This webinar, will highlight the Strand NGS Pipeline Manager feature. In this webinar, you will learn how to customize pipelines and share them with other Strand NGS users. This webinar will give a brief glimpse of an elaborate pipeline that aligns reads, filters poor-quality matches, computes coverage metrics, identifies variants, checks for sample cross-contamination, and emails quality reports – all from within Strand NGS. Vamsi will also be available for live questions at the event.
Speaker: Dr. Vamsi Veeramachaneni, Vice President – Bioinformatics, Strand Life Sciences
Register at http://www.strand-ngs.com/webinar_registration
We are excited to be a part of the Annual Meeting of The American Society of Human Genetics (ASHG) again, this time in Baltimore, Maryland from 6- 10 October 2015. Come and meet us to learn more about our best-in-class next-generation sequencing (NGS) data analysis software Strand NGS and Agilent Technologies state-of-the-art multi-omics analysis software GeneSpring.
You can meet our representatives for a one-on-one discussion or a live demo of Strand NGS and GeneSpring suite at Agilent Technologies booth #701. To schedule a demo / one-on-one meeting, please write to us at email@example.com
The Strand team will also present four posters at the ASHG conference this year. One of our posters titled ‘Detection of translocations in clinical cancer samples using targeted NGS data‘, presented as part of the ‘Clinical Genetic Testing’ has scored high points by the ASHG reviewers committee and will feature among the top 10%, so make sure you mark your calendars to come and take a look. The other three posters will be presented in the ‘Bioinformatics and Genomic Technology’ sessions. Listed below are the details
Date: 7th Oct 2015
Session: Bioinformatics and Genomic Technology
Date: 8th Oct 2015
Session: Clinical Genetic Testing
Session: Bioinformatics and Genomic Technology
Structural Variants (SVs) have long been implicated in many human diseases such as cancer, making their detection important in clinical genomics. Strand NGS 2.5 includes a new workflow step for detecting these variants based on split reads that span the breakpoints corresponding to the variants. Detection of SVs using split reads provides breakpoints with a higher precision compared to the methods based on paired-end reads. In this webinar, we will describe this method and demonstrate its application to detection of somatic gene fusions in targeted sequencing data. We will also show how the detected SVs can be visually validated in the elastic genome browser of Strand NGS.
Speaker: Dr. Shanmukh Katragadda, Vice President – Software Technology, Strand Life Sciences
Register here: http://www.strand-ngs.com/webinar_registration
In this month’s webinar, we will demonstrate and assess the algorithms in StrandNGS for both narrow and broad peak calling. Specifically, results from using ‘MACS’ algorithm for detecting the FOXA1 transcription factor binding sites and from ‘Find Enriched Regions’ approach for detecting histone H3K36 modification regions will be discussed.
Integrative RNA and ChIP-Seq analysis of regulatory T-cells , a Strand NGS application note describes how integrated multi-omics functionality in Strand NGS was used to find the regulatory role of FoxP3 in T-regulatory and T-helper cells. Learn how the gene expression profiles from RNA-Seq and FoxP3 DNA-protein binding sites from ChIP-Seq are integrated. For mor information, please write to us
Using a nasopharyngeal carcinoma case study, this paper highlights the integrated transcriptome analysis capabilities of Strand NGS demonstrating the identification of miRNA – mRNA interactions in regulatory networks.
Read the application note on Integrated mRNA and microRNA transcriptome analysis in Strand NGS by Veena Hedatale and Rohit Gupta. For more information, please contact us
Know about the state-of-the-art algorithms implemented in Strand NGS for detecting the binding sites of transcription factor (narrow peaks) and enriched regions of histone modification (broad peaks) from ChIP-Seq data.
Read the benchmarking study on Calling narrow and broad peaks from ChIP-Seq data in Strand NGS by Rohit Gupta and Anita Sathyanarayanan. For more information, please contact us
Happy to share the release of Strand NGS v2.5. This release comes with many new exciting features and enhancements. Some of the major enhancements include new workflow for MeDIP-Seq analysis, split read alignment, new structural variant caller using split reads, additional RNA QC plots, enhanced RNA-Seq workflow to handle large-scale projects, correlation analysis, meta-data analysis, new and improved CNV visualisations (genome browser and web browser).
Additionally several enhancements are made with respect to visualizations and for high confidence variant calling. All these new features are available once you update the product by clicking on Update Product from the Help menu. For more information, please see the release notes. In case you need any assistance, please write to us at firstname.lastname@example.org or email@example.com
Copy number variants constitute a significant fraction of genomic alterations responsible for cancer and various inherited disorders. In a clinical setting, performing focused NGS testing based on a panel of relevant genes is both economical and provides faster results. Thus the ability to detect CNVs from gene panel based NGS tests increases the diagnostic yield significantly. In this live webinar on Copy Number Detection in Inherited Disorders and Somatic Cancer, we will present few clinical case studies to demonstrate the new CNV analysis workflow in Strand NGS that enables researchers to detect and visualize copy number changes ranging from single exon to chromosome level events.
Dr. Smita Agrawal, Senior Scientist, Strand Life Sciences, has over 14 years of research experience applying analytical methods to biological problems in the fields of neuroscience, stem cell biology, immunology and genetics. Smita has a PhD in Chemical Engineering from the University of California, Berkeley and has experience working as a post-doctoral scholar in the division of Human Genetics at the University of Minnesota, and as a researcher in the early discovery division of Genentech Inc. At Strand, she heads the clinical data analysis group and also guides the product definition of StrandOmics, Strand’s clinical genomics interpretation and reporting software.
The year 2014 was a great year with exciting features and enhancements updated in Strand NGS. We take this opportunity to thank our clientele and well-wishers for their support and feedback. We wish you all a happy and prosperous new year and look forward to a more fruitful engagement in 2015.
In this blog on Interesting findings by ChIP-Seq and DNA-Seq analysis using Strand NGS, we present two recent publications that analyse ChIP-Seq and DNA-Seq data using Strand NGS.
1. A Comprehensive Profile of ChIP-Seq-Based PU.1/Spi1 Target Genes in Microglia by Satoh et al.
2. Localised Dominant Dystrophic Epidermolysis Bullosa with a Novel de Novo Mutation in COL7A1 Diagnosed by Next-generation sequencing by Nagai et al.
The paper by Satoh et al. investigates the biological role of the transcription factor PU.1 in regulation of microglial functions. Though PU.1 plays vital role in microgliogenesis, the comprehensive profile of PU.1/Spi1 target genes in microglia is unknown. In this paper, Strand NGS was used to analyse SRP036026 ChIP-Seq data set and identify the role of PU.1/ Spi1 in microglial gene regulation. Using Strand NGS, around 5,264 ChIP-Seq-based Spi1 target protein coding genes (Spi1, Irf8, Runx1, Csf1r, Csf1, Il34, Aif1 (Iba1), Cx3cr1, Trem2, and Tyrobp) were identified in BV2 mouse microglial cells. Motif analysis by GADEM revealed the PU-box consensus sequences (5’-GAGGAA-3’) were located on 80.3% of the peaks detected by MACS. By downstream pathway analysis, the ChIP-Seq-based Spi1 target genes were found to show significant relationship with diverse pathways essential for normal function of monocytes/ macrophages (like endocytosis, phagocytosis, lysosomal degradation). Hence PU.1/Spi1 was found to have an important role in microglial gene regulation and any aberrant regulation of these target genes would contribute to neurodegenerative diseases by activated microglia accumulation.
The second paper by Nagai et al. is a case study of a 10-month-old female infant with local Dominant Dystrophic Epidermolysis Bullosa. A targeted next generation sequencing was performed with the proband’s peripheral blood for 16 genes associated with Dystrophic Epidermolysis Bullosa. The sequenced data was aligned and analysed using the DNA variant analysis workflow in Strand NGS (formerly Avadis NGS). A heterozygous single nucleotide variation on chr.3: g.48616827C>T (negative strand) that corresponds to a missense mutation of p.Gly1761Asp in the triple helix domain of COL7A1 was detected. This de novo high confidence mutation was also confirmed by Sanger sequencing. This mutation was detected only in the proband and was not found in the parents, in 100 healthy Japanese alleles as well as in dbSNP.