lesion_data: Example T-ALL Lesion Dataset

In GRIN2: Genomic Random Interval (GRIN)

Example T-ALL Lesion Dataset

Description

Genomic lesion dataset including copy number variations, single nucleotide variants, and structural rearrangements affecting 265 newly diagnosed T-cell Acute Lymphoblastic Leukemia (T-ALL) patients, as reported by Liu, Yu, et al. (2017). The original lesion coordinates were based on the GRCh37 (hg19) human genome assembly. We converted these coordinates to GRCh38 (hg38) using the UCSC LiftOver tool (https://genome.ucsc.edu/cgi-bin/hgLiftOver) prior to running GRIN2 analyses.

Usage

lesion_data

Format

lesion_data

A data frame with 6,861 rows and 5 columns:

ID

Patient identifier for the individual affected by the lesion

chrom

Chromosome on which the lesion is located

loc.start

Lesion start position (in base pairs, hg38)

loc.end

Lesion end position (in base pairs, hg38)

lsn.type

Type of lesion (e.g., gain, loss, mutation, fusion, etc.)

Source

Adapted from the supplementary tables of Liu, Yu, et al. (2017), Nature Genetics (https://www.nature.com/articles/ng.3909#Sec27)

GRIN2 documentation built on June 17, 2025, 9:11 a.m.