CELLector

Genomics Guided Selection of Cancer in vitro Models

v1.0.3

Tutorial

Code

CELLector R Package

CELLector R Package interactive vignette

User Defined Binary genomic Event Matrices (BEMs)

Select Primary Tumour BEMs file:

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Select Cell Line BEMs file:

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Cancer Type:

Underlying data available at the GDSC1000 data portal.

Download Search Space

Representative Cell Line Selection

N. of Cell Lines to Select:

CELLect Cell Lines
Score cell lines Cell lines SubTypes Map

Signature Length weight (= 1 - n. Patients score weight)

Please cite: Najgebauer et al. 2018 - CELLector: Genomics Guided Selection of Cancer in vitro Models

Primary Tumours: Subtyping Criteria

Cancer Functional Events (CFEs) to consider:

Mutations in high confidence cancer genes

Recurrently CN altered chromosomal segments

Both

Include Methylation data

Alteration set size:

Global support (%):

Supervised Search Space Construction

1. Define subcohort based on the status of an individual CFE:

wild-type

2. Focus on CFEs in cancer pathways (max 3):

3. Consider only cell lines that are:

Microsatellite stable

Microsatellite instable

All

Show CNA id decoding table

Id decoding for recurrently CN altered chromosomal segments (values in Id column can be used in box 1)

Full decoding table available at the GDSC1000 data portal

Show HyperMeth. id decoding table

Id decoding for informative CpG island hyper-methylations (values in Id column can be used in box 1)

Full decoding table available at the GDSC1000 data portal

Legend

Genomic Binary Event Matrix (BEM) builder

v1.0.1

Tutorial

Code

CELLector R Package

CELLector R Package interactive vignette

Primary tumours

Variant catalogue to consider:

Use curated TCGA data from Iorio et al. 2016

Upload Variants

Cancer Type:

Genes to consider:

All Iorio et al. 2016 drivers CMPs drivers User defined list

Upload a plain .txt file with Gene identifiers (one per line):

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Variants to consider:

All Iorio et al. 2016 variants (COSMIC filtered) User defined list

Upload a plain .txt file with tab separated [Gene identifier - variant] (one pair per line):

Browse...

Upload the variant catalogue as a plain tab separated .txt file:

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BEM file format:

R object .tsv

Save BEM

in-vitro models

Variant catalogue to consider:

Use Variants Catalogue from Cell Model Passports (CMPs)

Upload Variants

Exclude organoids

Human derived only

Filter based on age at sampling

Gender:

Male

Female

All (including Unknown)

Filter based on etnicity

MSI status:

MSS

MSI

All (including NA)

Filter based on mutation burden

Filter based on ploidy

Tissue:

Genes to consider:

All Iorio et al. 2016 drivers CMPs drivers User defined list

Upload a plain .txt file with Gene identifiers (one per line):

Browse...

Variants to consider:

All Iorio et al. 2016 variants (COSMIC filtered) User defined list

Upload a plain .txt file with tab separated [Gene identifier - variant] (one pair per line):

Browse...

Upload the variant catalogue as a plain tab separated .txt file:

Browse...

BEM file format:

R object .tsv

Save BEM