Supplementary Figures S1-S25 from Late-Stage Metastatic Melanoma Emerges through a Diversity of Evolutionary Pathways
Authors: Spain Lavinia , Coulton Alexander , Lobon Irene , Rowan Andrew , Schnidrig Desiree , Shepherd Scott T.C. , Shum Benjamin , Byrne Fiona , Goicoechea Maria , Piperni Elisa , Au Lewis , Edmonds Kim , Carlyle Eleanor , Hunter Nikki , Renn Alexandra , Messiou Christina , Hughes Peta , Nobbs Jaime , Foijer Floris , van den Bos Hilda , Wardenaar Rene , Spierings Diana C.J. , Spencer Charlotte , Schmitt Andreas M. , Tippu Zayd , Lingard Karla , Grostate Lauren , Peat Kema , Kelly Kayleigh , Sarker Sarah , Vaughan Sarah , Mangwende Mary , Terry Lauren , Kelly Denise , Biano Jennifer , Murra Aida , Korteweg Justine , Lewis Charlotte , O'Flaherty Molly , Cattin Anne-Laure , Emmerich Max , Gerard Camille L. , Pallikonda Husayn Ahmed , Lynch Joanna , Mason Robert , Rogiers Aljosja , Xu Hang , Huebner Ariana , McGranahan Nicholas , Al Bakir Maise , Murai Jun , Naceur-Lombardelli Cristina , Borg Elaine , Mitchison Miriam , Moore David A. , Falzon Mary , Proctor Ian , Stamp Gordon W.H. , Nye Emma L. , Young Kate , Furness Andrew J.S. , Pickering Lisa , Stewart Ruby , Mahadeva Ula , Green Anna , Larkin James , Litchfield Kevin , Swanton Charles , Jamal-Hanjani Mariam , Turajlic Samra 
Published: June 2023

<p>Supplementary figure 1: Cohort overview. Number of samples sequenced with whole exome, panel or whole
RNA sequencing.
Supplementary figure 2: Phylogeny and WGD events in CRUKP1047.
Supplementary figure 3: Ploidy and SCNA burden.
Supplementary figure 4: Overview of each case.
Supplementary figure 5: MEDICC2 copy number sample trees.
Supplementary figure 6: MEDICC tree of all exome samples demonstrating that samples cluster together by patient, and not by melanoma subtype.
Supplementary figure 7: SCNA frequency of cutaneous (a), acral (b) and melanoma of unknown primary (MUP, c).
Supplementary figure 8: Correlation between liver copy number distance to other sites and time of emergence after stage IV diagnosis.
Supplementary figure 9: Examination of tumour heterogeneity of alterations to antigen-presentation machinery genes,with site and patient annotation.
Supplementary figure 10: Boxplots indicating the proportion of losses in the cohort for each segment.
Supplementary figure 11: Balance of expression between nonsynonymous mutations that were not predicted to be neoantigens and clonal predicted neoantigens.
Supplementary figure 12: Barplot of TIL infiltration score frequencies, determined by pathologist assessment of histology, across all samples.
Supplementary figure 13: Number of samples per patient that are classified as either none-low in terms of TILs or moderate-heavy.
Supplementary figure 14: Histogram of purity for samples with RNA-seq data.
Supplementary figure 15: TME deconvolution.
Supplementary figure 16: The effect of metastatic site on transcriptional profiles.
Supplementary figure 17: Association of PHF3 copy number with expression.
Supplementary figure 18: Overview of gene fusions identified in RNA-seq data.
Supplementary figure 19: Comparison of ploidy estimates from panel sequencing data, exome data and FISH.
Supplementary figure 20: Comparison of ploidy estimates in panel, exome, FISH and single cell data.
Supplementary figure 21: FACs sort plot for CRUKP2567 diaphragmatic metastasis.
Supplementary figure 22: Ploidy and wGII values from single cell sequencing of FACS-sorted tumour cells.
Supplementary figure 23: Copy number profiles on chromosome 5 for bulk samples from primary and DI_2_R2, a diaphragmatic metastasis.
Supplementary figure 24: Histogram of purity of samples for which RNA-seq was performed faceted by patient.
Supplementary figure 25: Histogram of purity of samples for which RNA-seq was performed faceted by tissue site.</p>