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--- ugli [2023/03/23 10:36]
bas
+++ ugli [2023/11/22 10:55] (current)
sylvia [UGLI Release 2]
@@ Line 91: / Line 91: @@
 ===== UGLI Release 2 =====
-As of March 2023, data of an additional +-30,000 genotyped participants has been made available. This release, called UGLI2, were genotyped using the FinnGen Thermo Fisher Axiom® custom array. Information on the QC of these samples can be found here: {{ :QC_report_UGLI2_(release_1)-v1.pdf |QC_report_UGLI2_(release_1)-v1.pdf}}
+As of March 2023, data of an additional 28,249 genotyped participants has been made available. Samples in this release, called UGLI2, were genotyped using the FinnGen Thermo Fisher Axiom® custom array.
+,166 participants were selected for UGLI 2 release and assessed using the pre mentioned array. All genotypes were included for QC screening, but the QC focussed on the the autosomes and chromosomes X for which there are N=617,715 and 22,405 markers available, respectively. A final set of 28,250 samples and 462,731 markers on autosomal and X chromosomes passed the QC steps described in
+ {{ :QC_report_UGLI2_(release_1)-v1.pdf |QC_report_UGLI2_(release_1)-v1.pdf}}.
+Please note that the array used for UGLI2 differs from the one used in UGLI1. Overlap in SNPs between these two arrays (GSA chip from Illumina=UGLI1 and FinnGen array from Affymetrix/ThermoFischer=UGLI2) is small, namely 1000-10000 SNPs.
@@ Line 110: / Line 106: @@
 UGLI consortium members receive temporary exclusive right to use the data for a period of 3 years, meaning that consortium members hold the first right to use the data should the non-UGLI member applicants proposed study overlap with a study from one of the UGLI consortium members. The 3-year period starts when UGLI-data is released on the UMCG cluster. After 3 years, UGLI consortium members must submit applications for the use of the data generated within UGLI via the regular Lifelines application procedure.
-A non-UGLI consortium member requesting UGLI data has the following options:
+A non-UGLI consortium member requesting UGLI data has the following option:
   * The applicant applies via the regular Lifelines application procedure. This means the applicant submits the proposal together with the dataset order using our online catalogue (https://data-catalogue.lifelines.nl/). UGLI data cannot be selected through the online catalogue. The applicant can request UGLI data by stating this in the written proposal. Current costs for data access will be charged. For more information on costs please visit our website: https://www.lifelines.nl/researcher/how-to-apply/costs-biobank-lifelines.
-  * The applicant joins the UGLI consortium by paying €10.000. This option holds the advantages that you will also gain the right of the 3 year embargo period, you will be able to submit multiple proposals within the 3-year embargo period with no costs being charged for access to the UMCG HPC and the data (Lifelines workspace access, data linkage, sample requests and add-ons do not fall within this agreement). Furthermore, as an UGLI consortium member you will gain access to all the available Lifelines phenotype data and get full support from other UGLI consortium members. If the applicant is considering this option, please contact the UGLI contact person: Harold Snieder.

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