Fragmentomics: The characteristics of a large number of DNA fragments. Fragmentomics involves the measurement and analysis of fragment lengths and the characteristics of the ends of the fragments (e.g., having a blunt or jagged end or having a specific sequence at the end, called an “end motif ”) and the patterns of the different lengths and fragment characteristics. There is a correlation between methylation and fragment end motif. DNA fragments from circulating tumor DNA, which can be in the blood of a person with cancer or precancer, are shorter, have more jagged ends, and have a different distribution of specific end motifs than the circulating free DNA in the blood from normal cells, which is present in the blood of all persons regardless of whether they have a tumor. Fragmentomics is also used in the study of cell-free DNA in the plasma of pregnant persons and transplant recipients. To learn more about this NEJM Illustrated Glossary term, read “Cell-free DNA for Colorectal Cancer Screening” by Y.M. Dennis Lo, BM, BCh, DPhil, DM: https://nej.md/43noybx Explore more terms: https://nej.md/glossary
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Read our newest publication in Cancers, Cell state and cell type: Deconvoluting circulating tumor cell populations in liquid biopsies by multi-omics. Great work by Lisa Welter and team! #liquidbiopsy #tumormicroenvironment https://lnkd.in/dQXbyfKB Summary: In addition to millions of normal red and white blood cells, the blood of cancer patients contains a variety of very rare cell types associated with the tumor. A simple blood draw or ‘liquid biopsy’ can, thus, provide important information about the state of the disease no matter where it exists in the body. In this paper, we describe a method for imaging all rare cells in a blood draw and the means to define each cell type using a combination of genomic, proteomic, and morphological measurements to distinguish tumor cells from mesenchymal and endothelial cells that are present in the tumor microenvironment. We compare the results of this assay among multiple prostate and breast cancer patients and show that this cellular profiling method is valid across patients and cancer types and may provide important biomarkers for assessing disease in real time.
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Prostate cancer is the 5th leading cause of male cancer mortality and its diagnosis is typically carried out using a prostate-specific antigen (PSA) test followed by a conventional tissue biopsy. However, the PSA test has a low positive predictive value (~30%) and poor specificity, and tissue biopsy can be painful and prone to complications and sampling errors. New liquid biopsy techniques that use biological fluids have emerged as a more accurate, less expensive, and minimally invasive method. Urine in particular, has gained popularity as a powerful tool for the diagnosis and treatment monitoring in prostate cancer patients. (https://hubs.la/Q015PTnz0) Meridian’s new Air-Dryable™ Direct DNA qPCR and Direct RNA/DNA qPCR Urine mixes are inhibitor-tolerant mixes designed for very fast, ultra-sensitive amplification of DNA and RNA directly from high concentrations of urine. The mixes are glycerol-free, provided at 4x concentration, and can be air-dried to create ambient-temperature stable assays or used in a liquid format. To learn more visit: https://lnkd.in/g3XRwqnv
