![]() A number of base-conversion chemistries have been developed to help differentiate unmodified C from its epigenetic variants, 5mC or 5hmC. Next-generation sequencing directly captures the canonical bases G, C, T and A in its readout 14. Hitherto, researchers have accessed either genetic or epigenetic information, without resolving 5mC from 5hmC.Ĭommonly used sequencing approaches do not capture full information from both genetics and epigenetics. More recently, 5-hydroxymethylcytosine (5hmC) has emerged as an important base modification that can provide information that goes beyond 5mC and genetics 12, 13. Epigenetic information in DNA has been retrieved principally via sequencing 5-methylcytosine (5mC). Noninvasive prenatal diagnostic analysis has also demonstrated that DNA methylation signal can determine fetal origin of DNA fragments 11. ![]() ![]() DNA methylation information can also inform on the tissue of origin of the circulating tumor DNA 10. Combining information on DNA methylation with genetic sequence in cell-free DNA (cfDNA) from blood has been shown to substantially increase sensitivity to detect tumor DNA 9. Germline genetic alterations cause changes in DNA methylation that ultimately dictate predisposition for disease 6, 7, 8. Both DNA methylation and genotype are required to determine the pluripotency of induced stem cells 4 and their maturation capacity 5. For instance, the analysis of somatic genetic mutations, together with DNA methylation marks, from blood DNA gave a substantially more accurate prediction of mortality than either genetics or DNA methylation alone 3. ![]() The combination of genetic and epigenetic information provides a more comprehensive view of biology. Epigenetic information in DNA provides insights into dynamic changes in biology that are closely associated with transcriptional programs 1 and cell fate 2. Genetic sequencing of the DNA bases G, C, T and A has been transformed by high-throughput sequencing approaches in the past two decades. There are multiple dimensions of information stored within DNA. Information encoded in nucleic acids is fundamental to the biology of living systems. Simultaneous, phased reading of genetic and epigenetic bases provides a more complete picture of the information stored in genomes and has applications throughout biomedicine. The approach is accurate, requires low DNA input and has a simple workflow and analysis pipeline. Methods are demonstrated on human genomic DNA and cell-free DNA from a blood sample of a patient with cancer. Coupled decoding of bases across the original and copy strand provides a phased digital readout. DNA is copied and bases are enzymatically converted. We present a single base-resolution sequencing methodology that sequences complete genetics and the two most common cytosine modifications in a single workflow. Methods widely used to detect epigenetic DNA bases fail to capture common C-to-T mutations or distinguish 5-methylcytosine from 5-hydroxymethylcytosine. Most DNA sequencing approaches address either genetics or epigenetics and thus capture incomplete information. Shankar Balasubramanian ORCID: /0000-0002-0281-5815 2, 3ĭNA comprises molecular information stored in genetic and epigenetic bases, both of which are vital to our understanding of biology.Simultaneous sequencing of genetic and epigenetic bases in DNA
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