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2021R1 Land Release Notes

With this content release, QIAGEN OncoLand and QIAGEN DiseaseLand provide hundreds of new projects. If you don't see a Land of interest listed under "Select Land", please ask your QIAGEN OmicSoft Server administrator to check the

In case you missed it

OmicSoft is in the process of re-analyzing all of our Human Lands on Human.B38 genome and the OmicsoftGenCode.V33 model. Several reprocessed Lands have been released, and the most up-to-date versions of the relevant Lands can be identified by the B38_GC33 suffix. Updated Lands include Blueprint_B38_GC33, CCLE_B38_GC33, GTEx_B38_GC33, TCGA_B38_GC33 and TRACERx_B38_GC33, as well as the controlled-access DLBCL_NCI_B38_GC33 Land.

QIAGEN OncoLand highlights

TCGA_B38_GC33

TCGA is now available based on alignment to GenCodeV33. With this Land, you can now build the latest VirtualLands, such as the popular CCLE.GTEx.TCGA VirtualLands. Later this year, we will update the extensive TCGA metadata to TCGA_B38_GC33, as well as comparisons between tumor samples that have key mutations in oncogenes and tumor suppressor genes vs samples that do not have these key mutations.

Figure 1. BMP2 expression in tissue samples from CCLE, GTEx and TCGA, using the latest Human.B38/Gencode.V33 releases. The Y-axis is profiled on Tissue Category, SourceLand and Tumor or Normal.

OncoGEO

In this release, we added 6591 new samples and 618 comparisons from 99 projects, with a focus on GI, reproductive and male urogenital cancers. Included in these are samples from studies of gene expression characterization of metastatic lesions (in which some cases are paired with primary tumors), pre- and post-treatment paired samples, explorations of the prognostic value of particular gene signatures, the effects of established treatments, comparisons of alternate therapeutic strategies and drug resistance.

Highlighted OncoGEO projects

  • Metastasis-specific gene expression profiles reflected in clinical, in vitro and in vivo experiments (GSE58708, GSE61723, GSE125989, GSE100534, GSE62837, GSE98281, GSE119968, GSE147043, GSE134405, GSE73652, GSE156178)
  • Gene classifiers and potential biomarkers for prognosis accuracy improvement (GSE147493, GSE141551, GSE148700, GSE143224, GSE109169, GSE102484)
  • In vitro and xenograft models (GSE101799, GSE101742, GSE137842, GSE138248, GSE134405, GSE146661)
  • Circulating tumor cells and their survival mechanisms (GSE153514, GSE144561, GSE144561, GSE140131, GSE111842, GSE150624)
  • Insights into disease progression in the context of drug resistance (GSE153470, GSE107040, GSE149723, GSE149724, GSE110948, GSE102124, GSE144248)
  • Pre- and post-treatment paired samples (GSE144794, GSE111177, GSE141484)

Figure 2. Distribution of new oncology-focused samples in OncoGEO 2021R1, grouped on the Y-axis by Tissue and color-coded according to DiseaseState.

Hematology

With 1303 new samples and 250 comparisons from 54 projects, this release adds Hodgkin and non-Hodgkin lymphoma, leukemia and myeloma samples, with experiments that explore the mechanisms of action of specific drugs, the discovery of potential biomarkers and the gene signatures that could predict patient outcome.

Highlighted Hematology projects

  • Potential biomarkers identified in transfection experiments (GSE13888, GSE25987, GSE22036, GSE14746, GSE20229)
  • Gene signatures for treatment-outcome prediction and disease classification (GSE17920, GSE22759, GSE14834, GSE148715)
  • Insights into drug mechanisms of action (GSE118558, GSE103143, GSE14834, GSE81267, GSE152497)
  • Gene fusions and alternative splicing events in hematologic cancers (GSE139614, GSE139616, GSE139619, GSE143986)

Figure 3. Distribution of new hematologic cancer-focused samples in Hematology 2021R1, grouped on the Y-axis by DiseaseState and color coded by CellType.

QIAGEN DiseaseLand highlights

This release contains datasets exploring the following: obesity, diabetes, immune-mediated diseases, vaccines (transcriptional response induced by influenza, BCG and Hantavirus vaccines in human and mouse) and vaccine adjuvants, viral and bacterial diseases, cellular-stress response and compound profiling (including genotoxicity studies). We've also added several profiling studies of the eye (cornea and retina).

HumanDisease

This release adds 3969 new samples and 949 comparisons from 108 projects, including a collection of studies on Zika virus and detailed profiling of eye expression, as well as new studies on cardiovascular, musculoskeletal and nervous system diseases.

Highlighted HumanDisease projects

  • Zika infection (GSE135413, GSE139181, GSE133396, GSE81637, GSE146423, GSE125554, GSE129882, GSE113636, GSE118305, GSE123835, GSE105884, GSE149775)
  • Eye profiling (GSE36695, GSE36695, GSE40524, GSE41616, GSE65991, GSE67645)

Figure 4. Distribution of new disease-focused samples in HumanDisease 2021R1, grouped on the Y-axis by DiseaseState and color coded by Tissue. Normal Control and Disease Control samples were hidden.

MouseDisease

This release adds 1559 new samples and 543 comparisons from 52 projects, with a focus on cellular stress in normal tissues and cells (GSE118660, GSE35681, GSE49598, GSE700, GSE84450, GSE90070, GSE54581, GSE29929, GSE11496, GSE11684, GSE122507).

Figure 5. Distribution of new disease-model samples in MouseDisease 2021R1, grouped on the Y-axis by DiseaseState and color coded by Tissue. Normal Control and Disease Control samples were hidden.

 

RatDisease

This release adds 2617 new samples and 2329 comparisons from 14 projects that focus on in vivo (SubjectTreatment metadata) and in vitro (Treatment metadata) compound-profiling and toxicity studies: GSE119122, GSE119129, GSE119133, GSE144219, GSE119933, GSE144219, GSE129814, GSE122184.

Figure 6. Subset of the distribution of new in vivo compound-profiling or toxicity samples, which are grouped on the Y-axis by SubjectTreatment.

Figure 7. Distribution of new in vitro compound-profiling or toxicity samples, grouped on the Y-axis by Treatment.

Did you know?

In addition to the unparalleled collection of normal tissue and blood expression data that can be found in GTEx and Blueprint, HumanDisease, MouseDisease, and RatDisease contain thousands of Normal Control samples from other tissue-profiling projects (i.e., projects not focused on comparing disease vs normal). These projects provide a complement for tissues (including fetal tissues) that are not covered by GTEx or Blueprint and that focus on precise definitions of samples.

To find these projects, use the Project filter tab Disease and select "Normal Control", which will include only studies that are focused on normal tissues.

If you don't select for "Normal Control" projects, Normal Control samples will be returned from thousands of additional studies that included both disease and normal tissues.

Subsequently, you can filter out any remaining disease samples with the Sample filter tab "Disease", selecting "Normal Control" (you can include "Disease Control" as well). Learn more about the difference between Normal Control and Disease Control.

At this point, you will probably want to group by Tissue to see the available tissues, and use the Sample level filter "TissueCategory" to hide hematopoietic and lymphoid system samples.

Finally, select the sample-level Treatment filter to "No Info" and "None", to eliminate samples that were treated.

To quickly apply these filters the next time you want to explore normal tissues, be sure to save this combination of filters by clicking “Manage Filters”.

Figure 8. Save your filters to quickly apply them in future sessions.

 

After applying these filters (or your saved filter set), you can perform searches to explore patterns of expression across diverse normal tissue samples.

Figure 9. Microarray expression of SerpinB6 across samples from Normal Control projects.