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The clonoSEQ Assay is an in vitro diagnostic that uses multiplex polymerase chain reaction (PCR) and next-generation sequencing (NGS) to identify and quantify rearranged IgH (VDJ), IgH (DJ), IgK and IgL receptor gene sequences, as well as translocated BCL1/1gH (J) and BCL2/1gH (J) sequences in DNA extracted from bone marrow from patients with B-cell acute lymphoblastic leukemia (ALL) or multiple myeloma (MM), and blood or bone marrow from patients with chronic lymphocytic leukemia (CLL).

The clonoSEQ Assay measures minimal residual disease (MRD) to monitor changes in burden of disease during and after treatment. The test is indicated for use by qualified healthcare professionals in accordance with professional guidelines for clinical decision-making and in conjunction with other clinicopathological features.

The clonoSEQ Assay is a single-site assay performed at Adaptive Biotechnologies Corporation.

The clonoSEQ Assay is a next-generation sequencing (NGS) based assay that identifies rearranged IgH (VDJ), IgH (DJ), IgK, and IgL receptor gene sequences, as well as translocated BCL1/IgH (J) and BCL2/IgH (J) sequences. The assay also includes primers that amplify specific genomic regions present as diploid copies in normal genomic DNA (gDNA) to allow determination of total nucleated cell content.

Testing begins with gDNA extracted from the specimen supplied (Figure 1). Extracted gDNA quality is assessed and rearranged immune receptors are amplified using a multiplex PCR. Reaction-specific index barcode sequences for sample identification are added to the amplified receptor sequences by PCR. Sequencing libraries are prepared from barcoded amplified DNA, which are then sequenced by synthesis using NGS. Raw sequence data are uploaded from the sequencing instrument to the Adaptive analysis pipeline. These sequence data are analyzed in a multi-step process: first, a sample's sequence data are identified using the sample index sequences. Next, data are processed using a proprietary algorithm with in-line controls to remove amplification bias. When the clonoSEQ Clonality (ID) assessment is conducted, the immune repertoire of the sample is checked for the presence of DNA sequences specific to "dominant" clone(s) consistent with the presence of a lymphoid malignancy. Each sequence that is being considered for MRD tracking is compared against a B cell repertoire database and assigned a uniqueness value that, together with its abundance relative to other sequences, is used to assign the sequence to a sensitivity bin which will be used in the estimation of the reported LoD and LoO on the patient report. During clonoSEQ Tracking (MRD) assessment, the complete immunoglobulin receptor repertoire is again assessed, and the previously identified dominant clonotype sequence(s) are detected and quantified to determine the sample MRD level. The clonoSEQ Assay MRD assessment measures residual disease in a biologic sample.

Here's a breakdown of the acceptance criteria and study details for the Adaptive Biotechnologies clonoSEQ Assay, based on the provided FDA 510(k) summary:

This device, the Adaptive Biotechnologies clonoSEQ Assay, is an in vitro diagnostic (IVD) that identifies and quantifies rearranged immune receptor gene sequences (IgH, IgK, IgL) and translocated BCL1/IgH and BCL2/IgH sequences using multiplex PCR and Next-Generation Sequencing (NGS). It measures Minimal Residual Disease (MRD) in patients with B-cell acute lymphoblastic leukemia (ALL), multiple myeloma (MM), and chronic lymphocytic leukemia (CLL) to monitor disease burden. The current submission is an expansion of indications to include blood samples from CLL patients.

1. A table of acceptance criteria and the reported device performance

The provided document doesn't explicitly list "acceptance criteria" in a single table, but rather describes the performance characteristics that were measured and the outcomes for each. I will compile these for the CLL in Blood indication, as this is the focus of the 510(k) expansion.

Acceptance Criteria & Reported Device Performance for clonoSEQ Assay (CLL in Blood)

• At 500 ng DNA input: 21.9% - 54.9% CV
• At 2 µg DNA input: 20.8% - 51.6% CV
• At 20 µg DNA input: 18.7% - 49.2% CV
  (Comparable to BMA precision) |
  | Precision (Malignant Cells Detected) | %CV within acceptable clinical/analytical limits, primarily influenced by cell number. | Range: 19% CV (at 765.70 cells) to 53% CV (at 3.10 cells).
  Primarily due to residual variability; other factors (operator, instruments, reagents, day, run) contributed 0%-10% CV. |
  | Linearity | Maximum deviation from linearity (based on quadratic or cubic fit) less than 5%. | Met for all DNA inputs (20µg, 2µg, 500ng) across the entire tested MRD frequency range (0 to 1x10^-3 / 4x10^-3).
• Slopes: 0.989 - 0.997 (indicating strong linearity)
• Intercepts: -0.009 to -0.075 |
  | Accuracy (Concordance with mpFC) | High positive percent agreement (PPA) and understanding of negative percent agreement (NPA) reflecting greater sensitivity. | PPA: 98.9% (95% CI: 94.3%-100%)
  NPA: 47.5% (95% CI: 40.5%-54.6%)
  (NPA lower due to clonoSEQ's higher sensitivity detecting MRD where mpFC calls negative) |
  | Limit of Blank (LoB) | LoB should be zero or negligible. | LoB was confirmed as zero (95th percentile of trackable sequences in healthy blood was zero). |
  | Limit of Detection (LoD) / Limit of Quantitation (LoQ) | LoD/LoQ for blood should be comparable to or lower than previously determined values for bone marrow. | LoD and LoQ for CLL in blood were lower or within the 95% CI of bootstrapped prior BMA data, confirming comparability. |
  | Analytical Specificity (Interfering Substances) | Mean MRD frequency difference ± 30% when comparing with and without interferent substances. | All tested endogenous and exogenous substances met acceptance criteria.
• Endogenous: Bilirubin (conjugated & unconjugated), Hemoglobin, Cholesterol, Triglycerides.
• Exogenous: K2EDTA, K3EDTA, Heparin, Chloroform.
  (MRD results not substantially influenced). |
  | Cross-Contamination/Sample Carryover | No significant contamination events leading to false positive ID or MRD results. | - No false calibrations for run-to-run (0/44 BMA, 0/44 BMMC).
• One single well-to-well false calibration (1/44 BMA) at a very low template count (83 templates), not associated with cell lines.
• Blood: No contamination or disease clone-sharing events leading to false positive ID/MRD results.
• PCR/Library/Sequencing: No run-to-run contamination (0/36 tests). 8/712 well-to-well events (likely vendor-related primer barcode issue)

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