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| Status |
Public on Dec 01, 2021 |
| Title |
Colon tumor from patient T108 |
| Sample type |
SRA |
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| Source name |
FFPE tumor
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| Organism |
Homo sapiens |
| Characteristics |
disease stage: Colon cancer stage II
tissue: FFPE tumor
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| Treatment protocol |
All patients were first-line treated with surgery, and none of them received adjuvant chemotherapy.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from each formalin-fixed paraffin-embedded (FFPE) tumor samples using the QIAmp DNA FFPE kit (Qiagen, Hilden, Germany) and then quantified using Qubit fluorometer assay (Thermo Fisher Scientific, MA, USA)
Enriched libraries were prepared from 50 ng of DNA per tumor sample using the SMARTer ThruPLEX DNA-seq Library Preparation kit (TaKaRa, Japan) and a predesigned gene capture pool of IDT xGen Lockdown probes (IDT, Coralville, Iowa, USA). Paired-end sequencing runs were performed on a MiSeq platform (Illumina, San Diego, CA, USA) following a protocol with 2x130 bp reads.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
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| Description |
Sequenced using MiSeq platform to profile mutations in tumor samples
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| Data processing |
Library strategy: Targeted Next-Generation DNA Sequencing
The Illumina MiSeq Reporter software (MSR, v2.6, Illumina) was used for initial base-calling and for generating FASTQ files.
Raw sequencing reads were trimmed for adaptor sequence, and masked of low-quality sequences using the MiSeq Reporter software (MSR, v2.6, Illumina). Alignment to human reference genome GRCh37/hg19 was executed with BWA-MEM aligner algorithm on MiSeq Reporter.
Variant calling was executed using two algorithms: MuTect2 (v2.2) from the GATK platform (Broad Institute, Cambridge, MA, USA) and the Illumina Somatic Variant Caller (integrated in the MiSeq Reporter, v2.6).
Variants on VCF files were annotated with SnpEff (v4.3) plus dbNSFP (v2.9.3) for downstream functional analysis.
Low quality calls were discarded to minimize false positive events: mapping quality below 30,TLOD <9 and read depth below 15x. Synonymous and germline variants were removed, along with polymorphisms having a worldwide population frequency above 1%, as reported in databases ExAC and 1000 Genomes Project.
Genome_build: Homo sapiens GRCh37/hg19
Supplementary_files_format_and_content: VCFs are tab-delimited text files including all detected DNA variants (rows) by sequencing in every sample. For each variant/row, functional information was subsequently annotated in column “INFO” using SnpEff (v4.3) plus dbNSFP (v2.9.3) databases.
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| Submission date |
Apr 16, 2021 |
| Last update date |
Dec 02, 2021 |
| Contact name |
Sara Lahoz |
| E-mail(s) |
saralahoz93@gmail.com, salahoz@clinic.cat
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| Organization name |
Institut D'Investigacions Sanitàries August Pi i Sunyer
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| Street address |
Carrer del Rosselló, 149
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| City |
Barcelona |
| ZIP/Postal code |
08036 |
| Country |
Spain |
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| Platform ID |
GPL15520 |
| Series (2) |
| GSE172190 |
Targeted Next-Generation Sequencing for profiling frequently mutated genes in early-stage colon cancer |
| GSE172191 |
Intratumor genomic heterogeneity in stage II colon cancer |
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| Relations |
| BioSample |
SAMN18753968 |
| SRA |
SRX10614541 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5243639_PASS-dbnsfp-Sorted_SnpEff-T108_S5.vcf.gz |
428.6 Kb |
(ftp)(http) |
VCF |
| GSM5243639_dbnsfp-SnpEff-PASS-FilterMutectCalls-Mutect2-T108_S5.vcf.gz |
99.6 Kb |
(ftp)(http) |
VCF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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