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Cancer staging statistics 11

The below statistics were taken from the cancer_staging_consolidated LabKey table from the Main Programme V11 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 15,233 12,337 80.99
Distinct Tumour Sample Plate-keys 16,350 13,101 (number of rows in cancer_staging_consolidated table) 80.13

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 = 13,101) 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 12,453 95.05
cancer_participant_tumour 5,840 44.58
sact 3,322 25.36

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 18 -69
median 16 39 -49
mean 31.55 57.56 -37.36
q3 48 69 -25
maximum 365 365 365
NA 7,261 648 9,779

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 = 13,101) 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 4,679
av_tumour 7,245
sact 1,177

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 = 13,101). 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 5,339
1 1 0 4,106
0 1 1 1,641
1 1 1 1,367
1 0 0 334
0 0 1 281
1 0 1 33