Introduction
The discovery of cell-free DNA in maternal plasma by our group has opened up new possibilities
for noninvasive prenatal testing (NIPT). Using the massive parallel sequencing technologies,
plasma DNA based NIPT has been employed worldwide and rapidly transformed the clinical practice
of prenatal testing. Most of the existing methods require the control group to establish the
reference ranges for determining the aneuploidy statuses, thus adding more cost and time to the
analysis particularly in laboratories with small test load. However, there is a paucity of
control-free approaches developed for NIPT.
Therefore, in this study, we developed a novel algorithm, named COFFEE (COntrol-Free noninvasive
FEtal chromosomal Examination), which employed the properties of plasma DNA sizes to obviate the
need of control samples. We had evaluated COFFEE using three datasets generating from different
sequencing settings. The accuracy of COFFEE was found to be 100% in trisomy 21 testing. On the
other hand, we found that the batch-to-batch variation in the control samples would cause false
positives using a control-based method but such false positives were not present in COFFEE. We
believe that COFFEE would be a valuable alternative or supplementary to the standard control-based
methods for NIPT.
License
COFFEE is free for academic, nonprofit, and personal use ONLY,
distributed under the Boost Software License.
Please contact us if you are interested in commercial uses
of this algorithm, program or any deviations.
Download
Download COFFEE package »
After downloading the file, uncompress it by
tar zxf COFFEE.tar.gz
The folder should contain the COFFEE package and testing dataset.
Please refer to README file in the package for more information on how to run COFFEE.
Contact
If there is any question, please feel free to contact us by Dr. Kun Sun or Prof. Peiyong Jiang.
Thanks for your interest!