Study

Pilot study for Illumina TST170 NGS panel on cutaneous T cell lymphoma samples

Study ID Alternative Stable ID Type
EGAS00001002567 Other

Study Description

A number of genomic studies using next generation sequencing (NGS) techniques have attempted to understand the underlying genetic basis of cutaneous T-cell lymphoma and found alterations in genes that are involved in T-cell activation, NF-kB and JAK-signal transducer and activator of transcription (STAT) pathways. 8 diagnostic skin biopsy samples (2xplaque, 6xtumour) on FFPE blocks were selected from 8 MF patients (stage IB:n=1, IIB:n=6, IVA2:n=1). An H&E was performed in order to assess percentage of tumor cells, viable cells, necrosis and immune infiltration, to determine the number of slides required for NGS. Freshly cut unstained slides were manually macrodissected prior to DNA and RNA extraction. Targeted deep sequencing was performed using panel of 170 genes associated with common solid tumours (Illumina TruSight Tumour 170 NGS panel). VCF files generated via the Illumina’s Basespace platform.

Study Datasets 6 datasets.

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 Technology Samples
EGAD00001005502
TST170 DNA FASTQ files
Illumina HiSeq 2500 16
EGAD00001005503
DNA BAM files
16
EGAD00001005710
TST170 Pilot RNA VCF
Illumina HiSeq 2500 16
EGAD00001005711
TST170 Pilot RNA FASTQ
Illumina HiSeq 2500 16
EGAD00001006043
TST170 Pilot DNA VCF files
16
EGAD00001006044
TST170 Pilot RNA BAM files
16

Who archives the data?

There are no publications available