DNA extraction on bio-chip: history and preeminence over conventional and solid-phase extraction methods

Ayoib, A.; Hashim, U.; Gopinath, Subash C. B.; Arshad, M. K. Md

doi:10.1007/s00253-017-8493-0

Cited by 33 publications

(25 citation statements)

References 96 publications

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“…The DNA of peripheral blood was extracted by the salting-out method according to the previous publications. 23 We performed an extensive literature search about the pharmacogenetics or pharmacogenomics of methotrexate on PubMed, and sixteen related polymorphisms were included (see Table S1). Sixteen single nucleotide polymorphisms (SNPs) of 259 samples were genotyped using Sequenom MassARRAY TM (Biomiao, Beijing, China) technology.…”

Section: Genotypingmentioning

confidence: 99%

The impacts of gene polymorphisms on methotrexate in Chinese psoriatic patients

Chen

et al. 2020

Acad Dermatol Venereol

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Background Methotrexate (MTX) is the first‐line treatment for psoriasis in China. The metabolic processes of MTX include various proteins and genes. Previous studies have shown that gene polymorphisms had significant impacts on the efficacy of MTX. However, the influence of gene polymorphisms has not been reported in the Chinese psoriatic patients. Objective The aim of this study was to verify the impacts of candidate genes polymorphisms on the effectiveness of MTX in a Chinese psoriatic population. Methods In this study, we enrolled 259 psoriasis patients from two clinical centres. Each of them received MTX treatment at 7.5–15 mg/week for at least 8 weeks. Patients were stratified as responders and non‐responders according to whether the Psoriasis Area and Severity Index score declined more than 75% (PASI75). According to previous reports, 16 single nucleotide polymorphisms (SNPs) were selected and genotyped for each patient using the Sequenom platform. Fisher’s exact test, the chi‐square test, Mann–Whitney tests and ANOVA analyses were used for statistical analysis. Results Among 259 patients, there were 182 males and 77 females, 63 patients with psoriatic arthritis and 196 patients without arthritis phenotype, and the age of all patients ranged from 19 to 70 years (49.7 ± 13.6). The baseline PASI value of patients was 13.8 ± 8.5, and 33.2% of patients achieved a PASI75 response after MTX treatment. Patients carrying the ATP‐binding cassette subfamily B member 1 gene (ABCB1) rs1045642 TT genotype were associated with more severe psoriasis skin lesion (P = 0.032). Furthermore, the ABCB1 rs1045642 TT genotype was found to be more frequent in non‐responders (P = 0.017), especially in moderate‐to‐severe patients (P = 0.002) and patients without psoriatic arthritis (P = 0.026) after MTX treatment. Conclusion We have demonstrated for the first time that polymorphism of the ABCB1 rs1045642 TT genotype is predictive of a worse clinical response of skin lesions to MTX therapy in a Chinese psoriatic population.

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Section: Genotypingmentioning

confidence: 99%

The impacts of gene polymorphisms on methotrexate in Chinese psoriatic patients

Chen

et al. 2020

Acad Dermatol Venereol

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Section: Dna Extractionmentioning

confidence: 99%

“…DNA extraction microfluidic modules [38] are involved with releasing the target DNA from the cells of interest, using a variety of techniques to this end. Extracting the required DNA is currently a basic molecular biology laboratory technique [38,39], with several commercial kits in the market for standard laboratory use. The process can be roughly divided into four steps [40], which can be modulated depending on the sample and downstream applications: (i) Cell disruption; (ii) removal of membrane lipids, proteins, and other nucleic acids; (iii) nucleic acid purification/binding from bulk; and (iv) nucleic acid concentration.…”

Section: Dna Extractionmentioning

confidence: 99%

Microfluidic Devices for Label-Free DNA Detection

et al. 2018

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Sensitive and specific DNA biomarker detection is critical for accurately diagnosing a broad range of clinical conditions. However, the incorporation of such biosensing structures in integrated microfluidic devices is often complicated by the need for an additional labelling step to be implemented on the device. In this review we focused on presenting recent advances in label-free DNA biosensor technology, with a particular focus on microfluidic integrated devices. The key biosensing approaches miniaturized in flow-cell structures were presented, followed by more sophisticated microfluidic devices and higher integration examples in the literature. The option of full DNA sequencing on microfluidic chips via nanopore technology was highlighted, along with current developments in the commercialization of microfluidic, label-free DNA detection devices.

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“…In genetic analysis of clinical samples, nucleic acid extraction from raw biosamples is the initial pre-treatment step to purify and concentrate the nucleic acid from other constituents of the samples including proteins, lipids, and other organic molecules. One of the mainstream solidphase extraction techniques is based on the charge interaction principle, using a surface modified binding media such as silica bead (or membrane) or magnetic bead to selectively collect the nucleic acid from the sample and ethanol-based buffers to wash out impurities [1][2][3][4][5].…”

Section: Introductionmentioning

confidence: 99%

“…The complexity of the conventional nucleic acid extraction method led to the introduction of alternative techniques, which have focused on simplifying the process and reducing the extraction time [4,6]. Among the reported strategies, lab-on-a-chip approaches targeted systemization of the procedure by integrating the extraction column, binding media, and buffers in a single device [5,6,[10][11][12]. In typical lab-on-a-chip experiments, a single microfluidic chip per extraction and small amounts of buffers were used to isolate DNA or RNA in a relatively short time (~ 30 min in general) [13][14][15][16][17][18][19].…”

Section: Introductionmentioning

confidence: 99%

Direct electrophoretic microRNA preparation from clinical samples using nanofilter membrane

et al. 2020

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A method to directly collect negatively charged nucleic acids, such as DNA and RNA, in the biosamples simply by applying an electric field in between the sample and collection buffer separated by the nanofilter membrane is proposed. The nanofilter membrane was made of low-stress silicon nitride with a thickness of 100 nm, and multiple pores were perforated in a highly arranged pattern using nanoimprint technology with a pore size of 200 nm and a pore density of 7.22 × 10 8 /cm 2 . The electrophoretic transport of hsa-mir-93-5p across the membrane was confirmed in pure microRNA (miRNA) mimic solution using quantitative reverse transcription-polymerase chain reactions (qRT-PCR). Consistency of the collected miRNA quantity, stability of the system during the experiment, and yield and purity of the prepared sample were discussed in detail to validate the effectiveness of the electrical protocol. Finally, in order to check the applicability of this method to clinical samples, liquid biopsy process was demonstrated by evaluating the miRNA levels in sera of hepatocellular carcinoma patients and healthy controls. This efficient system proposed a simple, physical idea in preparation of nucleic acid from biosamples, and demonstrated its compatibility to biological downstream applications such as qRT-PCR as the conventional nucleic acid extraction protocols.

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DNA extraction on bio-chip: history and preeminence over conventional and solid-phase extraction methods

Cited by 33 publications

References 96 publications

The impacts of gene polymorphisms on methotrexate in Chinese psoriatic patients

The impacts of gene polymorphisms on methotrexate in Chinese psoriatic patients

Microfluidic Devices for Label-Free DNA Detection

Direct electrophoretic microRNA preparation from clinical samples using nanofilter membrane

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