African American GeneticsNCT02770001
Suitability of Some Data Quality Controls Thresholds for Genetic Association Studies of Admixed Population
An observational study of African American Genetics, run by National Human Genome Research Institute (NHGRI).
Trial summary
Background: In genetic studies, the quality of DNA samples is tested first. Samples that are low-quality are not used. Some studies involve minority ethnic groups. And example is admixed African American. These studies often have small sample sizes. It is important to make sure samples are not discarded unnecessarily. Read more about this study
- Who is it for?
- Ages 50 years and older
- Conditions the study is for
- African American Genetics
- How many people
- 0 participants
- Where
- No sites listed yet
- Study dates
- 5 May 2016to 15 May 2017
- Phase
- Observational
- Are there results?
- None posted in the registry
Key requirements
Who can take part, as listed by the sponsor. Only the study team can confirm whether you are eligible, so take this list to your doctor.
- Ages 50 years and older
- All sexes
- No healthy volunteers
- Adult, Older adult
- All the genotype data will be used and no individual will be excluded based on any phenotype.
About this study
Official title: Investigating the Suitability of Some Data Quality Controls Thresholds for Genetic Association Studies of Admixed Population
Background: In genetic studies, the quality of DNA samples is tested first. Samples that are low-quality are not used. Some studies involve minority ethnic groups. And example is admixed African American. These studies often have small sample sizes. It is important to make sure samples are not discarded unnecessarily. This may happen by using quality control (QC) thresholds for homogenous groups. These may not be appropriate for an admixed group. Researchers want to study samples that failed certain QC tests. They want to see if this has to do with the ancestry of the outliers or the quality of the samples.
Objectives:
Read more
To study samples that fail heterozygosity and sample genotype call rate QC. To see if the failing rates have to do with the ancestry composition of the outliers or the quality of the samples.
Eligibility:
No new participants. Researchers will review data that has already been collected.
Design:
Researchers will study DNA samples in a lab.
The samples will not include data that can identify the person the sample came from.
Read the detailed description
The purpose of this IRB proposal is to gain access to genetic data generated from participants of publically-funded genomic studies and deposited into dbGaP. It is our intention to use dbGaP data to conduct secondary analysis of the influence of admixture on the outcome of data quality control (QC) in genetic association studies to inform future studies of the optimal QC metric for the genetic association analysis of admixed population. The data we intend to use is deposited in dbGaP and is from the Michigan University Health and Retirement Study (HRS). This protocol is being sent to you because of a dbGaP requirement for this specific de-identified dataset to be reviewed by an IRB as that was not in the protocol.
This work will require the use of statistical analyses tools to estimate the genetic ancestry make-up of each sample, from the genotype data, and determine how that ancestry relates to QC outcomes (i.e. whether or not the sample might be excluded from an analysis due to its ancestral genetic composition rather that the sample genetic quality).
Objectives and specific aims: This work aims to investigate samples failing heterozygosity and sample genotype call rate quality control (QC) to determine whether or not the samples call rate and heterozygosity rate have to do with the ancestry composition of the outliers rather than the quality of the samples and inform future studies of potential loss if general QC is applied to genetic data of admixed sample sets.
Rationale and Background: In genetic association studies DNA sample quality can vary largely across study participants and such variation has an impact on genotype call rate and genotype accuracy; samples of low DNA quality tend to have lower genotype call rate and genotype accuracy. Heterozygosity rate (proportion of heterozygous loci per individual) and genotype failure rate (proportion of missing genotypes per individual) are jointly and routinely used to identify samples with low DNA quality at the data quality control (QC) stage of genetic association studies. Excessive heterozygosity rate may indicate sample contamination whilst a reduced heterozygosity rate could indicate inbreeding [1]. Samples with 3-7% [2,3] genotype call-rate and heterozygosity > 2-3 standard deviations from the mean heterozygosity are usually excluded from genetic case-control studies.
Generally, the sample size of genetic association studies involving minority ethnic groups such as admixed African American tends to be small. It is hence important to ensure samples are not discarded unnecessarily, resulting into reduced statistical power, by using QC thresholds applied to homogenous groups which might not be appropriate for an admixed sample set. The aim of this analysis is to investigate samples failing heterozygosity and sample genotype call rate QC to determine whether or not the samples call rate and heterozygosity rate have to do with the ancestry composition of the outliers rather than the quality of the samples. The motivation is to inform future studies of potential loss if general
- Conditions
- African American Genetics
- Keywords
- Admixture, African American, African American Genetics
What is being measured
The primary outcome is the main question the study is designed to answer.
Continental genetic ancestry fraction
Measured: Study Completion
Secondary outcomes (1)
Heterozygosity rate
Measured: Study Completion
Timeline
From the start of the study to its completion; the mark is today. Estimated dates are the sponsor’s plan.
- First posted12 May 2016 (estimated)
- Study start5 May 2016
- Primary completion15 May 2017
- Study completion15 May 2017
Resources
- Official record on ClinicalTrials.govThe registry entry this page is built from, with its full change history.
- Other trials for African American GeneticsStudies of the same condition, open and under way.
- What the trial phases meanHow a treatment moves from first tests in people to approval.
More details
For doctors and researchers: how the study is designed, who runs it, and its registry IDs.
Study design
- Study type
- Observational
- Observational model
- Other
- Time perspective
- Other
- Enrolment
- 0 participants (actual)
Sponsor and investigators
- Lead sponsor
- National Human Genome Research Institute (NHGRI)
- Sponsor type
- US National Institutes of Health
- Responsible party
- Sponsor
- Investigators
- Sharon K Davis, Principal investigator, National Human Genome Research Institute (NHGRI)
IDs, dates and publications
- ClinicalTrials.gov ID
- NCT02770001
- Sponsor's protocol ID
- 999916110
- Other IDs
- 16-HG-N110
- Status last verified
- 15 May 2017
- First submitted
- 11 May 2016
- Last updated
- 17 Dec 2019
- Results posted
- No
Study at a glance
From the registry record, last updated by the sponsor on 17 Dec 2019. Recruitment status is as the sponsor reported it: confirm with the study team.
- Official title
- Investigating the Suitability of Some Data Quality Controls Thresholds for Genetic Association Studies of Admixed Population
- ClinicalTrials.gov ID
- NCT02770001
- Acronym / sponsor ID
- 999916110
- Conditions
- African American Genetics
- Keywords
- Admixture, African American, African American Genetics
- Study type
- Observational
- Recruitment status
- Withdrawn
- Enrolment
- 0 participants (actual)
- Lead sponsor
- National Human Genome Research Institute (NHGRI)US National Institutes of Health
- Study start
- 5 May 2016
- Primary completion
- 15 May 2017 (actual)
- Study completion
- 15 May 2017 (actual)
- First posted
- 12 May 2016 (estimated)
- Results
- Not posted in the source record
Clinical summary
The research question as the sponsor registered it. This describes what the study plans to test, not what it found.
Background: In genetic studies, the quality of DNA samples is tested first. Samples that are low-quality are not used. Some studies involve minority ethnic groups. And example is admixed African American. These studies often have small sample sizes. It is important to make sure samples are not discarded unnecessarily. This may happen by using quality control (QC) thresholds for homogenous groups. These may not be appropriate for an admixed group. Researchers want to study samples that failed certain QC tests. They want to see if this has to do with the ancestry of the outliers or the quality of the samples.
Objectives:
To study samples that fail heterozygosity and sample genotype call rate QC. To see if the failing rates have to do with the ancestry composition of the outliers or the quality of the samples.
Eligibility:
No new participants. Researchers will review data that has already been collected.
Design:
Researchers will study DNA samples in a lab.
The samples will not include data that can identify the person the sample came from.
Detailed description
The purpose of this IRB proposal is to gain access to genetic data generated from participants of publically-funded genomic studies and deposited into dbGaP. It is our intention to use dbGaP data to conduct secondary analysis of the influence of admixture on the outcome of data quality control (QC) in genetic association studies to inform future studies of the optimal QC metric for the genetic association analysis of admixed population. The data we intend to use is deposited in dbGaP and is from the Michigan University Health and Retirement Study (HRS). This protocol is being sent to you because of a dbGaP requirement for this specific de-identified dataset to be reviewed by an IRB as that was not in the protocol.
This work will require the use of statistical analyses tools to estimate the genetic ancestry make-up of each sample, from the genotype data, and determine how that ancestry relates to QC outcomes (i.e. whether or not the sample might be excluded from an analysis due to its ancestral genetic composition rather that the sample genetic quality).
Objectives and specific aims: This work aims to investigate samples failing heterozygosity and sample genotype call rate quality control (QC) to determine whether or not the samples call rate and heterozygosity rate have to do with the ancestry composition of the outliers rather than the quality of the samples and inform future studies of potential loss if general QC is applied to genetic data of admixed sample sets.
Rationale and Background: In genetic association studies DNA sample quality can vary largely across study participants and such variation has an impact on genotype call rate and genotype accuracy; samples of low DNA quality tend to have lower genotype call rate and genotype accuracy. Heterozygosity rate (proportion of heterozygous loci per individual) and genotype failure rate (proportion of missing genotypes per individual) are jointly and routinely used to identify samples with low DNA quality at the data quality control (QC) stage of genetic association studies. Excessive heterozygosity rate may indicate sample contamination whilst a reduced heterozygosity rate could indicate inbreeding [1]. Samples with 3-7% [2,3] genotype call-rate and heterozygosity > 2-3 standard deviations from the mean heterozygosity are usually excluded from genetic case-control studies.
Generally, the sample size of genetic association studies involving minority ethnic groups such as admixed African American tends to be small. It is hence important to ensure samples are not discarded unnecessarily, resulting into reduced statistical power, by using QC thresholds applied to homogenous groups which might not be appropriate for an admixed sample set. The aim of this analysis is to investigate samples failing heterozygosity and sample genotype call rate QC to determine whether or not the samples call rate and heterozygosity rate have to do with the ancestry composition of the outliers rather than the quality of the samples. The motivation is to inform future studies of potential loss if general
Study design
- Observational model
- Other
- Time perspective
- Other
Who may qualify
- Ages
- 50 years and older
- Sex
- All
- Healthy volunteers
- Not accepted
- Age groups
- Adult, Older adult
Eligibility is decided by the study team after screening; this overview does not establish that a patient qualifies. Full inclusion and exclusion criteria.
Primary outcome
Continental genetic ancestry fraction
Time frame: Study Completion
1 secondary outcome
Heterozygosity rate
Time frame: Study Completion
Results and safety
The study was withdrawn before enrolling participants, so there are no results.
Research links
- Official record on ClinicalTrials.govLast updated by the sponsor 17 Dec 2019.
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Referral and contact
AzTrials does not enrol participants or take referrals. Contact the study team or a site listed below; they decide who can take part. This study is not recruiting at the moment.
Sharon K Davis principal investigator
National Human Genome Research Institute (NHGRI)
Questions about this trial
What is this clinical trial studying?
An observational study of African American Genetics, run by National Human Genome Research Institute (NHGRI).
The full registered description is in the About this study section and the official record.
Who may be eligible to take part?
Eligibility is decided by the study team after screening, so read the full criteria and contact a listed site.
Is this clinical trial currently recruiting?
The record says: withdrawn, as of the sponsor's last update on 17 Dec 2019. Status can change between updates, so confirm with the study contact before making plans.
What are the possible benefits and risks?
They depend on the study and the treatment, and no study can promise a benefit. The study team explains the known risks during informed consent, before anyone joins; the record itself does not list them.
Are results available for this study?
The study was withdrawn before enrolling participants, so there are no results.
How can a doctor refer a patient or contact the research team?
The record lists no contact. The official record names the sponsor, who can be asked directly. AzTrials does not enrol participants or take referrals.
What does the primary outcome measure?
Continental genetic ancestry fraction (time frame: Study Completion). It is what the study was designed to measure, not a finding.
Where can I read the original study information?
Does a listing mean the treatment is approved or proven to work?
No. A listing means the study is registered. It does not show that the treatment is safe, works, or is approved by a regulator.
How often is this information updated?
AzTrials copies changed records from ClinicalTrials.gov every night and reloads the whole registry every week. The sponsor last updated this record on 17 Dec 2019.