NIPT and Next Generation Sequencing

Maternal plasma contains cell-free DNA from both mother and fetus. Next Generation Sequencing (NGS) of maternal plasma cell-free DNA allows fast and safe non-invasive prenatal testing (NIPT) for the screening of fetal aneuploidies: trisomy and monosomy. It is also possible to detect small copy number abnormalities (CNAs) like sub-chromosomal deletions or duplications and to determine the fetal sex.

Aneuploidies detection

The detection of fetal aneuploidies is based on a combination of high quality alignments against the human genome and read counts to identify chromosomal gain or loss. Different normalization are performed based on sequenced reads GC percentage to calculate high-quality z-scores.

The presence of a fetal aneuploidy is assessed by the value of three z-score calculations and some quality criterion computed for each samples: reads GC content, reads quality and number...

Small CNAs detection

The detection of small CNAs depends on a count analysis. Chromosomes are cut into bins and reads are counted. A z-score is computed to compare all chromosome bins representation. During z-score computation a normalization based on bins' reads GC percentage is performed. Finally, in order to eliminate the background noise, a deconvolution step is added to improve the detection of small CNA.

Fetal Fraction

The fetal fraction of plasma sample is of critical value for interpreting NIPT results. According to the sequencing method, the fetal fraction can be estimated by our solution. Our tool is also able to use an external fetal fraction estimation based on other experimental methods.

A modular solution

Our bioinformatics pipeline can be easily integrated with other tools to improve the analysis experience. For example, Micro LifePipe® can detects DNA viruses circulating in maternal plasma that would be important for a fetus’ development.