Laboratory Considerations for Releasing Next-Generation Sequencing Data to Patients.

CONTEXT.­: Title 45, section 164.524 of the Code of Federal Regulations states that health care systems must provide patient health records upon that patient's request. For complex testing, such as next-generation sequencing (NGS), this raises questions related to what data should be released and the laboratory considerations regarding the release of this data. OBJECTIVE.­: To describe the laboratory implications of releasing different NGS data files and the limitations for the clinical use of different NGS data files. DESIGN.­: The College of American Pathologists workgroup, composed of laboratorians with expertise regarding NGS testing, reviewed pertinent literature, including title 45, section 164.524, and the Health and Human Services "Guidance on Individuals' Right to Access Health Information." RESULT.­: From an accreditation standpoint, validation of NGS includes both the wet bench and data processing (bioinformatics) portions, and appropriately validated laboratory testing is required to ensure quality patient results. NGS testing generates intermediate data files that have not completed the fully validated process but are often kept by the laboratory. These files may be requested by patients, but most patients will not be aware of the test validation process and the limitations of data that have not gone through a fully validated process. CONCLUSIONS.­: Laboratories should encourage patients to receive their health data and to help individuals understand the content, uses, and limitations of laboratory data they have requested or received. NGS data used in a nonvalidated manner should not be used for clinical purposes without confirmation by a clinically validated method.

Prioritizing the Interview in Selecting Resident Applicants: Behavioral Interviews to Determine Goodness of Fit.

From our initial screening of applications, we assess that the 10% to 15% of applicants whom we will interview are all academically qualified to complete our residency training program. This initial screening to select applicants to interview includes a personality assessment provided by the personal statement, Dean's letter, and letters of recommendation that, taken together, begin our evaluation of the applicant's cultural fit for our program. While the numerical scoring ranks applicants preinterview, the final ranking into best fit categories is determined solely on the interview day at a consensus conference by faculty and residents. We analyzed data of 819 applicants from 2005 to 2017. Most candidates were US medical graduates (62.5%) with 23.7% international medical graduates, 11.7% Doctors of Osteopathic Medicine (DO), and 2.1% Caribbean medical graduates. Given that personality assessment began with application review, there was excellent correlation between the preinterview composite score and the final categorical ranking in all 4 categories. For most comparisons, higher scores and categorical rankings were associated with applicants subsequently working in academia versus private practice. We found no problem in using our 3-step process employing virtual interviews during the COVID pandemic.

Mater Artium Necessitas: The Birth of a COVID-19 Command Center.

In February of 2020, New York City was unprepared for the COVID-19 pandemic. Cases of SARS-CoV-2 infection appeared and spread rapidly. Hospitals had to repurpose staff and establish diagnostic testing for this new viral infection. In the background of the usual respiratory pathogen testing performed in the clinical laboratory, SARS-CoV-2 testing at the Montefiore Medical System grew exponentially, from none to hundreds per day within the first week of testing. The job of appropriately routing SARS-CoV-2 viral specimens became overwhelming. Additional staff was required to triage these specimens to multiple in-house testing platforms as well as external reference laboratories. Since medical school classes and many research laboratories shut down at the Albert Einstein College of Medicine and students were eager to help fight the pandemic, we seized the opportunity to engage and train senior MD-PhD students to assist in triaging specimens. This volunteer force enabled us to establish the "Pathology Command Center," staffed by these students as well as residents and furloughed dental associates. The Pathology Command Center staff were tasked with the accessioning and routing of specimens, answering questions from clinical teams, and updating ever evolving protocols developed in collaboration with a team of Infectious Disease clinicians. Many lessons were learned during this process, including how best to restructure an accessioning department and how to properly onboard students and repurpose staff while establishing safeguards for their well-being during these unprecedented times. In this article, we share some of our challenges, successes, and what we ultimately learned as an organization.

The New York State SARS-CoV-2 Testing Consortium: Regional Communication in Response to the COVID-19 Pandemic.

The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2, created an unprecedented need for comprehensive laboratory testing of populations, in order to meet the needs of medical practice and to guide the management and functioning of our society. With the greater New York metropolitan area as an epicenter of this pandemic beginning in March 2020, a consortium of laboratory leaders from the assembled New York academic medical institutions was formed to help identify and solve the challenges of deploying testing. This report brings forward the experience of this consortium, based on the real-world challenges which we encountered in testing patients and in supporting the recovery effort to reestablish the health care workplace. In coordination with the Greater New York Hospital Association and with the public health laboratory of New York State, this consortium communicated with state leadership to help inform public decision-making addressing the crisis. Through the length of the pandemic, the consortium has been a critical mechanism for sharing experience and best practices in dealing with issues including the following: instrument platforms, sample sources, test performance, pre- and post-analytical issues, supply chain, institutional testing capacity, pooled testing, biospecimen science, and research. The consortium also has been a mechanism for staying abreast of state and municipal policies and initiatives, and their impact on institutional and laboratory operations. The experience of this consortium may be of value to current and future laboratory professionals and policy-makers alike, in dealing with major events that impact regional laboratory services.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Qualitative Immunoglobulin G Assays: The Value of Numeric Reporting.

CONTEXT.­: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immunoglobulin G (IgG) testing is used for serosurveillance and will be important to evaluate vaccination status. Given the urgency to release coronavirus disease 2019 (COVID-19) serology tests, most manufacturers have developed qualitative tests. OBJECTIVE.­: To evaluate clinical performance of 6 different SARS-CoV-2 IgG assays and their quantitative results to better elucidate the clinical role of serology testing in COVID-19. DESIGN.­: Six SARS-CoV-2 IgG assays were tested using remnant specimens from 190 patients. Sensitivity and specificity were evaluated for each assay with the current manufacturer's cutoff and a lower cutoff. A numeric result analysis and discrepancy analysis were performed. RESULTS.­: Specificity was higher than 93% for all assays, and sensitivity was higher than 80% for all assays (≥7 days post-polymerase chain reaction testing). Inpatients with more severe disease had higher numeric values compared with health care workers with mild or moderate disease. Several discrepant serology results were those just below the manufacturers' cutoff. CONCLUSIONS.­: Severe acute respiratory syndrome coronavirus 2 IgG antibody testing can aid in the diagnosis of COVID-19, especially with negative polymerase chain reaction. Quantitative COVID-19 IgG results are important to better understand the immunologic response and disease course of this novel virus and to assess immunity as part of future vaccination programs.

Development of a Targeted Multi-Disorder High-Throughput Sequencing Assay for the Effective Identification of Disease-Causing Variants.

BACKGROUND: While next generation sequencing (NGS) is a useful tool for the identification of genetic variants to aid diagnosis and support therapy decision, high sequencing costs have limited its application within routine clinical care, especially in economically depressed areas. To investigate the utility of a multi-disease NGS based genetic test, we designed a custom sequencing assay targeting over thirty disease-associated areas including cardiac disorders, intellectual disabilities, hearing loss, collagenopathies, muscular dystrophy, Ashkenazi Jewish genetic disorders, and complex Mendelian disorders. We focused on these specific areas based on the interest of our collaborative clinical team, suggesting these diseases being the ones in need for the development of a sequencing-screening assay. RESULTS: We targeted all coding, untranslated regions (UTR) and flanking intronic regions of 650 known disease-associated genes using the Roche-NimbleGen EZ SeqCapV3 capture system and sequenced on the Illumina HiSeq 2500 Rapid Run platform. Eight controls with known variants and one HapMap sample were first sequenced to assess the performance of the panel. Subsequently, as a proof of principle and to explore the possible utility of our test, we analyzed test disease subjects (n = 16). Eight had known Mendelian disorders and eight had complex pediatric diseases. In addition to assess whether copy number variation may be of utility as a companion assay relative to these specific disease areas, we used the Affymetrix Genome-Wide SNP Array 6.0 to analyze the same samples. CONCLUSION: We identified potentially disease-associated variants: 22 missense, 4 nonsense, 1 frameshift, and 1 splice variants (16 previously identified, 12 novel among dbSNP and 15 novel among NHLBI Exome Variant Server). We found multi-disease targeted high-throughput sequencing to be a cost efficient approach in detecting disease-associated variants to aid diagnosis.

Finding those at risk: acute HIV infection in Newark, NJ.

BACKGROUND: A screening strategy combining rapid HIV-1/2 (HIV) antibody testing with pooled HIV-1 RNA testing increases identification of HIV infections, but may have other limitations that restrict its usefulness to all but the highest incidence populations. OBJECTIVE: By combining rapid antibody detection and pooled nucleic acid amplification testing (NAAT) testing, we sought to improve detection of early HIV-1 infections in an urban Newark, NJ hospital setting. STUDY DESIGN: Pooled NAAT HIV-1 RNA testing was offered to emergency department patients and outpatients being screened for HIV antibodies by fingerstick-rapid HIV testing. For those negative by rapid HIV and agreeing to NAAT testing, pooled plasma samples were prepared and sent to the University of Washington where real-time reverse transcription-polymerase chain reaction (RT-PCR) amplification was performed. RESULTS: Of 13,226 individuals screened, 6381 had rapid antibody testing alone, and 6845 agreed to add NAAT HIV screening. Rapid testing identified 115 antibody positive individuals. Pooled NAAT increased HIV-1 case detection by 7.0% identifying 8 additional cases. Overall, acute HIV infection yield was 0.12%. While males represent only 48.1% of those tested by NAAT, all samples that screened positive for HIV-1 RNA were obtained from men. CONCLUSION: HIV-1 RNA testing of pooled, HIV antibody-negative specimens permits identification of recent infections. In Newark, pooled NAAT increased HIV-1 case detection and provided an opportunity to focus on treatment and prevention messages for those most at risk of transmitting infection. Although constrained by client willingness to participate in testing associated with a need to return to receive further results, use of pooled NAAT improved early infection sensitivity.

Use of a rapid HIV testing algorithm to improve linkage to care.

BACKGROUND: Awaiting definitive diagnosis before scheduling healthcare visits complicates HIV screening and referral. Clients screened by rapid tests as initially reactive often fail to return to receive definitive test results, are not linked to care and enter care late or not at all. OBJECTIVES: To evaluate statewide, (1) the accuracy of a single-visit, two test HIV rapid testing algorithm (RTA) and (2) its effect on referral to care for positive clients. STUDY DESIGN: A two-test RTA was implemented at 24 sites in New Jersey beginning in December 2008. All clients with a reactive rapid HIV test were offered a second rapid HIV test, and RTA results were compared with Western blot (WB). Referral to care occurred based upon two sequential positive rapid tests. RESULTS: The RTA program has screened 51,413 individuals obtaining 426 reactive rapid test results; 394 (92.5%) were reactive by a second rapid test, 32 (7.5%) had a negative second rapid test. Twenty-eight individuals refused WB testing. Of 369 RTA-positive individuals who have WB results, 368 (99.5%) were confirmed positive. Of RTA-positive clients, 290 (73.6%), including 25 (6.6%) who refused Western blot, were immediately referred for care including one individual with a false-positive RTA. CONCLUSIONS: The RTA reduced false positive results by 6.2% and agreed with WB results 99.5% of the time. Improved referral to care compared to traditional rapid HIV screening occurs when immediate referral is based on RTA verification of a preliminary positive rapid test. WB confirmation is not essential for effective screening and contributes to difficulties linking individuals to care.

Rapid human immunodeficiency virus test quality assurance practices and outcomes among testing sites affiliated with 17 public health departments.

Rapid human immunodeficiency virus testing is often conducted in nonclinical settings by staff with limited training, so quality assurance (QA) monitoring is critical to ensure accuracy of test results. Rapid tests (n = 86,749) were generally conducted according to manufacturers' instructions, but ongoing testing competency assessments and on-site QA monitoring were not uniformly conducted.

Nomenclature and definitions for emergency department human immunodeficiency virus (HIV) testing: report from the 2007 conference of the National Emergency Department HIV Testing Consortium.

Early diagnosis of persons infected with human immunodeficiency virus (HIV) through diagnostic testing and screening is a critical priority for individual and public health. Emergency departments (EDs) have an important role in this effort. As EDs gain experience in HIV testing, it is increasingly apparent that implementing testing is conceptually and operationally complex. A wide variety of HIV testing practice and research models have emerged, each reflecting adaptations to site-specific factors and the needs of local populations. The diversity and complexity inherent in nascent ED HIV testing practice and research are associated with the risk that findings will not be described according to a common lexicon. This article presents a comprehensive set of terms and definitions that can be used to describe ED-based HIV testing programs, developed by consensus opinion from the inaugural meeting of the National ED HIV Testing Consortium. These definitions are designed to facilitate discussion, increase comparability of future reports, and potentially accelerate wider implementation of ED HIV testing.

Investigation of false positive results with an oral fluid rapid HIV-1/2 antibody test.

BACKGROUND: In March 2004, the OraQuick rapid HIV antibody test became the first rapid HIV test approved by the US Food and Drug Administration for use on oral fluid specimens. Test results are available in 20 minutes, and the oral fluid test is non-invasive. From August 2004-June 2005, we investigated a sudden increase in false-positive results occurring in a performance study of OraQuick oral-fluid rapid HIV tests in Minnesota. METHODOLOGY/PRINCIPAL FINDINGS: In a field investigation, we reviewed performance study data on oral-fluid and whole-blood OraQuick rapid HIV test device lots and expiration dates and assessed test performance and interpretation with oral-fluid and whole-blood specimens by operators who reported false-positive results. We used multivariate logistic regression to evaluate client demographic and risk characteristics associated with false-positive results. Next, we conducted an incidence study of false-positive OraQuick rapid HIV tests in nine US cities and tested both oral-fluid and finger-stick whole-blood specimens from clients; reactive tests were confirmed with Western blot. Sixteen (4.1%) false-positive oral-fluid results occurred in the performance study from April 15, 2004 through August 31, 2004 with unexpired devices from six test lots among 388 HIV-uninfected clients (specificity, 95.9%; 95% CI: 93.4-97.6). Three test operators who had reported false-positive results performed and interpreted the test according to package-insert instructions. In multivariate analysis, only older age was significantly associated with false-positive results (adjusted odds ratio = 4.5, 95% CI: 1.2-25.7). In the incidence study, all valid oral-fluid and whole-blood results from 2,268 clients were concordant and no false-positive results occurred (100% specificity). CONCLUSIONS/SIGNIFICANCE: The field investigation did not identify a cause for the increase in false-positive oral-fluid results, and the incidence study detected no false-positive results. The findings suggest this was an isolated cluster; the test's overall performance was as specified by the manufacturer.