Analysis of prostate cancer serum samples and healthy controls using recombinant antibody microarrays.

Serum samples collected from prostate cancer (PC) patients (nmPC=non-metastatic PC, mPC = metastatic PC) and healthy controls, HC (including the subgroups HC-1 and HC-2) were biotinylated and analyzed using antibody-based microarrays. Along the process, a quality control sample (QCpool) consisting of pooled human serum from five healthy individuals, biotinylated at one occasion, was also included in each assay.<br>In total, 363 serum samples (derived from prostate cancer patients and healthy controls) were analyzed using an antibody microarray consisting of 363 antibodies (scFv). The IMMray Evaluation Software (IES, Immunovia AB, Lund, Sweden) was used to align and quantify spot signal intensities. Using IES, local background was subtracted from each spot signal. Each data-point was represented by a mean spot intensity signal calculated based on three spot replicates per antibody. If the replicate coefficient of variation (CV) exceeded 15% from the mean value, the mean spot intensity was based on the two remaining replicates, which displayed most similar signals. In addition, all mean signals were trimmed, where 5% of the lower and upper extreme values were discarded, leading to the raw data file "Raw data_363 clinical samples and 136 QCpool samples_363 abs". Missing values (noted with NA) were replaced by bagged tree imputation, and acquired mean signal intensities were log2 transformed and normalized using Bayes algorithm ComBat to adjust for batch (print-to-print) variation. This data is available in the file "Normalized log2 data_363 clinical samples_363 abs".<br> In addition, 136 QCpool samples which were analyzed in the antibody microarray were also processed (separately) in a similar way as described above, and the data is available in the file "Normalized log2 _QCpool data".<br>

本研究采集了前列腺癌（prostate cancer, PC）患者（其中nmPC为非转移性前列腺癌，mPC为转移性前列腺癌）与健康对照（healthy controls, HC，包含HC-1与HC-2两个亚组）的血清样本，经生物素标记后，采用基于抗体的微阵列进行分析。实验过程中，每批次检测均纳入了1份质控混合样本（QCpool），该样本由5名健康个体的混合血清制备，且一次性完成生物素标记。
本次研究共纳入363份血清样本（来自前列腺癌患者与健康对照），使用包含363种单链抗体片段（single-chain variable fragment, scFv）的抗体微阵列进行检测。采用IMMray评估软件（IMMray Evaluation Software, IES, Immunovia AB, 瑞典隆德）对斑点信号强度进行校准与定量：首先从每个斑点的信号中扣除局部背景信号；每个数据点以对应抗体的3次重复斑点的平均信号强度表示，若重复样本的变异系数（coefficient of variation, CV）相对于平均值超过15%，则取信号最为接近的2次重复的平均强度作为结果。此外，对所有平均信号进行截尾处理，剔除上下各5%的极端值，最终得到原始数据文件"Raw data_363 clinical samples and 136 QCpool samples_363 abs"。对于标记为NA的缺失值，采用袋装树插补法进行填充；随后将得到的平均信号强度进行log2转换，并通过ComBat贝叶斯算法进行标准化以校正批次（打印批次间）差异，最终得到标准化log2数据文件"Normalized log2 data_363 clinical samples_363 abs"。
此外，本研究中在抗体微阵列上检测的136份QCpool样本亦按照上述流程单独进行了预处理，其对应数据已保存至文件"Normalized log2 _QCpool data"中。