title: Sensitivity of noninvasive prenatal detection of fetal aneuploidy from maternal plasma using shotgun sequencing is limited only by counting statistics.
abstract: We recently demonstrated noninvasive detection of fetal aneuploidy by shotgun sequencing cell-free DNA in maternal plasma using next-generation high throughput sequencer. However, GC bias introduced by the sequencer placed a practical limit on the sensitivity of aneuploidy detection. In this study, we describe a method to computationally remove GC bias in short read sequencing data by applying weight to each sequenced read based on local genomic GC content. We show that sensitivity is limited only by counting statistics and that sensitivity can be increased to arbitrary precision in sample containing arbitrarily small fraction of fetal DNA simply by sequencing more DNA molecules. High throughput shotgun sequencing of maternal plasma DNA should therefore enable noninvasive diagnosis of any type of fetal aneuploidy.
authors.affiliation: Department of Bioengineering, Stanford University and Howard Hughes Medical Institute, Stanford, California, United States of America.
authors.forename: H Christina
authors.initials: HC
authors.lastname: Fan
authors.forename: Stephen R
authors.initials: SR
authors.lastname: Quake
mesh_terms: D000782:Aneuploidy; D016477:Artifacts; D001482:Base Composition / Q000235:genetics; D005260:Female; D005333:Fetus / Q000378:metabolism*; D006801:Humans; D015233:Models, Statistical; D016012:Poisson Distribution; D011247:Pregnancy; D011296:Prenatal Diagnosis; D017422:Sequence Analysis, DNA / Q000379:methods*
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