Distant metastases-free survival Time and Events/Censored data

Question

[Masood]

I am trying to perform Kaplan-Meier analysis using histopathological information on its own and using the expression values. I am taking mets-dd-after-diagnosis as Time and Alive/Death as Events.

Could you please help in suggesting that I am taking the Event variable rightly? or please suggest what should I consider for the Events?

My data table looks like this: Original GEO data set http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40267

geo_accession   path. review % of tumour cells   ihc_pr     ihc_er     ihc_her2    node positive   grade    traditional histological type   diag_tumour_size     mets_dd_after_diagnosis     death_dd_after_diagnosis    mets_count    cause_of_death      age_at_diagnosis
GSM989445       70                               0          0          0           TRUE            3        NST                             -1                   NA                          NA                          0             NA                  46
GSM989446       95                               0          0          0           TRUE            3        NST                             2.5                  NA                          NA                          0             NA                  51
GSM989447       75                               0          0          0           FALSE           3        NST                             2                    341                         407                         1             Breast Cancer       66
GSM989448       95                               0          0          0           TRUE            3        NST                             5                    212                         788                         3             Breast Cancer       26
GSM989449       85                               1          0          NA          TRUE            3        MIXED NST AND METAPLASTIC       2                    1020                        1208                        2             Breast Cancer       50
GSM989450       70                               0          0          0           FALSE           3        NST                             3                    NA                          NA                          0             NA                  70
GSM989451       80                               0          0          0           FALSE           3        NST                             2.5                  NA                          NA                          0             NA                  33
GSM989452       90                               0          0          0           FALSE           3        NST                             4.5                  323                         542                         3             Breast Cancer       67
GSM989453       80                               1          0          0           NA              3        NST                             8.5                  194                         200                         4             Breast Cancer       57
GSM989454       75                               0          0          0           TRUE            3        NST                             5                    1463                        1650                        3             Breast Cancer       50
GSM989455       75                               0          0          0           FALSE           3        NST                             3                    NA                          6506                        0             NA                  59
GSM989456       80                               0          0          0           TRUE            3        NST                             1.5                  2163                        2541                        4             Breast Cancer       47
GSM989457       NA                               0          0          0           NA              3        NST                             2                    253                         271                         2             other_cause         48
GSM989458       80                               0          0          0           FALSE           3        NST                             4.5                  NA                          NA                          0             NA                  41
GSM989459       90                               1          0          0           TRUE            3        NST                             3.5                  384                         528                         3             Breast Cancer       67
GSM989460       80                               0          0          0           FALSE           3        METAPLASTIC MATRIX PRODUCING    2.5                  NA                          NA                          0             NA                  39
GSM989461       75                               1          0          0           FALSE           3        NST                             4                    NA                          NA                          0             NA                  41
GSM989462       75                               0          0          0           NA              3        NST                             2                    307                         368                         2             Breast Cancer       78
GSM989463       85                               0          0          0           FALSE           3        NST                             4                    NA                          NA                          0             NA                  51
GSM989464       70                               0          0          0           TRUE            3        NST                             2                    NA                          NA                          0             NA                  55
GSM989465       85                               0          0          0           FALSE           3        NST                             4.2                  NA                          NA                          0             NA                  61
GSM989466       70                               0          0          0           TRUE            3        NST                             5.5                  NA                          NA                          0             NA                  52
GSM989467       90                               0          0          0           FALSE           3        NST                             5                    783                         1009                        3             Breast Cancer       71
GSM989468       60                               0          0          0           FALSE           3        NST                             2                    NA                          NA                          0             NA                  55
GSM989469       70                               1          NA         0           TRUE            2        NST                             5.5                  NA                          940                         0             other_cause         74
GSM989470       50                               0          0          1           TRUE            3        NST                             4.5                  NA                          NA                          0             NA                  55
GSM989471       30                               0          0          0           FALSE           3        NST                             4.5                  NA                          NA                          0             NA                  41
GSM989472       85                               0          0          0           FALSE           3        NST                             5.5                  NA                          6763                        0             other_cause         70
GSM989473       80                               0          0          0           TRUE            3        NST                             4.5                  1579                        1652                        4             Breast Cancer       47
GSM989474       30                               0          0          0           FALSE           3        NST                             4                    NA                          NA                          0             NA                  50
GSM989475       75                               0          0          0           FALSE           3        NST                             2                    341                         407                         1             Breast Cancer       66
GSM989476       70                               0          0          0           NA              3        NST                             5.5                  NA                          NA                          0             NA                  73
GSM989477       90                               0          0          0           TRUE            2        PLEOMORPHIC LOBULAR             5                    1736                        1894                        2             Breast Cancer       72
GSM989478       50                               0          0          0           TRUE            3        NST                             5                    816                         1378                        2             Breast Cancer       49

Answer 1

[Sean Davis]

You are right to be confused about what to use for survival analysis for this study. Survival analysis needs two pieces of information to apply survival analysis for an event of interest:

1. Time to event OR last followup
2. Did the event occur

There are two possibilities for "event" in this study, metastasis and death. Interestingly, this study appears (I may be misunderstanding something) to give you the time to event only when the event occurred and does not tell you the amount of time the patients that did NOT experience an event were observed. This makes traditional survival analysis impossible. I would consider contacting the authors about getting complete information. Short of getting that additional information, you are going to be stuck with comparing "dead vs. alive" or "met vs. no met", neither of which is really ideal.