epiAneufinder: Single-cell ATAC-seq CNAs
Summary
EpiAneufinder is a novel algorithm designed to decipher genome-wide copy number alterations (CNAs) from single-cell open chromatin data, specifically scATAC-seq, enabling the examination of CNA variability in individual cells. Through its application to various cancer datasets, epiAneufinder adeptly reveals the intratumor clonal diversity among single cells based on their CNAs. Impressively, the CNA profiles identified by this method align well with the findings from single-cell whole genome sequencing of the same samples. This means epiAneufinder offers a unique way to uncover certain genomic variations without necessitating extra experiments.
Research Criteria
In the study, they present a method called "epiAneufinder" designed to detect single-cell genomic variations using scATAC-seq data. Through a unique combination of binary segmentation and a specific distance metric, this method pinpoints potential genome breakpoints. This procedure determines increases or decreases within these segments. Impressively, "epiAneufinder" can analyze scATAC-seq data without relying on a standard euploid sample or incorporating additional data types.
Result—epiAneufinder Algorithm
The epiAneufinder algorithm, an avant-garde computational tool, meticulously segments the genome into distinct regions, delineating gains, losses, and standard copy numbers at a single-cell granularity. Utilizing scATAC-seq data, it employs read counts as an indicative measure of DNA copy presence within specific genomic locales. To surmount the inherent coverage paucity of single-cell sequencing, the algorithm strategically bins the genome into uniform windows, typically set at 100,000 bp, whilst excluding regions with known mappability biases. Post data refinement, epiAneufinder harnesses the power of binary segmentation, a nuanced technique pinpointing shifts in data distribution. This process identifies genomic regions where variations in read distribution manifest, leveraging the Anderson–Darling distance as a metric of distribution congruence. Conclusively, each genomic segment is astutely categorized into states of gain, loss, or normalcy, based on nuanced read count analyses. The algorithm's output, a testament to its precision, includes detailed single-cell karyotypes and clustering results, offering invaluable insights into genomic intricacies.
Fig.1 epiAneufinder algorithm1.
Result—Other Single-Cell CNA Calling Methods are Outperformed by epiAneufinder
In an intricate evaluation of single-cell CNA calling methodologies, epiAneufinder emerges as a superior algorithm, especially when juxtaposed with other contenders in the realm of scRNA-seq and scATAC-seq data analysis. When scrutinized against datasets from various cell lines, including SNU601, HCT116, and Colo320, epiAneufinder consistently demonstrated a higher correlation with scWGS or WGS results. Specifically, in the SNU601 cell line, while the best scRNA-seq method, InferCNV, achieved a correlation of 0.61, epiAneufinder, representing scATAC-seq methods, boasted a more impressive correlation of 0.86. Furthermore, epiAneufinder's prowess was evident when contrasted with Copy-scAT, another scATAC-seq method, particularly in the SNU601 cell line, where it exhibited a superior correlation with WGS results (0.86 vs. 0.74). This comprehensive assessment unequivocally positions epiAneufinder as a more precise reflection of WGS outcomes, underscoring its preeminence in the domain of CNA detection.
Fig.2 Performance evaluation1.
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Single Cell ATAC Service
Creative Biolabs proudly provides a diverse array of bespoke, top-tier solutions within single-cell ATAC profiling to champion global scientific exploration. Delving into chromatin accessibility for gene regulation at the individual cellular tier holds the promise of profound insights into intricate mechanisms. Our offerings are meticulously crafted to align seamlessly with your unique research requisites, guaranteeing the utmost in quality outcomes. Through our single-cell ATAC profiling offerings, we wholeheartedly commit ourselves to propelling the frontiers of scientific inquiry and enlightenment.
Learn moreAt Creative Biolabs, our dedicated team offers an extensive array of bespoke, top-tier solutions in single-cell ATAC profiling, catering to the diverse needs of global scientific endeavors. Delving into gene regulation with meticulous scrutiny at the individual cellular echelon via chromatin accessibility analysis unveils profound insights into the intricate mechanisms orchestrating cellular function.
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Reference
- Ramakrishnan, Akshaya, et al. "epiAneufinder identifies copy number alterations from single-cell ATAC-seq data." Nature Communications 14.1 (2023): 5846.
