{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Sara Al-Badran"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15619"],"description":["This study used formalin-fixed paraffin-embedded (FFPE) human tissue collected for the Integrated teChnologies for Improved polyp SurveillancE (INCISE) collaborative from polypectomies performed within the Scottish BCSP in the NHS Greater Glasgow and Clyde health board between 2009-2016 in patients who underwent further colonoscopy between 6 months and 6 years after the index colonoscopy. The extracted DNA was then passed to the Genomics Innovation Alliance (formerly Glasgow Precision Oncology Laboratory; GPOL) for genomic sequencing using their bespoke Cancer Plus panel. Some patients had metachronous polyps, and synchronous polyps sequenced, in addition to their largest index polyp. The output from the sequencing is FASTQ files and VCF files."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - The HOLMES pipeline is used to process sequencing data and generate files containing single nucleotide variations, structural variations and copy-number variations. Raw .cblc files from the NovaSeq 6000 were converted to fastq files using Bcl2fastq. Alignment was performed with bwa. Variant calling was carried out using deepSNV/Shearwater for single nucleotide variations, and pindel for larger insertions and deletions. Variant annotation was performed using CAVA. Brass was used to find structural variation breakpoints by grouping discordant read pairs, and geneCN was used for copy-number calling.","Nucleic Acid Extraction - DNA was extracted from FFPE curls as per the exact instructions of the Promega Maxwell RSC DNA FFPE Kit (Products AS1450 and ASB1450).","Library Construction - Libraries were constructed following the instructions of the SureSelect XT HS2 DNA Library preparation method and pooled prior to target enrichment. Libraries are Illumina NGS compatible with in-read MBCs (trimmed) and dual 8bp indices.","Sample Collection - Two 10um thick serial section curls were cut from FFPE tissue blocks and stored in DNA/RNA-free tubes."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Normalization was done for copy number calling. GeneCN is designed to perform gene-specific copy number analysis from sequence capture data of cancer samples. It requires Bio-DB-HTS version 2.10 or higher. Preparation of the input bed file requires bedtools.  GeneCN consists of two scripts. The first is a Perl script, called depth-for-geneCN.pl, which generates coverage data for the sample of interest. The second is an R script, called geneCN.R, which normalises the coverage data from depth-for-geneCN.pl and generates copy number plots and calls for specific genes of interest."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["exome sequencing"],"species":["Homo sapiens"],"pubmed_authors":["Joanne Edwards","Sara Al-Badran"],"additional_accession":[]},"is_claimable":false,"name":"INCISE Mutational Data Subset: Index, Metachronous, and Synchronous Polyps","description":"This study used formalin-fixed paraffin-embedded (FFPE) human tissue collected for the Integrated teChnologies for Improved polyp SurveillancE (INCISE) collaborative from polypectomies performed within the Scottish BCSP in the NHS Greater Glasgow and Clyde health board between 2009-2016 in patients who underwent further colonoscopy between 6 months and 6 years after the index colonoscopy. The extracted DNA was then passed to the Genomics Innovation Alliance (formerly Glasgow Precision Oncology Laboratory; GPOL) for genomic sequencing using their bespoke Cancer Plus panel. Some patients had metachronous polyps, and synchronous polyps sequenced, in addition to their largest index polyp. The output from the sequencing is FASTQ files and VCF files.","dates":{"release":"2025-10-10T00:00:00Z","modification":"2026-05-27T16:43:31.924Z","creation":"2025-10-10T11:14:09.611Z"},"accession":"E-MTAB-15619","cross_references":{"ENA":["ERP181345"],"Biostudies":["E-MTAB-15346"],"EFO":["EFO_0002944","EFO_0005396","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0004184"]}}