METHODS FOR CLASSIFYING A SAMPLE INTO CLINICALLY RELEVANT CATEGORIES

The disclosure provides methods and kits for the classification of biological samples into clinically relevant categories. The method is a method of classifying a sample as comprising cell-free tumor DNA, the method comprising the steps of:(i) determining in a sample comprising a plurality of cell-f...

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Hauptverfasser:	LOIZIDES, Charalambos, ELIADES, Alexia, PATSALIS, Philippos, ACHILLEOS, Acilleas, TSANGARAS, Kyriakos, IOANNIDES, Marios, KOUMBARIS, George, KYPRI, Elena
Format:	Patent
Sprache:	eng
Schlagworte:	BEER BIOCHEMISTRY CHEMISTRY COMPOSITIONS OR TEST PAPERS THEREFOR CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL ORENZYMOLOGICAL PROCESSES ENZYMOLOGY MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEICACIDS OR MICROORGANISMS METALLURGY MICROBIOLOGY MUTATION OR GENETIC ENGINEERING PROCESSES OF PREPARING SUCH COMPOSITIONS SPIRITS VINEGAR WINE
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Beschreibung
Zusammenfassung:	The disclosure provides methods and kits for the classification of biological samples into clinically relevant categories. The method is a method of classifying a sample as comprising cell-free tumor DNA, the method comprising the steps of:(i) determining in a sample comprising a plurality of cell-free DNA (cfDNA) fragments the sequence coordinates of the start and/or stop of at least 100,000 cfDNA fragments by alignment to a reference sequence, (ii) determining in the reference sequence all nucleic acid motifs comprised of trinucleotides, tetranucleotides and pentanucleotides:a) within the range of 1 to 5 base pairs inwards but adjacent to each start and/or stop sequence coordinate determined in (i), and/orb) within a range of 1 to 5 base pairs outwards but adjacent to each start and/or stop sequence coordinate determined in (i),(iii) determining the frequency of:a) each sequence coordinate plus and/or minus 1 base pair determined in (i) in the plurality of cfDNA fragments comprised in the sample, b) each of the nucleic acid motifs determined in (ii) a) and b) in the plurality of cfDNA fragments comprised in the sample, (iv) calculating the ratio of each of the frequencies determined in (iii) a) and b) over a corresponding reference frequency, (v) calculating a diagnostic score separately for each ratio determined in step (iv), said score being the respective weighted sum of all respective frequency ratios of step (iv) (vi) calculating a combined diagnostic score from at least two or more of the diagnostic scores determined in (v) said score being the weighted sum of said two or more diagnostic scores determined in (v), and(vii) determining a classification of the sample by comparing the combined diagnostic score to a reference score, NIPD GENETICS PUBLIC COMPANY LIMITED CH Kilger Anwaltspartnerschaft mbBCyprus Fasanenstraße 29Our Ref.: B281-0029WO1 10719 Berlinwherein the sample is classified as comprising tumor cfDNA, if the combined diagnostic score value is higher than the mean of the reference score by at least one standard deviation of the reference score, wherein the reference score is calculated from one or more reference values.