Nucleic acid protocols: Extraction and optimization

El‐Ashram, Saeed; Nasr, Ibrahim Al; Suo, Xun

doi:10.1016/j.btre.2016.10.001

Cited by 56 publications

(34 citation statements)

References 11 publications

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“…Before covering the section of ctNA detection, it is pivotal to discuss the extraction and purification of NA, which follows four main stages: Cell lysis, protein denaturation, extraction of proteins from NA, and precipitation and dissolution of NA, more detailed information is provided by [ 50 ]. Figure 3 shows the step-by-step procedure for DNA and RNA extraction.…”

Section: Concept Of Liquid Biopsymentioning

confidence: 99%

Blood-Based Cancer Biomarkers in Liquid Biopsy: A Promising Non-Invasive Alternative to Tissue Biopsy

Marrugo-Ramírez

Mir

Samitier

2018

IJMS

343

202

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Cancer is one of the greatest threats facing our society, being the second leading cause of death globally. Currents strategies for cancer diagnosis consist of the extraction of a solid tissue from the affected area. This sample enables the study of specific biomarkers and the genetic nature of the tumor. However, the tissue extraction is risky and painful for the patient and in some cases is unavailable in inaccessible tumors. Moreover, a solid biopsy is expensive and time consuming and cannot be applied repeatedly. New alternatives that overcome these drawbacks are rising up nowadays, such as liquid biopsy. A liquid biopsy is the analysis of biomarkers in a non-solid biological tissue, mainly blood, which has remarkable advantages over the traditional method; it has no risk, it is non-invasive and painless, it does not require surgery and reduces cost and diagnosis time. The most studied cancer non-invasive biomarkers are circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), and exosomes. These circulating biomarkers play a key role in the understanding of metastasis and tumorigenesis, which could provide a better insight into the evolution of the tumor dynamics during treatment and disease progression. Improvements in isolation technologies, based on a higher grade of purification of CTCs, exosomes, and ctDNA, will provide a better characterization of biomarkers and give rise to a wide range of clinical applications, such as early detection of diseases, and the prediction of treatment responses due to the discovery of personalized tumor-related biomarkers.

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Section: Concept Of Liquid Biopsymentioning

confidence: 99%

Blood-Based Cancer Biomarkers in Liquid Biopsy: A Promising Non-Invasive Alternative to Tissue Biopsy

Marrugo-Ramírez

Mir

Samitier

2018

IJMS

343

202

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“…Genomic DNA was extracted from peripheral blood leukocytes using QIAamp DNA Blood Mini Kit (Qiagen, Berlin, Germany) following manufacturer's instructions and the procedure used by El‐Ashram, Al Nasr, and Suo (). Multiplex polymerase chain reaction (M‐PCR)‐ligase detection reaction was used to genotype blood DNA for three SNPs in HLA‐DPA1 (GenBank: ; rs3077), HLA‐DPB1 (GenBank: ; rs9277535), HLA‐DQB2 (GenBank: ; rs7453920) on an ABI3730XL Sequence Detection System (Applied Biosystems, Foster City, CA, USA).…”

Section: Methodsmentioning

confidence: 99%

Association of human leukocyte antigens‐DQB2/DPA1/DPB1 polymorphism and pulmonary tuberculosis in the Chinese Uygur population

Wang

Cao

Zhang

et al. 2019

Molec Gen & Gen Med

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Background Tuberculosis (TB) is the second‐leading cause of death globally. Genetic polymorphisms in human leukocyte antigens (HLA)‐DQB2, HLA‐DPA1, and HLA‐DPB1 may partly explain individual differences in TB susceptibility. Methods We performed a hospital‐based case–control study to assess the genetic influence of single‐nucleotide polymorphisms (SNPs) in the HLA (HLA‐DPA, HLA‐DPB, and HLA‐DQB) on the development of TB. There were 248 TB‐infected cases and 340 healthy controls in this study. Results The HLA‐DQB2 rs7453920 genotype GG was applied as the reference group, the GA genotype was related to a considerably magnified risk of TB (GA vs. GG: adjusted OR = 1.547, 95% CI = 1.039–2.304, p = 0.032). Nevertheless, the other two SNPs were not associated with TB risk. Stratified analyses suggested that tobacco was associated with an increased risk of TB in HLA‐DQB2 rs7453920 G>A. Conclusion These results suggested that the functional HLA‐DQB2 rs7453920 G>A polymorphism may contribute to the genetic susceptibility to TB. Nevertheless, the results were based on a limited sample size, and larger well‐designed studies are expected to confirm these preliminary findings.

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“…Therefore, DNases and RNases should preferably be eliminated from the samples to avoid degradation (Figure 1). Addition of, e.g., EDTA for preserving DNA and, e.g., RNAlater for preserving RNA in the sample, should be considered, as these preservatives inhibit DNase and RNase, respectively [19,20], and could thereby facilitate higher DNA or RNA yields from the sample. For molecular biomarkers, PCR-based techniques are commonly used to assess biomarker status.…”

Section: Collection Processing and Storage Of Liquid Biopsies For Bimentioning

confidence: 99%

Biobanking in Molecular Biomarker Research for the Early Detection of Cancer

Lommen

Odeh

Theije

et al. 2020

Cancers

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Although population-wide screening programs for several cancer types have been implemented in multiple countries, screening procedures are invasive, time-consuming and often perceived as a burden for patients. Molecular biomarkers measurable in non-invasively collected samples (liquid biopsies) could facilitate screening, as they could have incremental value on early diagnosis of cancer, but could also predict prognosis or monitor treatment response. Although the shift towards biomarkers from liquid biopsies for early cancer detection was initiated some time ago, there are many challenges that hamper the development of such biomarkers. One of these challenges is large-scale validation that requires large prospectively collected biobanks with liquid biopsies. Establishing those biobanks involves several considerations, such as standardization of sample collection, processing and storage within and between biobanks. In this perspective, we will elaborate on several issues that need to be contemplated in biobanking, both in general and for certain specimen types specifically, to be able to facilitate biomarker validation for early detection of cancer.

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Nucleic acid protocols: Extraction and optimization

Abstract: Graphical abstract

Cited by 56 publications

References 11 publications

Blood-Based Cancer Biomarkers in Liquid Biopsy: A Promising Non-Invasive Alternative to Tissue Biopsy

Blood-Based Cancer Biomarkers in Liquid Biopsy: A Promising Non-Invasive Alternative to Tissue Biopsy

Association of human leukocyte antigens‐DQB2/DPA1/DPB1 polymorphism and pulmonary tuberculosis in the Chinese Uygur population

Biobanking in Molecular Biomarker Research for the Early Detection of Cancer

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