cfDNA

Joint Fragmentomic and Methylation Signatures of cfDNA for Cancer Detection by Billy Lau at London Calling 2024

Billy Lau from Stanford University returned to London Calling 2024 and spoke about “Joint fragmentomic and methylation signatures of cfDNA for cancer detection.” They began by defining liquid biopsies for non-invasive cancer measurement as typically being blood draws used for sequencing and multi-omic analyses. They also explained how epigenetic reprogramming in cancer occurs and how […]
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Methylomics and Fragmentomics: Pioneering Cancer Detection Models

Hanlee Ji from Stanford University presented at London Calling 2024 on “Genomic sequencing for characterizing tumor minimal residual disease versus early cancer.” Ji spoke about apoptosis and circulating tumor DNA. Ji and the team evaluated the recurrence of metastatic colorectal cancer with circulating DNA monitoring. Early detection of breast cancer can benefit from nanopore sequencing […]
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Epstein-Barr Virus and Methylation Patterns

Christopher Oakes from The Ohio State University spoke at London Calling 2019 on “Discerning the origin of Epstein-Barr virus in patients using nanopore-derived DNA methylation signatures.” Oakes spoke about how they study tumor viruses and cancer. The Epstein-Barr virus is common, the “prototypical cancer virus,” according to Oakes. Immune cells suppress the virus, but the […]
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Cell-free DNA for Methylation-based Diagnostics

Billy Lau from Stanford University School of Medicine spoke at the Nanopore Community Meeting in Houston about “Nanopore sequencing of cell-free DNA for methylation-based breast cancer detection.” I have watched Lau speak at other ONT events. This session was about a research study to improve cancer detection. Lau spoke about breast cancer detection issues. Liquid […]
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Multi-modal Liquid Biopsy Analysis in Children with Cancer

Tonight I watched the London Calling 2023 session entitled “The potential application of nanopore sequencing for liquid biopsy analysis in children with cancer.” The second speaker was Carolin Sauer, a public research fellow at EMBL-EBI in the UK. Sauer focused on pediatric cancers and noted that they are the leading cause of death in the […]
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Deconvoluting Methylomes with Nanomix

Tonight I started watching videos from London Calling 2023! I started with the presentation by Jonathan Broadbent from the Ontario Institute for Cancer Research & the University of Toronto, Canada. Broadbent presented about “Nanomix: methylation-based cell-type deconvolution for low-pass nanopore sequencing.” They defined cell-free DNA (cfDNA) as “a mix of DNA from blood cells and […]
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CyclomicsSeq

jeroen de Ridder from Cyclomics and the University Medical Center Utrecht in the Netherlands presented “CyclomicsSeq: targeted and genome-wide detection of circulating tumor DNA using nanopore consensus sequencing” at London Calling 2022. They spoke about monitoring of treatment response and disease recurrence and avoiding invasive procedures. For this, they focused on cell-free tumor DNA: cfDNA […]
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You can’t sequence what you don’t have!

Tonight I continued watching masterclass sessions from the 2022 London Calling event. Vania Costa is an Applications Scientist with Oxford Nanopore Technologies and presented a masterclass on “Preparation: extracting high-quality DNA and RNA.” They spoke about pre-lab considerations, sample storage, DNA and RNA extraction, sample quality control, and several case studies. Pre-lab considerations mentioned by […]
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Methylation Profiles of Cell-Free DNA in Cancer Research

Billy Lau from Stanford University School of Medicine spoke at the Nanopore Community Meeting 2022. Lau’s 20-minute session was entitled “Single molecule methylation profiles of cell-free DNA in cancer with nanopore sequencing.” The study had the goal of exploring the “potential utility of nanopore sequencing for assessing cancer in cfDNA.” Lau explained that the conventional […]
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