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(a) Identification. The HIV drug resistance genotyping assay using next generation sequencing (NGS) technology is a prescription in vitro diagnostic device intended for use in detecting HIV genomic mutations that confer resistance to specific antiretroviral drugs. The device is intended to be used as an aid in monitoring and treating HIV infection.
(b) Classification. Class II (special controls). The special controls for this device are:
(1) The intended use of the device must:
(i) Specify the analyte (RNA or DNA), the genes in which mutations are detected, the clinical indications appropriate for test use, the sample type, and the specific population(s) for which the device in intended.
(ii) State that the device in not intended for use as an aid in the diagnosis of infection with HIV or to confirm the presence of HIV infection, or for screening donors of blood, plasma, or human cells, tissues, and cellular and tissue-based products.
(2) The labeling must include:
(i) A detailed device description, including but not limited to, all procedures from collection of the patient sample to reporting the final result, all device components, the control elements incorporated into the test procedure, instrument requirements, and reagents required for use but not provided as part of the device.
(ii) Performance characteristics from analytical studies and all intended specimen types.
(iii) A list of specific mutations detected.
(iv) The name and version of the standardized database used for sequence comparison and results derivation.
(v) A detailed explanation of the interpretation of test results, including acceptance criteria for evaluating the validity of a test run.
(vi) A limitation statement that the device is intended to be used in conjunction with clinical history and other laboratory findings. Results of this test are intended to be interpreted by a physician or equivalent.
(vii) A limitation statement that lack of detection of drug resistance mutations does not preclude the possibility of genetic mutation.
(viii) A limitation statement indicating the relevant genetic mutations that are included in the standardized database of HIV genomic sequences used for comparison and results derivation but that are not detected by the test.
(ix) A limitation statement that detection of a genomic drug resistance mutation may not correlate with phenotypic gene expression.
(x) A limitation statement that the test does not detect all genetic mutations associated with antiviral drugs.
(xi) A limitation statement listing the HIV types for which the test is not intended, if any.
(3) Device verification and validation must include:
(i) Design of primer sequences and rationale for sequence selection.
(ii) Computational path from collected raw data to reported result.
(iii) Detailed documentation of analytical studies including, but not limited to, characterization of the cutoff, analytical sensitivity, inclusivity, reproducibility, interference, cross reactivity, instrument and method carryover/cross contamination, sample stability, and handling for all genomic mutations claimed in the intended use.
(iv) Precision studies that include all genomic mutations claimed in the intended use.
(v) Detailed documentation of a multisite clinical study evaluating the sensitivity and specificity of the device. Clinical study subjects must represent the intended use population and device results for all targets claimed in the intended use must be compared to Sanger sequencing or other methods found acceptable by FDA. Drug resistance-associated mutations at or above the 20 percent frequency level must detect the mutations in greater than 90 percent of at least 10 replicates, for each of drug class evaluated.
(vi) Documentation that variant calling is performed at a level of coverage that supports positive detection of all genomic mutations claimed in the intended use.
(vii) Detailed documentation of limit of detection (LoD) studies in which device performance is evaluated by testing a minimum of 100 HIV-positive clinical samples including samples with analyte concentrations near the clinical decision points and near the LoD.
(A) The LoD for the device must be determined using a minimum of 10 HIV-1 group M genotypes if applicable. A detection rate at 1 * LoD greater than or equal to 95 percent must be demonstrated for mutations with a frequency greater than 20 percent.
(B) The LoD of genetic mutations at frequency levels less than 20 percent must be established.
(viii) A predefined HIV genotyping bioinformatics analysis pipeline (BAP). The BAP must adequately describe the bioinformatic analysis of the sequencing data, including but not limited to read alignment, variant calling, assembly, genotyping, quality control, and final result reporting.
(ix) A clear description of the selection and use of the standardized database that is used for sequence comparison and results derivation.
(4) Premarket notification submissions must include the information in paragraphs (b)(3)(i) through (ix) of this section.
[85 FR 7217, Feb. 7, 2020]
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