TP53 Mutations as Drivers of Chordoma Progression and Hallmarks of Aggressive Chordoma

TP53 Mutations as Drivers of Chordoma Progression and Hallmarks of Aggressive Chordoma

Methods

For the original dataset FFPE-derived DNA from three tumor samples of DC, one PDC, and 32 CCs was analyzed for the coding sequence of 664 cancer-related genes using the SeqCap EZ Custom Enrichment Kit (Roche, Basel, Switzerland). A complete list of genes is presented in details previously. One additional sample of primary CC and recurrent DC, DNA from a blood sample, as well as primary and recurrent tumors (CC and DC, respectively) from one patient, was subjected to whole-exome sequencing (WES). Exome enrichment was performed using the Agilent SureSelectXT Reagent Kit and Agilent SureSelect Human All ExonV6 (Cat No. G9611B). A sequencing library was constructed using the Novogene NGS DNA Library Prep Set (Cat No.PT004). Libraries were sequenced using the paired end 150 bp mode on Illumina NovaSeq X Plus instrument (Illumina, San Diego, CA). The procedures were performed by an NGS service provider, Novogene.

For the replication dataset, publically available data from Bai et al. were downloaded.

Whole-Genome Sequencing, panel sequencing, and WES datasets were aligned to the GRCh38p11 human reference genome, utilizing BWA. For WGS and WES data, somatic single nucleotide variants and small insertions/deletions were called using Strelka and Manta. Copy number alterations were identified and analyzed using the FACETS R package and samples with low tumor purity were rejected (ten WGS samples).

For panel sequencing data, given the absence of matched normal controls, variant calling was performed using Scalpel and bcftools. Variant annotation was subsequently conducted with vcf2maf, incorporating the Variant Effect Predictor (VEP). Variants were filtered at a minimum of 14x coverage and a Variant Allele Frequency (VAF) of at least 0.2, with a ratio of VAF in tumor to normal control of at least 4. For samples without a normal control, common variants were rejected, and SNPs were manually checked for benign variation.

Data

Table with somatic mutations from the ZJ case (ZJsomatic.zip)

Table with copy-number events from the ZJ case (ZJsegments.csv)

Table with somatic mutations from the mutation panel (PanelSomatic.zip)

Table with somatic mutations from the Bai et al. (BaiSomatic.zip)