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  • Archives of Pathology and Laboratory Medicine  (16)
  • 1
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    Comparative Performance of Breast Cancer Human Epidermal Growth Factor Receptor 2 Fluorescence In Situ Hybridization and Brightfield In Situ Hybridization on College of American Pathologists Proficiency Tests
    Archives of Pathology and Laboratory Medicine ; 2018
    In:  Archives of Pathology & Laboratory Medicine Vol. 142, No. 10 ( 2018-10-01), p. 1254-1259
    Details
    In: Archives of Pathology & Laboratory Medicine, Archives of Pathology and Laboratory Medicine, Vol. 142, No. 10 ( 2018-10-01), p. 1254-1259
    Abstract: Fluorescence in situ hybridization (FISH) and brightfield in situ hybridization (ISH) are 2 clinically approved laboratory methods for detecting ERBB2 (HER2) amplification in breast cancer. Objective.— To compare the performance of FISH and brightfield ISH on proficiency testing administered by the College of American Pathologists Laboratory Accreditation Program. Design.— Retrospective review was performed on 70 tissue core samples in 7 separate proficiency testing surveys conducted between 2009 and 2013. Results.— The samples included 13 consensus-amplified tissue cores, 53 consensus-nonamplified cores, and 4 cores that did not reach consensus for FISH and/or brightfield ISH. There were 2552 individual responses for FISH and 1871 individual responses for brightfield ISH. Consensus response rates were comparable for FISH (2474 of 2524; 98.0%) and brightfield ISH (2135 of 2189; 97.5%). The FISH analysis yielded an average HER2 copy number per cell that was significantly higher (by 2.86; P = .02) compared with brightfield ISH for amplified cores. For nonamplified cores, FISH yielded slightly, but not significantly, higher (by 0.17; P = .10) HER2 copy numbers per cell. There was no significant difference in the average HER2 to control ratio for either consensus-amplified or consensus-nonamplified cores. Participants reported “unable to analyze” more frequently for brightfield ISH (244 of 2453; 9.9%) than they did for FISH (160 of 2684; 6.0%). Conclusions.— Our study indicates a high concordance rate in proficiency testing surveys, with some significant differences noted in the technical performance of these assays. In borderline cases, updated American Society of Clinical Oncology/College of American Pathologists cutoff thresholds that place greater emphasis on HER2 copy number per cell could accentuate those differences between FISH and brightfield ISH.
    Type of Medium: Online Resource
    ISSN: 0003-9985 , 1543-2165
    URL: Article
    DOI: 10.5858/arpa.2017-0457-CP
    RVK:
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    Language: English
    Publisher: Archives of Pathology and Laboratory Medicine
    Publication Date: 2018
    detail.hit.zdb_id: 2028916-9
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  • 2
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    Current Laboratory Testing Practices for Assessment of ERBB2 /HER2 in Endometrial Serous Carcinoma and Colorectal Carcinoma
    Archives of Pathology and Laboratory Medicine ; 2023
    In:  Archives of Pathology & Laboratory Medicine Vol. 147, No. 10 ( 2023-10-01), p. 1148-1157
    Details
    In: Archives of Pathology & Laboratory Medicine, Archives of Pathology and Laboratory Medicine, Vol. 147, No. 10 ( 2023-10-01), p. 1148-1157
    Abstract: Therapy targeted at human epidermal growth factor receptor 2 (HER2; also known as ERBB2) was used initially for breast and gastroesophageal carcinoma and has more recently been adopted for endometrial serous carcinoma (ESC) and colorectal carcinoma (CRC). There is evidence that predictive biomarker testing algorithms for HER2 must be tumor type specific and that an algorithm validated for one tumor type cannot be applied to another. Objective.— To describe current laboratory practices for HER2 assessment in ESC and CRC. Design.— We surveyed laboratories participating in the 2021 College of American Pathologists (CAP) HER2 immunohistochemistry proficiency testing program. Results.— The survey was distributed to 1548 laboratories and returned by 1195, of which 83.5% (998) were in the United States. For ESC, 24.0% (287) of laboratories reported performing in-house testing for HER2 by immunohistochemical staining and/or in situ hybridization; of these, 44.3% (127) performed it reflexively on all cases of ESC. The most common criterion for evaluating HER2 was the American Society of Clinical Oncology/CAP 2018 guideline for breast carcinoma (69.0%; 194 of 281), whereas only 16.0% (45) of laboratories used guidelines specific to ESC. For CRC, 20.2% (239 of 1185) of laboratories performed in-house HER2 testing, and 82.0% of these (196) did the test only at the clinician’s request. A plurality (49.4%; 115 of 233) used gastroesophageal cancer guidelines when scoring CRC, 30.0% (70) used the CRC scoring system from the HERACLES trial, and 16.3% (38) used the American Society of Clinical Oncology/CAP 2018 guideline for breast carcinoma. Conclusions.— Laboratories vary in their approach to HER2 testing in ESC and CRC. Most laboratories did not report using tumor type–specific recommendations for HER2 interpretation. The lack of standardization could present a challenge to evidence-based practice when considering targeted therapy for these diseases.
    Type of Medium: Online Resource
    ISSN: 1543-2165 , 0003-9985
    URL: Article
    DOI: 10.5858/arpa.2022-0229-CP
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    Language: English
    Publisher: Archives of Pathology and Laboratory Medicine
    Publication Date: 2023
    detail.hit.zdb_id: 2028916-9
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  • 3
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    Next-Generation Sequencing Somatic and Germline Assay Troubleshooting Guide Derived From Proficiency Testing Data
    Archives of Pathology and Laboratory Medicine ; 2022
    In:  Archives of Pathology & Laboratory Medicine Vol. 146, No. 4 ( 2022-04-01), p. 451-461
    Details
    In: Archives of Pathology & Laboratory Medicine, Archives of Pathology and Laboratory Medicine, Vol. 146, No. 4 ( 2022-04-01), p. 451-461
    Abstract: Next-generation sequencing–based assays are increasingly used in clinical molecular laboratories to detect somatic variants in solid tumors and hematologic malignancies and to detect constitutional variants. Proficiency testing data are potential sources of information about challenges in performing these assays. Objective.— To examine the most common sources of unacceptable results from the College of American Pathologists Next-Generation Sequencing Bioinformatics, Hematological Malignancies, Solid Tumor, and Germline surveys and provide recommendations on how to avoid these pitfalls and improve performance. Design.— The College of American Pathologists next-generation sequencing somatic and germline proficiency testing survey results from 2016 to 2019 were analyzed to identify the most common causes of unacceptable results. Results.— On somatic and germline proficiency testing surveys, 95.9% (18 815/19 623) and 97.8% (33 890/34 641) of all variants were correctly identified, respectively. The most common causes of unacceptable results related to sequencing were false-negative errors in genomic regions that were difficult to sequence because of high GC content. False-positive errors occurred in the context of homopolymers and pseudogenes. Recurrent errors in variant annotation were seen for dinucleotide and duplication variants and included unacceptable transcript selection and outdated variant nomenclature. A small percentage of preanalytic or postanalytic errors were attributed to specimen swaps and transcription errors. Conclusions.— Laboratories demonstrate overall excellent performance for detecting variants in both somatic and germline proficiency testing surveys. Proficiency testing survey results highlight infrequent, but recurrent, analytic and nonanalytic challenges in performing next- generation sequencing–based assays and point to remedies to help laboratories improve performance.
    Type of Medium: Online Resource
    ISSN: 1543-2165 , 0003-9985
    URL: Article
    DOI: 10.5858/arpa.2020-0842-CP
    RVK:
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    Language: English
    Publisher: Archives of Pathology and Laboratory Medicine
    Publication Date: 2022
    detail.hit.zdb_id: 2028916-9
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  • 4
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    Most Frequently Cited Accreditation Inspection Deficiencies for Clinical Molecular Oncology Testing Laboratories and Opportunities for Improvement
    Archives of Pathology and Laboratory Medicine ; 2022
    In:  Archives of Pathology & Laboratory Medicine Vol. 146, No. 12 ( 2022-12-01), p. 1441-1449
    Details
    In: Archives of Pathology & Laboratory Medicine, Archives of Pathology and Laboratory Medicine, Vol. 146, No. 12 ( 2022-12-01), p. 1441-1449
    Abstract: The College of American Pathologists (CAP), a laboratory accreditation organization with deemed status under the Clinical Laboratories Improvement Amendments of 1988 administers accreditation checklists. Checklists are used by laboratories to ensure regulatory compliance. Peer-level laboratory professionals audit laboratory records during inspections to assess compliance. Objective.— To identify the most frequently cited deficiencies for molecular oncology laboratories undergoing CAP accreditation inspections and describe laboratory improvement opportunities. Design.— The CAP Molecular Oncology Committee (MOC), which is involved in maintaining the Molecular Pathology checklist, reviewed data and inspector comments associated with the most frequently observed citations related to molecular oncology testing from laboratories inspected by the CAP during a 2-year period (2018–2020). Results.— Of 422 molecular oncology laboratories that underwent accreditation inspections, 159 (37.7%) were not cited for any molecular oncology–related deficiencies. For the All Common (COM) and Molecular Pathology checklists, there were 364 and 305 deficiencies, corresponding to compliance rates of 98.8% and 99.6%, respectively. The most frequently cited deficiencies are described. The COM checklist deficiencies were associated most often with the analytic testing phase; the MOL checklist deficiencies were more evenly distributed across the preanalytic, analytic, and postanalytic phases of testing. Conclusions.— Molecular oncology laboratories demonstrated excellent compliance with practices that support high-quality results for patients and the health care providers who use those test results in patient management. This review includes a critical assessment of opportunities for laboratories to improve compliance and molecular oncology testing quality.
    Type of Medium: Online Resource
    ISSN: 1543-2165 , 0003-9985
    URL: Article
    DOI: 10.5858/arpa.2021-0448-CP
    RVK:
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    Language: English
    Publisher: Archives of Pathology and Laboratory Medicine
    Publication Date: 2022
    detail.hit.zdb_id: 2028916-9
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  • 5
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    Neoplastic Cellularity Assessment in Molecular Testing
    Archives of Pathology and Laboratory Medicine ; 2022
    In:  Archives of Pathology & Laboratory Medicine Vol. 146, No. 9 ( 2022-09-01), p. 1062-1071
    Details
    In: Archives of Pathology & Laboratory Medicine, Archives of Pathology and Laboratory Medicine, Vol. 146, No. 9 ( 2022-09-01), p. 1062-1071
    Abstract: Neoplastic cellularity assessment has become an essential component of molecular oncology testing; however, there are currently no best practice recommendations or guidelines for this potentially variable step in the testing process. Objective.— To describe the domestic and international practices of neoplastic cellularity assessment and to determine how variations in laboratory practices affect neoplastic cellularity assessment accuracy. Design.— Data were derived from 57 US and international laboratories that participated in the 2019 College of American Pathologists Neoplastic Cellularity Proficiency Testing Survey (NEO-B 2019). NEO-B 2019 included 29 laboratory practice questions and 5 images exhibiting challenging histologic features. Participants assessed the neoplastic cellularity of hematoxylin-eosin–stained digital images, and results were compared to a criterion standard derived from a manual cell count. Results.— The survey responses showed variations in the laboratory practices for the assessment of neoplastic cellularity, including the definition of neoplastic cellularity, assessment methodology, counting practices, and quality assurance practices. In some instances, variation in laboratory practice affected neoplastic cellularity assessment performance. Conclusions.— The results highlight the need for a consensus definition and improved standardization of the assessment of neoplastic cellularity. We put forth an initial set of best practice recommendations to begin the process of standardizing neoplastic cellularity assessment.
    Type of Medium: Online Resource
    ISSN: 1543-2165 , 0003-9985
    URL: Article
    DOI: 10.5858/arpa.2021-0166-CP
    RVK:
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    Language: English
    Publisher: Archives of Pathology and Laboratory Medicine
    Publication Date: 2022
    detail.hit.zdb_id: 2028916-9
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  • 6
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    Proficiency Testing of Standardized Samples Shows High Interlaboratory Agreement for Clinical Next-Generation Sequencing–Based Hematologic Malignancy Assays With Survey Material–Specific Differences in Variant Frequencies
    Archives of Pathology and Laboratory Medicine ; 2020
    In:  Archives of Pathology & Laboratory Medicine Vol. 144, No. 8 ( 2020-08-01), p. 959-966
    Details
    In: Archives of Pathology & Laboratory Medicine, Archives of Pathology and Laboratory Medicine, Vol. 144, No. 8 ( 2020-08-01), p. 959-966
    Abstract: As laboratories increasingly turn from single-analyte testing in hematologic malignancies to next-generation sequencing–based panel testing, there is a corresponding need for proficiency testing to ensure adequate performance of these next-generation sequencing assays for optimal patient care. Objective.— To report the performance of laboratories on proficiency testing from the first 4 College of American Pathologists Next-Generation Sequencing Hematologic Malignancy surveys. Design.— College of American Pathologists proficiency testing results for 36 different engineered variants and/or allele fractions as well as a sample with no pathogenic variants were analyzed for accuracy and associated assay performance characteristics. Results.— The overall sensitivity observed for all variants was 93.5% (2190 of 2341) with 99.8% specificity (22 800 of 22 840). The false-negative rate was 6.5% (151 of 2341), and the largest single cause of these errors was difficulty in identifying variants in the sequence of CEBPA that is rich in cytosines and guanines. False-positive results (0.18%; 40 of 22 840) were most likely the result of preanalytic or postanalytic errors. Interestingly, the variant allele fractions were almost uniformly lower than the engineered fraction (as measured by digital polymerase chain reaction). Extensive troubleshooting identified a multifactorial cause for the low variant allele fractions, a result of an interaction between the linearized nature of the plasmid and the Illumina TruSeq chemistry. Conclusions.— Laboratories demonstrated an overall accuracy of 99.2% (24 990 of 25 181) with 99.8% specificity and 93.5% sensitivity when examining 36 clinically relevant somatic single-nucleotide variants with a variant allele fraction of 10% or greater. The data also highlight an issue with artificial linearized plasmids as survey material for next-generation sequencing.
    Type of Medium: Online Resource
    ISSN: 0003-9985 , 1543-2165
    URL: Article
    DOI: 10.5858/arpa.2019-0352-CP
    RVK:
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    Language: English
    Publisher: Archives of Pathology and Laboratory Medicine
    Publication Date: 2020
    detail.hit.zdb_id: 2028916-9
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  • 7
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    SPOT/Dx Pilot Reanalysis and College of American Pathologists Proficiency Testing for KRAS and NRAS Demonstrate Excellent Laboratory Performance
    Archives of Pathology and Laboratory Medicine ; 2023
    In:  Archives of Pathology & Laboratory Medicine ( 2023-09-30)
    Details
    In: Archives of Pathology & Laboratory Medicine, Archives of Pathology and Laboratory Medicine, ( 2023-09-30)
    Abstract: The Sustainable Predictive Oncology Therapeutics and Diagnostics quality assurance pilot study (SPOT/Dx pilot) on molecular oncology next-generation sequencing (NGS) reportedly demonstrated performance limitations of NGS laboratory-developed tests, including discrepancies with a US Food and Drug Administration–approved companion diagnostic. The SPOT/Dx pilot methods differ from those used in proficiency testing (PT) programs. Objective.— To reanalyze SPOT/Dx pilot data using PT program methods and compare to PT program data. Design.— The College of American Pathologists (CAP) Molecular Oncology Committee reanalyzed SPOT/Dx pilot data applying PT program methods, adjusting for confounding conditions, and compared them to CAP NGS PT program performance (2019–2022). Results.— Overall detection rates of KRAS and NRAS single-nucleotide variants (SNVs) and multinucleotide variants (MNVs) by SPOT/Dx pilot laboratories were 96.8% (716 of 740) and 81.1% (129 of 159), respectively. In CAP PT programs, the overall detection rates for the same SNVs and MNVs were 97.2% (2671 of 2748) and 91.8% (1853 of 2019), respectively. In 2022, the overall detection rate for 5 KRAS and NRAS MNVs in CAP PT programs was 97.3% (1161 of 1193). Conclusions.— CAP PT program data demonstrate that laboratories consistently have high detection rates for KRAS and NRAS variants. The SPOT/Dx pilot has multiple design and analytic differences with established PT programs. Reanalyzed pilot data that adjust for confounding conditions demonstrate that laboratories proficiently detect SNVs and less successfully detect rare to never-observed MNVs. The SPOT/Dx pilot results are not generalizable to all molecular oncology testing and should not be used to market products or change policy affecting all molecular oncology testing.
    Type of Medium: Online Resource
    ISSN: 1543-2165 , 0003-9985
    URL: Article
    DOI: 10.5858/arpa.2023-0322-CP
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    Language: English
    Publisher: Archives of Pathology and Laboratory Medicine
    Publication Date: 2023
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  • 8
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    RNA Sequencing for Solid Tumor Fusion Gene Detection: Proficiency Testing Practice and Performance Comparison
    Archives of Pathology and Laboratory Medicine ; 2023
    In:  Archives of Pathology & Laboratory Medicine ( 2023-08-3)
    Details
    In: Archives of Pathology & Laboratory Medicine, Archives of Pathology and Laboratory Medicine, ( 2023-08-3)
    Abstract: Next-generation sequencing–based approaches using RNA have increasingly been used by clinical laboratories for the detection of fusion genes, intragenic rearrangements, and exon-skipping events. Correspondingly, the College of American Pathologists (CAP) has advanced RNA sequencing proficiency testing (PT) to ensure optimal performance of these assays. Objective.— To report on laboratory performance and practices of RNA sequencing for the detection of fusion genes, intragenic rearrangements, and exon-skipping events using CAP PT data from 8 mailings (2018-A through 2021-B). Design.— CAP PT RNA sequencing program results from 153 laboratories across 24 proficiency test specimens, interrogating 22 distinct engineered fusion transcripts, were analyzed for correct identification of the fusion event, associated performance variables, and laboratory practices. Results.— Overall, the 4-year program detection rate (sensitivity) was 95.5% (1486 of 1556 results). False-negative rates were 3.6% (53 of 1463) and 18.3% (17 of 93) for fusion gene and intragenic rearrangement/exon-skipping events, respectively. Only 19 false-positive results were reported among the 8 PT mailings, and most were likely the result of preanalytical or postanalytical errors. There were no practice characteristics (eg, instrumentation, sequencing method) significantly associated with the fusion detection results. Conclusions.— These data reveal a high overall sensitivity and specificity for fusion gene detection by participating laboratories using clinical RNA sequencing. Performance was comparable across all laboratories, regardless of methodology. The fraction of false-negative results for intragenic rearrangement/exon-skipping events was greater than that for the chimeric fusion genes. False-negative results could not be attributed to any specific practice characteristics.
    Type of Medium: Online Resource
    ISSN: 1543-2165 , 0003-9985
    URL: Article
    DOI: 10.5858/arpa.2023-0047-CP
    RVK:
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    Language: English
    Publisher: Archives of Pathology and Laboratory Medicine
    Publication Date: 2023
    detail.hit.zdb_id: 2028916-9
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  • 9
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    Tiered Somatic Variant Classification Adoption Has Increased Worldwide With Some Practice Differences Based on Location and Institutional Setting
    Archives of Pathology and Laboratory Medicine ; 2022
    In:  Archives of Pathology & Laboratory Medicine Vol. 146, No. 7 ( 2022-07-01), p. 822-832
    Details
    In: Archives of Pathology & Laboratory Medicine, Archives of Pathology and Laboratory Medicine, Vol. 146, No. 7 ( 2022-07-01), p. 822-832
    Abstract: The 2017 Association for Molecular Pathology/American Society of Clinical Oncology/College of American Pathologists (CAP) tier classification guideline provides a framework to standardize interpretation and reporting of somatic variants. Objective.— To evaluate the adoption and performance of the 2017 guideline among laboratories performing somatic next-generation sequencing (NGS). Design.— A survey was distributed to laboratories participating in NGS CAP proficiency testing for solid tumors (NGSST) and hematologic malignancies (NGSHM). Results.— Worldwide, 64.4% (152 of 236) of NGSST and 66.4% (87 of 131) of NGSHM participants used tier classification systems, of which the 2017 guideline was used by 84.9% (129 of 152) of NGSST and 73.6% (64 of 87) of NGSHM participants. The 2017 guideline was modified by 24.4% (30 of 123) of NGSST and 21.7% (13 of 60) of NGSHM laboratories. Laboratories implementing the 2017 guideline were satisfied or very satisfied (74.2% [89 of 120] NGSST and 69.5% [41 of 59] NGSHM), and the impression of tier classification reproducibility was high (mean of 3.9 [NGSST] and 3.6 [NGSHM] on a 5-point scale). Of nonusers, 35.2% (38 of 108) of NGSST and 39.4% (26 of 66) of NGSHM laboratories were planning implementation. For future guideline revisions, respondents favored including variants to monitor disease (63.9% [78 of 122] NGSST, 80.0% [48 of 60] NGSHM) and germline variants (55.3% [63 of 114] NGSST, 75.0% [45 of 60] NGSHM). Additional subtiers were not favored by academic laboratories compared to nonacademic laboratories (P & lt; .001 NGSST and P = .02 NGSHM). Conclusions.— The 2017 guideline has been implemented by more than 50.0% of CAP laboratories. While most laboratories using the 2017 guideline report satisfaction, thoughtful guideline modifications may further enhance the quality, reproducibility, and clinical utility of the 2017 guideline for tiered somatic variant classification.
    Type of Medium: Online Resource
    ISSN: 1543-2165 , 0003-9985
    URL: Article
    DOI: 10.5858/arpa.2021-0179-CP
    RVK:
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    Language: English
    Publisher: Archives of Pathology and Laboratory Medicine
    Publication Date: 2022
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  • 10
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    Proficiency Testing of Standardized Samples Shows Very High Interlaboratory Agreement for Clinical Next-Generation Sequencing–Based Oncology Assays
    Archives of Pathology and Laboratory Medicine ; 2019
    In:  Archives of Pathology & Laboratory Medicine Vol. 143, No. 4 ( 2019-04-01), p. 463-471
    Details
    In: Archives of Pathology & Laboratory Medicine, Archives of Pathology and Laboratory Medicine, Vol. 143, No. 4 ( 2019-04-01), p. 463-471
    Abstract: Next-generation sequencing–based assays are being increasingly used in the clinical setting for the detection of somatic variants in solid tumors, but limited data are available regarding the interlaboratory performance of these assays. Objective.— To examine proficiency testing data from the initial College of American Pathologists (CAP) Next-Generation Sequencing Solid Tumor survey to report on laboratory performance. Design.— CAP proficiency testing results from 111 laboratories were analyzed for accuracy and associated assay performance characteristics. Results.— The overall accuracy observed for all variants was 98.3%. Rare false-negative results could not be attributed to sequencing platform, selection method, or other assay characteristics. The median and average of the variant allele fractions reported by the laboratories were within 10% of those orthogonally determined by digital polymerase chain reaction for each variant. The median coverage reported at the variant sites ranged from 1922 to 3297. Conclusions.— Laboratories demonstrated an overall accuracy of greater than 98% with high specificity when examining 10 clinically relevant somatic single-nucleotide variants with a variant allele fraction of 15% or greater. These initial data suggest excellent performance, but further ongoing studies are needed to evaluate the performance of lower variant allele fractions and additional variant types.
    Type of Medium: Online Resource
    ISSN: 0003-9985 , 1543-2165
    URL: Article
    DOI: 10.5858/arpa.2018-0336-CP
    RVK:
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    Language: English
    Publisher: Archives of Pathology and Laboratory Medicine
    Publication Date: 2019
    detail.hit.zdb_id: 2028916-9
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