Determination of fetal DNA fraction from the plasma of pregnant women using sequence read counts

This study introduces a novel method, referred to as SeqFF, for estimating the fetal DNA fraction in the plasma of pregnant women and to infer the underlying mechanism that allows for such statistical modeling.

[1]  Matthew Rabinowitz,et al.  Non-invasive prenatal aneuploidy testing at chromosomes 13, 18, 21, X, and Y, using targeted sequencing of polymorphic loci , 2013 .

[2]  R. Rava,et al.  Optimal detection of fetal chromosomal abnormalities by massively parallel DNA sequencing of cell-free fetal DNA from maternal blood. , 2011, Clinical chemistry.

[3]  Wendy P Robinson,et al.  The human placenta methylome , 2013, Proceedings of the National Academy of Sciences.

[4]  J. Canick,et al.  High-Throughput Massively Parallel Sequencing for Fetal Aneuploidy Detection from Maternal Plasma , 2013, PLoS ONE.

[5]  Chunming Ding,et al.  Detection of the placental epigenetic signature of the maspin gene in maternal plasma. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[6]  D. Maddocks,et al.  Free fetal DNA in maternal plasma in anembryonic pregnancies: confirmation that the origin is the trophoblast , 2007, Prenatal diagnosis.

[7]  Stephen R Quake,et al.  Analysis of the size distributions of fetal and maternal cell-free DNA by paired-end sequencing. , 2010, Clinical chemistry.

[8]  Tze Kin Lau,et al.  Microfluidics digital PCR reveals a higher than expected fraction of fetal DNA in maternal plasma. , 2008, Clinical chemistry.

[9]  Tak Y. Leung,et al.  Digital PCR for the molecular detection of fetal chromosomal aneuploidy , 2007, Proceedings of the National Academy of Sciences.

[10]  S. Nelson,et al.  DNA sequencing of maternal plasma to detect Down syndrome: An international clinical validation study , 2011, Genetics in Medicine.

[11]  A. Hui,et al.  Size distributions of maternal and fetal DNA in maternal plasma. , 2004, Clinical chemistry.

[12]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[13]  J. Kitzman,et al.  Personalized Copy-Number and Segmental Duplication Maps using Next-Generation Sequencing , 2009, Nature Genetics.

[14]  Jian Wang,et al.  Clinical application of massively parallel sequencing‐based prenatal noninvasive fetal trisomy test for trisomies 21 and 18 in 11 105 pregnancies with mixed risk factors , 2012, Prenatal diagnosis.

[15]  Arnold Oliphant,et al.  Noninvasive prenatal detection and selective analysis of cell-free DNA obtained from maternal blood: evaluation for trisomy 21 and trisomy 18. , 2012, American journal of obstetrics and gynecology.

[16]  Peiyong Jiang,et al.  Noninvasive prenatal methylomic analysis by genomewide bisulfite sequencing of maternal plasma DNA. , 2013, Clinical chemistry.

[17]  A. Izenman.  Reduced-rank regression for the multivariate linear model , 1975 .

[18]  Trevor Hastie,et al.  Regularization Paths for Generalized Linear Models via Coordinate Descent. , 2010, Journal of statistical software.

[19]  Gary J. W. Liao,et al.  Size-based molecular diagnostics using plasma DNA for noninvasive prenatal testing , 2014, Proceedings of the National Academy of Sciences.

[20]  Amin R. Mazloom,et al.  Noninvasive prenatal detection of sex chromosomal aneuploidies by sequencing circulating cell‐free DNA from maternal plasma , 2013, Prenatal diagnosis.

[21]  J. Canick,et al.  The impact of maternal plasma DNA fetal fraction on next generation sequencing tests for common fetal aneuploidies , 2013, Prenatal diagnosis.

[22]  Yama W. L. Zheng,et al.  Maternal Plasma DNA Sequencing Reveals the Genome-Wide Genetic and Mutational Profile of the Fetus , 2010, Science Translational Medicine.

[23]  T. Jensen,et al.  Quantification of fetal DNA by use of methylation-based DNA discrimination. , 2010, Clinical chemistry.