Scientific posters

Saliva samples collected with OrageneTM devices and DNA extracted using Nanobind kits are a good alternative to blood for HiFi sequencing. High-throughput workflow from extraction using Nanobind HT kit through HiFi sequencing on the Revio system is available for saliva and blood samples.

Sawfish is a general-purpose structural variant (SV) caller for HiFi sequencing data. It has already been shown to provide best-in- class SV accuracy in both single-sample and joint-genotyping contexts1 . Sawfish2 adds depth-based CNV calling as a joint operation integrated with sawfish’s existing breakend-based SV calling methods.

Here, we combine IDT hybridization capture with PacBio full-length RNA sequencing for deep isoform characterization. We show that the new IDT xGen Hyb and Wash Kit v3 is compatible with the PacBio Kinnex full-length RNA kit and can achieve an on-target rate of 85%, increasing detection of low abundance isoforms by several thousand-fold.

Studies of structural variants (SVs) in large cohorts remain challenging due to high data volumes and imprecise breakpoints in low sequence complexity regions, such as tandem repeats. We developed SVX, a fast, memory-efficient SV merging tool implemented in Rust. SVX is in early development. It currently only works with Sawfish.

Despite advances in DNA sequencing, the causal mutations of many human diseases remain challenging to characterize with standard methods. The adoption of long-read sequencing can improve and simplify sequencing and analysis of these complex regions. The ability to detect methylation enables simultaneous generation of sequence- level and epigenetic data. We present new panel content for the PureTarget assay, which uses the CRISPR/Cas9 system to generate targeted sequencing libraries of native DNA, sequenced with long and accurate HiFi sequencing.

Here we apply PacBio HiFi to perform whole-genome sequencing of the newly described HG008 matched tumor- normal pair from the Genome in a Bottle (GIAB) consortium. 1 This reference sample includes an adherent, epithelial-like pancreatic adenocarcinoma (PDAC) cell line as the tumor material, with the matched normal obtained from adjacent duodenal and pancreatic tissue. We perform whole-genome sequencing of the tumor cell line and matched pancreatic normal tissue with PacBio HiFi, resulting in a more robust and comprehensive picture of somatic variation in this reference sample and contributing to the development of this novel benchmark.

The characterization of somatic variation, especially in complex genomic regions, is crucial for understanding the molecular drivers of cancer progression. Accurate PacBio long-read sequencing (HiFi) enables detection of all variant classes, from simple SNVs and INDELs up to complex structural variation, tandem repeats, and changes in epigenetic signatures. Complex and repetitive regions, while fully sequenced by HiFi reads, remain bioinformatically challenging, requiring tailored solutions. Here, we describe new tools to genotype understudied repetitive regions in cancer genomes, a task that has historically posed significant challenges for short-read sequencing.

In this proof-of-concept study, we demonstrate that high quality PacBio HiFi sequencing results can be obtained from DNA extracted from saliva collected in DNA Genotek Oragene devices and extracted using the Nanobind PanDNA or CBB kits.

StarPhase is a long-read pharmacogenomic diplotyper that provides highly accurate diplotype results from long-read observations, provides refined PGx diplotypes for GeT-RM benchmark samples, and generates full-length haplotype sequences and visualizations for complex pharmacogenes

Short tandem repeats (STRs) are DNA sequences composed of repetitions of 2 – 6 bp motifs. Expansions of STRs are the cause of over 60 monogenic diseases, including Huntington’s disease, fragile X syndrome, and amyotrophic lateral sclerosis1. In addition to their length, the pathogenicity of these STRs can be impacted by sequence composition, methylation status and mosaicism. One such example is the FMR1 repeat whose CGG repeat expansions are typically hypermethylated and where AGG interruption sequences can stabilize the repeat. Detecting all the characteristics associated with pathogenic repeat expansions traditionally required multiple assays, however high-accuracy long-read sequencing of unamplified DNA can resolve all these features in a single assay.

Targeted 16S sequencing is a cost-effective approach for assessing the bacterial composition of microbial communities. This is especially true for low bacterial biomass samples where amplicon sequencing is the best option. However, the high similarity between the 16S rRNA genes of related bacteria means that sequencing the entirety of the 16S gene (~1.5 kb) with high accuracy is essential for species- or strain-level characterization. Many recent comparative studies have shown that PacBio full-length (FL) 16S sequencing outperforms other sequencing methods for taxonomic resolution and data accuracy

Metagenome assembly of soil has been historically difficult using short reads. The combination of high species diversity and ultra-low relative abundances poses a challenge and requires a higher sequencing depth to achieve success. Here, we demonstrate that the amount of HiFi data from the high-throughput Revio system is sufficient to assemble high-quality MAGs in complex microbiomes such as wetland soil.

Here we describe our ocean genome laboratory workflow developed for processing marine vertebrates for HiFi sequencing on the PacBio Revio System. We outline methods optimised for High Molecular Weight (HMW) DNA extraction using the Nanobind PanDNA kit from various tissue types, our strategy for size selection, and the implementation of automated library preparation method using the Beckman Biomek i7 system.

Ovarian and endometrial cancers are the 4th highest (combined) cancer killer of Canadian women. In 2020, over 3000 women were diagnosed with an ovarian cancer, of which 75% were in the later stages. The goal of the DOvEEgene (Detecting Ovarian and Endometrial cancer Early using Genomics) project is to detect these cancers as early as the first stage through a low-cost, low invasiveness and widely available test, similar to what the Pap test has done for cervical cancers. In this assay, for each subject, an intra-uterine brush sample is collected along with a saliva sample. The genomic DNA is extracted from both these samples, captured using probes with a total size of 146.46 kb using SureSelect XT HS (see target design), sequenced at 20 million reads to a median DNA fragment depth of at least 80% at 1000x, and deduplicated using UMIs. In parallel, uncaptured libraries are also used for Low-pass whole genome sequencing (LP-WGS). Somatic and copy number variants are called, as well as germline variants for 10 genes, and microsatellite instability (MSI) status is determined for known microsatellite loci within the target region. Separately, clinical MSI testing is performed on each sample using a PCR-based assay. As the ability to detect early stage cancers relies on high sensitivity and specificity, we were interested in testing the PacBio Onso sequencing by binding (SBB) technology which promises much higher sequencing qualities and better performance in homopolymer regions, thus should potentially increase variant detection and MSI calling performance.

Liquid biopsy is revolutionizing the field of early cancer detection research through non-invasive detection of tumor DNA in the blood. However, existing liquid biopsy assays are limited in their sensitivity for ctDNA detection at low variant allele frequencies (VAFs). Here we describe the application of the PacBio Onso short-read sequencing system to help enable detecti