ImmuneLENS manuscript figure code
Creators: name: Bentham, Robert
Publisher: name: Zenodo
Year: 2025

description: ImmuneLENS characterizes systemic immune dysregulation in aging and cancer by Bentham et al. 

This folder contains the code and data necessary to reproduce all figures. 

The following cohorts were analysed:- Tx100 - TRACERx100 - previously published RNAseq, WES and coverage files from WGS data were used (available at https://zenodo.org/uploads/7785803)- 100KGP - 100,000 Genome Project. WGS and phenotypic data from the 100,000 Genomes Project can be accessed by application to Genomics England following the procedure outlined at https://www.genomicsengland.co.uk/about-gecip/joining-research-community/. Data necessary to run the figure code can be found on the Genomics England Research Environment within the folder ‘/re_gecip/shared_allGeCIPs/rbentham/ImmuneLENS_figure_code/' - TCGA - To access TCGA WES and low pass WGS data, researchers will need to apply to the TCGA Data Access Committee (DAC) via dbGaP (https://dbgap.ncbi.nlm.nih.gov/aa/wga.cgi?page=login). The calculated T cell ExTRECT TCRA T cell fraction scores along with the ImmuneLENS output for the low pass WGS samples used in this study is available at zenodo.org (10.5281/zenodo.7794867).- PCAWG - PCAWG data used in this study was obtained through our collaboration with MD Anderson. To gain access to the TCGA portion of the PCAWG data used in this study, researchers need to apply to the TCGA data access committee via dbGaP (https://dbgap.ncbi.nlm.nih.gov/aa/wga.cgi?page=login). The calculated ImmuneLENS output for these samples is available on zenodo.org (10.5281/zenodo.1109396)- 1000 genomes - The 1000 Genome Data used is publicly available and can be accessed on https://www.internationalgenome.org/data. Calculated ImmuneLENS output including class switching and polyclonal predictions for each LCL cell line included are available on zendodo (10.5281/zenodo.1109397). - single cell - All data used in this analysis is described in Salcher et al. available at https://cellxgene.cziscience.com/collections/edb893ee-4066-4128-9aec-5eb2b03f8287.

Below is the location of the code for each figure and the dataset used to produce the figure:

Figure 1:- 1a - biorender (see https://BioRender.com/m39r939)- 1b - Figure_TRACERx100_analysis.R - Tx100- 1c. Figure_TRACERx100_analysis.R - Tx100- 1d - Figure_blood_count.R - 100KGP

Figure 2:- 2 - Figure_immune_landscape.R - 100KGP

Figure 3:- 3a - Figure_age_ribbons.R - 100KGP- 3b - Figure_hes_post_seq.R - 100KGP- 3c,d -Figure_age_ribbons.R - 100KGP- 3e - Figure_PLINK_snps.R - 100KGP

Figure 4:- 4a - Figure_dnds_analysis.R - 100KGP- 4b - Figure_dnds_analysis.R - 100KGP

Figure 5:- 5a - Figure_survival.R - 100KGP- 5b - Figure_survival.R - 100KGP

Ext Fig 1:- Ext 1a - manually drawn on Illustrator- Ext 1b - Figure_ImmuneLENS_examples.R - Tx100- Ext 1c - Figure_ImmuneLENS_examples.R - Tx100- Ext 1d - Figure_TRACERx100_analysis.R - Tx100- Ext 1e - Figure_TRACERx100_analysis.R - Tx100- Ext 1f - Figure_TRACERx100_analysis.R - Tx100

Ext Fig 2:- Ext 2a, c-f - Figure_nested_downsampling.R- Tx100- Ext 2b  Figure_ImmuneLENS_examples.R - Tx100

Ext Fig 3:- Ext 3 -  Figure_blood_count.R - 100KGP

Ext Fig 4:- Ext 4a - biorender (see https://BioRender.com/k68l614)- Ext 4b - Figure_TRAV_diversity.R- Tx100- Ext 4c - Figure TRAV_diversity.R- Tx100- Ext 4d - Figure TRAV_diversity.R - Tx100

Ext Fig 5:- Ext 5 - Figure_immune_landscape.R - 100KGP

Ext Fig 6:- Ext 6a-b - Figure_immune_landscape.R - 100KGP

Ext Fig 7- Ext 7a-b - Figure_PLINK_snps.R - 100KGP

Ext Fig 8:- Ext 8a - Figure_dnds_analysis.R -100KGP- Ext 8b - Figure_dnds_analysis.R - 100KGP

Ext Fig 9- Ext 9a - Figure_survival.R - 100KGP- Ext 9b-c - Figure_survival.R - 100KGP

Ext Fig 10:- Ext 10A - Figure_TCGA_WES.R - TCGA- Ext 10B - Figure_TCGA_WES.R - TCGA

Sup Fig 1:- Sup Fig 1 - Figure_ig_s_regions.R - 100KGP

Sup Fig 2:- Sup Fig 2A - biorender (https://BioRender.com/h09e242)- Sup Fig 2B-D - Figure_IGH_germline_validation_RD.R - 100KGP- Sup Fig 2E,F, I(part) - Figure_IGH_germline_validation_tx100.R - Tx100- Sup Fig 2G,I,H - Figure_IGH_germline_validation_RD.R

Sup Fig 3:- Sup FIg 2A-C - Figure_ImmuneLENS_vs_TcellExTRECT - Tx100

Sup Fig 4:- Sup Fig 4A-F -  Figure_TRACERx100_analysis.R  - Tx100- Sup Fig 4G-H - Figure_scRNA_v2.R - singlecell

Sup Fig 5:- Sup Fig 5A-F - Figure_1000_genomes_analyis.R - 1000 genomes

Sup Fig 6:- Sup Fig 6A - Figure_PCAWG_analysis.R - PCAWG WGS- Sup Fig 6B - Figure_TCGA_WES.R - TCGA- Sup FIg 6C-D,E (part)  - Figure_PCAWG_analysis.R - PCAWG WGS- Sup Fig 6E (TCGA) - Figure_TCGA_WES.R - TCGA

Sup Fig 7:- Sup Fig 7A,B,C - Figure_PCAWG_analysis.R - PCAWG WGS- Sup Fig 7D,E - Figure_1000_genomes_analysis.R - 1000 genomes- Sup Fig 7F, G - Figure_1000_genomes_analysis_low_cov.R - 1000 genomes

Sup Fig 8:- Sup Fig 8 - Figure_TRAV_comparison.R - 100KGP

Sup Fig 9:- Sup Fig 9 - Figure_propensity_matched_FC.R - 100KGP

Sup Fig 10:- Sup Fig 10A,B,C,D,E,F - Figure_PLINK_SNPS.R - 100KGP