{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"study_type":["Other"],"full_dataset_link":["https://ega-archive.org/studies/EGAS00001003963"],"host":["EGA"],"description":["EGA study EGAS00001003963"],"dataset_title":["Sharc-prostate","Sharc-ovarian"],"category":["restricted"],"repository":["EGA"],"name_synonyms":["Biological Markers, Viral Marker, Viral, Surrogate Endpoints, Malignant Neoplasm, Surrogate Endpoint, whole blood, Clinical Markers, Laboratory, Clinical Marker, Neoplasms, Serum Markers, Benign Neoplasm, Biochemical, End Point, Endpoint, Biochemical Markers, Serum, Tumor, Biologic Marker, Malignant, Immune Marker, Surrogate End Points, Surrogate Markers, Laboratory Markers, MT, Benign, Marker, Biological, Surrogate End Point, Neoplasm, Biologic Markers, Biomarker, Serum Marker, primary cancer, Clinical, End Points, Genomes, Malignancy, Surrogate, Biological Marker, Endpoints, Benign Neoplasms, whole genome, Immunologic, Cancers, Laboratory Marker, malignant tumor, Surrogate Marker, Neoplasias, Immunologic Markers, Immune, Markers, Biochemical Marker, malignant neoplasm, Viral Markers, Malignancies, Immunologic Marker, Neoplasia, Biologic, Immune Markers, Cancer, Tumors, Malignant Neoplasms."],"description_synonyms":["Biological Markers, Viral Marker, Forestland, Surrogate Endpoints, Laboratory, Biochemical, Endpoint, Tumor, Serum, Long Term, Classifications, Laboratory Markers, Techniques, hierarchies, hierarchy, Biological, Method, systematics, responsivity, Forested, cytopathology, Polymerase Chain, Effect, average, treatment, thymus nucleic acid, me75, Biopsies, Genomes, long, Woodland, Inverse Polymerase Chain Reaction, D17Mit170, Fast, T1, Fgfr7, allergic reaction, Prostatic Neoplasm, Immune, Markers, Cancer of the Prostate, Methodological Studies, Bek, malignant neoplasm, Viral Markers, Reaction, sample, disease management, Therapies, svs, Double-Stranded DNA, Malignancies, deoxyribonucleic acids, DNAn, Nucleotide, Long-Term Effects, FAST, Tumors, Forested Area, Therapy, cancer of the prostate, Anchored Polymerase Chain Reaction, Viral, Surrogate Endpoint, familial, Systematics, Longterm Effect, Biochemical Markers, FASTK, Double-Stranded, Fgfr-7, Procedure, Tl3, Biologic Marker, Tl2, Nanopore, Fgfr-2, (Deoxyribonucleotide)n+m, Taxonomies, Benign, Marker, Areas, Area, NOS, desoxyribose nucleic acid, nucleotides, PCR, oligonucleotide random primer, Nanopore Sequencings, histopathology, End Points, Nested Polymerase Chain Reaction, Benign Neoplasms, Immunologic, whole genome, Methodological, Laboratory Marker, Methodological Study, cancer of prostate, Treatments, polymerase chain reaction, Malignant Neoplasms, Patient, Biochemical Marker, ds DNA, DNA, other neoplasm, Prostate, AU043015, DNS, Procedures, (Deoxyribonucleotide)n, Prostate Neoplasms, KGFR, Clinical Markers, taxonomy, Effects, Clinical Marker, Neoplasms, Benign Neoplasm, STK10, number, Polymerase Chain Reactions, Forested Areas, Inverse, Malignant, presence, Deoxyribonucleic acids, Prostate Cancers., Surrogate End Points, Surrogate Markers, method, Inverse PCR, Deoxyribonucleic Acid, sensitive, method used in an experiment, Studies, Prostatic Cancers, Low, Cancer of Prostate, sensitivity, Technique, Prostate Cancers, Biomarker, reactivity, Taxonomy, Woodlands, Clinical, Malignancy, Longterm, AW556123, Biological Marker, Double Stranded, Deoxyribonucleic acid, Long-Term, Sequencing, Neoplasias, Study, Immunologic Markers, RANDOM, ATP:Fas-activated serine/threonine protein phosphotransferase activity, Clients, Prostatic, liquid, Long-Term Effect, (Deoxyribonucleotide)m, Anchored PCR, Immunologic Marker, Biologic, Cancer, hereditary prostate cancer, Malignant Neoplasm, cou, DNAn+1, Serum Markers, End Point, Client, Immune Marker, read, count in organism, Lr, MT, Surrogate End Point, Long Term Effects, Prostatic Cancer, Neoplasm, ds-DNA, Biologic Markers, Random selection by shearing, KGFRTr, Anchored, primary cancer, Serum Marker, Reactions, Nested, Surrogate, Endpoints, Cancers, malignant tumor, Surrogate Marker, sample population, Longterm Effects, Prostate Neoplasm, plan specification, Forestlands, Therapeutic, Desoxyribonukleinsaeure, Bra, prostate cancer, Nested PCR, PC, Treatment, response, biopsy, Forest, Prostate Cancer, Neoplasia, Immune Markers"],"additional_accession":[]},"is_claimable":false,"name":"Rapid identification of somatic genome rearrangements as personalized biomarkers for blood-based cancer monitoring","description":"Increasing evidence shows the value of circulating tumour DNA (ctDNA) to detect cancer and monitor its progression. Somatic genomic structural variations (SVs) are promising personalized biomarkers for sensitive and specific detection of ctDNA in liquid biopsies. However, accurate, affordable, and fast identification of such SV biomarkers is challenging, which hinders routine use in the clinic. Here, we demonstrate a novel approach - termed SHARC - for rapid discovery of somatic SV breakpoints as personalized tumour biomarkers. SHARC combines low-coverage cancer genome sketching by using Oxford Nanopore portable sequencing with a random forest classification and a dedicated filtering pipeline to enrich for somatic SVs. Our method leverages the real-time and long-read capabilities of Nanopore sequencing to identify somatic SV breakpoints at nucleotide resolution from a tumour biopsy within two days. We applied SHARC to tumour samples of high-grade ovarian and prostate cancer and validated on average 10 somatic SVs per sample with the use of PCR mini-amplicons. Finally, we demonstrate that these somatic SV biomarkers can  be used to detect tumour presence from liquid biopsies in a quantitative manner and we retrospectively monitored treatment response in patients with prostate cancer, demonstrating its potential benefit for clinical practice.","dates":{"updated":"2019-12-02 10:51:53"},"accession":"EGAS00001003963","cross_references":{"TAXONOMY":["9606"],"EGA":["EGAD00001005472","EGAD00001005473","EGAC00001000432"]}}