Supplementary Table S17: Regression - SV count and Mutation Rates (per MB). All results are adjusted by sex, age of sampling and stage. Results with P < 0.05 are highlighted. ChRCC, chromophobe renal cell carcinoma; CN, copy number state; LoH, loss of heterozygosity; MB, megabase; pRCC, papillary renal cell carcinoma; SNV, single nucleotide variant; SV, structural variant.

Supplementary Figure S4: Tumour-normal discrepancy of telomere length between ChRCC (n = 61), further stratified by eosinophilic (n = 13) and classical (n = 48) subtypes, and pRCC (n = 103).

Supplementary Table S21: Summary of actionability of driver genes. “OncoKB Oncogenic Annotated” refers to mutations that do not meet the definitions of a “variant of unknown significance” (Supplementary Methods S1). Trials annotated in COSMIC targeting alterations in the MET gene are only mentioned for renal cell carcinoma cohorts with other cancer cohorts ignored. Trials annotated in COSMIC involving alterations in TP53 are ignored. ChRCC, chromophobe renal cell carcinoma; CN, copy number state; pRCC, papillary renal cell carcinoma; VEP, Variant Effect Predictor.

The identification of cancer drivers is a cornerstone to the delivery of precision oncology. So far, sequencing of renal cell cancer (RCC) has largely been confined to the clear cell subtype of RCC. In contrast, sequencing analyses of the less common forms of RCC, papillary RCC (pRCC) and chromophobe RCC (ChRCC), have so far been limited. We analyzed whole-genome sequencing data on 164 tumor-normal pairs from the Genomics England 100,000 Genomes Project, providing a comprehensive, high-resolution map of copy number alterations, structural variation, and key global genomic features, including mutational signatures, intratumor heterogeneity, and analysis of extrachromosomal DNA formation. Our research establishes correlations between genomic alterations and histologic diversification and the extent to which genetically-mediated immune escape contributes to the development of these RCC subtypes.Implications: We demonstrate the distinctive genetics that characterizes pRCC and ChRCC and how this information has the potential to inform patient treatment and clinical trials.

Supplementary Figure S8a-c: Structural variant (SV) hotspot regions in ChRCC (n = 61) tumours. A, Unclassified SVs at chr5:12448–1417975. B, Deletion SVs at chr6:31880903–32589555. C, Deletion SVs at chr20:2483222-15192528.

Supplementary Table S4: Software and data used in this study.

Supplementary Table S5: Germline mutations associated with RCC risk, and somatic mutations related to tumour hypermutation. Germline mutations of cancer susceptibility genes referenced in Yngvadottir and colleagues (2022) are also stated below. ChRCC, chromophobe renal cell carcinoma; MAF, minor allele frequency; pRCC, papillary renal cell carcinoma; SNP, single nucleotide polymorphism.

Supplementary Figure S16: Percentage of COSMIC signature mutational burden contribution for ChRCC (n = 61) samples, segregated by classical (n = 48) and eosinophilic (n = 13) subtypes, and pRCC (n = 103). ID1: slippage during DNA replication of the replicated DNA strand; ID2, slippage during DNA replication of the replicated DNA strand; ID12, unknown aetiology; SBS1, spontaneous deamination of 5-methylcytosine (clock-like signature); SBS5, unknown (clock-like signature); SBS26, defective DNA mismatch repair; SBS44, defective DNA mismatch repair.

Supplementary Table S16: Clinical Correlations with age, sex, stage and grade. Patient sex uses female sex as baseline. Results with P < 0.05 are highlighted. ChRCC, chromophobe renal cell carcinoma; CN, copy number state; LoH, loss of heterozygosity; MB, megabase; pRCC, papillary renal cell carcinoma; SNV, single nucleotide variant; SV, structural variant.

Supplementary Table S6: Summary of recurrent arm level CNA alterations. Recurrent focal regions were selected based on significance threshold Q < 0.05 from GISTIC output. ChRCC, Chromophobe renal cell carcinoma; CNA, copy number alteration; pRCC, papillary renal cell carcinoma.

Supplementary Figure S9: Number of extrachromosomal DNA (ecDNA) identified by AmpliconArchitect in ChRCC (n = 61) and pRCC (n = 103) samples.

Supplementary Figure S3: Overview of structural-variant-calling pipeline. BAM, binary sequence alignment map; PCAWG, The Pan-Cancer Analysis of Whole Genomes; SV, structural variant.

Supplementary Table S12: Summary of the distribution of mitochondria mutations. ChRCC, chromophobe renal cell carcinoma; HVI, high various I region; HV2, high various II region; pRCC, papillary renal cell carcinoma; VAF, variant allele frequency.

Supplementary Figure S15: Comparison of mitochondria features in ChRCC (n = 61), including stratified by classical (n = 48) and eosinophilic (n = 13) subtypes, and pRCC (n = 103). A, mitochondrial mutation rate (mutations with VAF > 1%). B,) mitochondrial copy number.

Supplementary Table S1: Number of fresh-frozen samples failing each quality control stage for RCC histologies. A sample is removed during quality control if it fails at least one quality control filter. Samples are further removed if they are not part of study aims. ChRCC,chromophobe renal cell carcinoma; pRCC, papillary renal cell carcinoma; SNV, single nucleotide variant; VAF, variant allele frequency.

Supplementary Figure S2: Overview of stage two of the copy-number-alteration-calling pipeline. SNV, single nucleotide variant; VAF, variant allele frequency.

Supplementary Table S20: Regression - Immune Escape. Logistic regression was applied. All results are adjusted by sex, age of sampling and stage. Results with P < 0.05 are highlighted. ChRCC, chromophobe renal cell carcinoma; CN, copy number state; LoH, loss of heterozygosity; MB, megabase; pRCC, papillary renal cell carcinoma; SNV, single nucleotide variant; SV, structural variant.

Supplementary Figure S5a-b: Distributions of copy number (CN) losses and gains in ChRCC (n = 61). A, Number of patients with simultaneous CN arm losses. B, Frequency of co-occurring arm level losses.

Supplementary Figure S14. Mutation and copy number timing. The relative ordering of driver mutations and arm level alterations. Copy number alterations refer to both gains and losses that encompass at least 50% of the chromosome arm. The odds ratio (OR) and 95% confidence intervals refer to the likelihood that a driver event is early (Log(OR) < 0) or late (Log(OR) > 0) and are calculated empirically from simulation (Supplementary Methods S1).A, ChRCC (n = 61). B, pRCC (n = 103).

Supplementary Table S15: Summary of mutations explained by COSMIC signatures. Signatures which are suspected to be signature artifacts are not included. Percentage of mutation burden refers to the percentage of either the total single base substitutions (SBS) or indels (ID) explained by a COSMIC signature for each patient. ChRCC, chromophobe renal cell carcinoma; ID1, slippage during DNA replication of the replicated DNA strand; ID2, slippage during DNA replication of the replicated DNA strand; ID12, unknown aetiology; pRCC, papillary renal cell carcinoma SBS1, spontaneous deamination of 5-methylcytosine (clock-like signature); SBS5, unknown (clock-like signature); SBS26, defective DNA mismatch repair; SBS44, defective DNA mismatch repair.