# 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](/emedgene/frequently-asked-questions/all-faq/how_do_i_analyze_mtdna_variants.md) 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*](/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/filters_presets_panel/filters/variant_type_filters.md). The filter can be added to your custom presets.

![](/files/Dcs3HdbYyqXbaR6G8uJA)

### mtDNA variant annotation

The [*Variant table*](/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/variant_table.md) and [*Variant page*](/emedgene/emedgene-analyze-manual/variant_page/variant_page.md) 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).

![](/files/TiZQq86q0ztdbxZCEMsN)

### mtDNA variant classification

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

![](/files/HiUeAB6RM45OHwMiti0C)

***

## **Related cases**

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

![](/files/0sojkrhO6ZzL4uZ42bkn)

Stay tuned for the curated data sharing between partner organizations!

***

## **Add virtual variants**

You can now [manually add variants](/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/variant_table/manually_add_variants_to_a_delivered_case.md) 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!

![](/files/qGa4II50B874b7bOgfon)

***

## **CNV calling from exomes**

We now support [CNV calling from exome data](/emedgene/frequently-asked-questions/all-faq/can_i_use_exome_data_for_cnv_detection.md) 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*](/emedgene/emedgene-analyze-manual/variant_page/visualization_section.md) now includes a *Test Subject VCF track* presenting proband's variants stored in the VCF file.

![](/files/8PsGyXLVzvWUx6dt9ST0)


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