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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:

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