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Liquid Biopsy Data Access Committee

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Ellen Heitzer
ellen.heitzer@medunigraz.at

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This DAC controls 13 datasets

Dataset ID	Description	Technology	Samples
EGAD00001007930	Mutation analysis of 77 frequently mutated genes in NSCLC in plasma DNA and corresponding PBMCs of NSCLC patients under ICI using the AVENIO Expanded Kit.	Illumina HiSeq 4000 NextSeq 550	516
EGAD00001008396	Targeted next-generation sequencing (NGS) of 93 frequently mutated genes in breast cancer using the QIAseq Human Breast Cancer Targeted Panel (QIAGEN), which uses digital sequencing by incorporating unique molecular barcodes (UMI).	Illumina MiSeq NextSeq 550	187
EGAD00001008397	Paired end shallow whole genome sequencing (sWGS) data for the identification of genomewide somatic copy number alterations (SCNA) and the estimation of tumor fractions.	NextSeq 550	185
EGAD00001009110	Extracted regions from WGS of Ewing sarcoma spanning fusion breakpoints +/- 100kb for ctDNA tracking in plasma	Illumina NovaSeq 6000	1
EGAD00001010100	These are aligned paired-end reads from Illumina NovaSeq 6000 whole-genome sequencing of 4 cfDNA samples extracted from blood plasma (plasma-Seq). Three samples from patients with breast cancer, prostate cancer, or colorectal cancer and one sample from a healthy individual were aligned to GRCh38 (GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set). The observed GC bias is different in each of these cfDNA samples which leads to different average GC content per sample. This bias is corrected using the GCparagon commandline tool.	Illumina NovaSeq 6000	2
EGAD00001010293	Paired end shallow whole genome sequencing (sWGS) data (FASTQ) for the identification of genomewide somatic copy number alterations (SCNA) and the estimation of tumor fractions.	NextSeq 550	30
EGAD00001010294	Aligned NGS data (BAM) of 77 frequently mutated genes in cancer using the AVENIO Expanded platform.	NextSeq 550	30
EGAD50000001586	Mutation analysis of cfDNA from urine (stored at various storage conditions) and plasma using the QIAseq HRR panel	Illumina NovaSeq 6000	82
EGAD50000001587	Shallow WGS data from cell-free DNA extracted from plasma and urine (stored under different storage conditions)	Illumina NovaSeq 6000	154
EGAD50000001588	Mutation analysis in cfDNA from plasma and urine (stored under different storage conditions) from CRC patients using the AVENIO Expanded Kit	Illumina NovaSeq 6000	36
EGAD50000001668	High resolution amplicon-bases sequencing o screen for PIK3CA hot spot mutations	NextSeq 550	156
EGAD50000001669	High resolution mutation analysis using the AVENIO ctDNA Expanded Kit V2, which targets 77 cancer-associated genes, in cfDNA in metastatic breast cancer.	Illumina NovaSeq 6000	158
EGAD50000001670	mFAST‑SeqS, or modified Fast Aneuploidy Screening Test‑Sequencing System, is a streamlined and cost-effective approach to estimate the fraction of ctDNA in blood samples by detecting genome-wide aneuploidy in cfDNA	NextSeq 500 NextSeq 550	161