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Patient-Derived Models Repository (PDMR)
Last Updated: 03/08/17

Limitations and Caveats

PDX Model-Associated Data:

  • Models are distributed only after the PDMR has performed multiple QC steps. As a general reminder, PDX fragments, sequence files, DNA, RNA, and protein vials are all generated from PDX tumors that are a mixture of human tumor and mouse stroma. The host mouse model used is NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG); the reference sequence can be found on the SOP page.
  • The provided PDX pathology, WES, RNASeq, and other model characterization information in the database are representative of that model. Recipients should perform their own analysis and characterization of the PDXs they grow from the distributed material.
  • A fragment from every PDX contributing to a distribution lot undergoes histopathology assessment to confirm diagnosis and PCR assessment for human:mouse DNA ratio. Models that have de-differentiated may also be reviewed by immunohistochemistry. Our standard IHC panel includes a human mitochondrial marker, cytokeratin, EBV, and CD45; additional markers may be used for certain cancer sub-types. Several models have stably low tumor content (20%-30%) relative to mouse stroma.
  • Identifiler (STR profile) is performed on a fragment from every PDX to confirm lineage identity.
  • Human pathogen assessment is performed using the hIMPACT panel from IDEXX. The PDMR does not distribute models that are positive for human immunodeficiency virus, Hepatitis B, or Hepatitis C.
  • Prior to distribution, all models must be proven to regrow from a viably cryopreserved fragment. For this QC step, five fragments are implanted and monitored for 300 days for regrowth since many models can take up to 200-250 days to regrow to 500-700 mm3 from a frozen sample. If the initial set of five implants fails to grow, five additional fragments from a different frozen lot are implanted and assessed. To date, very few models have failed this QC step, though some models have a higher percentage take-rate from frozen stock than others.
  • Many PDX models grow slowly, both when coming out of the freezer as well as between passages. For some models, you should expect initial implants to take as long as 200 days before tumor is of sufficient size for passage. Representative growth curves for each PDX model are available in the PDMR database in the specimen details.
  • Several models have stably low human tumor content (e.g., 20%-30%). The remaining content would be murine stroma.
  • The PDMR passages PDXs by lineage and tumor heterogeneity is observed in the models, we cannot guarantee which fragment a requestor will receive. For instance, there may be variation in differentiation level of the tumor or for a stomach adenocarcinoma in the signet ring cell content.

Model Expansion — Loss of PDX Material

  • The PDMR assesses every passage for the presence of xenograft-associated lymphoproliferative disorders (XALDs). We group the following PDX-associated issues into this classification for simplicity: human lymphoma outgrowth, murine tumor outgrowth, and graft-versus-host disease (GvHD).
  • The PDMR screens all PDX tumors that lose histological/morphological characteristics with an IHC panel including markers for human mitochondria, CD45, EBV, and cytokeratin or vimentin to confirm the presence of human tumor material (aka high-grade tumor) versus human lymphoma or murine tumor out-growth. We also perform PCR to assess the human:mouse DNA ratio on a fragment from all PDXs to verify presence or absence of human content.
  • Due to the nature of fragment passaging, EBV-driven human lymphomas occurring within a PDX model can develop, but not be identified during histopathologic assessment of one fragment. Not all fragments are created equal; some may maintain sufficient lymphoproliferative content to over-grow the PDX material.
    • Use of early-passage PDXs will carry this risk. The PDMR has observed XALD out-growth as late as passage 3 (P3) from fragment implantation and intermittently within sub-lineages of a model; these lineages are not distributed.
  • Outgrowth of a mouse tumor can also be observed during passaging, and in the PDMR’s experience is seen more often at later passages. Again, PDX tumors that lose histological/morphological characteristics are screened with an IHC panel and by PCR to confirm murine tumor out-growth has not occurred.

Associated Sequence Files

  • Sequence files associated with PDX models will, by definition, contain sequences associated with the murine host DNA. The host mouse model used is NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG); the reference sequence can be found on the SOP page.
  • The provided PDX pathology, WES, RNASeq, etc in the PDMR database are representative of the models. Recipients should perform their own analysis on PDXs they grow out to characterize them.
  • Currently, there has been no removal of somatic mutations from the sequences as tissue for germline sequencing was not obtained. The PDMR now preserves the white blood cell fraction from patient blood samples to be used for future germline sequencing.
  • DNA, RNA, and protein vials are from PDX tumors which are a mixture of human tumor and mouse stroma; these are not pure human extractions. The host mouse model used is NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG); the reference sequence can be found on the SOP page.