High-throughput molecular analysis of urine sediment for the detection of bladder cancer by high-density single-nucleotide polymorphism array

Mohammad Obaidul Hoque, Juna Lee, Shahnaz Begum, Keishi Yamashita, James M. Engles, Mark P. Schoenberg, William H. Westra, David Sidransky

Research output: Contribution to journalArticle

49 Citations (Scopus)

Abstract

The detection of urothelial malignancies remains challenging. The majority of patients diagnosed with bladder cancer require life-long surveillance for disease recurrence. Monitoring strategies rely predominantly on invasive endoscopic techniques, which are inconvenient and uncomfortable. Multiple in vitro diagnostic technologies have been developed to supplant the contemporary standard of care. The U.S. Food and Drug Administration has approved several assays, but [because of inferior performance characteristics (low sensitivity and specificity)] these tests have not made a significant impact on practice, to date. We sought to develop a test for bladder cancer with better performance characterization detection based on a novel molecular approach. Matched urine and peripheral blood lymphocyte samples were obtained before surgery from 31 patients with bladder cancer (10 pTa, 4 pT1, and 17 pT2≥). DNA from these samples was subjected to allelic imbalance analysis using HuSNP chips and was validated in parallel with microsatellite analysis for loss of heterozygosity and microsatellite instability. Peripheral blood lymphocyte and urine DNA obtained from 14 individuals without clinical evidence of genitourinary malignancy served as controls. Thirty-one of 31 (100%) urine DNA samples from patients with bladder tumors were found to have 24 or more single-nucleotide polymorphism (SNP) DNA alterations. In general, SNP alterations were more common in urine samples from pT2≥ tumors than pTa or pT1 tumors. SNP alterations were not identified in nine normal control subjects and in four of five patients with hematuria. These data support the noninvasive HuSNP chip assay in urine DNA as a valuable tool for the detection of bladder cancer (on a high-throughput-automated platform).

Original languageEnglish (US)
Pages (from-to)5723-5726
Number of pages4
JournalCancer Research
Volume63
Issue number18
StatePublished - Sep 15 2003
Externally publishedYes

Fingerprint

Urinary Bladder Neoplasms
Single Nucleotide Polymorphism
Urine
DNA
Neoplasms
Allelic Imbalance
Lymphocytes
Microsatellite Instability
Loss of Heterozygosity
Hematuria
United States Food and Drug Administration
Standard of Care
Microsatellite Repeats
Technology
Recurrence
Sensitivity and Specificity

ASJC Scopus subject areas

  • Cancer Research
  • Oncology

Cite this

High-throughput molecular analysis of urine sediment for the detection of bladder cancer by high-density single-nucleotide polymorphism array. / Hoque, Mohammad Obaidul; Lee, Juna; Begum, Shahnaz; Yamashita, Keishi; Engles, James M.; Schoenberg, Mark P.; Westra, William H.; Sidransky, David.

In: Cancer Research, Vol. 63, No. 18, 15.09.2003, p. 5723-5726.

Research output: Contribution to journalArticle

Hoque, MO, Lee, J, Begum, S, Yamashita, K, Engles, JM, Schoenberg, MP, Westra, WH & Sidransky, D 2003, 'High-throughput molecular analysis of urine sediment for the detection of bladder cancer by high-density single-nucleotide polymorphism array', Cancer Research, vol. 63, no. 18, pp. 5723-5726.
Hoque, Mohammad Obaidul ; Lee, Juna ; Begum, Shahnaz ; Yamashita, Keishi ; Engles, James M. ; Schoenberg, Mark P. ; Westra, William H. ; Sidransky, David. / High-throughput molecular analysis of urine sediment for the detection of bladder cancer by high-density single-nucleotide polymorphism array. In: Cancer Research. 2003 ; Vol. 63, No. 18. pp. 5723-5726.
@article{9c4cef8f20444227b653c1c33eb59bb5,
title = "High-throughput molecular analysis of urine sediment for the detection of bladder cancer by high-density single-nucleotide polymorphism array",
abstract = "The detection of urothelial malignancies remains challenging. The majority of patients diagnosed with bladder cancer require life-long surveillance for disease recurrence. Monitoring strategies rely predominantly on invasive endoscopic techniques, which are inconvenient and uncomfortable. Multiple in vitro diagnostic technologies have been developed to supplant the contemporary standard of care. The U.S. Food and Drug Administration has approved several assays, but [because of inferior performance characteristics (low sensitivity and specificity)] these tests have not made a significant impact on practice, to date. We sought to develop a test for bladder cancer with better performance characterization detection based on a novel molecular approach. Matched urine and peripheral blood lymphocyte samples were obtained before surgery from 31 patients with bladder cancer (10 pTa, 4 pT1, and 17 pT2≥). DNA from these samples was subjected to allelic imbalance analysis using HuSNP chips and was validated in parallel with microsatellite analysis for loss of heterozygosity and microsatellite instability. Peripheral blood lymphocyte and urine DNA obtained from 14 individuals without clinical evidence of genitourinary malignancy served as controls. Thirty-one of 31 (100{\%}) urine DNA samples from patients with bladder tumors were found to have 24 or more single-nucleotide polymorphism (SNP) DNA alterations. In general, SNP alterations were more common in urine samples from pT2≥ tumors than pTa or pT1 tumors. SNP alterations were not identified in nine normal control subjects and in four of five patients with hematuria. These data support the noninvasive HuSNP chip assay in urine DNA as a valuable tool for the detection of bladder cancer (on a high-throughput-automated platform).",
author = "Hoque, {Mohammad Obaidul} and Juna Lee and Shahnaz Begum and Keishi Yamashita and Engles, {James M.} and Schoenberg, {Mark P.} and Westra, {William H.} and David Sidransky",
year = "2003",
month = "9",
day = "15",
language = "English (US)",
volume = "63",
pages = "5723--5726",
journal = "Journal of Cancer Research",
issn = "0008-5472",
publisher = "American Association for Cancer Research Inc.",
number = "18",

}

TY - JOUR

T1 - High-throughput molecular analysis of urine sediment for the detection of bladder cancer by high-density single-nucleotide polymorphism array

AU - Hoque, Mohammad Obaidul

AU - Lee, Juna

AU - Begum, Shahnaz

AU - Yamashita, Keishi

AU - Engles, James M.

AU - Schoenberg, Mark P.

AU - Westra, William H.

AU - Sidransky, David

PY - 2003/9/15

Y1 - 2003/9/15

N2 - The detection of urothelial malignancies remains challenging. The majority of patients diagnosed with bladder cancer require life-long surveillance for disease recurrence. Monitoring strategies rely predominantly on invasive endoscopic techniques, which are inconvenient and uncomfortable. Multiple in vitro diagnostic technologies have been developed to supplant the contemporary standard of care. The U.S. Food and Drug Administration has approved several assays, but [because of inferior performance characteristics (low sensitivity and specificity)] these tests have not made a significant impact on practice, to date. We sought to develop a test for bladder cancer with better performance characterization detection based on a novel molecular approach. Matched urine and peripheral blood lymphocyte samples were obtained before surgery from 31 patients with bladder cancer (10 pTa, 4 pT1, and 17 pT2≥). DNA from these samples was subjected to allelic imbalance analysis using HuSNP chips and was validated in parallel with microsatellite analysis for loss of heterozygosity and microsatellite instability. Peripheral blood lymphocyte and urine DNA obtained from 14 individuals without clinical evidence of genitourinary malignancy served as controls. Thirty-one of 31 (100%) urine DNA samples from patients with bladder tumors were found to have 24 or more single-nucleotide polymorphism (SNP) DNA alterations. In general, SNP alterations were more common in urine samples from pT2≥ tumors than pTa or pT1 tumors. SNP alterations were not identified in nine normal control subjects and in four of five patients with hematuria. These data support the noninvasive HuSNP chip assay in urine DNA as a valuable tool for the detection of bladder cancer (on a high-throughput-automated platform).

AB - The detection of urothelial malignancies remains challenging. The majority of patients diagnosed with bladder cancer require life-long surveillance for disease recurrence. Monitoring strategies rely predominantly on invasive endoscopic techniques, which are inconvenient and uncomfortable. Multiple in vitro diagnostic technologies have been developed to supplant the contemporary standard of care. The U.S. Food and Drug Administration has approved several assays, but [because of inferior performance characteristics (low sensitivity and specificity)] these tests have not made a significant impact on practice, to date. We sought to develop a test for bladder cancer with better performance characterization detection based on a novel molecular approach. Matched urine and peripheral blood lymphocyte samples were obtained before surgery from 31 patients with bladder cancer (10 pTa, 4 pT1, and 17 pT2≥). DNA from these samples was subjected to allelic imbalance analysis using HuSNP chips and was validated in parallel with microsatellite analysis for loss of heterozygosity and microsatellite instability. Peripheral blood lymphocyte and urine DNA obtained from 14 individuals without clinical evidence of genitourinary malignancy served as controls. Thirty-one of 31 (100%) urine DNA samples from patients with bladder tumors were found to have 24 or more single-nucleotide polymorphism (SNP) DNA alterations. In general, SNP alterations were more common in urine samples from pT2≥ tumors than pTa or pT1 tumors. SNP alterations were not identified in nine normal control subjects and in four of five patients with hematuria. These data support the noninvasive HuSNP chip assay in urine DNA as a valuable tool for the detection of bladder cancer (on a high-throughput-automated platform).

UR - http://www.scopus.com/inward/record.url?scp=0141508014&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0141508014&partnerID=8YFLogxK

M3 - Article

VL - 63

SP - 5723

EP - 5726

JO - Journal of Cancer Research

JF - Journal of Cancer Research

SN - 0008-5472

IS - 18

ER -