Does the UCLA ATLAS Community Health Initiative have an IRB?

Patient Recruitment and Sample Collection for Precision Health Activities at UCLA is an approved study by the UCLA Institutional Review Board (UCLA IRB). IRB#17-001013

How are the genotype data generated and where are the data stored?

UCLA ATLAS Community Health Initiative DNA samples are genotyped on the Illumina Global Screening Array and microarray genotype data exit the Illumina scanner as binary .gtc files, one file per patient sample. These files are then processed and converted to single VCF and combined Plink files. VCF files are loaded into GenomicDB in the cloud. Combined Plink files are loaded into Discovery Data Repository (DDR) in Azure cloud.

How can I access clinical and/or genotype data on UCLA ATLAS Community Health Initiative patients?

De-identified clinical and genomics data for UCLA ATLAS Community Health Initiative patients can be accessed via the Discovery Data Repository (DDR) in the Azure cloud. Raw plink files are linked to the clinical data by a sample-id. To request access to DDR submit a ticket here.

De-identified genotype data (VCF files), may be accessed in GenomicDB, a repository for genomic data, via Scala (Zeppelin). To access the data, click here to fill out the data/sample request form.

How can I access samples?

All requests for DNA samples of UCLA ATLAS Community Health Initiative patients will be sent to the prioritization committee for review. Upon approval, the investigator is contacted by the UCLA ATLAS Precision Health Biobank for next steps.

How do I collaborate with IPH?

Please send an email to the Program Manager of IPH, Maryam Ariannejad - [email protected], to start a conversation.

How do I identify potential research cohort counts participating in the UCLA ATLAS Community Health Initiative?

Use the Informatics for Integrating Biology & the Bedside (i2b2) Cohort Discovery tool or Discovery Data Repository (DDR) to find out how many of your targeted patients already are participating in UCLA ATLAS Community Health Initiative and have been consented.

How to cite Institute for Precision Health in publications?

The sample and data gathered from UCLA ATLAS Community Health Initiative patients represent an unprecedented resource for genetic studies. Therefore, we require that researchers who receive financial support or utilize supported resources or services from the Institute for Precision Health (IPH) acknowledge IPH appropriately.

To this end, we have created the following guidelines for citing IPH. If you need further clarification, please contact IPH Program Manager, Maryam Ariannejad at [email protected].

1. If researchers used UCLA ATLAS Community Health Initiative biomaterials or accessed the genotypic or phenotypic data, UCLA ATLAS Community Health Initiative and IPH should be acknowledged as follows:

"We gratefully acknowledge the resources provided by the Institute for Precision Health (IPH) and participating UCLA ATLAS Community Health Initiative patients. The UCLA ATLAS Community Health Initiative and UCLA ATLAS Precision Health Biobank, is a program of the IPH, which directs and supports the biobanking and genotyping of biospecimen samples from participating UCLA patients in collaboration with the David Geffen School of Medicine, UCLA Clinical and Translational Science Institute grant number UL1TR001881, and UCLA Health.”

2. IPH faculty that receive financial support or utilize supported resources or services from the Institute for Precision Health are required to include their IPH affiliation in grants, presentation and other media.

3. Any researcher that publishes a manuscript based on IPH data or resources should forward a link to: Maryam Ariannejad, IPH Program Manager @ [email protected].

Is there a cost for accessing sample or data?

The UCLA ATLAS Precision Health Biobank charges UCLA investigators a nominal fee for its services. Please contact Dr. Clara Magyar - [email protected] for more details.
De-identified data are available to researchers at no cost. To access the data, click here to fill out the data/sample request form.
The UCLA Clinical and Translation Science Institue (CTSI) handles all requests for identified data. Click here to request a consult online at intranet.ctsi.ucla.edu.

What data are available on UCLA ATLAS Community Health Initiative patients?

De-identified clinical and genotype data from UCLA ATLAS Community Health Initiative patients are available for researchers upon request based on the Illumina Global Screening Array. Imputed data may also be available.

What is the DDR?

The DDR stands for the Discovery Data Repository - built upon a limited data set containing de-identified electronic health record data. It includes a selection of tools (Azure SQL Data Warehouse, Jupyter, Tableau), data sets (clinical data, genomics, waveform, devices and other Internet of Things) and technologies (Azure Platform, Linux, Citrix) to support growing data discovery requirements for UCLA Health Sciences and affiliated researchers across the UCLA campus. To request access to DDR submit a ticket here.

What kind of clinical and genotype data are available on UCLA ATLAS Community Health Initiative patients?

De-identified genotype data are available to UCLA researchers. Click here to submit a request.

Limited (date-shifted) data are available to UCLA researchers upon getting access to Discovery Data Repository (DDR). To request access to DDR submit a ticket here.

All requests for identified data will be reviewed by the CTSI scientific review committee first. Click here to request a consult online.

What SNPs are present on the UCLA ATLAS Community Health Initiative array?

Click here to use the Global Screening Array and Multi Disease SNP browser to look for the array content by gene name, chromosomal region (build 38 base pair position) or SNP name (primarily rs ID). Click here to download the entire manifest (29Mb).

What stock language is available for grant applications?

Please see the Institute for Precision Health Facilities document for the grant application language.

 

For questions about data security and protection visit The UCLA Health System's Compliance Program.