Extended Data Fig. 1 |. Study design to capture “wet lab” factors affecting sequencing quality.

DNA was extracted from either fresh cells or FFPE processed cells (formalin fixation time of 1, 2, 6, or 24 hours). Both fresh DNA and FFPE DNA were profiled on WGS and WES platforms. For fresh DNA, six centers (Fudan University (FD), Illumina (IL), Novartis (NV), European Infrastructure for Translational Medicine (EA), National Cancer Institute (NC), and Loma Linda University (LL)) performed WGS and WES in parallel following manufacturer recommended protocols with limited deviation. Three of the six sequencing centers (FD, IL, and NV) generated library preparation in triplicate. For FFPE samples, each fixation time point had six blocks that were sequenced at two different centers (IL and GeneWiz (GZ)). Three library preparation protocols (TruSeq PCR-free, TruSeq-Nano, and Nextera Flex) were used with four different quantities of DNA input (1, 10, 100, and 250 ng) and sequenced by IL and LL. DNAs from HCC1395 and HCC1395BL were pooled at various ratios to create mixtures of 75%, 50%, 20%, 10%, and 5%. All libraries from these experiments were sequenced in triplicate on the HiSeq series by Genentech (GT). In addition, nine libraries using the TruSeq PCR-free preparation were run on a NovaSeq for WGS analysis by IL. Sample naming convention (example: WGS_FD_N_1): First field was used for sequencing study: Whole genome sequencing (WGS), Whole exome sequencing (WES), WGS on FFPE sample (FFG), WES on FFPE sample (FFX), WGS on library preparation protocol (LBP), WGS on tumor purity (SPP); Second field was used for sequencing centers, EA, FD, IL, LL, NC, NV, GT, and GZ or sequencing technologies, HiSeq (HS) and NovaSeq (NS); Third field was used for tumor (T) or normal (N); The last field was used for the number of repeats. *WGS performed only on Mixture (tumor purity) samples. ^** WGS and WES performed only on FFPE samples.