Collection Kit Research Articles

Alternative direct-to-amplification cell lysis techniques for forensically relevant non-sperm cells.

While efforts have been made to reduce the pervasive backlog of sexual assault evidence collection kits, the actual laboratory process remains very time-consuming due to the requirement of a differential lysis step before DNA purification, as well as intricate mixture analysis towards the end of the DNA workflow. Recently, an alternative, direct-to-amplification sperm lysis method (using 1 M NaOH) was identified. However, a direct cell lysis method for non-sperm cells has not been identified yet. Thus, the primary objective of this work was to find an alternative method that is quick, inexpensive, and does not require multiple purification steps for the lysis of non-sperm cells in sexual assault samples. In this study, vaginal swab samples were lysed with the control method, prepGEM™, as well as six alternative reagents: alkaline buffer with 25-200 mM NaOH, high-salt stain extraction buffer, modified radioimmunoprecipitation assay (RIPA) buffer, mammalian protein extraction reagent (M-PER™), digitonin buffer, and urea/thiourea buffer. Quantification using Quantifiler® Trio of vaginal and semen lysates revealed that the alkaline (25 mM NaOH) and M-PER™ methods were efficient for the lysis of vaginal epithelial cells without substantial sperm cell lysis. Following quantification, analysis of STR profiles from vaginal lysates revealed that the M-PER™ method showed promising results across all metrics examined, including the percentage of detected STR alleles, mean peak heights, peak height ratio, and interlocus balance. Thus, this method was recommended as an alternative to the traditional differential lysis method for non-sperm cells given its ability to produce amplification-ready lysates without any DNA purification step.

Developing Clinical Phenotype Data Collection Standards for Research in Africa.

Modern biomedical research is characterised by its high-throughput and interdisciplinary nature. Multiproject and consortium-based collaborations requiring meaningful analysis of multiple heterogeneous phenotypic datasets have become the norm; however, such analysis remains a challenge in many regions across the world. An increasing number of data harmonisation efforts are being undertaken by multistudy collaborations through either prospective standardised phenotype data collection or retrospective phenotype harmonisation. In this regard, the Phenotype Harmonisation Working Group (PHWG) of the Human Heredity and Health in Africa (H3Africa) consortium aimed to facilitate phenotype standardisation by both promoting the use of existing data collection standards (hosted by PhenX), adapting existing data collection standards for appropriate use in low- and middle-income regions such as Africa, and developing novel data collection standards where relevant gaps were identified. Ultimately, the PHWG produced 11 data collection kits, consisting of 82 protocols, 38 of which were existing protocols, 17 were adapted, and 27 were novel protocols. The data collection kits will facilitate phenotype standardisation and harmonisation not only in Africa but also across the larger research community. In addition, the PHWG aims to feed back adapted and novel protocols to existing reference platforms such as PhenX.

A Web-Based, Mail-Order Sexually Transmitted Infection Testing Program: Qualitative Analysis of User Feedback.

The incidence of sexually transmitted infections (STIs) is increasing in the United States. The COVID-19 pandemic resulted in significant reductions in access to health care services, including STI testing and treatment, leading to underreporting of STI cases and a need for alternatives to clinic-based testing. Moreover, concerns around confidentiality, accessibility, and stigma continue to limit access to clinic-based STI testing, particularly for high-priority populations. IWantTheKit (IWTK) is a web-based platform that mails free, confidential, self-administered sample collection kits for testing for gonorrhea, chlamydia (both genital and extragenital sites), and vaginal trichomonas. Individuals visiting the IWTK website may select genital, pharyngeal, and rectal samples for chlamydia and gonorrhea testing. Vaginal samples are tested for trichomoniasis. Self-collected samples are processed in a College of American Pathologists-accredited laboratory, and results are posted to an individual's secure digital account. This study aimed to (1) describe users' experience with the IWTK service through analysis of routine data and (2) optimize retention among current users and expand reach among high-priority populations by responding to user needs through programmatic and functional changes to the IWTK service. Free-text entries were submitted by IWTK users via a confidential "Contact Us" page on the IWTK website from May 17, 2021, to January 31, 2022. All entries were deidentified prior to analysis. Two independent analysts coded these entries using a predefined codebook developed inductively for thematic analysis. A total of 254 free-text entries were analyzed after removing duplicates and nonsensical entries. Themes emerged regarding the functionality of the website and personal experiences using IWTK's services. Users' submissions included requests related to order status, address changes, replacement of old kits, clinical information (eg, treatment options and symptom reports), and reported risk behaviors. This analysis demonstrates how routine data can be used to propose potential programmatic improvements. IWTK implemented innovations on the website based on the study results to improve users' experience, including a tracking system for orders, address verification for each order, a physical drop box, additional textual information, direct linkage to care navigation, and printable results. Web-based, mail-order STI testing programs can leverage user feedback to optimize implementation and retention among current users and potentially expand reach among high-priority populations. This analysis is supported by other data that demonstrate how comprehensive support and follow-up care for individuals testing positive are critical components of any self-testing service. Additional formal assessments of the IWTK user experience and efforts to optimize posttesting linkage to care may be needed.

Two Interventions on Pathologic Nodal Staging in a Population-Based Lung Cancer Resection Cohort

BackgroundDespite its prognostic importance, poor pathologic nodal staging of lung cancer prevails. We evaluated the impact of 2 interventions to improve pathologic nodal staging. MethodsWe implemented a lymph node specimen collection kit to improve intraoperative lymph node collection (surgical intervention) and a novel gross dissection method for intrapulmonary node retrieval (pathology intervention) in nonrandomized stepped-wedge fashion, involving 12 hospitals and 7 pathology groups. We used standard statistical methods to compare surgical quality and survival of patients who had neither intervention (group 1), pathology intervention only (group 2), surgical intervention only (group 3), and both interventions (group 4). ResultsOf 4019 patients from 2009 to 2021, 50%, 5%, 21%, and 24%, respectively, were in groups 1 to 4. Rates of nonexamination of lymph nodes were 11%, 9%, 0%, and 0% and rates of nonexamination of mediastinal lymph nodes were 29%, 35%, 2%, and 2%, respectively, in groups 1 to 4 (P < .0001). Rates of attainment of American College of Surgeons Operative Standard 5.8 were 22%, 29%, 72%, and 85%; and rates of International Association for the Study of Lung Cancer complete resection were 14%, 21%, 53%, and 61% (P < .0001).Compared with group 1, adjusted hazard ratios for death were as follows: group 2, 0.93 (95% CI, 0.76-1.15); group 3, 0.91 (0.78-1.03); and group 4, 0.75 (0.64-0.87). Compared with group 2, group 4 adjusted hazard ratio was 0.72 (0.57-0.91); compared with group 3, it was 0.83 (0.69-0.99). These relationships remained after exclusion of wedge resections. ConclusionsCombining a lymph node collection kit with a novel gross dissection method significantly improved pathologic nodal evaluation and survival.

Self- and physician-collected high-risk human papillomavirus (HPV) testing to detect high-grade cervical lesions among Thai women

ObjectiveWe compared the performance of high-risk human papillomavirus (HPV) messenger RNA testing of physician- and self-collected specimens for detecting histological grade 2 or higher cervical intraepithelial neoplasia (CIN) among women...

Lessons from clinical implementation of a preemptive pharmacogenetic panel as part of a testing pilot program with an employer-sponsored medical plan.

Introduction: This manuscript reports on a pilot program focused on implementing pharmacogenetic testing within the framework of an employer-sponsored medical plan at University of Florida (UF) Health. The aim was to understand the challenges associated with program implementation and to gather insights into patient attitudes towards PGx testing. Methods: The pilot program adopted a partially preemptive approach, targeting patients on current prescriptions for medications with relevant gene-drug associations. Patients were contacted via phone or through the MyChart system and offered pharmacogenetic testing with no additional direct costs. Results: Of 244 eligible patients, 110 agreed to participate. However, only 61 returned the mailed DNA collection kits. Among these, 89% had at least one potentially actionable genotype-based phenotype. Post-test follow-up revealed that while the majority viewed the process positively, 71% preferred a consultation with a pharmacogenetic specialist for better understanding of their results. Barriers to implementation ranged from fatigue with the healthcare system to a lack of understanding of the pharmacogenetic testing and concerns about privacy and potential misuse of genetic data. Conclusion: The findings underscore the need for clearer patient education on pharmacogenetic results and suggest the importance of the role of pharmacogenetic-trained pharmacists in delivering this education. They also highlight issues with relying on incomplete or inaccurate medication lists in patients' electronic health record. The implementation revealed less obvious challenges, the understanding of which could be beneficial for the success of future preemptive pharmacogenetic implementation programs. The insights from the pilot program served to bridge the information gap between patients, providers, and pharmacogenetic -specialists, with the ultimate goal of improving patient care.

A Novel Home-Based Study of Circadian Rhythms: Design, Rationale, and Methods for the Circadia Study.

The Circadia Study (Circadia) is a novel "direct-to-participant" research study investigating the genetics of circadian rhythm disorders of advanced and delayed sleep phase and non-24 hour rhythms. The goals of the Circadia Study are twofold: (i) to create an easy-to-use toolkit for at-home circadian phase assessment for patients with circadian rhythm disorders through the use of novel in-home based surveys, tests, and collection kits; and (ii) create a richly phenotyped patient resource for genetic studies that will lead to new genetic loci associated with circadian rhythm disorders revealing possible loci of interest to target in the development of therapeutics for circadian rhythm disorders. Through these goals, we aim to broaden our understanding and elucidate the genetics of circadian rhythm disorders across a diverse patient population while increasing accessibility to circadian rhythm disorder diagnostics reducing health disparities through self-directed at-home dim light melatonin onset (DLMO) collections.

Development of an in-house bone marrow collection kit: The Catalan bone marrow transplantation group experience.

Bone marrow (BM) harvesting is one of the essential sources of stem cells for haematopoietic stem cell transplantation. In 2019, commercial BM collection kits became unavailable in Europe. Consequently, we created an in-house BM collection kit as an alternative. We compared two groups of BM collections. The first collections were taken using an in-house kit from June 2022 through February 2023 and the second with a commercial kit from February 2021 through May 2022. These all took place at seven collection centres (CC). We analysed the harvest quality (cell blood count, CD34+ cells, viability, potency and sterility), the incidents occurring with each kit and the time to neutrophil and platelet engraftment in recipients. A total of 23 donors underwent BM harvesting with the in-house kit and 23 with the commercial one. Both cohorts were comparable regarding donor characteristics, CC and time to procedure. No statistical differences were found in harvest quality between the in-house and commercial kits. A new transfusion set was required in three BM harvests (13%) with the in-house kit because of filter clogging. The median time to neutrophil and platelet engraftment was 21 days for both cohorts and 29 days (in-house) and 33 days (commercial), p = 0.284, respectively. The in-house BM collection kit offers a real approach to solve the diminished supply of commercial kits. A higher risk of filter clogging was observed compared with commercial kits due to the lack of 850 and 500 μm filters.

Sexually transmitted infections with Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma genitalium, and Trichomonas vaginalis in pregnant women as detected by molecular testing.

During pregnancy, sexually transmitted infections can be transmitted vertically to the fetus, leading to an increase in morbidity and mortality for both mother and child. This study aimed to determine the profile of cervical and vaginal infections in pregnant women receiving prenatal care in a single institute. The study was conducted in a tertiary hospital. Molecular testing was used to detect Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma genitalium, and Trichomonas vaginalis. Samples of vaginal secretions were collected from pregnant women using the Aptima® Multitest Swab Specimen Collection kit to test for the pathogens. The inclusion criteria consisted of pregnant women of 15-45 years of age receiving prenatal care at the institute, irrespective of gestational age, who agreed to provide vaginal swab. The exclusion criterion was the use of antibiotics in the preceding 3 months. Frequencies and percentages were calculated for the pathogens detected in the samples evaluated. Overall, 200 samples were tested. Of the pathogens detected, there was a predominance of T. vaginalis (15.5% of the samples) and C. trachomatis (14.5%), followed by M. genitalium (10.0%) and N. gonorrhoeae (0.5%). Identifying the microorganisms present in the microbiota of pregnant women is of the utmost importance in assuring the appropriate treatment for each pathogen, thus avoiding complications both for the woman and for her fetus. These results should serve to stimulate the debate on implementing these tests as routine during prenatal care.

Conductive vial electromembrane extraction of opioids from oral fluid.

The use of oral fluid as sample matrix has gained significance in the analysis of drugs of abuse due to its non-invasive nature. In this study, the 13 opioids morphine, oxycodone, codeine, O-desmethyl tramadol, ethylmorphine, tramadol, pethidine, ketobemidone, buprenorphine, fentanyl, cyclopropylfentanyl, etonitazepyne, and methadone were extracted from oral fluid using electromembrane extraction based on conductive vials prior to analysis with ultra-high performance liquid chromatography-tandem mass spectrometry. Oral fluid was collected using Quantisal collection kits. By applying voltage, target analytes were extracted from oral fluid samples diluted with 0.1% formic acid, across a liquid membrane and into a 300 μL 0.1% (v/v) formic acid solution. The liquid membrane comprised 8 μL membrane solvent immobilized in the pores of a flat porous polypropylene membrane. The membrane solvent was a mixture of 6-methylcoumarin, thymol, and 2-nitrophenyloctyl ether. The composition of the membrane solvent was found to be the most important parameter to achieve simultaneous extraction of all target opioids, which had predicted log P values in the range from 0.7 to 5.0. The method was validated in accordance to the guidelines by the European Medical Agency with satisfactory results. Intra- and inter-day precision and bias were within guideline limits of ± 15% for 12 of 13 compounds. Extraction recoveries ranged from 39 to 104% (CV ≤ 23%). Internal standard normalized matrix effects were in the range from 88 to 103% (CV ≤ 5%). Quantitative results of authentic oral fluid samples were in accordance with a routine screening method, and external quality control samples for both hydrophilic and lipophilic compounds were within acceptable limits.

Validating the ORACollect for the detection of cytomegalovirus

Targeted screening for Cytomegalovirus (CMV) in Deaf and Hard of Hearing (DHH) children is now internationally recommended. With newborn genomic screening for DHH children a future possibility, the commercially-available human genomic DNA collection kit (ORACollect, Oragene OCR-100) could enable one single sample to screen for CMV and genetic causes of deafness at scale with minimal additional costs. Our pilot study validated ORACollect against Copan FLOQswabs® (gold standard clinical procedure) for detecting CMV using 15 sets of saliva samples from 14 infants/children, comparing CMV PCR results using different testing protocols. ORACollect stored at room temperature had high sensitivity (up to 89%), specificity (up to 80%) and percent agreement (up to 86%) in detecting CMV DNA compared to FLOQswabs®. This suggests that ORACollect is an appropriate alternative to FLOQswabs® for collecting viral CMV DNA for PCR testing, independent of the DNA extraction approach. This could be revolutionary in facilitating dual genomic and viral screening in newborns and would enable CMV screening in non-tertiary hospital settings where laboratory facilities are not available.

Energetics and lifestyle in inherited syndromes (ELLIES Project): Feasibility of remote specimen collection for biomarker analysis.

e22545 Background: Hereditary breast cancer (BC) impacts ~39,000 individuals annually and about 10% of BCs result from an inherited mutation. Obesity is independently associated with an increased risk of BC and there is interest in studying modifiable risk factors such as nutrition, obesity, and physical activity in correlation to risk, but there is a paucity of data on the impact of lifestyle on risk and less is known about biomarkers specific to lifestyle interventions and mutation carriers. Biologic pathways are implicated in the association of obesity and cancer risk and several biomarkers have been adequately measured in fingerstick samples in controlled settings but not studied in remote specimens. To characterize metabolic risk factors and lifestyle habits over the lifetime and inform a future intervention, we explored the feasibility of obtaining sufficient specimens for biomarker analysis using home collection kits within a cohort of hereditary cancer mutation carriers. Methods: Cohort 1, recruited from a prospective registry of mutation carriers were mailed a home biospecimen collection kit containing a bloodspot collection card (BCC), a lancet for fingerstick blood collection, a tube containing a nucleic acid stabilizing buffer for saliva collection, return postage, and detailed instructions. Cohort 2, recruited from a High-Risk BC Clinic, provided a fasting intravenous blood draw and fingerstick for a BCC. Dried BCCs were analyzed for biomarkers: leptin, IGF-1, IGF binding proteins 1 and 2, glucose, and CRP. Variances between biomarker levels in home kits and plasma samples were examined. Saliva samples were evaluated for miRNA and SNPs. Results: 40 individuals were invited to participate in Cohort 1; 20 enrolled within 7 days and were mailed a kit; ~14 days occurred between mailing the kits and receiving specimens; 5 participants (25%) were unable to fill all circles on the BCCs, 1 (5%) was unable to draw blood with the lancet provided; 5 participants (25%) required additional postage and 5 (25%) were lost to follow-up. Rate of return of completed biomarker kits was 70% (15), with only one incomplete. 11 clinic patients were invited to participate in Cohort 2; 10 enrolled and provided a fasting intravenous blood draw and fingerstick for a BCC. Pearson coefficients between plasma samples and matching dried BCC samples indicated good correlations for most markers (leptin r = 0.97, p = 0.001; IGFBP1 r = 0.98, p = 0.001; IGFBP2 r = 0.97 p = 0.001; glucose r = 0.97, p = 0.003; CRP r = 0.98, p = 0.001; IGF1 r = 0.39, p = 0.30. Of the remote saliva collections, 14 of 15 samples had adequate quality and quantity of gDNA for SNP analysis and miRNA for miRNAseq. Conclusions: Remote self-collection of capillary blood and saliva was well-accepted in a cohort of hereditary mutation carriers and feasibility was established as specimens were adequate for measuring defined biomarkers.

Allelic Variants in the Warfarin-related Genes VKORC1 and CYP2C9 in a Western Saudi Population

Objectives To investigate the allele and genotype frequencies of the warfarin-related genes VKORC1 (-1639G&gt;A), CYP2C9*2, and CYP2C9*3 among healthy Saudis. Materials and Methods This cross-sectional study involved 125 unrelated healthy Saudis ages 18–60 years visiting the King Abdulaziz University Hospital (KAUH) in Jeddah, Western Saudi Arabia. The Oragene™ DNA saliva collection kits were used to collect and extract DNA from saliva samples. A polymerase chain reaction-restriction fragment length polymorphism analysis was used to detect the mutant alleles. Results Over 51.4% of the Saudi participants carried one or more mutant alleles. The frequency of the VKORC1 (-1639G&gt;A) allele in Saudi was relatively high at 54.8%. The frequencies of the CYP2C9 allele were 19.6% and 54% for the CYP2C9*2 and CYP2C9*3 alleles, respectively, which are substantially more abundant than in other populations. Conclusion The observed high frequencies of VKORC1 (-1639G&gt;A) and CYP2C9*2 and CYP2C9*3 polymorphisms suggest that genetic testing should be considered before initiating warfarin therapy to predict the optimal initial dose of warfarin and minimize warfarin-related side effects.

SPARK, studying pathways of resistance in KRAS-driven cancers: A remote plasma ctDNA participation study to identify mechanisms of resistance to KRAS inhibitors.

TPS3166 Background: KRAS mutations account for a significant proportion of oncogenic mutations in cancers of the lung, colon, pancreas, and other organs. Cancers with KRASG12C mutations are now targetable with direct KRASG12C inhibitors, and other allele-specific and pan-KRAS inhibitors are in clinical development. Recent work has shown that complex resistance mechanisms can arise after treatment with KRASG12C inhibitors, including polyclonal KRAS alterations, acquired bypass mechanisms, and acquired fusions. The SPARK protocol is a remote participation ctDNA collection study that will evaluate mechanisms of resistance to RAS inhibitors and combination therapies. Methods: SPARK (NCT05272423) is a non-interventional, single coordinating center, decentralized biospecimen collection study, with a planned accrual of up to 250 patients with a diagnosis of KRAS-mutant cancer who are experiencing disease progression on a specific KRAS inhibitor or combination of inhibitors. The study will enable a web-based remote consent (https://alcmi.net/research/spark/) and subjects will be sent blood collection kits with the necessary materials for local phlebotomy for the FoundationOne Liquid CDx (F1LCDx) Biopsy Assay. Plasma NGS results will be returned to the treating physician and the study team. Patients will initially be enrolled into two cohorts: Cohort 1A will be restricted to KRAS G12C mutant cancers who progressed after being treated with KRAS G12C inhibitors. Cohort 1B will enroll patients with KRAS mutant cancers whose tumors progressed on any KRAS inhibitor (other than a direct KRAS G12C inhibitor). Cohort 2 will enroll KRAS mutant patients that have progressed on KRAS inhibitors and who have already had a sequencing assay performed to determine the resistance mechanism to KRAS inhibitors. These patients will be invited to share their data and medical history with the study team. Plasma for F1LCDX analysis will be optional for Cohort 2. Mechanisms of acquired resistance will be summarized with descriptive statistics, and compared across drugs (e.g., sotorasib vs adagrasib), between tumor types (e.g., NSCLC vs CRC), and by regimen (e.g. monotherapy vs combination therapy) to determine if different resistance mutations arise in these settings. Progression-free survival (PFS), and overall survival (OS) with KRAS inhibitors will be analyzed depending on the resistance mechanism (e.g. on-target vs off-target). Kaplan-Meier method will be used estimate median survival, and log-rank test will be used to compare groups of interests. Cox-regression model will be used to estimate univariable and multivariable hazard ratios. Outcomes from subsequent treatment after the development of acquired resistance will also be explored with descriptive statistics. No interim analysis is planned. The study activated on November 1st 2022. Clinical trial information: NCT05272423 .

Facilitators and Barriers to HPV Self-Sampling as a Cervical Cancer Screening Option among Women Living with HIV in Rural Uganda.

Background: There is a paucity of studies exploring women living with HIV's (WLWH) experiences relating to human papillomavirus (HPV) self-sampling as cervical cancer (CC) screening approach, either at the clinic or at the home setting, using qualitative methods. Our study explored facilitators and barriers to HPV self-sampling as a CC screening approach among human immunodeficiency virus (HIV)-infected women, as supported by the new WHO guidelines of using the HPV test as a screening modality. Methods: The study was guided by the health promotion model (HPM), which helps individuals achieve higher levels of well-being. The phenomenology design was used to explore the deeper facilitators and barriers of women regarding self-sampling, either at home or in clinical settings, at Luweero District Hospital, Uganda. The in-depth interview (IDI) guide was translated from English to Luganda. Qualitative data analysis was guided by content analysis techniques. The transcripts were coded in NVivo 20.7.0. The coded text was used to generate categories of analytically meaningful data that guided the formation of themes, the interpretation of results, and the final write-up. Results: WLWH were motivated to screen for HPV using the clinic-based approach because of perceived early diagnosis and treatment, visualization of the cervix, and free service, while reduced distance, privacy and the smooth sample collection kit were motivators for the home-based approach. A barrier that cut across the two HPV self-sampling approaches was a lack of knowledge about HPV. The barriers to clinic-based HPV self-sampling screening included lack of privacy, perceived painful procedures for visual inception under acetic acid (VIA), and fear of finding the disease. Stigma and discrimination were reported as the major barriers to the home-based HPV self-sampling approach. The major reasons why some WLWH refused to screen were fear of finding the disease, stress, and financial disruptions related to being diagnosed with CC disease. Conclusions: Therefore, early diagnosis for HPV and CC enhances clinic-based HPV self-sampling, while privacy enhances the home-based HPV self-sampling approach. However, fear of finding a disease and the lack of knowledge of HPV and CC hinders HPV self-sampling. Finally, designing pre- and post-testing counselling programs in HIV care is likely to increase the demand for HPV self-sampling.

Emergency Department Preparedness to Care for Sexual Assault Survivors: A Nationwide Study.

Emergency departments (ED) provide trauma-informed care to sexual assault (SA) survivors and connect them with comprehensive services. Through surveying SA survivor advocates, we aimed to 1) document updated trends in the quality of care and resources offered to SA survivors and 2) identify potential disparities according to geographic regions in the US, urban vs rural clinic locations, and the availability of sexual assault nurse examiners (SANE). We conducted a cross-sectional study between June-August 2021, surveying SA advocates who were dispatched from rape crisis centers to support survivors during ED care. Survey questions addressed two major themes in quality of care: staff preparedness to provide trauma-response care; and available resources. Staff preparedness to provide trauma-informed care was assessed through observations of staff behaviors. We used Wilcoxon rank-sum and Kruskal-Wallis tests to analyze differences in responses according to geographic regions and SANE presence. A total of 315 advocates from 99 crisis centers completed the survey. The survey had a participation rate of 88.7% and a completion rate of 87.9%. Advocates who indicated that a higher proportion of their cases were attended by SANEs were more likely to report higher rates of trauma-informed staff behaviors. For example, the recalled rate of staff asking patients for consent at every step of the exam was significantly associated with SANE presence (P < 0.001). With respect to access to resources, 66.7% of advocates reported that hospitals often or always have evidence collection kits available; 30.6% reported that resources such as transportation and housing are often or always available, and 55.3% reported that SANEs are often or always part of the care team. The SANEs were reported to be more frequently available in the Southwest than in other US regions (P < 0.001) and in urban as opposed to rural areas (P < 0.001). Our study indicates that support from sexual assault nurse examiners is highly associated with trauma-informed staff behaviors and comprehensive resources. Urban-rural and regional disparities exist regarding access to SANEs, suggesting that elevating nationwide quality and equity in care of survivors of sexual assault requires increased investments in SANE training and coverage.

The microbiome of an outpatient rehabilitation clinic and predictors of contamination: A pilot study.

Understanding sources of microbial contamination in outpatient rehabilitation (REHAB) clinics is important to patients and healthcare providers. The purpose of this study was to characterize the microbiome of an outpatient REHAB clinic and examine relationships between clinic factors and contamination. Forty commonly contacted surfaces in an outpatient REHAB clinic were observed for frequency of contact and swiped using environmental sample collection kits. Surfaces were categorized based on frequency of contact and cleaning and surface type. Total bacterial and fungal load was assessed using primer sets specific for the 16S rRNA and ITS genes, respectively. Bacterial samples were sequenced using the Illumina system and analyzed using Illumina-utils, Minimum Entropy Decomposition, QIIME2 (for alpha and beta diversity), LEfSe and ANCOM-BC for taxonomic differential abundance and ADONIS to test for differences in beta diversity (p<0.05). Porous surfaces had more bacterial DNA compared to non-porous surfaces (median non-porous = 0.0016ng/μL, 95%CI = 0.0077-0.00024ng/μL, N = 15; porous = 0.0084 ng/μL, 95%CI = 0.0046-0.019 ng/μL, N = 18. p = 0.0066,DNA. Samples clustered by type of surface with non-porous surfaces further differentiated by those contacted by hand versus foot. ADONIS two-way ANOVA showed that the interaction of porosity and contact frequency (but neither alone) had a significant effect on 16S communities (F = 1.7234, R2 = 0.0609, p = 0.032). Porosity of surfaces and the way they are contacted may play an underestimated, but important role in microbial contamination. Additional research involving a broader range of clinics is required to confirm results. Results suggest that surface and contact-specific cleaning and hygiene measures may be needed for optimal sanitization in outpatient REHAB clinics.

Tale of Two Counties With the Same Telehealth Story: Experience with Cancer Genetics Testing During COVID-19 at a Community Hospital

Introduction: With the onset of the COVID-19 pandemic in 2020, the utilization of telemedicine now offered an alternative diagnostic and treatment resource to providers in many areas of medicine including oncology and cancer genetics. This care option paired with genetic testing labs’ ability to send saliva-based DNA collection kits to patients, enabled our community hospital in Detroit to offer diagnostic testing without the patient coming to a healthcare setting for a host of reasons. Social determinants of health have been found to influence success with telehealth, and this study sought to analyze how successful telehealth cancer genetics care was throughout the Detroit Metro area. Methods: Patient demographics for in person visits six months before COVID were analyzed, and then compared with demographics of patients during the 2020-2021 pandemic period where visits were telehealth. Results: Pre-pandemic there were , 192 unique patients seen in person with the top three cities patients were from were Detroit (12.1%), Clinton Township (8.3%), and Saint Clair Shores (10.4%). During the pandemic, with telehealth as the major modality, the top three cities were Macomb (7.2%), Detroit (7%), and Clinton Township (7%). Detroit is in Wayne County, while St.Clair Shores and Clinton Township are in Macomb County. Per the US Census Bureau Macomb county has a median income of $64,641 and Wayne county has a median income of $49,359, and poverty level in Macomb county is 9.2% versus in Wayne the level is 20%. Conclusions: This paper outlines the challenges of initiating a telemedicine program in an urban community area and highlights the benefits of a concierge service in serving cancer patients who may have economic and historically poor perceived technologic abilities.

Diagnostic yield of genetic screening in a diverse, community-ascertained cohort

BackgroundPopulation screening for genetic risk of adult-onset preventable conditions has been proposed as an attractive public health intervention. Screening unselected individuals can identify many individuals who will not be identified through current genetic testing guidelines.MethodsWe sought to evaluate enrollment in and diagnostic yield of population genetic screening in a resource-limited setting among a diverse population. We developed a low-cost, short-read next-generation sequencing panel of 25 genes that had 98.4% sensitivity and 99.98% specificity compared to diagnostic panels. We used email invitations to recruit a diverse cohort of patients in the University of Washington Medical Center system unselected for personal or family history of hereditary disease. Participants were sent a saliva collection kit in the mail with instructions on kit use and return. Results were returned using a secure online portal. Enrollment and diagnostic yield were assessed overall and across race and ethnicity groups.ResultsOverall, 40,857 people were invited and 2889 (7.1%) enrolled. Enrollment varied across race and ethnicity groups, with the lowest enrollment among African American individuals (3.3%) and the highest among Multiracial or Other Race individuals (13.0%). Of 2864 enrollees who received screening results, 106 actionable variants were identified in 103 individuals (3.6%). Of those who screened positive, 30.1% already knew about their results from prior genetic testing. The diagnostic yield was 74 new, actionable genetic findings (2.6%). The addition of more recently identified cancer risk genes increased the diagnostic yield of screening.ConclusionsPopulation screening can identify additional individuals that could benefit from prevention, but challenges in recruitment and sample collection will reduce actual enrollment and yield. These challenges should not be overlooked in intervention planning or in cost and benefit analysis.

GutAlive® enables DNA-based microbiome analysis without disrupting the original composition and diversity.

A precise fecal microbiome analysis requires normalized methods for microbiome sampling, transport and manipulation in order to obtain a representative snapshot of the microbial community. GutAlive® is the unique stool collection kit that generates an anaerobic atmosphere enabling oxygen sensitive bacteria to survive, maintaining the original microbiome composition and diversity. Five stool samples from different donors were collected using two different sampling devices, GutAlive® and Zymo DNA/RNA Shield®, and processed at four different time points. Shotgun metagenomics was used to evaluate the influence of the device and the processing timing on the microbial populations to unravel the potential fluctuations on the composition and diversity of the fecal microbiome and the metabolic pathways profiling. Additionally, RT-qPCR was used to quantify bacterial cell viability for downstream applications of microbiota samples beyond metagenomics. Our results show that GutAlive® enables bacterial cell viability overtime preserving DNA integrity, obtaining high-quantity and high-quality DNA to perform microbiome analysis using shotgun metagenomics. Based on the taxonomic profiling, metabolic pathways analysis, phylogeny and metagenome-assembled genomes, GutAlive® displayed greater performance without significant variability over time, showcasing the stabilization of the microbiome preserving the original composition and diversity. Indeed, this DNA stabilization is enabled with the preservation of bacterial viability on an anaerobic environment inside of the sampling device, without the addition of any reagents that interact directly with sample. All the above makes GutAlive® an user-friendly kit for self-collection of biological samples, suitable for microbiome analysis, diagnostics, fecal microbiota transplant and bacterial isolation, maintaining the stability and bacterial viability over time, preserving the original composition and diversity of the microbiome.