Dataset Information

Research on genomic test utilizing next generation sequencer for solid tumors and development of the genome database

ABSTRACT: Interventions: Genomic test CANCERPLEX-JP OncoGuide NCC oncopanel system FndationONe CDx genome profile GUARDANT360 MSI Analysis System BRACAnalysis Primary outcome(s): Development of genome database Study Design: Single arm Non-randomized

DISEASE(S): Solid Tumors (brain Tumor, Thyroid Cancer, Parathyroid Cancer, Breast Cancer, Lung Adenocarcinoma, Lung Squamous Cell Carcinoma, Tongue Cancer, Carcinoma Of The Oral Cavity, Pharyngeal Cancer, Esophageal Cancer, Gastric Cancer, Carcinoma Of The Small Intestine, Colon Cancer, Rectal Cancer, Gastrointestinal Stromal Tumor, Hepatocellular Carcinoma, Intrahepatic Bile Duct Cancer, Extrahepatic Bile Duct Cancer, Gallbladder Cancer, Ampullary Cancer, Pancreatic Cancer, Duodenal Cancer, Renal Cell Carcinoma, Urothelial Carcinoma, Bladder Cancer, Prostate Cancer, Carcinoma Of The Cervix Uteri, Carcinoma Of The Corpus Uteri, Ovarian Cancer, Skin Cancer)

PROVIDER: 2643590 | ecrin-mdr-crc |

REPOSITORIES: ECRIN MDR

ACCESS DATA

Similar Datasets

Project description:Targeted genomic enrichment followed by next-generation sequencing dramatically increased the efficiency of mutation discovery in human genomes. Here we demonstrate that these techniques also revolutionize traditional genetic approaches in model systems. We developed a two-step protocol utilizing a traditional bulk-segregant analysis (BSA) approach for positional cloning mutants in phenotype-driven forward genetic screens. First, BSA pools are 'light' sequenced for rough mapping, followed by targeted enrichment and deep-sequencing of the mutant BSA pool for the linked genomic region to fine-map and discover candidate mutations. We applied this method successfully to three Arabidopsis mutants and show that it can be scaled by multiplexing. Similarly, we applied these techniques to a gene-driven reverse genetics method (chemical driven target-selected mutagenesis or TILLING) that is used for generating gene knockouts in a wide range of organisms, including plants, invertebrates and vertebrates. We developed an efficient multiplexed genomic enrichment protocol for pre-barcoded samples. As a proof-of-principle, 770 genes were screened for induced mutations in 30 rats, which identified all but one known variants (30) as well as a large series of novel knockout and missense alleles. Mutations were retrieved at the expected frequency with a the false-positive rate of less than 1 in 6 million basepairs, which is much lower as compared to traditional mutation discovery approaches. Both methods are largely independent of the genome size due to the targeted enrichment and can thus be applied to any genetic model system of interest. Targeted genomic enrichment followed by next-generation sequencing dramatically increased the efficiency of mutation discovery in human genomes. Here we demonstrate that these techniques also revolutionize traditional genetic approaches in model systems. We developed a two-step protocol utilizing a traditional bulk-segregant analysis (BSA) approach for positional cloning mutants in phenotype-driven forward genetic screens. First, BSA pools are 'light' sequenced for rough mapping, followed by targeted enrichment and deep-sequencing of the mutant BSA pool for the linked genomic region to fine-map and discover candidate mutations. We applied this method successfully to three Arabidopsis mutants and show that it can be scaled by multiplexing. Similarly, we applied these techniques to a gene-driven reverse genetics method (chemical driven target-selected mutagenesis or TILLING) that is used for generating gene knockouts in a wide range of organisms, including plants, invertebrates and vertebrates. We developed an efficient multiplexed genomic enrichment protocol for pre-barcoded samples. As a proof-of-principle, 770 genes were screened for induced mutations in 30 rats, which identified all but one known variants (30) as well as a large series of novel knockout and missense alleles. Mutations were retrieved at the expected frequency with a the false-positive rate of less than 1 in 6 million basepairs, which is much lower as compared to traditional mutation discovery approaches. Both methods are largely independent of the genome size due to the targeted enrichment and can thus be applied to any genetic model system of interest.

Dataset Information

Research on genomic test utilizing next generation sequencer for solid tumors and development of the genome database

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure