Link to shared Google Document: https://docs.google.com/document/d/1H2WqmmUixjXviumAAubU8YsFVbx8pBvOCrgos3zVqgQ/edit?usp=sharing

Dr. Freese and I came up with a few title ideas for various possible abstract topics. Ann Loraine, could you let us know what you think of these titles/topics for the abstract?

1. Using the Integrated Genome Browser to visually analyze sequencing data from public resources, such as NCBI and EBI, to consumer genomics data, such as Nebula Genomics; why everyone should view their data
2. Expanding human genome visualization resources - adding consumer genetics data to the Integrated Genome Browser
3. A new genome visualization resource for viewing consumer genomics data such as Nebula Genomics
4. The Integrated Genome Browser: a platform for visualizing and quality checking whole genome sequencing data
5. Visual analysis of RNA-Seq data in the Integrated Genome Browser; why every researcher needs to view their data

Current working versions of both abstracts can be found below.

Title #1: Visual analysis of RNA-Seq data in the Integrated Genome Browser; why every researcher needs to view their data
Abstract #1:
Next-generation sequencing has become a go-to tool in the research toolkit. However, as with any tool or experiment, it is important to validate the data that are produced. Though many tools quality check sequencing data at various steps in the pipeline, an often overlooked step is to simply visualize the data. The Integrated Genome Browser is an open-source, free to use desktop genome browser designed to visualize aligned next-generation sequencing data, such as RNA-Seq, in the context of an annotated reference genome. We demonstrate how to use newly added features in the Integrated Genome Browser to identify problematic data, with examples encountered from the early stages of a project all the way to data published in publicly available data repositories. These examples include, visualizing soft-clipped reads in an RNA-Seq experiment where the reads failed to split across introns, layering data from multiple replicates to identify point mutations that indicate sample switching at a sequencing facility, and viewing RNA-Seq data where the intron length parameter was not set correctly, leading to chromosome-spanning introns.

Title #2: A new genome visualization resource for viewing consumer genomics data
Abstract #2:
Direct-to-consumer genomics provide a way for individuals to learn about their genetic information in a simple, cost-effective manner. Many consumer genomics companies produce basic products for the consumer like ancestral overviews or health panels. However, these companies do not provide a way for the consumer to interactively visualize and explore their data. The Integrated Genome Browser (IGB) is a freely-available open-source desktop genome browser that supports fast navigation through data-rich genomic datasets, such as whole genome sequencing data, as well as short-read sequencing data containing single nucleotide polymorphisms (SNPs). IGB is configurable with support for layering multiple data sources onto an annotated reference genome and includes customizable “LinkOuts” to the web so users can find out more information about various features. We have also recently released the IGB App Store so that users can customize IGB with features important to them, such as adding the ability to visualize SNP panels. As of the latest release, IGB can display Compressed Reference-oriented Alignment Map (CRAM) files, often used by biotechnology and consumer genomics companies to reduce the size of the data they distribute. This distributed data can be viewed directly on the user’s own personal computer without the need to upload data online. Here, we demonstrate how to visualize consumer CRAM data with IGB, as well as how to use an IGB app to view SNP data.

Please see Dropbox folder for my versions of the abstracts:

Dropbox / IGB / Outreach / Conferences / 2024-ASHG / 2024-ASHG-Abstracts.docx

Update:

• Nowlan Freese and Ann Loraine made edits yesterday in-office
• decided to submit abstracts today after another look in the morning, using fresh eyes

Submitted abstracts:

Title #1: Visual analysis of RNA-Seq data in the Integrated Genome Browser; why every researcher needs to view their data
Abstract #1:
Next-generation RNA sequencing (RNA-Seq) is a widely used and powerful method for detecting gene expression and understanding gene function. RNA-Seq data processing pipelines involve many steps, with many parameter choices along the way. Producing and processing RNA-Seq data requires diligent quality control to catch or avoid mistakes. One of the best ways to avoid mistakes is to visually examine the RNA-Seq alignments in a genome browser. To make visual inspection of RNA-Seq alignments more effective and convenient, we added several new features to Integrated Genome Browser (IGB), an open-source, highly interactive and customizable computational tool users can download and install from the BioViz project website. Here, we demonstrate how to use these IGB features to identify problems in RNA-Seq data arising from experimental or data processing errors. Examples to be presented include: visualizing soft-clipped reads in an RNA-Seq experiment where the reads failed to split across introns, layering data from multiple replicates to identify point mutations that indicate sample switching at a sequencing facility, and viewing RNA-Seq data where the intron length parameter was not set correctly, leading to chromosome-spanning introns. By documenting instances where visualization in a genome browser helps expose and ultimately correct mistakes, we hope to convince researchers that genomic visualization is essential to a successful RNA-Seq experiment.

Title #2: Upcoming version of Integrated Genome Browser will better support visualizing and exploring personal genome sequence data
Abstract #2:
Direct-to-consumer genomic sequencing services are relatively inexpensive now, making them accessible for families and individuals to explore the health and ancestry implications of their own personal genomes. To help personal genome sequencing clients better understand their own data, we added new capabilities to the Integrated Genome Browser (IGB), a freely available open-source desktop genome browser that supports fast navigation through vast data scenes. IGB supports layering multiple data sources onto an annotated reference genome. It includes customizable “LinkOuts” to external Web sites, enabling users to easily navigate to external data sources with information about genes and polymorphisms. As of upcoming IGB version 10.1.0, IGB will be able to display genome sequence data imported from Compressed Reference-oriented Alignment Map (CRAM) files, used by genome sequencing providers to distribute data. Because IGB runs locally, CRAM files can reside on a user’s personal computer, without requiring prior upload to a server or website. We also developed an IGB App for formatting of SNP array data for display. By comparing whole-genome sequencing to SNP array data, users can better understand and sanity-check results.

Both abstracts have been submitted to the 2024 ASHG conference. The submission information and receipts can be found in:
Dropbox / IGB / Outreach / Conferences / 2024-ASHG

Closing ticket.

Dear Nowlan Freese:

This confirms that your abstract (2024-A-4015-ASHG Visual analysis of RNA-Seq data in the Integrated Genome Browser; why every researcher needs to view their data) has been ACCEPTED for a poster presentation at the 2024 American Society of Human Genetics Annual Meeting in Denver, CO, from November 5-9.

Dear Paige Kulzer:

This confirms that your abstract (2024-A-4091-ASHG Upcoming version of Integrated Genome Browser will better support visualizing and exploring personal genome sequence data) has been ACCEPTED for a poster presentation at the 2024 American Society of Human Genetics Annual Meeting in Denver, CO, from November 5-9.