EGAGenomicsIllumina Genome Analyzer IIhttps://ega-archive.org/datasets/EGAD000010000369EGA dataset EGAD00001000036EGA<h4>Background</h4>Massively parallel sequencing technologies have brought an enormous increase in sequencing throughput. However, these technologies need to be further improved with regard to reproducibility and applicability to clinical samples and settings.<h4>Methods</h4>Using identification of genetic variations in prostate cancer as an example we address three crucial challenges in the field of targeted re-sequencing: Small nucleotide variation (SNV) detection in samples of formalin-fixed paraffin embedded (FFPE) tissue material, minimal amount of input sample and sampling in view of tissue heterogeneity.<h4>Results</h4>We show that FFPE tissue material can supplement for fresh frozen tissues for the detection of SNVs and that solution-based enrichment experiments can be accomplished with small amounts of DNA with only minimal effects on enrichment uniformity and data variance.Finally, we address the question whether the heterogeneity of a tumor is reflected by different genetic alterations, e.g. different foci of a tumor display different genomic patterns. We show that the tumor heterogeneity plays an important role for the detection of copy number variations.<h4>Conclusions</h4>The application of high throughput sequencing technologies in cancer genomics opens up a new dimension for the identification of disease mechanisms. In particular the ability to use small amounts of FFPE samples available from surgical tumor resections and histopathological examinations facilitates the collection of precious tissue materials. However, care needs to be taken in regard to the locations of the biopsies, which can have an influence on the prediction of copy number variations. Bearing these technological challenges in mind will significantly improve many large-scale sequencing studies and will - in the long term - result in a more reliable prediction of individual cancer therapies.Targeted high throughput sequencing in clinical cancer settings: formaldehyde fixed-paraffin embedded (FFPE) tumor tissues, input amount and tumor heterogeneity.Kerick Martin M, Isau Melanie M, Timmermann Bernd B, Sültmann Holger H, Herwig Ralf R, Krobitsch Sylvia S, Schaefer Georg G, Verdorfer Irmgard I, Bartsch Georg G, Klocker Helmut H, Lehrach Hans H, Schweiger Michal R MRDAT1, DAT, DA transporter, Dat1., Solute carrier family 6 member 3, PKDYShereditary prostate cancer, cancer of the prostate, Malignant Neoplasm, Prostate Neoplasms, Malignancy, Neoplasms, number, familial, Benign Neoplasm, Benign Neoplasms, Cancers, Tumor, cancer of prostate, Malignant, presence, Prostate Neoplasm, Neoplasias, count in organism, Prostatic Neoplasm, Cancer of the Prostate, Benign, cardinality, Prostatic Cancer, Neoplasm, Prostatic Cancers, Prostatic, prostate cancer, PC, NOS, Malignancies, Cancer of Prostate, Prostate Cancer, Neoplasia, Prostate, Cancer, Prostate Cancers, Tumors, Malignant Neoplasms.primary cancer, Formol, Malignant Neoplasm, heterogeneity., Malignancy, Neoplasms, Benign Neoplasm, Formaldehyd, Tissue, Oxomethane, Benign Neoplasms, Cancers, Tumor, Malignant, malignant tumor, Methylene oxide, Malignant Neoplasms, Neoplasias, MT, Benign, Formalin, Oxomethylene, malignant neoplasm, Methanal, Parafilm, Neoplasm, FORMALIN, Malignancies, other neoplasm, fixed, Neoplasia, Cancer, TumorsSingle Nucleotide Variant, Query, Formol, Needs, Nucleotide Sequencing, Massively-Parallel, clinical data, Addresses, Fresh Specimen, Tumor, Embedded, Long Term, Surgical Interventions, copy_number, Techniques, High-Throughput RNA Sequencing, sampling, sequencing assay, diseases, Roles, Method, Methanal, Parafilm, Concepts, Importance Rating Score 0, diseases and disorders, Newari, Ability Question, Influence, Effect, Detection, Deep Sequencing, FLD, In the Field, Targeting, thymus nucleic acid, human disease, Bearings, Copy Number Reported, Target Populations, Embedding, Biopsies, Identification, Focal, Illumina Sequencing, IMPROVED, Comparative Genomics, Large-Scale Sequencing, result, Formaldehyd, Tissue, hypoplasia, Oxomethane, procedures, Question, Based, genetic, Novel, Prostatic Neoplasm, Cancer of the Prostate, High Throughput RNA Sequencing, Methodological Studies, ARC11, Had, malignant neoplasm, Ability To, Taken, sample, Role Concepts, COPYNUM, Health Services Need, Homo sapiens disease, Double-Stranded DNA, Malignancies, Better, deoxyribonucleic acids, Outcome, DNAn, Nucleotide, Has, INCREASED, Importance Score 0, Tumors, Display, surgery, High-Throughput RNA, cancer of the prostate, Genomics, sequencing_assay, Difference, statistics and numerical data, Comparative, Needs and Demand, familial, Need, High-Throughput DNA Sequencing, FFPE, Importance 0, Double-Stranded, Functional Genomics, Procedure, DETECTION, Surgical Intervention, copy number, results, (Deoxyribonucleotide)n+m, ACCUMULATION AND REPLICATION OF CHLOROPLASTS 11, Ion Torrent Sequencing, Benign, Role Concept, Massively-Parallel Sequencing, Diseases, Next-Generation, Role, numerical data, NOS, simple tissue, Ion Torrent, Conflict, materials, Focus, desoxyribose nucleic acid, fixed, Deviation, nucleotides, Clinical Data, Enrichment, Surgically, Populations, VARIATION, Nucleic Acid Sequencing, Biological Detection Test, Health Services Needs, Bearing, Benign Neoplasms, Methodological, Improved, Methodological Study, cancer of prostate, Genomic, Malignant Neoplasms, High Throughput Sequencing, Identified, disease, Surgical, Request, Material, View, Base, ds DNA, inherited genetic, Nepal Bhasa, DNA, Detected, snv variant, other neoplasm, Sequence Analysis, Prostate, Surgical Procedure, Malignant Neoplasms., Fresh, other disease, Clinical Batch, Important, High Throughput DNA Sequencing, DNS, Procedures, Prostate Neoplasms, (Deoxyribonucleotide)n, Material Identification, Effects, Neoplasms, FRESH, Different, Importance, Benign Neoplasm, EMBEDDING, High-Throughput DNA, Surgery, Example, Available, Malignant, Illumina, Surgical Procedures, Next-Generation Sequencing, Deoxyribonucleic acids, Enrich, SEQUENCING, FIELD, New Lesion, Biopolymer Sequencing, Structural, It improved, reduced, Deoxyribonucleic Acid, utilization, Deep, Foci, Care, Studies, Prostatic Cancers, Variant, Functional, disease or disorder, tiny, Massively Parallel Sequencing, Cancer of Prostate, Technique, Prostate Cancers, snv_variant, Health Services, Embed, MZF18.10, Ion Proton Sequencing, Clinical, Malignancy, Target, BETTER/IMPROVED/RECOVERING, Double Stranded, Deoxyribonucleic acid, Pyrosequencing, Long-Term, Population, SNV, Sequencing, Solution, outcome, Focused, Heightened, non-neoplastic, Study, Neoplasias, Displayable, Formalin, Device Display Device, Newar Language, Dimension, heterogeneity, Prostatic, genome, High-Throughput, RNA Sequencing, disorder, (Deoxyribonucleotide)m, MZF18_10, constitutitional genetic, Variation, Cancer, Possess, small, hereditary prostate cancer, New, NEW, Molecular Biology, use, Question Text, Malignant Neoplasm, DNAn+1, Result, disorders, Targeted, Input, medical condition, Concept, Availability, MT, Clinical Lot, Have, DNA Sequencing, Prostatic Cancer, Neoplasm, clinical, condition, FORMALIN, background, techniques, ds-DNA, Next Generation Sequencing, Destination, Basic, Copy Number, New Lesion Identification, primary cancer, Type of Surgery, underdeveloped, Operation, Single Nucleotide Variants, Increased, Basis, Target Population, massively-parallel sequencing, Cancers, malignant tumor, Methylene oxide, sample population, introduction, massively parallel sequencing, NUCLEIC ACID SEQUENCING, Prostate Neoplasm, LAB_SEQ_METHOD, Differential, sample collection, ATMIND1, Formalin-Fixed Paraffin-Embedded, High-Throughput Sequencing, Oxomethylene, Embed Technique, Increase, Desoxyribonukleinsaeure, High Throughput Nucleotide Sequencing, prostate cancer, PC, Structural Genomics, Reproducibility, Bearing Device, Experimental Result, Ion Proton, hereditary, Prostate Cancer, Neoplasia, Genome, High-Throughput Nucleotide, methodologyfalseDAT_CancerMethodsPaper_CNVTumorFoci - samples"Copy number variant detection in multiple foci of three prostate cancer tumors"2017-07-26 15:39:24EGAD00001000036960621958464EGAC00001000030EGAS00001000136