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

Disclosed are methods for determining copy number variation (CNV) of a sequence of interest 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...

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Bibliographische Detailangaben
Hauptverfasser:	Skvortsov, Dimitri, Comstock, David A, Rava, Richard P, Duenwald, Sven, Barbacioru, Catalin, Chudova, Darya I, Jones, Keith W, Chen, Gengxin
Format:	Patent
Sprache:	eng
Schlagworte:	BEER BIOCHEMISTRY CHEMISTRY COMPOSITIONS OR TEST PAPERS THEREFOR CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL ORENZYMOLOGICAL PROCESSES ENZYMOLOGY HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATIONTECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING ORPROCESSING OF MEDICAL OR HEALTHCARE DATA INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTEDFOR SPECIFIC APPLICATION FIELDS MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEICACIDS OR MICROORGANISMS METALLURGY MICROBIOLOGY MUTATION OR GENETIC ENGINEERING PHYSICS PROCESSES OF PREPARING SUCH COMPOSITIONS SPIRITS VINEGAR WINE
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Beschreibung
Zusammenfassung:	Disclosed are methods for determining copy number variation (CNV) of a sequence of interest 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. The methods involve determining first and second coverages of sequence tags of the reference genome including the sequence of interest. The first coverages are based on sequence reads of cell-free nucleic acid fragments in a first size domain, and the second coverages are based on sequence reads of cell-free nucleic acid fragments in a second size domain. The methods also involve determining the copy number variation in the sequence of interest using a likelihood ratio calculated from the first coverages and the second coverages. Systems for performing the methods are also disclosed.