(509 days)
The Helix Genetic Health Risk App (HRA) uses qualitative genotyping to detect clinically relevant variants in genomic DNA isolated from human saliva collected from individuals ≥18 years with Oragene®Dx OGD-610 for the purpose of reporting and interpreting Genetic Health Risks (GHR):
The Helix Genetic Health Risk App (HRA) for late-onset Alzheimer's disease is indicated for reporting of the e2/e2, e2/e3, e2/e4 and e4/e4 genotypes in the APOE gene. The report describes if a person's genetic result is associated with an increased or decreased risk of developing late-onset Alzheimer's disease. The e2 and e4 variants included in this report are found and have been studied in many ethnicities. Detailed risk estimates have been studied the most in people of European descent.
The Helix Genetic Health Risk App (HRA) is to be used with the Helix Laboratory Platform.
The Helix Genetic Health Risk App is an over-the-counter (direct-to-consumer), DNA testing service that provides information and tools for consumers to learn about and explore their DNA.
The Helix Genetic Health Risk App is a currently marketed, non-invasive genetic information service that combines qualitative genotyping data indicate for late-onset Alzheimer's disease for reporting of the e2/e2, e2/e3, e2/e4, e3/e3, e3/e4 and e4/e4 genotypes in the APOE gene with descriptive information derived from peer reviewed, published genetic research studies. It is a home use, over-the-counter (direct-to-consumer) DNA testing service intended to provide information and tools for consumers to learn about and explore their DNA. Customer saliva is selfcollected using the FDA cleared Oragene®·Dx OGD-610 saliva collection kit manufactured by DNA Genotek, Inc. (K192920), which consists of a sealable collection tube containing a stabilizing buffer solution. Once the sample is collected, it is shipped to the CLIA-certified and College of American Pathologists (CAP) -accredited Helix laboratory for testing.
DNA is isolated from the saliva and tested using Helix's proprietary whole exome sequencing assay authorized under DEN190035 in the Helix laboratory. The genomic DNA is processed and sequenced using next generation sequencing (NGS) reagents and instrumentation manufactured by Illumina. The sequencing data is analyzed using Helix's proprietary software, where the genetic variants of interest are determined. All samples must pass Helix's stringent quality control metrics prior to analysis. Samples that do not pass quality thresholds will undergo re-sequencing and/or sample re-collection.
The genetic variant results are used to generate personalized reports that provide information about the detected genotype for the customer. These reports tell the user which genotype has/have been detected in their sample and provide information on the risk of disease associated with the genotype. If no genotype was determined, that information is also provided. The personalized reports are designed to present scientific concepts to users in an easy-tounderstand format. The reports provide scientifically valid information about the risks associated with the presence of a particular genetic 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.
N/A
FDA 510(k) Clearance Letter - Helix Genetic Health Risk App for Late-Onset Alzheimer's Disease
Page 1
U.S. Food & Drug Administration
10903 New Hampshire Avenue
Silver Spring, MD 20993
www.fda.gov
Doc ID # 04017.04.20
December 23, 2020
Helix OpCo, LLC
Gloria Lee
Senior Director Regulatory Affairs
96 Colbeck Street
Toronto, M6S1 V2 Ontario Canada
Re: K192073
Trade/Device Name: The Helix Genetic Health Risk app for late-onset Alzheimer's disease
Regulation Number: 21 CFR 866.5950
Regulation Name: Genetic health risk assessment system
Regulatory Class: Class II
Product Code: PTA
Dated: July 31, 2019
Received: August 2, 2019
Dear Gloria Lee:
We have reviewed your Section 510(k) premarket notification of intent to market the device referenced above and have determined the device is substantially equivalent (for the indications for use stated in the enclosure) to legally marketed predicate devices marketed in interstate commerce prior to May 28, 1976, the enactment date of the Medical Device Amendments, or to devices that have been reclassified in accordance with the provisions of the Federal Food, Drug, and Cosmetic Act (Act) that do not require approval of a premarket approval application (PMA). You may, therefore, market the device, subject to the general controls provisions of the Act. Although this letter refers to your product as a device, please be aware that some cleared products may instead be combination products. The 510(k) Premarket Notification Database located at https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfpmn/pmn.cfm identifies combination product submissions. The general controls provisions of the Act include requirements for annual registration, listing of devices, good manufacturing practice, labeling, and prohibitions against misbranding and adulteration. Please note: CDRH does not evaluate information related to contract liability warranties. We remind you, however, that device labeling must be truthful and not misleading.
If your device is classified (see above) into either class II (Special Controls) or class III (PMA), it may be subject to additional controls. Existing major regulations affecting your device can be found in the Code of Federal Regulations, Title 21, Parts 800 to 898. In addition, FDA may publish further announcements concerning your device in the Federal Register.
Please be advised that FDA's issuance of a substantial equivalence determination does not mean that FDA has made a determination that your device complies with other requirements of the Act or any Federal statutes and regulations administered by other Federal agencies. You must comply with all the Act's requirements, including, but not limited to: registration and listing (21 CFR Part 807); labeling (21 CFR Part
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K192073 - Gloria Lee Page 2
801 and Part 809); medical device reporting (reporting of medical device-related adverse events) (21 CFR 803) for devices or postmarketing safety reporting (21 CFR 4, Subpart B) for combination products (see https://www.fda.gov/combination-products/guidance-regulatory-information/postmarketing-safety-reporting-combination-products); good manufacturing practice requirements as set forth in the quality systems (QS) regulation (21 CFR Part 820) for devices or current good manufacturing practices (21 CFR 4, Subpart A) for combination products; and, if applicable, the electronic product radiation control provisions (Sections 531-542 of the Act); 21 CFR 1000-1050.
Also, please note the regulation entitled, "Misbranding by reference to premarket notification" (21 CFR Part 807.97). For questions regarding the reporting of adverse events under the MDR regulation (21 CFR Part 803), please go to https://www.fda.gov/medical-devices/medical-device-safety/medical-device-reporting-mdr-how-report-medical-device-problems.
For comprehensive regulatory information about medical devices and radiation-emitting products, including information about labeling regulations, please see Device Advice (https://www.fda.gov/medical-devices/device-advice-comprehensive-regulatory-assistance) and CDRH Learn (https://www.fda.gov/training-and-continuing-education/cdrh-learn). Additionally, you may contact the Division of Industry and Consumer Education (DICE) to ask a question about a specific regulatory topic. See the DICE website (https://www.fda.gov/medical-devices/device-advice-comprehensive-regulatory-assistance/contact-us-division-industry-and-consumer-education-dice) for more information or contact DICE by email (DICE@fda.hhs.gov) or phone (1-800-638-2041 or 301-796-7100).
Sincerely,
Ying (Katelin) Mao
Branch Chief
Division of Immunology and Hematology Devices
OHT7: Office of In Vitro Diagnostics and Radiological Health
Office of Product Evaluation and Quality
Center for Devices and Radiological Health
Enclosure
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DEPARTMENT OF HEALTH AND HUMAN SERVICES
Food and Drug Administration
Indications for Use
Form Approved: OMB No. 0910-0120
Expiration Date: 06/30/2020
See PRA Statement below.
510(k) Number (if known): K192073
Device Name: Helix Genetic Health Risk App for late-onset Alzheimer's disease
Indications for Use (Describe)
The Helix Genetic Health Risk App (HRA) uses qualitative genotyping to detect clinically relevant variants in genomic DNA isolated from human saliva collected from individuals ≥18 years with Oragene®•Dx OGD-610 for the purpose of reporting and interpreting Genetic Health Risks (GHR):
The Helix Genetic Health Risk App (HRA) for late-onset Alzheimer's disease is indicated for reporting of the e2/e2, e2/e3, e3/e3, e2/e4, e3/e4 and e4/e4 genotypes in the APOE gene. The report describes if a person's genetic result is associated with an increased or decreased risk of developing late-onset Alzheimer's disease. The e2 and e4 variants included in this report are found and have been studied in many ethnicities. Detailed risk estimates have been studied the most in people of European descent.
The Helix Genetic Health Risk App (HRA) is to be used with the Helix Laboratory Platform.
Type of Use (Select one or both, as applicable)
☐ Prescription Use (Part 21 CFR 801 Subpart D) ☑ Over-The-Counter Use (21 CFR 801 Subpart C)
CONTINUE ON A SEPARATE PAGE IF NEEDED.
This section applies only to requirements of the Paperwork Reduction Act of 1995.
DO NOT SEND YOUR COMPLETED FORM TO THE PRA STAFF EMAIL ADDRESS BELOW.
The burden time for this collection of information is estimated to average 79 hours per response, including the time to review instructions, search existing data sources, gather and maintain the data needed and complete and review the collection of information. Send comments regarding this burden estimate or any other aspect of this information collection, including suggestions for reducing this burden, to:
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"An agency may not conduct or sponsor, and a person is not required to respond to, a collection of information unless it displays a currently valid OMB number."
FORM FDA 3881 (7/17) Page 1 of 1
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510(k) SUMMARY
This summary of 510(k) safety and effectiveness information is being submitted in accordance with the requirements of Safe Medical Devices Act of 1990 and 21 CFR 807.92
The assigned 510(k) number is: K192073
Submitter / Company
Helix OpCo LLC (Head Office)
101 S Ellsworth Avenue, Suite 350
San Mateo, CA94401
www.helix.com
Company Contact
Gloria Lee, Ph.D.
Sr. Director Regulatory Affairs
gloria.lee@Helix.com
Phone: 647-248-2577
Date Prepared
December 1, 2020
5.1 Regulatory Information
Table 5.1 Proposed new device
| Type of Submission: | Traditional 510k |
|---|---|
| Common/ Usual Name: | Helix Genetic Health Risk App |
| Regulation Name: | Genetic Health Risk Assessment System |
| Regulation Description: | Genetic health risk assessment system is a qualitative in vitro molecular test that detects variants in genomic DNA isolated from human specimens. This assessment system provides users with a genetic health risk assessment of developing a disease and is intended to inform users of lifestyle choices and/or encourage conversations with a healthcare professional. This assessment system is for over-the-counter use. This device does not determine the person's overall risk of developing a disease. |
| Regulation Number: | 21 CFR 866.5950 |
| Product Code: | PTA |
| Class: | 2 |
Predicate Device: 23andMe PGS Genetic Health Risk Report for Late-onset Alzheimer's Disease
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5.2 Intended Use / Indications for Use
The Helix Genetic Health Risk App (HRA) uses qualitative genotyping to detect clinically relevant variants in genomic DNA isolated from human saliva collected from individuals ≥18 years with Oragene®•Dx OGD-610 for the purpose of reporting and interpreting Genetic Health Risks (GHR):
The Helix Genetic Health Risk App (HRA) for late-onset Alzheimer's disease is indicated for reporting of the e2/e2, e2/e3, e3/e3, e2/e4, e3/e4 and e4/e4 genotypes in the APOE gene. The report describes if a person's genetic result is associated with an increased or decreased risk of developing late-onset Alzheimer's disease. The e2 and e4 variants included in this report are found and have been studied in many ethnicities. Detailed risk estimates have been studied the most in people of European descent.
The Helix Genetic Health Risk App (HRA) is to be used with the Helix Laboratory Platform.
5.4. Substantially Equivalent Predicate Device
See Table 5.2 for list of similarities and differences with the predicate device.
Table 5.2 Substantial Equivalence
| Helix Genetic Health Risk App for late-onset Alzheimer's disease | 23andMe PGS Genetic Health Risk Report for Late-onset Alzheimer's Disease (DEN160026) | Similarities and Differences | |
|---|---|---|---|
| Intended Use / Indications for use | The Helix Genetic Health Risk App (HRA) uses qualitative genotyping to detect clinically relevant variants in genomic DNA isolated from human saliva collected from individuals ≥18 years with Oragene®•Dx OGD-610 for the purpose of reporting and | 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 | Similar |
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| Helix Genetic Health Risk App for late-onset Alzheimer's disease | 23andMe PGS Genetic Health Risk Report for Late-onset Alzheimer's Disease (DEN160026) | Similarities and Differences | |
|---|---|---|---|
| interpreting Genetic Health Risks (GHR): The Helix Genetic Health Risk App (HRA) for late-onset Alzheimer's disease is indicated for reporting of the e2/e2, e2/e3, e3/e3, e2/e4, e3/e4 and e4/e4 genotypes in the APOE gene. The report describes if a person's genetic result is associated with an increased or decreased risk of developing late-onset Alzheimer's disease. The e2 and e4 variants included in this report are found and have been studied in many ethnicities. Detailed risk estimates have been studied the most in people of European descent. The Helix Genetic Health Risk App (HRA) is to be used with the Helix Laboratory Platform. | for the purpose of reporting and interpreting Genetic Health Risks (GHR) The 23andMe PGS Genetic Health Risk Report for Late-onset Alzheimer's Disease is indicated for reporting of the e4 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 e4 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. | ||
| Target Population | ≥ 18 years old | ≥ 18 years old | Similar |
| Interpretation of Results | For over-the-counter use (OTC). Specialized interpretation by a physician not required | For over-the-counter use (OTC). Specialized interpretation by a physician not required | Similar |
| Human Factors | User comprehension testing | User comprehension testing | Similar |
| Compatibility with the environment and other devices | NA - it is a software application to be viewed on a mobile phone or desktop computer | NA - it is a software application to be viewed on a mobile phone or desktop computer | Similar |
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| Helix Genetic Health Risk App for late-onset Alzheimer's disease | 23andMe PGS Genetic Health Risk Report for Late-onset Alzheimer's Disease (DEN160026) | Similarities and Differences | |
|---|---|---|---|
| Design | Software application that includes product information page, e-commerce (registration and order DNA kit), secure login, download genetic report. | Software application that includes product information page, ecommerce (registration and order DNA kit), secure login, download genetic report. | Similar |
| Specimen Collection Kit | DNA Genotek Inc., Oragene®·Dx (OGD-610) | DNA Genotek Inc., Oragene®·Dx (OGD500.001) | Similar |
| Sample matrix | Saliva | Saliva | Similar |
| Variants detected | The APOE e2, e3, and e4 alleles at rs429358 and rs7412 SNPs. rs429358 is a SNP at position chr19::44908684 (GRCh38). rs7412 is a SNP at position chr19:44908822 (GRCh38). | Only reports at APOE e4, and looks at rs429358 SNPs that define APOE e4. The 23andMe PGS Genetic Health Risk Report for Late-onset Alzheimer's Disease only looks at: rs429358 is a SNP at position chr19: NC_000019.10:g.44908684 (GRCh38) | Different |
| Sequencing Platform | Helix Laboratory Platform, sequencing and pipeline analysis (authorized under DEN190035) | Tecan Evo Illumina iScan Illumina Infinium BeadChip genotyping chip customized for the PGS. The chip is designed to detect specific single nucleotide polymorphisms (SNPs) as well as other genetic variants; all markers refer to specific positions in the National Center for Biotechnology Information (NCBI) reference human genome. | Different |
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| Helix Genetic Health Risk App for late-onset Alzheimer's disease | 23andMe PGS Genetic Health Risk Report for Late-onset Alzheimer's Disease (DEN160026) | Similarities and Differences | |
|---|---|---|---|
| Software | Helix Bioinformatics Pipeline (authorized under DEN190035) | Genome Studio Coregen | Different |
| Technology | Next Generation Sequencing | Microarray genotyping | Different |
The Helix Genetic Health Risk App for late-onset Alzheimer's disease is intended for over-the-counter, direct-to-consumer use without prescription or physician order. When a customer purchases the Helix Genetic Health Risk App for late-onset Alzheimer's disease, the customer must first opt-in to receive the late-onset Alzheimer's disease risk report. As instructed in predicate device authorization DEN160026, similar healthcare provider limitations applicable to results for late-onset Alzheimer's disease are included in the package insert:
- This test is not intended to diagnose a disease, determine medical treatment or other medical intervention, or tell the user anything about their current state of health.
- This test is intended to provide users with their genetic information, which may inform health-related lifestyle decisions and conversations with their doctor or other healthcare professional.
- Any diagnostic or treatment decisions must be based on confirmatory prescription testing and/or other information that you determine to be appropriate for your patient, such as additional clinical testing and other risk factors that may affect individual risk and health care.
Thus, the Helix Genetic Health Risk App for late-onset Alzheimer's Disease is substantially equivalent to the predicate 23andMe Personal Genome Service (PGS) Genetic Health Risk Test for Alzheimer's disease authorized under DEN160026.
5.5 Device Description
The Helix Genetic Health Risk App is an over-the-counter (direct-to-consumer), DNA testing service that provides information and tools for consumers to learn about and explore their DNA. The Helix Genetic Health Risk App is a currently marketed, non-invasive genetic information service that combines qualitative genotyping data indicate for late-onset Alzheimer's disease for reporting of the e2/e2, e2/e3, e2/e4, e3/e3, e3/e4 and e4/e4 genotypes in the APOE gene with descriptive information derived from peer reviewed, published genetic research studies. It is a home use, over-the-counter (direct-to-consumer) DNA testing service intended to provide information and tools for consumers to learn about and explore their DNA. Customer saliva is self-collected using the FDA cleared Oragene®·Dx OGD-610 saliva collection kit manufactured by DNA Genotek, Inc. (K192920), which consists of a sealable collection tube containing a stabilizing
Page 9
buffer solution. Once the sample is collected, it is shipped to the CLIA-certified and College of American Pathologists (CAP) -accredited Helix laboratory for testing.
DNA is isolated from the saliva and tested using Helix's proprietary whole exome sequencing assay authorized under DEN190035 in the Helix laboratory. The genomic DNA is processed and sequenced using next generation sequencing (NGS) reagents and instrumentation manufactured by Illumina. The sequencing data is analyzed using Helix's proprietary software, where the genetic variants of interest are determined. All samples must pass Helix's stringent quality control metrics prior to analysis. Samples that do not pass quality thresholds will undergo re-sequencing and/or sample re-collection.
The genetic variant results are used to generate personalized reports that provide information about the detected genotype for the customer. These reports tell the user which genotype has/have been detected in their sample and provide information on the risk of disease associated with the genotype. If no genotype was determined, 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 genetic 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.
5.6 Technological Characteristics
Test Type: Qualitative genetic test for single nucleotide polymorphism detection in the APOE gene.
Sample Type: Genomic DNA obtained from a human saliva sample.
Target of detection: Single-nucleotide polymorphism.
DNA extraction: Automated method.
Gene: APOE
Alleles: e2, e3 and e4 alleles in the APOE gene
SNPs: rs429358 and rs7412.
Testing principle: DNA is isolated from saliva and tested on the Helix Laboratory Platform. The genomic DNA is processed and sequenced using next generation sequencing (NGS) reagents and instrumentation. The sequencing data is analyzed using Helix's proprietary software, where the genetic variants of interest are determined.
Instrument: Illumina HiSeq system.
Assay results: The raw sequencing data is analyzed, and the genotypes are determined and integrated into a report.
5.7 Performance Testing Summary
The laboratory may not be able to process a user's sample. The probability that the laboratory cannot process a sample can be up to 2.5%. The device performance was evaluated in the analytical and clinical studies as follows.
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All results presented below met the pre-defined acceptance criteria outlined in the Special Controls of 21 CFR 866.5950. Information regarding samples that failed quality control (FQC) was also evaluated and presented in each study below.
5.7.1 Method Comparison (Accuracy)
For evaluation of accuracy, three studies were conducted: the first study was conducted with human saliva samples with known genotypes and a second study was conducted with human cell line samples with known genotypes to determine the rates of correct APOE genotype calls. A third study was conducted with human saliva and/or human cell line samples with known variants in genes other than the APOE gene to determine the agreement of the genotype calls.
a) Accuracy study with human saliva samples:
Accuracy of the HRA for late-onset Alzheimer's disease was evaluated by testing human saliva samples with known APOE genotypes. Presence of the two variants in the APOE gene was analyzed on the HLP and the genotyping results were compared to the known genotypes confirmed by Sanger sequencing (comparator). The accuracy for detecting the two variants in the APOE gene on the HLP (genotype call) using DNA isolated from human saliva samples (n=99) was 100% with a lower bound of 96.3% using a 95% CI for all samples tested. The test results are shown in the table below.
| APOE Genotype | N | No. of Correct Genotype Calls | No. of Incorrect Genotype Calls | No. of FQC | Percent of FQC (%) | Percent Correct Genotype Calls (%) |
|---|---|---|---|---|---|---|
| e2/e2 | 12 | 12 | 0 | 0 | 0 | 100 |
| e2/e3 | 17 | 17 | 0 | 0 | 0 | 100 |
| e2/e4 | 10 | 10 | 0 | 0 | 0 | 100 |
| e3/e3 | 20 | 20 | 0 | 0 | 0 | 100 |
| e3/e4 | 20 | 20 | 0 | 0 | 0 | 100 |
| e4/e4 | 20 | 20 | 0 | 0 | 0 | 100 |
| All | 99 | 99 | 0 | 0 | 0 | 100 |
b) Accuracy study with human cell line samples:
Accuracy for detecting two variants, rs7412 and rs429358, in the APOE gene on the HLP was evaluated by using six cell lines with known APOE genotypes
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(e2/e3, e2/e4, e3/e3, e3/e4, e3/e4, and e4/e4). The accuracy of detecting the two variants in the APOE gene was 100% for all samples tested.
| Cell Line | N | APOE Genotype | No. of replicates | No. of Correct Genotype Calls | No. of Incorrect Genotype Calls | No. of FQC | Percent of FQC (%) | Percent Correct Genotype Calls (%) |
|---|---|---|---|---|---|---|---|---|
| NA24385 | 1 | e2/e3 | 1 | 1 | 0 | 0 | 0 | 100 |
| NA24149 | 1 | e2/e4 | 1 | 1 | 0 | 0 | 0 | 100 |
| NA12878 | 1 | e3/e3 | 1 | 1 | 0 | 0 | 0 | 100 |
| NA12877 | 1 | e3/e4 | 1 | 1 | 0 | 0 | 0 | 100 |
| NA24143 | 1 | e3/e4 | 1 | 1 | 0 | 0 | 0 | 100 |
| NA24631 | 1 | e4/e4 | 1 | 1 | 0 | 0 | 0 | 100 |
c) Accuracy study with 3,295 human saliva and cell line samples with known variants in genes other than APOE:
In addition to the two variants in the APOE gene, accuracy of the HLP for detecting variants in the genes associated with other clinical conditions included in DEN160026 was evaluated on the HLP using specimens carrying unique genetic variants linked to the specific clinical conditions as listed in the table below:
| Clinical condition | Gene | SNP |
|---|---|---|
| Hereditary Thrombophilia | FS | rs6025 |
| Hereditary Thrombophilia | F2 | rs1799963 |
| Alpha-1 Antitrypsin Deficiency | SERPINA1 | rs28929474 |
| Alpha-1 Antitrypsin Deficiency | SERPINA1 | rs17580 |
| Late-Onset Alzheimer's Disease | APOE | rs429358 |
| Parkinson's Disease | LRRK2 | rs34637584 |
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| Clinical condition | Gene | SNP |
|---|---|---|
| Parkinson's Disease; Gaucher Disease Type 1 | GBA | rs76763715 |
| Gaucher Disease Type 1 | GBA | rs387906315 |
| Gaucher Disease Type 1 | GBA | rs80356769 |
| Factor XI Deficiency | FXI | rs121965064 |
| Factor XI Deficiency | FXI | rs121965063 |
| Factor XI Deficiency | FXI | rs373297713 |
| Celiac Disease | HLA-DQA1 | rs2187668 |
| Glucose-6-Phosphate-Dehydrogenase Deficiency | G6PD | rs1050828 |
| Hereditary Hemochromatosis | HFE | rs1800562 |
| Hereditary Hemochromatosis | HFE | rs1799945 |
| Early-Onset Primary Dystonia | DYT1 | rs724159981 |
The overall number of true positive, false positives, true negative and false negatives were analyzed for seventeen (17) variants in eleven (11) genes. A total of 4,282 true positive and 51,731 true negative calls were reported. There were no false positive and no false negative results reported for the known variants tested. One no call was reported each for rs76763715 and rs429358.
5.7.2 Precision/Reproducibility
Reproducibility of the APOE genotype calls made by the HRA for late-onset Alzheimer's disease was assessed by testing 24 samples that include 6 human B-lymphocyte cell lines (6 cell lines hereafter) and 18 unique saliva-derived DNA samples) in two independent studies (Study 1 and Study 2). The calls for the APOE genotypes in the well-characterized cell line samples were compared to known APOE genotypes.
Study 1 tested 24 samples (6 cell lines and 18 unique saliva-derived DNA samples) with up to 72 replicates (3 replicates / sample / library prep plate x 3 plates x 2 enrichments x 4 independent runs of cBot and HiSeq instruments) for the APOE genotype calls. The test results are summarized below:
| Cell Line | N | APOE Genotype | No. of replicates | No. of Correct Genotype Calls | No. of Incorrect Genotype Calls | No. of FQC | Percent of FQC (%) | Percent Correct Genotype Calls (%) |
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Study 1: Cell lines
| Cell Line | N | APOE Genotype | No. of replicates | No. of Correct Genotype Calls | No. of Incorrect Genotype Calls | No. of FQC | Percent of FQC (%) | Percent Correct Genotype Calls (%) |
|---|---|---|---|---|---|---|---|---|
| NA24385 | 1 | e2/e3 | 72 | 72 | 0 | 0 | 0 | 100 |
| NA24149 | 1 | e2/e4 | 72 | 72 | 0 | 0 | 0 | 100 |
| NA12878 | 1 | e3/e3 | 72 | 72 | 0 | 0 | 0 | 100 |
| NA12877 | 1 | e3/e4 | 72 | 72 | 0 | 0 | 0 | 100 |
| NA24143 | 1 | e3/e4 | 72 | 72 | 0 | 0 | 0 | 100 |
| NA24631 | 1 | e4/e4 | 72 | 72 | 0 | 0 | 0 | 100 |
Study 1: Clinical Samples
| 4 | e2/e3 | 288 | 276 | 0 | 12 | 4.2 | 100 | |
| 2 | e2/e4 | 144 | 141 | 0 | 3 | 2.1 | 100 | |
| 7 | e3/e3 | 504 | 484 | 0 | 20 | 4.0 | 100 | |
| 2 | e3/e4 | 144 | 136 | 0 | 8 | 5.6 | 100 | |
| 2 | e4/e4 | 144 | 141 | 0 | 3 | 2.1 | 100 | |
| 1 | Unknown | 72 | N/A | N/A | 72 | 100 | N/A |
Study 2 tested 24 samples (6 cell lines and 18 unique saliva-derived DNA samples) with up to 54 replicates (3 replicates / sample / library prep plate x 3 plates x 2 enrichments x 3 reagent lots) for the APOE genotype calls. The test results are summarized below:
| Cell Line | N | APOE Genotype | No. of replicates | No. of Correct Genotype Calls | No. of Incorrect Genotype Calls | No. of FQC | Percent of FQC (%) | Percent Correct Genotype Calls (%) |
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Study 2: Cell lines
| Cell Line | N | APOE Genotype | No. of replicates | No. of Correct Genotype Calls | No. of Incorrect Genotype Calls | No. of FQC | Percent of FQC (%) | Percent Correct Genotype Calls (%) |
|---|---|---|---|---|---|---|---|---|
| NA24385 | 1 | e2/e3 | 54 | 54 | 0 | 0 | 0 | 100 |
| NA24149 | 1 | e2/e4 | 54 | 54 | 0 | 0 | 0 | 100 |
| NA12878 | 1 | e3/e3 | 54 | 54 | 0 | 0 | 0 | 100 |
| NA12877 | 1 | e3/e4 | 54 | 54 | 0 | 0 | 0 | 100 |
| NA24143 | 1 | e3/e4 | 54 | 54 | 0 | 0 | 0 | 100 |
| NA24631 | 1 | e4/e4 | 54 | 48 | 0 | 6 | 11.1 | 100 |
Study 2: Clinical Samples
| 2 | e2/e3 | 108 | 108 | 0 | 0 | 0 | 100 | |
| 7 | e3/e3 | 378 | 377 | 0 | 1 | 0.3 | 100 | |
| 7 | e3/e4 | 378 | 376 | 0 | 2 | 0.5 | 100 | |
| 2 | e4/e4 | 108 | 108 | 0 | 0 | 0 | 100 |
The calls for concordance on the APOE genotypes were analyzed in the clinical samples. Genotyping results produced 100% replicates that were called correctly for all APOE genotypes.
5.7.3 DNA Input
This study evaluated the impact of different levels of DNA input on the performance of the HRA for late-onset Alzheimer's disease. The study yielded concordant test results for all 19 saliva samples with known APOE genotypes when tested at sample DNA concentrations between 3.5 to 10 ng/µL, an input corresponding to a range of 35 to 100 ng of DNA in the library preparation.
| APOE Genotype | No. of replicates | No. of Correct Genotype Calls | No. of Incorrect Genotype Calls | No. of FQC | Percent of FQC (%) | Percent Correct Genotype Calls (%) |
|---|---|---|---|---|---|---|
| e2/e3 | 12 | 12 | 0 | 0 | 0 | 100 |
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| APOE Genotype | No. of replicates | No. of Correct Genotype Calls | No. of Incorrect Genotype Calls | No. of FQC | Percent of FQC (%) | Percent Correct Genotype Calls (%) |
|---|---|---|---|---|---|---|
| e3/e3 | 84 | 79 | 0 | 5 | 6 | 100 |
| e3/e4 | 18 | 18 | 0 | 0 | 0 | 100 |
5.7.4 Interfering Substances
Four studies were performed to determine the effects of substances found in saliva that may interfere with the performance of the HRA for late-onset Alzheimer's disease. Per study protocol, for sequenced samples to be included in the data analyses (e.g., evaluable samples), the sample(s) must pass pre-defined QC thresholds.
a. In study 1, four endogenous proteins commonly found in saliva, including alpha-amylase (395 U/mL), hemoglobin (20 mg/mL), immunoglobulin A (IgA) (0.43 mg/mL), and albumin (2.67mg/mL) were each added to saliva samples. These proteins did not affect test performance for saliva samples (n=29-30 evaluable samples across four endogenous proteins). The test results are shown below.
| APOE Genotype | No. of replicates | No. of Correct Genotype Calls | No. of Incorrect Genotype Calls | No. of FQC | Percent of FQC (%) | Percent Correct Genotype (%) |
|---|---|---|---|---|---|---|
| e2/e3 | 18 | 18 | 0 | 0 | 0 | 100 |
| e2/e4 | 4 | 4 | 0 | 0 | 0 | 100 |
| e3/e3 | 76 | 75 | 0 | 1 | 1.3 | 100 |
| e3/e4 | 18 | 18 | 0 | 0 | 0 | 100 |
| e4/e4 | 4 | 4 | 0 | 0 | 0 | 100 |
b. In study 2, saliva samples were tested before and after (either immediately or 30 minutes after) exposure to one of four exogenous substances: eating food, drinking liquids, using mouthwash, or chewing gum. This study showed that exogenous substances did not interfere with test performance for saliva samples (n=12-15 evaluable samples across testing time for four exogenous substances). The test results are shown below.
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| APOE Genotype | No. of replicates | No. of Correct Genotype Calls | No. of Incorrect Genotype Calls | No. of FQC | Percent of FQC (%) | Percent Correct Genotype Calls (%) |
|---|---|---|---|---|---|---|
| e2/e4 | 12 | 12 | 0 | 0 | 0 | 100 |
| e3/e3 | 90 | 83 | 0 | 7 | 7.8 | 100 |
| e3/e4 | 24 | 21 | 0 | 3 | 12.5 | 100 |
| Unknown | 6 | N/A | N/A | 6 | 100 | N/A |
c. In study 3, saliva samples were tested at 60 minutes before smoking, immediately after smoking, and 30 minutes after smoking and showed that smoking did not interfere with test performance (n=15 evaluable samples across three smoking conditions). The test results are shown below.
| APOE Genotype | No. of replicates | No. of Correct Genotype Calls | No. of Incorrect Genotype Calls | No. of FQC | Percent of FQC (%) | Percent Correct Genotype Calls (%) |
|---|---|---|---|---|---|---|
| e3/e3 | 18 | 18 | 0 | 0 | 0 | 100 |
| e3/e4 | 12 | 12 | 0 | 0 | 0 | 100 |
d. In study 4, bacterial DNA from a commercial source (American Type Culture Collection) was added in various amounts into six cell line DNA samples (NA24385, NA24149, NA12878, NA12877, NA24143, and NA24631) to evaluate the effects of bacterial contamination in the test performance. This bacterial sample (ATCC MSA-1003) is comprised of twenty (20) fully sequenced cultures that encompass a variety of characteristics including bacterial species found in mouse and oral cavity. The six cell lines were tested across five levels of bacterial content (0%, 10%, 20%, 30%, and 50%). This study showed that microbial DNA did not interfere with test performance (n=11-18 evaluable samples across five levels of bacterial content). In addition, study 4 tested various amounts of microbial and yeast DNA added to the saliva samples from 3 volunteers (0%, 10% Candida albicans, and 30% of ATCC MSA-1003). This study showed that yeast DNA did not interfere with test performance in clinical samples. The test results are shown below.
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| APOE Genotype | No. of replicates | No. of Correct Genotype Calls | No. of Incorrect Genotype Calls | No. of FQC | Percent of FQC (%) | Percent Correct Genotype Calls (%) |
|---|---|---|---|---|---|---|
| Cell lines | ||||||
| e2/e3 | 15 | 15 | 0 | 0 | 0 | 100 |
| e2/e4 | 15 | 13 | 0 | 2 | 13.3 | 100 |
| e3/e3 | 15 | 11 | 0 | 4 | 26.7 | 100 |
| e3/e4 | 30 | 28 | 0 | 2 | 6.7 | 100 |
| e4/e4 | 15 | 14 | 0 | 1 | 6.7 | 100 |
| Clinical samples | ||||||
| e3/e3 | 12 | 12 | 0 | 0 | 0 | 100 |
| e3/e4 | 6 | 6 | 0 | 0 | 0 | 100 |
5.7.5 Potentially Interfering Mutations
Not conducted
5.7.6 Matrix Comparison
Human saliva is the only suitable sample matrix, therefore Matrix Comparison studies are not applicable.
5.7.7 Shelf Life
The Helix Genetic Health Risk App requires the use of the same FDA-cleared saliva collection device that was reviewed and cleared in submission K192920. Shelf life data, summarized below, was previously reviewed and authorized in the clearance of the predicate device DEN160026.
5.7.8 Clinical Performance
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Three common versions of the APOE gene are: e2, e3, and e4 alleles. Genetic studies on late-onset Alzheimer's disease have associated this disease with the APOE gene and more specifically the APOE e2 and APOE e4 allele, as the main link for late-onset Alzheimer's disease in all ethnicities. The APOE e2 allele is associated with a decreased risk to develop late-onset Alzheimer's disease after the age of 65 years, whereas the APOE e4 allele is associated with an increased risk to develop late-onset Alzheimer's disease after the age of 65 years. This test looks at the 2 SNPs, rs429358 and rs7412, that define the APOE e2, e3, and e4 versions of the gene.
The different combinations of the APOE gene's versions (e2, e3 and e4) were grouped based on their association with developing late-onset Alzheimer's disease:
- Individuals with the APOE e3/e3 genotype are considered to have an average risk of developing late-onset Alzheimer's disease based on this genetic result.
- Individuals with the APOE e2/e2 or e2/e3 genotype are considered to have a decreased risk of developing late-onset Alzheimer's disease compared to individuals with the APOE e3/e3 genotype.
- Individuals with the APOE e2/e4, e3/e4, or e4/e4 genotypes are considered to have an increased risk of developing late-onset Alzheimer's disease compared to individuals with the APOE e3/e3 genotype.
- Individuals who have none of these APOE combinations will not receive information on their relative risk to develop late-onset Alzheimer's disease due to the lack of studies in the scientific literature.
The variants covered by this test are found in people of all ethnicities. The percentage of the population carrying each combination will vary from study to study based on the enrollment criteria to the genetic study. A summary of the frequency of each combination in different ethnicities gathered from multiple references is represented in the table below:
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Table 5.3a. Frequency of APOE e2, e3 and e4 combinations in different ethnicities
| e2/e2 | e2/e3 | e3/e3 | e2/e4 | e3/e4 | e4/e4 | Ref | |
|---|---|---|---|---|---|---|---|
| Decreased risk | Average risk | Increased risk | |||||
| European descent AD | 0.2% | 4.8% | 36.4% | 2.6% | 41.1% | 14.8% | Farrer et al., 1997 |
| European descent controls | 0.8% | 12.7% | 60.9% | 2.6% | 21.3% | 1.8% | |
| African descent AD | 0.6% | 7.4% | 37.7% | 3.7% | 37.7% | 13.0% | Murrell et al., 2006 |
| African descent controls | 1.9% | 15.1% | 51.3% | 4.1% | 24.2% | 3.5% | |
| South Asian descent AD | 0.2% | 6.2% | 44.8% | 6.2% | 37.2% | 5.3% | Agarwal et al., 2014 |
| South Asian descent controls | 2.0% | 11.8% | 72.0% | 1.5% | 11.7% | 0.9% | |
| East Asian descent AD | 0.9% | 7.9% | 51.0% | 3.3% | 29.3% | 7.6% | Liu et al., 2014 |
| East Asian descent controls | 0.8% | 11.8% | 73.1% | 1.7% | 12.4% | 0.3% |
AD = Alzheimer's disease.
Using the same references, it is possible to calculate likelihood ratios (LR), which represent an estimate of how the test result affects the chances of a condition.
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Table 5.3b: Alzheimer's disease likelihood ratios (LR) for APOE e2, e3 and e4 combinations in different ethnicities. The table was adapted from table on p.35 of DEN160026 decision summary.
| Ethnicity | Test result | Genotype | LR | 95% CI for LR | References | Study summary |
|---|---|---|---|---|---|---|
| European descent | Decreased risk | e2/e2 | 0.3 | 0.1-0.5 | Farrer et al., 1997 | A meta-analysis of 5,930 patients who met criteria for probable or definite Alzheimer's disease and 8,607 controls. Among study participants, there were 5,107 Alzheimer's disease patients from European descent, and 6,262 controls from European descent. |
| e2/e3 | 0.4 | 0.3-0.4 | ||||
| Average risk | e3/e3 | 0.6 | 0.57-0.62 | |||
| Increased risk | e2/e4 | 1 | 0.8-1.3 | |||
| e3/e4 | 1.9 | 1.8-2.1 | ||||
| e4/e4 | 8.2 | 6.8-10.0 | ||||
| African descent | Decreased risk | e2/e2 | 0.3 | 0.04-2.7 | Murrell et al., 2006 | This study included 162 individuals from African American descent with Alzheimer's disease and 318 controls from African American descent |
| e2/e3 | 0.5 | 0.3-0.9 | ||||
| Average risk | e3/e3 | 0.7 | 0.6-0.9 | |||
| Increased risk | e2/e4 | 0.9 | 0.4-2.3 | |||
| e3/e4 | 1.6 | 1.2-2.1 | ||||
| e4/e4 | 3.8 | 1.9-7.6 |
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| Ethnicity | Test result | Genotype | LR | 95% CI for LR | References | Study summary |
|---|---|---|---|---|---|---|
| South Asian descent | Decreased risk | e2/e2 | 0.1 | 0.02-0.9 | Agarwal et al., 2014 | A meta-analysis of 417 individuals from South Asian descent with Alzheimer's disease and 651 controls from South Asian descent. |
| e2/e3 | 0.5 | 0.3-0.8 | ||||
| Average risk | e3/e3 | 0.6 | 0.6-0.7 | |||
| Increased risk | e2/e4 | 4.1 | 2.0-8.3 | |||
| e3/e4 | 3.2 | 2.5-4.1 | ||||
| e4/e4 | 5.7 | 2.3-14.0 | ||||
| East Asian descent | Average risk | e2/e2* | 1.1 | 0.5-2.3 | Liu et al., 2014 | A meta-analysis of 1,576 individuals from East Asian descent with Alzheimer's disease and 1,741 controls from East Asian descent. (*limited number of e2/e2 samples used for analysis) |
| e2/e3 | 0.7 | 0.5-0.8 | ||||
| e3/e3 | 0.7 | 0.6-0.7 | ||||
| Increased risk | e2/e4 | 1.9 | 1.2-3.0 | |||
| e3/e4 | 2.5 | 2.2-2.9 | ||||
| e4/e4 | 25.6 | 10.5-62.6 |
5.7.9 Labeling Comprehension
All predefined demographic quotas and enrollment targets were met. Primary comprehension assessment addressed the following five core concepts: purpose of the test, limitations, relevant ethnicities, meaning of results, and appropriate follow-up. The average comprehension rate per comprehension category ranged from 85.2% to 100%, and the overall comprehension rate for all core concepts across each of the four study arms was greater than 90%. The representative Helix Genetic Health Risk report and supporting information provided in the pre-purchase page were effective in communicating relevant concepts to users unfamiliar with genetic testing sufficient for the safe use of the Helix Genetic Health Risk App for late-onset Alzheimer's disease.
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5.8. Discussion
The Helix Genetic Health Risk App (HRA) for late-onset Alzheimer's disease has a similar intended use as the predicate and therefore presents no new issues of safety or effectiveness when compared to the previously authorized predicate device (DEN160026).
5.9. Conclusion
The Helix Genetic Health Risk App (HRA) for late-onset Alzheimer's disease is substantially equivalent to the predicate device DEN160026 (23andMe PGS Genetic Health Risk Report for Late-onset Alzheimer's Disease). As presented, the Helix Genetic Health Risk App for late-onset Alzheimer's disease is a safe and effective consumer product that can safely and effectively assist and encourage users to discuss the report with their healthcare provider.
§ 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