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Exome sequencing

ABSTRACT: Exome sequencing in hereditary Colorectal cancer

PROVIDER: PRJEB7926 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	ERR696683_1.fastq.gz	Fastqsanger.gz
	ERR696683_2.fastq.gz	Fastqsanger.gz
	ERR753368_1.fastq.gz	Fastqsanger.gz
	ERR753368_2.fastq.gz	Fastqsanger.gz
	ERR753369_1.fastq.gz	Fastqsanger.gz

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Whole-exome sequencing (WES) of single glands from opposite side of two colorectal tumors and WES of colorectal cancer xenografts derived from single cell culture to study tumor growth dynamics

Project description:Single Gland Whole-exome sequencing: building on our prior description of multi-region WES of colorectal tumors and targeted single gland sequencing (E-MTAB-2247), we performed WES of multiple single glands from different sides (right: A and left: B) of two tumors in this study (tumor O and U) on the illumina platform using the Agilent SureSelect 2.0 or illumina Nextera Rapid Capture Exome kit (SureSelect or NRCE, as indicated in the naming of fastq files). Colorectal Cancer Xenograft Whole-exome sequencing: The HCT116 and LoVo Mismatch-Repair-deficient colorectal adenocarcinoma cell lines were obtained from the ATCC and cultured under standard conditions. For both cell lines, a single âfoundingâ cell was cloned and expanded in vitro to ~6M cells. Two aliquots of ~1M cells were subcutaneously injected into opposite flanks (right and left) of a nude mouse and tumors allowed to reach a size of ~1B cells (1cm3) before the animal was sacrificed. Tumor tissue was collected separately from the right and left lesions and DNA was extracted for WES using the illumina TruSeq Exome kit or Nextera Rapid Capture Exome expanded Kits (Truseq or NRCEe), as was DNA from the first passage population (a polyclonal tissue culture for HCT116 and a polyclonal xenograft sample for LoVo), which were employed as a control to study mutation accumulation in culture and post xenotransplantation.

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Project description:The raw data consist of whole exome sequencing data of cervical squamous samples

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Exome sequencing data analysis to characterize rare germline copy number variants involved in colorectal cancer predisposition

Project description:Colorectal cancer (CRC) represents the third most common cancer worldwide. Next generation sequencing (NGS) appearance has allowed us to produce huge amount of data and, in order to fully exploit its usage, copy number variants (CVN) detection software have been developed. In this study, we analyze germline DNA whole-exome sequencing (WES) data from 38 families with strong CRC aggregation without alterations in known hereditary genes to detect rare candidate CNVs to CRC predisposition using ExomeDepth and CoNIFER tools. Variants shared between family members were compared to Database of Genomic Variants (DGV) catalogue and our Spanish database. CNVs finally selected were validated and segregation analysis were performed using Comparative Genome Hybridization (CGH). Gene expression arrays and qRT-PCR were conducted in both germline and tumor cDNA to check possible effects at transcription level. Immunohistochemistry (IHC) studies were also carried out. Whith this, 21 candidate CNV corresponding to 16 duplications and 5 deletions were detected by calling tools. After multiple filtering steps, only the duplication in chromosome 1 in family 7 stood out as interesting. Validation by CGH confirmed the duplication and correct family segregation. TTF2, TRIM45, VTCN1 and miR942 are embedded in chromosome 1 duplication. Expression studies pointed to TTF2 and miR942 overexpression in carriers, and tumor IHC showed TTF2 protein overexpression and underexpression of the TMEM158 protein. Also known as RIS1, TMEM158 is a predicted target of miR942 and has been claimed to be a candidate tumor-supressor. All in all, chromosome 1 duplication may correspond to the mutational event involved in CRC predisposition in the carrier family by overexpressing TTF2 and miR942, leading to TMEM158 underexpression. Keywords: colorectal cancer, next generation sequencing, copy number variant, duplication, predisposition.

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