RESUMO
BACKGROUND: The clonoSEQ® Assay (Adaptive Biotechnologies Corporation, Seattle, USA) identifies and tracks unique disease-associated immunoglobulin (Ig) sequences by next-generation sequencing of IgH, IgK, and IgL rearrangements and IgH-BCL1/2 translocations in malignant B cells. Here, we describe studies to validate the analytical performance of the assay using patient samples and cell lines. METHODS: Sensitivity and specificity were established by defining the limit of detection (LoD), limit of quantitation (LoQ) and limit of blank (LoB) in genomic DNA (gDNA) from 66 patients with multiple myeloma (MM), acute lymphoblastic leukemia (ALL), or chronic lymphocytic leukemia (CLL), and three cell lines. Healthy donor gDNA was used as a diluent to contrive samples with specific DNA masses and malignant-cell frequencies. Precision was validated using a range of samples contrived from patient gDNA, healthy donor gDNA, and 9 cell lines to generate measurable residual disease (MRD) frequencies spanning clinically relevant thresholds. Linearity was determined using samples contrived from cell line gDNA spiked into healthy gDNA to generate 11 MRD frequencies for each DNA input, then confirmed using clinical samples. Quantitation accuracy was assessed by (1) comparing clonoSEQ and multiparametric flow cytometry (mpFC) measurements of ALL and MM cell lines diluted in healthy mononuclear cells, and (2) analyzing precision study data for bias between clonoSEQ MRD results in diluted gDNA and those expected from mpFC based on original, undiluted samples. Repeatability of nucleotide base calls was assessed via the assay's ability to recover malignant clonotype sequences across several replicates, process features, and MRD levels. RESULTS: LoD and LoQ were estimated at 1.903 cells and 2.390 malignant cells, respectively. LoB was zero in healthy donor gDNA. Precision ranged from 18% CV (coefficient of variation) at higher DNA inputs to 68% CV near the LoD. Variance component analysis showed MRD results were robust, with expected laboratory process variations contributing ≤3% CV. Linearity and accuracy were demonstrated for each disease across orders of magnitude of clonal frequencies. Nucleotide sequence error rates were extremely low. CONCLUSIONS: These studies validate the analytical performance of the clonoSEQ Assay and demonstrate its potential as a highly sensitive diagnostic tool for selected lymphoid malignancies.
Assuntos
Sequenciamento de Nucleotídeos em Larga Escala/instrumentação , Leucemia Linfocítica Crônica de Células B/diagnóstico , Mieloma Múltiplo/diagnóstico , Leucemia-Linfoma Linfoblástico de Células Precursoras/diagnóstico , Kit de Reagentes para Diagnóstico , Medula Óssea/patologia , Ciclina D1/genética , Rearranjo Gênico , Humanos , Cadeias Pesadas de Imunoglobulinas/genética , Cadeias lambda de Imunoglobulina/genética , Imunoglobulinas/genética , Leucemia Linfocítica Crônica de Células B/sangue , Leucemia Linfocítica Crônica de Células B/genética , Leucemia Linfocítica Crônica de Células B/terapia , Limite de Detecção , Mieloma Múltiplo/sangue , Mieloma Múltiplo/genética , Mieloma Múltiplo/terapia , Neoplasia Residual , Leucemia-Linfoma Linfoblástico de Células Precursoras/sangue , Leucemia-Linfoma Linfoblástico de Células Precursoras/genética , Leucemia-Linfoma Linfoblástico de Células Precursoras/terapia , Proteínas Proto-Oncogênicas c-bcl-2/genética , Translocação GenéticaRESUMO
We describe the development of a label-less ellipsometric imaging microarray reader. The ability of the ellipsometric microarray reader to measure binding of sample to microarray surface is verified using oligonucleotide complementary DNA (cDNA) microarrays. Polarized light illuminates the microarray surface through a glass substrate at an angle beyond the critical angle and changes in the polarization of totally internally reflected light resulting from binding events on the microarray surface are measured. This polarization change is used to measure the thickness of biomolecules bound to the microarray. A prototype ellipsometric imaging microarray reader is constructed and calibrated, and the performance is evaluated with cDNA microarrays. The microarray reader measures changes in refractive index changes as small as 0.0024 and thickness changes as small as 0.28 nm. The optimization of angle of incidence and substrate refractive index necessary to achieve high sensitivity is also described. This ellipsometric technique offers an attractive alternative to fluorescence-microarray readers in some genomic, proteomic, diagnostic, and sensing applications.
Assuntos
Algoritmos , Hibridização In Situ/instrumentação , Análise de Sequência com Séries de Oligonucleotídeos/instrumentação , Refratometria/instrumentação , Desenho de Equipamento , Análise de Falha de Equipamento , Hibridização In Situ/métodos , Análise de Sequência com Séries de Oligonucleotídeos/métodos , Projetos Piloto , Reprodutibilidade dos Testes , Sensibilidade e EspecificidadeRESUMO
Microarrays have become an extremely important research tool for life science researchers and are also beginning to be used in diagnostic, treatment and monitoring applications. This article provides a detailed description of microarrays prepared by in situ synthesis, deposition using microspotting methods, nonplanar bead arrays, flow-through microarrays, optical fiber bundle arrays and nanobarcodes. The problems and challenges in the development of microarrays, development of standards and diagnostic microarrays are described. Tables summarizing the vendor list of various derivatized microarray surfaces, commercially sold premade microarrays, bead arrays and unique microarray products in development are also included.