Mar 26, 2025
Version 2
TGD_Genotyping_Core_Instructions V.2
This protocol is a draft, published without a DOI.
- 1Stanford
Protocol Citation: Seth Sharp 2025. TGD_Genotyping_Core_Instructions. protocols.io https://protocols.io/view/tgd-genotyping-core-instructions-d6cx9axnVersion created by Swaraj Thaman
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: February 11, 2025
Last Modified: March 26, 2025
Protocol Integer ID: 125047
Abstract
This is the protocol to follow by the Stanford Genomics Core with regards to processing samples coming from the Translational Genomics of Diabetes Lab.
Receipt of batches of samples, arrays, and descriptive files
Receipt of batches of samples, arrays, and descriptive files
The Gloyn Lab will deliver the following to the Stanford Genotyping Core:
- Extracted sample DNA (either 96-well plates or tubes)
- Genotyping arrays (Illumina Omni2.5Exome V1.6 [Omni] or Global Diversity Array [GDA])
- Sample QC excel sheet containing sample identifiers, plate arrangements, and quality control information
Samples for genotyping are submitted as single batches (~50-200 samples per batch)
*Important note* each batch of samples delivered corresponds to one model of genotyping array, no batch should mix array types. For example, 64 samples may be delivered at once for GDA genotyping, Separately, 128 may be delivered as a separate batch for Omni genotyping.
Genotyping, clustering and export of data files
Genotyping, clustering and export of data files
Genotyping core runs the genotyping protocol
Genotyping arrays are run for all samples generating IDAT files containing intensity data.
*Important note* sample names as provided need to be preserved exactly. For instance, if a sample is listed as 'EDMN480DNA' on the Sample QC Sheet, please make sure that it is recorded as 'EDMN480DNA' in the genotyping data (please make sure that there are no extra underscores, no omissions of the 'DNA' suffix, etc). Previously we have had issues with sample names being changed, e.g. HIGI changed to HIG1, EDMNDNA changed to EDMN.
Genotyping core uses Illumina GenomeStudio to cluster and export genotyping data
Intensity files are clustered and exported as PLINK data files (ped/map) using GenomeStudio with the following settings:
- Manifest/strand A1 orientation (A1 in file name)
- Aligned to TOP strand (default if left unchanged)
- Tick "Remove zeroed SNPs from report"
- Any option to select manifest should correspond to GRCh37/hg19
*Important note* each type of array MUST be clustered with different input files
GDA - as per genome studio:
• Manifest file: default option corresponding to A1 / TOP
• Cluster file: default option corresponding to A1 / TOP
Omni - custom Gloyn lab files:
• Manifest file: "Omni2-5Exome-8v1-6_20098051_A1.bpm"
• Cluster file: "TGD_Omni2_5_v1_6_Exome_V1_5_A1.egt"
Naming and upload of data files
Naming and upload of data files
Genotyping core saves the output files with a new naming schema
We are changing to a new naming schema so Omni and GDA array files do not get mixed up
Omni arrays - Please continue with the V<XXX> naming schema e.g. V158, V159
GDA arrays - Please name all GDA arrays from now as G<XXX> naming schema starting at G043
*Important note* please keep the naming consistent, e.g. G043 not G_043 or G43
Genotyping core uploads data via Globus.
Please create a collection on your Globus endpoint. Please keep Omni and GDA arrays in separate collections and make sure to label which are GDA and which are Omni respectively
Gloyn lab will access the Globus endpoint and transfer the files to the Gloyn lab space (/oak/stanford/groups/agloyn/) using the SRCC_Oak endpoint.
*Important note* please only upload whole batches when complete rather than partial files
Gloyn dry lab team will copy and verify the files.