Supplementary Methods from Expression Profiling of Archival Tumors for Long-term Health Studies
Year: 2023
Type: supplementary-materials
Abstract: Methods Patient SamplesFor the NHS/HPFS CRC study, we collected paraffin-embedded tissue blocks from hospitals where participants underwent tumor resections(1).Tissue microarray (TMA) was constructed as previously described(2).Analyses of tumor characteristics (protein expression by immunohistochemistry, IHC or DNA methylation and microsatellite instability (MSI) analyses) were described as follows: CCND1(3); CDX2(4); CHFR(5); FASN(6); HIC1(5); HIF1A(7); IGF2 differentially methylated region (DMR0) methylation(8); IGFBP3(5); MGMT promoter hypermethylation(9) and IHC(10); microsatellite instability (MSI)(11); MLH1(9); MSH2(12); PTGER2(13); PTGS2(14); SIRT1(15); VDR(16); WRN(5).Similarly to the NHS/HPFS CRC samples, a pathologist supervised the enrichment of tumor cells via manual micro-dissection for the BC/A series.The Illumina DASL® HumanRef8 v3 chips were used for a series of 9 archival tumor samples termed the 'Autopsy' set, which consists of samples from the following organs (year of embedding in parenthesis); liver (1972, 1981), lymph node (1981), lung (1981, 1989, 1993), chest wall (1960), breast (1981), and spleen (1981).These samples were run in duplicate, with a duplicate negative control and a positive (internally regarded as positive based on previous success as determined by a high P95Grn and corresponding probe success) in triplicate.A series of primary invasive lobular breast cancers and matched lymph node metastases were also run on the same chips.Of these 66 patient samples, a sub-series of 12 matched tumor and metastasis pairs were run in duplicate, with negative and positive controls run in triplicate.
Authors: Levi Waldron, Shuji Ogino, Yujin Hoshida, Kaori Shima, Amy E. McCart Reed, Peter T. Simpson, Yoshifumi Baba, Katsuhiko Nosho, Nicola Segata, Ana Cristina Vargas, Margaret C. Cummings, Sunil R. Lakhani, Gregory J. Kirkner, Edward Giovannucci, John Quackenbush, Todd R. Golub, Charles S. Fuchs, Giovanni Parmigiani, Curtis Huttenhower
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
OpenAlex ID: W4361904558