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= Moores Cancer Center sample tracking for MONOD project = == 2014-03-04 == [[noi:MONOD%27s_project|Back]] * Plasma (P), serum (S), and buffy coat (BC) from 3 cases (4 aliquots/type/case) :{| {{table}} class = wikitable | align="center" style="background:#f0f0f0;"|'''Case/Accession #''' | align="center" style="background:#f0f0f0;"|'''Project ID #''' | align="center" style="background:#f0f0f0;"|'''Receiving Date''' | align="center" style="background:#f0f0f0;"|'''Type/ Amount''' | align="center" style="background:#f0f0f0;"|'''Anatomic site''' | align="center" style="background:#f0f0f0;"|'''Diagnosis''' |- | AA0005||UCSD-004-1||3/4/14||4-BC, P, S||N/A||Eosinophilia |- | AA0007||UCSD-004-2||3/4/14||4-BC, P, S||N/A||Anemia |- | AA0008||UCSD-004-3||3/4/14||4-BC, P,3-S||N/A||Anemia |} * [[Media:2014-03-04_plasma-serum-buffycoat_3cases-cancercenter.pdf| Original file of sample info.]] == 2014-05-27 == [[noi:MONOD%27s_project|Back]] ==== Serum (S) samples from 10 cases of pancreatic cancer patients ==== :{| {{table}} class =wikitable | align="center" style="width:120px; background:#f0f0f0;"|'''Project ID #''' | align="center" style="width:120px; background:#f0f0f0;"|'''Anatomic site''' | align="center" style="background:#f0f0f0;"|'''Diagnosis''' | align="center" style="width:120px; background:#f0f0f0;"|'''Ethnicity''' | align="center" style="width:100px; background:#f0f0f0;"|'''Sample type/ amount''' |- | UCSD-004-04||Pancreas||Adenocarcinoma, moderately to poorly differentiated, c/w pT3N0MX||Hispanic/ Latino||S/2 aliquots |- | UCSD-004-05||Pancreas||Adenocarcinoma, ductal type, moderately to poorly differentiated, pT3N1MX||White||S/2 aliquots |- | UCSD-004-06||Pancreas||Poorly differentiated adenocarcinoma, ductal type, pT3N1MX||White||S/2 aliquots |- | UCSD-004-07||Pancreas||Adenocarcinoma, ductal type, moderately to poorly differentiated, involving head and body of pancreas and invading into duodenal submucosa and peripancreatic soft tissue, c/w pT3N1MX||Hispanic/ Latino||S/2 aliquots |- | UCSD-004-08||Pancreas||Poorly differentiated pancreatic ductal adenocarcinoma, invading into duodenum, consistent with pT3N0MX||White||S/2 aliquots |- | UCSD-004-09||Pancreas||Invasive pancreatic duct adenocarcinoma, moderately to poorly differentiated, Stage: ypT3N1MX, Stage IIB||White||S/2 aliquots |- | UCSD-004-10||Pancreas||Invasice ductal adenocarcinoma of the pancreas, moderately to poorly differentiated, T3N1MX, stage IIB||White||S/2 aliquots |- | UCSD-004-11||Pancreas||Metastatic pancreatic adenocarcinoma||Hispanic/ Latino||S/2 aliquots |- | UCSD-004-12||Pancreas||Metastatic adenocarcinoma||Non-hispanic||S/2 aliquots |- | UCSD-004-13||Pancreas||Adenocarcinoma, moderately to poorly differentiated, c/w pT3N0MX||unknown||S/2 aliquots |} * [[Media:2014-05-27_10serum-samples-PANCREAS_cancercenter.pdf|Original file of sample info.]] * TNM staging system: [http://en.wikipedia.org/wiki/TNM_staging_system] * [[Noi/NOTES/2014-5-31| DNA extraction result]] * Assigne Zhang lab ID based on sample types :{| {{table}} class = wikitable | align="center" style="width:120px;background:#f0f0f0;"|'''Project ID #''' | align="center" style="width:120px;background:#f0f0f0;"|'''Zhang lab ID (S=serum)''' |- | UCSD-004-04||PC-S_1 |- | UCSD-004-05||PC-S_2 |- | UCSD-004-06||PC-S_3 |- | UCSD-004-07||PC-S_4 |- | UCSD-004-08||PC-S_5 |- | UCSD-004-09||PC-S_6 |- | UCSD-004-10||PC-S_7 |- | UCSD-004-11||PC-S_8 |- | UCSD-004-12||PC-S_9 |- | UCSD-004-13||PC-S_10 |} == 2014-06-05 == [[noi:MONOD%27s_project|Back]] ==== Plasma and tumor tissue samples from pancreatic cancer patients ==== * Plasma (P) and solid tumor tissue (T). ** Plasma samples from 10 cases. ** Tumor tissues from 5 cases (match with plasma samples) :{| {{table}} class = wikitable | align="center" style="width:120px;background:#f0f0f0;"|'''Project ID''' | align="center" style="width:120px;background:#f0f0f0;"|'''Anatomic site''' | align="center" style="width:90px;background:#f0f0f0;"|'''Date''' | align="center" style="width:120px;background:#f0f0f0;"|'''Ethinicity''' | align="center" style="width:100px;background:#f0f0f0;"|'''Amount/type''' |- | UCSD-004-04||Pancreas||6/5/14||Hispanic/ Latino||3P/20mg T |- | UCSD-004-05||Pancreas||6/5/14||White||3P/20mg T |- | UCSD-004-06||Pancreas||6/5/14||White||3P |- | UCSD-004-07||Pancreas||6/5/14||Hispanic/ Latino||3P/20mg T |- | UCSD-004-08||Pancreas||6/5/14||White||3P |- | UCSD-004-09||Pancreas||6/5/14||White||3P/20mg T |- | UCSD-004-10||Pancreas||6/5/14||White||3P/20mg T |- | UCSD-004-11||Pancreas||6/5/14||Hispanic/ Latino||3P |- | UCSD-004-12||Pancreas||6/5/14||Non-hispanic||3P |- | UCSD-004-13||Pancreas||6/5/14||unknown||3P |} * Note: Diagnosis is the same as sample info on 2014-05-27 * [[Noi/NOTES/2014-6-9| DNA extraction results]] * Assign Zhang lab ID based on sample types :{| {{table}} class = wikitable | align="center" style="width:120px;background:#f0f0f0;"|'''Project ID #''' | align="center" style="width:120px;background:#f0f0f0;"|'''Zhang lab ID (P=plasma)''' | align="center" style="width:120px;background:#f0f0f0;"|'''Zhang lab ID (T=tumor tissue)''' |- | UCSD-004-04||PC-P_1||PC-T_1 |- | UCSD-004-05||PC-P_2||PC-T_2 |- | UCSD-004-06||PC-P_3|| |- | UCSD-004-07||PC-P_4||PC-T_4 |- | UCSD-004-08||PC-P_5|| |- | UCSD-004-09||PC-P_6||PC-T_6 |- | UCSD-004-10||PC-P_7||PC-T_7 |- | UCSD-004-11||PC-P_8|| |- | UCSD-004-12||PC-P_9|| |- | UCSD-004-13||PC-P_10|| |} == 2014-06-26 == [[noi:MONOD%27s_project|Back]] ==== Plasma samples from 10 cases of colon cancer ==== * Project ID of '''colon samples''': '''UCSD-006''' * Now I know that different cancer types have different Project ID (pancreas UCSD-004, colon UCSD-006, lung UCSD-007). From this batch of sample, I will assign sample code to each sample based on project ID and sample type. Ex. 6-P_1 = colon cancer - plasma sample - sample #1 :{| {{table}} class = wikitable | align="center" style="width:120px;background:#f0f0f0;"|'''Project ID''' | align="center" style="width:120px;background:#f0f0f0;"|'''Anatomic site''' | align="center" style="width:90px;background:#f0f0f0;"|'''Date''' | align="center" style="background:#f0f0f0;"|'''Diagnosis''' | align="center" style="width:120px;background:#f0f0f0;"|'''Ethnicity''' | align="center" style="width:100px;background:#f0f0f0;"|'''Amount/type''' |- | UCSD-006.1||Colon||6/26/14||Poorly differentiated adenocarcinoma, consistent with recurrent colonic adenocarcinoma||White||3P aliquot/ case |- | UCSD-006.2||Colon||6/26/14||Metastatic malignant hemangiopericytoma/ malignant solitary fibrous tumor||White||3P aliquot/ case |- | UCSD-006.3||Colon||6/26/14||Sigmoid colon, rectum, and anus, resection. Recurrent invasive moderately- to poorly- differentiated||White/Non-hispanic||3P aliquot/ case |- | UCSD-006.4||Colon||6/26/14||Metastatic adenocarcinoma.||White/Non-hispanic||3P aliquot/ case |- | UCSD-006.5||Colon||6/26/14||Metastatic mucinous adenocarcinoma.||White/Non-hispanic||3P aliquot/ case |- | UCSD-006.6||Colon||6/26/14||Metastatic moderately-differentiated adenocarcinoma with mucinous features.||White||3P aliquot/ case |- | UCSD-006.7||Colon||6/26/14||Adenocarcinoma||White||3P aliquot/ case |- | UCSD-006.8||Colon||6/26/14||Metastatic moderately-differentiated adenocarcinoma with municous features||White||3P aliquot/ case |- | UCSD-006.9||Colon||6/26/14||Adenocarcinoma with municous features, moderately differentiated, pT4aN2b||White||3P aliquot/ case |- | UCSD-006.10||Colon||6/26/14||Mucinous adenocarcinoma, moderately differentiated||White||3P aliquot/ case |} * [[Noi/NOTES/2014-6-27#Part_2:_DNA_extraction_from_plasma_samples| DNA extraction result]] ==== Plasma samples from 10 cases of lung cancer ==== * Project ID of '''lung samples''': '''UCSD-007''' :{| {{table}} class = wikitable | align="center" style="width:120px;background:#f0f0f0;"|'''Project ID''' | align="center" style="width:120px;background:#f0f0f0;"|'''Anatomic site''' | align="center" style="width:90px;background:#f0f0f0;"|'''Date''' | align="center" style="background:#f0f0f0;"|'''Diagnosis''' | align="center" style="width:120px;background:#f0f0f0;"|'''Ethnicity''' | align="center" style="width:100px;background:#f0f0f0;"|'''Amount/type''' |- | UCSD-007.1||Lung||6/26/14||Invasive moderately differentiated adenocarcinoma, pT26N0||Asian||3P aliquot/case |- | UCSD-007.2||Lung||6/26/14||Poorly differentiated squamous cell carcinoma. Consistent with pT2N0MX, stage IB||White||3P aliquot/case |- | UCSD-007.3||Lung||6/26/14||Metastatic melanoma||White||3P aliquot/case |- | UCSD-007.4||Lung||6/26/14||Squamous cell carcinoma, clear cell variant, moderately differentiated||White||3P aliquot/case |- | UCSD-007.5||Lung||6/26/14||Squamous cell carcinoma, pT1bN0||White||3P aliquot/case |- | UCSD-007.6||Lung||6/26/14||Adenocarcinoma, mix subtype, including 60% bronchioalveolar carcinoma, mucinous subtype with 40% invasive carcinoma, acinar and papillary subtypes||White||3P aliquot/case |- | UCSD-007.7||Lung||6/26/14||Invasive squamous carcinoma, moderately differentiated, consistent with pT1N0MX||White||3P aliquot/case |- | UCSD-007.8||Lung||6/26/14||Invasive adenocarcinoma, poorly differentiated||White||3P aliquot/case |- | UCSD-007.9||Lung||6/26/14||Non-small-cell carcinoma||White||3P aliquot/case |- | UCSD-007.10||Lung||6/26/14||Poorly differentiated carcinoma, possibly adenoSCC||White||3P aliquot/case |} * [[Noi/NOTES/2014-6-27#Part_2:_DNA_extraction_from_plasma_samples| DNA extraction result]] == 2014-06-27 == [[noi:MONOD%27s_project|Back]] ==== Solid tumor tissue samples from 5 cases of colon cancer ==== :{| {{table}} class = wikitable | align="center" style="width:120px;background:#f0f0f0;"|'''Project ID''' | align="center" style="width:120px;background:#f0f0f0;"|'''Anatomic site''' | align="center" style="width:90px;background:#f0f0f0;"|'''Date''' | align="center" style="background:#f0f0f0;"|'''Diagnosis''' | align="center" style="width:120px;background:#f0f0f0;"|'''Ethnicity''' | align="center" style="width:100px;background:#f0f0f0;"|'''Amount/type''' |- | UCSD-006.1||Colon||6/27/14||Poorly differentiated adenocarcinoma, consistent with recurrent colonic adenocarcinoma.||White||20mg solid tissue |- | UCSD-006.2||Colon||6/27/14||Metastatic malignant hemagiopericytoma/malignant solitary fibrous tumor.||White||20mg solid tissue |- | UCSD-006.3||Colon||6/27/14||Sigmoid colon, rectum, and anus, resection. Recurrent invasive moderately- to poorly- differentiated adenocarcinoma, <u>ypT3N1cMX.</u> Underline was not stated in plasma sample sheet.||White/Non-hispanic||20mg solid tissue |- | UCSD-006.4||Colon||6/27/14||Metastatic adenocarcinoma.||White/Non-hispanic||20mg solid tissue |- | UCSD-006.5||Colon||6/27/14||Metastatic mucinous adenocarcinoma.||White/Non-hispanic||20mg solid tissue |} * [[Noi/NOTES/2014-6-27#Part_1:_DNA_extraction_from_solid_tumor_tissue_samples| DNA extraction result]] ==== Solid tumor tissue samples from 5 cases of lung cancer ==== :{| {{table}} class = wikitable | align="center" style="width:120px;background:#f0f0f0;"|'''Project ID''' | align="center" style="width:120px;background:#f0f0f0;"|'''Anatomic site''' | align="center" style="width:90px;background:#f0f0f0;"|'''Date''' | align="center" style="background:#f0f0f0;"|'''Diagnosis''' | align="center" style="width:120px;background:#f0f0f0;"|'''Ethnicity''' | align="center" style="width:100px;background:#f0f0f0;"|'''Amount/type''' |- | UCSD-007.1||Lung||6/27/14||Invasive moderately differentiated adenocarcinoma, pT26N0||Asian||20mg solid tissue |- | UCSD-007.2||Lung||6/27/14||Poorly differentiated squamous cell carcinoma. Consistent with pT2N0MX, stage IB||White||20mg solid tissue |- | UCSD-007.3||Lung||6/27/14||Metastatic melanoma||White||20mg solid tissue |- | UCSD-007.4||Lung||6/27/14||Squamous cell carcinoma, clear cell variants, moderately differentiated||White||20mg solid tissue |- | UCSD-007.5||Lung||6/27/14||Squamous cell carcinoma, pT1bN0||White||20mg solid tissue |} * Note: For both colon and lung solid tissues, the mass is estimated to be ~20mg, but the size seemed to be larger. * [[Noi/NOTES/2014-6-27#Part_1:_DNA_extraction_from_solid_tumor_tissue_samples| DNA extraction result]]
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