ABOUT EXOME Free Download

This web site is designed to disseminate exome sequencing data generated through federal funding from the NHLBI. This data is provided free-of-charge, provided the following permission statement is followed. There may be other information on the site, such as links to other sites, references to other project groups and federal grants. The University of Washington has no responsibility for these links and information.

The contents of the NHLBI ESP Exome Variant Server web site are intended for educational or research purposes. As stated above, a subset of exome variants on this website have been deposited in dbSNP, and the full dataset will be deposited in dbGaP as part of the ESP cohort data. We place no restrictions on the use of the data available from the EVS. You may download or copy the content and other downloadable items displayed on the Exome Variant Server portion of the web site, provided that in using the data, you follow the citation format given above.

Circulating cell-free DNA (cfDNA) released from cancerous tissues has been found to harbor tumor-associated alterations and to represent the molecular composition of the tumor. Recent advances in technologies, especially in next-generation sequencing, enable the analysis of low amounts of cfDNA from body fluids. We analyzed the exomes of tumor tissue and matched serum samples to investigate the molecular representation of the tumor exome in cfDNA. To this end, we implemented a workflow for sequencing of cfDNA from low serum volumes (200 μl) and performed whole-exome sequencing (WES) of serum and matched tumor tissue samples from six non-small cell lung cancer (NSCLC) patients and two control sera. Exomes, including untranslated regions (UTRs) of cfDNA were sequenced with an average coverage of 68.5x. Enrichment efficiency, target coverage, and sequencing depth of cfDNA reads were comparable to those from matched tissues. Discovered variants were compared between serum and tissue as well as to the COSMIC database of known mutations. Although not all tissue variants could be confirmed in the matched serum, up to 57% of the tumor variants were reflected in matched cfDNA with mutations in PIK3CA, ALK, and PTEN as well as variants at COSMIC annotated sites in all six patients analyzed. Moreover, cfDNA revealed a mutation in MTOR, which was not detected in the matched tissue, potentially from an untested region of the heterogeneous primary tumor or from a distant metastatic clone. WES of cfDNA may provide additional complementary molecular information about clinically relevant mutations and the clonal heterogeneity of the tumors.

In summary, we evaluated cfDNA to assess the exomes of six NSCLC patients in primary tumor and corresponding serum samples. We show that exome analysis of cfDNA is feasible for minimal-invasive characterization of tumor diseases. Our results provide evidence for cfDNA to inform about the molecular alteration in advanced cancer. Nevertheless, further evaluation and larger cohorts of different entities are needed to fully understand the value of WES of cfDNA as faithful representations of tumors.

A number of free software programs are available for viewing trace or chromatogram files. Click on the appropriate icon(s) to go to the respective Web page. You will find information about downloading, installing and using the software. Please make your choice based on your computer platform and operating system.

In this paper we describe a free web resource, named WEP (Whole Exome sequencing Pipeline web tool): it aims to analyze WES data produced by Illumina platforms [23], which are the most developed and used platforms currently available for WES data production [1, 24]. Our web tool automates the execution of an optimized WES pipeline. It is also capable to analyze a user-selected set of exome samples generating tables reporting variant information and their functional annotation.

SAMtools flagstat is used to generate alignment statistics, i.e. the calculation of the fraction of reads that successfully mapped to the reference, with number and percentages of the read mapped and unmapped, whereas NGSrich [53] provides detailed information about enrichment performance and target coverage, important quality criteria for the evaluation of the exome capture experiment.

The main results web page shows the summary of the statistics about the whole analysis: the input files, the number of short-reads, total and filtered (after the first step), mapped reads, number of reads after removing duplicates, exome coverage and the number of total variants detected.

WEP is a web tool which allows any user to freely submit and perform a complete WES optimized pipeline for Illumina sequenced exome samples. It performs a complete analysis starting from quality controls of submitted short reads produced in single or paired end to SNP/DIP identification and variant annotation.

Output files, status and information about each module of a running analysis are provided. Results can be filtered and managed through the GUI and can be downloaded as CSV standard formats as well. Codes and algorithms are regularly updated and tested.

In humans, there are about 180,000 exons with a combined length of 30 millionbase pairs (30 Mb). Thus, the exome represents only 1% of the human genome, buthas been estimated to harbor up to 85% of all disease-causing variants (Choiet al., 2009).

We offer a wide portfolio of Applied Biosystems software solutions for viewing and interpreting your Sanger sequencing and fragment analysis results. Learn about our free tools and commercially available products below.

Peak Scanner Software is a DNA sizing software that can either be downloaded for free or purchased for free as a software kit. Use this software to perform DNA fragment analysis, separate a mixture of DNA fragments according to their sizes, provide a profile of the separation, and precisely calculate the sizes of the fragments. The software allows you to view, edit, analyze, print, and export fragment analysis data generated using Applied Biosystems genetic analyzers.

The free, online Primer Designer Tool allows you to search for the right PCR/Sanger sequencing primer pair from a database of 650,000 predesigned primer pairs for resequencing the human exome and human mitochondrial genome.

Experimental Design: To study clonal evolution during treatment and follow-up, an innovative method based on circulating cell-free DNA (cfDNA) analysis by whole-exome sequencing (WES) paired with target sequencing was realized in sequential liquid biopsy samples of 19 neuroblastoma patients.

In cancer with genetic heterogeneity, the identification of clones resistant to upfront treatment will lead to new therapeutic strategies targeting these resistant clones. We present a new approach based on whole-exome sequencing (WES) techniques of cell-free DNA (cfDNA) samples in neuroblastoma patients, enabling for the first time sequential analyses of mutational profiles in these patients. We now show how the study of cfDNA by WES can contribute to the understanding of clonal evolution in this malignancy, indicating the emergence of subclonal events present at diagnosis to clonal events at disease progression. The modelization of clonal evolution highlights mechanisms of treatment resistance and of escape. The identification of treatment-resistant clones will enable adaptation of treatment strategies.

Get the Genomon-exome source from the github's Genomon-exome downloads page (see below) and download it on to your local machine. Please find the file with its file name extension, .tar.gz (or .zip). You'll need upload the archive, exome_for_HGC-RB_${version}.tar.gz (or .zip) to the supercomputer. (You can put it anywhere under your home directory) If you local machine runs Windows, it is better to use winSCP for the upload work.

Download the ANNOVAR package. The ANNOVAR perl scripts help you to download various databasese including the dbSNP build131. To user this software, you need to register at the ANNOVAR site and you will recieve an email directed to your email address used upon registration. The email has the link to the package. ANNOVAR should be placed under the exome/bin directory.

Whole-exome sequencing measures the regions of the genome (about 2%) that are involved in coding for proteins and is particularly suitable for identifying disease-causing and/or rare genetic variants.

Using Ethernet cable to connect to the UCSF network is a reliable way to download data. Also, your workstation/laptop may not have enough space to store the data. You should consider using an external hard-drive (1 TB or more) with USB 3.1 connection. If you are unsure about the best way to download your data, please feel free to discuss with us.

RefSeq and Ensembl gene annotations for the rat reference genome from assembly Rnor_6.0 (RGSC, 2014) were downloaded from the UCSC Genome Browser [9]. RefSeq and Ensembl annotations covered protein coding, lncRNAs and miRNAs with no RefSeq overlap and for which exons were removed that were completely contained in other longer exons. Merging the two annotations, the in-silico probe design covered a total of 223,636 exons (26,365 genes) of the reference rat exome. Based on the input targets, 120-base RNA probes were created iteratively by tiling at approximately 1X density (end-to-end) along the sense strand of the reference genome, Rnor_6.0 assembly. Probe filtering was based on the uniqueness criteria of an exon read having a single chromosome location within the Rn6 genome. Low complexity or repetitive probes not meeting the Rn6 genome criteria were removed from the pool. In total, 826,878 probe sequences were combined and used to manufacture a single biotinylated RNA library for target capture.

Current clinical next-generation sequencing is done by using gene panels and exome analysis, both of which involve selective capturing of target regions. However, capturing has limitations in sufficiently covering coding exons, especially GC-rich regions. We compared whole exome sequencing (WES) with the most recent PCR-free whole genome sequencing (WGS), showing that only the latter is able to provide hitherto unprecedented complete coverage of the coding region of the genome. Thus, from a clinical/technical point of view, WGS is the better WES so that capturing is no longer necessary for the most comprehensive genomic testing of Mendelian disorders. 59ce067264

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