Rapid DNA Testing Research Articles

Environmental detection of Fasciola hepatica by loop-mediated isothermal amplification.

Fasciola hepatica, commonly referred to as liver flukes, is a substantial zoonotic parasitic disease of humans and livestock globally. While infection is readily controlled by anthelmintics, namely triclabendazole, the heavy reliance on triclabendazole has resulted in drug resistance appearing worldwide. Due to drug resistance, it is imperative to adopt an integrated parasite management program to preserve the efficacy of currently available anthelmintics. A integrated liver fluke management plan would benefit from a simple rapid, field-deployable diagnostic for detection of F. hepatica in environment and the host. Therefore, a rapid DNA test using loop-mediated isothermal amplification was developed and optimised for the detection of F. hepatica from faecal and water samples to enable the detection of parasites both within the host and from the environment. The assay presented here is fast, with amplification in ≤20 min, and highly sensitive, with a detection limit of 5 × 10−4 ng/µL. The workflow presented here provides a time to result of ≤60 min without requiring a commercial kit for the extraction of DNA from faecal and water samples, and pending further validation from field-samples, could potentially be used to enable real-time decision making to mitigate parasite prevalence on a farming property and with no requirement for sample transportation.

The Return on Investment from Rapid DNA Testing of Sexual Assault Kits

The growing queue for DNA analysis in crime laboratories has prevented the analysis from providing investigative leads as turnaround time has grown, limiting the analytical results to a confirmatory role in the courtroom. Rapid DNA technology offers an opportunity to employ an automated system for the development of a DNA profile. The Rapid DNA technology permits a police booking station to take a buccal swab obtained from an arrestee, acquire a DNA profile, and test that profile against a DNA database, all while the arrestee remains in police custody during the booking process. Rapid DNA technologies are a capital-intensive system enabling sophisticated equipment designed for operation by individuals with limited technical training to provide investigative leads with immediate support. We present the testing of rapid DNA technology in a trial program conducted by the Kentucky State Police Forensic Laboratory. The Kentucky test confirms the efficacy of the rapid DNA testing as consistent with the findings from traditional laboratory testing. The economic analysis related to testing indicates that the time saving from the rapid DNA analysis yields benefits that far outweigh the costs from the change in technology.

Autosomal STR Profiling and Databanking in Malaysia: Current Status and Future Prospects.

Science and technology are extensively used in criminal investigation. From the mid- to late-1980s, one of the scientific discoveries that has had a particularly remarkable impact on this field has been the use of highly variable DNA sequence regions (minisatellites) in the human genome for individual identification. The technique was initially referred to as DNA fingerprinting, but is now more widely referred to as DNA profiling. Since then, many new developments have occurred within this area of science. These include the introduction of new genetic markers (microsatellites also known as short tandem repeats/STRs), the use of the polymerase chain reaction for target amplification, the development of DNA databases (databanking), and the advancement and/or improvement of genotyping protocols and technologies. In 2019, we described the progress of DNA profiling and DNA databanking in Malaysia for the first time. This report included information on DNA analysis regulations and legislation, STR genotyping protocols, database management, and accreditation status. Here, we provide an update on the performance of our DNA databank (numbers of DNA profiles and hits) plus the technical issues associated with correctly assigning the weight of evidence for DNA profiles in an ethnically diverse population, and the potential application of rapid DNA testing in the country. A total of 116,534 DNA profiles were obtained and stored in the Forensic DNA Databank of Malaysia (FDDM) by 2019, having increased from 70,570 in 2017. The number of hits increased by more than three-fold in just two years, where 17 and 69 hits between the DNA profiles stored in the FDDM and those from crime scenes, suspects, detainees, drug users, convicts, missing persons, or volunteers were recorded in 2017 and 2019, respectively. Forensic DNA analysis and databanking are thus progressing well in Malaysia and have already contributed to many criminal investigations. However, several other issues are discussed here, including the need for STR population data for uncharacterized population groups, and pilot trials for adopting rapid DNA profiling technology. These aspects should be considered by policy makers and law enforcement agencies in order to increase the reliability and efficiency of DNA profiling in criminal cases and in kinship analysis in Malaysia.

Studying the orientation of bio-objects by nematic liquid crystals

We have studied the ability of a liquid-crystal (LC) matrix to visualize and orient DNA molecules. It is established that the relief of the interface between the LC mesophase and conducting contact can be improved without using an additional high-ohmic polymer layer. Spectroscopic and ellipsometric techniques revealed changes in the refractive properties and structure of composites. The obtained results can be used in creating devices for rapid DNA testing with retained form of biostructures.

Tackling Technical Debt: Managing Advances in DNA Technology that Outpace the Evolution of Law

From its initial development in the 1980s as an identification tool, the use of DNA in criminal cases—both to convict defendants and exonerate the wrongly convicted—has been prolific. By the 1990s, Congress had focused on forensic DNA research and development. As DNA continues to expand its footprint as the ostensible “gold standard” in criminal investigations, an extraordinary amount of the federal funding allocated to crime labs was specifically earmarked for DNA expansion. Indeed, the funding abundance for DNA collection, testing, and retention far outstrip other crime lab allotments. Because of this, research and development of new DNA analytical techniques can be a lucrative business. Indeed, the next generation of DNA technology already has or inevitably will find its way into criminal investigations and the courtroom. The high rate of return on DNA-based investment almost dictates this result: As of December 2015, CODIS has produced over 315,410 hits that assisted in at least 303,201 investigations. But DNA technology may advance and outpace the testimonial claims, which are not yet reliable and scientifically defensible. Technology does not wait for the legal system to catch up with it. This article examines the new wave of DNA testing tools. It surveys the validity of these new forensic techniques, considers evidentiary uses in courts, and any addresses potential hurdles to admissibility. Part I covers the background of DNA testing. Part II assesses LCN DNA testing, Part III looks at phenotyping, and Part IV focuses on Rapid DNA testing. Finally, Part V concludes that additional validation studies are needed before these technologies become part of the routine criminal investigation process. From its initial development in the 1980s as an identification tool, the use of DNA in criminal cases—both to convict defendants and exonerate the wrongly convicted—has been prolific. By the 1990s, Congress had focused on forensic DNA research and development. As DNA continues to expand its footprint as the ostensible “gold standard” in criminal investigations, an extraordinary amount of the federal funding allocated to crime labs was specifically earmarked for DNA expansion. Indeed, the funding abundance for DNA collection, testing, and retention far outstrips other crime lab allotments. Because of this, research and development of new DNA analytical techniques can be a lucrative business. Indeed, the funding abundance for DNA collection, testing, and retention far outstripped other crime lab allotments, despite the fact that DNA analysis only represented a small portion of crime lab work at that time. Two decades later, DNA testing is now a primary hub of many labs—forcing other traditional forensic lab departments (such as trace evidence or fingerprints) to cut back or close shop.

The future of forensic DNA analysis.

The author's thoughts and opinions on where the field of forensic DNA testing is headed for the next decade are provided in the context of where the field has come over the past 30 years. Similar to the Olympic motto of 'faster, higher, stronger', forensic DNA protocols can be expected to become more rapid and sensitive and provide stronger investigative potential. New short tandem repeat (STR) loci have expanded the core set of genetic markers used for human identification in Europe and the USA. Rapid DNA testing is on the verge of enabling new applications. Next-generation sequencing has the potential to provide greater depth of coverage for information on STR alleles. Familial DNA searching has expanded capabilities of DNA databases in parts of the world where it is allowed. Challenges and opportunities that will impact the future of forensic DNA are explored including the need for education and training to improve interpretation of complex DNA profiles.

Does rapid genetic counseling and testing in newly diagnosed breast cancer patients cause additional psychosocial distress? results from a randomized clinical trial.

Female breast cancer patients carrying a BRCA1/2 mutation have an increased risk of second primary breast cancer. Rapid genetic counseling and testing (RGCT) before surgery may influence choice of primary surgical treatment. In this article, we report on the psychosocial impact of RGCT. Newly diagnosed breast cancer patients at risk for carrying a BRCA1/2 mutation were randomized to an intervention group (offer of RGCT) or a usual care control group (ratio 2:1). Psychosocial impact and quality of life were assessed with the Impact of Events Scale, Hospital Anxiety and Depression Scale, Cancer Worry Scale, and the EORTC QLQ-C30 and QLQ-BR23. Assessments took place at study entry and at 6- and 12-month follow-up visits. Between 2008 and 2010, 265 patients were recruited into the study. Completeness of follow-up data was more than 90%. Of the 178 women in the intervention group, 177 had genetic counseling, of whom 71 (40%) had rapid DNA testing and 59 (33%) received test results before surgery. Intention-to-treat and per-protocol analyses showed no statistically significant differences between groups over time in any of the psychosocial outcomes. In this study, RGCT in newly diagnosed breast cancer patients did not have any measurable adverse psychosocial effects.

Tuberculosis Peritonitis Patient with Septic Shock caused by Extended–Spectrum Beta Lactamases Producing Pseudomonas Aeruginosa

According to World Health Organization (WHO), tuberculosis (TB) is a worldwide pandemic. Up to 5% of patients with TB may have abdominal disease and 25-60% may have peritoneal involvement. Diagnosis of TB peritonitis is still challenging, and symptoms are usually insidious. The sensitivity of acid fast bacilli (AFB) is very low, ranging from 0-6%. Conventional mycobacterial culture takes up to 8 weeks to achieve results. Laparoscopic or laparotomy biopsy is uncomfortable for patient. The consequence of these problems is missing and delays in diagnosing TB peritonitis. In the end, it can results in significant morbidity and mortality. This case described a 20 year old female patient with TB peritonitis that suffered from septic shock caused by extended-spectrum beta lactamases (ESBL) producing Pseudomonas aeruginosa. In this case, TB peritonitis was diagnosed based on clinical features, high levels of adenosine deaminase (ADA) and a positive rapid DNA test with Xpert MTB/RIF. Keywords: tuberculosis peritonitis, extended-spectrum beta lactamases producing bacilli, adenosine deaminase, XpertMTB/RIF assay

Abstract P4-11-01: Rapid genetic counseling and testing in newly diagnosed breast cancer patients, findings from an RCT

Abstract Introduction: Female breast cancer patients carrying a BRCA1/2 mutation have an increased risk of second primary breast and ovarian tumors. Rapid genetic counseling and testing (RGCT) may aid in making informed decisions about therapeutic and preventive surgery and adjuvant treatment. Little is known about the effects of RGCT on treatment decisions and psychosocial well-being. We have performed a randomized controlled trial to investigate these issues. Methods: Newly diagnosed breast cancer patients from 12 Dutch hospitals with at least a 10% risk of carrying a BRCA1/2 mutation were randomized to an intervention group (RGCT) or a usual care control group (ratio 2:1). Study outcomes included uptake of RGCT, choice of type of surgery, cancer risk perception, cancer-specific distress, quality of life and decisional satisfaction. Assessments took place at study entry, and at 6 and 12 months follow-up. Results: Between 2008 and 2010, 271 patients were recruited, of whom 3 subsequently withdrew. The remaining 268 patients were randomized to the intervention (n = 181) or control (n = 87) group. Complete questionnaire data were available for 250 (93%) and 243 (91%) patients at 6 and 12 months follow-up, respectively. Of the 181 women in the intervention group, 180 (98%) underwent genetic counseling after a median of 4 days. One-hundred thirteen (63%) of them opted for accelerated DNA test procedures, of whom 72 underwent rapid testing (results available in <4 weeks) and 41 semi-rapid testing (results available in 4 weeks to 4 months). DNA test results were available before primary surgery for 65 patients (36%) in the intervention group. Of these 65 patients, 8 (12%) were BRCA1/2 carriers and 11 (20%) had a bilateral mastectomy. Of the remaining 68 patients in the intervention group, 67 opted for standard DNA test procedures at some time during the study period. In the control group, 8 patients (9%) underwent rapid genetic counseling, of whom 7 underwent rapid DNA testing. In total, 22/220 (10%) of patients who had their DNA tested were BRCA1/2 mutation carriers. There was no statistically significant difference between the intervention and control group in percentage of patients with unilateral breast cancer opting for a bilateral mastectomy (12% versus 9%, p = 0.33). Of the BRCA1/2 carriers in the intervention group with unilateral breast cancer, 27% opted for a bilateral mastectomy. There was also no significant difference observed between the intervention and control groups in the percentage of patients opting for breast-conserving surgery rather than unilateral mastectomy (45% and 46% in the intervention and control group, respectively). Data on additional surgery performed during follow-up and psychosocial outcomes will be available at the time of the conference. Conclusion: The uptake of rapid genetic counseling among high-risk breast cancer patients was high, and the majority of patients underwent accelerated DNA-testing procedures. However, RGCT did not have a significant effect on choice of type of primary surgery. In part, this may be explained by the fact that surgeons and patients often did not wait for DNA test results before primary surgery. Conclusions regarding the psychosocial impact of RGCT will be presented at the time of the conference. Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P4-11-01.

Polymerase Chain Reaction–Based Risk Assessment for Wilms Tumor in Sporadic Aniridia

Purpose: Sporadic cases of aniridia have a 30% risk for the development of Wilms tumor. Current guidelines for sporadic aniridia recommend screening by renal ultrasonography for the presence of tumors every 6 months until age 5 years. Deletions of chromosome 11p13 that affect both PAX6 (aniridia) and WT1 (Wilms tumor) loci are the basis for the association of these two uncommon disorders. We sought to develop a rapid polymerase chain reaction–based test that could rule out a chromosome 11p13 deletion covering the PAX6-WT1 region in sporadic aniridia. Methods: Five patients with sporadic aniridia were recruited. Polymerase chain reaction–based genotyping was carried out for six highly informative marker loci across the PAX6-WT1 region to determine whether these patients had one or two haplotypes. The results were compared with those obtained from two cell lines with known deletions in the PAX6-WT1 region. Results: All five patients were heterozygous at least at one of the four marker loci in the PAX6-WT1 region, indicating that there were no cases of gross chromosomal deletion. The cell lines showed hemizygosity in the four marker loci within the PAX6-WT1 region and in one of the two flanking marker loci. Conclusions: We have developed a rapid DNA test with an estimated sensitivity of 94.0% to 99.2%, using standard DNA diagnostic techniques and equipment, to rule out chromosomal deletion in sporadic aniridia. Patients in whom a chromosome 11p13 deletion has been ruled out do not require repeated renal imaging to screen for Wilms tumor.

Detection of Plasmodium falciparum DNA in a microtitration plate-based hybridization test

A rapid DNA-test, depending on the affinity based hybrid collection principle, was developed for the detection of Plasmodium falciparum DNA from clinical specimens. In this method, hybridization takes place in solution and the hybrids are collected onto a solid phase for measurement. Two probes are used, one labelled with an affinity tag (biotin) and the other with a detectable label ( 32P). In the present test a single oligonucleotide complementary to a 21-base pair sequence which is highly repeated in the parasite genome served both as capture and detector probe. The test is a 2-h hybridization performed in streptavidin coated microtitration plate wells, onto which the labelled hybrids simultaneously bind. The sensitivity of the assay with a crude erythrocyte lysate specimen was 1.6 × 10 9 repeat units corresponding to about 160 parasites in one μ1 blood. The results allowed quantification of the repeat sequences and thus estimation of the degree of parasitemia in clinical specimens.

Mutations causing aspartylglucosaminuria (AGU): a lysosomal accumulation disease.

This article provides a review of the mutations reported so far in the lysosomal storage disease aspartylglucosaminuria (AGU). The clinical symptoms, biochemical findings, and diagnostic possibilities of the disease are introduced. The prevalence and biological consequences of the found mutations are then described, as well as the availability of a new rapid DNA test suitable for carrier screening. This test will be especially applicable in the genetically isolated Finnish population, where the carrier frequency of AGU was found to be as high as 1:36. Finally, future prospects dealing with the foreseeable therapeutic interventions of the disease are discussed.