# New in Emedgene 2.19-2.22 (Apr 8, 2021)

1. [**New CNV Analysis Tools**](#h_5b8db3d6db)**:**
   1. [New *Gene Filters*: *LoF Genes*, *Established HI/TS Genes*](#h_9ee46b9dce)
   2. [New *Quality Filter*: *Bin Count*](#h_0161552ec6)
   3. [Extended CNV Quality Metrics](#h_ec7e4f7270)
2. [**UI & Workflow Improvements**](#h_0a399257ce)**:**
   1. [Variant page redesign: brand new *Summary tab* and updated *Quality tab*](#h_ad689eba5c)
   2. [Variant type filter & column](#h_77b805177f)
   3. [Full control over your gene lists](#h_617b7c8d6f)
   4. [Restricted access to *Finalized Case status*](#h_dd50122df7)

***

## **New CNV Analysis Tools**

### New *Gene Filters*: *LoF Genes, Established HI/TS Genes*

Two new CNV filters will help you focus on the genes that are most likely to be pathogenic:

* *LoF Genes* will present all genes with a gnomAD pLI≥0.9;
* *Established HI/TS Genes* filter will only return variants genes with an HI/TS score of 3.

Both are available under [*Gene Filters*](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab/analysis_tools_tab/filters_presets_panel/filters/gene_filters) and can be added to your preset filters.

![](https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-b7e09ec5b4f3c6a15b1b1433bf6bee60e3686bc0%2Fnew_in_emedgene_219-222_-apr_8-_2021_1.png?alt=media)

### New *Quality Filter*: Bin Count

If you’d like to focus on high-quality CNVs, you can now set a minimum bin count of 1, 5, 10, 25, 50, 100 or 500 in *CNV Bin Count* filter. The filter appears under [*Quality Filters*](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab/analysis_tools_tab/filters_presets_panel/filters/quality_filters) in *Advanced mode*.

![](https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-1c57484ba8c09c554aa15eb06ea4bbff408ae305%2Fnew_in_emedgene_219-222_-apr_8-_2021_2.png?alt=media)

### Extended CNV Quality Metrics

[*Quality tab*](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/quality_section) for CNVs got updated! For each sample, you can now see copy number, CNV quality, size, and bin count.

![](https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-cb4110debda367ffefe7ec96fc3efc7ef61e2cff%2Fnew_in_emedgene_219-222_-apr_8-_2021_3.png?alt=media)

***

## **UI & Workflow Improvements**

### Variant page redesign: brand new *Summary tab* and updated *Quality tab*

The [*Variant page*](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/variant_page) now features a clear [*Summary tab*](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/summary_section) that spotlights essential variant information - saving you precious clicks! If after the first glance you feel like diving deeper into the variant details - proceed to other *Variant page* tabs below.

![](https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-b066063139a9fe69bf37daae194f417df354a784%2Fnew_in_emedgene_219-222_-apr_8-_2021_4.png?alt=media)

We redesigned [*Quality tab*](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/quality_section): it has a slightly different style,

To change the sample in review for the particular variant, click on the corresponding icon in the family tree.

![](https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-30d35e9d57a52e403772b07f73c7808e9e3c6b65%2Fnew_in_emedgene_219-222_-apr_8-_2021_5.png?alt=media)

If you've read this far, here is a bonus insider tip! 🤫

Did you know that you can view the [*Evidence page*](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/evidence_page) for any tagged variant? We redesigned the *See evidence* button on the [*Evidence section*](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/evidence_section) to make it pop!

![](https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-65b6fd6ff3f6eaac9156f540bb3526f7faaa1142%2Fnew_in_emedgene_219-222_-apr_8-_2021_6.png?alt=media)

### **Variant type filter & column**

Piping hot [*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) at your command! Ready to filter variants by type (SNV, Indel, DEL, DUP). Additionally, variant type is shown in the variant table.

![](https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-8f34ab04d6a48a3406fa3793dede2c66fe30b077%2Fnew_in_emedgene_219-222_-apr_8-_2021_7.png?alt=media)

### **Full control over your gene lists**

Administrators of your account now have total control over [gene lists](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/launching-analysis/creating_a_single_case/gene_list) and can create and edit them in [*Settings*](https://help.connected.illumina.com/emedgene/release-notes/workbench-and-pipeline-updates/more-release-notes/broken-reference)*.*

![](https://1131024994-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FGCW0DnLlE7QjoZPNmKIi%2Fuploads%2Fgit-blob-3c7cf77adbe3ca18cad612459123901a5ae7fa0b%2Fnew_in_emedgene_219-222_-apr_8-_2021_8.png?alt=media)

### **Restricted access to *****Finalized*** ***Case status***

The *Finalized* [*Case status*](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/case_status) locks the case to prevent further changes to interpretation notes, ACMG tags, variant tags, pathogenicity and case-level interpretations.

Starting from this version, access to [finalizing a case](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/case-completion-and-reporting/finalizing_a_case) requires a dedicated [role](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/settings/user_roles), so the organization's manager can restrict access to a specific set of users.