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Science

Neoantigen Discovery Using Next-Generation Sequencing Data

Update (5/26/20) – Since originally publishing this post we’ve hosted a webinar on our Neoantigen Workflow. If you’d like an even deeper look at how to harness your NGS data, just click here! Leveraging neoantigens for guided treatment has become the definition of personalized cancer immunotherapy. Given their potential to …

Written by Vladimir Kovacevic
Useful Data

Biomedical Datasets for Large Scale Analysis

Biomedical data is growing at astonishing rates with the broadening of access to next-generation sequencing (NGS) and single-cell solutions. Not only is more data being generated, but it is also being generated with improvements in base-calling accuracy, read length and the generation of reads from each end of the library …

Written by Manisha Ray
Graph Genome

Pan-Genome Analysis Takes Center Stage

The concept of a pan-genome reference is straightforward: a reference structure that represents all the known genetic variation for a particular population or species. The representation of the human reference genome as a linear haploid DNA sequence poses limitations when trying to incorporate the known genetic diversity of human populations. …

Written by Devin Locke
Science

Sentieon Multi-instance Whole Genome Workflow

Organizations have adopted the use of Next Generation Sequencing (NGS) as a one of the primary tools of their discovery, diagnostic and clinical efforts. Simultaneously — the number of tools available for NGS analysis has ballooned, with each tool having different capabilities for speed, accuracy, cost, etc. Seven Bridges offers …

Written by Vladimir Kovacevic, Ana Popic, Luka Topalovic, Milan Kovacevic, Aleksandar Minic, Stefan Risteski
Platform

Data Cruncher Public Interactive Analyses

To help researchers transform raw NGS-based data into clinically actionable knowledge, Seven Bridges strives to efficiently bridge the gap between secondary and tertiary analysis. One of the features we offer to achieve this goal is Data Cruncher, which enables scientists to perform interactive computing and open-ended exploration of data on …

Written by Marko Milanovic, Nemanja Vucic, Milan Kovacevic, Boris Majic & Ana Damljanovic
Genomics

Taxanomic Profiling of Metagenomics Samples

Numerous colonies of different organisms live virtually everywhere on Earth, even in and on our bodies. They are called microbes and we think we know all about them. But do we really? Actually, the human race knew nothing about microbes before the 17th century. There were some assumptions and hypotheses, …

Written by Aleksandar Danicic, Nemanja Vucic, Srdjan Kasapovic and Vesna Pajic
Science

Accurate Analysis of Differential Methylation Data

With few exceptions, every human cell is composed of an identical DNA sequence. However, there are around 200 different cell types in our bodies. What is the underlying reason? Each different cell type represents a specific gene expression pattern. One of the main mechanisms that enables this is epigenetics. Epigenetics …

Written by Milos Nikolic, Tamara Stankovic, Milan Domazet, Sanja Mijalkovic
Science

Optimized Workflow for Bisulfite Sequencing Data Analysis

Epigenetics is an extra layer of information that is not encoded in the primary sequence of an organism’s DNA. While several mechanisms of epigenetic regulation exist, DNA methylation is one of the most commonly studied ones. Typically, the presence of methylated cytosines within a promoter region represses gene expression. The …

Written by Vesna Pajic, Tamara Jovanovic, Ana Damljanovic
Science

3-hour Whole Genome Analysis with GATK4

In the pursuit of accelerating next generation sequencing data processing for clinical applications,  Seven Bridges has developed a configurable GATK4 workflow 3.0 times faster than previous iterations. Following up on our initial push of the GATK4 workflow in 2017, and our recent update with the Broad’s Best Practices, we’ve worked …

Written by Vladimir Kovacevic, Teodora Aleksic, Jack DiGiovanna, Stefan Risteski

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