The Xenografts module

The Xenografts module is responsible for all the operations related to Xeno experiments. Each aliquot implantation defines a biological entity named Biomouse. Since multiple tumor aliquots may be implanted at different sites within the same animal, the physical animal can host several Biomice. Biomice can be grouped into Experimental Groups according to the purpose of the research. In this way, researchers can study tumor growth and treatment response on a subset of animals. The physical animals can assume different statuses which affect the life cycle of the hosted Biomice.

The Implant

  • Process description some aliquots are implanted on a biological mouse bound to physical mouse.
  • DBMS involved: Neo4j, MySQL.

The Explant

  • Process description some aliquots are created from a biological mouse. The relative physical mouse is sacrificed.
  • DBMS involved: Neo4j, MySQL

Data created

In the biobanca a new record for each aliquot is created in the table biobanca.aliquot. Each aliquot has a reference to the relative sampling event (e.g., 54398).

mysql> select * from biobanca.aliquot where uniqueGenealogyID like 'CRC0177LMX0C03005%';
id barcodeID uniqueGenealogyID idSamplingEvent idAliquotType availability timesUsed derived archiveDate
293941 20334 CRC0177LMX0C03005TUMFF0100 54398 4 1 0 0 NULL
293942 1156025086 CRC0177LMX0C03005TUMRL0100 54398 3 1 0 0 NULL
293943 1156025087 CRC0177LMX0C03005TUMRL0200 54398 3 1 0 0 NULL
293944 1156025088 CRC0177LMX0C03005TUMRL0300 54398 3 1 0 0 NULL
293945 1156025089 CRC0177LMX0C03005TUMRL0400 54398 3 1 0 0 NULL
293946 1156004068 CRC0177LMX0C03005TUMSF0100 54398 2 1 0 0 NULL
293947 1156004069 CRC0177LMX0C03005TUMSF0200 54398 2 1 0 0 NULL
293948 1156004070 CRC0177LMX0C03005TUMSF0300 54398 2 1 0 0 NULL
293949 1156004058 CRC0177LMX0C03005TUMSF0400 54398 2 1 0 0 NULL

The sampling event has a reference to a collection. The collection record is not usually created during the explant session. Therefore, if you need to delete explanted aliquots, do not delete the collection. The sampling event has a reference to a series.

mysql> select * from biobanca.samplingevent where id = 54398;
id idTissueType idCollection idSource idSerie samplingDate
54398 2 148 7 12081 2018-02-02

The series…

mysql> select * from biobanca.serie where id = 12081;
id operator serieDate
12081 user.name 2018-02-02

Besides, each aliquot has features in biobanca.aliquotfeature

mysql> select * from biobanca.aliquotfeature where idAliquot in (select id from aliquot where uniqueGenealogyID like 'CRC0177LMX0C03005%');
id idAliquot idFeature value
462254 293941 4 1
462255 293942 3 1
462256 293943 3 1
462257 293944 3 1
462258 293945 3 1
462259 293946 2 1
462260 293947 2 1
462261 293948 2 1
462262 293949 2 1

In the storage:…

In neo4j: …

Common operations for the help desk

Users usually request some of the following operations.

Adding aliquots to a performed explant

Problem: After an explant session, the mouse is not available anymore and the user cannot attach new explanted aliquots.

You can load other aliquots in the following way:

  • Go to Biological Experiments > Xenografts > Batch
  • Select Add aliquots to explant
  • Load the file with new aliquots. Click on Template to get the required format.

Recreate an implant

Here we exemplify the implant recovery procedure to restore the implant-related data to a consistent state in the database. The operations we are going to explain here are useful in all those cases in which the save operation has failed for whatever reason. First of all, we identify the experimental series the implant belongs to. In detail, there is a one-to-many relationship between a series and their related sampling events.

Supposing to investigate the experimental series related to the mouse barcodes B1, B2 and B3 respectively, we could run the following query.

mysql> select * from serie where id in (select idSerie from samplingevent where id in (select idSamplingEvent from aliquot where uniqueGenealogyID in ('B1','B2','B3')));

Once the experimental series has been identified, we use the Storage database

mysql> use storage;

Since the aliquots can be collected in multiple fashions, they must be treated accordingly during this recreation procedure.

  • FFPE blocks: delete both the container and the aliquot.
  • Tubes: make them available again (empty them setting attribute *full*=0 in the Container table) and delete the associated aliquot.

In order to access the containers related to the explants, we use their GenealogyIDs in the table Container

mysql> update Container set full=0 where id in (select idContainer from Aliquot where GenealogyID like 'Gen_ID%');

To delete the FFPE block, we delete its record in the Contanier table, along with the associated information in the ContainerFeature table.

mysql> delete from containerfeature where idContainer in (select idContainer from Aliquot where GenealogyID like 'Gen_ID%');

To simply delete an aliquot an automatic procedure is available at the URL http://las.ircc.it/biobank/canc/aliquot. Please refer to section Deleting an aliquot.