Supporting metadata for sequence data from Tracking plasma DNA mutation dynamics in estrogen receptor positive metastatic breast cancer with dPCR-SEQ

This metadata record is linked to plasma DNA sequence data from a study using dPCR-SEQ to track plasma DNA mutation dynamics in estrogen receptor positive metastatic breast cancer (ER+ MBC). dPCR-SEQ utilizes droplet PCR technology for target enrichment followed by next-generation sequencing. Data are deposited in the NCBI Sequence Read Archive.
The study reports the development of the dPCR-SEQ technique for the detection and monitoring of circulating tumor DNA (ctDNA) mutations in ER+ MBC, and its validation in a prospective biomarker cohort of 58 research participants with ER+ MBC. The study design involves droplet PCR for target enrichment at first step, recovery of DNA from droplets, adding illumina barcodes by secondary PCR, sample pooling and submission for Miseq.
See https://doi.org/10.6084/m9.figshare.7334507 for related dPCR data.
Type of data: DNA sequence
Format of data: FASTQ MiSeq files in compressed gzip .gz format
Number of files: 78. 2 files per sample (single time point samples from 24 individuals, two time point samples from 6 individuals and three time point samples from 1 individual)
Software required to view/access data files:The NCBI SRA database site includes an online tool to analyse FASTQ files.
Supporting Documentation available from the related publication:- Supplementary Table S1 provides the identifiers, names and sequences for the custom primers used in dPCR-SEQ- Supplementary Table S2 provides detailed cohort characteristics
- Supplementary Table S3 provides the ESR1 gBlocks and LNA probes

Data storage location: NCBI SRA (Sequence Read Archive) under accession number SRP162052: https://www.ncbi.nlm.nih.gov/sra/?term=SRP162052
Sample and cohort sizes and characteristics: The study cohort consisted of 58 individuals with ER+ MBC. Key inclusion criteria were histologically confirmed ER+ breast cancer, stage IV disease and a history of progression on a prior line of endocrine therapy.
Detailed cohort characteristics are available in Supplementary Table S2 of the related publication, grouped by ctDNA hotspot ESR1 mutation (n=16 positive, n=42 negative). None of the differences between groups are statistically significant (p<0.05) using a two-tailed Fisher’s exact test (categorical parameters) or a student’s t-test (continuous parameters).
All 58 research participants were analysed by droplet digital dPCR, but only 31 of these met the minimum requirement of 10ng of available plasma DNA input. The total sample number of 39 consists of single time point samples from 24 individuals, two time point samples from 6 individuals and three time point samples from 1 individual.
IRB: University of North Carolina at Chapel Hill Cancer Hospital. UNC IRB study 11-1924