[COPD-MICCAI 2018] Parse the new COPD Gene dataset tables

[sumedhasingla]

The tables are available at: /pghbio/dbmi/batmanlab/Data/COPDGene/ClinicalData

[sumedhasingla]

Key information

• Phase 1 phenotype data:
  • 10K subjects
  • Location: ClinicalData\phase 1 Final 10K\phase 1 Pheno
  • File name: Final10000_Phase1_Rev_28oct16.txt
• Phase 1 PRM data:
  • 8K subjects from phase 1
  • Location: ClinicalData\phase 1 Final 10K\phase 1 Pheno\phase 1 Imbio PRM
  • File name: COPDGene_Phase1_Imbio_PRM_STD.csv
  • Columns: prm_normal, prm_airtrapping, prm_emphysema and prm_uncharacterized
• Phase 1 ILD/Bronchiectasis data
  • 64 subjects not included in above 10k subjects
  • ILD (34) and Bronchiectasis (30)
  • Location: ClinicalData\phase 1 Final 10K\phase 1 separate ILD_Bronchiectasis
  • File name: COPDGene_ILD_Brnc_Phase1_31aug16.txt
  • Columns:
• Phase 1 Visual scoring data
  • 9K subjects from Phase 1
  • Location: ClinicalData\CT scan datasets\CT visual scoring
  • File name: COPDGene_CT_Visual_20JUL17.txt
  • Columns: Emph_Severity, Emph_Parasepta, Wall_Thickening, Adjudicated, CT_Subtype (categories)
• Mortality Analysis data
  • 9K subjects from Phase 1
  • Location: ClinicalData\MortalitySurvival Analysis
  • File name: COPDGene_Mortality_Surv_2016dec.txt
  • Mortality information using 2 cohort: SSDI (Social security death index) and LFU (Longitudinal followup program)
• Phase1 and Phase 2 combined data
  • 5K subjects
  • Location: ClinicalData\CT scan datasets\P1-P2 First 5K quantitative CT data, ClinicalData\P1-P2 First 5K Long Data
  • File name: first5000_p1p2_qct_24sep16.txt, First5000_P1P2_Pheno_Flat24sep16.txt, First5000_P1P2_Pheno_VisitLevel_24sep16
  • Phase 1 data is same as above.

[sumedhasingla]

"ClinicalData/Final Phase 1 subjects, Current Status-1:20:2017' have some status information.
Its not clear what "status" are they referring to.

[kayhan-batmanghelich]

@sumedhasingla I don't know what status is. Take a look at the html file or other pdf files to see if you can find any info. thanks

[sumedhasingla]

The status is the mortality status as of 01/20/2017.
N = 10,371.
Alive: 8963
Dead:1408