From a454536b0af9e7f62ee48b5e8d5d6cc681117552 Mon Sep 17 00:00:00 2001 From: "Matthew A. Wyczalkowski" Date: Thu, 20 May 2021 16:32:43 -0500 Subject: [PATCH] Updating counts of analyzed cases --- DCC_Analysis_Summary/README.Y3.md | 27 +++++++++++++-------------- DCC_Analysis_Summary/README.md | 8 ++++---- 2 files changed, 17 insertions(+), 18 deletions(-) diff --git a/DCC_Analysis_Summary/README.Y3.md b/DCC_Analysis_Summary/README.Y3.md index 4ffffdf..b39e4c8 100644 --- a/DCC_Analysis_Summary/README.Y3.md +++ b/DCC_Analysis_Summary/README.Y3.md @@ -1,22 +1,21 @@ -Last updated: 4/15/21 +Last updated: 5/20/21 -**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 |**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 +Methylation Array | 43 | 222 | 8 | 169 | 111 | 113 | 229 | 164 | 19 | 249 | 1327 +miRNA-Seq | 4 | 43 | 3 |**83**| 22 | 15 | 72 | 82 | 0 | 35 | **359** +RNA-Seq Expression | 42 | 222 | 8 |176| 111 | 113 | 229 | 164 | 19 | 252 | 1336 +RNA-Seq Fusion | 0 | 110 | 0 |**69**| 0 | 0 |**109**| 81 | 0 | 170 |**539** +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 +WGS SV | 0 | 222 | 0 |114| 111 | 85 |109| 89 | 0 | 203 | 1024 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** +WXS Somatic TD | 0 | 0 | 0 |57| 0 | 113 |109| 0 | 0 | 0 | 279 +WXS Somatic SW | 0 | 0 | 0 |**57**| 0 | 113 |**109**| 166 | 0 | 247 | **692** +WXS Germline | 0 | 110 | 0 |157|110 | 110 |218| 145 | 0 | 95 | 945 ## All results (Y1, Y2, Y3) - Case counts @@ -24,15 +23,15 @@ WXS Germline | 0 | 110 | 0 |**157**|110 | 110 |**218* Pipeline | AML | CCRCC | CM | GBM | HNSCC | LSCC | LUAD | PDA | SAR | UCEC | Total --- | --- | ----- | --- | --- | ----- | ---- | ---- | --- | --- | ---- | --- 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 +miRNA-Seq | 42 | 264 | 8 | 184 | 125 | 126 | 235 | 165 | 19 | 253 | 1341 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 Fusion | 11 | 222 | 8 | 188 | 111 | 113 | 273 | 164 | 19 | 247 | 1311 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 Somatic SW | 0 | 0 | 0 | 59 | 0 | 113 | 218 | 166 | 0 | 247 | 800 WXS Germline | 0 | 110 | 0 | 157 |110 | 110 | 218 | 145 | 0 | 95 | 945 diff --git a/DCC_Analysis_Summary/README.md b/DCC_Analysis_Summary/README.md index 6cfbe3f..10ab3b2 100644 --- a/DCC_Analysis_Summary/README.md +++ b/DCC_Analysis_Summary/README.md @@ -28,18 +28,18 @@ 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 (last updated 4/15/21) | AML | CCRCC | CM | GBM | HNSCC | LSCC | LUAD | PDA | SAR | UCEC | Total +Pipeline (last updated 5/20/21) | AML | CCRCC | CM | GBM | HNSCC | LSCC | LUAD | PDA | SAR | UCEC | Total --- | --- | ----- | --- | --- | ----- | ---- | ---- | --- | --- | ---- | --- 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 +miRNA-Seq | 42 | 264 | 8 | 184 | 125 | 126 | 235 | 165 | 19 | 253 | 1341 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 Fusion | 11 | 222 | 8 | 188 | 111 | 113 | 273 | 164 | 19 | 247 | 1311 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 Somatic SW | 0 | 0 | 0 | 59 | 0 | 113 | 218 | 166 | 0 | 247 | 800 WXS Germline | 0 | 110 | 0 | 157 |110 | 110 | 218 | 145 | 0 | 95 | 945