Alzheimer’s Disease Neuroimaging Initiative

Core Q&As

Genetics Core Q&A

Hi, I want to find Genotyping result about ADNI 4. Is there any result about it? I can not find result in ARC builder
10/08/24

I downloaded post-processed ADMC Duke p180 FIA and P180 UPLC (file ADMCDUKEP180FIA.LEVEL5 and ADMCDUKEP180UPLC.LEVEL5), however, I didn't find the dictionary for these two fil...
03/18/24

I downloaded the ADNI genetic data to do GWAS research, I get the data in plink format where I was able to get the three files of .bed, .bim and .fam, however as the fam file ...
03/13/24

For the methylation data, Vasanthakumar et al., 2020 indicated that blood cell composition could be substantially affect methylation differences between individuals and theref...
02/05/24

Hi ADNI experts, I'm interested in SNP rs2230288, which is a common SNP for some neurodegenerative disorders. The allele info is available in ADNI3 but not in ADNI1 and ADNI2/...
01/10/24

Hello, I would like to check how a specific genetic polymmorphism relates with tau pet burden. I have a collaborator with access to ADNI and that would perform the analysi...
09/27/23

Hello, I've downloaded the microarray data from https://ida.loni.usc.edu/pages/access/geneticData.jsp#207 and can't find a way to match the microarray column names (subject ID...
01/30/23

Hello, I am looking to pull a specific SNP (rs2233154) from the GWAS data and match the carrier status to the curated cohort of patients. I used PLINK 1.9 to analyze the .bed ...
01/19/23

Hello! I've got the WGS SNP data (i.e. GWAS type data) and I've been trying to match it to my phenotype information. I used the PTID from the roster file to make my IID and us...
09/12/22

Hello, I was wondering where I can find the APOE genotype of the ADNI database ? Thank you for your help Best, AÃ¯da
12/15/20

Hi, News said ADNI GO & 2 ApoE Genotypes ped and fam files were available. Do you know where I can download?
11/20/20

I am wondering how NAs are treated in the SNP data? For analyses where NAs are too cumbersome, is HapMap imputation utilized or something else? I plan on applying component an...
10/06/20

I was referring to a few published articles and found that ADNI has contributed 441(268 cases and 171 controls), to the ADGC study. Is it possible to get the IDs of these 441 ...
09/29/20

Hi, I am working with some data, and I found out that some of our snps Id is in "kgp" format. (For example: kgp6703048). How do I convert this id format into an rs snp id? ...
08/26/20

Dear professor, I used the SNP ID in the ADNI 1 GWAS and the SNP ID in the APOE gene (about 1000) to find duplicate values. The repeated part is only about sixty, why not all?...
06/20/20

Hi, for ADNI WGS VCFs, it has been mentioned that GATK VQSR (VariantRecalibrator + ApplyVQSR) variant QC steps were used. Can you please tell me how these were applied? For in...
06/04/20

Dear Genetics Core, A few days ago, I sent you a query re: a few questions I had. However, I still have not received any responses re: my specific questions. Could you plea...
06/02/20

Dear ADNI: I am planning a study using ADNI DNA methylation data. I am specifically interested in looking at the relationship between DNA methylation age in relation to MCI...
05/31/20

I'm using the ADNI 1 GWAS data and I need to extract specific SNPs by their "rs" value under the variable SNP.Name. However, when I download the csv files into R the SNP Name...
04/16/20

I'm interested in using DNA methylation data, but the normalized and QC-ed data files seem unavailable. Can you let me know how to have access to those? Also if I end up using...
03/05/20

Hi, I processed plink file of ADNIGO-2, noticing chr0-25, and dict says 1-22, X, Y, XY, MT. so chr23 is X and Chr24 is Y, is it right? However, when I sexcheck, it tells 167...
02/14/20

I downloaded the GWAS plink for ADNIGO-2. Want to merge APOE genotyping too. I noticed the news: New ADNI GO & 2 ApoE Genotypes are available in the Download section of the AD...
02/13/20

How is APOE4 coded in the ADNIMERGE dataset? 0, 1 and 2 stand for what?
01/27/20

Dear ADNI expert, I am using 'ADNI_GO_2' SNP database. Among the columns, 'Sample Index', 'Sample ID', 'GC Score', 'SNP Index', 'SNP Name', 'Allele1 - Top', 'Allele2 - Top', '...
11/10/19

Dear ADNI expert, I am using ADNI_Gene_Expression_Profile.csv to conduct some experiments. I wish to obtain the pathway information for the gene in the file. But it requires m...
09/24/19

Hiï¼ŒADNI, I will explain my questions with the following example: eg: In merged GATK vcf data of ID 141_S_4232, the ref is T, but there was three alt variants at chr3 119...
08/02/19

Dear ADNI, In CASAVA vcfs, what is the difference between GT 0/1 and 1/0? And whatâ€™s the meaning of MAXGT and POLY? Could you explain the two questions in details?
07/30/19

Hello, During the ADNI steering committee meeting it was mentioned that the ADNI-2 genetic imputation data would be made available around mid-2019. Is this data currently ava...
06/19/19

I've downloaded the genetic data in ADNI1, only including the .PLINK format. I wonder why the number of subjects in .PLINK file is 757 but not 818 and which procedures it had ...
01/21/19

I am new to the genetic data introduced by ADNI. I wanted to know how to extract the most-related SNPs to AD. Thanks in advance
12/04/18

Hello, Thank you very much for the incredible work that your team does with ADNI. My question relates to the APOE4 data in ADNI3. The majority of patients in ADNI3 do not s...
04/13/18

Hello, I have downloaded the dataset ADNI1/GO/2 WGS. However, I cannot find the diagnostic label. In the file "DXSUM_PDXCONV_ADNIALL.csv", there is only diagnostic labels for ...
04/08/18

Hello, I have downloaded the dataset ADNI1/GO/2 samples whole-genome sequenced, but I cannot find the diagnostic labels. Could you please let me know where I can find the diag...
04/08/18

Hello, How do the subject ID labels in the Plink files for ADNI1/2/GO relate to the subject IDs (i.e., ID, RID) in the file 'DXSUM_PDXCONV_ANDIALL.csv'? These labels don't ma...
03/24/18

I'm working with ADNI GWAS data, and I've discovered that these files use Illumina's kgp* format for naming SNPs rather than the rs* format used by NCBI. I'd like to find the ...
02/23/18

Dear ADNI Genetics Core, I have downloaded the "adni_mito_genomes.vcf" file and am trying to convert the file to PLINK format. However, my several tools (e.g., bcftools, PL...
02/20/18

Hello, I have obtained the bam files for a number of samples for my project. However, I am struggling to find within them the discordant/partially mapped reads. Having look...
01/17/18

Hello, I am working with ADNI WGS data, which is supplied in aligned bam format. The headers of the bam files state a reference fasta of either 'HumanNCBI37_UCSC_XX.fa' or ...
01/10/18

Hello I am a Post-doc working on reduced penetrance of familial AD and FTD. We have interested to identify the modifiers of AD and FTD using reduced penetrance subjects. We...
01/03/18

Hello, Is there a programmatic way to access the raw BAM data for ADNI? This is for the HLI (Human Longevity Inc.) team, ideally we would have access to this data availabl...
11/21/17

Hello. I have some questions while searching your database ADNI. What does that mean [APOE] and [TOMM40L] in 'ADNI_Gene_Expression_Profile.xlsx'. I want to know the exact...
11/20/17

Hello, Could you please advice how to combine GWAS data for ADNI1 (757 subjects) and ADNIGO/2 (432 subjects) before running QC? Thanks
11/16/17

Hello, I am interested in the longitudinal data for expression and looking at the 'ADNI_Gene_Expression_Profile' matrix I see that each subject has gene expression profile ...
11/08/17

I've recently downloaded the ADNI WGS alignment data (809 samples). How can I connect the bam filenames to the sample IDs?
11/01/17

How to interpret one's genotype? Where can i get the genotype of a human?
09/18/17

Hello, Could you please clarify the visit codes for ADNI2 for gene expression data? v02 v03 v04 v05 v06 v11 Thanks
07/11/17

Hi, Could you please advice if there's epigenetic longitudinal data for ADNI participants? Thanks
07/11/17

Dear ADNI, Some VCF files for WGS data have variants with genotype calls of ./. , instead of 0/0, 0/1, or 1/1, even though these variants pass all filters. Could you please...
06/28/17

Most samples in the vcf file have SITE_ID_S_RID, there is an upper case S, that sits in between the site and rid, but some samples, e.g., 041_s_4629, have a lower case s. Why ...
04/13/17

Hi folks, I'm working with ADNI GWAS data, and I've discovered that these files use Illumina's kgp* format for naming SNPs rather than the rs* format used by NCBI. I'd like...
01/06/17

For the VCF SNPs file, how do we genotype the participants. I found in an online guide that the '11AD40929_POLY' column gives you a key. They stated that 0/0 represents homozy...
12/01/16

Can you tell me how subjects were selected for Whole Genome Sequencing? Was there selection based on APOE genotype?
10/17/16

How can I know which sample in 818 ADNI paticipants of ADNI2 assigned to AD, MCI or controls
08/02/16

Do you know if there is any overlap in subjects between the ADNI samples and the IGAP summary data (http://web.pasteur-lille.fr/en/recherche/u744/igap/igap_download.php)?
05/26/16

When I extract the ADNI_cluster_01_forward_757LONI data. I found that the column where suppose to figure out the phenotype of the sample are all with value of -9. How could...
05/25/16

Hello sir, I downloaded WGS data how many participants(normal,MCI,AD) of WGS data after select baseline diagnosis only? thanks
05/03/16

To whom it may concern, I have questions regarding ADNI genetic data. Can you help to answer them? 1. How many samples were genotyped using Omni 2.5? I downloaded the O...
01/25/16

Dear Sir and Madam, I am working on ADNI GWAS data now. As I noticed, there is only SNPs information in the dataset. I am wondering if there is a way for me to get the geno...
01/08/16

Dear Sir or Madam, we're interested in SNP analyses using the ADNI Omni2.5M microarray SNP data. We can use Plink (or gPlink) to do first analyes, but as data related to init...
12/15/15

Could you please specify the visit on which were collected the blood samples that were used for generating the gene expression profiles posted on posted April 27, 2015 ?
11/24/15

Hi! I'm looking align the strand of the Omni 2.5M-8 chip using one of strand files from: http://www.well.ox.ac.uk/~wrayner/strand/index.html Are any of these the correct...
09/13/15

My colleagues and I have recently downloaded the ADNIgo/2 GWAS data from LONI IDA. We were missing data from 70 subjects but were told that data should be available for those ...
08/14/15

My question is about Gene Expression data. When I read its description pdf file, it seems like RNA expression level. And, I searched for the chip in the affymetrix web page...
05/21/15

Dear sirs, Please, correct me, if what I understood is wrong. Yesterday night (Dec 21th, 2014), I downloaded ADNI WGS vcf files. The sample IDs in vcf files were written in...
12/22/14

Today (Dec 22th, 2014), the sample IDs in vcf files of ADNI WGS GATK are still in the previous format such as 08AD6536, 08AD6540, and so on. Also, the csv file (ADNI_PTID_WG...
12/22/14

The vcf file (ADNI WGS GATK) for chr 9 unloaded in this website does not contain vcf for chr9 but "ADNI.808_indiv.minGQ_21.pass.ADNI_ID.tar" This file does not have any lines...
12/22/14

Dear ADNI group, ADNI news enounciates release of GATK WGS data, but the afformentioned links are missing in download section. Is the data unavailable at the momment?
12/17/14

Merging the ADNI_PTID_WGS_Sample_Correspondence with the ADNIMERGE table (by PTID = ADNI_PTID), I do not find the announced numbers of sequenced patients by disease category, ...
10/28/14

I find only 717 VCF files within the 25 zip archives I downloaded from (see listing below). I would expect 809 files, according to ADNI_WGS_Notice_20130917. Did I miss somethi...
10/27/14

I just downloaded the PLINK-format version of the variant calls derived from the ADNI WGS data. Having a quick look at the .bim file, I notice that location data is missing (...
10/14/14

kindly, i need the equivalent "rs" notations for the following two SNPs kgp8565253 and kgp5536625
10/08/14

Dear ADNI Genetics Core staff, I am downloading ADNI WGS data for analysis. However, I couldn't find an excel-like file for demographic information. Therefore, I checked WGS_...
09/08/14

Could you please give a description of the ADNI test data, which is imputed data? I have tried to open readme file, but unfortunately it seems to be corrupted and unreadable.I...
09/04/14

i want to know if the Whole genome sequencing (WGS)data in plink formats have APOE and TOMM40 genotyping data or not
08/13/14

In plink data i found 2 different SNP annotations one starting with rs(i know this annotation)and one with kgp what dose it mean? and what is the (rs) equivalent notation for ...
08/01/14

Please I have downloaded the genetic data and I have found more than one diagnosis value (1, 2, 3...) related to different times/ dates. I do not know which value can be taken...
07/08/14

I downloaded the plink data(812) with missing phynotype and after linking it with clinical data(879) to know AD,MCI and control subjects, i don't found 495 subjects and found ...
06/30/14

I downloaded the plink data(812) with missing phynotype and after linking it with clinical data(879) to know AD,MCI and control subjects, i don't found 495 subjects and found ...
06/29/14

i downloaded the complete plink data set for alzheimer (812) but with missing phenptype i want to know the case and control subjects
06/27/14

Dear ADNI Genetics Core, I was wondering what build have been used for the GWAS plink files? Further, I noticed a new addition to the ADNI genetic data, namely, AD Chall...
06/16/14

I have re-downloaded all available .zip files for the ADNI1 GWAS data and extracted successfully, however, there are only 757 subject files. I have read on the ADNI website th...
06/09/14

Dear ADNI scientist, After downloading whole-genome sequencing VCF files, I have faced a subject who lacks any SNP for X and mitochondrial chromosomes. The subject ID is...
06/06/14

I am trying to identify the current diagnosis status for samples in the WGS data (##_S_####). I have cross-referenced the last four digits of the PTID (RID) against the Diagno...
06/05/14

Is there now, or will there be in the future, a multi-sample VCF released for the WGS dataset?
04/15/14

There is an error in the data for the Everyday Cognition (ecog) test in the neuropsychological database. The test has 39 items but there are 40 items listed. There appears to ...
04/02/14

Hello. A PDF at http://adni.loni.usc.edu/wp-content/uploads/2010/09/ADNI_WGS_Notice_20130917.pdf has this infomation: In July 2012 the Brin-Wojcicki Foundation and th...
03/23/14

I want to know about detail APOE information. I know all ADNI data include *.xml file each patient. In xml file,I found below sentence. "3...
12/26/13

Dear Support, I would like to enquire how I can assign roster IDs to ADNI genetic data? For example, if I have 153_S_4172.csv, how do I know the RID of the subject this genet...
10/13/13

I have a question about ADNI sample IDs. I'd like to know how to connect FID and IID written in the plink file (ADNI_cluster_01_forward_757LONI.fam) in ADNI_1_GWAS_Plink.z...
08/09/13

Hi Genetic Core experts, I have a two-folded question. 1) Are the .csv files annotated raw files from Illumina? How do you match the SNP name with dbSNP id's? 2) Was the plin...
06/26/13

Hi ADNI team, I wonder why all of 819 ADNI1 participants' SNP data could not be provided. When I downloaded the ADNI1 PLINK format data, It has 757 participants\' SNPs. Would...
05/16/13

I'm an employee at LONI, currently using the ADNI2 subset for DTI analysis. I realized that ADNI2 participants weren't genotyped using the Illumina Quad-Core 610 Bead Chip. Wh...
04/25/13

I am trying to find the BDNF information (Homo, Hetro, non-carrier) for the ADNI data. The plink file under 'Genotype information' tab does not have the ped/map files. Could ...
04/23/13

Do we have ApoE genotyping for all ADNI 1 study participants? And what is GWAS?
04/11/13

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