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Informative priors on fetal fraction increase power of the noninvasive prenatal screen.

dc.contributor.author Guan, Yongtao
dc.contributor.author Xu, Hanli
dc.contributor.author Wang, Shaowei
dc.contributor.author Ma, Lin-Lin
dc.contributor.author Huang, Shuai
dc.contributor.author Liang, Lin
dc.contributor.author Liu, Qian
dc.contributor.author Liu, Yang-Yang
dc.contributor.author Liu, Ke-Di
dc.contributor.author Tan, Ze-Min
dc.contributor.author Ban, Hao
dc.contributor.author Lu, Zuhong
dc.date.accessioned 2018-07-25T17:58:51Z
dc.date.available 2018-07-25T17:58:51Z
dc.date.issued 2017-11-09
dc.identifier.issn 1098-3600
dc.identifier.issn 1530-0366
dc.identifier.uri https://hdl.handle.net/10161/17274
dc.description.abstract PurposeNoninvasive prenatal screening (NIPS) sequences a mixture of the maternal and fetal cell-free DNA. Fetal trisomy can be detected by examining chromosomal dosages estimated from sequencing reads. The traditional method uses the Z-test, which compares a subject against a set of euploid controls, where the information of fetal fraction is not fully utilized. Here we present a Bayesian method that leverages informative priors on the fetal fraction.MethodOur Bayesian method combines the Z-test likelihood and informative priors of the fetal fraction, which are learned from the sex chromosomes, to compute Bayes factors. Bayesian framework can account for nongenetic risk factors through the prior odds, and our method can report individual positive/negative predictive values.ResultsOur Bayesian method has more power than the Z-test method. We analyzed 3,405 NIPS samples and spotted at least 9 (of 51) possible Z-test false positives.ConclusionBayesian NIPS is more powerful than the Z-test method, is able to account for nongenetic risk factors through prior odds, and can report individual positive/negative predictive values.Genetics in Medicine advance online publication, 9 November 2017; doi:10.1038/gim.2017.186.
dc.language eng
dc.relation.ispartof Genetics in medicine : official journal of the American College of Medical Genetics
dc.relation.isversionof 10.1038/gim.2017.186
dc.title Informative priors on fetal fraction increase power of the noninvasive prenatal screen.
dc.type Journal article
dc.date.updated 2018-07-25T17:58:50Z
pubs.organisational-group School of Medicine
pubs.organisational-group Duke
pubs.organisational-group Biostatistics & Bioinformatics
pubs.organisational-group Basic Science Departments
pubs.publication-status Published
duke.contributor.orcid Guan, Yongtao|0000-0002-8055-2192


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