Cold Spring Harbor Laboratory

Koninklijke Philips Corporation N.V.

James Bruce Hicks

Michael H Wigler

Zihua Wang

Jennifer Troge

Nicholas Navin

Sitharthan Kamalakaran

Robert Lucito

Alexander Krasnitz

Anders P Zetterberg

A method for obtaining from genomic material genomic copy number information unaffected by amplification distortion, comprising obtaining segments of the genomic material, tagging the segments with substantially unique tags to generate tagged nucleic acid molecules, such that each tagged nucleic acid molecule comprises one segment of the genomic material and a tag, subjecting the tagged nucleic acid molecules to polymerase chain reaction (PCR) amplification, generating tag associated sequence reads by sequencing the product of the PCR reaction, assigning each tagged nucleic acid molecule to a location on a genome associated with the genomic material by mapping the subsequence of each tag associated sequence read corresponding to a segment of the genomic material to a location on the genome, and counting the number of tagged nucleic acid molecules assigned to the same location on the genome having a different tag, thereby obtaining genomic copy number information unaffected by amplification distortion.

Varietal counting of nucleic acids for obtaining genomic copy number information

A method for obtaining from genomic material genomic copy number information unaffected by amplification distortion, comprising obtaining segments of the genomic material, tagging the segments with substantially unique tags to generate tagged nucleic acid molecules, such that each tagged nucleic acid molecule comprises one segment of the genomic material and a tag, subjecting the tagged nucleic acid molecules to amplification by polymerase chain reaction (PCR), generating tag associated sequence reads by sequencing the product of the PCR reaction, assigning each tagged nucleic acid molecule to a location on a genome associated with the genomic material by mapping the subsequence of each tag associated sequence read corresponding to a segment of the genomic material to a location on the genome, and counting the number of tagged nucleic acid molecules having a different tag that have been assigned to the same location on the genome, thereby obtaining genomic copy number information unaffected by amplification distortion.

The invention relates to the fields of therapeutics and identifying candidates for therapy, in particular to a method of identifying candidates for trastuzumab (Herceptin&#xae;) therapy in a patient presenting with breast cancer based on the presence or absence of specific genetic markers in a tumor sample from said patient.

Genetic markers indicative of a cancer patient response to trastuzumab (herceptin)

The invention relates to a method for the analysis of ovarian cancer disorders, comprising determining the genomic methylation status of one or more CpG dinucleotides in a sequence selected from the group of sequences according to SEQ ID NO. 1 to 10 and/or SEQ ID NO. 50 to SEQ ID NO. 60. Optionally, additionally following steps are performed, the one or more results from the methylation status test is input into a classifier that is obtained from a Diagnostic Multi Variate Model, calculating a likelihood as to whether the sample is from a normal tissue or an ovarian cancer tissue and/or, calculating an associated p-value for the confidence in the prediction.

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Lattingtown, NY, United States of America

James Bruce Hicks