MMRd Project Update Nov 12 2020
Lingqi Luo
11/13/2020
Generate Baseline Characteristics
With original MMRd types
| ? (N=5) |
Complex (N=11) |
MLH1_PMS2 (N=251) |
MSH2_MSH6 (N=70) |
MSH6 (N=12) |
NORMAL (N=19) |
PMS2 (N=13) |
Total (N=381) |
|
|---|---|---|---|---|---|---|---|---|
| Age (years) | ||||||||
| Mean (SD) | 64.4 (12.8) | 63.8 (19.9) | 67.9 (13.2) | 56.8 (14.1) | 64.5 (11.2) | 61.1 (14.5) | 54.3 (16.7) | 64.8 (14.4) |
| Median [Min, Max] | 63.0 [46.0, 77.0] | 70.0 [26.0, 88.0] | 71.0 [25.0, 90.0] | 55.0 [30.0, 90.0] | 67.0 [36.0, 76.0] | 65.0 [31.0, 87.0] | 48.0 [37.0, 84.0] | 67.0 [25.0, 90.0] |
| Race | ||||||||
| BLACK OR AFRICAN AMERICAN | 1 (20.0%) | 0 (0%) | 15 (6.0%) | 4 (5.7%) | 0 (0%) | 1 (5.3%) | 1 (7.7%) | 22 (5.8%) |
| PT REFUSED TO ANSWER | 1 (20.0%) | 0 (0%) | 6 (2.4%) | 1 (1.4%) | 0 (0%) | 1 (5.3%) | 0 (0%) | 9 (2.4%) |
| WHITE | 3 (60.0%) | 8 (72.7%) | 208 (82.9%) | 57 (81.4%) | 10 (83.3%) | 16 (84.2%) | 9 (69.2%) | 311 (81.6%) |
| ASIAN-FAR EAST/INDIAN SUBCONT | 0 (0%) | 2 (18.2%) | 11 (4.4%) | 4 (5.7%) | 1 (8.3%) | 1 (5.3%) | 3 (23.1%) | 22 (5.8%) |
| OTHER | 0 (0%) | 1 (9.1%) | 9 (3.6%) | 4 (5.7%) | 1 (8.3%) | 0 (0%) | 0 (0%) | 15 (3.9%) |
| NATIVE AMERICAN-AM IND/ALASKA | 0 (0%) | 0 (0%) | 2 (0.8%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 2 (0.5%) |
| Ethnicity | ||||||||
| Non-Spanish; Non-Hispanic | 5 (100%) | 8 (72.7%) | 215 (85.7%) | 58 (82.9%) | 11 (91.7%) | 18 (94.7%) | 11 (84.6%) | 326 (85.6%) |
| "Spanish NOS; Hispanic NOS, Latino NOS" | 0 (0%) | 2 (18.2%) | 14 (5.6%) | 8 (11.4%) | 1 (8.3%) | 1 (5.3%) | 1 (7.7%) | 27 (7.1%) |
| Dominican Republic | 0 (0%) | 1 (9.1%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (0.3%) |
| 0 | 0 (0%) | 0 (0%) | 3 (1.2%) | 2 (2.9%) | 0 (0%) | 0 (0%) | 0 (0%) | 5 (1.3%) |
| Puerto Rican | 0 (0%) | 0 (0%) | 2 (0.8%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 2 (0.5%) |
| Unknown whether Spanish or not | 0 (0%) | 0 (0%) | 17 (6.8%) | 2 (2.9%) | 0 (0%) | 0 (0%) | 1 (7.7%) | 20 (5.2%) |
| Tumor Purity (%) | ||||||||
| Mean (SD) | 48.0 (19.2) | 38.2 (12.7) | 38.3 (16.0) | 39.6 (15.8) | 39.6 (16.3) | 47.2 (17.0) | 38.8 (19.4) | 39.2 (16.1) |
| Median [Min, Max] | 50.0 [20.0, 70.0] | 30.0 [25.0, 60.0] | 40.0 [10.0, 90.0] | 40.0 [5.00, 80.0] | 30.0 [25.0, 80.0] | 50.0 [20.0, 70.0] | 35.0 [10.0, 70.0] | 40.0 [5.00, 90.0] |
| Missing | 0 (0%) | 0 (0%) | 1 (0.4%) | 2 (2.9%) | 0 (0%) | 0 (0%) | 0 (0%) | 3 (0.8%) |
| Cancer Type | ||||||||
| Bladder | 1 (20.0%) | 0 (0%) | 0 (0%) | 5 (7.1%) | 2 (16.7%) | 0 (0%) | 1 (7.7%) | 9 (2.4%) |
| Endometrial | 1 (20.0%) | 1 (9.1%) | 62 (24.7%) | 14 (20.0%) | 1 (8.3%) | 4 (21.1%) | 0 (0%) | 83 (21.8%) |
| Esophagogastric | 2 (40.0%) | 1 (9.1%) | 33 (13.1%) | 4 (5.7%) | 0 (0%) | 2 (10.5%) | 0 (0%) | 42 (11.0%) |
| Small Bowel | 1 (20.0%) | 0 (0%) | 4 (1.6%) | 2 (2.9%) | 0 (0%) | 1 (5.3%) | 4 (30.8%) | 12 (3.1%) |
| Colon | 0 (0%) | 9 (81.8%) | 118 (47.0%) | 19 (27.1%) | 4 (33.3%) | 7 (36.8%) | 4 (30.8%) | 161 (42.3%) |
| Biliary | 0 (0%) | 0 (0%) | 5 (2.0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (7.7%) | 6 (1.6%) |
| Colorectal | 0 (0%) | 0 (0%) | 10 (4.0%) | 5 (7.1%) | 3 (25.0%) | 4 (21.1%) | 1 (7.7%) | 23 (6.0%) |
| CUP | 0 (0%) | 0 (0%) | 5 (2.0%) | 0 (0%) | 0 (0%) | 1 (5.3%) | 0 (0%) | 6 (1.6%) |
| Other | 0 (0%) | 0 (0%) | 2 (0.8%) | 5 (7.1%) | 0 (0%) | 0 (0%) | 0 (0%) | 7 (1.8%) |
| Ovarian | 0 (0%) | 0 (0%) | 1 (0.4%) | 2 (2.9%) | 0 (0%) | 0 (0%) | 1 (7.7%) | 4 (1.0%) |
| Pancreas | 0 (0%) | 0 (0%) | 1 (0.4%) | 2 (2.9%) | 1 (8.3%) | 0 (0%) | 0 (0%) | 4 (1.0%) |
| Prostate | 0 (0%) | 0 (0%) | 1 (0.4%) | 2 (2.9%) | 1 (8.3%) | 0 (0%) | 0 (0%) | 4 (1.0%) |
| Rectal | 0 (0%) | 0 (0%) | 9 (3.6%) | 10 (14.3%) | 0 (0%) | 0 (0%) | 1 (7.7%) | 20 (5.2%) |
| Sample Type | ||||||||
| Metastasis | 1 (20.0%) | 1 (9.1%) | 29 (11.6%) | 6 (8.6%) | 2 (16.7%) | 4 (21.1%) | 2 (15.4%) | 45 (11.8%) |
| Mixed | 1 (20.0%) | 1 (9.1%) | 17 (6.8%) | 5 (7.1%) | 2 (16.7%) | 1 (5.3%) | 1 (7.7%) | 28 (7.3%) |
| Primary | 3 (60.0%) | 9 (81.8%) | 205 (81.7%) | 59 (84.3%) | 8 (66.7%) | 14 (73.7%) | 10 (76.9%) | 308 (80.8%) |
With MMRd types collapsed by Multiplex or not
table1(~ Current_Age + Race + Ethnicity + Tumor_Purity + Cancer_Type_NEW + Sample_Type | Multiplex_or_not, data=df_2, overall="Total")| Singleton (N=25) |
? (N=5) |
Multiplex (N=332) |
NORMAL (N=19) |
Total (N=381) |
|
|---|---|---|---|---|---|
| Age (years) | |||||
| Mean (SD) | 59.2 (15.0) | 64.4 (12.8) | 65.4 (14.3) | 61.1 (14.5) | 64.8 (14.4) |
| Median [Min, Max] | 64.0 [36.0, 84.0] | 63.0 [46.0, 77.0] | 68.0 [25.0, 90.0] | 65.0 [31.0, 87.0] | 67.0 [25.0, 90.0] |
| Race | |||||
| ASIAN-FAR EAST/INDIAN SUBCONT | 4 (16.0%) | 0 (0%) | 17 (5.1%) | 1 (5.3%) | 22 (5.8%) |
| BLACK OR AFRICAN AMERICAN | 1 (4.0%) | 1 (20.0%) | 19 (5.7%) | 1 (5.3%) | 22 (5.8%) |
| OTHER | 1 (4.0%) | 0 (0%) | 14 (4.2%) | 0 (0%) | 15 (3.9%) |
| WHITE | 19 (76.0%) | 3 (60.0%) | 273 (82.2%) | 16 (84.2%) | 311 (81.6%) |
| PT REFUSED TO ANSWER | 0 (0%) | 1 (20.0%) | 7 (2.1%) | 1 (5.3%) | 9 (2.4%) |
| NATIVE AMERICAN-AM IND/ALASKA | 0 (0%) | 0 (0%) | 2 (0.6%) | 0 (0%) | 2 (0.5%) |
| Ethnicity | |||||
| "Spanish NOS; Hispanic NOS, Latino NOS" | 2 (8.0%) | 0 (0%) | 24 (7.2%) | 1 (5.3%) | 27 (7.1%) |
| Non-Spanish; Non-Hispanic | 22 (88.0%) | 5 (100%) | 281 (84.6%) | 18 (94.7%) | 326 (85.6%) |
| Unknown whether Spanish or not | 1 (4.0%) | 0 (0%) | 19 (5.7%) | 0 (0%) | 20 (5.2%) |
| 0 | 0 (0%) | 0 (0%) | 5 (1.5%) | 0 (0%) | 5 (1.3%) |
| Dominican Republic | 0 (0%) | 0 (0%) | 1 (0.3%) | 0 (0%) | 1 (0.3%) |
| Puerto Rican | 0 (0%) | 0 (0%) | 2 (0.6%) | 0 (0%) | 2 (0.5%) |
| Tumor Purity (%) | |||||
| Mean (SD) | 39.2 (17.6) | 48.0 (19.2) | 38.6 (15.8) | 47.2 (17.0) | 39.2 (16.1) |
| Median [Min, Max] | 30.0 [10.0, 80.0] | 50.0 [20.0, 70.0] | 40.0 [5.00, 90.0] | 50.0 [20.0, 70.0] | 40.0 [5.00, 90.0] |
| Missing | 0 (0%) | 0 (0%) | 3 (0.9%) | 0 (0%) | 3 (0.8%) |
| Cancer Type | |||||
| Colon | 8 (32.0%) | 0 (0%) | 146 (44.0%) | 7 (36.8%) | 161 (42.3%) |
| Biliary | 1 (4.0%) | 0 (0%) | 5 (1.5%) | 0 (0%) | 6 (1.6%) |
| Bladder | 3 (12.0%) | 1 (20.0%) | 5 (1.5%) | 0 (0%) | 9 (2.4%) |
| Colorectal | 4 (16.0%) | 0 (0%) | 15 (4.5%) | 4 (21.1%) | 23 (6.0%) |
| CUP | 0 (0%) | 0 (0%) | 5 (1.5%) | 1 (5.3%) | 6 (1.6%) |
| Endometrial | 1 (4.0%) | 1 (20.0%) | 77 (23.2%) | 4 (21.1%) | 83 (21.8%) |
| Esophagogastric | 0 (0%) | 2 (40.0%) | 38 (11.4%) | 2 (10.5%) | 42 (11.0%) |
| Other | 0 (0%) | 0 (0%) | 7 (2.1%) | 0 (0%) | 7 (1.8%) |
| Ovarian | 1 (4.0%) | 0 (0%) | 3 (0.9%) | 0 (0%) | 4 (1.0%) |
| Pancreas | 1 (4.0%) | 0 (0%) | 3 (0.9%) | 0 (0%) | 4 (1.0%) |
| Prostate | 1 (4.0%) | 0 (0%) | 3 (0.9%) | 0 (0%) | 4 (1.0%) |
| Rectal | 1 (4.0%) | 0 (0%) | 19 (5.7%) | 0 (0%) | 20 (5.2%) |
| Small Bowel | 4 (16.0%) | 1 (20.0%) | 6 (1.8%) | 1 (5.3%) | 12 (3.1%) |
| Sample Type | |||||
| Metastasis | 4 (16.0%) | 1 (20.0%) | 36 (10.8%) | 4 (21.1%) | 45 (11.8%) |
| Mixed | 3 (12.0%) | 1 (20.0%) | 23 (6.9%) | 1 (5.3%) | 28 (7.3%) |
| Primary | 18 (72.0%) | 3 (60.0%) | 273 (82.2%) | 14 (73.7%) | 308 (80.8%) |
With MMRd types collapsed by MSH6 or not
table1(~ Current_Age + Race + Ethnicity + Tumor_Purity + Cancer_Type_NEW + Sample_Type | MSH6_or_not, data=df_2, overall="Total")| MSH6 (N=82) |
Not_MSH6 (N=299) |
Total (N=381) |
|
|---|---|---|---|
| Age (years) | |||
| Mean (SD) | 57.9 (13.9) | 66.6 (14.0) | 64.8 (14.4) |
| Median [Min, Max] | 56.5 [30.0, 90.0] | 70.0 [25.0, 90.0] | 67.0 [25.0, 90.0] |
| Race | |||
| ASIAN-FAR EAST/INDIAN SUBCONT | 5 (6.1%) | 17 (5.7%) | 22 (5.8%) |
| BLACK OR AFRICAN AMERICAN | 4 (4.9%) | 18 (6.0%) | 22 (5.8%) |
| OTHER | 5 (6.1%) | 10 (3.3%) | 15 (3.9%) |
| PT REFUSED TO ANSWER | 1 (1.2%) | 8 (2.7%) | 9 (2.4%) |
| WHITE | 67 (81.7%) | 244 (81.6%) | 311 (81.6%) |
| NATIVE AMERICAN-AM IND/ALASKA | 0 (0%) | 2 (0.7%) | 2 (0.5%) |
| Ethnicity | |||
| "Spanish NOS; Hispanic NOS, Latino NOS" | 9 (11.0%) | 18 (6.0%) | 27 (7.1%) |
| 0 | 2 (2.4%) | 3 (1.0%) | 5 (1.3%) |
| Non-Spanish; Non-Hispanic | 69 (84.1%) | 257 (86.0%) | 326 (85.6%) |
| Unknown whether Spanish or not | 2 (2.4%) | 18 (6.0%) | 20 (5.2%) |
| Dominican Republic | 0 (0%) | 1 (0.3%) | 1 (0.3%) |
| Puerto Rican | 0 (0%) | 2 (0.7%) | 2 (0.5%) |
| Tumor Purity (%) | |||
| Mean (SD) | 39.6 (15.8) | 39.1 (16.2) | 39.2 (16.1) |
| Median [Min, Max] | 40.0 [5.00, 80.0] | 40.0 [10.0, 90.0] | 40.0 [5.00, 90.0] |
| Missing | 2 (2.4%) | 1 (0.3%) | 3 (0.8%) |
| Cancer Type | |||
| Colon | 23 (28.0%) | 138 (46.2%) | 161 (42.3%) |
| Biliary | 0 (0%) | 6 (2.0%) | 6 (1.6%) |
| Bladder | 7 (8.5%) | 2 (0.7%) | 9 (2.4%) |
| Colorectal | 8 (9.8%) | 15 (5.0%) | 23 (6.0%) |
| CUP | 0 (0%) | 6 (2.0%) | 6 (1.6%) |
| Endometrial | 15 (18.3%) | 68 (22.7%) | 83 (21.8%) |
| Esophagogastric | 4 (4.9%) | 38 (12.7%) | 42 (11.0%) |
| Other | 5 (6.1%) | 2 (0.7%) | 7 (1.8%) |
| Ovarian | 2 (2.4%) | 2 (0.7%) | 4 (1.0%) |
| Pancreas | 3 (3.7%) | 1 (0.3%) | 4 (1.0%) |
| Prostate | 3 (3.7%) | 1 (0.3%) | 4 (1.0%) |
| Rectal | 10 (12.2%) | 10 (3.3%) | 20 (5.2%) |
| Small Bowel | 2 (2.4%) | 10 (3.3%) | 12 (3.1%) |
| Sample Type | |||
| Metastasis | 8 (9.8%) | 37 (12.4%) | 45 (11.8%) |
| Mixed | 7 (8.5%) | 21 (7.0%) | 28 (7.3%) |
| Primary | 67 (81.7%) | 241 (80.6%) | 308 (80.8%) |
With MMRd types collapsed by PMS2 or not
table1(~ Current_Age + Race + Ethnicity + Tumor_Purity + Cancer_Type_NEW + Sample_Type | PMS2_or_not, data=df_2, overall="Total")| PMS2 (N=264) |
Not_PMS2 (N=117) |
Total (N=381) |
|
|---|---|---|---|
| Age (years) | |||
| Mean (SD) | 67.2 (13.7) | 59.3 (14.6) | 64.8 (14.4) |
| Median [Min, Max] | 70.0 [25.0, 90.0] | 59.0 [26.0, 90.0] | 67.0 [25.0, 90.0] |
| Race | |||
| ASIAN-FAR EAST/INDIAN SUBCONT | 14 (5.3%) | 8 (6.8%) | 22 (5.8%) |
| BLACK OR AFRICAN AMERICAN | 16 (6.1%) | 6 (5.1%) | 22 (5.8%) |
| NATIVE AMERICAN-AM IND/ALASKA | 2 (0.8%) | 0 (0%) | 2 (0.5%) |
| OTHER | 9 (3.4%) | 6 (5.1%) | 15 (3.9%) |
| PT REFUSED TO ANSWER | 6 (2.3%) | 3 (2.6%) | 9 (2.4%) |
| WHITE | 217 (82.2%) | 94 (80.3%) | 311 (81.6%) |
| Ethnicity | |||
| "Spanish NOS; Hispanic NOS, Latino NOS" | 15 (5.7%) | 12 (10.3%) | 27 (7.1%) |
| 0 | 3 (1.1%) | 2 (1.7%) | 5 (1.3%) |
| Non-Spanish; Non-Hispanic | 226 (85.6%) | 100 (85.5%) | 326 (85.6%) |
| Puerto Rican | 2 (0.8%) | 0 (0%) | 2 (0.5%) |
| Unknown whether Spanish or not | 18 (6.8%) | 2 (1.7%) | 20 (5.2%) |
| Dominican Republic | 0 (0%) | 1 (0.9%) | 1 (0.3%) |
| Tumor Purity (%) | |||
| Mean (SD) | 38.3 (16.1) | 41.1 (16.0) | 39.2 (16.1) |
| Median [Min, Max] | 40.0 [10.0, 90.0] | 40.0 [5.00, 80.0] | 40.0 [5.00, 90.0] |
| Missing | 1 (0.4%) | 2 (1.7%) | 3 (0.8%) |
| Cancer Type | |||
| Colon | 122 (46.2%) | 39 (33.3%) | 161 (42.3%) |
| Biliary | 6 (2.3%) | 0 (0%) | 6 (1.6%) |
| Bladder | 1 (0.4%) | 8 (6.8%) | 9 (2.4%) |
| Colorectal | 11 (4.2%) | 12 (10.3%) | 23 (6.0%) |
| CUP | 5 (1.9%) | 1 (0.9%) | 6 (1.6%) |
| Endometrial | 62 (23.5%) | 21 (17.9%) | 83 (21.8%) |
| Esophagogastric | 33 (12.5%) | 9 (7.7%) | 42 (11.0%) |
| Other | 2 (0.8%) | 5 (4.3%) | 7 (1.8%) |
| Ovarian | 2 (0.8%) | 2 (1.7%) | 4 (1.0%) |
| Pancreas | 1 (0.4%) | 3 (2.6%) | 4 (1.0%) |
| Prostate | 1 (0.4%) | 3 (2.6%) | 4 (1.0%) |
| Rectal | 10 (3.8%) | 10 (8.5%) | 20 (5.2%) |
| Small Bowel | 8 (3.0%) | 4 (3.4%) | 12 (3.1%) |
| Sample Type | |||
| Metastasis | 31 (11.7%) | 14 (12.0%) | 45 (11.8%) |
| Mixed | 18 (6.8%) | 10 (8.5%) | 28 (7.3%) |
| Primary | 215 (81.4%) | 93 (79.5%) | 308 (80.8%) |
