SAMPLE CONTAMINATION DETECTION OF CONTAMINATED FRAGMENTS FOR CANCER CLASSIFICATION

Methods and systems for detecting contaminated fragments in a biological sample for cancer classification are disclosed. The system identifies multiple SNP site contamination markers and indel site contamination markers. The multiple SNP site contamination markers include at least two SNP sites with...

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Bibliographische Detailangaben
Hauptverfasser:	GROSS, Samuel, S, BAGARIA, Siddhartha
Format:	Patent
Sprache:	eng ; fre ; ger
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:	Methods and systems for detecting contaminated fragments in a biological sample for cancer classification are disclosed. The system identifies multiple SNP site contamination markers and indel site contamination markers. The multiple SNP site contamination markers include at least two SNP sites within a threshold distance, having population haplotype frequency within a range of threshold frequencies, excluding guanine-adenine polymorphisms and/or cytosine-thymine polymorphisms, ensuring Hardy-Weinberg equilibrium, or any combination of the parameters above. The indel site contamination markers include indel sequences that are within a threshold length, having high complexity, having population haplotype frequency within a range of threshold frequencies, ensuring Hardy-Weinberg equilibrium, or any combination of the parameters above. The system identifies contamination markers for which the sample is homozygous. The system estimates the contamination level of the sample by identifying fragments having a haplotype that is different than the homozygous haplotype of the respective contamination marker site.