Laboratory-developed Tests Research Articles

Interlaboratory concordance of PD-L1 immunohistochemistry for non-small-cell lung cancer.

Programmed death ligand 1 (PD-L1) immunohistochemistry has become a mandatory diagnostic test in the treatment of lung cancer. Several research initiatives have started to harmonise the five PD-L1 immunohistochemistry assays that have been used in clinical trials. Here, we report data on interlaboratory and interassay concordance for commercial assays ('assays') and laboratory-developed tests (LDTs) at 10 German testing sites. To assess interlaboratory concordance, a tissue microarray containing 21 pulmonary carcinoma specimens was centrally prepared. Pre-cut sections were stained at 10 sites by the use of assays 28-8, 22C3, SP263, and SP142, as well as 11 LDTs. Assay performance was evaluated with a second tissue microarray containing 11 cell lines with defined PD-L1 expression. Quality control was centrally performed by manual and digital analyses. The assays yielded reproducible IHC staining patterns at all sites. In agreement with previous studies, 22C3, 28-8 and SP263 showed similar staining patterns, whereas SP142 was distinct. Among the LDTs, six of 11 protocols showed staining patterns similar to those of assays 22C3 and 28-8. Interlaboratory concordance of tumour cell scoring by use of a six-step system was moderate (Light's κ = 0.43-0.69), whereas the clinically approved cut-offs of ≥1% and ≥50% showed substantial concordance (κ = 0.73-0.89). Immune cell scoring by the use of SP142 yielded moderate concordance (κ = 0.42). The data confirm the previously described staining patterns of the assays, and show that they can be reproducibly employed at different sites. LDTs with staining results similar to those of the assays are implementable, but have to be carefully validated.

MS 18.04 PD-L1 Expression in Early Stage Lung Cancer

The significant activity of programmed cell death 1 (PD-1)/PD-1 ligand 1 (PD-L1) checkpoint inhibitors in heavily pre-treated patients with advanced non–small-cell lung cancer (NSCLC) marked the beginning of a new era of immunotherapy. Recently published randomized clinical trials’ data have led to the approval of 3 PD-1/PD-L1 inhibitors—nivolumab (Opdivo; Bristol-Myers Squibb Company), pembrolizumab (Keytruda; Merck Sharp & Dohme Corp), and atezolizumab (Tecentriq, Genentech/Roche)—for the treatment of advanced NSCLC after first-line therapy. Furthermore, pembrolizumab was recently approved by the FDA as a first-line therapy for patients with advanced NSCLC. However, the overall response rates to these agents in an unselected population are reportedly low, thus emphasising the need for predictive biomarkers that identify beneficial candidates. The recently approved tests for anti-PD-1/PD-L1 therapy in NSCLC include the assessment of PD-L1 expression using immunohistochemistry (IHC) as a companion diagnostic test (22C3 for pembrolizumab) and 2 complementary diagnostic tests (28-8 for nivolumab and SP142 for atezolizumab). Another PD-L1 assay is being currently tested in clinical trials (e.g. SP263). In addition to commercial assays, laboratories and research institutions may establish their own laboratory-developed tests (LDTs) using various antibodies available, most notably the E1L3N clone. Hence, the PD-L1 expression status, as well as its predictive and prognostic value, differ considerably based on the antibody clones, platforms, and interpretation criteria used. However, the current assays evaluating the predictive role of tumor PD-L1 expression remain without harmonization in terms of the staining analysis and scoring system. The intratumoral heterogeneity in PD-L1 expression is another important issue. At present, PD-L1 testing is mainly conducted on biopsy specimens, which may not represent the tumor as a whole, and it may lead to false results, particularly in cases where testing is conducted using small tissue specimens, such as bronchial or transthoracic biopsy specimens. The resulting false-negative results could lead to the under-treatment of patients. In this presentation, I’d like to introduce 1) the results of comparison study between 4 different PD-L1 IHC and scoring systems in the surgically resected early stage lung cancer specimen 2) the correlation of PD-L1 expression between TMA specimens and the corresponding resected specimen to better understand the intratumoral heterogeneity. PD-L1, immunohistochemistry, lung cancer

Accuracy of the cobas EGFR Mutation Assay in Non–small-cell Lung Cancer Compared With Three Laboratory-developed Tests

BackgroundThe reliability of the cobas EGFR assay to detect epidermal growth factor receptor (EGFR) mutations in non–small-cell lung cancer (NSCLC) as an in vitro diagnostic test was compared with 3 laboratory-developed tests (LDTs). Materials and MethodsAfter screening for EGFR mutations using formalin-fixed-paraffin-embedded NSCLC tissue sections using the cobas EGFR assay, 151 samples were further tested with 3 LDTs; the peptide nucleic acid-locked nucleic acid polymerase chain reaction (PCR) clamp, PCR invader, and Cycleave assays. The cobas EGFR assay performance was evaluated by determining the concordance rate and κ-coefficient between the assays. In samples exhibiting discrepancies in the EGFR mutation status in the 4 assays, next-generation sequencing was performed to confirm mutated sequences. ResultsConcordance rates and κ-coefficients between the cobas EGFR assay and the other tests were 96.0% and 0.921 for the peptide nucleic acid-locked nucleic acid PCR clamp assay, 94.0% and 0.881 for the PCR invader assay, and 96.7% and 0.934 for the Cycleave assay, respectively. Data showed very good agreement with the other assays. Precise mutated sequences or exons in the EGFR gene matched in 137 samples (90.7%). Different results were obtained in 4 samples (2.6%), owing to systemic limitations of the assay. Next-generation sequencing of 10 (6.6%) samples with discordant results exhibited a concordance rate of 60% to 80% in each assay. ConclusionsThe cobas EGFR assay showed high concordance rates and κ-coefficients between the 3 compared LDTs and can be used to select patients who would benefit from EGFR-tyrosine kinase inhibitors.

Correction: Use of the 22C3 anti-PD-L1 antibody to determine PD-L1 expression in multiple automated immunohistochemistry platforms

[This corrects the article DOI: 10.1371/journal.pone.0183023.].

Laboratory-Developed Tests: A Legislative and Regulatory Review.

Twenty-five years ago, the Food and Drug Administration (FDA) asserted in a draft document that "home brew" tests-now commonly referred to as laboratory-developed tests (LDTs)-are subject to the same regulatory oversight as other in vitro diagnostics (IVDs)4. In 2010, the FDA began work on developing a proposed framework for future LDT oversight. Released in 2014, the draft guidance sparked an intense debate over potential LDT regulation. While the proposed guidance has not been implemented, many questions regarding LDT oversight remain unresolved. This review provides an overview of federal statutes and regulations related to IVDs and clinical laboratory operations, with a focus on those potentially applicable to LDTs and proposed regulatory efforts. Sources reviewed include the Code of Federal Regulations, the Federal Register, congressional hearings, guidance and policy documents, position statements, published literature, and websites. Federal statutes regarding IVDs were passed without substantive evidence of congressional consideration toward the concept of LDTs. The FDA has clear oversight authority over IVD reagents introduced into interstate commerce. A 16-year delay in publicly asserting FDA authority over LDTs, the pursuit of a draft guidance approach toward oversight, and establishment of regulations under the Clinical Laboratory Improvement Amendments of 1988 (CLIA'88) applicable to LDTs contributed to community uncertainty toward LDT oversight. Future regulatory and/or legislative efforts may be required to resolve this uncertainty.

Competing Policy Windows in Biotechnology: The FDA, the 21st Century Cures Act, and Laboratory‐Developed Tests

AbstractIn 2014, the U.S. Food and Drug Administration (FDA) proposed taking a more active role in the regulation of laboratory‐developed tests (LDTs). Meanwhile, the U.S. House of Representatives embarked upon the 21st Century Cures initiative to develop legislation to expedite the development of new biotechnology innovations. During that initiative and in the public comments responding to the draft guidance, there was significant disagreement as to whether the increased FDA regulation of LDTs was beneficial or detrimental to biotechnology. Both the FDA guidance document and the 21st Century Cures Act came about due to the opening of a window of opportunity created by the convergence of circumstances. The question is whether the windows of opportunity are competing and how to resolve this competition. This study will investigate these questions through a qualitative case study. It will also provide recommendations for resolving policy disputes involving wicked problems like biotechnology policy.

Use of the 22C3 anti-PD-L1 antibody to determine PD-L1 expression in multiple automated immunohistochemistry platforms.

BackgroundFor non–small cell lung cancer (NSCLC), treatment with pembrolizumab is limited to patients with tumours expressing PD-L1 assessed by immunohistochemistry (IHC) using the PD-L1 IHC 22C3 pharmDx (Dako, Inc.) companion diagnostic test, on the Dako Autostainer Link 48 (ASL48) platform. Optimised protocols are urgently needed for use of the 22C3 antibody concentrate to test PD-L1 expression on more widely available IHC autostainers.MethodsWe evaluated PD-L1 expression using the 22C3 antibody concentrate in the three main commercially available autostainers Dako ASL48, BenchMark ULTRA (Ventana Medical Systems, Inc.), and Bond-III (Leica Biosystems) and compared the staining results with the PD-L1 IHC 22C3 pharmDx kit on the Dako ASL48 platform. Several technical conditions for laboratory-developed tests (LDTs) were evaluated in tonsil specimens and a training set of three NSCLC samples. Optimised protocols were then validated in 120 NSCLC specimens.ResultsOptimised protocols were obtained on both the VENTANA BenchMark ULTRA and Dako ASL48 platforms. Significant expression of PD-L1 was obtained on tissue controls with the Leica Bond-III autostainer when high concentrations of the 22C3 antibody were used. It therefore was not tested on the 120 NSCLC specimens. An almost 100% concordance rate for dichotomized tumour proportion score (TPS) results was observed between TPS ratings using the 22C3 antibody concentrate on the Dako ASL48 and VENTANA BenchMark ULTRA platforms relative to the PD-L1 IHC 22C3 pharmDx kit on the Dako ASL48 platform. Interpathologist agreement was high on both LDTs and the PD-L1 IHC 22C3 pharmDx kit on the Dako ASL48 platform.ConclusionAvailability of standardized protocols for determining PD-L1 expression using the 22C3 antibody concentrate on the widely available Dako ASL48 and VENTANA BenchMark ULTRA IHC platforms will expand the number of laboratories able to determine eligibility of patients with NSCLC for treatment with pembrolizumab in a reliable and concordant manner.

FDA-Cleared versus Laboratory-Developed Tests: Why Start from Scratch When Kits Are Available?

One of the most common questions facing laboratories when bringing up new clinical tests is deciding which specific assay best suits the needs of the lab, its patients, and its providers. At first glance, assays cleared by the Food and Drug Administration (FDA)2 for use in clinical testing would seem to have some obvious advantages: the validation requirements are less onerous than for laboratory-developed tests (LDTs) (1), and much of the legwork, e.g., sensitivity and specificity testing, is done by …

Standardization of Minimal Residual Disease Testing in Multiple Myeloma.

Multiple myeloma (MM)3 is an incurable neoplasm of the bone marrow characterized by a clonal expansion of plasma cells with presence of a monoclonal spike (M-spike) in the serum and/or urine (1). However, there have been major improvements in the way that MM is treated, prolonging overall survival (OS). As OS increases, clinicians and researchers have been increasingly investigating the utility of minimal residual disease (MRD) testing by flow cytometry and molecular diagnostics. Simultaneously, clinical hematology and hematopathology teams are driving efforts to achieve standardization of these laboratory-developed tests (LDTs). Historically, when a patient has a hematologic malignancy such as MM, residual disease is detected by morphologic examination of bone marrow by light microscopy as well as serum/urine protein electrophoresis. However, as technology has improved, we are now able to detect very small populations of clonal cells that cannot be seen by light microscopy—this is termed “MRD.” Some have suggested that the word “measurable” be substituted for “minimal,” because as our analytical approaches improve, the lower limit of detection changes (2). Multicolor flow cytometry has facilitated the relatively widespread adoption of flow cytometric MRD (FCMRD) testing. A recent survey estimates that there are more than 90 predominantly North American laboratories that perform FCMRD (3 …

Analytical Validation of Relative Average Telomere Length Measurement in a Clinical Laboratory Environment.

Average telomere length in whole blood has become a biomarker of aging, disease, and mortality risk across a broad range of clinical conditions. The most common method of telomere length measurement for large patient sample sets is based on quantitative PCR (qPCR). For laboratory-developed tests to be performed on clinical samples, they must undergo a rigorous analytical validation, currently regulated under CLIA. Whole blood samples from 40 donors were used in the analytical validation of methods for relative average telomere length (rATL) measurement. Three technical replicate DNA samples were extracted from each whole blood sample and placed in three independent wells on a sample plate. Each of these sample plates was assayed 12 times during the validation process. The study was conducted over a 20-day period, once in the morning and once in the evening, using 3 different operators. Our process of rATL measurement beginning with DNA extraction followed by qPCR-based assay resulted in repeatability and reproducibility CV of <5% and amplification efficiencies near 100%. The validated assay was used to establish a reference interval derived from 2 cohorts of individuals: (a) San Francisco Bay area (n = 504) and (b) a US cross-sectional, demographic population (n = 357). We present advances in the establishment of a highly reproducible analytically validated process for determining rATLs in a CLIA laboratory environment.

The Clinical and Economic Impact of Inaccurate EGFR Mutation Tests in the Treatment of Metastatic Non-Small Cell Lung Cancer.

Advances in personalized medicine are supported by companion diagnostic molecular tests. Testing accuracy is critical for selecting patients for optimal therapy and reducing treatment-related toxicity. We assessed the clinical and economic impact of inaccurate test results between laboratory developed tests (LDTs) and a US Food and Drug Administration (FDA)-approved test for detection of epidermal growth factor receptor (EGFR) mutations. Using a hypothetical US cohort of newly diagnosed metastatic non-small cell lung cancer (NSCLC) patients and EURTAC (erlotinib versus standard chemotherapy as first-line treatment for European patients with advanced EGFR mutation-positive non-small-cell lung cancer) clinical trial data, we developed a decision analytic model to estimate the probability of misclassification with LDTs compared to a FDA-approved test. We estimated the clinical and economic impact of inaccurate test results by quantifying progression-free and quality-adjusted progression-free life years (PFLYs, QAPFLYs) lost, and costs due to incorrect treatment. The base-case analysis estimated 2.3% (n = 1422) of 60,502 newly diagnosed metastatic NSCLC patients would be misclassified with LDTs compared to 1% (n = 577) with a FDA-approved test. An average of 477 and 194 PFLYs were lost among the misclassified patients tested with LDTs compared to the FDA-approved test, respectively. Aggregate treatment costs for patients tested with LDTs were approximately $7.3 million more than with the FDA-approved test, due to higher drug and adverse event costs among patients incorrectly treated with targeted therapy or chemotherapy, respectively. Invalid tests contributed to greater probability of patient misclassification and incorrect therapy. In conclusion, risks associated with inaccurate EGFR mutation tests pose marked clinical and economic consequences to society. Utilization of molecular diagnostic tests with demonstrated accuracy could help to maximize the potential of personalized medicine.

Validation and Implementation of Clinical Laboratory Improvements Act-Compliant Whole-Genome Sequencing in the Public Health Microbiology Laboratory.

ABSTRACTPublic health microbiology laboratories (PHLs) are on the cusp of unprecedented improvements in pathogen identification, antibiotic resistance detection, and outbreak investigation by using whole-genome sequencing (WGS). However, considerable challenges remain due to the lack of common standards. Here, we describe the validation of WGS on the Illumina platform for routine use in PHLs according to Clinical Laboratory Improvements Act (CLIA) guidelines for laboratory-developed tests (LDTs). We developed a validation panel comprising 10 Enterobacteriaceae isolates, 5 Gram-positive cocci, 5 Gram-negative nonfermenting species, 9 Mycobacterium tuberculosis isolates, and 5 miscellaneous bacteria. The genome coverage range was 15.71× to 216.4× (average, 79.72×; median, 71.55×); the limit of detection (LOD) for single nucleotide polymorphisms (SNPs) was 60×. The accuracy, reproducibility, and repeatability of base calling were >99.9%. The accuracy of phylogenetic analysis was 100%. The specificity and sensitivity inferred from multilocus sequence typing (MLST) and genome-wide SNP-based phylogenetic assays were 100%. The following objectives were accomplished: (i) the establishment of the performance specifications for WGS applications in PHLs according to CLIA guidelines, (ii) the development of quality assurance and quality control measures, (iii) the development of a reporting format for end users with or without WGS expertise, (iv) the availability of a validation set of microorganisms, and (v) the creation of a modular template for the validation of WGS processes in PHLs. The validation panel, sequencing analytics, and raw sequences could facilitate multilaboratory comparisons of WGS data. Additionally, the WGS performance specifications and modular template are adaptable for the validation of other platforms and reagent kits.

Analytic Validation of Immunohistochemistry Assays: New Benchmark Data From a Survey of 1085 Laboratories.

- A cooperative agreement between the College of American Pathologists (CAP) and the United States Centers for Disease Control and Prevention was undertaken to measure laboratories' awareness and implementation of an evidence-based laboratory practice guideline (LPG) on immunohistochemical (IHC) validation practices published in 2014. - To establish new benchmark data on IHC laboratory practices. - A 2015 survey on IHC assay validation practices was sent to laboratories subscribed to specific CAP proficiency testing programs and to additional nonsubscribing laboratories that perform IHC testing. Specific questions were designed to capture laboratory practices not addressed in a 2010 survey. - The analysis was based on responses from 1085 laboratories that perform IHC staining. Ninety-six percent (809 of 844) always documented validation of IHC assays. Sixty percent (648 of 1078) had separate procedures for predictive and nonpredictive markers, 42.7% (220 of 515) had procedures for laboratory-developed tests, 50% (349 of 697) had procedures for testing cytologic specimens, and 46.2% (363 of 785) had procedures for testing decalcified specimens. Minimum case numbers were specified by 85.9% (720 of 838) of laboratories for nonpredictive markers and 76% (584 of 768) for predictive markers. Median concordance requirements were 95% for both types. For initial validation, 75.4% (538 of 714) of laboratories adopted the 20-case minimum for nonpredictive markers and 45.9% (266 of 579) adopted the 40-case minimum for predictive markers as outlined in the 2014 LPG. The most common method for validation was correlation with morphology and expected results. Laboratories also reported which assay changes necessitated revalidation and their minimum case requirements. - Benchmark data on current IHC validation practices and procedures may help laboratories understand the issues and influence further refinement of LPG recommendations.

Interlaboratory-concordance of PD-L1 IHC for NSCLC.

e20508 Background: Immunohistochemistry (IHC) of the PD-L1 protein has become a mandatory diagnostic test for NSCLC. We conducted a two-step round robin test to analyze interobserver- and interlaboratory-concordance of PD-L1 IHC and to compare four clinical trial assays (CTAs; 28-8, 22C3, SP264, SP142) and laboratory-developed tests (LDTs). Results of step-one showed that reproducible PD-L1 IHC scoring is feasible; here we present the data on interlaboratory concordance Methods: Interlaboratory-concordance was tested by a centrally prepared tissue-microarray containing 21 NSCLC specimens that was stained at ten sites using CTAs and LDTs. Assay-performance was assessed with a second tissue-microarray containing eleven cell-lines with defined PD-L1 expression. Slides were evaluated by central quality-control and image-analysis. Results: The four CTAs yielded reproducible IHC-stainings at all sites while the results of the LDTs were mixed: Six protocols showed appropriate IHC quality with staining patterns similar to 22C3 and 28-8 CTAs, five protocols yielded less DAB-deposits and reduced staining intensity. Interlaboratory-concordance of carcinoma cell scoring using the 6-step system was moderate (κ = 0.43-0.69) while the included cut-offs ≥1% and ≥50% showed substantial concordance for the CTAs (κ = 0.73-0.89) and moderate concordance for the LDTs (κ = 0.50). No significant differences in interlaboratory-concordance were found among the CTAs. However, differences in the resulting staining patterns were noticed: While 22C3 and 28-8 showed similar staining patterns, SP263 showed minor differences in some cases and SP142 showed distinct patterns. Conclusions: The data show that the PD-L1 CTAs can be reproducibly employed and scored at different sites. LDTs with staining patterns similar to the CTAs are possible yet have to be carefully calibrated to match the appropriate intensity-range. The choice of assay and the set-up of the IHC-protocol may strongly influence the resulting staining.

Utility of NIST Whole-Genome Reference Materials for the Technical Validation of a Multigene Next-Generation Sequencing Test

The sensitivity and specificity of next-generation sequencing laboratory developed tests (LDTs) are typically determined by an analyte-specific approach. Analyte-specific validations use disease-specific controls to assess an LDT's ability to detect known pathogenic variants. Alternatively, a methods-based approach can be used for LDT technical validations. Methods-focused validations do not use disease-specific controls but use benchmark reference DNA that contains known variants (benign, variants of unknown significance, and pathogenic) to assess variant calling accuracy of a next-generation sequencing workflow. Recently, four whole-genome reference materials (RMs) from the National Institute of Standards and Technology (NIST) were released to standardize methods-based validations of next-generation sequencing panels across laboratories. We provide a practical method for using NIST RMs to validate multigene panels. We analyzed the utility of RMs in validating a novel newborn screening test that targets 70 genes, called NEO1. Despite the NIST RM variant truth set originating from multiple sequencing platforms, replicates, and library types, we discovered a 5.2% false-negative variant detection rate in the RM truth set genes that were assessed in our validation. We developed a strategy using complementary non-RM controls to demonstrate 99.6% sensitivity of the NEO1 test in detecting variants. Our findings have implications for laboratories or proficiency testing organizations using whole-genome NIST RMs for testing.

RHD alleles among pregnant women with serologic discrepant weak D phenotypes from a multiethnic population and risk of alloimmunization.

A considerable number of RHD alleles responsible for weak and partial D phenotypes have been identified. Serologic determination of these phenotypes is often doubtful and makes genetic analysis of RHD gene highly desirable in transfusion recipients and pregnant women. We analyzed the RHD gene in a cohort of pregnant women with doubtful D phenotypes. RHD genotyping was performed on 104 cases with D typing discrepancies or with history of serologic weak D phenotype. Laboratory-developed DNA tests, RHD BeadChip (Bioarray Solutions, Immucor), and sequencing were used to identify the RHD alleles. Molecular analyses showed 23 of 104 (22%) pregnant women were RHD*weak D types 1, 2, or 3 and not at risk for anti-D. Fifty-one (49%) were RHD*weak partial 4.0, 6 RHD*weak D type 38 (6%), 1 RHD*weak D type 45 (1%), 1 RHD*weak D type 67 (1%), and potentially at risk for being alloimmunized and making anti-D. Partial D was identified in 22 of 104 (21%) patients and definitively at risk for anti-D. Appropriate classification of RhD phenotypes is recommended for correct indication of RhIG in pregnant women. However, the serologic distinction between RhD-negative and RhD-positive phenotypes is a difficult task in the case of D variants due to the variations in serologic testing. Our results show a great variability in RHD variant alleles in pregnant women from this population of high admixture. According to these results, 78% of these obstetric patients are at risk for anti-D and candidates for RhIG.

Designing a standard of proof: the case for professional standards in next-generation sequencing laboratory-developed tests.

Designing a standard of proof: the case for professional standards in next-generation sequencing laboratory-developed tests.

Relative analytical sensitivity of donor nucleic acid amplification technology screening and diagnostic real-time polymerase chain reaction assays for detection of Zika virus RNA.

Zika virus (ZIKV) has spread rapidly in the Pacific and throughout the Americas and is associated with severe congenital and adult neurologic outcomes. Nucleic acid amplification technology (NAT) assays were developed for diagnostic applications and for blood donor screening on high-throughput NAT systems. We distributed blinded panels to compare the analytical performance of blood screening relative to diagnostic NAT assays. A 25-member, coded panel (11 half-log dilutions of a 2013 French Polynesia ZIKV isolate and 2015 Brazilian donor plasma implicated in transfusion transmission, and 3 negative controls) was sent to 11 laboratories that performed 17 assays with 2 to 12 replicates per panel member. Results were analyzed for the percentage reactivity at each dilution and by probit analysis to estimate the 50% and 95% limits of detection (LOD50 and LOD95 , respectively). Donor-screening NAT assays that process approximately 500 µL of plasma into amplification reactions were comparable in sensitivity (LOD50 and LOD95 , 2.5 and 15-18 copies/mL) and were approximately 10-fold to 100-fold more sensitive than research laboratory-developed and diagnostic reverse transcriptase-polymerase chain reaction tests that process from 10 to 30 µL of plasma per amplification. Increasing sample input volume assayed with the Centers for Disease Control and Prevention reverse transcriptase-polymerase chain reaction assays increased the LODs by 10-fold to 30-fold. Blood donor-screening ZIKV NAT assays demonstrate similar excellent sensitivities to assays currently used for screening for transfusion-transmitted viruses and are substantially more sensitive than most other laboratory-developed and diagnostic ZIKV reverse transcriptase-polymerase chain reaction assays. Enhancing sensitivities of laboratory-developed and diagnostic assays may be achievable by increasing sample input.

Variant call concordance between two laboratory-developed, solid tumor targeted genomic profiling assays using distinct workflows and sequencing instruments

Targeted genomic profiling (TGP) using massively parallel DNA sequencing is becoming the standard methodology in clinical laboratories for detecting somatic variants in solid tumors. The variety of methodologies and sequencing platforms in the marketplace for TGP has resulted in a variety of clinical TGP laboratory developed tests (LDT). The variability of LDTs is a challenge for test-to-test and laboratory-to-laboratory reliability. At the University of Vermont Medical Center (UVMMC), we validated a TGP assay for solid tumors which utilizes DNA hybridization capture and complete exon and selected intron sequencing of 29 clinically actionable genes. The validation samples were run on the Illumina MiSeq platform. Clinical specificity and sensitivity were evaluated by testing samples harboring genomic variants previously identified in CLIA-approved, CAP accredited laboratories with clinically validated molecular assays. The Molecular Laboratory at Dartmouth Hitchcock Medical Center (DHMC) provided 11 FFPE specimens that had been analyzed on AmpliSeq Cancer Hotspot Panel version 2 (CHPv2) and run on the Ion Torrent PGM. A Venn diagram of the gene lists from the two institutions is shown. This provided an excellent opportunity to compare the inter-laboratory reliability using two different target sequencing methods and sequencing platforms. Our data demonstrated an exceptionally high level of concordance with respect to the sensitivity and specificity of the analyses. All clinically-actionable SNV and InDel variant calls in genes covered by both panels (n=17) were identified by both laboratories. This data supports the proposal that distinct gene panel designs and sequencing workflows are capable of making consistent variant calls in solid tumor FFPE-derived samples.

On the Importance of Clinical Follow-up in the Establishment of Non-Invasive Prenatal Testing (NIPT) for Laboratory Developed Tests

Non-invasive prenatal genetic testing (NIPT) is an advance in the detection of fetal chromosomal aneuploidies that analyzes cell-free DNA (cfDNA) in the blood of a pregnant woman. NIPT has quickly spread across the globe after introduction into clinical practice earlier in this decade. Virtually all professional societies currently recommend that NIPT be used as a screening test rather than a diagnostic method. Due to the extraordinarily high specificity and sensitivity, it is clearly an attractive alternative to conventional serum biochemical screening tests-the current standard of care. We performed a clinical validation study of our Laboratory Developed Test (LDT) assessing equivalency to the verifi™ test by Illumina, Inc. The method uses next generation sequencing (NGS), and features interpretation based on the calculation of normalized chromosomal values (NCV). In our assay, samples from 3334 consecutive patients which had been tested with Illumina’s verifi test, were blinded by an independent third party and retested by the method developed for the Progenity LDT to be offered in our commercial laboratory. As an additional level of validation, we sought and achieved follow up contact on 1681 of the original Illumina cases, to further independently confirm our results and theirs. In the analysis of equivalence between the two tests, 111 trisomy 21 samples, 43 trisomy 18 samples and 21 trisomy 13 samples were identified by both tests, indicating an equivalency of >99.9%. Although the results between the verifi “gold standard” test and our LDT proved identical (i.e., 100% concordance), the verifi test is not promoted by Illumina as having a 100% sensitivity and specificity. Therefore, certain discrepancies can only be appreciated by clinical follow up. In the NCV analyses, categories are created for “affected” or “suspected trisomy” based on the magnitude of the NCV value. Our findings suggest that the very few discrepancies were between the “aneuploidy suspected” categories of the verify reference standard and our LDT’s confirmed “not affected” or “affected” categories. Our conclusion is that NIPT LDTs must be validated by a process including clinical follow-up, not just equivalency to a reference testing method.