Johns Hopkins University

Other

James Gordon Herman

Stephen B Baylin

Curtis C Harris

David Sidransky

Yoshimitsu Akiyama

Hiromu Suzuki

Hirohide Yoshikawa

Manel Esteller

Nita Ahuja

Malcolm V Brock

Jeff Wang

Vasudev Bailey

Mi J Yi

Simon Daniel Spivack

Weiguo Han

Joo-Mi Yi

The present invention provides methods for identifying metastases by detecting nucleic acid hypermethylation of one or more genes in one or more samples, and in particular in the lymph nodes. The invention further relates to DNA methylation as a predictor of disease recurrence and patient prognosis, specifically in the field of cancer biology.

DNA methylation markers and methods of use

The invention provides compositions and methods for detecting a neoplasia (e.g., pancreatic cancer, lung cancer, colon cancer) in a subject sample (e.g., serum, blood, plasma, tissue). In particular embodiments, the invention provides methods for detecting BNC1 and ADAMTS1 promoter methylation in circulating DNA in serum.

Compositions and methods for detecting a neoplasia

Methods are provided for identifying the presence of cancer cells in a sample by detecting hypermethylation of the promoter region of a GATA-4 transcription factor gene, a GATA-5 transcription factor gene, or both. Methods for ameliorating a cancer by effecting expression of a hypermethylation silenced GATA-4 and/or GATA-5 transcription also are provided.

Hypermethylation of GATA-4 and GATA-5 transcription factor genes in cancer

The present invention relates to a tag-modified bisulfite genomic sequencing (tBGS) method developed for simplified evaluation of DNA methylation sites. The method employs direct cycle sequencing of PCR products at kilobase scale, without conventional DNA fragment cloning. The method entails subjecting bisulfite-modified genomic DNA to a second-round PCR amplification employing GC-tagged primers. The invention also relates to a method for identifying a patient at risk for lung cancer using the tBGS technique disclosed.

GC tag-modified bisulfite genomic DNA sequencing for continuous methylation spectra

A method of identifying epigenetically silenced genes, e.g., methylation silenced genes, in cancer cells is provided. In addition, methods of identifying a cancer by detecting epigenetic silencing of gene expression are provided, as are methods of treating a subject having such a cancer, for example, a colorectal cancer and/or gastric cancer. Reagents for practicing such methods also are provided.

Genomic screen for epigenetically silenced genes associated with cancer

Methods of genomic screening to identify epigenetically silenced genes, including epigenetically silenced tumor suppressor genes are provided. Also provided are methods of detecting a cancer, for example, an esophageal squamous cell carcinoma or a head and neck squamous cell carcinoma, as are methods of treating a subject having such a cancer.

Genomic screen for epigenetically silenced tumor suppressor genes

Methods are provided for identifying a cell exhibiting unregulated growth associated with methylation-silenced transcription of a suppressor of cytokine signaling (SOCS)/cytokine-inducible SH2 protein (CIS) family member (SOCS/CIS) gene such as the SOCS-1 gene. In addition, methods of treating a cancer patient, wherein cancer cells in the patient exhibit methylation-silenced transcription of SOCS/CIS gene such as a SOCS-1 gene, are provided, as are reagents for practicing such methods.

SOCS-1 gene methylation in cancer

The present invention provides methods relating to chemotherapeutic treatment of a cell proliferative disorder. In particular, a method is provided for predicting the clinical response to certain types of chemotherapeutic agents. Alkylating agents, used for the treatment of certain types of tumors including tumors of the nervous system and lymph system, are efficacious agents when the damage they do to tumor cell DNA is not repaired by cellular DNA repair mechanisms. The present invention provides a method for determining the activity of a gene encoding a DNA repair enzyme, thus providing a prediction of the clinical response to alkylating agents.

Method of predicting the clinical response to chemotherapeutic treatment with alkylating agents

The present invention provides a method for detecting a methylated CpG-containing nucleic acid present in a specimen by contacting the specimen with an agent that modifies unmethylated cytosine and amplifying the CpG-containing nucleic acid using CpG-specific oligonucleotide primers. The present invention provides an improved method of methylation detection by facilitating the rapid identification of DNA methylation patterns in a CpG-containing nucleic acid.

Method of detection of methylated nucleic acid using agents which modify unmethylated cytosine and distinguish modified methylated and non-methylated nucleic acids

The present invention provides a method for detecting a methylated CpG-containing nucleic acid present in a specimen by contacting the specimen with an agent that modifies unmethlyated cytosine and amplifying the CpG-containing nucleic acid using CpG-specific oligonucleotide primers. The present invention provides an improved method of methylation detection by facilitating the rapid identification of DNA methylation patterns in a CpG-containing nucleic acid.

Methods for identifying methylation patterns in a CpG-containing nucleic acid

Method of detection of methylated nucleic acid using agents which modify

The present invention provides a method of PCR, methylation specific PCR (MSP), for rapid identification of DNA methylation patterns in a CpG-containing nucleic acid. MSP uses agents to modify unmethylated cytosine in a nucleic acid of interest, and then uses the PCR reaction to amplify the CpG-containing nucleic acid in the specimen by means of CpG-specific oligonucleotide primers. The oligonecleotide primers distinguish between modified methylated and nonmethylated nucleic acid. Kits utilizing MSP for the detection of methylated CpG-containing nucleic acids are also provided.

Growing community of inventors

Lutherville, MD, United States of America

James Gordon Herman