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--- ugli [2020/01/21 13:46]
sylvia [Table]
+++ ugli [2023/11/22 10:55] (current)
sylvia [UGLI Release 2]
@@ Line 1: / Line 1: @@
-====== UGLI release 1======
+====== UGLI ======
 UGLI is one of [[cohort|Lifelines]]' [[additional assessments]]. UGLI is the abbreviation for UMCG Genetics Lifelines Initiative. UGLI aims at facilitating and accelerating genetic data generation and data analysis and thereby scientific output through using the Lifelines genomics data.
@@ Line 5: / Line 5: @@
 ===== Background =====
 Genome-wide association (GWAS) data is highly valuable for biobanks such as Lifelines in identifying disease/trait associations, predicting future disease development and personalized treatment.\\
-To facilitate the generation, analysis and study of genetic data in Lifelines, the UGLI consortium was founded. UGLI brings together many groups and PIs within the UMCG, RUG and beyond that are interested in performing such research with Lifelines data. They have brought the funding together which led to the initial genotyping of a total of 38,030 Lifelines participants, including [[children]], as part of the HUGE consortium in Rotterdam on the Infinium Global Screening Array® (GSA) MultiEthnic Disease Version. In combination with 15,400 samples already genotyped on the Cytochip ([[GWAS]]), a single quality controlled GWAS dataset of n~50,000 subjects will be made available to members of the UGLI consortium based on specific proposals approved by the UGLI steering committee and by Lifelines.\\
+To facilitate the generation, analysis and study of genetic data in Lifelines, the UGLI consortium was founded. UGLI brings together many groups and PIs within the UMCG, RUG and beyond that are interested in performing such research with Lifelines data. They have brought the funding together which led to the initial genotyping of a total of 38,030 Lifelines participants, including [[children]], as part of the [[http://glimdna.org|HUGE]] consortium in Rotterdam on the Infinium Global Screening Array® (GSA) MultiEthnic Disease Version 1.0. Together with 15,400 samples already genotyped on the Cytochip ([[GWAS]]), two quality controlled GWAS datasets with a combined sample size of n~50,000 subjects will be made available to members of the UGLI consortium based on specific proposals approved by the UGLI steering committee and by Lifelines.\\
 The UGLI consortium is actively raising funding for the genotyping of additional samples. The genotyped additional samples are generally referred to as UGLI2. With additional funding of new UGLI members, the consortium will increase the number of genotyped Lifelines participants. These efforts will make Lifelines a more interesting partner for national and international collaborations as well as with non-academic partners that work on healthy ageing.
-===== Subcohort =====
+===== UGLI Release 1 =====
 ,030 Lifelines participants were selected for UGLI release 1 using the following criteria:
   *  availability of isolated DNA-samples of adequate volume and concentration at Lifelines
   *  Caucasian-ancestry samples
-The genotype of 38,030 participants was assessed using the Infinium Global Screening Array® (GSA) MultiEthnic Disease Version. In the QC screening all genotyped samples were included, and the focuss of the QC of genetic
+The genotype of 38,030 participants was assessed using the Infinium Global Screening Array® (GSA) MultiEthnic Disease Version 1.0. In the QC screening all genotyped samples were included, and the focuss of the QC of genetic
 markers was on the autosomes and chromosomes X (N=691,072 markers).
-A final set of 36,339 samples and 571,420 markers on autosomal and X chromosomes passed the QC steps described in QC_report_UGLI_R1.pdf.
+A final set of 36,339 samples and 571,420 markers on autosomal and X chromosomes passed the QC steps described in {{ :qc_report_ugli_r1.pdf |QC_report_UGLI_R1.pdf}}.
 ^ UGLI release 1 cohort - samples that passed QC           ||
@@ Line 27: / Line 27: @@
 | Age* >64                                        | 2,401   |
 Table 1: UGLI release 1 cohort information. These are samples that passed QC. Age at [[1a_visit_1|Baseline assessment first visit]]. *One participant did not visit during [[1a|Baseline]], but did visit during [[2a|2nd screening]]. Since participant was under 18 years of age at [[2a_visit_1|2nd screening visit 1]], this participant has been added to the children 8-17 group.
+{{:ugli_age_distribution.jpg?400|}}
 ==== Overlap between studies====
@@ Line 38: / Line 40: @@
 ===== SNP Genotyping Array =====
-The Infinium Global Screening Array® (GSA) MultiEthnic Disease Version was used for SNP genotyping of the UGLI release 1 cohort. This array contains approximately 1,000,000 SNPs and combines multi-ethnic genome-wide content, curated clinical research variants, and quality control (QC) markers for precision medicine research((https://www.illumina.com/content/dam/illumina-marketing/documents/products/datasheets/infinium-commercial-gsa-data-sheet-370-2016-016.pdf)).
+The Infinium Global Screening Array® (GSA) MultiEthnic Disease Version 1.0 was used for SNP genotyping of the UGLI release 1 cohort. This array contains approximately 1,000,000 SNPs and combines multi-ethnic genome-wide content, curated clinical research variants, and quality control (QC) markers for precision medicine research((https://www.illumina.com/content/dam/illumina-marketing/documents/products/datasheets/infinium-commercial-gsa-data-sheet-370-2016-016.pdf)).
 ===== Quality Checks =====
 An UGLI (release 1.0) Quality Control Report is available, describing in detail the QC steps that were taken during the quality control (QC) process of the first release of UGLI comprising the genotype of 38,030 participants
-assessed using the Infinium Global Screening Array® (GSA) MultiEthnic Disease Version. In this QC screening all genotyped samples were included, but the focus was on QC of genetic markers on the autosomes and chromosomes X (N=691,072 markers).\\
+assessed using the Infinium Global Screening Array® (GSA) MultiEthnic Disease Version 1.0. In this QC screening all genotyped samples were included, but the focus was on QC of genetic markers on the autosomes and chromosomes X (N=691,072 markers).\\
 \\
 In brief, first translations and corrections specific from the GSA platform to a general
@@ Line 88: / Line 90: @@
 In UGLI, samples for which biological sex does not match registrated sex will be excluded from the main dataset, but not completely neglected (as opposed to [[gwas|GWAS]]). These samples will still undergo quality check analyses and will be made available for analyses to the researchers.
+===== UGLI Release 2 =====
+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.
 =====UGLI-data release=====
-UGLI data is currently being generated, analysed and quality checked. This data is not yet available for release.
-UGLI data will be made available on the HPC (Linux environment) of the UMCG once it is available and therefore the data is only accessible to researchers who are working at or are affiliated with the University Medical Center Groningen (UMCG). The data will not be accessible through the Lifelines workspace. The applicant’s proposal will be reviewed by both Lifelines and the UGLI steering committee (UGLI SC).
+UGLI data is available on the HPC (Linux environment) of the UMCG. The data will not be accessible through the Lifelines workspace. The applicant’s proposal will be reviewed by both Lifelines and the UGLI steering committee (UGLI SC).
-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 applicant’s 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.
+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-UMCG researcher requesting UGLI data has three options:
+A non-UGLI consortium member requesting UGLI data has the following option:
-  * The applicant joins the UGLI consortium by paying €10.000. After joining the consortium you will receive an UMCG account so that you can access the UGLI data. 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 (non-UGLI consortium members can only submit one proposal and get access to the data for 1 year). 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, get the applicant into contact with the UGLI contact person Harold Snieder.
+  * 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 establishes a partnership with an UGLI consortium member. The applicant and the UGLI consortium partner will discuss the terms of this partnership, i.e. co-autorship, costs for analyses. To gain access to the data for 1 year, costs will be involved which still have to be determined. Phenotypic data that has been requested specifically in your proposal will be made available together with access to the UGLI release folder.
-  * The applicant hires an in-house UMCG analyst who would be available to analyse the data. That UMCG analyst (or PhD student or postdoc) can have access to the data if the applicant’s application is approved. Extra costs may be involved and it needs to be clear to the applicant that Lifelines can not ensure that willing partners or willing analysts are available. This is up to the UGLI steering group. Furthermore, to gain access to the data for 1 year, costs will be involved which still have to be determined.  Phenotypic data that has been requested specifically in your proposal will be made available together with access to the UGLI release folder.

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