PacBio - Monthly Newsletter (July)

pacbio_shortlogo_color_rgb-01.jpgWelcome to the PacBio News and Events Update!


Events

Webinar: SMRT Sequencing Application for Human Genomics and Medicine

Date: Wednesday 8th July, 2020
Time: 5:00pm AEST

adam-ameur.jpeg Special Guest Speaker:

Adam Ameur, Ph.D.
Associate Professor and Senior Bioinformatician, SciLifeLab, National Genomics Infrastructure, Sweden

Abstract:

At SciLifeLab, Uppsala University, we have for a long time been developing new SMRT sequencing applications for medical diagnostics and human genetics research. This includes many different types of projects, from sequencing of single genes to de novo assembly of complete human genomes. My presentation will give an overview of some of our key developments, including a new method to study CRISPR-Cas9 off-target effects using long reads.

Highlighted Publications:

  1. Amplification-free long read sequencing reveals unforeseen CRISPR-Cas9 off-target activity. Höijer I, Johansson J, Gudmundsson S, Chin CS, Bunikis I, Häggqvist S, Emmanouilidou A, Wilbe M, den Hoed M, Bondeson ML, Feuk L, Gyllensten U, Ameur A. bioRxiv 2020.02.09.940486.
  2. Single-Molecule Sequencing: Towards Clinical Applications. Ameur A, Kloosterman WP, Hestand MS. Trends Biotechnol. 2019 Jan;37(1):72-85.

Register Now




Research Highlights

Seriously Good Methods - Using Xdrop - A Long Range DNA Capture Technology for Long Read Sequencing

Xdrop has jumped on the scene recently to be used together with SMRT Sequencing. Check out the recent publication on Xdrop technology and how it was used with SMRT sequencing in solving viral integration sites for HPV.
View Publication

Also check out this recorded webinar where Adam Ameur, the lead researcher, where he talks about the technique
View Recording

Lastly, be sure to attend our upcoming webinar where Adam Ameur will be discussing, as one of the many topics, how they use Xdrop for clinical cases together with SMRT Sequencing. See details in the Events section above!
Register now!



Celebrating 10 Years of Direct DNA Modification Detection

Ten years ago this month, Benji Flusberg et al. 2010 showed that SMRT sequencing can detect a DNA modification.  PacBio data continues to have this feature because the methylation event causes a little lag in the nucleotide incorporation by our polymerase.

graph.pngFast-forward to 2020 and 2 recent publications harness this same phenomenon to study chromatin and transcription factor states in humans at the single molecule level.  The trick is that they treat the chromatin-packaged genome with a methyltransferase enzyme, then use SMRT sequencing to read out the sequences in the genome where the enzyme can access dsDNA and leave behind a methyl group.

  1. Stergachis et al. call this type of chromatin profiling, Fiber-seq, and they use it to infer regulatory elements, nucleosome positioning and transcription factor occupancy amongst chromatin fibers.  The average fiber they read with the is over 10kb!
  2. Ardulhay et al. uses the same concept for methyltransferase accessibility of the genome and adds in another -omic measurement, nuclease accessibility. This lets them tease apart "oligonucleosomes", a one of the units of chromatin.  These authors came up with the tasty acronym SAMOSA for Single molecule Adenine Methylated Oligonucleosome Sequencing Assay.


A Comprehensive View of the Soybean Genome (the pangenome)

There was recently a fantastic paper that came out titled "Pan-Genome of Wild and Cultivated Soybeans" in Cell. It's a very comprehensive look at variation within the soybean genome. They sequenced and assembled 26 different cultivars using PacBio, created a graph-based pangenome for mapping resequencing data, identified thousands of structural variants and dozens of gene fusions, and linked variants to agronomically important traits. Having a comprehensive view of a species' genome (the pangenome) enables better understanding of biology - Read about the many interesting biological findings they presented.

Hope you all enjoy this paper as much as we did.

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Genome in a Bottle Consortium Releases Structural Variant Calling Benchmark Data

genome-in-a-bottle.pngPacBio sequencing technology is featured in this GenomeWeb article, which highlights a new Structural Variant Calling Benchmark available for human genome Reference Material from the U.S. National Institute of Standards and Technology (NIST).
Read the Blog Post Now




Spotlight on Microbiology and Infectious Disease

Missing your favourite microbial conference? Check out some terrific microbiology talks from our recent virtual SMRT Leiden conference and a Shoreline Biome poster from AGBT, minus the jet lag and sore feet. Then take in the big picture with an editorial on methylation research.

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SMRT Leiden: A HiFi view of cow and sheep microbiomes
Listen to the Talk Now!

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A plan for taking on bacterial epigenetics
Hear a Perspective Now!

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Beyond phage defense: The C. difficile epigenome
Watch the Poster Presentation Now!

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Using 16S+ITS to understand the microbiome and sepsis
Learn a Method Now!




PacBio Updates

SMRT Sequencing Datasets Webpage

You can now find all Sequel II datasets released by PacBio on one webpage! This includes applications in Whole Genome Sequencing, RNA sequencing, Targeted Sequencing and Complex Populations. Older datasets are still available on DevNet.



2020 Plant and Animal Sciences SMRT Grant Program

The 2020 Plant & Animal Sciences SMRT Grant and program website has gone LIVE!

Click here to find out more!



New DNA Resource

We are pleased to let you know we have a new Technical Note that focuses on DNA extraction and QC.

View the Tech Note Now!




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