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An Outstanding Year of SMRT Science: 2018 Publication Review

Thursday, December 27, 2018

Scientists were certainly sequencing with confidence in 2018, as evidenced by the number of significant and wide-ranging advancements made using SMRT Sequencing technology, several of which made the cover of high-impact journals. As the year draws to a close, we have taken this opportunity to reflect on the many achievements made by members of our community, from newly sequenced plant and animal species to human disease breakthroughs that even captivated the popular press.

 

“It’s been a phenomenal year for science. We are proud of our partners and honored that our technology is helping to drive such discovery across all fields of the life science.”

Jonas Korlach, Chief Scientific Officer

Human Biomedical Research

 

Our understanding of human health and disease increased with new population-specific genomes, breast cancer cell line variants, on-target mutagenesis of CRISPR-Cas9 editing and insights into genomic cDNAs and their potential role in in Alzheimer’s disease.

 

  • Work from A. Ameur et al. from Uppsala University, “De Novo Assembly of Two Swedish Genomes Reveals Missing Segments from the Human Grch38 Reference and Improves Variant Calling of Population-Scale Sequencing Data,” featured in Genes and on our blog
  • “Complex Rearrangements and Oncogene Amplifications Revealed by Long-read DNA and RNA Sequencing of a Breast Cancer Cell Line” by M. Nattestad et al. garnered lots of reads in Genome Research and on our blog
  • A study by scientists at the Sanger Institute, “Repair of Double-Strand Breaks Induced by CRISPR-Cas9 Leads to Large Deletions and Complex Rearrangements” in Nature Biotechnology (and our blog) added to the gene editing debate
  • Nature featured a “remarkable phenomenon” observed by Lee et al. in “Somatic APP Gene Recombination in Alzheimer’s Disease and Normal Neurons.”

Plant & Animal Sciences

Research in plant and animal genomes uncovered exciting biology, including a tiny animal with a huge genome that gave us a glimpse into tissue regeneration and great apes that are helping us better understand human evolution. In addition to big achievements from international consortiums such as the Vertebrate Genome Project, the Earth Biogenome Project, and the Sanger 25, we also shared in the sweet success of the sugarcane genome and explored architectural differences between maize and sorghum.

 

  • Nature’s report on “The Axolotl Genome and the Evolution of Key Tissue Formation Regulators” by S. Nowoshilow and colleagues around the world captured the attention of the popular press, and our blog
  • Kronenberg’s “High-Resolution Comparative Analysis of Great Ape Genomes” graced the cover of Science, and our blog
  • “Allele-defined Genome of The Autopolyploid Sugarcane Saccharum spontaneum L” by J. Zhang et al. was also a cover star, in Nature Genetics and our blog
  • Our RNA sequencing capabilities featuring the Iso-Seq method were nicely showcased in “A Comparative Transcriptional Landscape of Maize and Sorghum Obtained by Single-molecule Sequencing” by B. Wang et al. in Genome Research

Microbiology & Infectious Disease

From selfish symbiotic bacteria to HIV variants in the brain, we were enthralled by new views into the microbial world. In addition to the release of 3,000 bacterial genomes  by the UK’s National Collection of Type Cultures (NCTC), scientists also contributed new methods to distinguish between microbial genomes.

 

  • RL Brese et al. made important inroads in understanding why patients with HIV develop neurological disorders in their Journal of Neurovirology paper, “Ultradeep Single-molecule Real-time Sequencing of HIV Envelope Reveals Complete Compartmentalization of Highly Macrophage-Tropic R5 Proviral Variants in Brain and CXCR4-Using Variants in Immune and Peripheral Tissues,” also featured on our blog
  • AP Douglass et al. made a concerning discovery in their PLoS Pathogens paper “Population Genomics Shows No Distinction Between Pathogenic Candida krusei and Environmental Pichia kudriavzevii: One Species, Four Names,” also featured on our blog
  • Nature featured a discovery by Swiss researchers, with potential implications for insect control in other species, “Male-Killing Toxin in a Bacterial Symbiont of Drosophila,” also featured on our blog
  • Nature Biotechnology described a new method of sequence binning by researchers at Icahn School of Medicine at Mount Sinai, “Metagenomic Binning and Association of Plasmids with Bacterial Host Genomes Using DNA Methylation,” also featured on our blog

Did we miss one of your favorite publications of 2018? Tweet us @PacBio, using #PoweredbyPacBio. And check out our searchable publications database for more than 1500 examples of outstanding SMRT Science from 2018.

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