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Update changelog.md
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mbaudis committed Sep 15, 2024
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Expand Up @@ -4,6 +4,26 @@ This page lists changes for the [Beacon+](http://beacon.progenetix.org/ui/)
implementation of the ["Beacon" genomics API](http://beacon-project.io), as well
as related updates for the [Progenetix](http://progenetix.org) front-end.

## 2024-09-10: Ongoing removal of samples from pure germline series

So far of the currently 145264 samples the Progenetix collection consisted of
besides data from

* 112674 cancer samples (including primary tumors, recurrences and metastases)
* 5742 cancer cell line samples
* 26848 germline samples consisting of
- germline references of tumor patients
- 3201 reference profiles from the 1000 genomes project
- samples from 58 "accidental" germline series (_i.e._ such being analyzed
in automated download & processing and then being kept for comparative purposes)

We are now in the process of creating a new resource for the germline samples
which will become available in the near future under the [refcnv.org](https://refcnv.org)
address. While strengthening the focus of the Progenetix database this will provide
a new general resource for germline CNV data e.g. as reference for rare disease
applications.


## 2024-06-18 Switching ontology use for `individual.sex`

While we had previously used the PATO terms for `genotypic sex` (PATO:0020001
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