scholarly journals Putative Origins of Cell-Free DNA in Humans: A Review of Active and Passive Nucleic Acid Release Mechanisms

2020 ◽  
Vol 21 (21) ◽  
pp. 8062 ◽  
Author(s):  
Stefan Grabuschnig ◽  
Abel Jacobus Bronkhorst ◽  
Stefan Holdenrieder ◽  
Ingund Rosales Rodriguez ◽  
Klaus Peter Schliep ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Host Cells ◽  
Clinical Tool ◽  
Cell Free Dna ◽  
Genomic Changes ◽  
Free Dna ◽  
Release Mechanisms ◽  
Passive Release ◽  
Genetic Complexity ◽  
Efficient Extraction

Through various pathways of cell death, degradation, and regulated extrusion, partial or complete genomes of various origins (e.g., host cells, fetal cells, and infiltrating viruses and microbes) are continuously shed into human body fluids in the form of segmented cell-free DNA (cfDNA) molecules. While the genetic complexity of total cfDNA is vast, the development of progressively efficient extraction, high-throughput sequencing, characterization via bioinformatics procedures, and detection have resulted in increasingly accurate partitioning and profiling of cfDNA subtypes. Not surprisingly, cfDNA analysis is emerging as a powerful clinical tool in many branches of medicine. In addition, the low invasiveness of longitudinal cfDNA sampling provides unprecedented access to study temporal genomic changes in a variety of contexts. However, the genetic diversity of cfDNA is also a great source of ambiguity and poses significant experimental and analytical challenges. For example, the cfDNA population in the bloodstream is heterogeneous and also fluctuates dynamically, differs between individuals, and exhibits numerous overlapping features despite often originating from different sources and processes. Therefore, a deeper understanding of the determining variables that impact the properties of cfDNA is crucial, however, thus far, is largely lacking. In this work we review recent and historical research on active vs. passive release mechanisms and estimate the significance and extent of their contribution to the composition of cfDNA.

scholarly journals DISMIR: a deep learning-based cancer-detection method by integrating DNA sequence and methylation information of individual cell-free DNA reads

2021 ◽  
Author(s):  
Jiaqi Li ◽  
Lei Wei ◽  
Xianglin Zhang ◽  
Wei Zhang ◽  
Haochen Wang ◽  
...  
Keyword(s):  
Deep Learning ◽  
Dna Sequence ◽  
Cancer Detection ◽  
High Throughput Sequencing ◽  
Detection Method ◽  
Low Cost ◽  
Sequencing Data ◽  
Cell Free Dna ◽  
Free Dna ◽  
Novel Approach

ABSTRACTDetecting cancer signals in cell-free DNA (cfDNA) high-throughput sequencing data is emerging as a novel non-invasive cancer detection method. Due to the high cost of sequencing, it is crucial to make robust and precise prediction with low-depth cfDNA sequencing data. Here we propose a novel approach named DISMIR, which can provide ultrasensitive and robust cancer detection by integrating DNA sequence and methylation information in plasma cfDNA whole genome bisulfite sequencing (WGBS) data. DISMIR introduces a new feature termed as “switching region” to define cancer-specific differentially methylated regions, which can enrich the cancer-related signal at read-resolution. DISMIR applies a deep learning model to predict the source of every single read based on its DNA sequence and methylation state, and then predicts the risk that the plasma donor is suffering from cancer. DISMIR exhibited high accuracy and robustness on hepatocellular carcinoma detection by plasma cfDNA WGBS data even at ultra-low sequencing depths. Analysis showed that DISMIR tends to be insensitive to alterations of single CpG sites’ methylation states, which suggests DISMIR could resist to technical noise of WGBS. All these results showed DISMIR with the potential to be a precise and robust method for low-cost early cancer detection.

scholarly journals A cell-free DNA metagenomic sequencing assay that integrates the damage response to infection

2019 ◽  
Author(s):  
Alexandre Pellan Cheng ◽  
Philip Burnham ◽  
John Richard Lee ◽  
Matthew Pellan Cheng ◽  
Manikkam Suthanthiran ◽  
...  
Keyword(s):  
Urinary Tract ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Viral Infections ◽  
Clinical Samples ◽  
Metagenomic Sequencing ◽  
Kidney Transplant Recipients ◽  
Bladder Tissue ◽  
Cell Free Dna ◽  
Free Dna

ABSTRACTHigh-throughput metagenomic sequencing offers an unbiased approach to identify pathogens in clinical samples. Conventional metagenomic sequencing however does not integrate information about the host, which is often critical to distinguish infection from infectious disease, and to assess the severity of disease. Here, we explore the utility of high-throughput sequencing of cell-free DNA after bisulfite conversion to map the tissue and cell types of origin of host-derived cell-free DNA, and to profile the bacterial and viral metagenome. We applied this assay to 51 urinary cfDNA isolates collected from a cohort of kidney transplant recipients with and without bacterial and viral infection of the urinary tract. We find that the cell and tissue types of origin of urinary cell-free DNA can be derived from its genome-wide profile of methylation marks, and strongly depend on infection status. We find evidence of kidney and bladder tissue damage due to viral and bacterial infection, respectively, and of the recruitment of neutrophils to the urinary tract during infection. Through direct comparison to conventional metagenomic sequencing as well as clinical tests of infection, we find this assay accurately captures the bacterial and viral composition of the sample. The assay presented here is straightforward to implement, offers a systems view into bacterial and viral infections of the urinary tract, and can find future use as a tool for the differential diagnosis of infections.

scholarly journals Separating the signal from the noise in metagenomic cell-free DNA sequencing

2019 ◽  
Author(s):  
Philip Burnham ◽  
Nardhy Gomez-Lopez ◽  
Michael Heyang ◽  
Alexandre Pellan Cheng ◽  
Joan Sesing Lenz ◽  
...  
Keyword(s):  
Amniotic Fluid ◽  
High Throughput Sequencing ◽  
False Positive Rate ◽  
Normal Pregnancy ◽  
True Positive Rate ◽  
Total Biomass ◽  
Metagenomic Sequencing ◽  
Cell Free Dna ◽  
Free Dna ◽  
Positive Rate

Abstract Background: Cell-free DNA (cfDNA) in blood, urine and other biofluids provides a unique window into human health. A proportion of cfDNA is derived from bacteria and viruses, creating opportunities for the diagnosis of infection via metagenomic sequencing. The total biomass of microbial-derived cfDNA in clinical isolates is low, which makes metagenomic cfDNA sequencing susceptible to contamination and alignment noise. Results: Here, we report Low Biomass Background Correction (LBBC), a bioinformatics noise filtering tool informed by the uniformity of the coverage of microbial genomes and the batch variation in the absolute abundance of microbial cfDNA. We demonstrate that LBBC leads to a dramatic reduction in false positive rate while minimally affecting the true positive rate for a cfDNA test to screen for urinary tract infection. We next performed high throughput sequencing of cfDNA in amniotic fluid collected from term uncomplicated pregnancies or those complicated with clinical chorioamnionitis with and without intra-amniotic infection. Conclusions: The data provide unique insight into the properties of fetal and maternal cfDNA in amniotic fluid, demonstrate the utility of cfDNA to screen for intra-amniotic infection, support the view that the amniotic fluid is sterile during normal pregnancy, and reveal cases of intra-amniotic inflammation without infection at term.

scholarly journals Separating the signal from the noise in metagenomic cell-free DNA sequencing

2020 ◽  
Author(s):  
Philip Burnham ◽  
Nardhy Gomez-Lopez ◽  
Michael Heyang ◽  
Alexandre Pellan Cheng ◽  
Joan Sesing Lenz ◽  
...  
Keyword(s):  
Amniotic Fluid ◽  
High Throughput Sequencing ◽  
False Positive Rate ◽  
Normal Pregnancy ◽  
True Positive Rate ◽  
Total Biomass ◽  
Metagenomic Sequencing ◽  
Cell Free Dna ◽  
Free Dna ◽  
Positive Rate

Abstract Background: Cell-free DNA (cfDNA) in blood, urine and other biofluids provides a unique window into human health. A proportion of cfDNA is derived from bacteria and viruses, creating opportunities for the diagnosis of infection via metagenomic sequencing. The total biomass of microbial-derived cfDNA in clinical isolates is low, which makes metagenomic cfDNA sequencing susceptible to contamination and alignment noise. Results: Here, we report Low Biomass Background Correction (LBBC), a bioinformatics noise filtering tool informed by the uniformity of the coverage of microbial genomes and the batch variation in the absolute abundance of microbial cfDNA. We demonstrate that LBBC leads to a dramatic reduction in false positive rate while minimally affecting the true positive rate for a cfDNA test to screen for urinary tract infection. We next performed high throughput sequencing of cfDNA in amniotic fluid collected from term uncomplicated pregnancies or those complicated with clinical chorioamnionitis with and without intra-amniotic infection. Conclusions: The data provide unique insight into the properties of fetal and maternal cfDNA in amniotic fluid, demonstrate the utility of cfDNA to screen for intra-amniotic infection, support the view that the amniotic fluid is sterile during normal pregnancy, and reveal cases of intra-amniotic inflammation without infection at term.

scholarly journals cfDNA deconvolution via NIPT of a pregnant woman after bone marrow transplant and donor egg IVF

2021 ◽  
Vol 15 (1) ◽  
Author(s):  
Jianjiang Zhu ◽  
Feng Hui ◽  
Xuequn Mao ◽  
Shaoqin Zhang ◽  
Hong Qi ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Bone Marrow Transplant ◽  
High Throughput Sequencing ◽  
Prenatal Testing ◽  
Clinical Information ◽  
Marrow Transplant ◽  
Cell Free Dna ◽  
Free Dna ◽  
Donor Egg ◽  
Active Research

AbstractCell-free DNA is known to be a mixture of DNA fragments originating from various tissue types and organs of the human body and can be utilized for several clinical applications and potentially more to be created. Non-invasive prenatal testing (NIPT), by high throughput sequencing of cell-free DNA (cfDNA), has been successfully applied in the clinical screening of fetal chromosomal aneuploidies, with more extended coverage under active research.In this study, via a quite unique and rare NIPT sample, who has undergone both bone marrow transplant and donor egg IVF, we investigated the sources of oddness observed in the NIPT result using a combination of molecular genetics and genomic methods and eventually had the case fully resolved. Along the process, we devised a clinically viable process to dissect the sample mixture.Eventually, we used the proposed scheme to evaluate the relatedness of individuals and the demultiplexed sample components following modified population genetics concepts, exemplifying a noninvasive prenatal paternity test prototype. For NIPT specific applicational concern, more thorough and detailed clinical information should therefore be collected prior to cfDNA-based screening procedure like NIPT and systematically reviewed when an abnormal report is obtained to improve genetic counseling and overall patient care.

scholarly journals Cell-free DNA Reveals Potential Zoonotic Reservoirs in Non-Human Primates

2018 ◽  
Author(s):  
Mark Kowarsky ◽  
Iwijn De Vlaminck ◽  
Jennifer Okamoto ◽  
Norma F Neff ◽  
Matthew LeBreton ◽  
...  
Keyword(s):  
Species Diversity ◽  
High Throughput Sequencing ◽  
Geographic Location ◽  
Zoonotic Diseases ◽  
Primate Species ◽  
Cell Free Dna ◽  
Wildlife Reservoirs ◽  
Free Dna ◽  
Unbiased Manner ◽  
Insight Into

Abstract:The microbiome of non-human primates is relatively neglected compared with humans, and yet it is a source of many zoonotic diseases. We used high throughput sequencing of circulating cell-free DNA to identify the bacteria, archaea, eukaryotic parasites and viruses from over 200 individual non-human primates across 17 species from Africa. Many of the assembled sequences have low or no homology to previously sequenced microorganisms, while those that do have homology support prior observations of specific taxa present in primate microbiomes. The structure of the total microbiome is correlated with geographic location, even between distinct primate species which are co-located. However, we find that viruses have a particularly notable association with host taxa independent of geography. Numerous potentially zoonotic taxa were discovered in an unbiased manner, thereby expanding knowledge of host species diversity and strengthening the case for monitoring wildlife reservoirs.One Sentence SummaryBlood from non-human primates provides insight into potential pathogens which might eventually infect humans.

scholarly journals A cell-free DNA metagenomic sequencing assay that integrates the host injury response to infection

2019 ◽  
Vol 116 (37) ◽  
pp. 18738-18744 ◽  
Author(s):  
Alexandre Pellan Cheng ◽  
Philip Burnham ◽  
John Richard Lee ◽  
Matthew Pellan Cheng ◽  
Manikkam Suthanthiran ◽  
...  
Keyword(s):  
Urinary Tract ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Viral Infections ◽  
Clinical Samples ◽  
Metagenomic Sequencing ◽  
Kidney Transplant Recipients ◽  
Bladder Tissue ◽  
Cell Free Dna ◽  
Free Dna

High-throughput metagenomic sequencing offers an unbiased approach to identify pathogens in clinical samples. Conventional metagenomic sequencing, however, does not integrate information about the host, which is often critical to distinguish infection from infectious disease, and to assess the severity of disease. Here, we explore the utility of high-throughput sequencing of cell-free DNA (cfDNA) after bisulfite conversion to map the tissue and cell types of origin of host-derived cfDNA, and to profile the bacterial and viral metagenome. We applied this assay to 51 urinary cfDNA isolates collected from a cohort of kidney transplant recipients with and without bacterial and viral infection of the urinary tract. We find that the cell and tissue types of origin of urinary cfDNA can be derived from its genome-wide profile of methylation marks, and strongly depend on infection status. We find evidence of kidney and bladder tissue damage due to viral and bacterial infection, respectively, and of the recruitment of neutrophils to the urinary tract during infection. Through direct comparison to conventional metagenomic sequencing as well as clinical tests of infection, we find this assay accurately captures the bacterial and viral composition of the sample. The assay presented here is straightforward to implement, offers a systems view into bacterial and viral infections of the urinary tract, and can find future use as a tool for the differential diagnosis of infection.

scholarly journals Separating the signal from the noise in metagenomic cell-free DNA sequencing

2019 ◽  
Author(s):  
Philip Burnham ◽  
Nardhy Gomez-Lopez ◽  
Michael Heyang ◽  
Alexandre Pellan Cheng ◽  
Joan Sesing Lenz ◽  
...  
Keyword(s):  
Amniotic Fluid ◽  
High Throughput Sequencing ◽  
False Positive Rate ◽  
Normal Pregnancy ◽  
True Positive Rate ◽  
Total Biomass ◽  
Metagenomic Sequencing ◽  
Cell Free Dna ◽  
Free Dna ◽  
Positive Rate

ABSTRACTCell-free DNA (cfDNA) in blood, urine and other biofluids provides a unique window into human health. A proportion of cfDNA is derived from bacteria and viruses, creating opportunities for the diagnosis of infection via metagenomic sequencing. The total biomass of microbial-derived cfDNA in clinical isolates is low, which makes metagenomic cfDNA sequencing susceptible to contamination and alignment noise. Here, we report Low Biomass Background Correction (LBBC), a bioinformatics noise filtering tool informed by the uniformity of the coverage of microbial genomes and the batch variation in the absolute abundance of microbial cfDNA. We demonstrate that LBBC leads to a dramatic reduction in false positive rate while minimally affecting the true positive rate for a cfDNA test to screen for urinary tract infection. We next performed high throughput sequencing of cfDNA in amniotic fluid collected from term uncomplicated pregnancies or those complicated with clinical chorioamnionitis with and without intra-amniotic infection. The data provide unique insight into the properties of fetal and maternal cfDNA in amniotic fluid, demonstrate the utility of cfDNA to screen for intra-amniotic infection, support the view that the amniotic fluid is sterile during normal pregnancy, and reveal cases of intra-amniotic inflammation without infection at term.

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