{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"study_type":["Other"],"full_dataset_link":["https://ega-archive.org/studies/EGAS00001003382"],"host":["EGA"],"description":["EGA study EGAS00001003382"],"dataset_title":["Mannheim Liquid Biopsy Unit, Heidelberg University & DKFZ"],"repository":["EGA"],"category":["restricted"],"name_synonyms":["Colorectal Neoplasm, Carcinoma, dTAF[[II]]230, TAF[[II]]250, d230, DNS, Colorectal Cancer, (Deoxyribonucleotide)n, DNAn+1, Neoplasms, TAF200, l(3)84Ab, dTAFII250, BG:DS00004.13, Double-Stranded, TAFII-250, Tumor, TAF250/230, EfW1, autosomal dominant, Cell, Deoxyribonucleic acids, dTAF230, (Deoxyribonucleotide)n+m, dmTAF[[II]]230, Colorectal, colorectal cancer, TAFII250, Deoxyribonucleic Acid, dmTAF1, Taf230, p230, Neoplasm, TAF[[II]]250/230, TFIID, CRC, Colorectal Cancers, ds-DNA, desoxyribose nucleic acid, TAF250, Colorectal Tumors, Carcinomas, Taf[[II]]250, large bowel cancer, Taf200, thymus nucleic acid, dTAF[[II]]250, TAF[[II]]230, TFIID TAF250, cel, cell, susceptibility to, Colorectal Carcinoma, Double Stranded, Taf1p, Colorectal Carcinomas, TAF[II]250, Deoxyribonucleic acid, Cancers, Colorectal Tumor, CG17603, TAF[[II]], free, cancer of large bowel, large intestine cancer, cancer of the large intestine, dTAF250, DmelCG17603, colon cancer, Taf250, SR3-5, ds DNA, Desoxyribonukleinsaeure, cancer of the large bowel, Double-Stranded DNA, (Deoxyribonucleotide)m, DNA, deoxyribonucleic acids, cancer of large intestine, DNAn, colorectal (colon or rectal) cancer., TAF, somatic mutation, TAF230, TAF1, Tumors, Cancer"],"description_synonyms":["DER/faint little ball, Colorectal Neoplasm, determination, Elp-B1, der, Elp-1, Errb1, B-cell receptor complex, Tumor, PIG61, Mutations, dmTAF[[II]]230, Techniques, Personal, diseases, Method, epidermal growth factor-activated receptor activity, AI552599, diseases and disorders, Software Engineering, Polymerase Chain, Work Flow, d-egf-r, drug resistance, Computer Program, Colorectal Tumors, Progression, Psychological, treatment, thymus nucleic acid, human disease, TFIID TAF250, cel, membrane bound, Open, Computer Programs and Programming, Inverse Polymerase Chain Reaction, Colorectal Carcinomas, Colorectal Tumor, free, flb, large intestine cancer, genetic, Social, Methodological Studies, malignant neoplasm, Reaction, disease management, Therapies, Exacerbation, 9030024J15Rik, Homo sapiens disease, D-EGFR, Malignancies, Double-Stranded DNA, deoxyribonucleic acids, Social Power, DNAn, B-lymphocyte receptor complex, somatic mutation, NISBD2, colorectal (colon or rectal) cancer, Power, Tumors, DER1, Therapy, Carcinoma, dTAF[[II]]230, Anchored Polymerase Chain Reaction, Elp, Wa5, l(2)09261, DEgfr, frequency, familial, Disease Exacerbation, TAF200, Double-Stranded, Psychological Powers, TAFII-250, Procedure, TAF250/230, antibodies, Source Softwares, CG10079, Software Tools, Programs, (Deoxyribonucleotide)n+m, Program, Computer Applications, torpedo/egfr, TAFII250, Workflows, Benign, wa2, Computer Applications Software, Diseases, Computer Applications Softwares, Softwares, Colorectal Cancers, desoxyribose nucleic acid, END, PCR, Carcinomas, egfr, Software Applications, HD-33, El, death rate, Nested Polymerase Chain Reaction, Source Software, DER/EGFR, EGFR, EGfr, EgfR, susceptibility to, dEgfr, Benign Neoplasms, DER flb, Methodological, Torpedo/Egfr, CG17603, TAF[[II]], Methodological Study, surveillance, Treatments, cancer of large bowel, morbidity, polymerase chain reaction, Malignant Neoplasms, experimental procedures, Degfr, disease, metastatic, Applications, immunoglobulin, B cell receptor accessory molecule complex, Taf250, Patient, SR3-5, DEGFR, ds DNA, l(2)57DEFa, l(2)05351, B lymphocyte receptor complex, cancer of the large bowel, dEGFR, inherited genetic, DNA, cancer of large intestine, DmHD-33, Powers, other neoplasm, Work Flows, TAF230, Computer Software Applications, Psychological Power, other disease, d230, DNS, Colorectal Cancer, D-Egf, Procedures, (Deoxyribonucleotide)n, experimental, Professional Power, C-erb, Neoplasms, drug susceptibility/resistance, Benign Neoplasm, mor1, dTAFII250, Polymerase Chain Reactions, Computer, mENA, Inverse, EK2-6, Malignant, EfW1, autosomal dominant, Deoxyribonucleic acids, Colorectal, colorectal cancer, antibody, method, Inverse PCR, BCR complex, Deoxyribonucleic Acid, dmTAF1, Taf230, method used in an experiment, c-erbB, EGFr, Egfr, Studies, Clinical Progression, disease or disorder, torpedo/Egfr, EGF receptor activity, TOP, Egf-r, immunoglobulin complex, Technique, Application, TAF250, Open Source Softwares, Taf200, EGF-R, methods, dTAF[[II]]250, Clinical, Malignancy, occurrence, cell, experimental section, Software Application, prevalence, Open Source Software, Double Stranded, top, Taf1p, Torpedo/DER, Deoxyribonucleic acid, Computer Software Application, top/flb, non-neoplastic, cancer of the large intestine, Neoplasias, Study, dTAF250, Tools, Clinical Course, l(2)57EFa, time of survival, Clients, disorder, l(2)57Ea, (Deoxyribonucleotide)m, Anchored PCR, TAF, constitutitional genetic, HHT1, incidence, Cancer, Applications Software, Elp-B1RB1, Open Source, Disease, TAF[[II]]250, Malignant Neoplasm, Computer Software, Edg, Drug resistance, TGF-alpha receptor activity, ERBB, dEGFR1, DNAn+1, disorders, l(3)84Ab, BG:DS00004.13, medical condition, Client, Cell, Tool, dTAF230, Software Tool, disease management., MT, survival, epidermal growth factor receptor activity, DmelCG10079, p230, chemical analysis, Neoplasm, Resistance, TAF[[II]]250/230, TFIID, condition, Professional, CRC, ds-DNA, DER/top, Software, outbreaks, opsonin activity, Taf[[II]]250, large bowel cancer, Anchored, primary cancer, TAF[[II]]230, Reactions, Nested, top/DER, Colorectal Carcinoma, response to drug, Engineering, TAF[II]250, patient, ERBB1, Cancers, wa-2, malignant tumor, endemics, Drug, plan specification, Computer Programs, Personal Power, Egf, DmelCG17603, colon cancer, EFG-R, Applications Softwares, Therapeutic, Errp, Erbb, Power (Psychology), Desoxyribonukleinsaeure, Der, DER, B cell receptor activity, Nested PCR, Treatment, epidemics, assay, transforming growth factor-alpha receptor activity, ORW1, hereditary, Neoplasia, DER/torpedo, HER1, TAF1"],"additional_accession":[]},"is_claimable":false,"name":"Detection of mutational patterns in cell free DNA (cfDNA) of colorectal cancer by custom amplicon sequencing","description":"Monitoring the mutational patterns of solid tumors during cancer therapy is a major challenge in oncology. Analysis of mutations in cell free (cf) DNA offers a non-invasive approach to detect mutations that may be prognostic for disease survival or predictive for primary or secondary drug resistance. A main challenge for the application of cfDNA as a diagnostic tool is the diverse mutational landscape of cancer. Here, we developed a flexible end-to-end experimental and bioinformatics workflow to analyze mutations in cfDNA using custom amplicon sequencing. Our approach relies on open software tools to select primers suitable for multiplex PCR using minimal cfDNA as input. In addition, we developed a robust linear model to identify specific genetic alterations from sequencing data of cfDNA. We used our method to design a custom amplicon panel suitable for detection of hotspot mutations relevant for colorectal cancer and analyzed mutations in serial cfDNA samples from 34 patients with advanced colorectal cancer. Our data demonstrates that recurrent and patient-specific mutational patterns can be reliably detected for the majority of patients. Furthermore, we show that the allele frequency of mutations in cfDNA correlates well with disease progression. Finally, we demonstrate that monitoring of cfDNA can outperform the predictive power of currently used tumor markers and reveal mechanisms of resistance to anti-EGFR antibody treatment.","dates":{"updated":"2019-06-28 12:53:11"},"accession":"EGAS00001003382","cross_references":{"TAXONOMY":["9606"],"EGA":["EGAD00001004574","EGAC00001001113"]}}