Special course on the analysis of metagenomic data (2021–2022)
Special course on the analysis of metagenomic data
New version of Genomenal 2.4.0
Sun, 10/29/2023 - 09:00
Main updates:
- Introducing CNV Viewer - Copy Number Variation analysis tool with filtering, sorting, and prioritizing, integrated with IGV and Decipher database, records pinning, user custom interpretation, pathogenicity and boundary refinement, hierarchical and flat full/split record view modes.
- The new homepage for easy analysis, interpretation, work step tracking.
- User notifications on completion of sample processing and batch analyses.
New version of Genomenal 2.3.0
Thu, 07/20/2023 - 09:00
Key changes:
- Genomenal can now combine any number of samples into a single table (in VCF format), with unsequenced parts of the samples marked in a special way (with "./." genotype). This capability provides the basis for qualitative population analysis, variant frequency calculations and other population genetics tasks. The results of such analyses can be loaded into Genomenal as user annotations.
- A feature has been developed to merge images into a single image at the data loading stage.
- This is particularly relevant when sequencers produce multiple files for a single sample, spread across multiple lanes of the sequencer. It is also possible to combine heterogeneous data into a single sample.
- Population and panel analysis functionality for large numbers of samples has been introduced.
- RefSeq annotation has been introduced.
- Users can now analyze the effects of variants on both Ensembl and RefSeq transcripts. Easily select the annotation system you are familiar with.
- Grouping of filter fields in the query builder has been added to improve navigation and usability.
- Introduced the ability to resume interrupted sample downloads, making it easier to work with large amounts of data.
- If communication is interrupted, the sample download can almost always be resumed from the same location.
- The Variant Viewer tool now has the ability to display the "HGVSp long" column, allowing you to view the variant annotation in the format recommended by the International Human Genetic Variant Consortium.
- GRM has been improved with an interface to manage organization, add interpretation steps and notify other users of changes to steps. Working in a team is now even more convenient.
New version of Genomenal 2.2.0
Mon, 05/22/2023 - 09:00
New features:
- A new, unique interpreter collaboration system - Genomic Relationship Management.
- A new pipeline has been introduced that allows for the prediction of polygenic traits for samples in FASTQ format.
- The display now includes the interpretation of identical variants in other samples that have been uploaded to the account and previously interpreted.
- A new setting, "Compound Heterozygotes", has been added to the query builder. This setting, used after applying other filters, allows for the extraction of those variants that may be in a compound heterozygous form from the filtered ones. This setting is particularly relevant for group analysis.
- The display now includes the interpretation of identical variants in other samples uploaded to the account and previously interpreted.
- The ability to add tracks of other samples uploaded to the account to the Integrative Genomics Viewer (IGV) has been implemented.
Improvements:
- Databases updated to the latest versions.
- Added support for variant phase groups (new column in VV "Phase group status", by default the column is not shown).
- Added Enigma database annotation (new columns in VV "ENIGMA clinical significance" and "ENIGMA clinical significance comment", by default the columns are not shown).
- Added new scorers MaxEntScan, MutationAssessor, added precalculated CADD and SpliceAI.
- Added ability to export variants whose parameters (interpretation, anchoring, pathogenicity, etc.) have been changed.
- Added a new "Label" column in the Variant Viewer (VV) to allow the significance of a variant to be marked or to indicate that a variant is a sequencing error (by default the column is not displayed).
- Added the ability to filter by multiple HPO terms.
- Added the ability to sort by multiple columns.
- Added additional external links to open databases (UCSC, Franklin).
- Added color coding of ClinVar pathogenicity, shortened pathogenicity names.
- Copying variant positions from the variant table to VV is now done with a single mouse click.
- In VV, a frequency filter (using gnomAD) with defined thresholds has been added to the basic filters. The option is enabled in the VV settings in the user profile.
- The ability to add new samples to a previously created run has been implemented.
- The Variant Interpretation/Comment field can now be edited in the General tab at the bottom of the VV window.
- Variant details can be opened in a separate tab for easier comparison and analysis by right clicking on the "Show Variant Details" icon in the variant row.
- Finding the required parameters to set filter conditions for variants in the Query Builder has been improved.
The Journal of Molecular and Cellular Cardiology Plus has released a paper on transcriptome changes in coronary heart disease
Wed, 04/05/2023 - 09:00
Employees of NOVEL collaborated in the publication of the article "RNAseq profiling of blood from patients with coronary artery disease: "Signature of a T cell imbalance" in the Journal of Molecular and Cellular Cardiology Plus.
The investigation of regulatory T cell dysfunction in CAD is the focus of the article. Researchers have accurately analyzed the biggest sample of gene activity in CAD using cutting-edge sequencing and bioinformatics methods.
It has been demonstrated that transcripts connected to the immunological synapse (interaction) are particularly connected to CAD. T-cells and B-cells can communicate with diverse antigen-presenting and immunomodulatory cells at the immunological synapse, which is contact-dependent. Fibromodulin (FMOD; upregulated 2.8-fold in CAD) is one of the most differentially expressed genes and is known to be associated with atherosclerosis, cardiomyopathy, and iron-dependent programmed cell death.
Moreover, transcripts for proteins connected to the immunological synapse's formation and operation have been found. Nebulette is involved in the binding of actin and desmin for the operation of the cytoskeleton and vesicular movement (increases 2.4 times in CAD). Transcripts that were directly connected to T cell activity and the regulation of differentiation were present in the immunological synapses' signaling pathways. T-cell activation is mediated by butyrophilin, which is elevated 1.7-fold in coronary artery disease.
The paper demonstrates how alternative sequencing technologies (SeqLL and Illumnina) enable the identification of transcripts linked to alterations in T regulatory cells, but with distinctly distinct transcripts linked to CAD.
The full text of the article can be found here: https://www.sciencedirect.com/science/article/pii/S277297612300003X?via%3Dihub
New version of Genomenal 2.1.0
Fri, 03/03/2023 - 09:00
Main changes in Genomenal version 2.1.0:
- Implemented a new filter "Compound heterozygote (Genotype)" for group analysis in Variant Viewer, adding which it will display variants in genes that have at least two variants with the alt_het genotype (ref/alt heterozygote).
- The number of variants in the Variant Viewer page now can be changed.
- Implemented the ability to load FASTQ data from different sequencer lanes and process them as a solid sample.
- Now Genomenal can automatically determine the reference genome for custom Capture Kit.
- Improved clinical susceptibility sorting in ClinVar.
- Updated guidelines for cancer reporting.
- Increased sample processing speed with the storage performance improved.
New version of Genomenal 1.9.5
Mon, 10/24/2022 - 09:00
Major updates for Genomenal 1.9.5:
- CADD and SpliceAI scores have been added to Variant Viewer to improve quality and convenience of data interpretation.
- ClinVar and 1000Genomes (1KG) databases were updated.
- The Molecular Genetic Testing Report Designer has been improved.
More details at https://genomenal.com/
New version of Genomenal 1.9.0
Fri, 07/29/2022 - 09:00
The main changes in Genomenal ver. 1.9.0:
- The official recommendations of RUSSCO, NCCN and ESMO for convenience and improved quality of the cancer specimen interpreter were integrated.
- Special tools for genotype analysis in family trios (proband/mother/father) were improved.
- Sample interpretation statuses were added.
- Now you can save the state of filters and sorting in the Variant Viewer for each sample.
- NCBI RefSeq transcript codes (NM_...) were added to Variant Viewer.
- Now you can switch the Genomenal interface language in the user profile.
- Automatic status updates on the All Patients page were implemented.
More details at https://genomenal.com/
NOVEL at the III All-Russian Conference "High-performance Sequencing in Genomics”
Mon, 07/04/2022 - 09:00
The III All-Russian Conference "High-performance Sequencing in Genomics" (HSG-2022) was held June 19-24, 2022 in Novosibirsk Akademgorodok. The event brings together such fields as eukaryotic and prokaryotic genomics, metagenomics of microorganism communities, medical genomics, transcriptomics, protein-nucleic acid interactions, and translation.
New methods based on high-performance sequencing and their practical application were discussed at the conference.
Leading experts from Novel participated in this conference.
Mikhail Pomaznoy: "The most important thing at any conference is new contacts. This event is important for us, because NGS Wizard is not yet familiar to everyone. Surprisingly, we managed to make new contacts with people who are working in the neighboring building and did not know about our project. The variety of topics makes the reports interesting, because it allows me to hear about areas that I have nothing to do with. For example, research of bacterial communities of the Barents Sea is something distant, unfamiliar and fascinating for me.”
Maria Starchevskaya: “My report at the conference "High-performance sequencing in genomics" was devoted to metagenomic analysis of Colorado potato beetle genomes. The search for viral genetic sequences is an urgent and challenging task and we developed an analytical software pipeline that performs identification and annotation of viral material in NGS data.”
New version of Genomenal 1.8.0
Mon, 05/16/2022 - 09:00
Updates in new version of Genomenal 1.8.0:
- Analysis pipeline is substantially reworked and improved. It is now faster and more precise.
Improvements were achieved by using updated version of GATK, bwa-mem2, and revisiting mechanisms of raw read filtration and other steps of the pipeline. Precision was controlled using benchmarks shared by Genome In a Bottle and SEQC-2.
- Persistent custom pathogenicity classes.
Variants marked as pathogenic while working on an arbitrary sample, will be marked as pathogenic in other samples automatically. Moreover it is possible to upload pathogenic variants in bulk to use later in annotation pipeline.
- Improvements of basic filtering mode in Variant Viewer.
Panel of basic filter is now customizable. It allows to use several new filtering creteria. Multiselection is now enabled in the fields where it is possible.
- Customizable UI features.
User can adjust several interface features. For example, hide variant details panel in Variant Viewer, customize navigation panel etc.