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2020R3 Land Release Notes

In this content release, we added hundreds of new projects to OncoLand and DiseaseLand, and a new Land focused on non-small cell lung cancer (NSCLC). If you are not able to access a Land of interest to you, please ask your OmicSoft Server administrator to check the Cloud Land Publishing function for available data.

Oncoland Highlights

  • New Land: TRACERx Land for Non-small cell lung cancer
  • Updated CCLE and Blueprint B38 Lands to GenCode.V33
  • Curation focus on colorectal cancer projects and immunotherapy, including anti-PD1/PD-L1 and CTLA4 checkpoint modulators
  • MMRC dataset update in Hematology_B37

TRACERx

The TRACERx (TRAcking Cancer Evolution through therapy (Rx)) study focuses on the progression of NSCLC.

In this new TRACERx_B38_GC33 Land, 447 samples from 100 patients, with somatic mutation, copy number, clinical covariates and survival data, are available for analysis.

Figure 1. Sample distribution of lung samples in TRACERx_B38_GC33. Using the filters for Sample Origin (excluding peripheral blood and lymph node samples) and Sampling Time (excluding post-treatment samples) and grouping on Histology, the number of samples from different subtypes of NSCLC are displayed. Multiple tumor regions (up to 8) were sampled per tumor.

Figure 2. Differential mutation frequency in pre-treatment invasive vs. squamous NSCLC samples in TRACERx Land. After filtering for pre-treatment lung samples with histology indicating either invasive or squamous adenocarcinoma NSCLC, a Sample Set was generated to compare the two histologies for mutation frequencies with the OmicSoft Lands "Sample Grouping to Mutation" function. Among the top mutations found enriched in one group vs. the other, TP53, PIK3CA, CDKN2A and many other genes were more frequently mutated in squamous (green) samples, whereas KRAS and AMER3 were more frequently mutated in invasive (blue) samples.

Blueprint and CCLE B38/Gencode.V33 update

Lands continue to be updated to the new OmicsoftGenCode.V33 gene model on Human.B38 genome, with Blueprint (normal blood cell type expression) and CCLE (cancer cell line expression) updated this release. Look for the "B38_GC33" suffixes to find these latest data; your QIAGEN OmicSoft Administrator will need to add these to your OmicSoft Server with Publish Cloud Lands.

CCLE_B38_GC33 also includes a significant update to available data, with new RNA-seq, mutation, copy number and protein data, along with the DepMap CRISPR/RNAi gene dependency data.

OncoGEO

In this release, 3314 samples from 65 projects were added to OncoGEO, with a focus on immune checkpoint therapies targeting PD-1 pathway and CTLA4, CNS cancers, female reproductive cancers, liver, prostate, and colorectal cancers, prostate cancer, lung cancers and skin cancers.

Figure 3. Sample distribution of OncoGEO 2020R3 additions, filtering out disease control and normal control samples.

Hematology

In this release, we added 6781 samples from 109 projects to Hematology_B37. New studies for a variety of leukemias and lymphomas were added.

MMRC update

MMRC-related projects (ProjectIDs GSE26760, GSE26849, and MMRC) were updated with new metadata to enhance the interpretation of these datasets. For ProjectID MMRC, the columns Translocation[IGH], Cytogenetics, Gender, AgeAtDiagnosis[years], SampleMaterial, CellType, CellMarkers, and CellPurity were added. For ProjectIDs GSE26760 and GSE26849, DiseaseHistory, PatientStatus, SampleMaterial, and CellPurity were added; and HeavyChainClass and LightChainClass columns were merged in ImmunoglobulinClass.

Figure 4. Sample distribution of Hematology 2020R3 additions, filtering out normal control samples.

OncoMouse - disease areas

In this release, we added 511 samples from 24 projects to OncoMouse_B38, with new studies relevant to anti-PD1/PD-L1 and anti-CTLA4 immunotherapy agents, Female Reproductive Cancers of Breast and Ovary, lung cancers, and kidney and bladder cancers.

Figure 5. Sample distribution of OncoMouse 2020R3 additions, filtering out disease control and normal control samples.

DiseaseLand

Highlights:
  • Includes new studies on aging of various organs and systems, neurodegeneration, skin disorders, and immune-mediated disorders
  • New studies on viral infections, including coronavirus, and infection responses, including acute respiratory distress syndrome (ARDS)

HumanDisease

In this release, we added 7021 samples from 133 projects to HumanDisease_B37. Among the many diseases covered in the new projects, a particular focus was on aging-related gene expression changes in aging of the brain, eye, immune system, liver, muscle, skin and more (use the project filter Keywords to find "aging" studies).

In addition, new studies relevant to coronavirus research were added (COVID-19, SARS, MERS, ARDS and other complications), as well as Alzheimer's Disease, Huntington's Disease, Parkinson's Disease, arthritis, asthma, chronic obstructive pulmonary disease (COPD) and skin disorders.

Figure 6. Sample distribution of HumanDisease 2020R3 additions, filtering out disease control and normal control samples.

MouseDisease

With 2362 samples from 83 projects, MouseDisease_B38 has new content on aging, Alzheimer's Disease and Parkinson's Disease models, immune-related diseases such as graft-vs-host disease and lupus, as well as skin diseases.

Figure 7. Sample distribution of MouseDisease 2020R3 additions, filtering out disease control and normal control samples.

RatDisease

In RatDisease_B6, we added 637 samples from 21 projects, with studies focused on aging, cirrhosis, Alzheimer's disease and Parkinson's disease.

Figure 8. Sample distribution of RatDisease 2020R3 additions.