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mwyczalkowski committed Apr 16, 2021
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50 changes: 25 additions & 25 deletions DCC_Analysis_Summary/README.Y3.md
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Last updated: 2/18/21
Last updated: 4/15/21

**Bold fields** are new since 20210115
**Bold fields** are new since 20210318

## Analysis Summaries - Case counts - Y3 only
Pipeline | AML | CCRCC | CM | GBM | HNSCC | LSCC | LUAD | PDA | SAR | UCEC | Total
--- | --- | ----- | --- | --- | ----- | ---- | ---- | --- | --- | ---- | ---
Methylation Array | 43 | 222 | 8 | 116 | 111 | 113 | 229 | 164 | 19 | 246 | 1271
RNA-Seq Expression | 42 | 222 | 8 | 118 | 111 | 113 | 229 | 164 | 19 | 249 | 1275
RNA-Seq Fusion | 0 | 110 | 0 | 0 | 0 | 0 | 0 | 81 | 0 | 167 | 358
RNA-Seq Transcript + Splicing | 0 | 110 | 0 | 0 | 0 | 0 | 0 | 81 | 0 | 167 | 358
WGS CNV Somatic | 0 | 105 | 0 | 115 | 111 | 113 | 0 | 166 | 0 | 239 | 849
WGS SV | 0 | 222 | 0 | 56 | 111 | 85 | 0 | 89 | 0 | 200 | 854
miRNA-Seq | 4 | **43**| 3 | 14 | 22 | 15 | 72 | 82 | 0 | 32 | **287**
WXS MSI | 0 | 117 | 0 | 0 | 0 | 0 | 0 | 166 | 0 | 101 | 384
WXS Somatic | 0 | **40** | 0 | 0 | 0 | 113 | 0 | 0 | 0 | 0 | **153**
WXS Somatic SW | 0 | 0 | 0 | 0 | 0 | 113 | 0 | 166 | 0 | 244 | 523
<!--WXS Germline | 0 | 110 | 0 | 99 | 110 | 110 | 110 | 145 | 0 | 95 | 779-->
Methylation Array | 43 | 222 | 8 |**169**| 111 | 113 | 229 | 164 | 19 | 249 | **1327**
RNA-Seq Expression | 42 | 222 | 8 |**176**| 111 | 113 | 229 | 164 | 19 | 252 | **1336**
RNA-Seq Fusion | 0 | 110 | 0 | 0 | 0 | 0 | 0 | 81 | 0 | 170 | 361
RNA-Seq Transcript + Splicing | 0 | 110 | 0 |**69**| 0 | 0 |**109**| 81 | 0 | 170 | 539
WGS CNV Somatic | 0 | 146 | 0 | 115 | 111 | 113 | 0 | 166 | 0 | 242| 893
WGS SV | 0 | 222 | 0 |**114**| 111 | 85 |**109**| 89 | 0 | 203 | **1024**
miRNA-Seq | 4 | 43| 3 | 14 | 22 | 15 | 72 | 82 | 0 | 35 | 290
WXS MSI | 0 | 156 | 0 | 0 | 0 | 0 | 0 | 166 | 0 | 104 | 426
WXS Somatic TD | 0 | 0 | 0 |**57**| 0 | 113 |**109**| 0 | 0 | 0 | **279**
WXS Somatic SW | 0 | 0 | 0 | 0 | 0 | 113 | 0 | 166 | 0 | 247 | 526
WXS Germline | 0 | 110 | 0 |**157**|110 | 110 |**218**| 145 | 0 | 95 | **945**

<!-- Note, WXS Somatic CCRCC was not reported to DCC analysis summary -->
## All results (Y1, Y2, Y3) - Case counts

Pipeline | AML | CCRCC | CM | GBM | HNSCC | LSCC | LUAD | PDA | SAR | UCEC | Total
--- | --- | ----- | --- | --- | ----- | ---- | ---- | --- | --- | ---- | ---
Methylation Array | 43 | 222 | 8 | 116 | 111 | 113 | 229 | 164 | 19 | 246 | 1271
miRNA-Seq | 42 | 222 | 8 | 114 | 111 | 113 | 229 | 164 | 19 | 247 | 1269
RNA-Seq Expression | 42 | 225 | 8 | 120 | 118 | 117 | 230 | 164 | 19 | 251 | 1275
RNA-Seq Fusion | 11 | 222 | 8 | 119 | 111 | 113 | 164 | 164 | 19 | 244 | 1174
RNA-Seq Transcript + Splicing | 1 | 222 | 3 | 119 | 111 | 113 | 53 | 164 | 0 | 244 | 1029
WGS SV | 0 | 222 | 0 | 115 | 132 | 113 | 111 | 166 | 0 | 239 | 1168
WGS CNV Somatic | 0 | 222 | 0 | 115 | 111 | 113 | 121 | 166 | 0 | 239 | 1087
WXS MSI | 0 | 222 | 0 | 118 | 111 | 113 | 111 | 166 | 0 | 244 | 1085
WXS Normal Adjacent | 0 | 80 | 0 | 0 | 5 | 22 | 101 | 0 | 0 | 21 | 229
WXS Somatic | 0 | **40** | 0 | 0 | 0 | 113 | 0 | 0 | 0 | 0 | **153**
WXS Somatic SW | 0 | 0 | 0 | 0 | 0 | 113 | 109 | 166 | 0 | 244 | 632
<!--WXS Germline | 0 | 110 | 0 | 99 | 110 | 110 | 110 | 145 | 0 | 95 | 779-->
Methylation Array | 43 | 222 | 8 | 169 | 111 | 113 | 229 | 164 | 19 | 249 | 1327
miRNA-Seq | 42 | 222 | 8 | 114 | 111 | 113 | 229 | 164 | 19 | 250 | 1272
RNA-Seq Expression | 42 | 222 | 8 | 176 | 111 | 113 | 229 | 164 | 19 | 252 | 1336
RNA-Seq Fusion | 11 | 222 | 8 | 119 | 111 | 113 | 164 | 164 | 19 | 247 | 1177
RNA-Seq Transcript + Splicing | 1 | 222 | 3 | 188 | 111 | 113 | 162 | 164 | 0 | 247 | 1167
WGS SV | 0 | 222 | 0 | 173 | 132 | 113 | 220 | 166 | 0 | 242 | 1337
WGS CNV Somatic | 0 | 222 | 0 | 115 | 111 | 113 | 121 | 166 | 0 | 242 | 1090
WXS MSI | 0 | 222 | 0 | 118 | 111 | 113 | 111 | 166 | 0 | 247 | 1088
WXS Somatic TD | 0 | 0 | 0 | 57 | 0 | 113 | 109 | 0 | 0 | 0 | 279
WXS Somatic SW | 0 | 0 | 0 | 0 | 0 | 113 | 109 | 166 | 0 | 247 | 635
WXS Germline | 0 | 110 | 0 | 157 |110 | 110 | 218 | 145 | 0 | 95 | 945


### Technical
Generate Y3 counts with,
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25 changes: 13 additions & 12 deletions DCC_Analysis_Summary/README.md
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Expand Up @@ -28,19 +28,20 @@ Pipelines which generate multiple result files per case will have multiple entri

Counts of cases processed per disease and pipeline. Counts of results to reference other than GDC hg38 excluded.

Pipeline | AML | CCRCC | CM | GBM | HNSCC | LSCC | LUAD | PDA | SAR | UCEC | Total
Pipeline (last updated 4/15/21) | AML | CCRCC | CM | GBM | HNSCC | LSCC | LUAD | PDA | SAR | UCEC | Total
--- | --- | ----- | --- | --- | ----- | ---- | ---- | --- | --- | ---- | ---
Methylation Array | 43 | 222 | 8 | 116 | 111 | 113 | 229 | 164 | 19 | 246 | 1271
miRNA-Seq | 42 | 222 | 8 | 114 | 111 | 113 | 229 | 164 | 19 | 247 | 1269
RNA-Seq Expression | 42 | 225 | 8 | 120 | 118 | 117 | 230 | 164 | 19 | 251 | 1275
RNA-Seq Fusion | 11 | 222 | 8 | 119 | 111 | 113 | 164 | 164 | 19 | 244 | 1174
RNA-Seq Transcript + Splicing | 1 | 222 | 3 | 119 | 111 | 113 | 53 | 164 | 0 | 244 | 1029
WGS SV | 0 | 222 | 0 | 115 | 132 | 113 | 111 | 166 | 0 | 239 | 1077
WGS CNV Somatic | 0 | 222 | 0 | 115 | 111 | 113 | 121 | 166 | 0 | 239 | 1087
WXS MSI | 0 | 222 | 0 | 118 | 111 | 113 | 111 | 166 | 0 | 244 | 1085
WXS Normal Adjacent | 0 | 80 | 0 | 0 | 5 | 22 | 101 | 0 | 0 | 21 | 229
WXS Somatic | 0 | 0 | 0 | 0 | 0 | 113 | 0 | 0 | 0 | 0 | 113
WXS Somatic SW | 0 | 0 | 0 | 0 | 0 | 113 | 109 | 166 | 0 | 244 | 632
Methylation Array | 43 | 222 | 8 | 169 | 111 | 113 | 229 | 164 | 19 | 249 | 1327
miRNA-Seq | 42 | 222 | 8 | 114 | 111 | 113 | 229 | 164 | 19 | 250 | 1272
RNA-Seq Expression | 42 | 222 | 8 | 176 | 111 | 113 | 229 | 164 | 19 | 252 | 1336
RNA-Seq Fusion | 11 | 222 | 8 | 119 | 111 | 113 | 164 | 164 | 19 | 247 | 1177
RNA-Seq Transcript + Splicing | 1 | 222 | 3 | 188 | 111 | 113 | 162 | 164 | 0 | 247 | 1167
WGS SV | 0 | 222 | 0 | 173 | 132 | 113 | 220 | 166 | 0 | 242 | 1337
WGS CNV Somatic | 0 | 222 | 0 | 115 | 111 | 113 | 121 | 166 | 0 | 242 | 1090
WXS MSI | 0 | 222 | 0 | 118 | 111 | 113 | 111 | 166 | 0 | 247 | 1088
WXS Somatic TD | 0 | 0 | 0 | 57 | 0 | 113 | 109 | 0 | 0 | 0 | 279
WXS Somatic SW | 0 | 0 | 0 | 0 | 0 | 113 | 109 | 166 | 0 | 247 | 635
WXS Germline | 0 | 110 | 0 | 157 |110 | 110 | 218 | 145 | 0 | 95 | 945


<!--
### QC Pipelines
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