Translation of an STR-based biomarker into a clinically compatible SNP-based platform for loss of heterozygosity.

PubWeight™: 0.87‹?›

🔗 View Article (PMC 2861428)

Published in Cancer Biomark on January 01, 2009

Authors

Heather D Kissel1, Patricia C Galipeau, Xiaohong Li, Brian J Reid

Author Affiliations

1: Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA. hkissel@fhcrc.org

Articles cited by this

BLAT--the BLAST-like alignment tool. Genome Res (2002) 126.78

Hospital volume and surgical mortality in the United States. N Engl J Med (2002) 25.79

The IARC TP53 database: new online mutation analysis and recommendations to users. Hum Mutat (2002) 12.39

Phases of biomarker development for early detection of cancer. J Natl Cancer Inst (2001) 10.37

Updated guidelines 2008 for the diagnosis, surveillance and therapy of Barrett's esophagus. Am J Gastroenterol (2008) 7.94

Principles of tumor suppression. Cell (2004) 5.52

Loss-of-heterozygosity analysis of small-cell lung carcinomas using single-nucleotide polymorphism arrays. Nat Biotechnol (2000) 4.10

Single-nucleotide polymorphism analysis by pyrosequencing. Anal Biochem (2000) 3.21

INK4a/ARF: a multifunctional tumor suppressor locus. Mutat Res (2005) 3.08

Predictors of progression to cancer in Barrett's esophagus: baseline histology and flow cytometry identify low- and high-risk patient subsets. Am J Gastroenterol (2000) 2.99

Barrett's esophagus, dysplasia, and adenocarcinoma. Hum Pathol (1994) 2.97

Use of allelic loss to predict malignant risk for low-grade oral epithelial dysplasia. Clin Cancer Res (2000) 2.71

p16(MTS-1/CDKN2/INK4a) in cancer progression. Exp Cell Res (2001) 2.34

Predicting cancer development in oral leukoplakia: ten years of translational research. Clin Cancer Res (2000) 2.34

Frequent microsatellite alterations at chromosomes 9p21 and 3p14 in oral premalignant lesions and their value in cancer risk assessment. Nat Med (1996) 2.29

NSAIDs modulate CDKN2A, TP53, and DNA content risk for progression to esophageal adenocarcinoma. PLoS Med (2007) 2.23

Predictors of progression in Barrett's esophagus III: baseline flow cytometric variables. Am J Gastroenterol (2001) 2.21

Predictors of progression in Barrett's esophagus II: baseline 17p (p53) loss of heterozygosity identifies a patient subset at increased risk for neoplastic progression. Am J Gastroenterol (2001) 2.17

SNP arrays in heterogeneous tissue: highly accurate collection of both germline and somatic genetic information from unpaired single tumor samples. Am J Hum Genet (2008) 2.00

Loss of heterozygosity analysis using whole genome amplification, cell sorting, and fluorescence-based PCR. Genome Res (1999) 1.90

Mortality rates in patients with Barrett's oesophagus. Aliment Pharmacol Ther (2007) 1.81

High-resolution copy number analysis of paraffin-embedded archival tissue using SNP BeadArrays. Genome Res (2007) 1.61

Mortality in Barrett's oesophagus: results from a population based study. Gut (2003) 1.60

Combined array-comparative genomic hybridization and single-nucleotide polymorphism-loss of heterozygosity analysis reveals complex changes and multiple forms of chromosomal instability in colorectal cancers. Cancer Res (2006) 1.56

Meta analysis: Cancer risk in Barrett's oesophagus. Aliment Pharmacol Ther (2007) 1.50

Genome-wide copy number analysis in esophageal adenocarcinoma using high-density single-nucleotide polymorphism arrays. Cancer Res (2008) 1.50

Single nucleotide polymorphism-based genome-wide chromosome copy change, loss of heterozygosity, and aneuploidy in Barrett's esophagus neoplastic progression. Cancer Prev Res (Phila) (2008) 1.43

A high-throughput method for quantifying alleles and haplotypes of the malaria vaccine candidate Plasmodium falciparum merozoite surface protein-1 19 kDa. Malar J (2006) 1.41

Characterization of 26 miniSTR loci for improved analysis of degraded DNA samples. J Forensic Sci (2007) 1.35

Claudin-18: a dominant tight junction protein in Barrett's esophagus and likely contributor to its acid resistance. Am J Physiol Gastrointest Liver Physiol (2007) 1.29

Combined array-comparative genomic hybridization and single-nucleotide polymorphism-loss of heterozygosity analysis reveals complex genetic alterations in cervical cancer. BMC Genomics (2007) 1.24

Genotypic analysis of multiple loci in somatic cells by whole genome amplification. Nucleic Acids Res (1995) 1.24

Rare CpG island methylator phenotype in ulcerative colitis-associated neoplasias. Gastroenterology (2007) 1.23

Genome-wide screening of copy number alterations and LOH events in renal cell carcinomas and integration with gene expression profile. Mol Cancer (2008) 1.22

Comparison of methods for extracting DNA from formalin-fixed paraffin sections for nonisotopic PCR. Diagn Mol Pathol (1996) 1.20

Comprehensive analysis of loss of heterozygosity events in glioblastoma using the 100K SNP mapping arrays and comparison with copy number abnormalities defined by BAC array comparative genomic hybridization. Genes Chromosomes Cancer (2008) 1.17

DNA/protein flow cytometry as a predictive marker of malignancy in dysplasia-free Barrett's esophagus: thirteen-year follow-up study on a cohort of patients. Cytometry (1998) 1.13

A comparison of conventional cytology, DNA ploidy analysis, and fluorescence in situ hybridization for the detection of dysplasia and adenocarcinoma in patients with Barrett's esophagus. Hum Pathol (2008) 1.12

Potential use of quantitative tissue phenotype to predict malignant risk for oral premalignant lesions. Cancer Res (2008) 1.10

Gains and amplifications of c-myc, EGFR, and 20.q13 loci in the no dysplasia-dysplasia-adenocarcinoma sequence of Barrett's esophagus. Cancer Epidemiol Biomarkers Prev (2008) 1.08

Direct inference of SNP heterozygosity rates and resolution of LOH detection. PLoS Comput Biol (2007) 1.06

Molecular defense mechanisms of Barrett's metaplasia estimated by an integrative genomics. J Mol Med (Berl) (2007) 1.06

Esophageal mucin: an adherent mucus gel barrier is absent in the normal esophagus but present in columnar-lined Barrett's esophagus. Am J Gastroenterol (2001) 1.05

Improvements to bead-based oligonucleotide ligation SNP genotyping assays. Biotechniques (2008) 1.04

Electrical parameters and ion species for active transport in human esophageal stratified squamous epithelium and Barrett's specialized columnar epithelium. Am J Physiol Gastrointest Liver Physiol (2007) 1.02

Determination of CYP2D6 gene copy number by pyrosequencing. Clin Chem (2005) 1.01

Assessment of chromosomal gains as compared to DNA content changes is more useful to detect dysplasia in Barrett's esophagus brush cytology specimens. Genes Chromosomes Cancer (2008) 0.98

Current status of biomarkers in head and neck cancer. J Surg Oncol (2008) 0.98

Concordant loss of MTAP and p16/CDKN2A expression in gastroesophageal carcinogenesis: evidence of homozygous deletion in esophageal noninvasive precursor lesions and therapeutic implications. Am J Surg Pathol (2005) 0.97

A sensitive method for detecting variation in copy numbers of duplicated genes. Genome Res (2003) 0.94

Loss of heterozygosity on chromosome 17p predicts neoplastic progression in Barrett's esophagus. J Gastroenterol Hepatol (2003) 0.89

Exploring allelic imbalance within paraffin-embedded tumor biopsies using pyrosequencing technology. Clin Chem Lab Med (2006) 0.78

NIST mixed stain study 3: signal intensity balance in commercial short tandem repeat multiplexes. Anal Chem (2004) 0.77

Articles by these authors

Cancer as an evolutionary and ecological process. Nat Rev Cancer (2006) 9.33

Genetic clonal diversity predicts progression to esophageal adenocarcinoma. Nat Genet (2006) 6.71

High frequency targeted mutagenesis in Arabidopsis thaliana using zinc finger nucleases. Proc Natl Acad Sci U S A (2010) 4.78

Barrett's oesophagus and oesophageal adenocarcinoma: time for a new synthesis. Nat Rev Cancer (2010) 3.27

Extent of low-grade dysplasia is a risk factor for the development of esophageal adenocarcinoma in Barrett's esophagus. Am J Gastroenterol (2007) 3.00

Nf1-dependent tumors require a microenvironment containing Nf1+/-- and c-kit-dependent bone marrow. Cell (2008) 2.84

Maternal malaria and gravidity interact to modify infant susceptibility to malaria. PLoS Med (2005) 2.72

Non-steroidal anti-inflammatory drugs and risk of neoplastic progression in Barrett's oesophagus: a prospective study. Lancet Oncol (2005) 2.40

Leukocyte telomere length predicts cancer risk in Barrett's esophagus. Cancer Epidemiol Biomarkers Prev (2007) 2.39

Transcription activator-like effector nucleases enable efficient plant genome engineering. Plant Physiol (2012) 2.36

Progress in chemoprevention drug development: the promise of molecular biomarkers for prevention of intraepithelial neoplasia and cancer--a plan to move forward. Clin Cancer Res (2006) 2.24

NSAIDs modulate CDKN2A, TP53, and DNA content risk for progression to esophageal adenocarcinoma. PLoS Med (2007) 2.23

Gene expression analyzed by high-resolution state array analysis and quantitative proteomics: response of yeast to mating pheromone. Mol Cell Proteomics (2004) 2.22

Selectively advantageous mutations and hitchhikers in neoplasms: p16 lesions are selected in Barrett's esophagus. Cancer Res (2004) 2.15

Analysis of inflammatory cytokines in the tears of dry eye patients. Cornea (2009) 1.96

A comprehensive survey of clonal diversity measures in Barrett's esophagus as biomarkers of progression to esophageal adenocarcinoma. Cancer Prev Res (Phila) (2010) 1.89

The combination of genetic instability and clonal expansion predicts progression to esophageal adenocarcinoma. Cancer Res (2004) 1.76

MyD88 signaling in nonhematopoietic cells protects mice against induced colitis by regulating specific EGF receptor ligands. Proc Natl Acad Sci U S A (2010) 1.73

A likelihood-based approach to mixed modeling with ambiguity in cluster identifiers. Biostatistics (2008) 1.72

Enhanced sensitivity to DSS colitis caused by a hypomorphic Mbtps1 mutation disrupting the ATF6-driven unfolded protein response. Proc Natl Acad Sci U S A (2009) 1.69

A genome-wide association study identifies new susceptibility loci for esophageal adenocarcinoma and Barrett's esophagus. Nat Genet (2013) 1.67

Lethal mitochondrial cardiomyopathy in a hypomorphic Med30 mouse mutant is ameliorated by ketogenic diet. Proc Natl Acad Sci U S A (2011) 1.59

Focus on Barrett's esophagus and esophageal adenocarcinoma. Cancer Cell (2004) 1.57

Slc15a4, AP-3, and Hermansky-Pudlak syndrome proteins are required for Toll-like receptor signaling in plasmacytoid dendritic cells. Proc Natl Acad Sci U S A (2010) 1.55

Common variants at the MHC locus and at chromosome 16q24.1 predispose to Barrett's esophagus. Nat Genet (2012) 1.52

Retracted Alteration of astrocytes and Wnt/β-catenin signaling in the frontal cortex of autistic subjects. J Neuroinflammation (2012) 1.51

Reproducible two-dimensional capillary electrophoresis analysis of Barrett's esophagus tissues. Anal Chem (2006) 1.49

Nf1+/- mast cells induce neurofibroma like phenotypes through secreted TGF-beta signaling. Hum Mol Genet (2006) 1.48

Single nucleotide polymorphism-based genome-wide chromosome copy change, loss of heterozygosity, and aneuploidy in Barrett's esophagus neoplastic progression. Cancer Prev Res (Phila) (2008) 1.43

Alginate production by Pseudomonas putida creates a hydrated microenvironment and contributes to biofilm architecture and stress tolerance under water-limiting conditions. J Bacteriol (2007) 1.41

Single nucleotide polymorphism array analysis of flow-sorted epithelial cells from frozen versus fixed tissues for whole genome analysis of allelic loss in breast cancer. Am J Pathol (2002) 1.39

An Slfn2 mutation causes lymphoid and myeloid immunodeficiency due to loss of immune cell quiescence. Nat Immunol (2010) 1.39

Extended lifespan of Barrett's esophagus epithelium transduced with the human telomerase catalytic subunit: a useful in vitro model. Carcinogenesis (2003) 1.39

Stromal transforming growth factor-beta signaling mediates prostatic response to androgen ablation by paracrine Wnt activity. Cancer Res (2008) 1.36

Temporal and spatial evolution of somatic chromosomal alterations: a case-cohort study of Barrett's esophagus. Cancer Prev Res (Phila) (2013) 1.31

Electrospun fibrous mats with high porosity as potential scaffolds for skin tissue engineering. Biomacromolecules (2008) 1.31

Association between markers of obesity and progression from Barrett's esophagus to esophageal adenocarcinoma. Clin Gastroenterol Hepatol (2013) 1.29

Synthesis and characterization of biocompatible Fe3O4 nanoparticles. J Biomed Mater Res A (2007) 1.28

ENU-induced phenovariance in mice: inferences from 587 mutations. BMC Res Notes (2012) 1.28

Preventable maternal mortality: geographic/rural-urban differences and associated factors from the population-based Maternal Mortality Surveillance System in China. BMC Public Health (2011) 1.27

Increasing genomic instability during premalignant neoplastic progression revealed through high resolution array-CGH. Genes Chromosomes Cancer (2007) 1.26

Germline genetic contributions to risk for esophageal adenocarcinoma, Barrett's esophagus, and gastroesophageal reflux. J Natl Cancer Inst (2013) 1.25

Cancer prevention strategies that address the evolutionary dynamics of neoplastic cells: simulating benign cell boosters and selection for chemosensitivity. Cancer Epidemiol Biomarkers Prev (2004) 1.22

Geographical detector-based risk assessment of the under-five mortality in the 2008 Wenchuan earthquake, China. PLoS One (2011) 1.22

Hyperactivation of p21ras and PI3K cooperate to alter murine and human neurofibromatosis type 1-haploinsufficient osteoclast functions. J Clin Invest (2006) 1.20

Erk1 positively regulates osteoclast differentiation and bone resorptive activity. PLoS One (2011) 1.19

Adriamycin-induced autophagic cardiomyocyte death plays a pathogenic role in a rat model of heart failure. Int J Cardiol (2008) 1.19

A forward genetic screen reveals roles for Nfkbid, Zeb1, and Ruvbl2 in humoral immunity. Proc Natl Acad Sci U S A (2012) 1.19

Multiple increased osteoclast functions in individuals with neurofibromatosis type 1. Am J Med Genet A (2011) 1.18

Role for stromal heterogeneity in prostate tumorigenesis. Cancer Res (2011) 1.18

Maternal mortality in China, 1996-2005. Int J Gynaecol Obstet (2010) 1.18

Chromosomal instability and copy number alterations in Barrett's esophagus and esophageal adenocarcinoma. Clin Cancer Res (2009) 1.17

IL-6 is increased in the cerebellum of autistic brain and alters neural cell adhesion, migration and synaptic formation. J Neuroinflammation (2011) 1.17

Nonsteroidal anti-inflammatory drug use, body mass index, and anthropometry in relation to genetic and flow cytometric abnormalities in Barrett's esophagus. Cancer Epidemiol Biomarkers Prev (2002) 1.14

Neosquamous epithelium does not typically arise from Barrett's epithelium. Clin Cancer Res (2006) 1.14

Chromosomal instability in Barrett's esophagus is related to telomere shortening. Cancer Epidemiol Biomarkers Prev (2006) 1.12

Natural selection in neoplastic progression of Barrett's esophagus. Semin Cancer Biol (2005) 1.10

The changes in maternal mortality in 1000 counties in mid-Western China by a government-initiated intervention. PLoS One (2012) 1.09

Mucin core polypeptide expression in the progression of neoplasia in Barrett's esophagus. Hum Pathol (2006) 1.08

iRhom2 is required for the secretion of mouse TNFα. Blood (2012) 1.08

The role of tobacco, alcohol, and obesity in neoplastic progression to esophageal adenocarcinoma: a prospective study of Barrett's esophagus. PLoS One (2013) 1.08

Knockdown of Oct4 and Nanog expression inhibits the stemness of pancreatic cancer cells. Cancer Lett (2013) 1.08

Neurofibroma-associated growth factors activate a distinct signaling network to alter the function of neurofibromin-deficient endothelial cells. Hum Mol Genet (2006) 1.07

BDNF-Akt-Bcl2 antiapoptotic signaling pathway is compromised in the brain of autistic subjects. J Neurosci Res (2010) 1.07

Bone marrow derived mesenchymal stem cells incorporate into the prostate during regrowth. PLoS One (2010) 1.07

Investigation of drug release and matrix degradation of electrospun poly(DL-lactide) fibers with paracetanol inoculation. Biomacromolecules (2006) 1.07

Hydroxyapatite nucleation and growth mechanism on electrospun fibers functionalized with different chemical groups and their combinations. Biomaterials (2010) 1.06

Direct inference of SNP heterozygosity rates and resolution of LOH detection. PLoS Comput Biol (2007) 1.06

Expression of inflammatory cytokines, Bcl2 and cathepsin D are altered in lymphoblasts of autistic subjects. Immunobiology (2010) 1.06

Twenty-five cases of adult prostate sarcoma treated at a high-volume institution from 1989 to 2009. Urology (2013) 1.05

Geographical disparities of infant mortality in rural China. Arch Dis Child Fetal Neonatal Ed (2012) 1.05

Household catastrophic medical expenses in eastern China: determinants and policy implications. BMC Health Serv Res (2013) 1.05

Preparation and characterization of a novel electrospun spider silk fibroin/poly(D,L-lactide) composite fiber. J Phys Chem B (2008) 1.04

Stable knockdown of polycystin-1 confers integrin-alpha2beta1-mediated anoikis resistance. J Am Soc Nephrol (2006) 1.03

Inhibition of HER-2(neu/ErbB2) restores normal function and structure to polycystic kidney disease (PKD) epithelia. Biochim Biophys Acta (2006) 1.03

Transcriptional analyses of Barrett's metaplasia and normal upper GI mucosae. Neoplasia (2002) 1.03

Molecular phenotype of spontaneously arising 4N (G2-tetraploid) intermediates of neoplastic progression in Barrett's esophagus. Cancer Res (2003) 1.02

Promotion of skin regeneration in diabetic rats by electrospun core-sheath fibers loaded with basic fibroblast growth factor. Biomaterials (2011) 1.02

Neonatal mortality due to preterm birth at 28-36 weeks' gestation in China, 2003-2008. Paediatr Perinat Epidemiol (2011) 1.01

MiR-200a inhibits epithelial-mesenchymal transition of pancreatic cancer stem cell. BMC Cancer (2014) 0.99

Serum selenium levels in relation to markers of neoplastic progression among persons with Barrett's esophagus. J Natl Cancer Inst (2003) 0.99

Yes-associated protein expression in head and neck squamous cell carcinoma nodal metastasis. PLoS One (2011) 0.99