ugli
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ugli [2022/06/02 11:15] sylvia [UGLI-data release] |
ugli [2023/11/22 10:55] (current) sylvia [UGLI Release 2] |
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| - | ====== 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. | 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. | ||
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| - | ===== Subcohort ===== | + | ===== UGLI Release 1 ===== |
| 38,030 Lifelines participants were selected for UGLI release 1 using the following criteria: | 38,030 Lifelines participants were selected for UGLI release 1 using the following criteria: | ||
| * availability of isolated DNA-samples of adequate volume and concentration at Lifelines | * availability of isolated DNA-samples of adequate volume and concentration at Lifelines | ||
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| 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 | 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). | 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 || | ^ UGLI release 1 cohort - samples that passed QC || | ||
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| 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. | 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. | ||
| + | 29,166 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. | |
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| 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. | 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 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. 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, please contact the UGLI contact person: Harold Snieder. | ||
ugli.1654161327.txt.gz · Last modified: 2022/06/02 11:15 by sylvia
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