hum0608-v1Release info

Exploratory study on the diagnosis of cutaneous malignant tumors

Aims

This exploratory study aims to characterize gene expression and mutations in cutaneous malignant tumors—particularly nail apparatus tumors, which are difficult to diagnose by skin biopsy—using nucleic acids from FFPE specimens, toward minimally invasive preoperative and differential diagnosis. The deposited data, a foundational analysis preceding that goal, consist of bulk RNA-sequencing data of cutaneous melanoma, primarily nail unit melanoma. Specifically, we analyzed (1) transcriptomic changes associated with progression in the main nail unit melanoma cohort (early- and late-stage) and (2) molecular differences between nail unit and non-nail (plantar acral and non-acral) melanoma.

Methods

Total RNA was extracted from formalin-fixed, paraffin-embedded (FFPE) sections using the AllPrep DNA/RNA FFPE Kit (QIAGEN). RNA-sequencing libraries were prepared using the SMART-Seq Stranded Kit (Takara Bio), and 150-bp paired-end sequencing was performed on Illumina NovaSeq 6000 or NovaSeq X Plus instruments. Library preparation and sequencing were outsourced to Takara Bio Inc.

Participants/materials

The subjects were 55 patients with cutaneous melanoma, using FFPE tumor specimens. They comprised a main cohort of 43 nail unit melanoma patients (22 early-stage, 21 late-stage) and 12 late-stage (AJCC stage IIB or higher) non-nail melanoma patients (6 plantar acral, 6 non-acral) for cross-subtype comparison. Paired-end bulk RNA-sequencing was performed with one tumor specimen per patient (55 in total).

Principal investigator

Atsushi Otsuka

Affiliation

Department of Dermatology, Kindai University Faculty of Medicine

No research projects.

No grants.

No use of the controlled access data has been recorded.