cfDNA papers 📚 NucPosDB database

Papers on cell-free DNA (#cfDNA). Maintained by @TeifLab. Also see @nucleosome_bot, @CTCF_papers, @DNAbinding, @TF_binding_bot @generegulation

[Teif Lab @TeifLab]

Nucleosome aficionados! Our new review "Nucleosome spacing across cell types, diseases, and ages" is out in NAR: https://t.co/Z1TgEYxBH8

A huge effort to pull together what we’ve learned about nucleosome spacing in many systems. Enjoy!
#nucleosomics #nucleosome #chromatin #cfDNA

[Teif Lab @TeifLab]

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

[Teif Lab @TeifLab]

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!

[Alex Wyatt @ResearchWyatt]

💡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

[Teif Lab @TeifLab]

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 https://t.co/tZyM0AAENU

[Teif Lab @TeifLab]

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

[Teif Lab @TeifLab]

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: https://t.co/wT5EuK5GmS

[Anirban Maitra @Aiims1742]

Based on the ECLIPSE trial, @US_FDA today approved the Guardant SHIELD blood test for #ColorectalCancer.
@matthewherper in @statnews
https://t.co/8F4TO9gmL9
See ECLIPSE data below & why individuals undergoing this assay should clearly understand - this is NOT a test for CRC PREVENTION (it has very low sensitivity for adenomas, including adenomas with high grade dysplasia, where sensitivity is in the low teens).
SHIELD is at best a test for DETECTION of CRC, and even in this setting, half to a third of Stage 1 cancers might be missed.
The full details are on this document that detail the FDA approval label accompanying SHIELD:
https://t.co/E34bZjDRZQ

[Andrew Beggs @adbeggs]

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

[Teif Lab @TeifLab]

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

[James Hadfield @coregenomics]

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.

[Teif Lab @TeifLab]

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!

[Ellen Heitzer @EllenHeitzer]

Read our perspective on how to surpass sensitivity limits in liquid biopsy https://t.co/9XC5ttmdpf

[cfDNA papers 📚 NucPosDB database @cfDNA_papers]

Keeping a track on leptomeningeal disease in non-small cell lung cancer: A single-institution experience with CNSideTM https://t.co/H6Qa996MPF

[cfDNA papers 📚 NucPosDB database @cfDNA_papers]

Plasma cell-free DNA as a sensitive biomarker for multi-cancer detection and immunotherapy outcomes prediction https://t.co/II7WVcDf87

[cfDNA papers 📚 NucPosDB database @cfDNA_papers]

Circulating free DNA and its potential in the diagnostics and therapy of malignant lymphoma https://t.co/ME3bjLv8VX

[cfDNA papers 📚 NucPosDB database @cfDNA_papers]

The role of microRNAs involved in the disorder of blood-brain barrier in the pathogenesis of multiple sclerosis https://t.co/WQ5EaY3tji

[cfDNA papers 📚 NucPosDB database @cfDNA_papers]

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

[cfDNA papers 📚 NucPosDB database @cfDNA_papers]

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

[cfDNA papers 📚 NucPosDB database @cfDNA_papers]

Liquid Biopsy: An Evolving Paradigm for Non-invasive Disease Diagnosis and Monitoring in Medicine https://t.co/N3nT5GEF2j