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QIAGEN OmicSoft Lands 2021R4 Release Notes

Invitation to request new data curations

The QIAGEN OmicSoft Team invites you to request new OncoLand, DiseaseLand and Single Cell Land expression projects to be curated for upcoming releases, which will be included as part of your subscription.

Let us know if there are important datasets that you would like to have curated and represented in the Lands. Public (GEO, SRA and Array Express) expression studies for human, mouse and rat will be evaluated; single-cell transcriptomic projects, projects for bulk RNA-seq and commercial expression arrays from Affymetrix, Illumina and Agilent are compatible platforms. Contact us at omicsoft.support@qiagen.com for more information.

We are also evaluating proteomics datasets for curation starting later this year.

 

Updated Land versions

The QIAGEN OmicSoft Team continues to reprocess our most popular Land databases to move from human genome B37 to human genome B38 and Gencode Gene Model version 33. We recommend that you use the latest version (“B38_GC33”) as soon as it becomes available, as this version contains the newest and most comprehensively curated data.

Lands available in B38_GC33 include GTEx, TCGA, Blueprint, CCLE, HumanDisease and TRACERx, in addition to the latest Single Cell Lands. Upcoming B38_GC33 Lands include OncoGEO and TARGET.

 

Flat-file “text dumps”

If your subscription includes access to QIAGEN OmicSoft Land “text dump” flat-file exports, you can request the latest data in the form of a series of indexed, tab-delimited tables. These files are perfect for larger exploratory meta-analysis and machine learning studies. If you are interested in accessing the latest data via flat file, ask your QIAGEN OmicSoft account administrator to request the links.

OncoLand updates

New projects were added to OncoGEO (including Cancer Moonshot consortium projects) and Hematology, and a comprehensive update of CCLE metadata was performed. In the next release, OncoGEO will be available on human genome B38/GenCode.33.

CCLE Land

The latest release of CCLE Land includes hundreds of new samples, new data types and extensive new curated metadata fields sourced from DepMap and other sources.

 

Figure 1. CCLE Cell Lines, grouped on the Y-axis by DiseaseCategory and subgrouped by CancerType.

The 2021R4 release of CCLE_B38_GC33 increases the number of cell lines profiled from 1114 to 1805 cell lines, corresponding to the 2021R3 DepMap release. All data use Human.B38 and OmicSoft Gencode.V33 as the reference genome and gene model.

The QIAGEN OmicSoft Team of scientists spent over 1300 hours reviewing the latest available data from over 40 publications and applied our curation standards to standardize the newest information about cell-line origins and features. New metadata fields have clearly explained ToolTips to describe the purpose of the field. Download the full dictionary here: https://resources.omicsoft.com/downloads/land/CCLE/CCLE_B38_GC33_2021R4_Updates.xlsx

Key columns, such as DiseaseState, are updated to the latest OmicSoft controlled vocabularies and standards that have been used in other QIAGEN OmicSoft Lands. These standards are based on the curation of information from DepMap, CCLE publications, and original papers. Additional metadata columns can be harnessed to select general cancer types or specific histological types.

  • DiseaseState uses OmicSoft controlled-vocabulary terms to describe cell lines as one of 29 cancer disease states or “control”.
  • CancerType (disease subtype) and CancerClassification (for histological types) provide additional curated disease information.

Tissue and DiseaseLocation[PrimarySite] were added to reflect the best current information about the tissue of origin for each cell line.

Finally, CancerType[Cellosaurus] captures the disease classification of these cell lines from Cellosaurus – Expasy, which reflects the observed discrepancies between various sources.

Two comment fields (Comment and Comment[PMID22460905]) provide additional free-text notes from QIAGEN OmicSoft curators that were added during the review process.

Important note: With the latest update, cell lines now use DepMapID instead of the deprecated CCLE ID as SampleID. DepMapID has been adopted by Cellosaurus and other resources for easier cross-reference.

OncoGEO Land updates

This release adds 9666 new samples and 408 new comparisons from 54 projects (54 unique project IDs), focusing on prostate, lung, breast, gastrointestinal system, thyroid, pancreas, kidney, melanoma, lung and central nervous system cancers.

This release encompasses studies that explore gene expression profiles associated with drug-induced gene modulation, patient outcome, tumor/non-tumor paired samples, metastases and organoids, or that focus on alternative splicing. The release also includes studies that investigate gene signatures as a prognostic factor and insights into the tumor micro-environment.

Figure 2. Distribution of samples by DiseaseState in OncoGEO 2021R4.

Highlighted OncoGEO projects: 

  • Drug screening on NCI60 cell panel: GSE116438, GSE116439, GSE116440, GSE116441, GSE116442, GSE116443, GSE116444, GSE116445, GSE116446, GSE116447, GSE116448, GSE116451, GSE116449, GSE116450
    To select these projects, use “NCI60 cell panel;drug screening” as keywords.
  • Paired tumor-/non-tumor samples: GSE149609, GSE58561, GSE117230, GSE151165, GSE5364, GSE162102
  • Tumor micro-environment: GSE101665, GSE123375, GSE117230
  • Gene signatures for prognosis accuracy improvement: GSE17891, GSE85047, GSE107850, GSE157009, GSE157010, GSE109857, GSE31519
  • Cancer Moonshot: GSE114052, GSE116728, GSE120720, GSE121217, GSE123860, GSE126917, GSE134147, GSE139335, GSE139962, GSE141633, GSE144319, GSE147976, GSE149609, GSE164141, GSE97398
    To identify Cancer Moonshot projects, one of the following keywords can be used: “Cancer Moonshot”, “Adult Immunotherapy Network”, “Immuno-Oncology Translational Network”, “IOTN”)
  • Other new projects: E-MTAB-8412, GSE112037, GSE142102, GSE152395, GSE162436, GSE163986, GSE166991, GSE167025, GSE169321, GSE60979, GSE67742

Figure 3. Find Cancer Moonshot consortium projects using the Project-level “Keywords” filter.

 

Hematology Land

This release adds 2291 new samples and 226 new comparisons from 19 projects (17 unique project IDs), focusing on leukemia and different subtypes of lymphoma.

Included in this release are studies that explore the gene expression profiling associated with the mechanisms of action of certain drugs in vitro, pre-post treatment paired samples, CAR-T cell therapy and CRISPR-Cas9 genome editing.

Figure 4. New samples in Hematology Land profiled by DiseaseState, sub-grouped by Project ID. A large number of projects focusing on DLBCL were added to this release.

 

Highlighted Hematology projects:

  • CRISPR-Cas9: GSE127266, GSE158303
  • Drug resistance mechanism: GSE138126
  • Molecular subtypes for a large DLBCL cohort: GSE181063
  • Other projects this release: CRA000746, GSE127761, GSE132929, GSE134480, GSE138282, GSE151612, GSE159472, GSE159852, GSE160608, GSE160609, GSE56313, GSE56314, GSE57611

 

DiseaseLand updates

HumanDisease

Figure 5. New samples in HumanDisease, grouped by DiseaseState and colored by TissueCategory (Normal Control and Disease Control samples are hidden).

This release adds 2651 new samples and 1404 comparisons from 80 projects (79 unique project IDs).

This release includes studies on the following:

  • T-cell types from various tissues (easily found with string filter “T cell” in CellType): GSE102751, GSE112899, GSE126116, GSE132790, GSE132932, GSE133397, GSE135291, GSE135390, GSE136200, GSE141508, GSE148970, GSE150805, GSE151586, GSE152381, GSE158489, GSE163405, GSE163605, GSE166375, GSE166445, GSE166866, GSE169009, GSE169761, GSE173377, GSE176191
  • Type 1 diabetes mellitus: GSE131526
  • Aging (muscular tissue): GSE113165, GSE164471, GSE25941, GSE28392, GSE28422
  • Arthritis: GSE111357, GSE114007, GSE123492, GSE169077, GSE171952, PRJNA505578
  • Nervous system diseases (Parkinson’s disease and multiple sclerosis): GSE111972, GSE123496, GSE138614, GSE20333, GSE68719
  • Retina profiling: E-MTAB-4377, GSE60570, GSE71831,PRJNA232850, PRJNA274213, PRJNA298886
  • Profiling of gene expression in 30 brain regions : GSE127898
  • Other studies: E-MTAB-5965, GSE109439, GSE114519, GSE120847, GSE124381, GSE124474, GSE131089, GSE131523, GSE131524, GSE132044, GSE132931, GSE134881, GSE137869, GSE150540, GSE151086, GSE151924, GSE155176, GSE157652, GSE158395, GSE159266, GSE160016, GSE165498, GSE172100, GSE173895, GSE37686, GSE65469, GSE83443, GSE83482, GSE84639, GSE93801, PRJNA284254

 

MouseDisease

Figure 6. New samples in MouseDisease, grouped by DiseaseState and colored by Tissue (Normal Control and Disease Control samples are hidden).

This release adds 1750 new samples and 1678 comparisons from 45 projects and includes studies of the following:

  • Aging: GSE120290, GSE122061
  • Liver disease: GSE138779, GSE153703, GSE154021,GSE154724
  • Cardiovascular disease (including aortic dissection): GSE138484, GSE138558, GSE147078
  • Endocrine and metabolic diseases (including obesity and diabetes mellitus): GSE120290, GSE122061, GSE125637, GSE133577, GSE136582, GSE138779, GSE139440, GSE141826, GSE142874, GSE144829, GSE145404, GSE145620, GSE147039, GSE149231, GSE150485, GSE151268, GSE152539, GSE153703, GSE154021, GSE154325, GSE154611, GSE154724, GSE156838, GSE172283
  • Infectious disease (bacterial and viral): GSE124688, GSE140943, GSE140944, GSE149425, GSE150664
  • Nervous system diseases: GSE132044, GSE144459, GSE147039, GSE152539, GSE156646, GSE79812
  • Potential biomarkers of vaccine inflammation in mice: GSE120661
  • Other projects: GSE123124, GSE135844, GSE151303, GSE155892, GSE158057, GSE159207, GSE167248, GSE99701

 

Did you know?

QIAGEN OmicSoft Studio includes powerful functions for importing and exploring “measurement data”, quantitative data for samples in Lands.

For CCLE Land, extensive data (drug sensitivity, metabolomics, proteomics) from studies performed on cancer cell lines can be added and analyzed alongside CCLE 'omics data, including the following:

Adding new measurement data is pretty simple, but new data can only be added by an OmicSoft Server administrator.

If you use CCLE Land but don’t see measurement data, talk to your administrator and review this wiki page for information: http://www.arrayserver.com/wiki/index.php?title=Manage_Measurement_Data_in_ArrayLand.

In case you missed it: Major TCGA Update

We recently released a major update to TCGA Land. With this update, we released the TCGA metadata dictionary, a lookup guide that you may find useful. This is available in both pdf and xlsx formats.  Please find the links and explanation about the utility in the whitepaper titled: Navigating TCGA metadata

2021R3 Land Release Notes

In this content release, OncoLand and DiseaseLand added hundreds of new projects, and Human Disease data are now available on Human Genome B38!

If you don't see a Land of interest listed under "Select Land", please ask your OmicSoft Server administrator to check the Cloud Land Publishing function for available data.

Invitation to request new data curation

The OmicSoft team is inviting requests for new OncoLand or DiseaseLand expression projects to curate for upcoming releases, which will be included as part of your subscription.

Let us know if there are important datasets that you would like to see curated and represented in the Lands. Public (GEO, SRA or Array Express) expression studies for human, mouse, and rat will be evaluated; single-cell transcriptomic projects, projects for bulk RNA-seq and commercial expression arrays from Affymetrix, Illumina and Agilent are compatible platforms. Please email omicsoft.support@qiagen.com for more information.

OncoLand

Figure 1. Distribution of disease samples in OncoGEO and Hematology update by Disease Category.

OncoGEO

This release adds 2058 new samples and 399 new comparisons from 63 projects, focusing on breast, melanoma, lung, central nervous system and stomach cancer.
Some highlights in this release are studies that explore the following:

 

  • CAR-T cells: GSE164902 (SynNotch CAR-T cells), GSE163400, GSE136432, GSE135379, GSE161942, GSE158144
  • Paired pre- and post-treatment, and tumor and non-tumor samples: GSE155164, GSE106128, GSE144020, GSE94104, GSE110114, GSE133039
  • Gene signatures for prognosis accuracy improvement: GSE33331, GSE126870, GSE168009, GSE133713, GSE131769, GSE139050, GSE122220, GSE126044, GSE135565
  • Cancer progression: GSE80609, GSE144020
  • Xenograft models: GSE66346, GSE148310, GSE100066, GSE104020, GSE100669
  • And more!

Hematology

This release adds 1830 new samples from 44 unique project IDs  with 222 comparisons, focusing on subtypes of leukemia, lymphoma and myeloma.
Some highlights in this release are studies that explore the following:

  • CAR-T cells: GSE134937, GSE153437 (axicabtagene ciloleucel), GSE156190, GSE166976 (NK cell), GSE160311 (synthetic T cell antigen receptor (STAR)), GSE147046, GSE156207
  • Paired pre- and post-treatment samples: GSE122934, GSE75086, GSE117090
  • Xenograft models: GSE123485, GSE75086, GSE156207, GSE121007

 

 

TCGA major update coming soon

Figure 2. The comprehensive update of TCGA metadata included the review of over 1200 files, the definition of over 1000 fields, the unification and grouping of hundreds of columns, the update of fields representing TCGA publication results and the curation of hundreds of treatment labels.

We are in the final stages of a comprehensive update of TCGA Land (TCGA_B38_GC33).

Look for comprehensive metadata field definitions and tooltips, improved metadata field names, curated treatment information, additional marker paper and PanCanAtlas cluster information, and more!

 

 

DiseaseLand

Figure 3. Distribution of disease samples in the latest release of DiseaseLand by Disease Category.

HumanDisease

With this release the Human Disease collection is now available on Human Genome B38/GenCode version 33. All new content requests will be added to HumanDisease_B38_GC33.

If you don't see HumanDisease_B38_GC33, be sure to ask your OmicSoft Server administrator to use "Publish Cloud Land" to select the new Land.

This release adds 7749 new samples and 2297 comparisons from 102 unique project IDs.
This release includes the following:

  • NK cells (CellType: NK Cell) from peripheral blood, umbilical cord blood, lung, liver, spleen and more
  • Infectious diseases and vaccines: over 30 projects in the “Infectious Diseases” Therapeutic Area
  • Arthritis: E-MTAB-6266, E-MTAB-7466, GSE104113, GSE148395, GSE41038, GSE49604, GSE57218, GSE75181, GSE89484, GSE98918
  • Female reproductive diseases: GSE35287, GSE40400, GSE5850
  • Nervous system diseases: GSE121569, GSE122647, GSE135511, GSE136666, GSE137619, GSE138064, GSE141381, GSE150174, GSE151936, GSE22779
  • Tissue-profiling projects: GSE2004; GSE2361; GSE803

MouseDisease

This release adds 1200 new samples and 357 comparisons from 59 projects, including studies on the following:

  • Kidney disease: 13 new projects in Therapeutic Area “Renal Disease”, including chronic kidney disease, acute kidney injury and renal fibrosis
  • Liver disease: NAFLD, acute liver failure and acute liver injury models in projects such as GSE102489, GSE104302, GSE111828, GSE120484, GSE124694, GSE128284, GSE130528 and GSE132298
  • Arthritis: E-MTAB-5326, GSE101573, GSE104793, GSE104794, GSE33754, GSE43663, and GES53857
  • Nervous system diseases (migraine, anxiety, addiction, obsessive compulsive disorder, amyotrophic lateral sclerosis): 14 new projects in Therapeutic Area “Neurology” and “Psychiatry”
  • Systemic lupus erythematosus: GSE128692, GSE145422, and GSE147359
  • Drug screen: GSE110256

RatDisease

This release adds 383 new samples and 125 comparisons from 13 projects on nervous system disease, cardiovascular and metabolic diseases and aging.

Single Cell Lands

With the latest Single Cell Lands content update, new datasets on ophthalmology, oncology, neurology, gastroenterology, endocrinology, dermatology and more are now available.

  • 29 human projects (23 UMI + 6 non-UMI), 79 datasets and 801 comparisons
  • 9 mouse projects (8 UMI + 1 non-UMI), 15 datasets and 166 comparisons

Figure 4. Human UMI datasets in the latest release, plotting the number of cell clusters with different cell types (colored) by tissue.

 

Looking ahead to the next release, expect 55 additional projects with 96 "cell map" dimension reduction datasets, profiling 3.2 million cells from 847 samples.

Our new "Single Cell Lite" protocol for integrating pre-quantified datasets with full manual curation enables us to bring in datasets without raw data. Key datasets to be integrated include Tabula Sapiens (UMI and nonUMI) profiling normal tissue expression in humans, and Allen Mouse Brain Atlas (GSE116470).

 

 

Did you know?

In OmicSoft curation, we annotate in vivo and in vitro treatment studies in different columns.

  • Treatment: For in vitro studies, describes the treatment performed on a sample, using OmicSoft controlled vocabularies
  • Subject Treatment: For in vivo studies, describes the treatment using OmicSoft controlled vocabularies
    • If the same subject was sampled before and after treatment, Subject Treatment will be the same, but Treatment Status will indicate which sample is post-treatment
  • Treatment Status: Indicates the treatment applied to an individual sample, when the sample came from a Subject (i.e., patient) that was sampled pre- and post-treatment
  • Pre Treatment: treatment given in vivo or in vitro before the main treatment. Many times the pre-treatment is the disease-induction model for mouse studies.
  • Maternal Treatment: in vivo treatment given to the mother prior to or during gestation. The sample collected from is from the offspring.

OmicSoft curates controlled vocabulary terms from PubChem, NCIT, DrugBank, ChemSpider and the company web site of the treatment source.

 

Using the SubjectTreatment and TreatmentStatus columns, you can group and subset in vivo treatment studies to reveal interesting patterns in the data, for example, by showing pre-treatment gene expression between patients with differential response to a treatment.

Figure 5. KCNB2 is up-regulated in pre- and post-treatment samples of pancreatic ductal adenocarcinoma from GSE131050. All samples are curated as SubjectTreatment=5-fluorouracil;irinotecan;leucovorin;oxaliplatin;PF-4136309. Pre-treatment samples are identified by TreatmentStatus=none, post-treatment samples are identified by TreatmentStatus=5-fluorouracil;irinotecan;leucovorin;oxaliplatin;PF-4136309. Treatment response is indicated by Response (partial response or stable disease).

2021R2 Land Release Notes

In this content release, OncoLand and DiseaseLand added hundreds of new projects.

If you don't see a Land of interest listed under "Select Land", please ask your OmicSoft Server administrator to check the Cloud Land Publishing function for available data.

Invitation to request new data curation

The OmicSoft team is inviting requests for new OncoLand or DiseaseLand expression projects to curate for upcoming releases, which will be included as part of your subscription.

Let us know if there are important datasets that you would like to see curated and represented in the Lands. Public (GEO, SRA or Array Express) expression studies for human, mouse and rat will be evaluated; single-cell transcriptomic projects, projects for bulk RNA-seq and commercial expression arrays from Affymetrix, Illumina and Agilent are compatible platforms. Please email omicsoft.support@qiagen.com for more information.

BodyMaps

Tissue-specific comparisons from GTEx

GTEx_B38_GC33 now has comparisons revealing the top up- and down-regulated genes for 52 tissues.

Figure 1. Search for a gene and see in which tissues it is enriched; use “Specify Profile Columns” to change to Case.tissueDetail_GTEx or similar, color by Case.TissueCategory.

 

Figure 2. Discover co-enriched genes with the Comparison Correlation View to find additional genes that are enriched or depleted in a similar pattern as your gene of interest.

 

 

Figure 3. Browse and filter the comparisons to find the most up- and down-regulated genes (the top genes are so significant that they are compressed to the top)

 

 

OncoGEO

Figure 4. Distribution of new oncology-focused samples in OncoGEO 2021R2, grouped on the Y-axis by Tissue and colored by DiseaseState.

 

 

This release adds 5246 new samples and 598 new comparisons from 106 projects, focusing on melanomas, breast, liver and pancreatic cancers. Included in this release are studies that explore the gene expression profiling associated with the mechanisms of action of various drugs both in vivo and in vitro, pre- vs. post-treatment paired samples, tumor vs. non-tumor paired samples, potential biomarkers and gene signatures that could predict patient outcome, xenograft models and drug resistance.

Highlighted OncoGEO projects: 

  • Paired tumor and non-tumor samples: E-MTAB-1503, GSE104310, GSE117361, GSE136247, GSE36376, GSE36411, GSE57957, GSE76427, GSE98383, GSE98617, E-MTAB-6389, GSE100684, GSE127559, GSE138485, GSE171485, GSE22780, GSE41368, GSE43795, GSE56560, GSE71989, GSE126076
  • Paired pre- and post-treatment samples: GSE87455, GSE131050
  • In vivo applied treatments: GSE102723, GSE128515, GSE131050, GSE153262, GSE60646, GSE87455
  • In vitro applied treatments: GSE133568, GSE127760, GSE155570, GSE119832, GSE102744, GSE123250, GSE163950, GSE136613, GSE136614, GSE100269, GSE127948, GSE95189, GSE68836, GSE100169, GSE146850
  • Xenograft models: GSE128515, GSE1099030
  • Gene signatures and potential biomarkers for prognosis accuracy improvement: GSE131050, GSE138485, GSE158309, GSE39409, GSE57495, GSE62165, GSE76427, GSE77435, GSE84219, GSE104580
  • Tumor-educated platelet (TEP) characterization: GSE160252
  • Purity Independent Subtyping of Tumors (PurIST), a clinically robust single-sample classifier for tumor subtyping in pancreatic cancer: GSE131050

Hematology

Figure 5. Distribution of new hematologic cancer-focused samples in Hematology 2021R2, grouped on the Y-axis by DiseaseState and colored by CellType.

 

 

This release adds 1231 new samples and 364 new comparisons from 30 projects, focusing on different subtypes of lymphoma and leukemia, the most highly represented subtypes are acute myeloid leukemia (LAML) followed by acute lymphoblastic leukemia (ALL) and chronic myeloid leukemia (CML). Included in this release are studies that explore the mechanisms of action of certain drugs both in vivo and in vitro and discovery of potential biomarkers and gene signatures that could predict drug resistance.

Highlighted Hematology projects:

  • Gene fusions and alternative splicing events in hematologic cancers: GSE139620, GSE139621
  • Gene signatures and potential biomarkers for treatment-response prediction: GSE103424, GSE130404, GSE143166
  • Insights on drug mechanisms of action: GSE139620, GSE139617, GSE139618, GSE149624, GSE138322, GSE125437
  • Paired pre- vs. post-treatment samples: GSE136634

 

HumanDisease

Figure 6. Distribution of new Disease-focused samples in HumanDisease 2021R2, grouped on the Y-axis by DiseaseState and colored by Tissue. Normal control and Disease Control samples were hidden.

 

 

This release adds 15,358 new samples and 2099 comparisons from 126 projects, including a collection of studies on immune mediated diseases (systemic lupus erythematosus, Sjogren’s syndrome, psoriasis and others), amyotrophic lateral sclerosis, obesity, as well as new studies on respiratory diseases, infectious diseases, muscular dystrophy  and nervous system diseases.

Highlighted HumanDisease projects

  • Tissue profiling for transplanted organs (kidney; heart): GSE124203; GSE124897
  • Leukocyte subsets from different immune-mediated conditions: E-MTAB-2713

MouseDisease

Figure 7. Distribution of new Disease model samples in MouseDisease 2021R2, grouped on the Y-axis by DiseaseState and colored by Tissue.

 

 

This release adds 1589 new samples and 1413 comparisons from 28 projects on vaccines, degenerative diseases of the CNS, aging, metabolic and immune mediated diseases.

Highlighted MouseDisease projects

  • Vaccines: GSE100288; GSE107116; GSE107543; GSE129133; GSE131914; GSE143617

 

Single Cell Lands

With the latest Single Cell Lands content update, new datasets on ophthalmology, oncology, neurology, gastroenterology, endocrinology, dermatology and more are now available.

  • 29 human projects (23 UMI + 6 non-UMI), 79 datasets and 801 comparisons
  • 9 mouse projects (8 UMI + 1 non-UMI), 15 datasets and 166 comparisons

Figure 8. Human UMI datasets in 2021R2, plotting the number of clusters with different cell types (colored) by tissue.

 

Figure 9. Human UMI datasets in 2021R2, plotting the number of clusters with different cell types (colored) by tissue.

 

Figure 10. Mouse UMI datasets in 2021R2, plotting the number of clusters with different cell types (colored) by tissue.

 

Figure 11. Mouse non-UMI datasets in 2021R2, plotting the number of clusters with different cell types (colored) by tissue.

 

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.

2020R4 Land Release Notes

In this content release, OncoLand and DiseaseLand added hundreds of new projects. If you don't see a Land of interest listed under "Select Land", please ask your OmicSoft Server administrator to check the Cloud Land Publishing function for available data.

In Case You Missed It

The latest versions of OmicSoft GTEx, Blueprint and CCLE Lands were released and mapped to Human.B38 and OmicsoftGenCode.V33. Be sure to use these Lands to get the most up-to-date data!

  • GTEx_B38_GC33: 17,000 RNA-seq samples from 51 normal tissues, as well as expression microarray data.
  • CCLE_B38_GC33: Over 1000 cancer cell lines, profiled for RNA-seq, DNA-seq mutation, CNV, DepMap Gene Dependency (CRISPR and RNAi), MS, and RPPA proteomic data.
  • Blueprint_B38_GC33: 628 normal hematopoietic cell expression profiles.

In addition, TRACERx_B38_GC33 (multi-omics non-small cell lung cancer) and DLBCL_NCI_B38_GC33 (diffuse large cell B cell lymphoma, controlled-access application required) are available on the latest gene model.

Oncoland Highlights

  • Hundreds of new projects added to OncoGEO and OncoMouse
  • Coming Soon: TCGA_B38, reprocessed on OmicSoftGenCode.V33

OncoGEO

In this release, there are 4110 new samples and 1245 new comparisons from 102 projects added to OncoGEO, focusing on renal clear cell carcinoma, hepatocellular carcinoma, glioblastoma, colon and colorectal cancers, cervix carcinoma and breast carcinoma.

Figure 1. Distribution of new oncology-focused samples in OncoGEO 2020R4, grouped on the Y-axis by Tissue and colored by DiseaseState.

Hematology

We added 1822 samples and 557 comparisons from 55 projects in this release, with new studies on multiple myeloma, acute myeloid leukemia, diffuse large B-cell lymphoma, chronic lymphocytic leukemia and more.

Figure 2. Distribution of new hematologic cancer-focused samples in Hematology 2020R4, grouped on the Y-axis by DiseaseState and colored by CellType.

OncoMouse

In this release, we added 361 samples and 121 comparisons from 19 projects to OncoMouse_B38, with new studies relevant to chronic lymphocytic leukemia, myelodysplastic syndrome, multiple myeloma, mantle cell lymphoma and more.

Figure 3. Distribution of new oncology model samples in OncoMouse 2020R4, grouped on the Y-axis by DiseaseState and colored by Tissue.

 

DiseaseLand Highlights

  • New studies on viral infections, including COVID-19 and HIV
  • New studies on psychiatric disorders, neurodegenerative disorders, celiac disease and more
  • Coming soon: HumanDisease on Human Genome B38, OmicSoftGenCode.V33

HumanDisease

In this release, we added 7579 samples and 3234 comparisons from 137 projects to HumanDisease_B37. Among the many diseases covered in the new projects, a particular focus was on viral infection, including further studies on COVID-19, MERS and HIV, as well as studies on schizophrenia, autism spectrum, bipolar, celiac disease, diabetes and more.

Figure 4. Distribution of new Disease-focused samples in HumanDisease 2020R4, grouped on the Y-axis by DiseaseState and colored by Tissue. Normal control and Disease Control samples were hidden.

 

MouseDisease

With 4364 samples and 994 comparisons from 97 projects, MouseDisease_B38 has new content on allergy, Alzheimer's disease, autism spectrum, chronic kidney disease, graft-vs-host disease, Huntington's disease, toxoplasmosis and diabetes.

Figure 5. Distribution of new Disease model samples in MouseDisease 2020R4, grouped on the Y-axis by DiseaseState and colored by Tissue. Normal control and Disease Control samples were hidden.

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.

2020R2 Land Release notes

Our latest Land content updates, released July 1, bring you new datasets, ready to be explored to discover patterns of gene and transcript expression across normal tissue and disease expression. Check out the new projects added to HumanDisease, MouseDisease and OncoGEO, and the thousands of new normal tissue samples in GTEx_B38.

GTEx_B38 V8 - First Land on GenCode.V33

With 2020R2, we released our first Land on Human_B38/OmicSoftGenCode.V33, with over 16,000 RNA-seq samples profiling normal tissue expression.

To maintain compatibility with older Virtual Lands that include GTEx_B38, we released this update as GTEx_B38_GC33 (B38 refers to Human Genome version B38; GC33 refers to GenCode Version 33).

Figure 1. Gene FPKM of ACE2 across 16,963 samples from GTEx_B38_GC33.

 

This Land has been added automatically to hosted servers; if you have an onsite Land installation, please use Cloud Land Publishing to add it to your collection.

Figure 2. GTEx_B38_GC33 and other Lands, ready to be installed to the Land collection.

We will continue to release updated versions on this new genome and gene model, starting with the most popular Lands. We will continue to use the OmicSoft Aligner (OSA) and RSEM quantification; a benchmark white paper is in progress.

DiseaseLand

DiseaseLand content highlights:

Coronavirus-related research: In this release, we added 1119 samples and 920 comparisons from 23 projects to HumanDisease, and 357 samples and 203 comparisons from 11 projects MouseDisease. These provide insights into coronavirus infection, associated lung damage, treatment and immune response.

New data: With the latest release, we've added the following data:

  • HumanDisease_B37: 7812 new samples and 1856 new comparisons from 118 projects
  • MouseDisease_B38: 1533 new samples and 729 new comparisons from 87 projects
  • Areas of focus:
    • Coronavirus-related: (SARS, MERS), acute lung injury, acute respiratory distress syndrome (ARDS)
    • Liver disease (NAFLD, NASH, liver fibrosis)
    • Autoimmune disorders
    • Type 2 diabetes

 

Figure 3. Sample distribution of new data added to HumanDisease_B37 in 2020R2.

 

HumanDisease Projects:

MouseDisease Projects:

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OncoLand

With the latest update to OncoGEO, we added 4622 new samples and 832 comparisons from 112 projects.

Areas of focus:

  • Prostate cancer
  • Bladder cancer
  • Kidney cancer
  • Lung cancer

Fig 4. Sample distribution of new data added to OncoGEO_B37 in 2020R2.

 

Note to OmicSoft Server Administrators

If you haven't restarted your Land server recently, consider doing this during a period of low usage. We've released several new improvements, and this also ensures that the latest files have been synchronized.

 

What's new in the QIAGEN OmicSoft 2020R1 and 2020R1.1 releases

QIAGEN OmicLand 2020R1 release notes

The OncoLand and DiseaseLand 2020R1 release is out! Servers should automatically update during low-traffic periods overnight.

Release Schedule

To enable the fastest release of data, this release was released in two batches: GTEx_B37, OncoGEO and HumanDisease were released on April 24, 2020; OncoMouse, MouseDisease and RatDisease were released on May 11, 2020.

In case you missed it...

OncoLand has several new Lands available, be sure to check them out! If you do not see this in your OncoLand collection, please contact your OmicSoft Server administrator to add the Lands to your server.

    • OncoMouse_B38: Curated oncology studies in mouse model.
    • BeatAML_B37/B38: In-depth investigation of the various genetic classes of AML that have recently been discovered, with expression and mutation data, as well as ex-vivo drug sensitivity data that can be added as measurements.
  • CCLE_DepMap_Preview_B37/B38: All the data in CCLE Lands, with additional gene dependency measurements from CRISPR and RNAi knockdown experiments, as well as new visualizations to correlate these data.

Body Maps

GTEx_B37 has 8,711 new RNA-seq samples, with16,964 total RNA-seq samples. GTEx_B38 is scheduled to be updated to GTEx V8 with 2020R2.

Figure 1: Sample distribution of GTEx samples across tissues, colored by whether they were added in the latest release.

 

 

The Tissue metadata column now uses OmicSoft's controlled vocabularies, making it simpler to build virtual Lands. GTEx metadata terms can be found in Tissue_GTEx and TissueDetail_GTEx.

 

New projects in OncoLand 2020R1

Figure 2: New projects in OncoGEO and OncoMouse.

 

  • OncoGEO_B37: 117 new projects, 8236 new samples and 1777 new comparisons
    • This release is focused on breast, ovarian, bladder and prostate cancers. New comparisons explore treatment responsiveness, mutation status, and more!
  • OncoMouse_B38: 33 new projects, 545 new samples and 192 new comparisons
  • Hematology_B37: 5 new projects

 

New projects in DiseaseLand 2020R1

 

Figure 3: New projects in Human, Mouse, and Rat Disease.

 

  • HumanDisease_B37: 111 new projects, 6724 new samples and 3849 new comparison
    • A new developmental map of 7 organs from 4 weeks post-conception to adulthood (E-MTAB-6814)
    • Inflammatory disease: Effect of stimuli of blood samples from Systemic Juvenile Idiopathic Arthritis (GSE103500)
  • RatDisease_B6: 14 new projects, over 6112 new samples, 3102 new comparisons
    • A new developmental map of 7 organs (E-MTAB-6811)
    • Compound profiling in Rat tissues: GSE57822
  • MouseDisease_B38: 79 new projects, 2437 new samples, 1102 new comparisons
    • A new developmental map of 7 organs (E-MTAB-6798)

 

Figure 4: Comparisons from E-MTAB-6814, a developmental map of the human transcriptome across 7 tissues. Similar datasets are in MouseDisease (E-MTAB-6798) and RatDisease (E-MTAB-6811). In the Comparisons Distribution View, the ProjectName filter was used to find E-MTAB-6814. Comparison groups were specified by "Specify Histogram Columns: Case.ExperimentGroup", and subgrouped with "Specify Group Column: Case.ExperimentGroup".

 

QIAGEN OmicSoft Array Suite 2020 R1.1 release notes

This release includes several minor improvements. Please review these latest improvements and update if any would be useful for your research.

OmicSoft Studio improvements:

  • The Single Cell Quantification function now supports antisense strand reads (commonly generated from 5' chemistry) in addition to sense strand reads (generated from 3' chemistry), increasing the flexibility to support new workflows.

  • Users of the "Studio on the Cloud" AWS add-on can now specify the Amazon Machine Image (AMI), expanding the capabilities for studio-based cloud analysis.

 

 

  • The "Import and Unstack Table" function now supports the option not to prepend each column name with a label of the source row. This is useful when importing results from external tools.

  • In "Map RNA-seq reads to genome", there is a new option to pair input files in the order they were submitted, instead of pre-sorting the files by name. This is useful in exceptional situations, such as when data for the same sample are stored across multiple files in multiple directories, and the file names are identical among directories.

For example, if your data were run across multiple lanes, and the output files for Read1 are saved as "Batch2_1_S1_L001_R1_001.fastq.gz" in multiple directories (each directory holding data from one lane), you can ensure proper file pairing by specifying the order with "Add List" or during sample registration, and by selecting "pair files in order" when specifying alignment options.

 

 

In this example, "Pair Files In Order" will take all the files for Sample201 in the listed order, and properly pair those in folders "aRename" and "bRename".

  • QIAGEN Digital Insights has a unified EULA now; you will be automatically prompted to review it the next time you start OmicSoft Studio, and can review it at any time here.

Server improvements:

  • Now you can download FASTQ files up to 100 GB from the Short Read Archive. Previously, downloading FASTQ data from the NCBI Short Read Archive (SRA) database supported files only up to 20 GB.
  • Logs for External Script (Escript) analyses will include the named External Script, e.g., Performing Escript action (Mode=EScript for observation KallistoQuant).
  • If OmicSoft Server is configured in "Master/Analytic Server" configuration, Reference Library and Gene Models built on either Master or Analytic server will be listed in drop-down menus. Previously, only Reference Libraries and Gene Models on the Master Server would have been listed, regardless of Analytic Server connected.

Bug fixes:

  • In Land Explorer, internal Lands with comparison data missing PubMedID entries will successfully load.
  • The "Remove Comparisons from Land" now generates a properly-formatted oscript.
  • An issue that created a non-working desktop shortcut to "QIAGEN OmicSoft Studio Launcher" when launching OmicSoft Studio is now fixed.
  • When exporting Land data using "Download Selected Samples Across All Genes", specifying a VariableSet to limit the metadata columns will now fetch only metadata for the selected samples.

QIAGEN OmicSoft Suite 2020 R1 Release notes

A new version of QIAGEN OmicSoft Suite has been released. Please review the latest improvements and update your OmicSoft Server at the next available opportunity to take advantage of these new features included in version 10.2.7!

  • Array Suite is now OmicSoft Suite! This is purely a name change to reflect the wide variety of Omics data supported by OmicSoft.
    • OmicSoft Studio=Array Studio. OmicSoft Server=Array Server. OmicSoft Viewer=Array Viewer.

  • Support for Docker images and cloud analysis with External Scripts improvements
    • OmicSoft Suite now supports External Scripts on AWS Cloud, and can run analyses on Docker images.
      These new capabilities substantially expand the options for QIAGEN OmicSoft Suite as an 'omics data and analysis hub, allowing advanced users who would like to run third-party bioinformatics tools to do so from OmicSoft Suite, and even build pipelines to analyze data and import into OmicSoft projects. Talk with your account manager to learn more about some of the possibilities, or check out these links.
  • Improvements to single-cell preprocessing (oscript only)
    • Single-cell preprocessing (non-10x) now supports cell barcode correction, matching the 10x preprocessing function's capability of "fuzzy" matching to cell barcode white lists
    • 10x preprocessing and non-10x preprocessing oscript support /DeleteSkippedReads and /ExportSkippedReads options to manage output files
    • 10x and non-10x preprocessing functions will summarize the top reasons for skipped reads for each sample with /SummarizeSkippedReads
  • Server startup optimizations
    • DisableParallelLandLoading enforces Land Loading individually, instead of using all CPUs specified with CPUNumber in ArrayServer.cfg
  • Improved BAM CIGAR handling
    • SAM/BAM reads that contain '=' or 'X' will be loaded and reads will be displayed
    • "Validate SAM/BAM" will validate files that contain a read with '=' or 'X'

Software maintenance to consider:

Additional details on major improvements:

Docker support and cloud support for External Scripts

With version 10.2.1 we are proud to support for Docker images in "External Scripts". This is considered an advanced feature for OmicSoft "power-users" who want to extend their OmicSoft Suite capabilities beyond tools integrated into the software. Because of the wide variety of tools that can run in Docker images, OmicSoft Support cannot provide debugging support for each tool, but will be happy to answer questions about External Scripts syntax, provide tutorials and example scripts. The QIAGEN Discovery Services team can also work with you to build full pipelines and workflows using External Scripts and Docker images for a variety of bioinformatics needs.

To support External Scripts on AWS, you will need to use an updated AMI. Please visit http://www.arrayserver.com/wiki/index.php?title=Build_AWS_Ubuntu_AMI_for_OmicSoft_Cloud_Computing

To support Docker in External Scripts on your onsite OmicSoft Server installation, please install Docker v19.

More useful resources:

A full log of all the changes is located in the Help menu of the Analysis tab in OmicSoft Studio. To download this log, click here:

 

 

New features in the QIAGEN OmicSoft 10.1.2 release

Land visualizations: CRISPR/RNAi dependency screen data with multi-'omics integration views. Directly explore correlations of expression, mutation and gene dependency data in the updated CCLE Land, updated with DepMap data. Use the “Add Measurement Data” function to bring in additional data such as drug sensitivity and metabolomic data.

Cloud Analysis: Map S3 buckets from multiple AWS accounts, and on master/analytic server setup. More flexible cloud configurations allow you to map buckets from collaborators and other shared buckets with your access/secret keys.

 

 

In case you missed it: Find out what was included in the 10.1 release (October 2019)

Cloud analysis: Spot Instance support. AWS spot instances use idle EC2 resources, which can be requested at significant cost savings over on-demand instances.

Single-cell analysis: Improved importing of Single Cell Expression Matrices. Merge memory-efficient Zero-Inflated Matrix (ZIM) data from multiple samples to compare single-cell data from multiple experiments.

.NET 4.5 Framework: Update from .NET 3.5 framework.

IPA integration: Multi-identifier uploads. Now you can specify up to five molecule identifier columns in your inference table when uploading from OmicSoft to IPA. This feature is especially useful for metabolomic studies.

 

DiseaseLand updates – 2019R3

Human disease updates: 48 new projects, with a focus on amyotrophic lateral sclerosis, Alzheimer’s disease, Huntington’s disease and HIV.

Mouse disease updates: 50 new projects, with a focus on models of amyotrophic lateral sclerosis, Alzheimer’s disease and Huntington’s disease.

In case you missed it: We added 67 projects and 1285 samples, with a focus on ophthalmology.

OncoLand updates – 2019R3

New Land: OncoMouse. Oncology-focused studies in mouse models, with 48 projects in the initial release.

OncoGEO updates: 68 new projects, with a focus on cancers of the reproductive system, GI system, respiratory system, urinary system, skin and CNS.

CCLE update: CRISPR/RNAi screen data have been integrated into CCLE Lands, enabling new multi-'omics comparisons.

In case you missed it: We added a new Land. BeatAML includes RNA-seq, DNA-seq and ex-vivo drug responses for over 500 patients.

OncoGEO/hematology added 58 new projects and 3653 samples, with an emphasis on hematologic cancers.

February 2019: New Features with this Release

  • Access new hereditary disease variant annotations and functional prediction tools
  • Get instant annotation of hereditary diseases from HGMD Professional in Array Suite, along with functional predictions from SIFT, PolyPhen2, MutationTaster, and LRT
  • Take greater control of your data using Python programming
  • Perform Land queries, customized data analysis, and Array Server system management using the OmicPython Application Programming Interface (API).

Land Explorer Updates

Customize and share your gene expression, protein level and mutation views with ease

Land Explorer now supports web-based access to Land data with over 100 visualizations for expression, fusions, protein levels and mutations. Custom visualizations can easily be shared with colleagues using customized web links. Access and explore all the Land data that are important to you
The Sample Explorer and Comparison Explorer pages summarize data across every Land in interactive plots. Use filters to identify the samples of interest to you and discover every Land with data relevant to your research.

GeneticsLand Updates

  • First GeneticsLand content on GRCh38
  • GWAS results from the UK Biobank lifted to GRCh38, with a new phenome plot available to visualize all the associations for a given variant
  • Access more OmicSoft curated genome-wide association data from the GWAS Catalog
  • Explore 11,382 phenotypes and millions of variant association summary statistics, including 3,975 studies from the GWAS Catalog
  • Explore non-coding somatic cancer mutations from TCGA with potential regulatory effects
  • Access 828 whole-genome somatic mutation samples across 22 cancer types, from the PanCancer Analysis of Whole Genomes

DiseaseLand Updates

  • Identify key oncogenes and tumor suppressors in cell lines from CRISPR and RNAi knockdowns
  • Brand-new Lands with CRISPR/RNAi dependency screen data from Project Achilles and Project DRIVE. Discover how hundreds of cell lines are affected by individual knockdowns of genes across the transcriptome
  • Access enhanced viral infection, cardiovascular disease, obesity and diabetes data
  • DiseaseLand added projects, samples and comparisons with a focus on dermatology, viral infection, cardiovascular disease, obesity and diabetes
  • A new MouseDisease gene model featuring miRNA gene annotations is now available.
  • Quantify and normalize gene expression of Single-Cell RNA sequencing data
  • Single-Cell Lands now feature new cell types, including hematopoietic stem cells (HSC), peripheral blood stem cells (PBSC), lung epithelial stem cells and olfactory receptor cells. In Array Studio’s Single Cell analysis, you can now quantify and normalize gene expression to Reads Per Million in a single step, and quickly overlay expression in tSNE clustering views.

OncoLand Updates

Access the largest Land of published oncology projects

  • Explore new immuno-oncology studies in OncoGEO_B37, our largest Land of published oncology projects: Explore even more miRNA data from gastrointestinal, reproductive and urinary system cancer samples.
  • Get more new insights from The Cancer Genome Atlas (TCGA) Land: You get more insights with the addition of new metadata content from the recent PanCancer Atlas publications, along with updated copy number (CNV) and protein quantification data.
  • Explore enhanced cancer genomic data: Hundreds of new projects have been added, as well as updates to consortium datasets including Broad Institute Cancer Cell Line Encyclopedia (CCLE), Genotype-Tissue Expression (GTEx) project, International Cancer Genome Consortium (ICGC), AACR Project Genomics Evidence Neoplasia Information Exchange (GENIE), and Sanger Lands.

August 2018 Release: New Features with this Release

GeneticsLand Updates

  • Now access electronic health record phenotypes with the addition of PheWAS data
  • As part of the GeneticsLand data service, we curated Phenome-Wide Association Study (PheWAS) results from the UK Biobank and the PheWAS Catalog, giving you access to 3,777 new phenotypes and 26 billion variant association summary statistics
  • Improve the identification of interesting variants
    • Each variant is annotated with 1000 Genomes, gnomAD, ClinVar, Conservation, dbNSFP, GTEx, GWAS Catalog, GRASP, GWAVA, RegulomeDB, OMIM, HGNC, InterPro, and DGIdb. More annotation sources are available upon request.

DiseaseLand Updates

  • Access more expression data for autoimmune disorders, heart disease, and stroke-related projects
  • HumanDisease, MouseDisease, and RatDisease Lands now contain over 360 additional projects that include 12,000 new samples and 1,700 new comparisons
  • Explore new cell types in single cell lands
  • Single Cell Lands (SCHuman, SCMouse, and SCRat) have 27 new projects with over 21,000 new samples. New cell types include hair follicle stem and progenitor populations, innate immune cells, and in vitro cultured neurons.

OncoLand Updates

Improve your genetic characterization of human cancer cell lines

  • The Cancer Cell Line Encyclopedia (CCLE) Land contains updated DNA-seq mutation and RPPA data recently released on the Broad portal
  • New drug measurements from the Cancer Therapeutics Response Portal are also available upon request
  • New clinical features curated from TCGA PanCancer Atlas publications
  • The Cancer Genome Atlas (TCGA) Land now features over 150 new metadata columns, including additional survival metrics derived from recent PanCancer Atlas publications
  • Enhanced data content (DNA mutation, copy number, and expression)
  • MET500 (metastatic cancer cohort) Land now available for genome reference library B38
  • American Association for Cancer Research GENIE Land has been updated to version 3 with over 21,000 new samples
  • OncoGEO B37 Land has approximately 10,000 additional samples.
  • The Human Protein Atlas (HPA) Land has new tissue microarray data