as a noninvasive biomarker to monitor graft health and diagnose graft rejection after solid-organ transplantation. However, current approaches used to measure dscfDNA can be costly and/or laborious. A probe-free droplet digital PCR (ddPCR) methodology using small deletion/insertion polymorphisms (DIPs) was developed to circumvent these limitations without compromising the quantification of dscfDNA. This method was called PHABRE-PCR (Primer to Hybridize across an Allelic BREakpoint-PCR). The strategic placement of one primer to hybridize across an allelic breakpoint ensured highly specific PCR amplification, which then enabled the absolute quantification of donor-specific alleles by probe-free ddPCR. METHODS dscfDNA was serially measured in 3 liver transplant recipients. Donor and recipient genomic DNA was first genotyped against a panel of DIPs to identify donor-specific alleles. Alleles that differentiated donor-specific from recipient-specific DNA were then selected to quantify dscfDNA in the recipient plasma. RESULTS Lack of amplification of nontargeted alleles confirmed that PHABRE-PCR was highly specific. In recipients who underwent transplantation, dscfDNA was increased at day 3, but decreased and plateaued at a low concentration by 2 weeks in the 2 recipients who did not develop any complications. In the third transplant recipient, a marked increase of dscfDNA coincided with an episode of graft rejection. CONCLUSIONS PHABRE-PCR was able to quantify dscfDNA with high analytical specificity and sensitivity. The implementation of a DIP-based approach permits surveillance of dscfDNA as a potential measure of graft health after solid-organ transplantation.
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Affiliation(s)
- Su Kah Goh
- Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia.,Department of Surgery, University of Melbourne, Austin Health, Heidelberg, Victoria, Australia
| | | | - Christopher Christophi
- Department of Surgery, University of Melbourne, Austin Health, Heidelberg, Victoria, Australia
| | - Hongdo Do
- Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia.,School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia.,Department of Pathology, University of Melbourne, Parkville, Victoria, Australia
| | - Alexander Dobrovic
- Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia; .,School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia.,Department of Pathology, University of Melbourne, Parkville, Victoria, Australia
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