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1.
Addict Sci Clin Pract ; 18(1): 70, 2023 11 18.
Article in English | MEDLINE | ID: mdl-37980494

ABSTRACT

BACKGROUND: Preventing progression to moderate or severe opioid use disorder (OUD) among people who exhibit risky opioid use behavior that does not meet criteria for treatment with opioid agonists or antagonists (subthreshold OUD) is poorly understood. The Subthreshold Opioid Use Disorder Prevention (STOP) Trial is designed to study the efficacy of a collaborative care intervention to reduce risky opioid use and to prevent progression to moderate or severe OUD in adult primary care patients with subthreshold OUD. METHODS: The STOP trial is a cluster randomized controlled trial, randomized at the PCP level, conducted in 5 distinct geographic sites. STOP tests the efficacy of the STOP intervention in comparison to enhanced usual care (EUC) in adult primary care patients with risky opioid use that does not meet criteria for moderate-severe OUD. The STOP intervention consists of (1) a practice-embedded nurse care manager (NCM) who provides patient participant education and supports primary care providers (PCPs) in engaging and monitoring patient-participants; (2) brief advice, delivered to patient participants by their PCP and/or prerecorded video message, about health risks of opioid misuse; and (3) up to 6 sessions of telephone health coaching to motivate and support behavior change. EUC consists of primary care treatment as usual, plus printed overdose prevention educational materials and an educational video on cancer screening. The primary outcome measure is self-reported number of days of risky (illicit or nonmedical) opioid use over 180 days, assessed monthly via text message using items from the Addiction Severity Index and the Current Opioid Misuse Measure. Secondary outcomes assess other substance use, mental health, quality of life, and healthcare utilization as well as PCP prescribing and monitoring behaviors. A mixed effects negative binomial model with a log link will be fit to estimate the difference in means between treatment and control groups using an intent-to-treat population. DISCUSSION: Given a growing interest in interventions for the management of patients with risky opioid use, and the need for primary care-based interventions, this study potentially offers a blueprint for a feasible and effective approach to improving outcomes in this population. TRIAL REGISTRATION: Clinicaltrials.gov, identifier NCT04218201, January 6, 2020.


Subject(s)
Analgesics, Opioid , Opioid-Related Disorders , Adult , Humans , Analgesics, Opioid/adverse effects , Quality of Life , Opioid-Related Disorders/drug therapy , Research Design , Patient Acceptance of Health Care
2.
Addict Sci Clin Pract ; 18(1): 56, 2023 09 20.
Article in English | MEDLINE | ID: mdl-37726839

ABSTRACT

BACKGROUND: Screening for substance use in rural primary care clinics faces unique challenges due to limited resources, high patient volumes, and multiple demands on providers. To explore the potential for electronic health record (EHR)-integrated screening in this context, we conducted an implementation feasibility study with a rural federally-qualified health center (FQHC) in Maine. This was an ancillary study to a NIDA Clinical Trials Network study of screening in urban primary care clinics (CTN-0062). METHODS: Researchers worked with stakeholders from three FQHC clinics to define and implement their optimal screening approach. Clinics used the Tobacco, Alcohol, Prescription Medication, and Other Substance (TAPS) Tool, completed on tablet computers in the waiting room, and results were immediately recorded in the EHR. Adult patients presenting for annual preventive care visits, but not those with other visit types, were eligible for screening. Data were analyzed for the first 12 months following implementation at each clinic to assess screening rates and prevalence of reported unhealthy substance use, and documentation of counseling using an EHR-integrated clinical decision support tool, for patients screening positive for moderate-high risk alcohol or drug use. RESULTS: Screening was completed by 3749 patients, representing 93.4% of those with screening-eligible annual preventive care visits, and 18.5% of adult patients presenting for any type of primary care visit. Screening was self-administered in 92.9% of cases. The prevalence of moderate-high risk substance use detected on screening was 14.6% for tobacco, 30.4% for alcohol, 10.8% for cannabis, 0.3% for illicit drugs, and 0.6% for non-medical use of prescription drugs. Brief substance use counseling was documented for 17.4% of patients with any moderate-high risk alcohol or drug use. CONCLUSIONS: Self-administered EHR-integrated screening was feasible to implement, and detected substantial alcohol, cannabis, and tobacco use in rural FQHC clinics. Counseling was documented for a minority of patients with moderate-high risk use, possibly indicating a need for better support of primary care providers in addressing substance use. There is potential to broaden the reach of screening by offering it at routine medical visits rather than restricting to annual preventive care visits, within these and other rural primary care clinics.


Subject(s)
Cannabis , Illicit Drugs , Substance-Related Disorders , Humans , Adult , Ethanol , Substance-Related Disorders/diagnosis , Substance-Related Disorders/epidemiology , Primary Health Care
3.
J Addict Med ; 17(4): 471-473, 2023.
Article in English | MEDLINE | ID: mdl-37579113

ABSTRACT

OBJECTIVES: This secondary analysis evaluated opioid-specific validation results of the Tobacco, Alcohol, Prescription Medication, and Other Substances (TAPS) tool for screening in primary care. METHODS: This study is a secondary data analysis of the TAPS validation study. Performance of the TAPS tool for screening for unhealthy opioid use (with a score of 1+ for heroin and/or prescription opioids representing a positive screen) was evaluated. Discriminative ability was examined in comparison with reference standard measures across the spectrum of unhealthy opioid use: timeline follow-back with and without oral fluid testing identifying past-month use and the modified Composite International Diagnostic Interview for past-year problem use, opioid use disorder (OUD), and moderate-severe OUD. RESULTS: In a sample of 2000 primary care patients, 114 screened positive for opioids on the TAPS tool. With a TAPS cutoff equal to 1+, the TAPS accurately identified past-month use, problem use, any OUD, and moderate-severe OUD (sensitivities = 68%-85%, specificities = 97%-98%, area under the curve = 0.80-0.91). When past-month use was expanded to include timeline follow-back with oral fluid testing, accuracy declined (52% sensitivity [95% confidence interval, 43%-60%], 98% specific [95% confidence interval, 97%-98%]). CONCLUSIONS: While further testing in a larger population sample may be warranted, given their brevity, simplicity, and accuracy when self-administered, the TAPS opioid items can be used in primary care settings for a spectrum of unhealthy opioid use; however, self-disclosure remains an issue in primary care settings.


Subject(s)
Opioid-Related Disorders , Prescription Drugs , Tobacco Use Disorder , Adult , Humans , Analgesics, Opioid/adverse effects , Opioid-Related Disorders/diagnosis , Opioid-Related Disorders/epidemiology , Ethanol , Prescriptions
4.
JAMA Netw Open ; 6(5): e2314422, 2023 05 01.
Article in English | MEDLINE | ID: mdl-37213103

ABSTRACT

Importance: Efficient screening tools that effectively identify substance use disorders (SUDs) among youths are needed. Objective: To evaluate the psychometric properties of 3 brief substance use screening tools (Screening to Brief Intervention [S2BI]; Brief Screener for Tobacco, Alcohol, and Drugs [BSTAD]; and Tobacco, Alcohol, Prescription Medication, and Other Substances [TAPS]) with adolescents aged 12 to 17 years. Design, Setting, and Participants: This cross-sectional validation study was conducted from July 1, 2020, to February 28, 2022. Participants aged 12 to 17 years were recruited virtually and in person from 3 health care settings in Massachusetts: (1) an outpatient adolescent SUD treatment program at a pediatric hospital, (2) an adolescent medicine program at a community pediatric practice affiliated with an academic institution, and (3) 1 of 28 participating pediatric primary care practices. Participants were randomly assigned to complete 1 of the 3 electronic screening tools via self-administration, followed by a brief electronic assessment battery and a research assistant-administered diagnostic interview as the criterion standard measure for Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5) diagnoses of SUDs. Data were analyzed from May 31 to September 13, 2022. Main Outcomes and Measures: The main outcome was a DSM-5 diagnosis of tobacco/nicotine, alcohol, or cannabis use disorder as determined by the criterion standard World Mental Health Composite International Diagnostic Interview Substance Abuse Module. Classification accuracy of the 3 substance use screening tools was assessed by examining the agreement between the criterion, using sensitivity and specificity, based on cut points for each tool for use disorder, chosen a priori from previous studies. Results: This study included 798 adolescents, with a mean (SD) age of 14.6 (1.6) years. The majority of participants identified as female (415 [52.0%]) and were White (524 [65.7%]). High agreement between screening results and the criterion standard measure was observed, with area under the curve values ranging from 0.89 to 1 for nicotine, alcohol, and cannabis use disorders for each of the 3 screening tools. Conclusions and Relevance: These findings suggest that screening tools that use questions on past-year frequency of use are effective for identifying adolescents with SUDs. Future work could examine whether these tools have differing properties when used with different groups of adolescents in different settings.


Subject(s)
Nicotine , Substance-Related Disorders , Humans , Adolescent , Female , Child , Cross-Sectional Studies , Substance-Related Disorders/diagnosis , Substance-Related Disorders/epidemiology , Sensitivity and Specificity , Mass Screening/methods , Ethanol
5.
Anal Bioanal Chem ; 412(19): 4749-4760, 2020 Jul.
Article in English | MEDLINE | ID: mdl-32474725

ABSTRACT

Digital polymerase chain reaction (dPCR) methodology has been asserted to be a "potentially primary" analytical approach for assigning DNA concentration. The essence of dPCR measurements is the independent dispersal of fragments into multiple reaction partitions, amplifying fragments containing a target nucleotide sequence until the signal from all partitions containing at least one such fragment rises above threshold, and then determining the proportion of partitions with an above-threshold signal. Should originally double-stranded DNA (dsDNA) fragments be converted into two single strands (ssDNA) prior to dispersal, the dPCR measurements could be biased high by as much as a factor of two. Realizing dPCR's metrological potential therefore requires analytical methods for determining the proportion of ssDNA in nominally dsDNA samples. To meet this need, we have investigated several approaches to this determination: A260 ratio, dPCR ratio, cdPCR staircase, and ddPCR enzyme. In our hands, only the endonuclease-based approach provides adequately accurate estimates for relatively small ssDNA proportions. We present four (enzyme, assay) pairs that provide self-consistent results for human nuclear DNA extracts. However, the proportion of ssDNA differs by as much as 50% between assays, apparently related to the guanine-cytosine (GC) content of the fragment near the assay's target sequence. While materials extracted by us have no more than 6% ssDNA content even after long storage, a commercially obtained PCR assay calibrant contains ≈18% ssDNA. Graphical abstract.


Subject(s)
Cell Nucleus/chemistry , DNA/analysis , Polymerase Chain Reaction/methods , Cell Nucleus/genetics , DNA/genetics , DNA, Single-Stranded/analysis , DNA, Single-Stranded/genetics , Female , Hot Temperature , Humans , Male , Nucleic Acid Denaturation
6.
J Am Geriatr Soc ; 67(2): 363-370, 2019 02.
Article in English | MEDLINE | ID: mdl-30548594

ABSTRACT

BACKGROUND/OBJECTIVES: Of older adults, 42% report problems with daily function, and physical function is the most important consideration for aging individuals. Thus, we implemented a model of care focused on improving physical function and examined health and use outcomes and satisfaction. DESIGN: A 3-year participatory, single-group pretrial/posttrial benchmarked to a usual care cohort that was evaluated prior to the study. SETTING: Four Medicaid home and community-based waiver sites in Michigan. PARTICIPANTS: The participants included 34 clinicians and 270 Medicaid beneficiaries 50 years and older. INTERVENTION: Community Aging in Place, Advancing Better Living for Elders (CAPABLE), an evidence-based model of care that improved physical function in older adults, was implemented using evidence-based strategies. MEASUREMENT: Characteristics (age, race, and sex), health outcomes (comorbidities, instrumental/activities of daily living [I/ADLs], pain, depression, and falls), and emergency department and hospitalization visits preintervention/postintervention and in the usual care cohort were examined. We also measured Medicaid beneficiary's satisfaction with care for those who received CAPABLE. RESULTS: Improved mean ± SD ADLs (preintervention, 8.51 ± 3.08; postintervention, 7.80 ± 2.86; P = .01) and IADLs (preintervention, 6.43 ± 1.31; postintervention, 5.62 ± 1.09; P < .01), a decrease in falls by 14% (from 34.8% preintervention to 20.8% postintervention; P < .01), and fewer hospitalizations (from 0.43 ± 1.51 preintervention to 0.23 ± 0.60 postintervention; P = .03) were found. Post-CAPABLE means were significantly better compared with a usual care cohort for IADLs (6.73 ± 1.27; P < .01) and hospitalizations (0.47 ± 2.66; P < .01). Satisfaction with care was high, and 98.1% recommended CAPABLE as a way to help remain living in the community. CONCLUSION: Improved ADLs and IADLs, a reduction in fall rates, fewer hospitalizations, and high satisfaction with care occurred in this population as a result of the use of CAPABLE. CAPABLE may be one solution to helping vulnerable, low-income older adults with poor physical function to remain living in the community. J Am Geriatr Soc 67:363-370, 2019.


Subject(s)
Health Services for the Aged , Independent Living , Medicaid , Activities of Daily Living , Aged , Aged, 80 and over , Female , Geriatric Assessment , Hospitalization/statistics & numerical data , Humans , Male , Michigan , Middle Aged , Patient Satisfaction , Physical Functional Performance , Program Evaluation , United States
7.
Forensic Sci Int Genet ; 37: 81-94, 2018 11.
Article in English | MEDLINE | ID: mdl-30103146

ABSTRACT

Interlaboratory studies are a type of collaborative exercise in which many laboratories are presented with the same set of data to interpret, and the results they produce are examined to get a "big picture" view of the effectiveness and accuracy of analytical protocols used across participating laboratories. In 2005 and again in 2013, the Applied Genetics Group of the National Institute of Standards and Technology (NIST) conducted interlaboratory studies involving DNA mixture interpretation. In the 2005 NIST MIX05 study, 69 laboratories interpreted data in the form of electropherograms of two-person DNA mixtures representing four different mock sexual assault cases with different contributor ratios. In the 2013 NIST MIX13 study,108 laboratories interpreted electropherogram data for five different case scenarios involving two, three, or four contributors, with some of the contributors potentially related. This paper describes the design of these studies, the variations observed among laboratory results, and lessons learned.


Subject(s)
DNA Fingerprinting , DNA/genetics , Laboratories/statistics & numerical data , Microsatellite Repeats , Alleles , Canada , Electrophoresis , Female , Forensic Genetics/standards , Forensic Genetics/statistics & numerical data , Government Agencies , Humans , Laboratories/standards , Male , Polymerase Chain Reaction , Sex Offenses , United States
8.
Anal Bioanal Chem ; 410(12): 2879-2887, 2018 May.
Article in English | MEDLINE | ID: mdl-29556737

ABSTRACT

The highly multiplexed polymerase chain reaction (PCR) assays used for forensic human identification perform best when used with an accurately determined quantity of input DNA. To help ensure the reliable performance of these assays, we are developing a certified reference material (CRM) for calibrating human genomic DNA working standards. To enable sharing information over time and place, CRMs must provide accurate and stable values that are metrologically traceable to a common reference. We have shown that droplet digital PCR (ddPCR) limiting dilution end-point measurements of the concentration of DNA copies per volume of sample can be traceably linked to the International System of Units (SI). Unlike values assigned using conventional relationships between ultraviolet absorbance and DNA mass concentration, entity-based ddPCR measurements are expected to be stable over time. However, the forensic community expects DNA quantity to be stated in terms of mass concentration rather than entity concentration. The transformation can be accomplished given SI-traceable values and uncertainties for the number of nucleotide bases per human haploid genome equivalent (HHGE) and the average molar mass of a nucleotide monomer in the DNA polymer. This report presents the considerations required to establish the metrological traceability of ddPCR-based mass concentration estimates of human nuclear DNA. Graphical abstract The roots of metrological traceability for human nuclear DNA mass concentration results. Values for the factors in blue must be established experimentally. Values for the factors in red have been established from authoritative source materials. HHGE stands for "haploid human genome equivalent"; there are two HHGE per diploid human genome.


Subject(s)
DNA/genetics , Polymerase Chain Reaction/methods , Algorithms , DNA/analysis , Gene Dosage , Genome, Human , Haploidy , Humans
9.
Anal Chem ; 89(8): 4648-4654, 2017 04 18.
Article in English | MEDLINE | ID: mdl-28347134

ABSTRACT

Digital polymerase chain reaction (dPCR) end point platforms directly estimate the number of DNA target copies per reaction partition, λ, where the partitions are fixed-location chambers (cdPCR) or aqueous droplets floating in oil (ddPCR). For use in the certification of target concentration in primary calibrant certified reference materials (CRMs), both λ and the partition volume, V, must be metrologically traceable to some accessible reference system, ideally, the International System of Units (SI). The fixed spatial distribution of cdPCR chambers enables real-time monitoring of PCR amplification. Analysis of the resulting reaction curves enables validation of the critical dPCR assumptions that are essential for establishing the SI traceability of λ. We know of no direct method for validating these assumptions for ddPCR platforms. The manufacturers of the cdPCR and ddPCR systems available to us do not provide traceable partition volume specifications. Our colleagues at the National Institute of Standards and Technology (NIST) have developed a reliable method for determining ddPCR droplet volume and have demonstrated that different ddPCR reagents yield droplets of somewhat different size. Thus, neither dPCR platform by itself provides metrologically traceable estimates of target concentration. We show here that evaluating split samples with both cdPCR and ddPCR platforms can transfer the λ traceability characteristics of a cdPCR assay to its ddPCR analogue, establishing fully traceable ddPCR estimates of CRM target concentration.


Subject(s)
DNA/analysis , Genome, Human , Polymerase Chain Reaction/methods , DNA/metabolism , Humans , Plasmids/genetics , Plasmids/metabolism
11.
Anal Chem ; 88(4): 2132-9, 2016 Feb 16.
Article in English | MEDLINE | ID: mdl-26751276

ABSTRACT

Polymerase chain reaction (PCR) multiplexed assays perform best when the input quantity of template DNA is controlled to within about a factor of √2. To help ensure that PCR assays yield consistent results over time and place, results from methods used to determine DNA quantity need to be metrologically traceable to a common reference. Many DNA quantitation systems can be accurately calibrated with solutions of DNA in aqueous buffer. Since they do not require external calibration, end-point limiting dilution technologies, collectively termed "digital PCR (dPCR)", have been proposed as suitable for value assigning such DNA calibrants. The performance characteristics of several commercially available dPCR systems have recently been documented using plasmid, viral, or fragmented genomic DNA; dPCR performance with more complex materials, such as human genomic DNA, has been less studied. With the goal of providing a human genomic reference material traceably certified for mass concentration, we are investigating the measurement characteristics of several dPCR systems. We here report results of measurements from multiple PCR assays, on four human genomic DNAs treated with four endonuclease restriction enzymes using both chamber and droplet dPCR platforms. We conclude that dPCR does not estimate the absolute number of PCR targets in a given volume but rather the number of accessible and amplifiable targets. While enzymatic restriction of human genomic DNA increases accessibility for some assays, in well-optimized PCR assays it can reduce the number of amplifiable targets and increase assay variability relative to uncut sample.


Subject(s)
DNA/analysis , Genome, Human , Polymerase Chain Reaction , DNA/metabolism , DNA Primers/metabolism , DNA Restriction Enzymes/metabolism , Humans
12.
Anal Chem ; 88(24): 12169-12176, 2016 12 20.
Article in English | MEDLINE | ID: mdl-28193036

ABSTRACT

Enumeration-based determination of DNA copy-concentration was assessed through an international comparison among national metrology institutes (NMIs) and designated institutes (DIs). Enumeration-based quantification does not require a calibration standard thereby providing a route to "absolute quantification", which offers the potential for reliable value assignments of DNA reference materials, and International System of Units (SI) traceability to copy number 1 through accurate counting. In this study, 2 enumeration-based methods, flow cytometric (FCM) counting and the digital polymerase chain reaction (dPCR), were compared to quantify a solution of the pBR322 plasmid at a concentration of several thousand copies per microliter. In addition, 2 orthogonal chemical-analysis methods based on nucleotide quantification, isotope-dilution mass spectrometry (IDMS) and capillary electrophoresis (CE) were applied to quantify a more concentrated solution of the plasmid. Although 9 dPCR results from 8 laboratories showed some dispersion (relative standard deviation [RSD] = 11.8%), their means were closely aligned with those of the FCM-based counting method and the orthogonal chemical-analysis methods, corrected for gravimetric dilution factors. Using the means of dPCR results, the RSD of all 4 methods was 1.8%, which strongly supported the validity of the recent enumeration approaches. Despite a good overall agreement, the individual dPCR results were not sufficiently covered by the reported measurement uncertainties. These findings suggest that some laboratories may not have considered all factors contributing to the measurement uncertainty of dPCR, and further investigation of this possibility is warranted.


Subject(s)
DNA/analysis , Flow Cytometry/methods , Plasmids/analysis , Polymerase Chain Reaction/methods , Electrophoresis, Capillary , Mass Spectrometry , Nucleotides/analysis
13.
Anal Bioanal Chem ; 407(30): 9061-9, 2015 Dec.
Article in English | MEDLINE | ID: mdl-26438478

ABSTRACT

Polymerase chain reaction (PCR) end-point limiting dilution techniques, collectively termed "digital PCR (dPCR)", have been proposed as providing a potentially primary method for DNA quantification. We are evaluating several commercially available dPCR systems for use in certifying mass concentration in human genomic DNA reference materials. To better understand observed anomalies among results from chamber- and droplet-dPCR (cdPCR and ddPCR) systems, we have developed a graphical tool for evaluating and documenting the performance of PCR assays in real-time cdPCR systems: the ogive plot, the cumulative distribution of crossing threshold values. The ogive structure appears to embed information about early amplification events. We have successfully simulated ogives observed with different assays and reaction conditions using a four-stage amplification model parameterized by the probability of creating an intact 1) first generation "long" amplicon of indeterminate length from an original DNA target, 2) second generation defined-length amplicon from a long amplicon, and 3) defined-length amplicon from another defined-length amplicon. We are using insights from this model to optimize dPCR assay design and reaction conditions and to help validate assays proposed for use in value-assigning DNA reference materials.


Subject(s)
DNA/genetics , Polymerase Chain Reaction/instrumentation , Adult , Humans , Male , Polymerase Chain Reaction/methods
14.
Forensic Sci Int Genet ; 13: 195-205, 2014 Nov.
Article in English | MEDLINE | ID: mdl-25178681

ABSTRACT

The PowerPlex(®) ESI 16 Fast, ESI 17 Fast, ESX 16 Fast, and ESX 17 Fast Systems represent faster cycling versions (50min or less) of the PowerPlex(®) ESI and ESX Systems released by Promega in 2009 to accommodate the ENFSI and EDNAP groups' call for new STR multiplexes for Europe. In addition to amplification of purified DNA samples, these new faster cycling systems allow for direct amplification from single-source blood and buccal samples deposited on FTA(®) and nonFTA paper as well as from SwabSolution™ extracts of buccal swabs without the need for purification and quantitation. There are no changes to the autosomal primer pair sequences in the PowerPlex(®) ESI Fast and ESX Fast Systems compared to the original multiplexes, and full concordance at all autosomal loci and amelogenin was observed with data generated previously with the original PowerPlex(®) ESI and ESX Systems. This paper describes the developmental validation study performed on these new fast systems following guidelines issued by the Scientific Working Group on DNA Analysis Methods (SWGDAM) and those of the DNA Advisory Board (DAB). Validation data demonstrate that these systems are sensitive for detecting low levels of DNA while also being capable of generating robust profiles from the high amount of input DNA present in direct-amplification samples. These systems are also tolerant to both high concentrations of PCR inhibitors as well as to slight variations in the final concentration of master mix and primer pair present in the amplification reaction that might be encountered due to pipetting error. The results of this validation study demonstrate that these systems may be used on multiple thermal cyclers and capillary electrophoresis platforms.


Subject(s)
DNA Fingerprinting , Microsatellite Repeats , Multiplex Polymerase Chain Reaction/instrumentation , Animals , DNA Degradation, Necrotic , Electrophoresis, Capillary , Humans , Male , Reproducibility of Results , Species Specificity , Specimen Handling/methods
17.
J Mol Diagn ; 15(2): 177-85, 2013 Mar.
Article in English | MEDLINE | ID: mdl-23321018

ABSTRACT

Human cytomegalovirus (CMV), classified as human herpesvirus 5, is ubiquitous in human populations. Infection generally causes little illness in healthy individuals, but can cause life-threatening disease in those who are immunocompromised or in newborns through complications arising from congenital CMV infection. An important aspect in diagnosis and treatment is to track circulating viral load with molecular methods, particularly with quantitative PCR. Standardization is vital, because of interlaboratory variability (due in part to the variety of assays and calibrants). Toward that end, the U.S. National Institute of Standards and Technology produced a Standard Reference Material 2366 appropriate for establishing metrological traceability of assay calibrants. This standard is composed of CMV DNA (Towne(Δ147) bacterial artificial chromosome DNA). Regions of the CMV DNA that are commonly used as targets for PCR assays were sequenced. Digital PCR was used to quantify the DNA, with concentration expressed as copies per microliter. The materials were tested for homogeneity and stability. An interlaboratory study was conducted by Quality Control for Molecular Diagnostics (Glasgow, UK), in which one component of SRM 2366 was included for analysis by participants in a CMV external quality assessment and proficiency testing program.


Subject(s)
Cytomegalovirus Infections/diagnosis , Cytomegalovirus/genetics , DNA, Viral/genetics , Reference Standards , Viral Load/standards , Gene Order , Genome, Viral , Humans , Reproducibility of Results , Sequence Analysis, DNA
18.
Forensic Sci Int Genet ; 7(1): 129-35, 2013 Jan.
Article in English | MEDLINE | ID: mdl-22921483

ABSTRACT

As short tandem repeat markers remain the foundation of human identification throughout the world, new STR multiplexes require rigorous testing to ensure the assays are sufficiently robust and reliable for genotyping purposes. The PowerPlex(®) 18D System was created for the direct amplification of buccal and blood samples from FTA(®) storage cards and reliably accommodates other sample materials. The PowerPlex(®) 18D System allows simultaneous amplification of the 13 CODIS loci and amelogenin along with four additional loci: Penta E, Penta D, D2S1338, and D19S433. To demonstrate suitability for human identification testing, the PowerPlex(®) 18D System was tested for sensitivity, concordance, inhibitor tolerance, and performance with thermal cycling and reaction condition variation following SWGDAM developmental validation guidelines. Given these results, PowerPlex(®) 18D System can confidently be used for forensic and human identification testing.


Subject(s)
Forensic Anthropology/methods , Microsatellite Repeats , Electrophoresis, Capillary , Gene Frequency , Humans , Reference Standards
19.
Int J Cancer ; 132(11): 2510-9, 2013 Jun 01.
Article in English | MEDLINE | ID: mdl-23136038

ABSTRACT

Continuous human cell lines have been used extensively as models for biomedical research. In working with these cell lines, researchers are often unaware of the risk of cross-contamination and other causes of misidentification. To reduce this risk, there is a pressing need to authenticate cell lines, comparing the sample handled in the laboratory to a previously tested sample. The American Type Culture Collection Standards Development Organization Workgroup ASN-0002 has developed a Standard for human cell line authentication, recommending short tandem repeat (STR) profiling for authentication of human cell lines. However, there are known limitations to the technique when applied to cultured samples, including possible genetic drift with passage. In our study, a dataset of 2,279 STR profiles from four cell banks was used to assess the effectiveness of the match criteria recommended within the Standard. Of these 2,279 STR profiles, 1,157 were grouped into sets of related cell lines-duplicate holdings, legitimately related samples or misidentified cell lines. Eight core STR loci plus amelogenin were used to unequivocally authenticate 98% of these related sets. Two simple match algorithms each clearly discriminated between related and unrelated samples, with separation between related samples at ≥80% match and unrelated samples at <50% match. A small degree of overlap was noted at 50-79% match, mostly from cell lines known to display variable STR profiles. These match criteria are recommended as a simple and effective way to interpret results from STR profiling of human cell lines.


Subject(s)
Algorithms , Gene Expression Profiling/methods , Genotyping Techniques/standards , Microsatellite Repeats/genetics , Cell Line , Humans , Polymerase Chain Reaction
20.
Eur J Hum Genet ; 20(1): 20-6, 2012 Jan.
Article in English | MEDLINE | ID: mdl-21811303

ABSTRACT

Huntington's disease results from a CAG repeat expansion within the Huntingtin gene; this is measured routinely in diagnostic laboratories. The European Huntington's Disease Network REGISTRY project centrally measures CAG repeat lengths on fresh samples; these were compared with the original results from 121 laboratories across 15 countries. We report on 1326 duplicate results; a discrepancy in reporting the upper allele occurred in 51% of cases, this reduced to 13.3% and 9.7% when we applied acceptable measurement errors proposed by the American College of Medical Genetics and the Draft European Best Practice Guidelines, respectively. Duplicate results were available for 1250 lower alleles; discrepancies occurred in 40% of cases. Clinically significant discrepancies occurred in 4.0% of cases with a potential unexplained misdiagnosis rate of 0.3%. There was considerable variation in the discrepancy rate among 10 of the countries participating in this study. Out of 1326 samples, 348 were re-analysed by an accredited diagnostic laboratory, based in Germany, with concordance rates of 93% and 94% for the upper and lower alleles, respectively. This became 100% if the acceptable measurement errors were applied. The central laboratory correctly reported allele sizes for six standard reference samples, blind to the known result. Our study differs from external quality assessment (EQA) schemes in that these are duplicate results obtained from a large sample of patients across the whole diagnostic range. We strongly recommend that laboratories state an error rate for their measurement on the report, participate in EQA schemes and use reference materials regularly to adjust their own internal standards.


Subject(s)
Diagnostic Errors/statistics & numerical data , Genetic Testing/standards , Huntington Disease/genetics , Nerve Tissue Proteins/genetics , Nuclear Proteins/genetics , Trinucleotide Repeats , Alleles , Genetic Testing/methods , Guidelines as Topic , Humans , Huntingtin Protein , Huntington Disease/diagnosis , International Cooperation , Mutation , Reference Standards , Reproducibility of Results , Sensitivity and Specificity
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