(300 days)
The AncestryDNA Saliva Collection Kit is intended for use in the noninvasive collection of saliva samples for in vitro diagnostic testing of human DNA. Saliva may be collected by spitting directly into the AncestryDNA Saliva Collection Kit by a lay user. Saliva samples collected using the AncestryDNA Saliva Collection Kit are stabilized and isolated for use with over-the-counter AncestryDNA Genetic Health Risk Tests. Saliva samples collected using the AncestryDNA Saliva Collection Kit can be transported and/or stored long term at ambient conditions.
The AncestryDNA Saliva Collection Kit consists of: saliva collection tube, funnel, cap, blister pack, collection bag with absorbent pad, return mailer, and Instructions for Use. The collection device consists of the saliva collection tube, funnel, and cap. The cap contains DNA stabilization solution. Saliva is delivered directly by spitting into the collection tube via the funnel. Once the user has provided the saliva sample, s/he removes the funnel from the saliva collection tube and affixes the cap. Affixing the cap by screwing on releases the stabilization solution. The user is then instructed to shake the tube for at least five seconds to mix the saliva sample with the stabilization solution. After collecting the saliva sample, the user places the closed saliva collection tube in the collection bag. The collection bag with the enclosed saliva collection tube is shipped to a designated Ancestry Genomics location for testing via the pre-addressed postage paid return mailer.
Acceptance Criteria for the AncestryDNA Saliva Collection Kit and Supporting Study
The AncestryDNA Saliva Collection Kit is intended for non-invasive collection, stabilization, transportation, and long-term storage of saliva samples for in vitro diagnostic testing of human DNA, specifically for use with the AncestryDNA Factor V Leiden Genetic Health Risk Test. The following acceptance criteria were established and demonstrated through analytical and user studies.
1. Table of Acceptance Criteria and Reported Device Performance
| Acceptance Criteria Category | Specific Criteria | Reported Device Performance |
|---|---|---|
| Analytical Performance | ||
| Reproducibility/Precision | Overall precision and per genotype point estimate > 99% agreement for genotyping with true variant status. | Lab 1: Overall Percent Agreement (OPA) = 100.00% (95% CI: 99.79 – 100.00%) Lab 2: OPA = 100.00% (95% CI: 99.41 – 100.00%) All operator teams combined: OPA = 100.00% (95% CI: 99.84 – 100.00%) All AncestryDNA SCK lot combinations combined: OPA = 100.00% (95% CI: 99.84 – 100.00%) Within-run repeatability: OPA = 100.00% (95% CI: 92.13 – 100.00%) Inter-lab data at Lab 1 & 2: OPA = 100.00% (95% CI: 95.55 – 100.00%) All "GG", "GA", "AA" genotypes: OPA = 100.00% (95% CI: 99.53 – 100.00%) |
| Analytical Sensitivity (LoD) | Lowest DNA concentration at which at least 95% of samples yielded the correct call. Concentrations between LoD and upper limit should produce genotypes concordant with bidirectional sequencing. | Limit of Detection (LoD): 1.53 ng/uL. Upper limit of concentration: 50 ng/uL. All genotyping attempts on samples with call rates ≥ 98% and concentrations between 1.53 ng/uL and 50 ng/uL produced genotypes 100% concordant with bidirectional sequencing. |
| Interfering Substances | ≥ 95% agreement with true variant status as determined by bi-directional sequencing for samples with endogenous, exogenous, and microbial interferents. | Endogenous Interference: 100% OPA for all tested interferents (PBS, Salivary α-amylase, Hemoglobin, IgA, Total Protein). Exogenous Interference: 100% OPA for all tested interferents (Chicken, Alcohol, Mouthwash, Beef, Gum, Smoking) at various time points, where QC passed. Microbial Interference: 100% OPA for all tested microbial interferents (S. epidermis, S. mutans, L. casei, A. odontolyticus, C. albicans) at low/normal and high concentrations. |
| Sample Volume Tolerance | For all samples that passed quality control for each collection volume (under-filled, normally filled, over-filled), ≥ 95% agreement with true variant status. | 100% OPA for all fill volumes (control, under, over) and all genotypes (Wild Type, Heterozygous, Variant). |
| Specimen Stability | Post-collection samples stored at 15°C to 30°C for up to 12 months should maintain performance. Transport at temperatures ranging from -29°C to 50°C and up to 85% RH should not impact performance. | Demonstrated through testing that post-collection samples can be stored at 15°C to 30°C for up to 12 months and transported at -29°C to 50°C and up to 85% RH while maintaining DNA integrity for genotyping. |
| Method Comparison | ||
| Accuracy (vs. Predicate) | > 99% agreement with true variant determination overall and per genotype tested, when comparing against bi-directional sequencing. | Overall Percent Agreement: 100% (95% CI: 98.2–100%) for all genotypes (GG, GA, AA) combined. Per Genotype: GG (100%, 94.8–100%), GA (100%, 94.5–100%), AA (100%, 94.4–100%). 100% concordance with true variant status for all 198 samples that passed QC. |
| Clinical Studies | ||
| User Comprehension | Flesch-Kincaid reading level of instructions for use shall meet or exceed the 8th grade threshold. High user satisfaction and understanding of instructions. Sufficient viable DNA yield from lay user collected samples. | Flesch-Kincaid reading level: 6.0 (total SCK instructions), 7.1 (text alone). This met the ≥ 8th grade threshold. Viable DNA yield: 257 out of 271 (94.8%) submitted saliva samples passed all three evaluated failure points and had a sample call rate of ≥ 98%. User feedback: 98.1% rated overall usability as somewhat easy or higher; 99.2% rated kit instructions as somewhat easy to understand or better; 98.1% indicated instructions were somewhat easy to follow or better; 99.6% found illustrations helpful. |
2. Sample Size Used for the Test Set and Data Provenance
The primary test set for demonstrating accuracy (Method Comparison) involved 209 donors (200 initial + 9 alternate).
Data Provenance: The study was conducted by a CLIA-certified laboratory (Ancestry Genomics' designated location) on collected saliva samples. The bi-directional sequencing for ground truth was performed by a third-party laboratory. The country of origin of the data is not explicitly stated, but the submission is to the U.S. FDA, suggesting the data is likely from the U.S. (or at least collected with U.S. regulatory oversight in mind). The study appears to be prospective as samples were collected specifically for the purpose of the study and then processed.
3. Number of Experts Used to Establish the Ground Truth for the Test Set and Their Qualifications
The ground truth for the test set (Factor V Leiden genotypes) was established using bi-directional sequencing analysis performed by a third-party laboratory. The document does not specify the number of individual experts (e.g., geneticists or laboratory personnel) involved in interpreting the sequencing results, nor their specific qualifications (e.g., years of experience). However, the use of "bi-directional sequencing" by a "third-party laboratory" implies a robust and standard method for genotype determination.
4. Adjudication Method for the Test Set
The document does not describe an adjudication method involving multiple human readers for discrepancies in the ground truth for the test set. The ground truth (true variant status) was determined solely by bi-directional sequencing.
5. If a Multi-Reader Multi-Case (MRMC) Comparative Effectiveness Study Was Done
No, an MRMC comparative effectiveness study was not conducted. This device is a saliva collection kit, and the performance evaluation focuses on the analytical accuracy of DNA collection and subsequent genotyping, not on human interpretation of images or other data where AI might assist.
6. If a Standalone Study Was Done
Yes, a standalone performance study was done for the AncestryDNA Factor V Leiden GHR Test in combination with the AncestryDNA Saliva Collection Kit. The reported performance metrics (reproducibility, analytical sensitivity, interference, sample volume tolerance, and accuracy) directly reflect the algorithm's (genotyping test's) ability to correctly identify genotypes from samples collected by the device, without human intervention in the genotype determination process itself. The user comprehension study also evaluated the standalone usability of the collection kit by lay users.
7. The Type of Ground Truth Used
The ground truth used for determining the true variant status of the Factor V Leiden genotype was bi-directional sequencing. This is considered a gold standard method for confirming genetic sequences.
8. The Sample Size for the Training Set
The document does not provide information regarding a specific "training set" sample size for the AncestryDNA Factor V Leiden GHR Test algorithm. It describes analytical and clinical validation studies for the device and its compatibility with the GHR test. Since this is for a collection kit and an established genotyping method (Illumina Infinium array platform), it's less likely to involve a distinct "training set" in the same way machine learning models typically do for image analysis, for example. The genotyping methodology itself has inherent validation processes, and the studies here validate the use of the collection kit with that methodology.
9. How the Ground Truth for the Training Set Was Established
As a specific "training set" is not explicitly mentioned or relevant in the common AI/ML sense for this type of device (a collection kit and a genotyping test on an array platform), the method for establishing ground truth for a training set is not applicable and therefore not described in the document.
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Image /page/0/Picture/0 description: The image shows the logo of the U.S. Food and Drug Administration (FDA). The logo consists of two parts: the Department of Health & Human Services logo on the left and the FDA logo on the right. The FDA logo is a blue square with the letters "FDA" in white, followed by the words "U.S. FOOD & DRUG ADMINISTRATION" in blue.
August 13, 2020
Ancestry Genomics, Inc. Raajdeep Venkatesan Vice President of Regulatory Affairs & Quality Assurance 153 Townsend Street. Suite 800 San Francisco, CA 94107
Re: K192947
Trade/Device Name: AncestryDNA Saliva Collection Kit Regulation Number: 21 CFR 862.1675 Regulation Name: Blood specimen collection device Regulatory Class: Class II Product Code: OYJ Dated: July 17, 2020 Received: July 20, 2020
Dear Raajdeep Venkatesan:
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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801 and Part 809); medical device 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-reportingcombination-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-device-safety/medical-device-reportingmdr-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/medicaldevices/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-device-advice-comprehensive-regulatoryassistance/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,
Marianela Perez-Torres, Ph.D. Acting Deputy Director Division of Chemistry and Toxicology 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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Indications for Use
510(k) Number (if known) K192947
Device Name AncestryDNA Saliva Collection Kit
Indications for Use (Describe)
The AncestryDNA Saliva Collection Kit is intended for use in the noninvasive collection of saliva samples for in vitro diagnostic testing of human DNA. Saliva may be collected by spitting directly into the AncestryDNA Saliva Collection Kit by a lay user. Saliva samples collected using the AncestryDNA Saliva Collection Kit are stabilized and isolated for use with over-the-counter AncestryDNA Genetic Health Risk Tests. Saliva samples collected using the AncestryDNA Saliva Collection Kit can be transported and/or stored long term at ambient conditions.
| Type of Use (Select one or both, as applicable) |
|---|
| ------------------------------------------------- |
| | Prescription Use (Part 21 CFR 801 Subpart D)
|X | Over-The-Counter Use (21 CFR 801 Subpart C)
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510(K) SUMMARY
A. GENERAL INFORMATION
| Date Prepared: | August 7, 2020 |
|---|---|
| Submitter Information: | |
| Submitted By: | Ancestry Genomics, Inc.153 Townsend Street, Suite 800San Francisco, CA 94107 |
| Contact Person: | Raajdeep Venkatesan, MS, RAC, CMQ-OE, CBA, CQEVice President of RA/QAAncestry Genomics, Inc.Phone: (415) 795-6110 |
| Alternate Contact Person: | Julie WoodDirector, QualityAncestry Genomics, Inc.Phone: (415) 795-6000 |
B. PURPOSE FOR SUBMISSION
To obtain a substantial equivalence determination for the AncestryDNA Saliva Collection Kit for use in the noninvasive collection of saliva samples. DNA from the saliva sample is isolated, stabilized and suitable for over-the-counter use with the AncestryDNA Factor V Leiden Genetic Health Risk Test.
C. MEASURAND
Not applicable.
D. TYPE OF TEST
Collection and stabilization of genomic DNA from saliva for use in molecular genotyping testing
E. APPLICANT
Ancestry Genomics, Inc.
F. PROPRIETARY AND ESTABLISHED NAMES
AncestryDNA Saliva Collection Kit
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G. REGULATORY INFORMATION
| Trade Name: | AncestryDNA Saliva Collection Kit |
|---|---|
| Classification: | Class II |
| Regulation Number | 21 CFR 862.1675 |
| Device Classification Name: | DNA Specimen Collection, Saliva |
| Product Code: | OYJ |
| Panel: | Clinical Chemistry |
H. INTENDED USE
-
- Intended Use:
See Indications for Use below.
- Intended Use:
-
- Indications for Use:
The AncestryDNA Saliva Collection Kit is intended for use in the noninvasive collection of saliva samples for in vitro diagnostic testing of human DNA. Saliva may be collected by spitting directly into the AncestryDNA Saliva Collection Kit by a lay user. Saliva samples collected using the AncestryDNA Saliva Collection Kit are stabilized and isolated for use with over-the-counter AncestryDNA Genetic Health Risk Tests. Saliva samples collected using the AncestryDNA Saliva Collection Kit can be transported and/or stored long term at ambient conditions.
- Indications for Use:
-
- Special Conditions for Use:
For over-the-counter use.
- Special Conditions for Use:
AncestryDNA Saliva Collection Kit is for use with AncestryDNA Factor V Leiden Genetic Health Risk Test.
AncestryDNA Saliva Collection Kit is only for use in adults 18 years of age and older.
-
- Special Instrument Requirements:
None.
- Special Instrument Requirements:
I. DEVICE DESCRIPTION
The AncestryDNA Saliva Collection Kit consists of: saliva collection tube, funnel, cap, blister pack, collection bag with absorbent pad, return mailer, and Instructions for Use. The collection device consists of the saliva collection tube, funnel, and cap. The cap contains DNA stabilization solution. Saliva is delivered directly by spitting into the collection tube via the funnel. Once the user has provided the saliva sample, s/he removes the funnel from the saliva collection tube and affixes the cap. Affixing the cap by screwing on releases the
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stabilization solution. The user is then instructed to shake the tube for at least five seconds to mix the saliva sample with the stabilization solution. After collecting the saliva sample, the user places the closed saliva collection tube in the collection bag. The collection bag with the enclosed saliva collection tube is shipped to a designated Ancestry Genomics location for testing via the pre-addressed postage paid return mailer.
J. SUBSTANTIAL EQUIVALENCE INFORMATION
-
- Predicate device name(s): Oragene Dx OGD-500.001
-
- Predicate 510(k) number(s): K141410
-
- Comparison with predicate:
| AncestryDNA Saliva Collection Kit | Oragene Dx OGD-500.001(Predicate Device) | |
|---|---|---|
| K Number | K192947 | K141410 |
| SIMILARITIES | ||
| Intended Use | The AncestryDNA Saliva CollectionKit is intended for use in the non-invasive collection of saliva samples.Human DNA from the saliva sampleis isolated, stabilized and suitable foruse with over-the-counterAncestryDNA Genetic Health RiskTests. Saliva samples collected usingthe AncestryDNA Saliva CollectionKit are stabilized and can betransported and/or stored long term atambient conditions. | Oragene®•Dx OGD-500.001 isintended for use in the non-invasivecollection of saliva samples. DNAfrom the saliva sample is isolated,stabilized, and suitable for over-thecounter use with FDA cleared,approved, or legally marketed exemptDNA carrier screening genotypingtests. Saliva samples collected usingOragene•Dx OGD-500.001 arestabilized and can be transportedand/or stored long term at ambientconditions. |
| Specialconditions foruse | Over the counter | Same |
| Classification | Class II | Same |
| Analyte | DNA | Same |
| SampleCollection | Non-invasive collection of biologicalsamples delivered into a non-sterileplastic collection tube | Same |
| Tube Material | Plastic | Same |
| SampleSource | Human saliva | Same |
| Additive | Nucleic acid stabilization solution | Same |
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| AncestryDNA Saliva Collection Kit | Oragene Dx OGD-500.001(Predicate Device) | |
|---|---|---|
| Transport andStability | Pre-collection AncestryDNA SalivaCollection Kits can be transported attemperatures ranging from -29°C to50°C and up to 85% RH. | Pre-collection Oragene Dx kits can betransported at temperatures rangingfrom -20°C to 50°C |
| Post-collection AncestryDNA SalivaCollection Kits can be transported attemperatures ranging from -29°C to50°C and up to 85% RH | Post-collection Oragene·Dx kits canbe transported at temperaturesranging from -20°C to 50°C | |
| Pre-collection AncestryDNA SalivaCollection Kits can be stored at roomtemperature for up to 12 months | Pre-collection Oragene Dx kits can bestored at room temperature for up to24 months | |
| Post-collection AncestryDNA SalivaCollection samples can be stored atroom temperature for up to 12months | Post-collection Oragene Dx samplescan be stored at room temperature forup to 12 months | |
| DIFFERENCES | ||
| SpecialConditions forUse | AncestryDNA Saliva Collection Kitis for use with AncestryDNA FactorV Leiden Genetic Health Risk Test.For use in adults 18 years and older. | For over-the-counter use. For use inadults of reproductive age. |
| Performance | Performance has been establishedwith the AncestryDNA Factor VLeiden Genetic Health Risk (GHR)Test | Performance has been establishedwith the 23andMe Personal GenomeService (PGS) Carrier Screening Test |
K. STANDARDS/GUIDANCE DOCUMENTS REFERENCED
- CLSI Guideline EP07-A3, Interference Testing in Clinical Chemistry; Approved Guideline . – Third Edition.
- CLSI Guideline EP12-A2, User Protocol for Evaluation of Qualitative Test Performance; . Approved Guideline—Second Edition
- . CLSI Guideline EP17-A2, Evaluation of Detection Capability for Clinical Laboratory Measurement Procedures; Approved Guideline - Second Edition.
- CLSI Guideline EP25-A, Evaluation of Stability of In Vitro Diagnostic Reagents; ● Approved Guideline.
- CLSI Guideline EP37-A1, Supplemental Tables for Interference Testing in Clinical . Chemistry.
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M. TEST PRINCIPLE
The AncestryDNA Saliva Collection Kit is used for collecting and stabilizing human DNA from saliva and for the transportation and long-term ambient room temperature storage of a saliva sample. The collection device consists of the saliva collection tube, funnel, and cap. The cap contains DNA stabilization solution. Saliva is delivered directly by expectorating into the collection tube via the funnel. Once the user has provided the saliva sample, s/he removes the funnel from the saliva collection tube and affixes the cap. Affixing the cap by screwing on releases the stabilization solution. The Instructions for Use instruct the user to shake the tube for at least five seconds to mix the saliva sample with the stabilization solution. Samples can be immediately processed, transported, or stored for future use. Device and sample integrity are preserved during typical ambient transport and storage conditions for up to 12 months.
N. PERFORMANCE CHARACTERISTICS
The analytical and clinical studies conducted to support the intended use and substantial equivalence claim to the predicate device are summarized below. Execution of the analytical and clinical studies and genotyping using the AncestryDNA Factor V Leiden Genetic Health Risk Test was performed by a CLIA-certified laboratory on the Illumina Infinium array platform. Results were analyzed using the Illumina iScan System and Genome Studio software to generate genotypes and to calculate call rates. Ancestry Genomics performed quality control of genotype results and associated the genotype variants to donor identification.
1. Analytical Performance
a. Reproducibility/Precision
The purpose of this study was to determine the precision and reproducibility of the AncestryDNA Factor V Leiden GHR Test at multiple sites, on multiple days, using multiple operator teams, with samples collected using multiple lots of the AncestryDNA SCK. Execution of the study protocol and genotyping using the AncestryDNA Factor V Leiden GHR Test was performed at two CLIA-certified laboratories (Lab 1 and Lab 2) on the Illumina Infinium array platform by six different operator teams (3 per laboratory).
Saliva samples were collected from nine donors with known Factor V Leiden genotypes as determined using bi-directional sequencing: three donors each with homozygous common, heterozygous, and homozygous rare. Each of the nine donors provided 19 saliva samples into three lots of AncestryDNA SCKs. This study was performed over multiple days for the AncestryDNA Factor V Leiden GHR Test evaluated in Lab 1 and Lab 2. Genotyping with the AncestryDNA Factor V Leiden GHR Test was conducted over a minimum of six non-consecutive starting days at Lab 1 and two non-consecutive days at Lab 2.
Each of the donor collections within a given AncestryDNA SCK lot were pooled and mixed, then returned to the AncestryDNA SCK tubes for double extraction. Replicates
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that did not pass SCR QC in the first genotyping run underwent second, and when eligible, third genotyping run.
Single Site Precision and Repeatability
At the Lab 1 testing site, repeatability (within-run) and intermediate precision (within laboratory, across days, operator teams, and lots) was performed. Each of three operator teams tested each of the nine donor DNA samples in singlicate 20 times over five nonconsecutive dates. In addition, within-run repeatability was conducted at the Lab 1 testing site. Each donor DNA sample was genotyped an additional four times on one plate (batch). Testing for this batch was performed by one operator team within a single day.
At the Lab 2 testing site, intermediate precision (within laboratory, across days, and operator teams) was performed. Each of three operator teams tested each of the nine donor DNA samples in singlicate 20 times over five non-consecutive dates.
Inter-laboratory Reproducibility
For the inter-laboratory reproducibility study, two AncestryDNA SCK Lot A saliva tubes from each donor were extracted at Lab 1 and plated to DNA plates for processing. DNA samples were tested in triplicate at Lab 1, and tested in triplicate at Lab 2. This resulted in 18 additional genotyping events per specimen (9 total replicates at Lab 1 and 9 total replicates at Lab 2). Each donor's saliva specimen was genotyped in singlet 260 times: 191 genotyping events at the Lab 1 laboratory and 69 genotyping events at the Lab 2.
The final genotyping results for the Labs 1 and 2 are summarized in the tables below. For Lab 1, testing was conducted by three different operator teams as well as saliva collection in three different AncestryDNA SCK lot combinations. For the Lab 2, testing was conducted across three different operator teams, and three different AncestryDNA SCK lot combinations. The number of concordant calls includes replicates that pass call rate QC and have genotypes concordant with the expected genotype as determined by bidirectional sequencing.
| DonorID | ExpectedGenotype | TotalNumber ofReplicates | Number ofConcordantCalls | Number of"No-Calls" | Number ofCall Rate QCFailures | Proportionof FQC(%) |
|---|---|---|---|---|---|---|
| 1 | GG | 191 | 191 | 0 | 0 | 0.00 |
| 2 | GA | 191 | 191 | 0 | 0 | 0.00 |
| 3 | AA | 191 | 191 | 0 | 0 | 0.00 |
| 4 | GG | 191 | 191 | 0 | 0 | 0.00 |
| 5 | AA | 191 | 191 | 0 | 0 | 0.00 |
| 6 | GA | 191 | 191 | 0 | 0 | 0.00 |
| 7 | AA | 191 | 191 | 0 | 0 | 0.00 |
| 8 | GG | 191 | 191 | 0 | 0 | 0.00 |
| 9 | GA | 191 | 188 | 0 | 3 | 1.57 |
| Total | 1,719 | 1,716 | 0 | 3 | 0.17 |
Summary of Lab 1 Testing Results
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| DonorID | ExpectedGenotype | TotalNumber ofReplicates | Number ofConcordantCalls | Number of"No-Calls" | Number ofCall Rate QCFailures | Proportionof FQC(%) |
|---|---|---|---|---|---|---|
| 1 | GG | 69 | 69 | 0 | 0 | 0.00 |
| 2 | GA | 69 | 69 | 0 | 0 | 0.00 |
| 3 | AA | 69 | 69 | 0 | 0 | 0.00 |
| 4 | GG | 69 | 69 | 0 | 0 | 0.00 |
| 5 | AA | 69 | 69 | 0 | 0 | 0.00 |
| 6 | GA | 69 | 69 | 0 | 0 | 0.00 |
| 7 | AA | 69 | 69 | 0 | 0 | 0.00 |
| 8 | GG | 69 | 69 | 0 | 0 | 0.00 |
| 9 | GA | 69 | 69 | 0 | 0 | 0.00 |
| Total | 621 | 621 | 0 | 0 | 0.00 |
Summary of the Lab 2 Testing Results
Single Site Precision and Repeatability
Results by Site and Operator Team
The final genotyping results by site per operator team per genotype, across three AncestryDNA SCK lots is in the table below. The number of concordant calls includes replicates that pass call rate QC and have genotypes concordant with the expected genotype as determined by bi-directional sequencing.
| Site and Operator Combination Results | ||
|---|---|---|
| Caracterial Controller Company Comments of Children Comments of Children |
| Site/OperatorTeam | ExpectedGenotype | TotalNumber ofReplicates | Number ofConcordantCalls | Number of"No-Calls" | Number ofCall RateQC Failures* | Proportionof FQC(%) |
|---|---|---|---|---|---|---|
| Lab 1Team 1 | AA | 195 | 195 | 0 | 0 | 0.00 |
| GA | 195 | 194 | 0 | 1 | 0.51 | |
| GG | 195 | 195 | 0 | 0 | 0.00 | |
| Total | 585 | 584 | 0 | 1 | 0.17 | |
| Lab 1Team 2 | AA | 189 | 189 | 0 | 0 | 0.00 |
| GA | 189 | 188 | 0 | 1 | 0.53 | |
| GG | 189 | 189 | 0 | 0 | 0.00 | |
| Total | 567 | 566 | 0 | 1 | 0.18 | |
| Lab 1Team 3 | AA | 189 | 189 | 0 | 0 | 0.00 |
| GA | 189 | 188 | 0 | 1 | 0.53 | |
| GG | 189 | 189 | 0 | 0 | 0.00 | |
| Total | 567 | 566 | 0 | 1 | 0.18 | |
| Lab 2Team 1 | AA | 69 | 69 | 0 | 0 | 0.00 |
| GA | 69 | 69 | 0 | 0 | 0.00 | |
| GG | 69 | 69 | 0 | 0 | 0.00 | |
| Total | 207 | 207 | 0 | 0 | 0.00 | |
| Lab 2 | AA | 69 | 69 | 0 | 0 | 0.00 |
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| Site/OperatorTeam | ExpectedGenotype | TotalNumber ofReplicates | Number ofConcordantCalls | Number of"No-Calls" | Number ofCall RateQC Failures* | Proportionof FQC(%) |
|---|---|---|---|---|---|---|
| Team 2 | GA | 69 | 69 | 0 | 0 | 0.00 |
| GG | 69 | 69 | 0 | 0 | 0.00 | |
| Total | 207 | 207 | 0 | 0 | 0.00 | |
| Lab 2Team 3 | AA | 69 | 69 | 0 | 0 | 0.00 |
| GA | 69 | 69 | 0 | 0 | 0.00 | |
| GG | 69 | 69 | 0 | 0 | 0.00 | |
| Total | 207 | 207 | 0 | 0 | 0.00 | |
| All teams'totalscombined | GG, GA,AA | 2,340 | 2,337 | 0 | 3 | 0.13 |
- The heterozygous donor failures in each of the Lab 1 operator teams are from Donor 9 listed above.
Results by Site and AncestryDNA SCK Lot Combination
The final genotyping results by site per AncestryDNA SCK lot combination per genotype across six different operator teams and three AncestryDNA SCK lots are in the table below. The number of genotype calls includes replicates that pass the QC call rate and have genotypes concordance with the expected genotype as determined by bi-directional sequencing.
Site and AncestryDNA SCK Lot Combination Results
| Site/AncestryDNASCK Lot | ExpectedGenotype | TotalNumber ofReplicates | Number ofConcordantCalls | Numberof "No-Calls" | Number ofCall RateQCFailures | Proportionof FQC(%) |
|---|---|---|---|---|---|---|
| Lab 1-Lot A | AA | 213 | 213 | 0 | 0 | 0.00 |
| GA | 213 | 213 | 0 | 0 | 0.00 | |
| GG | 213 | 213 | 0 | 0 | 0.00 | |
| Total | 639 | 639 | 0 | 0 | 0.00 | |
| Lab 1-Lot B | AA | 180 | 180 | 0 | 0 | 0.00 |
| GA | 180 | 177 | 0 | 3 | 1.67 | |
| GG | 180 | 180 | 0 | 0 | 0.00 | |
| Total | 540 | 537 | 0 | 3 | 0.56 | |
| Lab 1-Lot C | AA | 180 | 180 | 0 | 0 | 0.00 |
| GA | 180 | 180 | 0 | 0 | 0.00 | |
| GG | 180 | 180 | 0 | 0 | 0.00 | |
| Total | 540 | 540 | 0 | 0 | 0.00 | |
| Lab 2-Lot A | AA | 87 | 87 | 0 | 0 | 0.00 |
| GA | 87 | 87 | 0 | 0 | 0.00 | |
| GG | 87 | 87 | 0 | 0 | 0.00 | |
| Total | 261 | 261 | 0 | 0 | 0.00 |
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| Site/AncestryDNASCK Lot | ExpectedGenotype | TotalNumber ofReplicates | Number ofConcordantCalls | Numberof “No-Calls” | Number ofCall RateQCFailures | Proportionof FQC(%) |
|---|---|---|---|---|---|---|
| Lab 2-Lot B | AA | 60 | 60 | 0 | 0 | 0.00 |
| GA | 60 | 60 | 0 | 0 | 0.00 | |
| GG | 60 | 60 | 0 | 0 | 0.00 | |
| Total | 180 | 180 | 0 | 0 | 0.00 | |
| Lab 2-Lot C | AA | 60 | 60 | 0 | 0 | 0.00 |
| GA | 60 | 60 | 0 | 0 | 0.00 | |
| GG | 60 | 60 | 0 | 0 | 0.00 | |
| Total | 180 | 180 | 0 | 0 | 0.00 | |
| All AncestryDNASCK lots' totalscombined | GG, GA,AA | 2,340 | 2,337 | 0 | 3 | 0.13 |
Within-Run Repeatability
Within-run repeatability was conducted at the Lab 1 testing site and the results are in the table below. Each donor DNA sample was genotyped four additional times on one plate (batch). There were no genotyping repeats.
| DonorID | ExpectedGenotype | Total Numberof Replicates | Number ofConcordantCalls | Number of"No-Calls" | Number of CallRate QC Failures | Proportion ofFQC (%) |
|---|---|---|---|---|---|---|
| 1 | GG | 5 | 5 | 0 | 0 | 0.00 |
| 2 | GA | 5 | 5 | 0 | 0 | 0.00 |
| 3 | AA | 5 | 5 | 0 | 0 | 0.00 |
| 4 | GG | 5 | 5 | 0 | 0 | 0.00 |
| 5 | AA | 5 | 5 | 0 | 0 | 0.00 |
| 6 | GA | 5 | 5 | 0 | 0 | 0.00 |
| 7 | AA | 5 | 5 | 0 | 0 | 0.00 |
| 8 | GG | 5 | 5 | 0 | 0 | 0.00 |
| 9 | GA | 5 | 5 | 0 | 0 | 0.00 |
| Totals | 45 | 45 | 0 | 0 | 0.00 |
Within-Run Repeatability Results from Lab 1
Inter-laboratory Reproducibility
The final genotyping results for the inter-laboratory reproducibility study (n=2) across six operator teams is in the table below. The number of concordant calls includes replicates that pass call rate quality control and also have genotypes concordant with the expected genotype (bi-directional sequencing genotype result).
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| DonorID | ExpectedGenotype | Total Numberof Replicates(Lab 1 Lab 2) | Number ofConcordantCalls(Lab 1 Lab 2) | Number of"No-Calls"(Lab 1 Lab 2) | Number of CallRate QCFailures(Lab 1 Lab 2) | Proportion ofFQC (%)(Lab 1 Lab 2) | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | GG | 9 | 9 | 9 | 9 | 0 | 0 | 0 | 0 | 0.00 | 0.00 |
| 2 | GA | 9 | 9 | 9 | 9 | 0 | 0 | 0 | 0 | 0.00 | 0.00 |
| 3 | AA | 9 | 9 | 9 | 9 | 0 | 0 | 0 | 0 | 0.00 | 0.00 |
| 4 | GG | 9 | 9 | 9 | 9 | 0 | 0 | 0 | 0 | 0.00 | 0.00 |
| 5 | AA | 9 | 9 | 9 | 9 | 0 | 0 | 0 | 0 | 0.00 | 0.00 |
| 6 | GA | 9 | 9 | 9 | 9 | 0 | 0 | 0 | 0 | 0.00 | 0.00 |
| 7 | AA | 9 | 9 | 9 | 9 | 0 | 0 | 0 | 0 | 0.00 | 0.00 |
| 8 | GG | 9 | 9 | 9 | 9 | 0 | 0 | 0 | 0 | 0.00 | 0.00 |
| 9 | GA | 9 | 9 | 9 | 9 | 0 | 0 | 0 | 0 | 0.00 | 0.00 |
| Totals | 81 | 81 | 81 | 81 | 0 | 0 | 0 | 0 | 0.00 | 0.00 |
Inter-Laboratory Reproducibility
Overall Percent Agreement (OPA) for Repeatability and Genotyping
The OPA point estimates for repeatability exceeded the 99% predefined protocol acceptance criteria, and the OPA point estimates for each genotype exceeded the 99% predefined protocol acceptance criteria as seen in the table below.
| Attribute | Concordant Replicates(Total QC PassingReplicates) | Point Estimate PercentAgreement (%)(95% Confidence Interval) |
|---|---|---|
| Lab 1 laboratory | 1,716 (1,716) | 100.00 (99.79 – 100.00) |
| Lab 2 laboratory | 621 (621) | 100.00 (99.41 – 100.00) |
| Lab 1 operator team 1 | 584 (584) | 100.00 (99.37 – 100.00) |
| Lab 1 operator team 2 | 566 (566) | 100.00 (99.35 – 100.00) |
| Lab 1 operator team 3 | 566 (566) | 100.00 (99.35– 100.00) |
| Lab 2 operator team 1 | 207 (207) | 100.00 (98.23 – 100.00) |
| Lab 2 operator team 2 | 207 (207) | 100.00 (98.23 – 100.00) |
| Lab 2 operator team 3 | 207 (207) | 100.00 (98.23 – 100.00) |
| All operator teams | 2,337 (2,337) | 100.00 (99.84 – 100.00) |
| Lab 1 AncestryDNA SCK lot A | 639 (639) | 100.00 (99.42 – 100.00) |
| Lab 1 AncestryDNA SCK lot B | 537 (537) | 100.00 (99.32 – 100.00) |
| Lab 1 AncestryDNA SCK lot C | 540 (540) | 100.00 (99.32 – 100.00) |
| Lab 2 AncestryDNA SCK lot A | 261 (261) | 100.00 (98.60– 100.00) |
| Lab 2 AncestryDNA SCK lot B | 180 (180) | 100.00 (97.97 – 100.00) |
| Lab 2 AncestryDNA SCK lot C | 180 (180) | 100.00 (97.97 – 100.00) |
| All AncestryDNA SCK lotcombinations | 2,337 (2,337) | 100.00 (99.84 – 100.00) |
| Within-run repeatability | 45 (45) | 100.00 (92.13 – 100.00) |
| Inter-lab data at Lab 1 | 81 (81) | 100.00 (95.55 – 100.00) |
| Inter-lab data at Lab 2 | 81 (81) | 100.00 (95.55 – 100.00) |
| All “GG” | 780 (780) | 100.00 (99.53 – 100.00) |
| All “GA” | 777 (777) | 100.00 (99.53 – 100.00) |
Point Estimates for Overall Percent Agreement for Repeatability and Genotype
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| Attribute | Concordant Replicates(Total QC PassingReplicates) | Point Estimate PercentAgreement (%)(95% Confidence Interval) |
|---|---|---|
| All "AA" | 780 (780) | 100.00 (99.53 - 100.00) |
The AncestryDNA Factor V Leiden GHR Test was evaluated at multiple labs, on multiple days, by multiple personnel teams. The results demonstrate that the AncestryDNA Factor V Leiden GHR Test met the acceptance criteria for overall precision > 99% point estimate, and for each genotype > 99% agreement. The AncestryDNA Factor V Leiden GHR Test also delivered precise and reproducible results across multiple AncestryDNA SCK lots. The AncestryDNA SCK in combination with the AncestryDNA Factor V Leiden GHR Test consistently produced results that were in agreement with the true variant status, which was determined by bidirectional sequencing.
b. Linearity/Assay Reportable Range
Not applicable.
c. Traceability, Stability, Expected Values (controls, calibrators, or methods)
Pre-collection AncestryDNA Saliva Collection Kits can be stored at 15°C to 30°C for up to 12 months.
Pre-collection AncestryDNA Saliva Collection Kits can be transported at temperatures ranging from -29℃ to 50℃ and up to 85% RH.
d. Analytical Sensitivity
The study was designed around the regression (probit/logit) approach from section 5.5 of the CLSI EP17-A2 to determine Limit of Blank (LoB) and Limit of Detection (LoD). Each sample was serially diluted to different DNA concentrations and genotyped. To confirm the genotype call, each sample was also sequenced by bi-directional sequencing to determine the rates of correct genotype calls at each DNA concentration. The Limit of Detection (LoD) was defined as the lowest DNA concentration at which at least 95% of samples yielded the correct call.
Limit of Blank Test Method
Due to the noisy nature of UV-Vis spectroscopy and potentially erroneous fluorescence signal in the assay, to establish the Limit of Blank (LoB) samples were extracted and quantified on a plate of 95 blanks containing 1 mL of molecular grade water and the standard volume of DNA stabilizing solution from the AncestryDNA SCK. The samples were extracted, quantified, and genotyped.
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Limit of Detection Test Method
Saliva samples were collected from 15 donors with known Factor V Leiden genotypes as determined using bi-directional sequencing: five (5) donors each with homozygous common, heterozygous, and homozygous rare. Samples were collected using the Oragene® Dx Collection Device, model OGD-500.001 (OGD) (n=1) and the AncestryDNA SCK (n=4). DNA extracted from each donor's saliva samples were pooled to create a homogenous solution. The pooled DNA was used to create a two-fold dilution series, including a neat sample and four additional dilutions for a total of five samples per donor per genotype in the series. Six replicates of each dilution series were genotyped using the AncestryDNA Factor V Leiden GHR Test. Testing was performed under standard protocol for the AncestryDNA GHR Test, except that each donor sample in the series was genotyped in duplicate. A total 450 replicates were tested in the LoD study.
The LoB = 1.004 ng/uL, based on the non-parametric rank method from section 5.3.3.1 of EP17-A2 to account for sources of measurement variability in the both UV-Vis spectrophotometry and the bead-based fluorescence assay.
The LoD = 1.53 ng/uL, a limit concentration that is statistically distinguishable from blank samples.
The upper limit of concentration = 50 ng/uL.
All genotyping attempts on samples containing the measurand with call rates ≥ 98% and concentrations between 1.53 ng/uL and 50 ng/uL produced genotypes concordant with bidirectional sequencing.
e. Interfering Substances
The analytical specificity studies were designed using CLSI EP07 - Interference Testing in Clinical Chemistry; Approved Guideline – Third Edition for determining potential interference with the AncestryDNA Factor V Leiden GHR Test. Endogenous, exogenous, and microbial DNA were evaluated as part of the analytical specificity study.
Endogenous Interference
Four potential common endogenous interferents were evaluated to determine the effect on the performance of the AncestryDNA Factor V Leiden GHR Test as listed in the table below.
| Endogenous Substance | Final Concentration (1x) in Saliva |
|---|---|
| PBS (reference/control) | N/A |
| Salivary α-amylase | 395 U/mL |
| Hemoglobin | 20 mg/mL |
| IgA | 0.44 mg/mL |
| Total Protein | 0.185 mg/mL Salivary α-amylase0.44 mg/mL IgA |
Endogenous Interferent Concentrations
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| Endogenous Substance | Final Concentration (1x) in Saliva |
|---|---|
| 2.05 mg/mL human serum albumin |
A total of ten total saliva donors with unknown Factor V Leiden genotypes were utilized in the specificity study. A saliva sample from each donor was collected with the Oragene® Dx Collection Device, model OGD-500.001 (OGD) (K141410) and sent to a third party laboratory to determine the true variant status using bi-directional sequencing analysis. Each donor provided five saliva samples into five AncestryDNA SCK Saliva Collection Tubes that were shipped to the laboratory. The endogenous substances were individually spiked into saliva prior to DNA extraction and genotyping. Saliva that was spiked with PBS served as the reference/control. The assay was executed by the same two (2) operators for each genotyping replicate. Each sample was genotyped in triplicate for a total of 30 replicate genotyping attempts (3 replicates for each of 10 donors) per each interferent and 30 control replicate genotyping attempts (450 total initial genotyping attempts).
For all samples (control samples and samples with endogenous interferents) that passed quality control, the concordance was 100%, exceeding the acceptance criterion of ≥ 95% agreement with true variant status as determined by bi-directional sequencing. The point estimate of overall percent agreement from each of the endogenous interferents is provided in the table below. The results indicate that the performance of the AncestryDNA Factor V Leiden GHR Test when tested from samples collected with the AncestryDNA SCK are not affected by the tested interferents.
| Endogenous Interferent | Overall Percent Agreement Point Estimate |
|---|---|
| PBS (reference/control) | 100% (30/30) |
| Salivary α-amylase | 100% (30/30) |
| Hemoglobin | 100% (30/30) |
| IgA | 100% (30/30) |
| Total Protein | 100% (30/30) |
Overall Percent Agreement for the Endogenous Interference Study
Exogenous Interference
Six potential exogenous interferents were evaluated to determine its effect on the performance of the AncestryDNA Factor V Leiden GHR Test. The exogenous interference study included samples from non-smokers and smokers. Saliva samples were collected from 10 non-smokers in 15 AncestryDNA SCKs over the course of five (5) days. Each day, the donor performed one (1) of the five (5) activities (eating beef, eating chicken, drinking alcohol, chewing gum, or using mouthwash). The donors provided three (3) tubes per day as follows: before consuming the exogenous substance (control/baseline), immediately after, and 30-minutes after performing the activity. Saliva samples were also collected from 10 smokers into 3 AncestryDNA SCK per day as follows: before smoking (control/baseline), immediately after smoking, and 30-minutes after smoking. There was a total of 594 data points as summarized in the table below.
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| Exogenous Activity | Donor Count | Time Point | Replicates | Total |
|---|---|---|---|---|
| Eating 3 oz. chicken | 12 | 3 | 3 | 108 |
| Drinking 1.5 oz. alcohol | 12 | 3 | 3 | 108 |
| Using mouthwash | 12 | 3 | 3 | 108 |
| Eating 3 oz beef | 10 | 3 | 3 | 90 |
| Chewing gum | 10 | 3 | 3 | 90 |
| Smoking | 10 | 3 | 3 | 90 |
| Total | 594 |
Overview of Exogenous Interferent Study Design
For all samples where the control samples and replicates containing the interfering substances passed QC, the concordance for all interfering substances was 100% met the acceptance criterion of ≥ 95% agreement with true variant status from bi-directional sequencing for all samples that have passed OC. Results indicate that the performance of the AncestryDNA Factor V Leiden GHR Test when tested from samples collected with the AncestryDNA SCK are not affected by the tested interferents. The table below summarizes the overall percent agreement (OPA) point estimate calculated on genotyping events with control samples that passed QC for each interferent and time point.
| Exogenous Substance | OPA Point Estimate(Concordant Replicates / Total QC Passing Replicates) | |
|---|---|---|
| T0 | T30 | |
| Chicken | 100% (33/33) | 100% (36/36) |
| Alcohol | 100% (36/36) | 100% (36/36) |
| Mouthwash | 100% (36/36) | 100% (36/36) |
| Beef | 100% (27/27) | 100% (30/30) |
| Gum | 100% (30/30) | 100% (30/30) |
| Smoking | 100% (30/30) | 100% (30/30) |
Overall Percent Agreement for Exogenous Interferents
For the eating chicken and eating beef activities, a higher rate of QC failures for samples collected immediately after completing the activity (T0) when matched donor control samples passed QC was observed. Therefore, the AncestryDNA Saliva Collection Kit will include in the labeling the following sentence as part of the saliva collection warning: "Do NOT eat, drink, smoke or chew gum for 30 minutes before giving your saliva sample.
Microbial Interference
Microbial DNA from five (5) different species (Staphylococcus epidermis, Streptococcus mutans, Lactobacillus casei, Actinomyces odontolyticus, and Candida albicans) were evaluated to determine its impact on the performance of the AncestryDNA Factor V Leiden GHR Test. DNA from six (6) human cell lines was obtained for this study:
- Four cell lines were Factor V Leiden homozygous common (wild type; GG), ●
- One cell line was Factor V Leiden heterozygous (GA), and ●
- . One cell line was Factor V Leiden homozygous rare (Variant; AA).
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All cell lines were subjected to bi-directional sequencing by a third-party laboratory to verify the Factor V Leiden genotype as part of the study. DNA from each of the six human cell lines was spiked with two concentrations (1ow/normal (2.8 ng/uL) and high (12.5 ng/uL)) of the five different species of microbial DNA. Human cell line DNA spiked with buffer functioned as a spike-in control at both concentrations. Each of the human cell lines was spiked a total of 12 times (5 microbial interferents and a control at 2 levels per cell line). The resulting 72 DNA mixtures were genotyped in replicates of 6 using the AncestryDNA Factor V Leiden GHR Test, for a total of 432 genotyping results (6 cell lines x 6 microbe/control x 2 concentrations x 6 replicates = 432).
Each sample and replicate, spiked with two levels of microbial interferent, and unspiked (spiked with PBS) was compared directly to bidirectional sequencing results. The assay produced concordant genotypes with bidirectional sequencing in all genotyping events. The point estimate of overall percent agreement (OPA) with true variant status from each condition is provided below. The Factor V Leiden GHR Test performs to the internal specifications and meets the study acceptance criteria of a > 95% agreement with true variant status. The assay reproduced the true variant status, as determined by bidirectional sequencing, for each replicate that was tested, including all control genotyping replicates and all interferent-spiked genotyping replicates. The results indicate that there is no significant impact of common microbial interferents on the performance of the Factor V Leiden GHR Test in either low/normal or higher-than-average concentrations.
| Microbial Interferent | OPA Point Estimate | |
|---|---|---|
| Low/Normal Concentration | High Concentration | |
| Buffer (reference/control) | 100% (36/36) | 100% (36/36) |
| S. epidermis | 100% (36/36) | 100% (36/36) |
| S. mutans | 100% (36/36) | 100% (36/36) |
| L. casei | 100% (36/36) | 100% (36/36) |
| A. odontolyticus | 100% (36/36) | 100% (36/36) |
| C. albicans | 100% (36/36) | 100% (36/36) |
Microbial Interferent Testing Results for Overall Percent Agreement
f. Assav Cut-off
Not applicable.
g. Sample Volume Tolerance
Saliva sample volume in the AncestryDNA SCK was evaluated to determine its effect on the performance of the AncestryDNA Factor V Leiden GHR Test. Saliva samples were collected from 80 donors with known Factor V Leiden genotypes: 60 homozygous common (wild type), 15 heterozygous, and five homozygous rare (variant). Each of the 80 donors provided saliva samples into four tubes for a total of n=320 tubes for testing with the AncestryDNA Factor V Leiden GHR Test (240 tubes) and bi-directional sequencing analysis (80 tubes). For each donor, one AncestryDNA SCK Saliva
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Collection Tube was under-filled, one was filled per the instructions for use, and one was over-filled. All of the AncestryDNA SCK Saliva Collection Tubes were genotyped with the AncestryDNA Factor V Leiden GHR Test.
Nine out of 240 samples failed sample call rate QC. The AncestryDNA Factor V Leiden GHR Test reproduced the true variant status for all samples that passed QC irrespective of fill volume as determined by bi-directional sequencing. For all target fill volumes evaluated, the acceptance criterion was met which stated, for all samples that passed quality control for each collection volume (under-filled, normally filled, over-filled), ≥ 95% agreement with true variant status. The point estimates of overall percent agreement (OPA) with the bidirectional sequencing and AncestryDNA Factor V Leiden GHR Test showed 100% agreement across all fills and genotypes evaluated in the tables below.
| Fill | Fill Line | Concordant QC Passing Samples /Total QC Passing Samples | Point Estimate OPA(%) |
|---|---|---|---|
| Control | 1.0 mL | 79/79 | 100 |
| Under | 0.5 mL | 79/79 | 100 |
| Over | 1.5 mL | 73/73 | 100 |
Overall Percent Agreement Point Estimates Stratified by Fill Line
| Overall Percent Agreement Point Estimates Stratified by Genotype | |
|---|---|
| Genotype by | Sequencing | Concordant QC Passing Samples /Total QC Passing Samples | Point Estimate OPA(%) |
|---|---|---|---|
| Wild Type | GG | 172/172 | 100 |
| Heterozygous | GA | 44/44 | 100 |
| Variant | AA | 15/15 | 100 |
h. Specimen Stability
Post-collection AncestryDNA Saliva Collection samples can be stored at 15°C to 30°C for up to 12 months.
Post-collection AncestryDNA Saliva Collection Kits can be transported at temperatures ranging from -29°C to 50°C and up to 85% RH.
2. Comparison Studies
a. Method Comparison with the Predicate
The accuracy of the AncestryDNA Factor V Leiden GHR Test was established by comparing the results of the test to the true variant status as determined by bi-directional sequencing analysis at a third-party laboratory.
Saliva samples were collected from 209 donors with known Factor V Leiden genotypes: 200 initial study donors plus nine alternate study donors. The genotypes of the donors as determined by bi-directional sequencing were 73 homozygous common, 69
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heterozygous, and 67 homozygous rare. Samples were collected using Oragene Dx Ogd-500.001 (OGD) and the AncestryDNA SCK.
- Each sample collected using the OGD device was subjected to bi-directional ● sequencing by a third-party laboratory to verify the Factor V Leiden genotype,
- Each donor sample collected using the AncestryDNA SCK was used in the accuracy . study with the AncestryDNA Factor V Leiden GHR Test.
Of the 200 samples initially genotyped, 185 passed the first pass genotyping quality control sample-level call rate (SCR) of ≥ 98% and 15 did not (<98%). Nine alternate samples were added to the sample cohort, all of which passed the first pass genotyping SCR of ≥ 98%. The 15 samples that were regenotyped, four passed SCR quality control in second pass genotyping attempts, and 11 failed SCR quality control in the second pass genotyping attempt and were not eligible for a third genotyping attempt based on sample call rate criteria. The table below summarizes the genotype counts for all samples passing SCR quality control for the AncestryDNA Factor V Leiden GHR Test and the genotyping results for the bi-directional sequencing. Zero (0) 'no-call' events were observed in any of the samples that passed quality control.
| Bi-directional SequencingGenotypes | Total | ||||
|---|---|---|---|---|---|
| GG | GA | AA | |||
| AncestryDNAFactor VLeiden | GG (homozygouscommon) | 69 | 0 | 0 | 69 |
| GHR Test | GA (heterozygous) | 0 | 65 | 0 | 65 |
| Genotypes | AA (homozygous rare) | 0 | 0 | 64 | 64 |
| 00 (no-call) | 0 | 0 | 0 | 0 | |
| Total | 69 | 65 | 64 | 198 |
Comparison of the Genotyping Results for Bi-directional Sequencing and AncestryDNA Factor V Leiden GHR Test
For all samples that passed quality control, the overall percent agreement and the percent agreement for each genotype with bi-directional sequencing genotypes was 100% as outlined below.
Percent Agreement and Confidence Intervals for AncestryDNA Factor V Leiden GHR Test Genotypes as Compared with Bi-directional Sequencing
| Genotype | Observed/Expected | Percent Agreement | 95% Confidence Interval |
|---|---|---|---|
| GG | 69/69 | 100% | 94.8–100% |
| GA | 65/65 | 100% | 94.5–100% |
| AA | 64/64 | 100% | 94.4–100% |
| All genotypes | 198/198 | 100% | 98.2–100% |
The calculated overall percent agreement and 95% confidence intervals based on a binomial distribution between genotypes obtained from donors using the AncestryDNA SCK with the AncestryDNA Factor V Leiden GHR Test and using the Oragene Dx Ogd-500.001 (OGD) for bi-directional sequencing.
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| Overall Percent Agreement and Confidence Interval for Genotypes Obtained Using | |
|---|---|
| AncestryDNA SCK Compared to OGD |
| Proportion Concordant Genotypes(AncestryDNA SCK vs. OGD) | Genotype OPA BetweenSaliva Collection Devices | 95% ConfidenceInterval |
|---|---|---|
| 198/198 | 100% | 98.2 - 100% |
The genotype frequencies for Factor V Leiden in various US population were obtained from the 2018 ACMG reporting standard (Zhang et al., 2018): "In the United States, factor V Leiden heterozygosity is present in 5.1%, 2.0%, and 1.2% of Caucasians, Hispanics, and African Americans respectively; the frequencies of homozygosity for the above populations are 65, 10, and 4 per 100,000 individuals correspondingly."
In the accuracy study for the AncestryDNA Factor V Leiden GHR Test, point estimates of PA(GG|GG) = PA(GA|GA)=PA(AA|AA) = 100%. The point estimate for the Technical Positive Predictive Value (TPPV) for such a scenario is 100% for both heterozygotes and homozygotes. While this point estimate may have larger uncertainty about the TPPV than an estimate from a larger test population, no discordant genotypes were observed in any of the 198 genotyping events that passed quality control.
For all samples that passed SCR quality control (198/209, 95%), the AncestryDNA Factor V Leiden GHR Test genotypes were 100% concordant with true variant status, determined by bi-directional sequencing from saliva samples collected in the OGD. This result met the predefined protocol acceptance criterion of > 99% agreement with true variant determination overall and per genotype tested. These results show that the AncestryDNA SCK is capable of noninvasive collection of saliva samples for the purpose of supporting DNA tests that evaluate genomic DNA isolated from the collection device.
b. Matrix Comparison
Not applicable.
3. Clinical Studies
a. User Comprehension Study
Ancestry Genomics sponsored a study to assess naive user comprehension of labeling provided with the AncestryDNA SCK. The user comprehension study was performed using a sampling of individuals that was demographically diverse, using quota-based sampling methods and was conducted in a controlled environment at four sites across the U.S. In addition to the assessment of user comprehension of the SCK labeling, the study was moderated in order to collect observational data on participants' overall experience.
The user comprehension study was designed to assess the comprehension of representative labeling contained in the AncestryDNA Sample Collection Kit. The study was conducted with demographically diverse individuals to evaluate the reading level required for comprehension of the instructions for use.
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The user comprehension study was conducted to:
- a) evaluate readability of all written materials and instructions in the SCK
- b) document the SCK user experience, including submitting samples to the lab for testing to determine their viability to generate a genotype
Participants were representative of the intended use population: adults aged 18 years and older in the U.S. Participants were recruited to match the demographics (education, age, sex/gender, and race/ethnicity) of the adult U.S. population as of the most recent estimates released by the U.S. Census Bureau. Geographic diversity was addressed through participant recruitment and comprehension testing from each of the four (4) U.S. Census geographic regions: Northeast, Midwest, South, and West.
351 individuals were recruited for the study using quota sampling methods. Of the 351 individuals recruited. 271 participants were enrolled in the study. They were provided with the AncestryDNA SCK, instructed to open the kit, and follow all instructions to prepare the kit exactly as they would if they were doing so at home. After the procedure, the participant responded to an online post survey and was interviewed about the experience using the AncestryDNA SCK. The samples were shipped to a central CLIA certified laboratory, processed for viability and reported any failures in accessioning, extraction, or deficiency in DNA. AncestryDNA SCKs were only processed to determine that the sample contained an adequate amount of viable DNA to pass the call rate of ≥ 98%.
Out of the 271 individuals who completed the user comprehension survey and provided a saliva sample for analysis, 257 (94.8%) of the submitted saliva collection kit samples passed through all three evaluated failure points, and passed sample call rate of 98%. See Ancestry Genomics co-submission K192944 for additional user study information.
The AncestryDNA SCK instructions for use was calculated to have a Flesch-Kincaid reading level of 6.0, and the text alone reading level result was 7.1. The success criterion, that the Flesch-Kinkaid reading level shall meet or exceed the 8th grade threshold, was met.
Participants rated the AncestryDNA SCKs instructions as easy to understand and easy to follow and rated the illustrations as helpful.
- 98.1% rated the overall usability of the test as somewhat easy or higher. .
- 99.2% rated the kit instructions as somewhat easy to understand or better. .
- 98.1% indicated that the instructions were somewhat easy to follow or better. ●
- 99.6% said the illustrations on the card were somewhat helpful or better. .
b. Expected Values/Reference Range
Not applicable.
O. INSTRUMENT NAME
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Not applicable.
P. PROPOSED LABELING
The labeling satisfies the requirements of 21 CFR Parts 801 and 809.
Q. CONCLUSION
The results of the analytical, clinical and user studies submitted in this 510(k) Premarket Notification are complete and demonstrate that the AncestryDNA Saliva Collection Kit meets the established specifications necessary for consistent performance for the intended use of noninvasive collection, stabilization, transportation, and storage of saliva samples. The results support a conclusion that the AncestryDNA Saliva Collection Kit is substantially equivalent to the predicate.
§ 862.1675 Blood specimen collection device.
(a)
Identification. A blood specimen collection device is a device intended for medical purposes to collect and to handle blood specimens and to separate serum from nonserum (cellular) components prior to further testing. This generic type device may include blood collection tubes, vials, systems, serum separators, blood collection trays, or vacuum sample tubes.(b)
Classification. Class II.