Tony E. Godfrey

Arjun Pennathur4
James D Luketich4
Santhoshi Bandla3
Anders Ståhlberg2
James D. Luketich2
4Arjun Pennathur
4James D Luketich
3Santhoshi Bandla
2Anders Ståhlberg
2James D. Luketich
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The incidence of esophageal adenocarcinoma (EAC) has risen 600% over the last 30 years. With a 5-year survival rate of ~15%, the identification of new therapeutic targets for EAC is greatly important. We analyze the mutation spectra from whole-exome sequencing of 149 EAC tumor-normal pairs, 15 of which have also been subjected to whole-genome sequencing. We(More)
Alternative processing of pre-mRNA transcripts is a major source of protein diversity in eukaryotes and has been implicated in several disease processes including cancer. In this study we have performed a genome wide analysis of alternative splicing events in lung adenocarcinoma. We found that 2369 of the 17 800 core Refseq genes appear to have alternative(More)
BACKGROUND Several recent reports have described the detection of circulating, cancer-related RNA molecules in serum or plasma from cancer patients, but little is known about the biology of this extracellular RNA. We aimed to determine how RNA is protected against degradation in serum, to optimize RNA isolation from large volumes of serum, and to test our(More)
BACKGROUND Microarray studies in cancer compare expression levels between two or more sample groups on thousands of genes. Data analysis follows a population-level approach (e.g., comparison of sample means) to identify differentially expressed genes. This leads to the discovery of 'population-level' markers, i.e., genes with the expression patterns A > B(More)
BACKGROUND PCR-based assays can improve clinical care, but they remain technically demanding and labor-intensive. We describe a new instrument, the GeneXpert, that performs automated nucleic acid isolation, reverse transcription, and fluorescence-based quantitative PCR in approximately 35 min. METHODS Yield and integrity of RNA isolated on the GeneXpert(More)
  • Bonnie Choy, Santhoshi Bandla, Yinglin Xia, Dongfeng Tan, Arjun Pennathur, James D Luketich +4 others
  • 2012
BACKGROUND High expression of Bmi-1, a key regulatory component of the polycomb repressive complex-1, has been associated with many solid and hematologic malignancies including esophageal squamous cell carcinoma. However, little is known about the role of Bmi-1 in esophageal adenocarcinoma. The aim of this study is to investigate the amplification and high(More)
  • Zhongren Zhou, Santhoshi Bandla, Jiqing Ye, Yinglin Xia, Jianwen Que, James D Luketich +4 others
  • 2014
BACKGROUND Cyclin E is a cell cycle regulator which is critical for driving G1/S transition. Abnormal levels of cyclin E have been found in many cancers. However, the level changes of cyclin E in esophageal adenocarcinoma and its precancerous lesion have not been well studied. Here, we focus on the gene amplification and expression of cyclin E in these(More)
OBJECTIVE Quantification of small molecule numbers often requires preamplification to generate enough copies for accurate downstream enumerations. Here, we studied experimental parameters in targeted preamplification and their effects on downstream quantitative real-time PCR (qPCR). METHODS To evaluate different strategies, we monitored the(More)
Detection of cell-free DNA in liquid biopsies offers great potential for use in non-invasive prenatal testing and as a cancer biomarker. Fetal and tumor DNA fractions however can be extremely low in these samples and ultra-sensitive methods are required for their detection. Here, we report an extremely simple and fast method for introduction of barcodes(More)
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