ArticleBMC genomics2019
A ligation-based single-stranded library preparation method to analyze cell-free DNA and synthetic oligos.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed, 86 citations in OpenAlex.
- Fragmentation patterns of human telomeric chromatin in plasma cfDNA.Nature communications · 2026Article
- Three thousand five hundred years of sheeppox virus evolution inferred from archaeological and codicological genomes.Science advances · 2026Article
- Biological basis and clinical translation prospects of circulating cell-free DNA in precision management of breast cancer (Review).Oncology letters · 2026Review
- Holistic determination of ends of cfDNA molecules.Cell genomics · 2026Article
- End-repair causes methylation underestimation in cell-free DNA sequencing libraries.The journal of liquid biopsy · 2026Article
- Cell-Free DNA-Based Methods to Map Chromatin.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Hidden in the woods: A new species ofZooKeys · 2026Article
- A novel one-step multiplex PCR method (OS-MPCR) for efficient NGS library preparation in cancer.PloS one · 2026Article
- Direct measurement of sub-kilobase chromatin structure reveals that linker histone H1 broadly compacts chromatin, with differential impact amongst epigenetic states.bioRxiv : the preprint server for biology · 2025Article
- Bacterial cell-free DNA profiling reveals the co-elevation of multiple bacteria in newborn foals with suspected sepsis.iScience · 2025Article
- Expanding the Genome in a Bottle Truth Set: Detection and Validation of Novel Low-frequency Variants Using High-accuracy NanoSeq.bioRxiv : the preprint server for biology · 2025Article
- Wide-spectrum profiling of plasma cell-free RNA and the potential for health-monitoring.RNA biology · 2025Article
- Pliocene Forest Fragmentation Shaped Speciation in Tropical Asia's Giant Squirrels (Ratufa).Molecular ecology · 2025Article
- Whole-genome profiling of age- and sex-associated DNA methylation signatures in human plasma cell-free DNA.Communications medicine · 2025Article
- Fragment end motif analysis to distinguish pathogens from contaminants in enriched plasma microbial DNA.medRxiv : the preprint server for health sciences · 2025Article
- Circulating Cell-free DNA Fragmentomics Detection and Beyond.Aging and disease · 2025Review
- Uncovering new lineages in the Sunda pangolin (Biology letters · 2025Article
- Article
- Single-stranded pre-methylated 5mC adapters uncover the methylation profile of plasma ultrashort Single-stranded cell-free DNA.Nucleic acids research · 2024Article
- Can novel methods replace the gold standard chimerism method after allogeneic hematopoietic stem cell transplantation?Annals of hematology · 2024Review
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Authors and funding
9 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundCell-free DNA (cfDNA), present in circulating blood plasma, contains information about prenatal health, organ transplant reception, and cancer presence and progression. Originally developed for the genomic analysis of highly degraded ancient DNA, single-stranded DNA (ssDNA) library preparation methods are gaining popularity in the field of cfDNA analysis due to their efficiency and ability to convert short, fragmented DNA into sequencing libraries without altering DNA ends. However, current ssDNA methods are costly and time-consuming.
resultsHere we present an efficient ligation-based single-stranded library preparation method that is engineered to produce complex libraries in under 2.5 h from as little as 1 nanogram of input DNA without alteration to the native ends of template molecules. Our method, called Single Reaction Single-stranded LibrarY or SRSLY, ligates uniquely designed Next-Generation Sequencing (NGS) adapters in a one-step combined phosphorylation/ligation reaction that foregoes end-polishing. Using synthetic DNA oligos and cfDNA, we demonstrate the efficiency and utility of this approach and compare with existing double-stranded and single-stranded approaches for library generation. Finally, we demonstrate that cfDNA NGS data generated from SRSLY can be used to analyze DNA fragmentation patterns to deduce nucleosome positioning and transcription factor binding.
conclusionsSRSLY is a versatile tool for converting short and fragmented DNA molecules, like cfDNA fragments, into sequencing libraries while retaining native lengths and ends.
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