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FEMER: Noninvasive reconstruction of placental methylome
by analysis of circulating cell-free DNA in maternal plasma

Source package

Click here to download FEMER (v1.0 Oct 2017; for x86_64 platform).

FEMER is free for academic, nonprofit, and personal use ONLY under the BOOST License.
A license is required for all kinds of commercial usage of FEMER and/or its deviations. Please contact the author for more inquires.

Testing datasets

FEMER had been applied on a pregnancy dataset collected from our previous study (Lun et al. Clin Chem 2013).
A shell script is provided to run FEMER on this dataset (for x86_64 platform):

    user@linux$ ./run.testing.dataset.sh


Note that this script will download the sequencing files from our server which are very large (~95 GB in total).

If it is not convenient for you to download this large dataset, we also provide a shell script run FEMER on a light dataset
which only contains data for chr1:

    user@linux$ ./run.testing.dataset.light.sh


This script will only download ~5 GB data.
NOTE: the results are slightly different between this light dataset and the whole dataset. The reason is
that the fetal DNA fraction calculation is only based on the informative SNPs on chr1, which is much
smaller than the whole dataset thus affects the accuracy. However, the difference is very subtle.

Supplementary files for performance evaluation

The following files are related to the testing dataset, which could be used to evaluate the performance of FEMER.

Citation

When referencing, please cite "Sun K, Lun FMF, Leung TY, Chiu RWK, Lo YMD and Sun H (2018):
Noninvasive reconstruction of placental methylome from maternal plasma DNA: potential for prenatal testing and monitoring.
Prenat Diagn. 2018 Feb;38(3):196-203." PubMed   Full Text

Contact

For more inquiries, please contact the authors.

Last update: Jan 31, 2018