Lengthening and shortening of plasma DNA in hepatocellular carcinoma patients

The impact of digital DNA counting technologies on noninvasive prenatal testing

The discovery of cell-free DNA molecules in maternal plasma has opened up numerous opportunities for noninvasive prenatal testing. The advent of new digital counting technologies, including digital polymerase chain reaction and massive parallel sequencing, has provided the opportunity to quantify the cell-free DNA molecules in maternal plasma in an unprecedentedly precise manner. Powered by these technologies, prenatal testing of different kinds of hereditary conditions, ranging from monogenic diseases to chromosome aneuploidies, has been shown to be possible through the analysis of maternal plasma DNA. Discussed here are the principles of the approaches used in the noninvasive testing of different fetal conditions, with an emphasis on the impact that different digital DNA counting strategies have made on the development of these tests.

Bioinformatics analysis of circulating cell-free DNA sequencing data

The discovery of cell-free DNA molecules in plasma has opened up numerous opportunities in noninvasive diagnosis. Cell-free DNA molecules have become increasingly recognized as promising biomarkers for detection and management of many diseases. The advent of next generation sequencing has provided unprecedented opportunities to scrutinize the characteristics of cell-free DNA molecules in plasma in a genome-wide fashion and at single-base resolution. Consequently, clinical applications of circulating cell-free DNA analysis have not only revolutionized noninvasive prenatal diagnosis but also facilitated cancer detection and monitoring toward an era of blood-based personalized medicine. With the remarkably increasing throughput and lowering cost of next generation sequencing, bioinformatics analysis becomes increasingly demanding to understand the large amount of data generated by these sequencing platforms. In this Review, we highlight the major bioinformatics algorithms involved in the analysis of cell-free DNA sequencing data. Firstly, we briefly describe the biological properties of these molecules and provide an overview of the general bioinformatics approach for the analysis of cell-free DNA. Then, we discuss the specific upstream bioinformatics considerations concerning the analysis of sequencing data of circulating cell-free DNA, followed by further detailed elaboration on each key clinical situation in noninvasive prenatal diagnosis and cancer management where downstream bioinformatics analysis is heavily involved. We also discuss bioinformatics analysis as well as clinical applications of the newly developed massively parallel bisulfite sequencing of cell-free DNA. Finally, we offer our perspectives on the future development of bioinformatics in noninvasive diagnosis.

Assessment of DNA Integrity, Applications for Cancer Research

Many methods have been developed for DNA integrity assessment including electrophoresis-based procedures, quantitative PCR, and, more recently, microfluidics-based procedures. DNA integrity evaluation can be employed for characterizing biological samples quality before extensive genomic analysis and also finds applications in reproductive medicine, prenatal diagnostics, or cancer research. In this chapter, we will focus on the assessment of DNA integrity in cancer research. In particular, we will present the application of the determination of DNA integrity for tracking of circulating tumor DNA. Finally, we will conclude by illustrating the potential innovative application of DNA integrity as a biomarker in clinical research, especially for prognostic purposes, patient follow-up, or early diagnosis.