APOE4 Discrepancy between APORES file and ADNIMERGE

[Victor E]

I’m currently working with APOE genotype data from ADNI and noticed a number of discrepancies between the APOE4 values in the ADNIMERGE dataset and those derived from the APOERES file based on participants’ genotypes.

Below is a summary of the participants with conflicting APOE4 values:

To ensure accuracy in my analyses, I wanted to confirm the following:

1. Are these discrepancies due to data entry or merging errors, or do they reflect historical updates that have not yet propagated across datasets?

2. Is the APOERES file considered the authoritative source for APOE genotype and APOE4 allele count?

3. Are there any forthcoming updates or best practices for resolving such inconsistencies?

[Danielle J Harvey]

Hi Victor,

 

Thank you for bringing this to our attention. I have an older APOERES file (downloaded several years ago) and the genotype results there match what is in ADNIMERGE…so the newer APOERES file is different from the older one. I will reach out to the Genetics Core for clarification.

 

Danielle

 

From: adni...@googlegroups.com <adni...@googlegroups.com> On Behalf Of Victor E
Sent: Tuesday, July 8, 2025 6:45 AM
To: Alzheimer's Disease Neuroimaging Initiative (ADNI) Data <adni...@googlegroups.com>
Subject: [adni-data] APOE4 Discrepancy between APORES file and ADNIMERGE

 

I’m currently working with APOE genotype data from ADNI and noticed a number of discrepancies between the APOE4 values in the ADNIMERGE dataset and those derived from the APOERES file based on participants’ genotypes.

Below is a summary of the participants with conflicting APOE4 values:

 

To ensure accuracy in my analyses, I wanted to confirm the following:

1. Are these discrepancies due to data entry or merging errors, or do they reflect historical updates that have not yet propagated across datasets?
2. Is the APOERES file considered the authoritative source for APOE genotype and APOE4 allele count?
3. Are there any forthcoming updates or best practices for resolving such inconsistencies?

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[Danielle J Harvey]

Hi Victor,

 

I was able to get clarification from the Genetics Core. Because they also do WGS on samples, they are able to cross-check genotypes and make any corrections that are needed. The APOERES table should be considered the most accurate. They doublechecked the ones you flagged below and confirmed that the GENOTYPE column (from APOERES) matches their records. ADNIMERGE was using an older version of the table, which was causing the discrepancy. I will let the team responsible for ADNIMERGE know to see if they can fix it.

 

Danielle

 

 

 

From: adni...@googlegroups.com <adni...@googlegroups.com> On Behalf Of Victor E
Sent: Tuesday, July 8, 2025 6:45 AM
To: Alzheimer's Disease Neuroimaging Initiative (ADNI) Data <adni...@googlegroups.com>
Subject: [adni-data] APOE4 Discrepancy between APORES file and ADNIMERGE

 

I’m currently working with APOE genotype data from ADNI and noticed a number of discrepancies between the APOE4 values in the ADNIMERGE dataset and those derived from the APOERES file based on participants’ genotypes.

Below is a summary of the participants with conflicting APOE4 values:

 

To ensure accuracy in my analyses, I wanted to confirm the following:

1. Are these discrepancies due to data entry or merging errors, or do they reflect historical updates that have not yet propagated across datasets?
2. Is the APOERES file considered the authoritative source for APOE genotype and APOE4 allele count?
3. Are there any forthcoming updates or best practices for resolving such inconsistencies?

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You received this message because you are subscribed to the Google Groups "Alzheimer's Disease Neuroimaging Initiative (ADNI) Data" group.
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To view this discussion visit https://groups.google.com/d/msgid/adni-data/7e3248aa-14b6-43a3-988f-876ccb29a2e7n%40googlegroups.com.

[Victor E]

Thanks Danielle! Very much appreciate you following up on this and the quick turnaround

-Victor