# New in Emedgene 2.24-2.25 (Aug 11, 2021)

1. [mtDNA variants are here!](#h_91b0a861ad)
   1. [mtDNA variant callers](#h_91b0a861ad)
   2. [mtDNA variant filter](#h_624fed85a4)
   3. [mtDNA variant annotation](#h_2f418b18ec)
   4. [mtDNA variant classification](#h_7e29619f84)
2. [Related cases](#h_3ac7c65f49)
3. [Add virtual variants](https://github.com/illumina-swi/emedgene-docs/blob/prod/docs/release-notes/workbench_version_updates/http:/Add%20virtual%20variants/README.md)
4. [CNV calling from exomes](https://github.com/illumina-swi/emedgene-docs/blob/prod/docs/release-notes/workbench_version_updates/http:/CNV%20Calling%20from%20Exomes/README.md)
5. [Visualize variants from a VCF](https://github.com/illumina-swi/emedgene-docs/blob/prod/docs/release-notes/workbench_version_updates/http:/Visualize%20variants%20from%20a%20VCF/README.md)

***

## **mtDNA variants are here!** ✨

You can now [analyze and interpret mtDNA variants](https://help.connected.illumina.com/emedgene/frequently-asked-questions/all-faq/how_do_i_analyze_mtdna_variants) on the Emedgene platform, using a streamlined workflow that makes it easy to focus your analysis on the clinically meaningful variants.

### mtDNA variant callers

* Our secondary analysis pipeline uses [DRAGEN](https://www.illumina.com/products/by-type/informatics-products/dragen-bio-it-platform.html) and leverages improved quality metrics to help reduce the number of variants for review,
* We also support VCF files from [mity](https://github.com/KCCG/mity), [MuTect](https://software.broadinstitute.org/cancer/cga/mutect), and [CNVkit](https://cnvkit.readthedocs.io/en/stable/).

### mtDNA variant filter

You can focus on mtDNA variants by using the updated mtDNA filter in the [*Variant Type Filters*](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab/analysis_tools_tab/filters_presets_panel/filters/variant_type_filters). The filter can be added to your custom presets.

![](https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-d72a49cef59c120699e94734fe57255f63962c3b%2Fnew_in_emedgene_224-225_-aug_11-_2021_1_image.png?alt=media)

### mtDNA variant annotation

The [*Variant table*](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab/analysis_tools_tab/variant_table) and [*Variant page*](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/variant_page) reflect basic mtDNA variant annotations including:

* genes,
* transcripts,
* population annotations (gnomAD and [MITOMAP](https://academic.oup.com/nar/article/24/1/177/2359869)),
* *Missense Prediction* scores ([APOGEE](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5501658/) and [MitoTIP](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005867)),
* known disease-causing variants (MITOMAP).

![](https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-f5e68cea9cabf1c7a06a997f9d21fe7f2d8f87de%2Fnew_in_emedgene_224-225_-aug_11-_2021_2_unnamed.png?alt=media)

### mtDNA variant classification

The *ACMG SNV Classification wizard* is now [available for tagged mtDNA variants](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/evidence_section/acmg_snv_classification_wizard). It utilizes only relevant ACMG criteria and automatically defines the resulting ACMG class based on the manually assigned criteria.

![](https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-56b52cf1c06f4df6b62d418254e79386879e8ad0%2Facmg_snv_classification_wizard_7_acmg_mtdna.png?alt=media)

***

## **Related cases**

[*Related Cases*](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/related_cases_section) is a new tab of the [*Variant page*](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/variant_page) that highlights information on previous variant curation activity (i.e., assigning a [variant tag](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/variant_tagging_widget) and/or assigning *Pathogenicity* and/or adding *Variant Interpretation* notes).

![](https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-e37360b921d5da35c1677edb76a8f805a84d7ca4%2Frelated_cases_section_4_related_cases.gif?alt=media)

Stay tuned for the curated data sharing between partner organizations!

***

## **Add virtual variants**

You can now [manually add variants](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab/analysis_tools_tab/variant_table/manually_add_variants_to_a_delivered_case) not present in the VCF or not called from FASTQ to your case. This is useful when:

* you need to complement NGS with data from other genetic tests (long-read sequencing, optical mapping, CGH, SNP array, karyotyping/FISH, repeat-primed PCR, MLPA, Southern blot, etc);
* you want to report a few adjacent variants as a single multi-nucleotide variant.

Supported variant types are SNV, CNV, UPD, ROH, and STR. SV is coming soon!

![](https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-c8fa8427814deee165dd57cd51967275a97478e0%2Fnew_in_emedgene_224-225_-aug_11-_2021_5_unnamed%2B1.png?alt=media)

***

## **CNV calling from exomes**

We now support [CNV calling from exome data](https://help.connected.illumina.com/emedgene/frequently-asked-questions/all-faq/can_i_use_exome_data_for_cnv_detection) using DRAGEN. High precision and recall are achieved through a lab-optimized panel of normals (PON). Results vary per laboratory/sample preparation protocol, and validation is performed upon request.

***

## **Visualize variants from a VCF**

The [*Visualization tab*](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/visualization_section) now includes a *Test Subject VCF track* presenting proband's variants stored in the VCF file.

![](https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-570c59ee1293ae6de7335a90da87189a86ba639a%2Fnew_in_emedgene_224-225_-aug_11-_2021_6_viz_vcf_tr.png?alt=media)