Distribution of ctDNA levels in plasma of early-stage non-small cell lung cancer patients measured using personalised ctDNA analysis
Blood-based assays have shown increasing ability to detect circulating tumour DNA (ctDNA) in patients with early-stage cancer. However, detection of ctDNA in patients with non-small cell lung cancer (NSCLC) has continued to prove challenging. We performed retrospective analysis to quantify ctDNA levels in a cohort of 100 patients with early-stage NSCLC prior to treatment with curative intent. Where tumour tissue was available for whole exome sequencing, mutations identified were used to define patient-specific sequencing assays. For those 90 patients, plasma cell-free DNA was sequenced to high depth across capture panels targeting a median of 328 mutations specific to each patient. Data was analysed using Integration of Variant Reads (INVAR), detecting ctDNA in 66.7% of patients, including 52.7% (29 of 55) patients with stage I disease and >88% detection for patients with stage II and III disease (16/18 and 15/17). ctDNA was detected in plasma at fractional concentrations as low as 9.1x10-6, and in patients with tumour volumes as low as 0.23 cm3. A 36-gene sequencing panel (InVisionFirst-LungTM) was used to analyse plasma DNA in 27 samples including the 10 cases without tumour exome data, and detected ctDNA in 59% of samples tested (16 of 27). Across the entire cohort, detection rates were higher in squamous cell carcinoma patients compared to adenocarcinoma patients (81% vs. 59%). Detection of ctDNA prior to treatment was associated with significantly shorter time free from relapse, across all patients and in patient subgroups, with Hazard Ratios ranging from 2.25 to >11. Our analysis indicates that for patients with stage I NSCLC, the median ctDNA fraction in plasma is approx. 12 parts per million (0.0012%). This indicates the limits of detection that would be required for ctDNA-based liquid biopsies to detect ctDNA in the majority of patients with early-stage NSCLC.
- 29 samples
- DAC: EGAC00001001633
Policy for access to data included in the following publication; ctDNA monitoring using patient-specific sequencing and integration of variant reads
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Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.
Study ID | Study Title | Study Type |
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Other |
This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.
ID | File Type | Size | Located in | |
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EGAF00004043095 | fq.gz | 3.2 GB | ||
EGAF00004043096 | fq.gz | 3.6 GB | ||
EGAF00004043097 | fq.gz | 3.2 GB | ||
EGAF00004043098 | fq.gz | 3.6 GB | ||
EGAF00004043099 | fq.gz | 4.8 GB | ||
EGAF00004043100 | fq.gz | 5.6 GB | ||
EGAF00004043101 | fq.gz | 1.0 GB | ||
EGAF00004043102 | fq.gz | 1.1 GB | ||
EGAF00004043103 | fq.gz | 3.4 GB | ||
EGAF00004043104 | fq.gz | 3.9 GB | ||
EGAF00004043105 | fq.gz | 6.9 GB | ||
EGAF00004043106 | fq.gz | 8.0 GB | ||
EGAF00004043107 | fq.gz | 921.4 MB | ||
EGAF00004043108 | fq.gz | 1.0 GB | ||
EGAF00004043109 | fq.gz | 962.0 MB | ||
EGAF00004043110 | fq.gz | 1.1 GB | ||
EGAF00004043111 | fq.gz | 1.0 GB | ||
EGAF00004043112 | fq.gz | 1.2 GB | ||
EGAF00004043113 | fq.gz | 6.7 GB | ||
EGAF00004043114 | fq.gz | 7.6 GB | ||
EGAF00004043115 | fq.gz | 991.0 MB | ||
EGAF00004043116 | fq.gz | 1.1 GB | ||
EGAF00004043117 | fq.gz | 4.7 GB | ||
EGAF00004043118 | fq.gz | 5.5 GB | ||
EGAF00004043119 | fq.gz | 3.6 GB | ||
EGAF00004043120 | fq.gz | 4.1 GB | ||
EGAF00004043121 | fq.gz | 6.9 GB | ||
EGAF00004043122 | fq.gz | 7.5 GB | ||
EGAF00004043123 | fq.gz | 1.0 GB | ||
EGAF00004043124 | fq.gz | 1.2 GB | ||
EGAF00004043125 | fq.gz | 863.8 MB | ||
EGAF00004043126 | fq.gz | 944.6 MB | ||
EGAF00004043127 | fq.gz | 7.6 GB | ||
EGAF00004043128 | fq.gz | 8.4 GB | ||
EGAF00004043129 | fq.gz | 971.1 MB | ||
EGAF00004043130 | fq.gz | 1.1 GB | ||
EGAF00004043131 | fq.gz | 3.4 GB | ||
EGAF00004043132 | fq.gz | 3.9 GB | ||
EGAF00004043133 | fq.gz | 6.3 GB | ||
EGAF00004043134 | fq.gz | 7.0 GB | ||
EGAF00004043135 | fq.gz | 3.7 GB | ||
EGAF00004043136 | fq.gz | 4.4 GB | ||
EGAF00004043137 | fq.gz | 3.4 GB | ||
EGAF00004043138 | fq.gz | 4.0 GB | ||
EGAF00004043139 | fq.gz | 3.2 GB | ||
EGAF00004043140 | fq.gz | 3.7 GB | ||
EGAF00004043141 | fq.gz | 4.4 GB | ||
EGAF00004043142 | fq.gz | 5.1 GB | ||
EGAF00004043143 | fq.gz | 7.6 GB | ||
EGAF00004043144 | fq.gz | 8.8 GB | ||
EGAF00004043145 | fq.gz | 903.9 MB | ||
EGAF00004043146 | fq.gz | 990.7 MB | ||
EGAF00004043147 | fq.gz | 7.1 GB | ||
EGAF00004043148 | fq.gz | 8.1 GB | ||
EGAF00004043149 | fq.gz | 966.9 MB | ||
EGAF00004043150 | fq.gz | 1.1 GB | ||
EGAF00004043151 | fq.gz | 6.3 GB | ||
EGAF00004043152 | fq.gz | 7.1 GB | ||
EGAF00004150991 | csv | 562.8 kB | ||
59 Files (226.7 GB) |