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Plasma DNA - GIS

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Anders Skanderup
skanderupamj@gis.a-star.edu.sg

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This DAC controls 6 datasets

Dataset ID	Description	Technology	Samples
EGAD00001006419	WGS data of plasma samples from CRC patients (N=12)	Illumina HiSeq 4000	12
EGAD00001006420	WGS data of plasma samples from BRCA patients (N=10)	Illumina HiSeq 4000	10
EGAD00001006421	WGS data of plasma samples from healthy individuals (N=29)	Illumina HiSeq 4000	29
EGAD00001008352	WGS data of buffy coat from CRC patients	Illumina HiSeq 4000	7
EGAD50000000167	Fragle is a deep learning based two stage model that quantifies ctDNA from blood plasma derived cfDNA bam files. Fragle was developed using some previously published datasets and some newly generated data. Fragle was evaluated using some validation cohorts and some unseen cohorts. Some of these cohorts are newly created consisting of total 365 low pass (2-3X) whole genome sequencing bam files mapped to hg19/GRCh37. This dataset contains these newly generated bam files.	Illumina NovaSeq 6000	365
EGAD50000001870	This study provides a comprehensive benchmarking resource for somatic variant detection in cell-free DNA (cfDNA) from cancer patients. Longitudinal plasma samples from colorectal and breast cancer cohorts were selected to create patient-matched dilution series spanning ultra-low to high circulating-tumour-DNA (ctDNA) fractions, while preserving each individual’s germline and clonal haematopoiesis background. Deep whole-genome sequencing (150×) and ultra-deep whole-exome sequencing (2,000×) generated a reference call set of ~37,000 single-nucleotide variants and ~58,000 insertions/deletions. These data enabled systematic evaluation of nine somatic variant callers across variable ctDNA levels and sequencing depths, and were further used to explore machine-learning–guided parameter tuning. The resulting dataset offers an openly accessible framework for developers and clinicians to assess and optimize somatic variant calling in liquid biopsy applications.	Illumina NovaSeq 6000	12