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Genome-wide cell-free DNA fragmentation in patients with cancer

ABSTRACT: Genome-wide cell-free DNA fragmentation in patients with cancer

PROVIDER: PRJNA543358 | ENA |

REPOSITORIES: ENA

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Genome-wide cell-free DNA fragmentation in patients with cancer

Project description:Genome-wide cell-free DNA fragmentation in patients with cancer

| PRJNA543357 | ENA

Genome-wide cell-free DNA fragmentation in patients with cancer

Project description:Cell-free DNA (cfDNA) in the blood provides a noninvasive diagnostic avenue for patients with cancer. However, characteristics of the origins and molecular features of cfDNA are poorly understood. We developed an approach to evaluate fragmentation patterns of cfDNA across the genome and found that cfDNA profiles of healthy individuals reflected nucleosomal patterns of white blood cells, while patients with cancer had altered fragmentation profiles. We applied this method to analyze fragmentation profiles of 236 patients with breast, colorectal, lung, ovarian, pancreatic, gastric, or bile duct cancers and 245 healthy individuals. A machine learning model incorporating genome-wide fragmentation features had sensitivities of detection ranging from 57% to >99% among the seven cancer types at 98% specificity, with an overall AUC of 0.94. Fragmentation profiles could be used to identify the tissue of origin of the cancers to a limited number of sites in 75% of cases. Combining our approach with mutation based cfDNA analyses detected 91% of cancer patients. The results of these analyses highlight important properties of cfDNA and provide a proof of principle approach for screening, early detection, and monitoring of human cancer.

| EGAS00001003611 | EGA

Genome-wide cell-free DNA fragmentation in patients with cancer.

Project description:Cell-free DNA in the blood provides a non-invasive diagnostic avenue for patients with cancer1. However, characteristics of the origins and molecular features of cell-free DNA are poorly understood. Here we developed an approach to evaluate fragmentation patterns of cell-free DNA across the genome, and found that profiles of healthy individuals reflected nucleosomal patterns of white blood cells, whereas patients with cancer had altered fragmentation profiles. We used this method to analyse the fragmentation profiles of 236 patients with breast, colorectal, lung, ovarian, pancreatic, gastric or bile duct cancer and 245 healthy individuals. A machine learning model that incorporated genome-wide fragmentation features had sensitivities of detection ranging from 57% to more than 99% among the seven cancer types at 98% specificity, with an overall area under the curve value of 0.94. Fragmentation profiles could be used to identify the tissue of origin of the cancers to a limited number of sites in 75% of cases. Combining our approach with mutation-based cell-free DNA analyses detected 91% of patients with cancer. The results of these analyses highlight important properties of cell-free DNA and provide a proof-of-principle approach for the screening, early detection and monitoring of human cancer.

| S-EPMC6774252 | biostudies-literature

FinaleMe: Predicting DNA Methylation by the Fragmentation Patterns of Plasma Cell-free DNA

Project description:FinaleMe: Predicting DNA Methylation by the Fragmentation Patterns of Plasma Cell-free DNA

| PRJNA965897 | ENA

FinaleMe: Predicting DNA Methylation by the Fragmentation Patterns of Plasma Cell-free DNA

Project description:FinaleMe: Predicting DNA Methylation by the Fragmentation Patterns of Plasma Cell-free DNA

| PRJNA965896 | ENA

De novo Characterization of Cell-free DNA Fragmentation Hotspots in Plasma Whole-genome Sequencing.

Project description:De novo Characterization of Cell-free DNA Fragmentation Hotspots in Plasma Whole-genome Sequencing.

| PRJNA881452 | ENA

De novo Characterization of Cell-free DNA Fragmentation Hotspots in Plasma Whole-genome Sequencing.

Project description:De novo Characterization of Cell-free DNA Fragmentation Hotspots in Plasma Whole-genome Sequencing.

| PRJNA881451 | ENA

Genome-wide plasma cell-free DNA methylation profiling in pancreatic cancer patients using MeDIP-seq

Project description:Genome-wide plasma cell-free DNA methylation profiling in pancreatic cancer patients using MeDIP-seq

| PRJEB40875 | ENA

Genome-wide plasma cell-free DNA methylation profiling in lung cancer patients using MeDIP-seq

Project description:Genome-wide plasma cell-free DNA methylation profiling in lung cancer patients using MeDIP-seq

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DNA methylation and gene expression as determinants of genome-wide cell-free DNA fragmentation.

Project description:Circulating cell-free DNA (cfDNA) is emerging as an avenue for cancer detection, but the characteristics of cfDNA fragmentation in the blood are poorly understood. We evaluate the effect of DNA methylation and gene expression on genome-wide cfDNA fragmentation through analysis of 969 individuals. cfDNA fragment ends more frequently contained CCs or CGs, and fragments ending with CGs or CCGs are enriched or depleted, respectively, at methylated CpG positions. Higher levels and larger sizes of cfDNA fragments are associated with CpG methylation and reduced gene expression. These effects are validated in mice with isogenic tumors with or without the mutant IDH1, and are associated with genome-wide changes in cfDNA fragmentation in patients with cancer. Tumor-related hypomethylation and increased gene expression are associated with decrease in cfDNA fragment size that may explain smaller cfDNA fragments in human cancers. These results provide a connection between epigenetic changes and cfDNA fragmentation with implications for disease detection.

| S-EPMC11303779 | biostudies-literature

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