Whole genome sequencing of primary and metastatic Melanoma cases in an Australian cohort.

Melanoma is the fourth most common cancer in Australia and the leading cause of cancer death in young adults. The Australian Melanoma Genome Project (AMGP) is analysing whole genomes from melanomas. We include the results of whole genome sequencing (WGS) for a number of datasets that include cutaneous, acral and mucosal melanoma subtypes.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

14 Datasets 23 Publications

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Samples
EGAD00001003353	BAM outputs from STAR (https://github.com/alexdobin/STAR) analysis of RNASeq sequencing on HiSeq platform of 56 tumour samples from 46 melanoma cases. Gene model = Ensembl version 70	-
EGAD00001003357	Aligned, merged and deduplicated BAM files from HiSeq whole exome sequencing of 106 samples: matched tumour-normal pairs from 53 melanoma patients.	-
EGAD00001003388	Aligned, merged and deduplicated BAM files from HiSeq whole genome sequencing of 366 samples: matched tumour-normal pairs from 183 melanoma cases comprising 48 primary melanomas, 15 cell lines, and 120 metastases. Sequencing was performed on the Illumina HiSeq 2000 and Xten platforms at Australian and Korean sequencing centres. Data was aligned to the human genome (GRCh37) using BWA-MEM.	-
EGAD00001004409	Aligned, merged and deduplicated BAM files from HiSeq whole genome sequencing of 134 samples: matched tumour-normal pairs from 67 mucosal melanoma cases	-
EGAD00001004474	Aligned, merged and deduplicated BAM files from HiSeq whole genome sequencing of 28 samples: matched tumour-normal pairs from 14 melanocytic nevi cases	-
EGAD00001004869	Illumina platform sequencing data for matched tumour-normal DNA samples from 77 melanoma patients participating in a study investigating response to immunotherapy. Selected cases also have RNA sequencing of the tumour.	-
EGAD00001005454	Illumina platform sequencing of whole genome libraries prepared from paired tumour/normal samples from 103 cases of melanoma Uveal subtype	-
EGAD00001005500	Illumina platform sequencing of whole genome libraries prepared from paired tumour/normal samples from 87 cases of melanoma Acral subtype. 63 cases also have RNASeq sequencing from the tumour sample.	-
EGAD00001005501	Illumina RNASeq sequencing of tumour samples from 41 cases of melanoma	-
EGAD00001005738	79 RNAseq samples from 56 patients with melanoma who have undergone immune checkpoint blockade immunotherapy.	-
EGAD00001006439	Illumina RNASeq sequencing of tumour samples from 53 cases of cutaneous melanoma and 61 cases of acral melanoma	-
EGAD00001007055	RNAseq of 55 melanoma tumors that were used as a validation dataset in Garg et al Nat Commun, 2021 Feb 18;12(1):1137. doi: 10.1038/s41467-021-21207-2.	-
EGAD00001008798	Illumina platform whole genome sequencing data for matched tumour-normal DNA samples from 570 melanoma patients	1139
EGAD00001008837	Illumina RNASeq sequencing of tumour samples from 230 cases of melanoma	230

Publications	Citations
Whole-genome landscapes of major melanoma subtypes. Hayward NK, Wilmott JS, Waddell N, Johansson PA, Field MA, Nones K, Patch AM, Kakavand H, Alexandrov LB, Burke H, Jakrot V, Kazakoff S, Holmes O, Leonard C, Sabarinathan R, Mularoni L, Wood S, Xu Q, Waddell N, Tembe V, Pupo GM, De Paoli-Iseppi R, Vilain RE, Shang P, Lau LMS, Dagg RA, Schramm SJ, Pritchard A, Dutton-Regester K, Newell F, Fitzgerald A, Shang CA, Grimmond SM, Pickett HA, Yang JY, Stretch JR, Behren A, Kefford RF, Hersey P, Long GV, Cebon J, Shackleton M, Spillane AJ, Saw RPM, López-Bigas N, Pearson JV, Thompson JF, Scolyer RA, Mann GJ. Nature 545: 2017 175-180	656
Identification of Cancer Drivers at CTCF Insulators in 1,962 Whole Genomes. Liu EM, Martinez-Fundichely A, Diaz BJ, Aronson B, Cuykendall T, MacKay M, Dhingra P, Wong EWP, Chi P, Apostolou E, Sanjana NE, Khurana E. Cell Syst 8: 2019 446-455.e8	45
Whole-genome landscape of mucosal melanoma reveals diverse drivers and therapeutic targets. Newell F, Kong Y, Wilmott JS, Johansson PA, Ferguson PM, Cui C, Li Z, Kazakoff SH, Burke H, Dodds TJ, Patch AM, Nones K, Tembe V, Shang P, van der Weyden L, Wong K, Holmes O, Lo S, Leonard C, Wood S, Xu Q, Rawson RV, Mukhopadhyay P, Dummer R, Levesque MP, Jönsson G, Wang X, Yeh I, Wu H, Joseph N, Bastian BC, Long GV, Spillane AJ, Shannon KF, Thompson JF, Saw RPM, Adams DJ, Si L, Pearson JV, Hayward NK, Waddell N, Mann GJ, Guo J, Scolyer RA. Nat Commun 10: 2019 3163	121
Transcriptional downregulation of MHC class I and melanoma de- differentiation in resistance to PD-1 inhibition. Lee JH, Shklovskaya E, Lim SY, Carlino MS, Menzies AM, Stewart A, Pedersen B, Irvine M, Alavi S, Yang JYH, Strbenac D, Saw RPM, Thompson JF, Wilmott JS, Scolyer RA, Long GV, Kefford RF, Rizos H. Nat Commun 11: 2020 1897	140
Whole genome landscapes of uveal melanoma show an ultraviolet radiation signature in iris tumours. Johansson PA, Brooks K, Newell F, Palmer JM, Wilmott JS, Pritchard AL, Broit N, Wood S, Carlino MS, Leonard C, Koufariotis LT, Nathan V, Beasley AB, Howlie M, Dawson R, Rizos H, Schmidt CW, Long GV, Hamilton H, Kiilgaard JF, Isaacs T, Gray ES, Rolfe OJ, Park JJ, Stark A, Mann GJ, Scolyer RA, Pearson JV, van Baren N, Waddell N, Wadt KW, McGrath LA, Warrier SK, Glasson W, Hayward NK. Nat Commun 11: 2020 2408	67
Whole-genome sequencing of acral melanoma reveals genomic complexity and diversity. Newell F, Wilmott JS, Johansson PA, Nones K, Addala V, Mukhopadhyay P, Broit N, Amato CM, Van Gulick R, Kazakoff SH, Patch AM, Koufariotis LT, Lakis V, Leonard C, Wood S, Holmes O, Xu Q, Lewis K, Medina T, Gonzalez R, Saw RPM, Spillane AJ, Stretch JR, Rawson RV, Ferguson PM, Dodds TJ, Thompson JF, Long GV, Levesque MP, Robinson WA, Pearson JV, Mann GJ, Scolyer RA, Waddell N, Hayward NK. Nat Commun 11: 2020 5259	71
Ultraviolet radiation drives mutations in a subset of mucosal melanomas. Mundra PA, Dhomen N, Rodrigues M, Mikkelsen LH, Cassoux N, Brooks K, Valpione S, Reis-Filho JS, Heegaard S, Stern MH, Roman-Roman S, Marais R. Nat Commun 12: 2021 259	16
Tumour gene expression signature in primary melanoma predicts long-term outcomes. Garg M, Couturier DL, Nsengimana J, Fonseca NA, Wongchenko M, Yan Y, Lauss M, Jönsson GB, Newton-Bishop J, Parkinson C, Middleton MR, Bishop DT, McDonald S, Stefanos N, Tadross J, Vergara IA, Lo S, Newell F, Wilmott JS, Thompson JF, Long GV, Scolyer RA, Corrie P, Adams DJ, Brazma A, Rabbie R. Nat Commun 12: 2021 1137	29
Pathway signatures derived from on-treatment tumor specimens predict response to anti-PD1 blockade in metastatic melanoma. Du K, Wei S, Wei Z, Frederick DT, Miao B, Moll T, Tian T, Sugarman E, Gabrilovich DI, Sullivan RJ, Liu L, Flaherty KT, Boland GM, Herlyn M, Zhang G. Nat Commun 12: 2021 6023	23
Characterisation of the spectrum and genetic dependence of collateral mutations induced by translesion DNA synthesis. Póti Á, Szikriszt B, Gervai JZ, Chen D, Szüts D. PLoS Genet 18: 2022 e1010051	4
Anatomic position determines oncogenic specificity in melanoma. Weiss JM, Hunter MV, Cruz NM, Baggiolini A, Tagore M, Ma Y, Misale S, Marasco M, Simon-Vermot T, Campbell NR, Newell F, Wilmott JS, Johansson PA, Thompson JF, Long GV, Pearson JV, Mann GJ, Scolyer RA, Waddell N, Montal ED, Huang TH, Jonsson P, Donoghue MTA, Harris CC, Taylor BS, Xu T, Chaligné R, Shliaha PV, Hendrickson R, Jungbluth AA, Lezcano C, Koche R, Studer L, Ariyan CE, Solit DB, Wolchok JD, Merghoub T, Rosen N, Hayward NK, White RM. Nature 604: 2022 354-361	43
Integrated genomic analyses of acral and mucosal melanomas nominate novel driver genes. Wang M, Banik I, Shain AH, Yeh I, Bastian BC. Genome Med 14: 2022 65	11
The impact of rare germline variants on human somatic mutation processes. Vali-Pour M, Park S, Espinosa-Carrasco J, Ortiz-Martínez D, Lehner B, Supek F. Nat Commun 13: 2022 3724	12
Comparative Genomics Provides Etiologic and Biological Insight into Melanoma Subtypes. Newell F, Johansson PA, Wilmott JS, Nones K, Lakis V, Pritchard AL, Lo SN, Rawson RV, Kazakoff SH, Colebatch AJ, Koufariotis LT, Ferguson PM, Wood S, Leonard C, Law MH, Brooks KM, Broit N, Palmer JM, Couts KL, Vergara IA, Long GV, Barbour AP, Nieweg OE, Shivalingam B, Robinson WA, Stretch JR, Spillane AJ, Saw RPM, Shannon KF, Thompson JF, Mann GJ, Pearson JV, Scolyer RA, Waddell N, Hayward NK. Cancer Discov 12: 2022 2856-2879	27
streammd: fast low-memory duplicate marking using a Bloom filter. Leonard C. Bioinformatics 39: 2023 btad181	1
Generalising uncertainty improves accuracy and safety of deep learning analytics applied to oncology. MacDonald S, Foley H, Yap M, Johnston RL, Steven K, Koufariotis LT, Sharma S, Wood S, Addala V, Pearson JV, Roosta F, Waddell N, Kondrashova O, Trzaskowski M. Sci Rep 13: 2023 7395	0
Long-molecule scars of backup DNA repair in BRCA1- and BRCA2-deficient cancers. Setton J, Hadi K, Choo ZN, Kuchin KS, Tian H, Da Cruz Paula A, Rosiene J, Selenica P, Behr J, Yao X, Deshpande A, Sigouros M, Manohar J, Nauseef JT, Mosquera JM, Elemento O, Weigelt B, Riaz N, Reis-Filho JS, Powell SN, Imieliński M. Nature 621: 2023 129-137	3
A tumor-associated endothelial signature score model in immunotherapy and prognosis across pan-cancers. Chen S, Zhang L, Huang M, Liang Y, Wang Y. Front Pharmacol 14: 2023 1190660	2
Landscape of enhancer disruption and functional screen in melanoma cells. Wang Z, Luo M, Liang Q, Zhao K, Hu Y, Wang W, Feng X, Hu B, Teng J, You T, Li R, Bao Z, Pan W, Yang T, Zhang C, Li T, Dong X, Yi X, Liu B, Zhao L, Li M, Chen K, Song W, Yang J, Li MJ. Genome Biol 24: 2023 248	4
Most large structural variants in cancer genomes can be detected without long reads. Choo ZN, Behr JM, Deshpande A, Hadi K, Yao X, Tian H, Takai K, Zakusilo G, Rosiene J, Da Cruz Paula A, Weigelt B, Setton J, Riaz N, Powell SN, Busam K, Shoushtari AN, Ariyan C, Reis-Filho J, de Lange T, Imieliński M. Nat Genet 55: 2023 2139-2148	8
Functional analysis of recurrent CDC20 promoter variants in human melanoma. Godoy PM, Oyedeji A, Mudd JL, Morikis VA, Zarov AP, Longmore GD, Fields RC, Kaufman CK. Commun Biol 6: 2023 1216	0
Inflammatory response signature score model for predicting immunotherapy response and pan-cancer prognosis. Chen S, Huang M, Zhang L, Huang Q, Wang Y, Liang Y. Comput Struct Biotechnol J 23: 2024 369-383	2
Base-excision repair pathway shapes 5-methylcytosine deamination signatures in pan-cancer genomes. Silveira AB, Houy A, Ganier O, Özemek B, Vanhuele S, Vincent-Salomon A, Cassoux N, Mariani P, Pierron G, Leyvraz S, Rieke D, Picca A, Bielle F, Yaspo ML, Rodrigues M, Stern MH. Nat Commun 15: 2024 9864	0