Genomics Archives - Canadian Centre for Computational Genomics

Research Spotlight: Optimal Sequencing Strategies for Human Genome Variant Detection

Designing a sequencing project? A recent Genome Biology study offers a practical framework for choosing the right technologies based on your budget and research objectives.

Accurately identifying every genetic variation in the human genome is essential for both research and clinical applications. This Genome Biology study brings together expertise from the Canadian Centre for Computational Genomics (C3G) (Robert Eveleigh, Jose Hector Galvez, Mathieu Bourgey, and Guillaume Bourque) and the Advanced Genomic Technologies Laboratory (Sarah Reiling and Jiannis Ragoussis) to benchmark state-of-the-art sequencing platforms and variant detection approaches across both small and large variant classes.

Methodology

Using the Genome in a Bottle (GIAB) HG002 reference sample, the team systematically compared short-read (SRS; Illumina, MGI) and long-read (LRS; PacBio Sequel/Revio, ONT R9/R10) technologies against Telomere-to-Telomere (T2T) and Clinically Medically Relevant Genes (CMRG) benchmarks, spanning a range of sequencing depths, genomic contexts, and bioinformatic pipelines.

Findings

Their findings confirm that platform and workflow selection should be driven by research objectives. SRS excels at identifying small variants in well-mapped regions, while LR, particularly PacBio Revio, delivers superior accuracy for structural variants and small variants in complex or repetitive regions, achieving accuracy saturation at markedly lower sequencing depths (20–45×) than short-reads (>60×).

While SRS remains a practical choice for high-throughput genotyping, LRS provides the resolution required for clinical applications at challenging loci.

Learn More

To stay current with the latest algorithms, technologies, and benchmarking practices, C3G also maintains a live dashboard!

Read the full article

A beginner’s Guide to Manual Curation of Transposable Elements

In the study of transposable elements (TEs), the generation of a high confidence set of consensus sequences that represent the diversity of TEs found in a given genome is a key step in the path to investigating these fascinating genomic elements.

C3G Bioinformatics Platform at the Rosalind and Morris Goodman Cancer Institute

With next-generation sequencing and other high-throughput technologies revolutionizing life sciences and health care research, data processing and interpretation, rather than data production, has become the major limiting factor for discovery and innovation. Large genomics centers, and increasingly smaller research labs, are facing significant data analysis challenges.

Gene fusion meta-calling with MetaFusion

The Toronto Node of C3G has developed MetaFusion, a flexible meta-calling tool that amalgamates outputs from any number of fusion callers. Designed to overcome inconsistencies among frequently used fusion callers, MetaFusion is among the first ensemble fusion calling tools currently available.

Working with Genomics Coming From a Pure Software Engineering Background

While pursuing a Bachelor of Science in Software Engineering at McGill University, I joined the Canadian Centre for Computational Genomics as an intern in 2020. I started working at the C3G with no background whatsoever in the field of computational genomics.

Understanding why persons living with HIV are at increased risk of tuberculosis

Persons living with HIV (PLWH) are at increased risk of tuberculosis (TB). HIV-associated TB is often the result of a recent infection with Mycobacterium tuberculosis (Mtb) followed by rapid progression to the disease.

A Coordinated Progression of Progenitor Cell States Initiates Urinary Tract Development

Oraly Sanchez-Ferras from the Goodman Cancer Research Centre recently published a paper in Nature Communications. She reveals how the formation of tissues proceeds through a progression of different progenitors.

New study analyzes different mechanisms in the establishment of sex-phenotype dependent methylation in mouse livers

Recently, using mice with different combinations of genetic and phenotypic sex, we were able to identify sex-associated differentially methylated regions (sDMRs) that depended on the sex phenotype (see this related study).

How do jumping genes contribute to human diversity?

In recognition of Transposons Day 2021 (June 16th), let’s take a look at the importance of active mobile genomic elements (once called “junk DNA”) to human health and diseases.

Why better Data Sharing means better health Care

Guillaume Bourque and Yann Jolly sitting together

Using big data techniques to analyze the function of human genes is already helping develop treatments tailored to individual patients. The more data researchers can access from across the world, the better chances of treating even rare diseases. But privacy and consent regulations differ by country, making sharing this information across borders slow and frustrating.

Data sharing Health care