(282 days)
The 23andMe Personal Genome Service (PGS) Test uses qualitative genotyping to detect the following clinically relevant variants in genomic DNA isolated from human saliva collected from individuals ≥18 years with the Oragene Dx model OGD-500.001 for the purpose of reporting and interpreting Genetic Health Risks (GHR):
The 23andMe PGS Genetic Health Risk Report for Hereditary Thrombophilia is indicated for reporting of the Factor V Leiden variant in the F5 gene, and the Prothrombin G20210A variant in the F2 gene. This report describes if a person has variants associated with a higher risk of developing harmful blood clots, but it does not describe a person's overall risk of developing harmful blood clots. This test is most relevant for people of European descent.
The 23andMe PGS Genetic Health Risk Report for Alpha-1 Antitrypsin Deficiency is indicated for reporting of the PIZ and PIS variants in the SERPINA1 gene. This report describes if a person has variants associated with AAT deficiency and a higher risk for lung or liver disease, but it does not describe a person's overall risk of developing lung or liver disease. This test is most relevant for people of European descent.
The 23andMe PGS Genetic Health Risk Report for Late-onset Alzheimer's Disease is indicated for reporting of the £4 variant in the APOE gene. The report describes if a person's genetic result is associated with an increased risk of developing Late-onset Alzheimer's Disease, but it does not describe a person's overall risk of developing Alzheimer's Disease. The £4 variant included in this report is found and has been studied in many ethnicities. Detailed risk estimates have been studied the most in people of European descent.
The 23andMe PGS Genetic Health Risk Report for Parkinson's Disease is indicated for reporting of the G2019S variant in the LRRK2 gene and the N370S variant in the GBA gene. The report describes if a person's genetic result is associated with an increased risk of developing Parkinson's disease, but it does not describe a person's overall risk of developing Parkinson's disease. The test is most relevant for people of European, Ashkenazi Jewish, and North African Berber descent.
The 23andMe PGS Genetic Health Risk Report for Gaucher Disease Type 1 is indicated for reporting of the N370S, 84GG, and V394L variants in the GBA gene. This report describes if a person has variants associated with an increased risk for developing symptoms of Gaucher Disease Type 1, but it does not describe a person's overall risk of developing Gaucher Disease Type 1. This test is most relevant for people of Ashkenazi Jewish descent.
The 23andMe PGS Genetic Health Risk Report for Factor XI Deficiency is indicated for reporting of the variants F283L. E117X. IVS14+1G>A in the F11 gene. This report describes if a person has a variant associated with Factor XI deficiency and the potential for a higher risk of excessive bleeding following trauma or surgery, but it does not describe a person's overall risk for excessive bleeding. This test is most relevant for people of Ashkenazi Jewish descent.
The 23andMe PGS Genetic Health Risk Report for Celiac Disease is indicated for reporting of a variant associated with the HLA-DQ2.5 haplotype. The report describes if a person has a haplotype associated with an increased risk of developing celiac disease, but it does not describe a person's overall risk for developing celiac disease. This report is most relevant for people of European descent.
The 23andMe PGS Genetic Health Risk Report for Glucose-6-Phosphate-Dehydrogenase Deficiency is indicated for reporting of the Val68Met variant in the G6PD gene. This report describes if a person has a variant associated with G6PD deficiency and a higher risk for episodes of anemia, but it does not describe a person's overall risk of developing anemia. This test is most relevant for people of African descent.
The 23andMe PGS Genetic Health Risk Report for Hereditary Hemochromatosis is indicated for reporting of the C282Y and H63D variants in the HFE gene. This report describes if a person has variants associated with hereditary hemochromatosis and a higher risk for iron overload, but it does not describe a person's overall risk of developing iron overload. This report is most relevant for people of European descent.
The 23andMe PGS Genetic Health Risk Report for Early-Onset Primary Dystonia (DYT1/TOR1A-Related) is indicated for reporting of the deltaE302/303 variant in the DYT1 gene. This report describes if a person has variants associated with a higher risk for early-onset primary dystonia, but it does not describe a person's overall risk of developing dystonia. This report is most relevant for people of Ashkenazi Jewish descent.
The 23andMe PGS is a currently-marketed, non-invasive genetic information service that combines qualitative genotyping data covering genetic ancestry, traits, and certain heritable health conditions from a single multiplex assay with descriptive information derived from peer reviewed, published genetic research studies. It is a direct-toconsumer, over-the-counter, non-diagnostic, DNA genetic testing service intended to provide information and tools for individual users.
A user's saliva is self-collected using the Oragene-Dx device manufactured by DNA Genotek, Inc. (previously cleared under K141410), which consists of a sealable collection tube containing a stabilizing buffer solution. Once the sample is collected, it is shipped to one of two Clinical Laboratory Improvement Amendments (CLIA)-certified laboratories for processing.
DNA is isolated from the saliva and tested in a multiplex assay using a customized genotyping chip and instrumentation manufactured by Illumina. The multiplex assay simultaneously tests for more than 500,000 variants, including those for the indications proposed herein.
The raw data is generated using Illumina GenomeStudio software, and then sent to 23andMe (the Manufacturer). The data are analyzed using the Manufacturer's proprietary Coregen software, and a genotype is determined for each tested variant. The results for certain of these variants are used to generate personalized reports for users that provide information about the diseases associated with the detected variant.
Personalized reports are generated for each user that provide results of the testing performed. These reports tell the user which variant(s) has/have been detected in their sample and provide information on the risk of disease associated with the variant(s). If no variant was detected, that information is also provided. The personalized reports are designed to present scientific concepts to users in an easy-to-understand format. The reports provide scientifically valid information about the risks associated with the presence of a particular variant. The reports are designed to help users understand the meaning of their results and any appropriate actions that may be taken based on their results.
Acceptance Criteria and Device Performance Study for 23andMe Personal Genome Service (PGS) Genetic Health Risk Test
The 23andMe Personal Genome Service (PGS) Genetic Health Risk Test is a qualitative in vitro molecular diagnostic system for detecting genetic variants associated with various diseases. The regulatory approval details the acceptance criteria and performance study results.
1. Table of Acceptance Criteria and Reported Device Performance
The acceptance criteria for analytical performance (Precision/Reproducibility, Limit of Detection, and Accuracy) are derived from the Special Controls outlined in 21 CFR 866.5950, specifically paragraph (b)(3)(iii)(J).
| Acceptance Criteria Category | Specific Criterion (from 21 CFR 866.5950, (b)(3)(iii)(J)) | Reported Device Performance (Extracts from Document) |
|---|---|---|
| Analytical Performance | ||
| Accuracy (Comparison to Gold Standard) | Point estimates of percent agreement for each genotype must be calculated as the number of correct calls for that genotype divided by the number of samples known to contain that genotype excluding 'no calls' or 'invalid calls'. The accuracy point estimates for percent agreements for DD, Dd, and dd must be ≥99 percent per reported variant and overall. (b)(3)(iii)(J)(I)(vi) & (vii) | Hereditary Thrombophilia (Factor V Leiden F5): |
- PA (CC|CC) = 100% (95% CI: 94.7% to 100%)
- PA (CT|CT) = 100% (95% CI: 94.7% to 100%)
- PA (TT|TT) = 100% (95% CI: 94.6% to 100%)
Hereditary Thrombophilia (Prothrombin G20210A F2): - PA (GG|GG) = 100% (95% CI: 94.7% to 100%)
- PA (AG|AG) = 100% (95% CI: 94.6% to 100%)
- PA (AA|AA) = 100% (95% CI: 94.5% to 100%)
Alpha-1 Antitrypsin Deficiency (PI*Z SERPINA1): - PA (CC|CC) = 100% (95% CI: 94.8% to 100%)
- PA (CT|CT) = 100% (95% CI: 94.7% to 100%)
- PA (TT|TT) = 100% (95% CI: 94.7% to 100%)
Alpha-1 Antitrypsin Deficiency (PI*S SERPINA1): - PA (TT|TT) = 100% (95% CI: 94.4% to 100%)
- PA (AT|AT) = 100% (95% CI: 94.7% to 100%)
- PA (AA|AA) = 100% (95% CI: 94.7% to 100%)
Late-onset Alzheimer's Disease (APOE s4): - PA (TT|TT) = 100% (95% CI: 98.8% to 100%)
- PA (CT|CT) = 99.2% (95% CI: 95.7% to 99.9%)
- PA (CC|CC) = 100% (95% CI: 96.3% to 100%)
Parkinson's Disease (G2019S LRRK2): - PA (GG|GG) = 100% (95% CI: 86.7% to 100%)
- PA (AG|AG) = 100% (95% CI: 93% to 100%)
- PA (AA|AA) = 100% (95% CI: 51.0% to 100%)
Parkinson's Disease (N370S GBA): - PA (TT|TT) = 100% (95% CI: 86.7% to 100%)
- PA (CT|CT) = 100% (95% CI: 94% to 100%)
- PA (CC|CC) = 100% (95% CI: 87.1% to 100%)
Gaucher Disease Type 1 (N370S GBA): - PA (TT|TT) = 100% (95% CI: 86.7% to 100%)
- PA (CT|CT) = 100% (95% CI: 94% to 100%)
- PA (CC|CC) = 100% (95% CI: 87.1% to 100%)
The Manufacturer affirmed that comparison studies for other variants (84GG, V394L in GBA; F283L, E117X, IVS14+1G>A in Factor XI; HLA-DQA1 for Celiac Disease; Val68Met in G6PD; C282Y, H63D in HFE; deltaE302/303 in DYT1) were completed with identical study design, acceptance criteria, and results as the reported variants, including 100% accuracy for all valid calls. |
| Precision/Reproducibility | The percentage of samples that failed quality control must be indicated (i.e., the total number of sample replicates for which a sequence variant cannot be called (no calls) or that fail sequencing quality control criteria divided by the total number of replicates tested). (b)(3)(iii)(J)(2) | General: All analytical performance studies met the pre-determined acceptance criteria.
Factor V Leiden: 98.0% correct calls, 2.01% FQCs (0.04% anticipated 2 FQCs).
Prothrombin G20210A: 98.1% correct calls, 1.85% FQCs (0.03% anticipated 2 FQCs).
PI*Z SERPINA1: 98.4% correct calls, 1.63% FQCs (0.03% anticipated 2 FQCs).
PI*S SERPINA1: 98.2% correct calls, 1.76% FQCs (0.03% anticipated 2 FQCs).
APOE s4: 98.5% correct calls, 1.54% FQCs (0.02% anticipated 2 FQCs).
G2019S LRRK2: 98.5% correct calls, 1.54% FQCs (0.02% anticipated 2 FQCs).
N370S GBA (Parkinson's): 96.2% correct calls, 3.81% FQCs (0.15% anticipated 2 FQCs).
N370S GBA (Gaucher): 97.5% correct calls, 3.12% FQCs (0.10% anticipated 2 FQCs).
All valid calls in these studies were 100% correct at both sites. The Manufacturer affirmed that reproducibility studies were completed for all other listed variants (84GG, V394L in GBA; F283L, E117X, IVS14+1G>A in Factor XI; HLA-DQA1 for Celiac Disease; Val68Met in G6PD; C282Y, H63D in HFE; deltaE302/303 in DYT1) with identical study design, acceptance criteria, and results. |
| Limit of Detection (LoD) | Data must be provided demonstrating the minimum amount of DNA that will enable the test to perform correctly in 95 percent of runs. (b)(3)(iii)(J)(5) | The LoD study yielded 100% correct genotype calls for all samples and all reagent lots tested at sample DNA concentrations of 5, 15, and 50 ng/uL. The study passed LoD acceptance criteria at 5 ng/uL. Manufacturer claimed LoD of 15 ng/uL.
The Manufacturer affirmed that LoD studies were completed for all other listed variants (84GG, V394L in GBA; F283L, E117X, IVS14+1G>A in Factor XI; HLA-DQA1 for Celiac Disease; Val68Met in G6PD; C282Y, H63D in HFE; deltaE302/303 in DYT1) with identical study design, acceptance criteria, and results. |
| User Comprehension | The user study must meet predefined primary endpoint criteria, including a minimum of a 90 percent or greater overall comprehension rate (i.e., selection of the correct answer) for each comprehension concept. (b)(3)(iii)(M)(4)(vi) | The overall comprehension score for all concepts across all test reports studied was greater than 90%. For the G6PD Deficiency report scenario ("1 Variant Detected"), the report-specific comprehension score was 73.3%, which the Manufacturer mitigated with planned labeling changes in the FAQ section. |
2. Sample Sizes and Data Provenance for Test Set
Test Set for Analytical Accuracy (Comparison to Sanger Bidirectional Sequencing):
- Hereditary Thrombophilia (Factor V Leiden): 68 Homozygous Common (CC), 68 Heterozygous (CT), 67 Homozygous Rare (TT) samples. Total = 203.
- Hereditary Thrombophilia (Prothrombin G20210A): 68 Homozygous Common (GG), 67 Heterozygous (AG), 66 Homozygous Rare (AA) samples. Total = 201.
- Alpha-1 Antitrypsin Deficiency (PI*Z SERPINA1): 70 Homozygous Common (CC), 68 Heterozygous (CT), 69 Homozygous Rare (TT) samples. Total = 207.
- Alpha-1 Antitrypsin Deficiency (PI*S SERPINA1): 65 Homozygous Common (TT), 68 Heterozygous (AT), 69 Homozygous Rare (AA) samples. Total = 202.
- Late-onset Alzheimer's Disease (APOE s4): 316 Homozygous Common (TT), 126 Heterozygous (CT), 101 Homozygous Rare (CC) samples with correct calls. (Total raw samples: 320 TT, 129 CT, 106 CC, including those with "no calls" or "invalid"). Total = 555.
- Parkinson's Disease (G2019S LRRK2): 25 Homozygous Common (GG), 51 Heterozygous (AG), 4 Homozygous Rare (AA) samples. Total = 80.
- Parkinson's Disease (N370S GBA): 25 Homozygous Common (TT), 60 Heterozygous (CT), 26 Homozygous Rare (CC) samples. Total = 111.
- Gaucher Disease Type 1 (N370S GBA): 25 Homozygous Common (TT), 60 Heterozygous (CT), 26 Homozygous Rare (CC) samples. Total = 111.
- Other variants: For Gaucher Disease Type 1 (84GG, V394L), Factor XI Deficiency (F283L, E117X, IVS14+1G>A), Celiac Disease (HLA-DQA1), G6PD Deficiency (Val68Met), Hereditary Hemochromatosis (C282Y, H63D), and Early-Onset Primary Dystonia (deltaE302/303), the manufacturer affirmed that comparison studies were completed with the same design, acceptance criteria, and results as the explicitly detailed studies, testing wild-type, heterozygous, and homozygous samples where applicable, adhering to minimum sample size requirements (e.g., at least 20 unique samples for common genotypes, 3 for rare heterozygous, 3-20 for rare homozygous based on frequency).
Data Provenance: Saliva samples were selected from the 23andMe customer biobank based on their predetermined genotype. The data origin is not explicitly stated geographically, but it is indicated that genotype frequencies are considered for "individuals of European descent," "Ashkenazi Jewish descent," "North African Berber descent," "African descent," "South Asian," and "East Asian" depending on the variant, implying a diverse customer base. The samples are retrospective, as they were chosen from an existing biobank.
3. Number of Experts and Qualifications for Ground Truth
No external experts were explicitly mentioned for establishing the ground truth of the genetic variants in the test set. The ground truth for the test set was established by Sanger bidirectional sequencing, which is considered the "gold standard" for genetic variant determination. This method is an intrinsic, highly accurate laboratory technique, rather than requiring expert consensus interpretation.
4. Adjudication Method for the Test Set
Not applicable. The ground truth was established by Sanger bidirectional sequencing, an objective laboratory method, which means there was no human adjudication process involved for the genetic variant calls.
5. Multi-Reader Multi-Case (MRMC) Comparative Effectiveness Study
No MRMC comparative effectiveness study was performed in the context of human readers improving with or without AI assistance. This device is a direct-to-consumer genetic test for detecting specific variants, not an AI-assisted diagnostic imaging or interpretation tool.
6. Standalone (Algorithm-Only) Performance Study
Yes, the analytical performance studies (Accuracy, Precision/Reproducibility, Limit of Detection) represent the standalone performance of the 23andMe PGS device. The device's genotyping results were compared directly against the gold standard (Sanger bidirectional sequencing) without human intervention in the interpretation of the device's output for genetic calls.
7. Type of Ground Truth Used
The type of ground truth used for the analytical performance studies (accuracy, LoD) was Sanger bidirectional sequencing, which is a highly accurate molecular biology laboratory method for DNA sequencing, serving as the "truth" for genetic variants. This is an objective laboratory measure, not expert consensus, pathology, or outcomes data.
8. Sample Size for the Training Set
The document does not explicitly mention a "training set" in the context of machine learning or AI algorithm development for genetic variant detection. The methodologies described are for analytical validation of a qualitative genetic test. The robustness of the test is demonstrated through extensive reproducibility and accuracy studies using defined sets of samples (both cell lines and customer biobank samples).
For the analytical performance studies (Precision/Reproducibility and Limit of Detection), a range of sample sizes were used:
- Precision/Reproducibility for Hereditary Thrombophilia (Factor V Leiden): 10 DNA samples (3 wild type, 2 heterozygous, 1 homozygous rare, repeated multiple times) used for 1890 replicates.
- Precision/Reproducibility for Hereditary Thrombophilia (Prothrombin G20210A): 10 DNA samples (3 wild type, 1 heterozygous, 1 homozygous rare, repeated multiple times) used for 1620 replicates.
- Precision/Reproducibility for Alpha-1 Antitrypsin Deficiency (PI*Z SERPINA1): 8 DNA samples (2 wild type, 1 heterozygous, 1 homozygous rare, repeated multiple times) used for 1350 replicates.
- Similar numbers of DNA samples and replicates were used for other variants in the reproducibility studies.
- Limit of Detection: Samples were diluted to three different DNA concentrations (5, 15, and 50 ng/uL) and genotyped. The text does not specify the number of individual donor samples used for LoD beyond "each sample was diluted," implying the same initial set of samples used for accuracy/precision.
9. How the Ground Truth for the Training Set Was Established
As mentioned above, a "training set" in the conventional machine learning sense for algorithm development is not explicitly described. The ground truth for the samples used in the analytical validation studies (which could be considered analogous to a "development/test set" for a traditional assay) was established through bidirectional Sanger sequencing, performed by an independent laboratory. This external, highly accurate, and objective method served as the reference standard for confirming the genotypes of the samples used in the performance evaluations.
§ 866.5950 Genetic health risk assessment system.
(a)
Identification. A genetic health risk assessment system is a qualitative in vitro molecular diagnostic system used for detecting variants in genomic deoxyribonucleic acid (DNA) isolated from human specimens that will provide information to users about their genetic risk of developing a disease to inform lifestyle choices and/or conversations with a health care professional. This assessment system is for over-the-counter use. This device does not determine the person's overall risk of developing a disease.(b)
Classification. Class II (special controls). The genetic health risk assessment system device, when it has previously received a first-time FDA marketing authorization (e.g., 510(k) clearance) for the genetic health risk assessment system (a “one-time FDA reviewed genetic health risk assessment system”), is exempt from the premarket notification procedures in part 807, subpart E, of this chapter subject to the limitations in § 866.9. The device must comply with the following special controls:(1) The 21 CFR 809.10 compliant labeling and any prepurchase page and test report generated, unless otherwise specified, must include:
(i) A section addressed to users with the following information:
(A) The limiting statement explaining that this test provides genetic risk information based on assessment of specific genetic variants but does not report on a user's entire genetic profile. This test [does not/may not, as appropriate] detect all genetic variants related to a given disease, and the absence of a variant tested does not rule out the presence of other genetic variants that may be related to the disease.
(B) The limiting statement explaining that other companies offering a genetic risk test may be detecting different genetic variants for the same disease, so the user may get different results using a test from a different company.
(C) The limiting statement explaining that other factors such as environmental and lifestyle risk factors may affect the risk of developing a given disease.
(D) The limiting statement explaining that some people may feel anxious about getting genetic test health results. This is normal. If the potential user feels very anxious, such user should speak to his or her doctor or other health care professional prior to collection of a sample for testing. This test is not a substitute for visits to a doctor or other health care professional. Users should consult with their doctor or other health care professional if they have any questions or concerns about the results of their test or their current state of health.
(E) Information about how to obtain access to a genetic counselor, board-certified clinical molecular geneticist, or equivalent health care professional about the results of a user's test.
(F) The limiting statement explaining that this test is not intended to diagnose a disease, tell you anything about your current state of health, or be used to make medical decisions, including whether or not you should take a medication or how much of a medication you should take.
(G) A limiting statement explaining that the laboratory may not be able to process a sample, and a description of the next steps to be taken by the manufacturer and/or the customer, as applicable.
(ii) A section in your 21 CFR 809.10 labeling and any test report generated that is for health care professionals who may receive the test results from their patients with the following information:
(A) The limiting statement explaining that this test is not intended to diagnose a disease, determine medical treatment, or tell the user anything about their current state of health.
(B) The limiting statement explaining that this test is intended to provide users with their genetic information to inform lifestyle decisions and conversations with their doctor or other health care professional.
(C) The limiting statement explaining that any diagnostic or treatment decisions should be based on testing and/or other information that you determine to be appropriate for your patient.
(2) The genetic test must use a sample collection device that is FDA-cleared, -approved, or -classified as 510(k) exempt, with an indication for in vitro diagnostic use in over-the-counter DNA testing.
(3) The device's labeling must include a hyperlink to the manufacturer's public Web site where the manufacturer shall make the information identified in paragraph (b)(3) of this section publicly available. The manufacturer's home page, as well as the primary part of the manufacturer's Web site that discusses the device, must provide a hyperlink to the Web page containing this information and must allow unrestricted viewing access. If the device can be purchased from the Web site or testing using the device can be ordered from the Web site, the same information must be found on the Web page for ordering the device or provided in a publicly accessible hyperlink on the Web page for ordering the device. Any changes to the device that could significantly affect safety or effectiveness would require new data or information in support of such changes, which would also have to be posted on the manufacturer's Web site. The information must include:
(i) An index of the material being provided to meet the requirements in paragraph (b)(3) of this section and its location.
(ii) A section that highlights summary information that allows the user to understand how the test works and how to interpret the results of the test. This section must, at a minimum, be written in plain language understandable to a lay user and include:
(A) Consistent explanations of the risk of disease associated with all variants included in the test. If there are different categories of risk, the manufacturer must provide literature references that support the different risk categories. If there will be multiple test reports and multiple variants, the risk categories must be defined similarly among them. For example, “increased risk” must be defined similarly between different test reports and different variant combinations.
(B) Clear context for the user to understand the context in which the cited clinical performance data support the risk reported. This includes, but is not limited to, any risks that are influenced by ethnicity, age, gender, environment, and lifestyle choices.
(C) Materials that explain the main concepts and terminology used in the test that include:
(
1 )Definitions: Scientific terms that are used in the test reports.(
2 )Prepurchase page: This page must contain information that informs the user about what information the test will provide. This includes, but is not limited to, variant information, the condition or disease associated with the variant(s), professional guideline recommendations for general genetic risk testing, the limitations associated with the test (e.g., test does not detect all variants related to the disease) and any precautionary information about the test the user should be aware of before purchase. When the test reports the risk of a life-threatening or irreversibly debilitating disease or condition for which there are few or no options to prevent, treat, or cure the disease, a user opt-in section must be provided. This opt-in page must be provided for each disease that falls into this category and must provide specific information relevant to each test result. The opt-in page must include:(
i ) An option to accept or decline to receive this specific test result;(
ii ) Specification of the risk involved if the user is found to have the specific genetic test result;(
iii ) Professional guidelines that recommend when genetic testing for the associated target condition is or is not recommended; and(
iv ) A recommendation to speak with a health care professional, genetic counselor, or equivalent professional before getting the results of the test.(
3 )Frequently asked questions (FAQ) page: This page must provide information that is specific for each variant/disease pair that is reported. Information provided in this section must be scientifically valid and supported by corresponding publications. The FAQ page must explain the health condition/disease being tested, the purpose of the test, the information the test will and will not provide, the relevance of race and ethnicity to the test results, information about the population to which the variants in the test is most applicable, the meaning of the result(s), other risk factors that contribute to disease, appropriate followup procedures, how the results of the test may affect the user's family, including children, and links to resources that provide additional information.(iii) A technical information section containing the following information:
(A) Gene(s) and variant(s) the test detects using standardized nomenclature, Human Genome Organization nomenclature and coordinates as well as Single Nucleotide Polymorphism Database (dbSNP) reference SNP numbers (rs#).
(B) Scientifically established disease-risk association of each variant detected and reported by the test. This risk association information must include:
(
1 ) Genotype-phenotype information for the reported variants.(
2 ) Table of expected frequency and risks of developing the disease in relevant ethnic populations and the general population.(
3 ) A statement about the current professional guidelines for testing these specific gene(s) and variant(s).(
i ) If professional guidelines are available, provide the recommendations in the professional guideline for the gene, variant, and disease, for when genetic testing should or should not be performed, and cautionary information that should be communicated when a particular gene and variant is detected.(
ii ) If professional guidelines are not available, provide a statement that the professional guidelines are not available for these specific gene(s) and variant(s).(C) The specimen type (
e.g., saliva, capillary whole blood).(D) Assay steps and technology used.
(E) Specification of required ancillary reagents, instrumentation, and equipment.
(F) Specification of the specimen collection, processing, storage, and preparation methods.
(G) Specification of risk mitigation elements and description of all additional procedures, methods, and practices incorporated into the directions for use that mitigate risks associated with testing.
(H) Information pertaining to the probability of test failure (
i.e., percentage of tests that failed quality control) based on data from clinical samples, a description of scenarios in which a test can fail (i.e., low sample volume, low DNA concentration, etc.), how users will be notified of a test failure, and the nature of followup actions on a failed test to be taken by the user and the manufacturer.(I) Specification of the criteria for test result interpretation and reporting.
(J) Information that demonstrates the performance characteristics of the test, including:
(
1 ) Accuracy of study results for each claimed specimen type.(
i ) Accuracy of the test shall be evaluated with fresh clinical specimens collected and processed in a manner consistent with the test's instructions for use. If this is impractical, fresh clinical samples may be substituted or supplemented with archived clinical samples. Archived samples shall have been collected previously in accordance with the instructions for use, stored appropriately, and randomly selected. In some limited circumstances, use of contrived samples or human cell line samples may also be appropriate and used as an acceptable alternative. The contrived or human cell line samples shall mimic clinical specimens as much as is feasible and provide an unbiased evaluation of the device accuracy.(
ii ) Accuracy must be evaluated by comparison to bidirectional Sanger sequencing or other methods identified as appropriate by FDA. Performance criteria for both the comparator method and the device must be predefined and appropriate to the device's intended use. Detailed study protocols must be provided.(
iii ) Test specimens must include all genotypes that will be included in the tests and reports. The number of samples tested in the accuracy study for each variant reported must be based on the variant frequency using either the minimum numbers of samples identified in this paragraph or, when determined appropriate and identified by FDA, a minimum number of samples determined using an alternative method. When appropriate, the same samples may be used in testing to demonstrate the accuracy of testing for multiple genotypes by generating sequence information at multiple relevant genetic locations. At least 20 unique samples representing the wild-type genotype must be tested. To test samples that are heterozygous for the reported variant(s), common variants (>0.1 percent variant frequency in the relevant population) must be tested with at least 20 unique samples. Rare variants (≤0.1 percent variant frequency in the relevant population) must be tested with at least three unique samples. To test samples that are homozygous for the reported variant(s), variants with ≥2 percent variant frequency in a relevant population must be tested with at least 20 unique samples. Variants with a frequency in the relevant population