Changes between Initial Version and Version 1 of BIOS_Phenotype


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Timestamp:
Sep 20, 2016 1:03:39 PM (8 years ago)
Author:
jamverlouw
Comment:

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  • BIOS_Phenotype

    v1 v1  
     1= Phenotype data and metadata =
     2This file contains data on the core phenotypes, data on DNA/RNA samples and measurements (meta-data) and agreement that samples and data are made available to analyses within RP3.
     3
     4== Format ==
     5 ||Biobank  || CODAM, LL, LLS, NTR, PAN, RS ||
     6 ||pheno_id  || ID linked to phenotypic data in line with sample_id list provided [[BR]] for data uploads (can be person_id if no special id for phenotype exists) ||
     7 ||Ascertainment_criterion  || Inclusion criterion biobank/selected samples ||
     8 ||GWAS_Chip  || comma separated in case of multiple chips ||
     9 ||GWAS_DataGeneration_Date  || YYYY ||
     10 ||DNA_BloodSampling_Age  || xx.x (i.e. years + 1 decimal) ||
     11 ||DNA_BloodSampling_Date  || YYYY-MM-DD ||
     12 ||DNA_BloodSampling_Time  || HH:MM ||
     13 ||DNA_Source  || Whole blood, other ||
     14 ||DNA_Extraction_Method  ||   ||
     15 ||DNA_Extraction_Date  || YYYY-MM-DD ||
     16 ||DNA_QuantificationMethod  ||   ||
     17 ||DNA_A260A280ratio  || A260/A280 ||
     18 ||RNA_BloodSampling_Age  || xx.x (i.e. years + 1 decimal) ||
     19 ||RNA_Sampling_Date  || YYYY-MM-DD ||
     20 ||RNA_Sampling_Time  || HH:MM ||
     21 ||RNA_Source  || Pax gene, other ||
     22 ||RNA_Extraction_Date  || YYYY-MM-DD ||
     23 ||RNA_Extraction_Method  ||   ||
     24 ||RNA_RIN  || RIN or equivalent score ||
     25 ||RNA_A260280ratio  || A260/A280 ||
     26 ||!BirthYear  || xxxx (e.g. 1969) ||
     27 ||Sex  || 0=male/1=female ||
     28 ||Smoking_Age  || xx.x (i.e. years + 1 decimal) ||
     29 ||Smoking  || 0=non-smoker/1=former smoker/2=current smoker ||
     30 ||Lipids_BloodSampling_Age  || xx.x (i.e. years + 1 decimal) ||
     31 ||Lipids_BloodSampling_Date  || DD/MM/YYYY ||
     32 ||Lipids_BloodSampling_Time  || HH:MM ||
     33 ||Lipids_BloodSampling_Fasting  || 0=no/1=yes ||
     34 ||!TotChol  || in mmol/L ||
     35 ||HDLchol  || in mmol/L ||
     36 ||Triglycerides  || in mmol/L ||
     37 ||LDLchol  || in mmol/L ||
     38 ||LDLcholMethod  || 1=Friedewald estimation/2=measured ||
     39 ||LipidsMed_Age  || xx.x (i.e. years + 1 decimal) ||
     40 ||!LipidMed  || 0=no/1=statins/2=yes, but no statins ||
     41 ||Anthropometry_Age  || xx.x (i.e. years + 1 decimal) ||
     42 ||Height  || xxx.x in cm ||
     43 ||Weight  || xx.x in kg ||
     44 ||CRP_BloodSampling_Age  || xx.x (i.e. years + 1 decimal) ||
     45 ||CRP_BloodSampling_Date  || YYYY-MM-DD ||
     46 ||CRP_BloodSampling_Time  || HH:MM ||
     47 ||hsCRP  || in mg/L ||
     48 ||CellCount_BloodSampling_Age  || xx.x (i.e. years + 1 decimal) ||
     49 ||CellCount_BloodSampling_Date  || YYYY-MM-DD ||
     50 ||CellCount_BloodSampling_Time  || HH:MM ||
     51 ||WBC  || WhiteBloodcellCount_WBC in x10^9cells/L ||
     52 ||RBC  || !RedBloodcellCount in x10^12cells/L ||
     53 ||HGB  || Hemoglobulin in mmol/L ||
     54 ||HCT  || Hematocrit L/L ||
     55 ||MCV  || !MeanCorpuscularVolume in fL ||
     56 ||MCH  || !MeanCorpuscularHemoglobin fmol ||
     57 ||MCHC  || !MeanCorpuscularHemoglobinConcentration in mmol/L ||
     58 ||CHCM  || !CorpuscularHemoglobinConcentrationMean in mmol/L ||
     59 ||CH  || !CorpuscularHemoglobinContent in fmol/L ||
     60 ||RDW  || !RedCellVolumeDistributionWidth in % ||
     61 ||HDW  || !HemoglobinConcentrationDistributionWidth in mmol/L ||
     62 ||PLT  || !PlateletCount in x10^9cells/L ||
     63 ||MPV  || !MeanPlateletVolume in fL ||
     64 ||Neut  || !NeutrophilCount in 10^9/L ||
     65 ||Lymph  || !LymphocyteCount in 10^9/L ||
     66 ||Mono  || !MonocyteCount in 10^9/L ||
     67 ||Eos  || !EosinophilCount in 10^9/L ||
     68 ||Baso  || !BasophilCount in 10^9/L ||
     69 ||LUC  || !LargeUnstainedCells in 10^9/L ||
     70 ||Neut_Perc  || in % of white bloodcell count ||
     71 ||Lymph_Perc  || in % of white bloodcell count ||
     72 ||Mono_Perc  || in % of white bloodcell count ||
     73 ||Eos_Perc  || in % of white bloodcell count ||
     74 ||Baso_Perc  || in % of white bloodcell count ||
     75 ||LUC_Perc  || in % of white bloodcell count ||
     76 
     77== Data ==
     78
     79=== V02 ===
     80* Corrected smoking age of 0 for non smoking sample
     81* Added unique id <biobank>-<biobankSampleId>
     82
     83attachment:RP3_pheno_V02.txt
     84
     85=== V01 ===
     86The complete table with all phenotype data can be found here: attachment:RP3_pheno_V01.txt
     87
     88Comparative plots have been generated and can be downloaded here: attachment:RP3_pheno_V01_plots.pdf
     89
     90== File name ==
     91All phenotype data is stored at srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/RP3/<biobank>/Phenotypes:
     92{{{
     93<biobank>-phen-<YYYYMMDD>.txt
     94}}}