Fragmentomic cfDNA Patterns in Noninvasive Prenatal Testing and Beyond

Abstract

The release of fetoplacental cell-free DNA (cfDNA) into the maternal bloodstream opened up new avenues towards noninvasive prenatal testing (NIPT) for aneuploidies, hereditary DNA mutations and other pregnancy-related developmental disorders. Increasingly, cfDNA catches interest for its noninvasive screening value in other areas as well, including oncology. Although there are indications that cfDNA fragmentation is a non-random process, the etiology and different structural aspects of cfDNA are still not well known. The emerging field of cfDNA fragmentomics investigates the existence of tissue and disease specific cfDNA signatures and the chemistry and biology underlying the fragmentation process. This review sheds light on recent developments in cfDNA fragmentomics and illustrates their significance in NIPT improvement and beyond.We discuss aspects of fragment size distributions, epigenetic correlations and putatively enriched cfDNA fragment-end compositions. Combinatorial fragmentomic efforts have provided more insights into the roles of different enzymes that contribute to the fragmentation process in the tissue of origin and in the bloodstream. Altogether, these studies revealed multiple fragmentomic-related biomarkers that can be used to make noninvasive screening and other types of clinical use of cfDNA more robust, by raising its distinctive capacities. This includes multiple complementary approaches to determine the fetal fraction, a key determinant in NIPT. Furthermore, these developments translate to a better understanding of the encountered cfDNA patterns and will catalyze the expansion of screening possibilities in NIPT and beyond

In Vitro CRISPR-Cas12a-Based Detection of Cancer-Associated TP53 Hotspot Mutations Beyond the crRNA Seed Region

“…This study made use of cell culture medium to extract cell-free fragmented oligonucleosomal DNA that reflects size patterns as found in plasma DNA. 29 Such cfDNA mimics can be of good use in translational liquid biopsy research that requires cfDNA as input. As we demonstrated, these cfDNA mimics can be combined to simulate more complex allele compositions, which allowed us to approach different tumor fractions.…”

Noninvasive Prenatal Test Results Indicative of Maternal Malignancies: A Nationwide Genetic and Clinical Follow-Up Study

“…In the future, the emerging field of cfDNA fragmentomics offers possibilities to further link cfDNA and NIPT profiles to the tissue of origin. 32,33 In addition, for future studies, it might be interesting to apply bioinformatics tools such as ichorCNA to assess a correlation between the tumor fraction in cfDNA and the copy-number changes. 34 In conclusion, this study provides important insights into the management of a rare, but challenging group of pregnant women with a malignancy suspicious-NIPT result.…”

“…In the future, the emerging field of cfDNA fragmentomics offers possibilities to further link cfDNA and NIPT profiles to the tissue of origin. 32,33 In addition, for future studies, it might be interesting to apply bioinformatics tools such as ichorCNA to assess a correlation between the tumor fraction in cfDNA and the copy-number changes. 34…”

Minimal Residual Disease Monitoring in Radically Treated Non-Small Cell Lung Cancer: Challenges and Future Directions

“… 34 This technology has been in use for years in non-invasive prenatal testing due to the fragment length of fetal cfDNA being shorter than that of maternal cfDNA. 35 The DELFI assay (DNA evaluation of fragments for early interception) uses a machine learning model incorporating genome-wide fragmentation. The genome-wide pattern from an individual can be compared to reference populations to determine if the fragmentation pattern is likely healthy or cancer-derived.…”