Size Selection Has Utility for Cell-Free DNA Studies

The rise of research studies and diagnostic tests looking at cell-free DNA — particularly fetal DNA in a mother’s bloodstream — has happened with astonishing speed. Prenatal genetic testing, for instance, has already supplanted many invasive clinical tests such as amniocentesis or chorionic villus sampling. Cell-free DNA is now considered an important source of information about cancer, and will no doubt have many other applications as we learn more about it.

These studies are particularly interesting to us because isolating cell-free DNA involves accurate size selection. Foundational research has consistently found that cell-free fetal DNA is shorter than cell-free maternal DNA: this early study determined that fetal DNA was less than 300 bp, while maternal DNA was larger than 1 Kb, while another study reported a dominant peak of about 160 bp for fetal DNA.

A more recent publication explored various methods of analyzing fragment sizes for a study of cell-free fetal DNA. With paired-end sequencing as well as basic electrophoresis (sizes were read with a Bioanalyzer), the scientists were able to distinguish maternal from fetal DNA. With extremely specific findings of fragment size, they were also able to detect some cases of fetal chromosomal aneuploidy just by observing size aberrations.

We’re excited about the possibilities of applying automated DNA size selection to cell-free DNA studies. Other methods of size selection have not been terribly successful due to the yield challenge; DNA derived from a fetus or tumor is already such a small proportion of DNA in these samples. But with a platform like ours, which significantly boosts yield compared to other sizing techniques, we think there is great potential for enhancing cell-free DNA research.

We’re presenting a poster on this topic at the AGBT Precision Health meeting right now. If you’re attending the conference, check out poster #107 — and if not, we’ll have more details on our blog next week.

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