Molecular correlates for HPV-negative head and neck cancer engraftment prognosticate patient outcomes

Head and neck squamous cell carcinoma (HNSCC) tumors were sampled from 88 patients. Samples were implanted subcutaenously into the flank of NOD/SCID/IL2R-/- mice. Mice were then monitored weekly for tumor growth and the time of initial palpation was recorded. Mice were euthanized when tumors reached 15 mm in diameter or after 6 months. If no tumor formed by 6 months, the patient tumor was defined as Non-engrafter (N). RNA-seq was performed on all primary tumor samples and successfully engrafted patient-derived xenograft (PDX) samples.

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

1 Dataset 1 Publication

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Dataset ID	Description	Technology	Samples
EGAD50000000995	This dataset includes transcriptome profiling of 88 head and neck primary patient tumor samples and 45 paired patient-derived xenograft samples that successfully engrafted in mice. NGS was performed using the Illumina TruSeq stranded total RNA sample preparation kit on the Illumina NovaSeq X Plus platform at the Princess Margaret Genomics Centre. This dataset consists of paired-end fastq files.	Illumina NovaSeq X	133

Publications	Citations
Molecular correlates for HPV-negative head and neck cancer engraftment prognosticate patient outcomes. Waas M, Karamboulas C, Wu BZ, Khan S, Poon S, Meens J, Govindarajan M, Khoo A, Mejia-Guerrero S, Ha A, Liu LY, Nixon KCJ, Walton J, Bratman SV, Huang SH, Goldstein D, Gaiti F, Ailles L, Kislinger T. Nat Commun 15: 2024 10869	0