Rossa W. K. Chiu
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View article: Fragmentation landscape of cell-free DNA revealed by deconvolutional analysis of end motifs
Fragmentation landscape of cell-free DNA revealed by deconvolutional analysis of end motifs Open
Cell-free DNA (cfDNA) fragmentation is nonrandom, at least partially mediated by various DNA nucleases, forming characteristic cfDNA end motifs. However, there is a paucity of tools for deciphering the relative contributions of cfDNA cleav…
View article: Fragment Ends of Circulating Microbial DNA as Signatures for Pathogen Detection in Sepsis
Fragment Ends of Circulating Microbial DNA as Signatures for Pathogen Detection in Sepsis Open
Background Nuclear-derived cell-free DNA (cfDNA) molecules in blood plasma are nonrandomly fragmented, bearing a wealth of information related to tissues of origin. DNASE1L3 (deoxyribonuclease 1 like 3) is an important player in shaping th…
View article: Comparison of Single Molecule, Real-Time Sequencing and Nanopore Sequencing for Analysis of the Size, End-Motif, and Tissue-of-Origin of Long Cell-Free DNA in Plasma
Comparison of Single Molecule, Real-Time Sequencing and Nanopore Sequencing for Analysis of the Size, End-Motif, and Tissue-of-Origin of Long Cell-Free DNA in Plasma Open
Background Recent studies using single molecule, real-time (SMRT) sequencing revealed a substantial population of analyzable long cell-free DNA (cfDNA) in plasma. Potential clinical utilities of such long cfDNA in pregnancy and cancer have…
View article: Epigenetic analysis of cell-free DNA by fragmentomic profiling
Epigenetic analysis of cell-free DNA by fragmentomic profiling Open
Cell-free DNA (cfDNA) fragmentation patterns contain important molecular information linked to tissues of origin. We explored the possibility of using fragmentation patterns to predict cytosine-phosphate-guanine (CpG) methylation of cfDNA,…
View article: <i>Clinical Chemistry</i>’s Invited Reviewers 2022
<i>Clinical Chemistry</i>’s Invited Reviewers 2022 Open
Journal Article Clinical Chemistry’s Invited Reviewers 2022 Get access Clinical Chemistry, Volume 68, Issue 12, December 2022, Pages 1585–1586, https://doi.org/10.1093/clinchem/hvac181 Published: 06 December 2022 Article history Received: …
View article: Fragmentomics of urinary cell-free DNA in nuclease knockout mouse models
Fragmentomics of urinary cell-free DNA in nuclease knockout mouse models Open
Urinary cell-free DNA (ucfDNA) is a potential biomarker for bladder cancer detection. However, the biological characteristics of ucfDNA are not well understood. We explored the roles of deoxyribonuclease 1 (DNASE1) and deoxyribonuclease 1-…
View article: Single-Molecule Sequencing Enables Long Cell-Free DNA Detection and Direct Methylation Analysis for Cancer Patients
Single-Molecule Sequencing Enables Long Cell-Free DNA Detection and Direct Methylation Analysis for Cancer Patients Open
Background Analysis of circulating tumor DNA has become increasingly important as a tool for cancer care. However, the focus of previous studies has been on short fragments of DNA. Also, bisulfite sequencing, a conventional approach for me…
View article: Effects of nucleases on cell-free extrachromosomal circular DNA
Effects of nucleases on cell-free extrachromosomal circular DNA Open
Cell-free extrachromosomal circular DNA (eccDNA) as a distinct topological form from linear DNA has recently gained increasing research interest, with possible clinical applications as a class of biomarkers. In this study, we aimed to expl…
View article: The Next Frontier in Noninvasive Prenatal Diagnostics: Cell-Free Fetal DNA Analysis for Monogenic Disease Assessment
The Next Frontier in Noninvasive Prenatal Diagnostics: Cell-Free Fetal DNA Analysis for Monogenic Disease Assessment Open
With the widespread clinical adoption of noninvasive screening for fetal chromosomal aneuploidies based on cell-free DNA analysis from maternal plasma, more researchers are turning their attention to noninvasive prenatal assessment for sin…
View article: Jagged Ends on Multinucleosomal Cell-Free DNA Serve as a Biomarker for Nuclease Activity and Systemic Lupus Erythematosus
Jagged Ends on Multinucleosomal Cell-Free DNA Serve as a Biomarker for Nuclease Activity and Systemic Lupus Erythematosus Open
Background Jagged ends of plasma DNA are a recently recognized class of fragmentomic markers for cell-free DNA, reflecting the activity of nucleases. A number of recent studies have also highlighted the importance of jagged ends in the con…
View article: High-resolution analysis for urinary DNA jagged ends
High-resolution analysis for urinary DNA jagged ends Open
Single-stranded ends of double-stranded DNA (jagged ends) are more abundant in urinary DNA than in plasma DNA. However, the lengths of jagged ends in urinary DNA remained undetermined, as a previous method used for urinary DNA jagged end s…
View article: Single-molecule sequencing reveals a large population of long cell-free DNA molecules in maternal plasma
Single-molecule sequencing reveals a large population of long cell-free DNA molecules in maternal plasma Open
Significance We revealed a large population of long cell-free DNA molecules (up to 23,635 bp in length) in maternal plasma and developed an approach which leveraged the abundance of CpG sites on long molecules to deduce the tissue of origi…
View article: Nuclease deficiencies alter plasma cell-free DNA methylation profiles
Nuclease deficiencies alter plasma cell-free DNA methylation profiles Open
The effects of DNASE1L3 or DNASE1 deficiency on cell-free DNA (cfDNA) methylation were explored in plasma of mice deficient in these nucleases and in DNASE1L3-deficient humans. Compared to wild-type cfDNA, cfDNA in DNASE1L3-deficient mice …
View article: Dissection of PIK3CA Aberration for Cervical Adenocarcinoma Outcomes
Dissection of PIK3CA Aberration for Cervical Adenocarcinoma Outcomes Open
Personalized treatment of genetically stratified subgroups has the potential to improve outcomes in many malignant tumors. This study distills clinically meaningful prognostic/predictive genomic marker for cervical adenocarcinoma using sig…
View article: Single Cell and Plasma RNA Sequencing for RNA Liquid Biopsy for Hepatocellular Carcinoma
Single Cell and Plasma RNA Sequencing for RNA Liquid Biopsy for Hepatocellular Carcinoma Open
Background Human plasma contains RNA transcripts released by multiple cell types within the body. Single-cell transcriptomic analysis allows the cellular origin of circulating RNA molecules to be elucidated at high resolution and has been …
View article: Cell‐free fetal DNA coming in all sizes and shapes
Cell‐free fetal DNA coming in all sizes and shapes Open
Cell‐free fetal DNA analysis has an established role in prenatal assessments. It serves as a source of fetal genetic material that is accessible non‐invasively from maternal blood. Through the years, evidence has accumulated to show that c…
View article: Applications of genetic-epigenetic tissue mapping for plasma DNA in prenatal testing, transplantation and oncology
Applications of genetic-epigenetic tissue mapping for plasma DNA in prenatal testing, transplantation and oncology Open
We developed genetic-epigenetic tissue mapping (GETMap) to determine the tissue composition of plasma DNA carrying genetic variants not present in the constitutional genome through comparing their methylation profiles with relevant tissues…
View article: Genome-wide detection of cytosine methylation by single molecule real-time sequencing
Genome-wide detection of cytosine methylation by single molecule real-time sequencing Open
Significance Single molecule real-time (SMRT) sequencing theoretically offers the opportunity to directly assess certain base modifications of native DNA molecules without any prior chemical/enzymatic conversions and PCR amplification, usi…
View article: Characteristics of Fetal Extrachromosomal Circular DNA in Maternal Plasma: Methylation Status and Clearance
Characteristics of Fetal Extrachromosomal Circular DNA in Maternal Plasma: Methylation Status and Clearance Open
Background Although the characterization of cell-free extrachromosomal circular DNA (eccDNA) has gained much research interest, the methylation status of these molecules is yet to be elucidated. We set out to compare the methylation densit…
View article: Jagged Ends of Urinary Cell-Free DNA: Characterization and Feasibility Assessment in Bladder Cancer Detection
Jagged Ends of Urinary Cell-Free DNA: Characterization and Feasibility Assessment in Bladder Cancer Detection Open
Background Double-stranded DNA in plasma is known to carry single-stranded ends, called jagged ends. Plasma DNA jagged ends are biomarkers for pathophysiologic states such as pregnancy and cancer. It remains unknown whether urinary cell-fr…
View article: Fetal mitochondrial <scp>DNA</scp> in maternal plasma in surrogate pregnancies: Detection and topology
Fetal mitochondrial <span>DNA</span> in maternal plasma in surrogate pregnancies: Detection and topology Open
Objectives Due to the maternally‐inherited nature of mitochondrial DNA (mtDNA), there is a lack of information regarding fetal mtDNA in the plasma of pregnant women. We aim to explore the presence and topologic forms of circulating fetal a…
View article: International Society for Prenatal Diagnosis Position Statement: cell free (cf)<scp>DNA</scp> screening for Down syndrome in multiple pregnancies
International Society for Prenatal Diagnosis Position Statement: cell free (cf)<span>DNA</span> screening for Down syndrome in multiple pregnancies Open
The aim of this Position Statement from the International Society for Prenatal Diagnosis (ISPD) is to review the relevant published literature and make evidence-based recommendations regarding screening twin and triplet pregnancies for Dow…
View article: Detection and characterization of jagged ends of double-stranded DNA in plasma
Detection and characterization of jagged ends of double-stranded DNA in plasma Open
Cell-free DNA in plasma has been used for noninvasive prenatal testing and cancer liquid biopsy. The physical properties of cell-free DNA fragments in plasma, such as fragment sizes and ends, have attracted much recent interest, leading to…