RESUMEN
BACKGROUND: Control charting is routine in the quality assurance of traditional clinical laboratory testing. Genomic tests are not typically managed by control charting. We examined control charting to monitor the performance of a clinical next-generation sequencing (NGS) assay. METHODS: We retrospectively examined 3 years of control material (NA12878) data from clinical genomic epilepsy testing. Levey-Jennings plots were used to visualize changes in control material depth of sequencing coverage in genomic regions of an epilepsy genomic panel. Changes in depth of coverage were correlated with changes in the manufactured lot of capture probe reagent. Depth of coverage was also correlated between quality control material and clinical samples. RESULTS: Fifty-seven sequencing runs of NA12878 were analyzed for 1811 genomic regions targeting 108 genes. Manufactured probe lot changes were associated with significant changes in the average coverage of 537 genomic regions and the lowest coverage of 173 regions (using a critical cut-off of P < 5.52 x 10-6). Genomic regions with the highest sensitivity to lot-to-lot variation by average sequencing depth of coverage were not the same regions with the highest sensitivity by lowest sequencing depth of coverage. Levey-Jennings plots displayed differences in genomic depth of coverage across capture probe reagent lot changes. There was moderate correlation between the changes in depth of sequencing across lot changes for control material and clinical cases (r2 = 0.45). CONCLUSIONS: Genomic control charting can be used routinely by clinical laboratories to monitor assay performance and ensure the quality of testing.
Asunto(s)
Genómica , Secuenciación de Nucleótidos de Alto Rendimiento , Técnicas de Laboratorio Clínico , Humanos , Control de Calidad , Estudios RetrospectivosRESUMEN
BACKGROUND: Detection of SARS-CoV-2 viral RNA is important for the diagnosis and management of COVID-19. METHODS: We present a clinical validation of a reverse transcription PCR (RT-PCR) assay for the SARS-CoV-2 nucleocapsid (N1) gene. Off-board lysis on an automated nucleic acid extraction system was optimized with endemic coronaviruses (OC43 and NL63). Genomic RNA and SARS-CoV-2 RNA in a recombinant viral protein coat were used as control materials and compared for recovery from nucleic acid extraction. RESULTS: Nucleic acid extraction showed decreased recovery of endemic Coronavirus in vitro transcribed RNA (NL63) compared with attenuated virus (OC43). SARS-CoV-2 RNA had more reliable recovery from extraction through amplification than genomic RNA. Recovery of genomic RNA was improved by combining lysis buffer with clinical matrix before adding RNA. The RT-PCR assay demonstrated 100% in silico sensitivity and specificity. The accuracy across samples was 100% (75 of 75). Precision studies showed 100% intra-run, inter-run, and inter-technologist concordance. The limit of detection was 264 copies per milliliter (estimated 5 copies per reaction; 35.56 mean threshold cycle value). CONCLUSIONS: This SARS-CoV-2 assay demonstrates appropriate characteristics for use under an Emergency Use Authorization. Endemic coronavirus controls were useful in optimizing the extraction procedure. In the absence of live or attenuated virus, recombinant virus in a protein coat is an appropriate control specimen type for assay validation during a pandemic.
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Betacoronavirus , Técnicas de Laboratorio Clínico/métodos , Infecciones por Coronavirus/diagnóstico , Proteínas de la Nucleocápside , Neumonía Viral/diagnóstico , Betacoronavirus/genética , Betacoronavirus/aislamiento & purificación , COVID-19 , Prueba de COVID-19 , Vacunas contra la COVID-19 , Infecciones por Coronavirus/terapia , Servicios Médicos de Urgencia/métodos , Humanos , Proteínas de la Nucleocápside/análisis , Proteínas de la Nucleocápside/genética , Pandemias , Neumonía Viral/terapia , ARN Viral/análisis , Reproducibilidad de los Resultados , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa/métodos , SARS-CoV-2RESUMEN
Fibrous hamartoma of infancy (FHI) is a benign mesenchymal tumor histologically characterized by a mixture of intersecting fascicles of fibroblasts/myofibroblasts in collagenous stroma, nests of primitive oval or stellate cells in basophilic mucoid stroma, and mature adipose tissue. We hypothesized that FHI, because of histologic overlap with mesenchymal overgrowth tumors seen in CLOVES (Congenital Lipomatous Overgrowth with Vascular, Epidermal, Skeletal anomalies) and Proteus syndromes, may harbor mutations in signaling pathways associated with cellular proliferation. Formalin-fixed paraffin-embedded material from a discovery set of 4 cases of FHI was investigated by targeted next-generation sequencing of a panel of cancer-associated genes. The results were confirmed by targeted Sanger sequencing of EGFR exon 20. A validation set of 8 cases of FHI and 10 cases of other pediatric fatty tumors were investigated by targeted Sanger sequencing of EGFR exon 20. All 12 cases of FHI, and none of the 10 control tumors, showed EGFR exon 20 insertion/duplication mutations. This is the first report of molecular aberrations in FHI. The consistent occurrence of EGFR exon 20 insertion/duplication mutations in 100% of cases of FHI studied suggests that they must play a principal role in the pathogenesis of FHI, likely by conferring a potential for growth and local infiltration. Although surgical treatment will remain the mainstay of FHI treatment, tyrosine kinase inhibitors may have an adjunctive role in cases that are difficult to resect.
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Exones , Duplicación de Gen , Genes erbB-1 , Hamartoma/genética , Mutagénesis Insercional , Estudios de Casos y Controles , Preescolar , Femenino , Marcadores Genéticos , Hamartoma/diagnóstico , Hamartoma/patología , Humanos , Lactante , Masculino , Análisis de Secuencia de ADNRESUMEN
Distinction of hydatidiform moles from nonmolar specimens and their subclassification as complete (complete hydatidiform mole) versus partial hydatidiform mole (PHM) are important for clinical practice and investigational studies to refine ascertainment of risk of persistent gestational trophoblastic disease, which differs among these entities. Immunohistochemical analysis of p57 expression, a paternally imprinted maternally expressed gene on 11p15.5, and molecular genotyping are useful for improving diagnosis. Here, we describe a first trimester abortus with morphologic features consistent with a hydatidiform mole and p57 expression pattern supporting a diagnosis of PHM. Short tandem repeat (STR) genotyping and fluorescent in-situ hybridization analysis showed tetraploidy with 3 paternal and 1 maternal chromosome complements. To our knowledge, this is the first description of a tetraploid PHM confirmed to be triandric by STR analysis, and the first description of p57 immunostaining in a confirmed triandric tetraploid PHM. This case highlights the complex nature of the genetics that can be encountered in molar specimens and illustrates that STR genotyping, in contrast to fluorescent in-situ hybridization or ploidy analysis, offers the advantage of determining the parental origin of chromosome complements for refined diagnosis of hydatidiform moles.