cfDNA papers 📚 NucPosDB database
@cfDNA_papers
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Papers on cell-free DNA (#cfDNA). Maintained by @TeifLab. Also see @nucleosome_bot, @CTCF_papers, @DNAbinding, @TF_binding_bot @generegulation
Joined July 2019
Great to see that this preprint used our software NucTools to calculate NRL, and reached conclusions confirming our previous paper, which reported effect of linker histones H1 on cfDNA fragmentation patterns and nucleosome spacing in cancer tissues/cfDNA https://t.co/eaPqOWINHN
Excited to share our latest preprint by Alexis Yang and Gary Lee, in collab with the @jberchuck lab: https://t.co/cb3pRjketO. We found that transcription of enhancers (a mark of activation) causes distinct fragmentation patterns in #cfDNA.
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We have a postdoctoral opening for a researcher with experience in bioinformatics of DNA sequencing and machine learning to work on the development of new methods for cancer diagnostics related to nucleosomes, chromatin and more https://t.co/7btyVTeDR8. Apply by 21st April 2025!
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💡Will #ctDNA serve as a treatment response biomarker in metastatic cancers? Here’s a thorough evaluation in @CCR_AACR from the RECIST working group, looking at the next steps towards using ctDNA for novel early endpoints in clinical trials and beyond. 👉 https://t.co/VQmuHaWBTw
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Very happy to contribute to this paper about cfDNA in SCLC, led by the team of Anish Thomas. It's already online in Genome Medicine: Takahashi et al., Genomic alterations and transcriptional phenotypes in circulating free DNA and matched metastatic tumor
link.springer.com
Genome Medicine - Profiling circulating cell-free DNA (cfDNA) has become a fundamental practice in cancer medicine, but the effectiveness of cfDNA at elucidating tumor-derived molecular features...
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Interesting preprint on nucleosome spacing from cfDNA [Johnston et al., 2024] https://t.co/VNg6W2QPc0. The authors refer to NRL changes 10n -> 10n-5 bp. Earlier we showed that NRL decrease in cancer is more complex & context-specific [Jacob et al., 2024] https://t.co/eaPqOWINHN
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We have an opening for a three-year postdoctoral position for a researcher with expertise in machine learning and genome bioinformatics, to work on cancer diagnostics (liquid biopsies). Please apply here:
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Based on the ECLIPSE trial, @US_FDA today approved the Guardant SHIELD blood test for #ColorectalCancer. @matthewherper in @statnews
https://t.co/BXWWNfB1Yb See ECLIPSE data below & why individuals undergoing this assay should clearly understand - this is NOT a test for CRC
statnews.com
The FDA approved a blood test intended to detect colon cancer, which many experts hope will help catch cases of the disease early enough so that they can be more easily treated.
Two studies in @nejm on non-invasive detection of #ColorectalCancer 1: Blood based cfDNA assay (@GuardantHealth) https://t.co/qehcJM02d5 2: Stool based multi target DNA test (@ExactSciences). A🧵 on comparative numbers 👉🏽 Sensitivity for ALL CANCER Dx: cfDNA: ~83%; Stool:
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Interesting news from @GrailBio trial in the UK - accuracy in the article given as 56% One of the main issues I think with Galleri is its model trained on late stage disease, and is a “fixed” panel. We need broader WG assays trained on early disease https://t.co/gYTaIffHgd
hsj.co.uk
NHS England has decided not to extend the use of a high-profile emerging cancer screening technology, casting further doubt on its target to improve early detection.
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Our paper on nucleosome repositioning in breast cancer is now published in Clinical Epigenetics! https://t.co/nCEWTcRzPO ▶️Nucleosome gain marks deregulated TFs ▶️Shorter distances between nucleosomes in cancer ▶️NRL affected by gene expression, methylation, H1 histones, repeats
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Read the latest from @enseqlopedia on my blog: https://t.co/JBTDYPfQYr Priming agents to increase cfDNA levels for #liquidbiopsy by @broadinstitute @MIT
@OmicsOmicsBlog @AlbertVilella @SanDiegOmics @mehtamanal this is some pretty #coolscience I know you'll be interested in.
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Excited to present the first ageing clock based on nucleosomics of cell-free DNA (cfDNA)! https://t.co/f2XmODzbA2 ✅ Nucleosome repeat length increases with age ✅ Can predict age with ~3 year precision Congrats to @MShtumpf, @nrnflowers, @Milena_Bikova, @hulkar_m, @LumiRuje!
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Read our perspective on how to surpass sensitivity limits in liquid biopsy
science.org
Attenuation of cell-free DNA clearance in vivo is an alternative strategy to maximize recovery
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Keeping a track on leptomeningeal disease in non-small cell lung cancer: A single-institution experience with CNSideTM https://t.co/H6Qa996MPF
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Plasma cell-free DNA as a sensitive biomarker for multi-cancer detection and immunotherapy outcomes prediction https://t.co/II7WVcDf87
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Circulating free DNA and its potential in the diagnostics and therapy of malignant lymphoma https://t.co/ME3bjLv8VX
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The role of microRNAs involved in the disorder of blood-brain barrier in the pathogenesis of multiple sclerosis https://t.co/WQ5EaY3tji
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Comprehensive Genomic Analysis of Patients With Non-Small-Cell Lung Cancer Using Blood-Based Circulating Tumor DNA Assay: Findings From the BFAST Database of a Single Center in Taiwan https://t.co/iGPPzmn672
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Exploratory Biomarker Analysis Using Plasma Angiogenesis-Related Factors and Cell-Free DNA in the TRUSTY Study: A Randomized, Phase II/III Study of Trifluridine/Tipiracil Plus Bevacizumab as Second-Line Treatment for Metastatic Colorectal Cancer https://t.co/Dzzj9W8oL2
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Liquid Biopsy: An Evolving Paradigm for Non-invasive Disease Diagnosis and Monitoring in Medicine https://t.co/N3nT5GEF2j
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Serum Cell-free DNA-based Detection of Mycobacterium Avium Complex Infection https://t.co/tnsV5D6ojc
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