The PDXliver database was designed to provide a data storage, search, and analysis system for liver cancer mouse xenografts (Fig.
1a). Currently, it contained three datasets. One dataset were obtained from a public literature [
24]. Another two datasets came from our in-house PDX experimental platform (the Liver Cancer Institute of ZhongShan Hospital, Fudan University, Shanghai, China); some PDX models are firstly publicly available in PDXliver. Table
1 gives the source of each dataset, the number of PDX models with molecular profiles or drug treatment. A total of 116 patients have stable PDX models, some patients have multiple serially passaged xenografts. All patients have been comprehensively annotated with clinical information, such as age, gender, virus infection and tumor stage (Table
2, Fig.
1b). Since all patients are Chinese, most of them are HBV positive (
n = 88). Hepatocellular carcinoma (HCC) is the major histopathologic subtype (
n = 100), followed by cholangiocarcinoma (
n = 11). A part of models have genome-wide expression profiles (
n = 88), germline variations (
n = 40), somatic mutations (
n = 69) and copy number alterations (
n = 42). Expression profiles of 72 HCC were available and they were classified into three subgroups using a previous public method [
27]: S1 (23.6%), S2 (23.6%) and S3 (41.7%) (Fig.
1c). TP53 (69.5%) is the most frequently mutated gene in liver cancer PDX models; its frequency is higher than the reported frequency (25%~ 35%) in liver cancer patients [
28,
29]. Mutation frequency of another four genes (APOB, CTNNB1, AXIN1, TSC2) are higher than 10%. We also provide histological staining (
n = 40), tumor growth curve (
n = 40), and drug response data (
n = 26) for the in-house PDX models.
Table 1
Data source and statistics of PDXliver database. Multiple PDX models from the same patient were counted only once
DataSet1 | 46 | 40 | Affymetrix Human Genome U133 Plus 2.0 Array (GPL570) | 40 | Affymetrix Genome-Wide Human SNP 6.0 Array | 21 | ZhongShan Hospital | unpublished |
13 | Exome sequencing |
DataSet2 | 65 | 43 | Affymetrix Human Gene Expression Array (GPL15207) | 42 | Affymetrix Genome-Wide Human SNP 6.0 Array | 0 | WuXi AppTech | |
56 | Exome sequencing |
DataSet3 | 5 | 5 | RNA sequencing | / | 5 | ZhongShan Hospital | unpublished |
Table 2
Clinical information of 116 liver cancer patients
Age (y) | < 50 | 43 |
≥50 | 73 |
Gender | Female | 20 |
Male | 96 |
Tumor differentiation | Early stage (I-II) | 16 |
Late stage (III-IV) | 96 |
HBV | Positive | 88 |
Negative | 16 |
HCV | Positive | 1 |
Negative | 47 |
Tumor encapsulate | Complete | 30 |
None | 20 |
Tumor subtype | Hepatocellular carcinoma | 100 |
Cholangiocarcinoma | 11 |
Other | 5 |