Biomaterial Database

Global Characterization of Circulating Nucleic Acids. 2020

Marina Dunaeva, and Ger J M Pruijn

Department of Biomolecular Chemistry, Institute for Molecules and Materials, Radboud University Nijmegen, Nijmegen, The Netherlands. m.dunaeva@ncmls.ru.nl.

Circulating nucleic acids (CNAs) include genomic and mitochondrial DNA fragments, small RNAs, and bacterial and viral DNA/RNA. Different mechanisms such as cell apoptosis, necrosis, and active CNA release from cells have been proposed to result in nucleic acids in the circulation. Application of next generation sequencing technology demonstrated that CNAs contain specific mutations, indels, microsatellite alterations, and epigenetic changes (DNA methylation) associated with various diseases. Their clinical implications have been demonstrated for diseases such as cancer, stroke, trauma, myocardial infarction, autoimmune disorders, and pregnancy-associated complications. Thus, CNAs in blood represent an attractive family of molecules that can serve as biomarkers and the analysis of CNAs can be alternative for immunohistochemical analyses of conventional biopsies. The methods described in this chapter provides details for circulating DNA and small RNA isolation, CNA(-derived cDNA) library preparation, and sequencing data analysis.

UI	MeSH Term	Description	Entries
D011247	Pregnancy	The status during which female mammals carry their developing young (EMBRYOS or FETUSES) in utero before birth, beginning from FERTILIZATION to BIRTH.	Gestation,Pregnancies
D004272	DNA, Mitochondrial	Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial GENOME is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins.	Mitochondrial DNA,mtDNA
D004273	DNA, Neoplasm	DNA present in neoplastic tissue.	Neoplasm DNA
D005260	Female		Females
D005819	Genetic Markers	A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.	Chromosome Markers,DNA Markers,Markers, DNA,Markers, Genetic,Genetic Marker,Marker, Genetic,Chromosome Marker,DNA Marker,Marker, Chromosome,Marker, DNA,Markers, Chromosome
D006801	Humans	Members of the species Homo sapiens.	Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D000073888	Cell-Free Nucleic Acids	Nucleic acids (DNA or RNA) found circulating in SERUM; PLASMA; or other BODY FLUIDS.	Circulating Cell-Free Nucleic Acid,Circulating Nucleic Acid,Cell-Free DNA,Cell-Free Deoxyribonucleic Acid,Cell-Free Nucleic Acid,Cell-Free RNA,Cell-Free Ribonucleic Acid,Circulating Cell-Free Nucleic Acids,Circulating DNA,Circulating Nucleic Acids,Circulating RNA,cfDNA,cfRNA,cirDNA,cirRNA,Acid, Cell-Free Deoxyribonucleic,Acid, Cell-Free Ribonucleic,Acid, Circulating Nucleic,Acids, Circulating Nucleic,Cell Free DNA,Cell Free Deoxyribonucleic Acid,Cell Free Nucleic Acid,Cell Free Nucleic Acids,Cell Free RNA,Cell Free Ribonucleic Acid,Circulating Cell Free Nucleic Acid,Circulating Cell Free Nucleic Acids,DNA, Cell-Free,DNA, Circulating,Deoxyribonucleic Acid, Cell-Free,Nucleic Acid, Cell-Free,Nucleic Acid, Circulating,Nucleic Acids, Cell-Free,Nucleic Acids, Circulating,RNA, Cell-Free,RNA, Circulating,Ribonucleic Acid, Cell-Free
D001483	Base Sequence	The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.	DNA Sequence,Nucleotide Sequence,RNA Sequence,DNA Sequences,Base Sequences,Nucleotide Sequences,RNA Sequences,Sequence, Base,Sequence, DNA,Sequence, Nucleotide,Sequence, RNA,Sequences, Base,Sequences, DNA,Sequences, Nucleotide,Sequences, RNA
D016415	Sequence Alignment	The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.	Sequence Homology Determination,Determination, Sequence Homology,Alignment, Sequence,Alignments, Sequence,Determinations, Sequence Homology,Sequence Alignments,Sequence Homology Determinations
D058727	RNA, Small Untranslated	Short RNA, about 200 base pairs in length or shorter, that does not code for protein.	Short Noncoding RNA,Small Non-Coding RNA,Small Non-Messenger RNA,Small Non-Protein-Coding RNA,Small Noncoding RNA,Small Untranslated RNA,sncRNA,sncRNAs,Non-Coding RNA, Small,Non-Messenger RNA, Small,Non-Protein-Coding RNA, Small,Noncoding RNA, Short,Noncoding RNA, Small,RNA, Short Noncoding,RNA, Small Non-Coding,RNA, Small Non-Messenger,RNA, Small Non-Protein-Coding,RNA, Small Noncoding,Small Non Coding RNA,Small Non Messenger RNA,Small Non Protein Coding RNA,Untranslated RNA, Small