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Cancer staging statistics 18

The below statistics were taken from the cancer_staging_consolidated LabKey table from the Main Programme V18 data release. The table is built from the participant IDs and Tumour Sample Plate-key IDs from the cancer_analysis table which comprises QC-passed and interpreted tumour-normal genome pairs.

Completion as a percent of samples in the cancer_analysis table

This table shows the rate of data completion as a percentage of the total number of distinct participants and distinct tumour sample plate-keys in the cancer_analysis table vs the cancer_staging_consolidated table. Please note that this indicates the number of entries (participants or tumour sample plate-keys, respectively) for which we have stage information from one of the three input sources (cancer_participant_tumour, av_tumour, sact) within 12 months of acquiring the tumour sample. No additional checks were conducted.

# cancer_analysis cancer_staging_consolidated % complete
Distinct Participants 15,206 12,621 83
Distinct Tumour Sample Plate-keys 16,321 13,445 (number of rows in cancer_staging_consolidated table) 82.38

Completion rates of cancer_staging_consolidated by each source of staging

This table shows the number and rate of completion of tumour_sample plate-keys (n = 13,445) that are linked each of the three sources of staging. Note the link must be within a year of the tumour_clinical_sample_time field from the cancer_analysis table.

Source Number of tumour sample plate-keys % complete
av_tumour 12,835 95.46
cancer_participant_tumour 5,831 43.37
sact 3,522 26.20

Summary and Distribution of time-difference days between tumour clinical sample time and staging information

This table shows the summary statistics of the distribution of time (in days) between the tumour_clinical_sample_time and the date of staging data acquisition. This is broken down by the three sources of staging.

NB: Note that in the below table and histogram, positive values indicate that the date of staging data acquisition is before the tumour_clinical_sample_time. Negative values indicate that the date of staging data acquisition is after the tumour_clinical_sample_time.

Stat cancer_participant_tumour av_tumour sact
minimum -365 -360 -365
q1 0 17 -70
median 16 39 -49
mean 31.64 57.57 -39.23
q3 48 70 -23
maximum 365 365 365
NA 7,614 610 9,923

The below histograms show the same data but as a frequency distribution.

Frequency of the nearest staging source to the tumour clinical sample time for each tumour sample plate-key

The below table shows the break down of the tumour_sample plate-keys (n = 13,445) by the nearest source of staging data. For example if a tumour_sample plate-key has both linked av_tumour and sact staging entries, then the nearest entry to the tumour_clinical_sample_time is taken.

Staging Source Frequency
cancer_participant_tumour 4,652
av_tumour 7,516
sact 1,277

Frequency of breakdown by combination of data sources for each tumour sample plate-key

This table shows the frequency breakdown of the three sources of staging data across the tumour_sample plate-keys (n = 13,445). For example, if a tumour_sample plate-key has only cancer_participant_tumour and sact data available, then these two data sources are marked as Y.

cancer_participant_tumour av_tumour sact Frequency
0 1 0 5,519
1 1 0 4,142
0 1 1 1,748
1 1 1 1,390
1 0 0 312
0 0 1 262
1 0 1 37