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US 12,644,892 B2Granted
Biomarkers for clear cell renal cell carcinoma
AssigneeVenn Biosciences Corporation
InventorsDaniel Serie, Klaus Lindpaintner
Life of this patent
Estimating the term…
Abstract
Set forth herein are methods useful for identifying disease biomarkers, particularly for diseases such as clear cell renal cell carcinoma (ccRCC). In some examples, the methods set forth herein are useful for monitoring the prognosis of patients having disease such as ccRCC.
Claims35
A method for classifying a biological sample from an individual having clear cell renal cell carcinoma (ccRCC), the method comprising:
- quantifying one or more glycopeptides to obtain quantification information,
- wherein the quantifying is based on information obtained from a liquid chromatography/mass spectrometry (LC/MS) analysis of a prepared sample from the biological sample for the LC/MS analysis,
- wherein the one or more glycopeptides include one or more of SEQ ID NO:1 comprising glycan 7603 at residue 271;
- SEQ ID NO:2 comprising glycan 5402 at residue 402-MC;
- SEQ ID NO:3 comprising glycan 7614 at residue 72;
- SEQ ID NO:4 comprising glycan 5401 at residue 3411;
- SEQ ID NO:5 comprising glycan 1111 at residue 74;
- SEQ ID NO:6 comprising glycan 1300 at residue 74;
- SEQ ID NO:7 comprising glycan 2110 at residue 74;
- SEQ ID NO:8 comprising glycan 1102 at residue 74-Aoff;
- SEQ ID NO:9 comprising glycan 5402 at residue 98;
- SEQ ID NO:10 comprising glycan 5410 at residue 98;
- SEQ ID NO:11 comprising glycan 6510 at residue 98;
- SEQ ID NO:12 comprising glycan 6530 at residue 98;
- SEQ ID NO:13 comprising glycan 9800 at residue 98;
- SEQ ID NO:14 comprising glycan 5421 at residue 135;
- SEQ ID NO:15 comprising glycan 8500 at residue 135;
- SEQ ID NO:16 comprising glycan 5402 at residue 174;
- SEQ ID NO:17 comprising glycan 6503 at residue 366;
- SEQ ID NO:18 comprising glycan 6513 at residue 366;
- SEQ ID NO:19 comprising glycan 5400 at residue 291;
- SEQ ID NO:20 comprising glycan 6503 at residue 291;
- SEQ ID NO:21 comprising glycan 5402 at residue 437;
- SEQ ID NO:22 comprising glycan 5402 at residue 156;
- SEQ ID NO:23 comprising glycan 6503 at residue 176;
- SEQ ID NO:24 comprising glycan 6513 at residue 176;
- SEQ ID NO:25 comprising glycan 6513 at residue 241;
- SEQ ID NO:26 comprising glycan 5411 at residue 297;
- SEQ ID NO:27 comprising glycan 5411 at residue 71;
- SEQ ID NO:28 comprising glycan 5402 at residue 494;
- SEQ ID NO:29 comprising glycan 6503 at residue 494;
- SEQ ID NO:30 comprising glycan 5420 at residue 324;
- SEQ ID NO:31 comprising glycan 6501 at residue 324;
- SEQ ID NO:32 comprising glycan 6502 at residue 324;
- SEQ ID NO:33 comprising glycan 5401 at residue 121;
- SEQ ID NO:34 comprising glycan 5402 at residue 121;
- SEQ ID NO:35 comprising glycan 5400 at residue 630;
- SEQ ID NO:36 comprising glycan 6502 at residue 630;
- SEQ ID NO:37 comprising glycan 5431 at residue 1005;
- SEQ ID NO:38 comprising glycan 7420 at residue 1005;
- or SEQ ID NO:39 comprising glycan 5412 at residue 112;
- inputting the quantification information of the one or more glycopeptides into a trained machine learning model to generate an output probability;
- and
- outputting the output probability for ccRCC progression-free survival classification of the biological sample.
41 more elements
A method for classifying a biological sample from an individual having clear cell renal cell carcinoma (ccRCC), the method comprising:
- quantifying one or more glycopeptides to obtain quantification information,
- wherein the quantifying is based on information obtained from a liquid chromatography/mass spectrometry (LC/MS) analysis of a prepared sample from the biological sample for the LC/MS analysis,
- wherein the one or more glycopeptides include one or more of SEQ ID NO:1 comprising glycan 7603 at residue 271;
- SEQ ID NO:2 comprising glycan 5402 at residue 402-MC;
- SEQ ID NO:3 comprising glycan 7614 at residue 72;
- SEQ ID NO:4 comprising glycan 5401 at residue 3411;
- SEQ ID NO:5 comprising glycan 1111 at residue 74;
- SEQ ID NO:6 comprising glycan 1300 at residue 74;
- SEQ ID NO:7 comprising glycan 2110 at residue 74;
- SEQ ID NO:8 comprising glycan 1102 at residue 74-Aoff;
- SEQ ID NO:9 comprising glycan 5402 at residue 98;
- SEQ ID NO:10 comprising glycan 5410 at residue 98;
- SEQ ID NO:11 comprising glycan 6510 at residue 98;
- SEQ ID NO:12 comprising glycan 6530 at residue 98;
- SEQ ID NO:13 comprising glycan 9800 at residue 98;
- SEQ ID NO:14 comprising glycan 5421 at residue 135;
- SEQ ID NO:15 comprising glycan 8500 at residue 135;
- SEQ ID NO:16 comprising glycan 5402 at residue 174;
- SEQ ID NO:17 comprising glycan 6503 at residue 366;
- SEQ ID NO:18 comprising glycan 6513 at residue 366;
- SEQ ID NO:19 comprising glycan 5400 at residue 291;
- SEQ ID NO:20 comprising glycan 6503 at residue 291;
- SEQ ID NO:21 comprising glycan 5402 at residue 437;
- SEQ ID NO:22 comprising glycan 5402 at residue 156;
- SEQ ID NO:23 comprising glycan 6503 at residue 176;
- SEQ ID NO:24 comprising glycan 6513 at residue 176;
- SEQ ID NO:25 comprising glycan 6513 at residue 241;
- SEQ ID NO:26 comprising glycan 5411 at residue 297;
- SEQ ID NO:27 comprising glycan 5411 at residue 71;
- SEQ ID NO:28 comprising glycan 5402 at residue 494;
- SEQ ID NO:29 comprising glycan 6503 at residue 494;
- SEQ ID NO:30 comprising glycan 5420 at residue 324;
- SEQ ID NO:31 comprising glycan 6501 at residue 324;
- SEQ ID NO:32 comprising glycan 6502 at residue 324;
- SEQ ID NO:33 comprising glycan 5401 at residue 121;
- SEQ ID NO:34 comprising glycan 5402 at residue 121;
- SEQ ID NO:35 comprising glycan 5400 at residue 630;
- SEQ ID NO:36 comprising glycan 6502 at residue 630;
- SEQ ID NO:37 comprising glycan 5431 at residue 1005;
- SEQ ID NO:38 comprising glycan 7420 at residue 1005;
- or SEQ ID NO:39 comprising glycan 5412 at residue 112;
- and
- generating a multivariable score based on the quantification information for ccRCC progression-free survival classification of the biological sample,
- wherein the multivariable score is based on a sum of instances of the one or more glycopeptides being above an associated cut-off value.
41 more elements
A method comprising:
- (a) obtaining a biological sample from an individual having clear cell renal cell carcinoma (ccRCC);
- (b) preparing the biological sample for a liquid chromatography/mass spectrometry (LC/MS) analysis comprising multiple-reaction-monitoring (MRM);
- and
- (c) performing the MRM LC/MS analysis comprising monitoring one or more of transitions 1-39.
1 more element
Dependencies are inferred from the claim text.