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71,389 result(s) for "DNA testing"
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Differences in intention to receive clinician-collected and self-collected samples for HPV DNA testing and its determinants between heterosexual males and females in Hong Kong, China: findings of a territory-wide household survey
Background Human papillomavirus (HPV) infection is prevalent among people who are sexually active. This study aimed to compare the levels of behavioral intention to receive free clinician-collected and self-collected samples for HPV DNA testing and its determinants between heterosexual males and females in Hong Kong, China. Methods This is a secondary analysis of a territory-wide survey conducted in Hong Kong between May 2021 and March 2022. Participants were sexually active adult Hong Kong residents who were able to communicate in English or Chinese. Invitation letters were mailed to residential addresses that were geographically randomly selected. All sexually active adult household members were invited to complete a self-administered online survey. Multivariate logistic regression analyses were fitted. Results Out of 45,394 invitations, 1265 surveys were collected, and 487 heterosexual males and 741 females were included in the analysis. More females than heterosexual males intended to take up free clinician-collected samples for HPV DNA testing (76.7% versus 62.2%, p  < 0.001). Similar proportion of heterosexual males and females intended to receive free self-collected samples for HPV DNA testing (67.8% versus 72.6%, p  = 0.20). Perceived existing treatment could control sexually transmitted infections (STI) (treatment control), more concerned about STI (concern), perceived more benefits, cue to action (suggested by significant others), and self-efficacy related to HPV testing were associated with higher intention to receive clinician-collected samples for HPV testing in both groups. Heterosexual males who perceived more severe symptoms if contracted STI (identity), longer duration of STI (timeline), more negative effects of STI on their lives (consequences), more understanding of STI (coherence), and stronger negative emotions if contracted STI (emotions) also had higher behavioral intention to take up clinician-collected samples for HPV testing. In addition, perceived more benefits, cue to action, and self-efficacy related to self-collected samples for HPV DNA testing were associated with behavioral intention to take up such testing in both groups. Conclusions HPV DNA testing was under-utilized in Hong Kong. Free self-collected samples for HPV testing were highly acceptable by both heterosexual males and females. Illness representation of STI and the Health Belief Model could explain intentions to take up HPV DNA testing.
Transcriptomic Analysis of Green Leaf Plants and White–Green Leaf Mutants in IHaworthia cooperi/I var. Ipilifera/I
Haworthia cooperi var. pilifera is a succulent plant with ornamental value. The white–green leaf mutant (wl) showed a significant difference in leaf color from the wild-type plant (WT). In this study, we integrated the transcriptomes of wl and WT plants to screen differentially expressed genes related to leaf color variation. The results of transcriptome analysis showed that 84,163 unigenes were obtained after de novo assembly and the NR database annotated the largest number of unigenes, which accounted for 57.13%, followed by NT (43.02%), GO (39.84%), Swiss-Prot (39.25%), KEGG (36.06%), and COG (24.88%). Our finding showed that 2586 genes were differentially expressed in the two samples, including 1996 down-regulated genes and 590 up-regulated genes. GO analysis predicted that these differentially expressed genes (DEGs) participate in 12 cellular components, 20 biological processes, and 13 molecular function terms and KEGG analysis showed that metabolic pathways, plant–pathogen interaction, glycerophospholipid metabolism, endocytosis, plant hormone signal transduction, and ether lipid metabolism were enriched among all identified pathways. Through functional enrichment analysis of DEGs, we found that they were involved in chloroplast division and the biosynthesis of plant pigments, including chlorophyll, carotenoids, anthocyanin, and transcription factor families, which might be related to the formation mechanism of leaf color. Taken together, these results present insights into the difference in gene expression characteristics in leaves between WT and wl mutants and provide a new insight for breeding colorful leaf phenotypes in succulent plants.
Molecular stool testing as an alternative for surveillance colonoscopy: a cross-sectional cohort study
Background As in many other European countries, a nationwide screening program for colorectal cancer (CRC) has recently been introduced in the Netherlands. As a side effect, such a screening program will inherently yield an increase in the demand for surveillance after removal of polyps/adenomas or CRC. Although these patients are at increased risk of metachronous colorectal neoplasia, solid evidence on CRC-related mortality reduction as a result of colonoscopy-based surveillance programs is lacking. Furthermore, colonoscopy-based surveillance leads to high patient burden, high logistic demands and high costs. Therefore, new surveillance strategies are needed. The aim of the present study, named Molecular stool testing for Colorectal CAncer Surveillance (MOCCAS), is to determine the performance characteristics of two established non-invasive tests, i.e., the multitarget stool DNA test Cologuard® and the faecal immunochemical test (FIT) in the detection of CRC and advanced adenomas as an alternative for colonoscopy surveillance. Methods In this observational cross-sectional cohort study, subjects aged 50 to 75 years will be approached to collect (whole-) stool samples for molecular testing and a FIT prior to their scheduled surveillance colonoscopy. The results of the tests will allow calculation of test sensitivities and specificities in the context of surveillance. This will provide the required input for the Dutch ASCCA model (Adenoma and Serrated pathway to Colorectal CAncer) to simulate surveillance strategies differing in frequency and duration. The model will allow predictions of lifetime health effects and costs. Multiple centres in the Netherlands will participate in the study that aims to include 4,000 individuals. Discussion The outcome of this study will inform on the (cost-) effectiveness of stool based molecular testing as an alternative for colonoscopy in the rapidly expanding surveillance population. Trial registration ClinicalTrials.gov ( https://clinicaltrials.gov/ ): NCT02715141 . Retrospectively registered 17 February 2016.
DNA evidence: Current perspective and future challenges in India
•DNA fingerprinting has extensively been used in the court room for civil as well as criminal adjudication worldwide.•DNA evidence may be used only as corroborative evidence and not as a conclusive proof especially in criminal cases.•Indian courts are relying on DNA evidence both in civil and criminal matters but there is no legal regime on DNA profiling.•Since half a decade, India is attempting to legislate on DNA profiling; the bill is awaiting placement in the Parliament.•This article reviews the consequences of admissibility of DNA as ‘evidence’ in the judicial dominion in India. Since the discovery of DNA fingerprinting technology in 1985 it has been used extensively as evidence in the court of law world-wide to establish the individual identity both in civil and criminal matters. In India, the first case of parentage dispute solved by the use of DNA fingerprinting technology was in 1989. Since then till date, the DNA technology has been used not only to resolve the cases of paternity and maternity disputes, but also for the establishment of individual identity in various criminal cases and for wildlife forensic identification. Since last half a decade, India is exercising to enact legislation on the use of DNA in the judicial realm and the draft ‘Human DNA Bill-2012’ is pending in the parliament. Largely, the promoters of forensic DNA testing have anticipated that DNA tests are nearly infallible and DNA technology could be the greatest single advance step in search for truth, conviction of the perpetrator, and acquittal of the innocent. The current article provides a comprehensive review on the status of DNA testing in India and elucidates the consequences of the admissibility of DNA as ‘evidence’ in the judicial dominion. In this backdrop of civil and criminal laws and changing ethical and societal attitudes, it is concluded that the DNA legislation in India and world-wide needs to be designed with utmost care.
Short tandem repeat
One thousand sixty-one individuals were sampled from the cities of Anbar, Baghdad, Basra, Diyala, Najaf, and Wasit in Iraq and typed for 15 forensic STRs to explore the genetic structure of Iraq and develop a forensic DNA database. The total number of alleles that were identified was 203. Analyses of molecular variance (AMOVA) were then conducted Baghdad provides a good representation of the rest of the country, while Anbar is the most genetically distinct. The average heterozygosities of these loci was 0.779, homozygosities was 0.221, polymorphism information content was 0.77, power of discrimination was 0.927, and power of exclusion was 0.563. At these loci, a matching genotype will occur, on average, in 1 in 8.152 x 1017 individuals. For paternity tests, the average paternity probability for a matching profile is 99.9997%. These loci are appropriate for use in forensic and paternity testing for this population. Iraq is similar to other countries in the Middle East, particularly Iran and Turkey, and is more similar to Europe than either Asia or Africa.
Enhanced detection of minimal residual disease by targeted sequencing of phased variants in circulating tumor DNA
Circulating tumor-derived DNA (ctDNA) is an emerging biomarker for many cancers, but the limited sensitivity of current detection methods reduces its utility for diagnosing minimal residual disease. Here we describe phased variant enrichment and detection sequencing (PhasED-seq), a method that uses multiple somatic mutations in individual DNA fragments to improve the sensitivity of ctDNA detection. Leveraging whole-genome sequences from 2,538 tumors, we identify phased variants and their associations with mutational signatures. We show that even without molecular barcodes, the limits of detection of PhasED-seq outperform prior methods, including duplex barcoding, allowing ctDNA detection in the ppm range in participant samples. We profiled 678 specimens from 213 participants with B cell lymphomas, including serial cell-free DNA samples before and during therapy for diffuse large B cell lymphoma. In participants with undetectable ctDNA after two cycles of therapy using a next-generation sequencing-based approach termed cancer personalized profiling by deep sequencing, an additional 25% have ctDNA detectable by PhasED-seq and have worse outcomes. Finally, we demonstrate the application of PhasED-seq to solid tumors. The sensitivity of circulating tumor DNA detection is improved by identifying sequences with two or more mutations.
Chloroplast Genome Analysis for Genetic Information and Authentication in Five IBarleria/I Species
In order to authenticate the genomic information of Barleriacristata L., B. lupulina Lindl., B. repens Nees, B. siamensis Craib, and B. strigosa Willd, cp genomes were investigated. They revealed a general structure with a total size of 151,997–152,324 bp. The genomes encoded a total of 131 genes, including 86 CDS, 37 tRNA, and 8 rRNA genes. Other details found were as follows: different numbers and types of SSRs; identical gene content, which is adjacent to the border regions, except for B. strigosa, that revealed a shorter ndhF gene sequence and lacked the ycf1 gene; slightly different genetic distance values, which can be used for species identification; three distinct gaps of nucleotide variations between the species located at the intergenic spacer regions of the LSC and CDS of the SSC; three effective molecular markers derived from divergent hotspot regions, including the ccsA-ndhD, ndhA-ndhH-rps15, and ycf1. The genetic relationships derived from the cp genome and the CDS phylogenetic trees of Barleria and the 13 genera in Acanthaceae and different families, Scrophulariaceae and Phrymaceae, showed similar results. The six Barleria species as monophyletic groups with inner and outer outgroups were found to have perfect discrimination. These results have helped to authenticate the five Barleria species and the six genera in Acanthaceae.
Sequencing-based counting and size profiling of plasma Epstein–Barr virus DNA enhance population screening of nasopharyngeal carcinoma
Circulating tumor-derived DNA testing for cancer screening has recently been demonstrated in a prospective study on identification of nasopharyngeal carcinoma (NPC) among 20,174 asymptomatic individuals. Plasma EBV DNA, a marker for NPC, was detected using real-time PCR. While plasma EBV DNA was persistently detectable in 97.1% of the NPCs identified, ∼5% of the general population had transiently detectable plasma EBV DNA. We hypothesized that EBV DNA in plasma of subjects with or without NPC may have different molecular characteristics. We performed target-capture sequencing of plasma EBV DNA and identified differences in the abundance and size profiles of EBV DNA molecules within plasma of NPC and non-NPC subjects. NPC patients had significantly higher amounts of plasma EBV DNA, which showed longer fragment lengths. Cutoff values were established from an exploratory dataset and tested in a validation sample set. Adopting an algorithm that required a sample to concurrently pass cutoffs for EBV DNA counting and size measurements, NPCs were detected at a positive predictive value (PPV) of 19.6%. This represented superior performance compared with the PPV of 11.0% in the prospective screening study, which required participants with an initially detectable plasma EBV DNA result to be retested within 4 weeks. The observed differences in the molecular nature of EBV DNA molecules in plasma of subjects with or without NPC were successfully translated into a sequencing-based test that had a high PPV for NPC screening and achievable through single time-point testing.
Paper-based microfluidics for DNA diagnostics of malaria in low resource underserved rural communities
Rapid, low-cost, species-specific diagnosis, based upon DNA testing, is becoming important in the treatment of patients with infectious diseases. Here, we demonstrate an innovation that uses origami to enable multiplexed, sensitive assays that rival polymerase chain reactions (PCR) laboratory assays and provide high-quality, fast precision diagnostics for malaria. The paper-based microfluidic technology proposed here combines vertical flow sample-processing steps, including paper folding for whole-blood sample preparation, with an isothermal amplification and a lateral flow detection, incorporating a simple visualization system. Studies were performed in village schools in Uganda with individual diagnoses being completed in <50 min (faster than the standard laboratory-based PCR). The tests, which enabled the diagnosis of malaria species in patients from a finger prick of whole blood, were both highly sensitive and specific, detecting malaria in 98% of infected individuals in a double-blind first-in-human study. Our method was more sensitive than other field-based, benchmark techniques, including optical microscopy and industry standard rapid immunodiagnostic tests, both performed by experienced local healthcare teams (which detected malaria in 86% and 83% of cases, respectively). All assays were independently validated using a real-time double-blinded reference PCR assay. We not only demonstrate that advanced, low-cost DNA-based sensors can be implemented in underserved communities at the point of need but also highlight the challenges associated with developing and implementing new diagnostic technologies in the field, without access to laboratories or infrastructure.