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Detection of renal cell carcinoma using plasma and urine cell-free DNA methylomes

Improving early cancer detection has the potential to substantially reduce cancer-related mortality. Cell-free methylated DNA immunoprecipitation and high-throughput sequencing (cfMeDIP-seq) is a highly sensitive assay capable of detecting early-stage tumors. We report accurate classification of pat... Full description

Journal Title: Nature medicine 2020-07, Vol.26 (7), p.1041-1043
Main Author: Nuzzo, Pier Vitale
Other Authors: Berchuck, Jacob E , Korthauer, Keegan , Spisak, Sandor , Nassar, Amin H , Abou Alaiwi, Sarah , Chakravarthy, Ankur , Shen, Shu Yi , Bakouny, Ziad , Boccardo, Francesco , Steinharter, John , Bouchard, Gabrielle , Curran, Catherine R , Pan, Wenting , Baca, Sylvan C , Seo, Ji-Heui , Lee, Gwo-Shu Mary , Michaelson, M Dror , Chang, Steven L , Waikar, Sushrut S , Sonpavde, Guru , Irizarry, Rafael A , Pomerantz, Mark , De Carvalho, Daniel D , Choueiri, Toni K , Freedman, Matthew L
Format: Electronic Article Electronic Article
Language: English
Subjects:
DNA
Publisher: United States: Nature Publishing Group
ID: ISSN: 1078-8956
Link: https://www.ncbi.nlm.nih.gov/pubmed/32572266
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title: Detection of renal cell carcinoma using plasma and urine cell-free DNA methylomes
format: Article
creator:
  • Nuzzo, Pier Vitale
  • Berchuck, Jacob E
  • Korthauer, Keegan
  • Spisak, Sandor
  • Nassar, Amin H
  • Abou Alaiwi, Sarah
  • Chakravarthy, Ankur
  • Shen, Shu Yi
  • Bakouny, Ziad
  • Boccardo, Francesco
  • Steinharter, John
  • Bouchard, Gabrielle
  • Curran, Catherine R
  • Pan, Wenting
  • Baca, Sylvan C
  • Seo, Ji-Heui
  • Lee, Gwo-Shu Mary
  • Michaelson, M Dror
  • Chang, Steven L
  • Waikar, Sushrut S
  • Sonpavde, Guru
  • Irizarry, Rafael A
  • Pomerantz, Mark
  • De Carvalho, Daniel D
  • Choueiri, Toni K
  • Freedman, Matthew L
subjects:
  • Assaying
  • Biomarkers, Tumor - genetics
  • Cancer
  • Carcinoma, Renal cell
  • Carcinoma, Renal Cell - blood
  • Carcinoma, Renal Cell - diagnosis
  • Carcinoma, Renal Cell - genetics
  • Carcinoma, Renal Cell - urine
  • Cell-Free Nucleic Acids - blood
  • Cell-Free Nucleic Acids - genetics
  • Cell-Free Nucleic Acids - urine
  • Deoxyribonucleic acid
  • Diagnosis
  • DNA
  • DNA methylation
  • DNA Methylation - genetics
  • DNA sequencing
  • Early Detection of Cancer
  • Epigenome - genetics
  • Ethylenediaminetetraacetic acid
  • Gene sequencing
  • Genetic aspects
  • Genetic research
  • Health aspects
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Immunoprecipitation
  • Kidney cancer
  • Methylation
  • Next-generation sequencing
  • Oncology, Experimental
  • Renal cell carcinoma
  • Tumors
  • Urine
ispartof: Nature medicine, 2020-07, Vol.26 (7), p.1041-1043
description: Improving early cancer detection has the potential to substantially reduce cancer-related mortality. Cell-free methylated DNA immunoprecipitation and high-throughput sequencing (cfMeDIP-seq) is a highly sensitive assay capable of detecting early-stage tumors. We report accurate classification of patients across all stages of renal cell carcinoma (RCC) in plasma (area under the receiver operating characteristic (AUROC) curve of 0.99) and demonstrate the validity of this assay to identify patients with RCC using urine cell-free DNA (cfDNA; AUROC of 0.86).
language: eng
source:
identifier: ISSN: 1078-8956
fulltext: no_fulltext
issn:
  • 1078-8956
  • 1546-170X
url: Link


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titleDetection of renal cell carcinoma using plasma and urine cell-free DNA methylomes
creatorNuzzo, Pier Vitale ; Berchuck, Jacob E ; Korthauer, Keegan ; Spisak, Sandor ; Nassar, Amin H ; Abou Alaiwi, Sarah ; Chakravarthy, Ankur ; Shen, Shu Yi ; Bakouny, Ziad ; Boccardo, Francesco ; Steinharter, John ; Bouchard, Gabrielle ; Curran, Catherine R ; Pan, Wenting ; Baca, Sylvan C ; Seo, Ji-Heui ; Lee, Gwo-Shu Mary ; Michaelson, M Dror ; Chang, Steven L ; Waikar, Sushrut S ; Sonpavde, Guru ; Irizarry, Rafael A ; Pomerantz, Mark ; De Carvalho, Daniel D ; Choueiri, Toni K ; Freedman, Matthew L
creatorcontribNuzzo, Pier Vitale ; Berchuck, Jacob E ; Korthauer, Keegan ; Spisak, Sandor ; Nassar, Amin H ; Abou Alaiwi, Sarah ; Chakravarthy, Ankur ; Shen, Shu Yi ; Bakouny, Ziad ; Boccardo, Francesco ; Steinharter, John ; Bouchard, Gabrielle ; Curran, Catherine R ; Pan, Wenting ; Baca, Sylvan C ; Seo, Ji-Heui ; Lee, Gwo-Shu Mary ; Michaelson, M Dror ; Chang, Steven L ; Waikar, Sushrut S ; Sonpavde, Guru ; Irizarry, Rafael A ; Pomerantz, Mark ; De Carvalho, Daniel D ; Choueiri, Toni K ; Freedman, Matthew L
descriptionImproving early cancer detection has the potential to substantially reduce cancer-related mortality. Cell-free methylated DNA immunoprecipitation and high-throughput sequencing (cfMeDIP-seq) is a highly sensitive assay capable of detecting early-stage tumors. We report accurate classification of patients across all stages of renal cell carcinoma (RCC) in plasma (area under the receiver operating characteristic (AUROC) curve of 0.99) and demonstrate the validity of this assay to identify patients with RCC using urine cell-free DNA (cfDNA; AUROC of 0.86).
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languageeng
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subjectAssaying ; Biomarkers, Tumor - genetics ; Cancer ; Carcinoma, Renal cell ; Carcinoma, Renal Cell - blood ; Carcinoma, Renal Cell - diagnosis ; Carcinoma, Renal Cell - genetics ; Carcinoma, Renal Cell - urine ; Cell-Free Nucleic Acids - blood ; Cell-Free Nucleic Acids - genetics ; Cell-Free Nucleic Acids - urine ; Deoxyribonucleic acid ; Diagnosis ; DNA ; DNA methylation ; DNA Methylation - genetics ; DNA sequencing ; Early Detection of Cancer ; Epigenome - genetics ; Ethylenediaminetetraacetic acid ; Gene sequencing ; Genetic aspects ; Genetic research ; Health aspects ; High-Throughput Nucleotide Sequencing ; Humans ; Immunoprecipitation ; Kidney cancer ; Methylation ; Next-generation sequencing ; Oncology, Experimental ; Renal cell carcinoma ; Tumors ; Urine
ispartofNature medicine, 2020-07, Vol.26 (7), p.1041-1043
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0Nuzzo, Pier Vitale
1Berchuck, Jacob E
2Korthauer, Keegan
3Spisak, Sandor
4Nassar, Amin H
5Abou Alaiwi, Sarah
6Chakravarthy, Ankur
7Shen, Shu Yi
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11Bouchard, Gabrielle
12Curran, Catherine R
13Pan, Wenting
14Baca, Sylvan C
15Seo, Ji-Heui
16Lee, Gwo-Shu Mary
17Michaelson, M Dror
18Chang, Steven L
19Waikar, Sushrut S
20Sonpavde, Guru
21Irizarry, Rafael A
22Pomerantz, Mark
23De Carvalho, Daniel D
24Choueiri, Toni K
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0Detection of renal cell carcinoma using plasma and urine cell-free DNA methylomes
1Nature medicine
addtitleNat Med
descriptionImproving early cancer detection has the potential to substantially reduce cancer-related mortality. Cell-free methylated DNA immunoprecipitation and high-throughput sequencing (cfMeDIP-seq) is a highly sensitive assay capable of detecting early-stage tumors. We report accurate classification of patients across all stages of renal cell carcinoma (RCC) in plasma (area under the receiver operating characteristic (AUROC) curve of 0.99) and demonstrate the validity of this assay to identify patients with RCC using urine cell-free DNA (cfDNA; AUROC of 0.86).
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1Biomarkers, Tumor - genetics
2Cancer
3Carcinoma, Renal cell
4Carcinoma, Renal Cell - blood
5Carcinoma, Renal Cell - diagnosis
6Carcinoma, Renal Cell - genetics
7Carcinoma, Renal Cell - urine
8Cell-Free Nucleic Acids - blood
9Cell-Free Nucleic Acids - genetics
10Cell-Free Nucleic Acids - urine
11Deoxyribonucleic acid
12Diagnosis
13DNA
14DNA methylation
15DNA Methylation - genetics
16DNA sequencing
17Early Detection of Cancer
18Epigenome - genetics
19Ethylenediaminetetraacetic acid
20Gene sequencing
21Genetic aspects
22Genetic research
23Health aspects
24High-Throughput Nucleotide Sequencing
25Humans
26Immunoprecipitation
27Kidney cancer
28Methylation
29Next-generation sequencing
30Oncology, Experimental
31Renal cell carcinoma
32Tumors
33Urine
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12Curran, Catherine R
13Pan, Wenting
14Baca, Sylvan C
15Seo, Ji-Heui
16Lee, Gwo-Shu Mary
17Michaelson, M Dror
18Chang, Steven L
19Waikar, Sushrut S
20Sonpavde, Guru
21Irizarry, Rafael A
22Pomerantz, Mark
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titleDetection of renal cell carcinoma using plasma and urine cell-free DNA methylomes
authorNuzzo, Pier Vitale ; Berchuck, Jacob E ; Korthauer, Keegan ; Spisak, Sandor ; Nassar, Amin H ; Abou Alaiwi, Sarah ; Chakravarthy, Ankur ; Shen, Shu Yi ; Bakouny, Ziad ; Boccardo, Francesco ; Steinharter, John ; Bouchard, Gabrielle ; Curran, Catherine R ; Pan, Wenting ; Baca, Sylvan C ; Seo, Ji-Heui ; Lee, Gwo-Shu Mary ; Michaelson, M Dror ; Chang, Steven L ; Waikar, Sushrut S ; Sonpavde, Guru ; Irizarry, Rafael A ; Pomerantz, Mark ; De Carvalho, Daniel D ; Choueiri, Toni K ; Freedman, Matthew L
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1Biomarkers, Tumor - genetics
2Cancer
3Carcinoma, Renal cell
4Carcinoma, Renal Cell - blood
5Carcinoma, Renal Cell - diagnosis
6Carcinoma, Renal Cell - genetics
7Carcinoma, Renal Cell - urine
8Cell-Free Nucleic Acids - blood
9Cell-Free Nucleic Acids - genetics
10Cell-Free Nucleic Acids - urine
11Deoxyribonucleic acid
12Diagnosis
13DNA
14DNA methylation
15DNA Methylation - genetics
16DNA sequencing
17Early Detection of Cancer
18Epigenome - genetics
19Ethylenediaminetetraacetic acid
20Gene sequencing
21Genetic aspects
22Genetic research
23Health aspects
24High-Throughput Nucleotide Sequencing
25Humans
26Immunoprecipitation
27Kidney cancer
28Methylation
29Next-generation sequencing
30Oncology, Experimental
31Renal cell carcinoma
32Tumors
33Urine
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1Berchuck, Jacob E
2Korthauer, Keegan
3Spisak, Sandor
4Nassar, Amin H
5Abou Alaiwi, Sarah
6Chakravarthy, Ankur
7Shen, Shu Yi
8Bakouny, Ziad
9Boccardo, Francesco
10Steinharter, John
11Bouchard, Gabrielle
12Curran, Catherine R
13Pan, Wenting
14Baca, Sylvan C
15Seo, Ji-Heui
16Lee, Gwo-Shu Mary
17Michaelson, M Dror
18Chang, Steven L
19Waikar, Sushrut S
20Sonpavde, Guru
21Irizarry, Rafael A
22Pomerantz, Mark
23De Carvalho, Daniel D
24Choueiri, Toni K
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7Shen, Shu Yi
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9Boccardo, Francesco
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notes
0Author Contributions: P.V.N., J.E.B., S.S., M.P., T.K.C., M.L.F. conceived and designed experiments. P.V.N., J.E.B., S.S. performed experiments. P.V.N., J.E.B., S.S., K.K., S.C.B., R.A.I., M.P., D.D.D.C., T.K.C., M.L.F. analyzed and interpreted data. M.D.M, S.L.C., S.S.W., G.S. contributed patient samples. A.H.N., S.A.A., Z.B., J.S., G.B., C.R.C., W.P., G.-S.M.L., M.D.M. collected patient data and samples. P.V.N., J.E.B., S.S., K.K., A.C., S.Y.S., F.B., S.C.B., J.-H.S., R.A.I., M.P., D.D.D.C., T.K.C., M.L.F. provided guidance and scientific input. P.V.N., J.E.B., S.S., D.D.D.C., T.K.C., M.L.F. drafted the manuscript. All authors read and approved the final manuscript.
1equal contribution (P.V.N., J.E.B., K.K., S.S.)
2equal contribution (D.D.D.C., T.K.C., M.L.F.)
abstractImproving early cancer detection has the potential to substantially reduce cancer-related mortality. Cell-free methylated DNA immunoprecipitation and high-throughput sequencing (cfMeDIP-seq) is a highly sensitive assay capable of detecting early-stage tumors. We report accurate classification of patients across all stages of renal cell carcinoma (RCC) in plasma (area under the receiver operating characteristic (AUROC) curve of 0.99) and demonstrate the validity of this assay to identify patients with RCC using urine cell-free DNA (cfDNA; AUROC of 0.86).
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