Webinars and Conference Talks

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ESHG 2021 – Samplix Corporate Session

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Long-read whole genome analysis of single human cells

Talk by DR. ADAM AMEUR, Uppsala University and Science for Life Laboratory (SciLifeLab), at ESHG 2021 Virtual.

Leveraging the unbiased droplet multiple displacement amplification (dMDA) step of Xdrop®, Dr. Ameur prepared long fragments of gDNA from a single cell for HiFi PacBio sequencing. 2.5 million reads per cell and up to 40% genome coverage revealed comparable numbers of SNV as seen with short-read sequencing, but four times as many structural variants. The method presented goes far beyond limits of current long-read sequencing protocols, which normally require at least 5 ng of input DNA.

Samplix Webinar – Pitfalls and best practices for CRISPR/Cas9-based gene editing

BENJAMIN SCHMID, Bioneer, and PETER MOURITZEN, Samplix

Another two-part webinar featuring a collaboration with Bioneer. Benjamin gives specific recommendations for planning a successful gene editing strategy in "Ten things you should think of when designing a good gene editing strategy". Then, Peter provides advice for subsequent validation of your edits in "How to ensure your gene editing validation accounts for larger unintended rearrangements."

Samplix Webinar – Certainty After CRISPR

PAUL ERIC BENNETT, COBO Technologies, and KEYI GENG, Karolinska Institute.

A two-part webinar discussing unanticipated alterations happening after gene editing and ways to detect and characterize expected and unexpected outcomes. In "Fast and sensitive detection of indels induced by precise gene targeting", Paul surveys the pros and cons of current InDel detection methods and how to choose the one that is fit for purpose. Keyi describes her detective work in uncovering and fully characterizing unexpected outcomes of a gene editing strategy in "Where did the target region go? Unravelling odd CRISPR/Cas9-induced genomic alterations in human cells."

Genome Editing Oxford 2021 Virtual

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Validation of Genome Editing Through Indirect Sequence Capture and Long-Read Sequencing

Talk by PETER MOURITZEN, Vice President Application and Market Development, Samplix, at Genome Editing 2021 Virtual.

• Methods commonly used to validate genome editing may fail to detect unintended modifications occuring during editing with considerable ramifications for results.
• By enriching long DNA fragments over and around the region of interest, the Xdrop® indirect sequence capture provided by Samplix® offers a novel high-resolution alternative validation.
• Show case: Xdrop-based validation reveals an unwanted alteration in an engineered human cell line.

Festival of Genomics 2021

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Identification of functional proteins densely co-encoded in the human genome

Talk by ALEX KHITUN, Postdoctoral Researcher at Harvard Medical School

  •  Description of small open reading frame (ORF)-encoded proteins
  •  Discovery via buttom-up proteomics of small ORF-encoded proteins overlapping RPL36
  •  Assessment of structure and function of these densely encoded proteins
  •  Validation of knockout cell lines using Xdrop®
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CRISPR validation and resolving complex genomics landscapes with Xdrop

Talk by PETER MOURITZEN, VP Application & Market Development at Samplix

  •  Indirect Sequence Capture of any genomic region: the Xdrop® microfluidics system
  • Validation of CRISPR edited cell lines detecting unintended kb-long insertions
  • Identification of integration sites and structural variation in transgenic mice
  • Reconstruction of complex genomic regions: CYP2D6 gene without confounding effects of pseudogenes
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Genomically humanized mouse models of neurodegenerative disease

Talk by TOM CUNNINGHAM, Senior Investigator Scientist at MRC Harwell

  • Engineering and studying a new generation of knock-in mouse models of motor neuron disease and frontal temporal dementia
  • Genomic humanisation refers to replacement of entire mouse genes with the human orthologous sequence
  • Allele QC is critical in order to accurately study the consequences of pathogenic mutations

NextGen Omics Nov 2020 Virtual

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Tackling Disease Related Repeat- Expansion Analysis By Xdrop® Indirect Sequence Capture

Talk by MARZIA ROSSATO, Researcher in Genetics, University of Verona, at the NextGen Omics conference 2020.

• The analysis of long DNA fragments provides consistent benefits in the characterization of clinically-relevant regions with challenging features, such as tandem repeats, structural variants, and high CG-content
• The Xdrop indirect sequence capture provided by Samplix® represents a flexible approach to enrich for long DNA fragments of interest and sequence them using either short or long reads
• Show case: Xdrop can be efficiently applied for the analysis of SNV, tandem repeat length and interruption in genes underlying neurological disorders

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Xdrop – Validation Of Correct CRISPR Gene Editing

Talk by PETER MOURITZEN, Vice President Application and Market Development, Samplix, at NextGen Omics conference 2020

The Xdrop concept of Indirect Sequence Capture allows on-target analysis of 40 kb or more of the genomic region surrounding gene editing sites
• Case study: Detection of unintended on-target editing in a set of IPS cell lines
• Additional strategies for targeted enrichment to analyse for CRISPR on- and off- target events, CRISPR knock-in and other transgene integration patterns

Samplix Webinar June 2020

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Samplix Webinar: Capture the dark genome: From repeat-expansions to CRISPR unintended mutations

PART 1 (01:30): Tackling Disease-Related Repeat-Expansion Analysis - Dr. Marzia Rossato, Researcher, Functional Genomic Lab, University of Verona, Italy

PART 2 (20:44): Validation of CRISPR in a 100 kb Region Surrounding the Editing Site - Dr. Peter Mouritzen, Application Development Services, Samplix, Denmark

PART 3 (37:50): The Launch of a Grant Program and Q&A