Verinata Health, Inc.

Illumina Corporation

Dimitri Skvortsov

Richard P Rava

Darya Chudova

Keith W Jones

David A Comstock

Catalin Barbacioru

Gengxin Chen

Sven Duenwald

Cosmin Deciu

Sarah L Kinnings

Badri Padhukasahasram

Darya I Chudova

Provided are methods and systems for sample quality control in CNV detection using test samples comprising cell-free nucleic acid fragments originating from a mother and a fetus. The method involves determining an exclusion region defined by at least a fetal fraction limit of detection (LOD) curve. The fetal fraction LOD curve varies with coverage values and indicates minimum values of fetal fractions needed to achieve a detection criterion given different coverages.

Limit of detection based quality control metric

Disclosed are methods for determining copy number variation (CNV) known or suspected to be associated with a variety of medical conditions. In some embodiments, methods are provided for determining copy number variation of fetuses using maternal samples comprising maternal and fetal cell free DNA. In some embodiments, methods are provided for determining CNVs known or suspected to be associated with a variety of medical conditions. Some embodiments disclosed herein provide methods to improve the sensitivity and/or specificity of sequence data analysis by deriving a fragment size parameter. In some implementations, information from fragments of different sizes are used to evaluate copy number variations. In some implementations, one or more t-statistics obtained from coverage information of the sequence of interest is used to evaluate copy number variations. In some implementations, one or more fetal fraction estimates are combined with one or more t-statistics to determine copy number variations.

Using cell-free DNA fragment size to determine copy number variations

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Orinda, CA, United States of America

Dimitri Skvortsov