Whole genome and whole transcriptome sequencing of patients diagnosed with angiosarcoma.

Angiosarcomas are rare, clinically-aggressive tumors with a predilection for the elderly and immunosuppressed, which has incited suspicion of an oncogenic virus. We studied the metagenomic landscape of angiosarcomas and identified reads mapping to human herpesvirus-7 (HHV-7). Overall, HHV-7 was present in two-thirds of angiosarcomas, particularly in cases with low tumor mutation burden and lacking signatures of ultraviolet-induced DNA damage. Transcriptomic profiling revealed the enrichment of tumor inflammation signatures in HHV7-positive angiosarcomas. In conclusion, we identified a distinct “inflammatory” subtype of angiosarcoma associated with HHV-7.

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

2 Datasets 2 Publications

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Dataset ID	Description	Technology	Samples
EGAD00001005366	Whole-genome sequencing (WGS) was performed for 13 pairs of tumor-normal and 5 tumor-only samples from patients diagnosed with angiosarcoma. Genomic DNA from tumor tissue was extracted with QIAamp DNA Mini Kit. The DNA for the matching normal was obtained from blood or buccal swabs and purified by Blood and Cell Culture DNA Mini kit or E.Z.N.A. Tissue DNA Kit (Omega Bio-tek) according to manufacturer’s instructions. The quantity and quality were assessed by Quant-iT PicoGreen dsDNA Assay Kit (Invitrogen) and agarose gel electrophoresis. All sequencing libraries were prepared using TruSeq Nano DNA Library Prep Kit (Illumina). Paired-end sequencing was performed on Illumina HiSeq X Ten as 2x151 bp.	HiSeq X Ten Illumina HiSeq 2000	31
EGAD00001005367	Whole-transcriptome sequencing (WTS) of 6 tumor-normal and 6 tumor-only samples from patients diagnosed with angiosarcoma. Total RNA from snap frozen EITL tumor samples was extracted using TRIzol (Invitrogen) and purified with RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions. The integrity of RNA was determined by electrophoresis using 2100 Bioanalyzer (Agilent Technologies). 500 ng of total RNA was reverse transcribed with iScript cDNA Synthesis Kit (Bio-Rad, Hercules, CA, USA). Quantification was performed using SsoFast EvaGreen Supermix and CFX96 Real-Time PCR System (both Bio-Rad). Sequencing libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero (Illumina) and WTS was performed on HiSeq 2500 and HiSeq 3000 (Illumina) with 2x101 bp and 2x151 bp read length, respectively.	Illumina HiSeq 2500	18

Publications	Citations
Multiomic analysis and immunoprofiling reveal distinct subtypes of human angiosarcoma. Chan JY, Lim JQ, Yeong J, Ravi V, Guan P, Boot A, Tay TKY, Selvarajan S, Md Nasir ND, Loh JH, Ong CK, Huang D, Tan J, Li Z, Ng CC, Tan TT, Masuzawa M, Sung KW, Farid M, Quek RHH, Tan NC, Teo MCC, Rozen SG, Tan P, Futreal A, Teh BT, Soo KC. J Clin Invest 130: 2020 5833-5846	41
Spatial transcriptomics reveal topological immune landscapes of Asian head and neck angiosarcoma. Loh JW, Lee JY, Lim AH, Guan P, Lim BY, Kannan B, Lee ECY, Gu NX, Ko TK, Ng CC, Lim JCT, Yeong J, Lim JQ, Ong CK, Teh BT, Chan JY. Commun Biol 6: 2023 461	7