wiki:BIOS_Phenotype

Version 1 (modified by jamverlouw, 9 months ago) (diff)

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Phenotype data and metadata

This 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.

Format

Biobank CODAM, LL, LLS, NTR, PAN, RS
pheno_id ID linked to phenotypic data in line with sample_id list provided
for data uploads (can be person_id if no special id for phenotype exists)
Ascertainment_criterion Inclusion criterion biobank/selected samples
GWAS_Chip comma separated in case of multiple chips
GWAS_DataGeneration_Date YYYY
DNA_BloodSampling_Age xx.x (i.e. years + 1 decimal)
DNA_BloodSampling_Date YYYY-MM-DD
DNA_BloodSampling_Time HH:MM
DNA_Source Whole blood, other
DNA_Extraction_Method
DNA_Extraction_Date YYYY-MM-DD
DNA_QuantificationMethod
DNA_A260A280ratio A260/A280
RNA_BloodSampling_Age xx.x (i.e. years + 1 decimal)
RNA_Sampling_Date YYYY-MM-DD
RNA_Sampling_Time HH:MM
RNA_Source Pax gene, other
RNA_Extraction_Date YYYY-MM-DD
RNA_Extraction_Method
RNA_RIN RIN or equivalent score
RNA_A260280ratio A260/A280
BirthYear xxxx (e.g. 1969)
Sex 0=male/1=female
Smoking_Age xx.x (i.e. years + 1 decimal)
Smoking 0=non-smoker/1=former smoker/2=current smoker
Lipids_BloodSampling_Age xx.x (i.e. years + 1 decimal)
Lipids_BloodSampling_Date DD/MM/YYYY
Lipids_BloodSampling_Time HH:MM
Lipids_BloodSampling_Fasting 0=no/1=yes
TotChol in mmol/L
HDLchol in mmol/L
Triglycerides in mmol/L
LDLchol in mmol/L
LDLcholMethod 1=Friedewald estimation/2=measured
LipidsMed_Age xx.x (i.e. years + 1 decimal)
LipidMed 0=no/1=statins/2=yes, but no statins
Anthropometry_Age xx.x (i.e. years + 1 decimal)
Height xxx.x in cm
Weight xx.x in kg
CRP_BloodSampling_Age xx.x (i.e. years + 1 decimal)
CRP_BloodSampling_Date YYYY-MM-DD
CRP_BloodSampling_Time HH:MM
hsCRP in mg/L
CellCount_BloodSampling_Age xx.x (i.e. years + 1 decimal)
CellCount_BloodSampling_Date YYYY-MM-DD
CellCount_BloodSampling_Time HH:MM
WBC WhiteBloodcellCount_WBC in x109cells/L
RBC RedBloodcellCount in x1012cells/L
HGB Hemoglobulin in mmol/L
HCT Hematocrit L/L
MCV MeanCorpuscularVolume in fL
MCH MeanCorpuscularHemoglobin fmol
MCHC MeanCorpuscularHemoglobinConcentration in mmol/L
CHCM CorpuscularHemoglobinConcentrationMean in mmol/L
CH CorpuscularHemoglobinContent in fmol/L
RDW RedCellVolumeDistributionWidth in %
HDW HemoglobinConcentrationDistributionWidth in mmol/L
PLT PlateletCount in x109cells/L
MPV MeanPlateletVolume in fL
Neut NeutrophilCount in 109/L
Lymph LymphocyteCount in 109/L
Mono MonocyteCount in 109/L
Eos EosinophilCount in 109/L
Baso BasophilCount in 109/L
LUC LargeUnstainedCells in 109/L
Neut_Perc in % of white bloodcell count
Lymph_Perc in % of white bloodcell count
Mono_Perc in % of white bloodcell count
Eos_Perc in % of white bloodcell count
Baso_Perc in % of white bloodcell count
LUC_Perc in % of white bloodcell count

Data

V02

  • Corrected smoking age of 0 for non smoking sample
  • Added unique id <biobank>-<biobankSampleId>

attachment:RP3_pheno_V02.txt

V01

The complete table with all phenotype data can be found here: attachment:RP3_pheno_V01.txt

Comparative plots have been generated and can be downloaded here: attachment:RP3_pheno_V01_plots.pdf

File name

All phenotype data is stored at srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/RP3/<biobank>/Phenotypes:

<biobank>-phen-<YYYYMMDD>.txt

Attachments (3)