Got an impossible polyploid or highly repetitive plant gene, or perhaps an enormous fungal genome or complex microbial community? Have an impossible dream of cracking pandemic, epidemic & endemic biology, or uncovering neurological disorders and rare diseases?
What was once impossible has become possible with HiFi Sequencing, scientists heard at the 2021 PacBio Global Virtual User Meeting.
The event, “HiFi Sequencing: Around the World in 24 Hours,” featured 32 speakers and 22 panelists from every region of the globe, covering human biomedical research, plant and animal sciences, and microbiology and infectious disease. There were also Ask the Experts sessions and panel discussions about trending topics, such as the COVID-19 pandemic.
If you missed it, it is now available for on-demand viewing, and here are some highlights:
When genomics gets tough, the tough get HiFi: more stories of HiFi enabled science
Keynote speaker Jeremy Schmutz of HudsonAlpha and the Joint Genome Institute discussed some of the most difficult genomic challenges he and his colleagues face, including “the known hard stuff” like the FCGR region of the human immune system, an enormous 1.17 Gb ‘zombie’ fungi, and the gigantic, super complex polyploid 10 Gb, 130 chromosome sugarcane.
Want to know how to get to the ultimate genome? Schmutz’s advice: Start with good DNA. Sequence with HiFi. Add Hi-C, assembly curation, and polishing. Use RNA sequencing for annotation.
Unravelling the mysteries of sex determination in reptiles using HiFi sequencing
The bearded dragon lizard, Pogona vitticeps, is an increasingly popular model organism with a unique sex determination, shaped by both genotype and temperature. In his talk, Ira Deveson of the Kinghorn Centre for Clinical Genomics at the Garvan Institute of Medical Research discussed how he used PacBio HiFi sequencing for genome assembly, phasing, and isoform profiling to elucidate the mechanisms of reptile sex determination.
Rapid, accurate surveillance of SARS-CoV-2 variants across the commonwealth of Kentucky
At the University of Louisville Sequencing Technology Center, Melissa Smith (@SmithLab_UofL) was able to create nearly complete genomes for several lineages of SARS-CoV-2 circulating in Kentucky at the end of 2021, including Beta, Gamma, and Delta, using an early access version of the new PacBio HiFiViral Kit. The new HiFiViral kit enables researchers to see a more comprehensive view of viral variation of all types and enables laboratories to identify viral mutations of all kids. Out of 646 samples run with the early access HiFiViral Kit, she saw 80% genome completion; previous methods had yielded complete genomes in only about 50% of cases, she said at the summit. She noted that she appreciated the protocol’s high multiplexing capacity (384 samples at a time in her lab), reduced hands-on time (by about 80%), and the end-to-end kitted solution, allowing her to avoid having to source reagents from multiple different vendors (especially during the pandemic, when supply chains have at times been unreliable). Melissa now intends to use the HiFiViral Kit to sequence more than 7,000 samples as part of a statewide virus surveillance effort.
Increased risk of severe clinical course of COVID-19 in carriers of HLA-C*04:01
Bettina Heidecker and Phillip Suwalski of Charité Universitätsmedizin Berlin presented their research investigating HLA as a risk factor for COVID-19. Adjusting for other known confounding factors such as age, BMI, and sex, their data suggests that HLA-C* 04:01 increases susceptibility to SARS-CoV-2 and risk for severe course of COVID-19; the results were reproduced in GWAS data of 7,796 cases and 875,694 controls. HLA typing on the Sequel System also helped contribute to an improved understanding of the pathophysiology of COVID-19.
Characterization of HBV integration patterns with HiFi long reads
How does the hepatitis B virus (HBV) induce hepatocellular carcinoma (HCC), the most common type of primary liver cancer? Professor Kai Ye of Xi’an Jiaotong University explained how he conducted a genome-wide analysis of HBV cell lines and clinical samples and characterized novel recurrent genome rearrangement types associated with HBV integration, finding that different DNA repair mechanisms activated by virus integration were the major cause of virus-specific genome rearrangements.
A new era for marine microbial research
Taylor Priest (@taylorpriest2) of the Max Planck Institute for Marine Microbiology talked about the value of HiFi sequencing in his study on the ecology of microbial communities in arctic marine ecosystems, particularly microbial carbon degradation. One of the most important, but also the most difficult, aspects of elucidating the ecology of microbial populations is accurately linking phylogeny and function, he said. Using HiFi reads and the PacBio ultra-low input library prep protocol, Priest was able to recover a higher quantity and quality of metagenome assembled genomes (MAGs). And with several complete genes obtained per read, genes could be functionally annotated for community-level analysis without any assembly required.