Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving nucleic acid
Reexamination Certificate
1998-05-20
2001-12-25
Fredman, Jeffrey (Department: 1655)
Chemistry: molecular biology and microbiology
Measuring or testing process involving enzymes or...
Involving nucleic acid
C435S091200, C536S023100, C536S024300, C536S024310, C536S024320, C536S024330
Reexamination Certificate
active
06333152
ABSTRACT:
TECHNICAL FIELD OF THE INVENTION
This invention is related to the diagnosis of cancer, and tools for carrying out such diagnosis.
BACKGROUND OF THE INVENTION
Much of cancer research over the past 50 years has been devoted to the analyses of genes that are expressed differently in tumor cells compared to their normal counterparts. Although hundreds of studies have pointed out differences in the expression of one or a few genes, no comprehensive study of gene expression in the cancer cell has been reported. It is therefore not known how many genes are expressed differentially in tumor versus normal cells, whether the bulk of these differences are cell autonomous rather than being dependent on the tumor microenvironment, and whether most differences are cell-type specific or tumor specific. Thus there is a need in the art for information on the molecular changes that occur in cells during cancer development and progression.
SUMMARY OF THE INVENTION
According to one embodiment of the invention, a method is provided for diagnosing colon cancer in a sample suspected of being neoplastic. The method comprises the steps of:
comparing the level of at least one transcript in a first sample of a tissue to a second sample, wherein the first sample is of a colonic tissue suspected of being neoplastic and the second sample is of a normal human colonic tissue, and wherein the transcript is identified by a tag selected from the group consisting of those shown in Table 3;
identifying the first sample as neoplastic when the level of the at least one transcript is found to be lower in the first sample than in the second sample.
According to another embodiment of the invention, another method is provided for diagnosing colon cancer in a sample suspected of being neoplastic. The method comprises the steps of:
comparing the level of at least one transcript in a first sample of a tissue to a second sample, wherein the first sample is of a colonic tissue suspected of being neoplastic and the second sample is of a normal human colonic tissue, and wherein the transcript is identified by a tag selected from the group consisting of those shown in Table 2;
identifying the first sample as neoplastic when the level of the at least one transcript is found to be higher in the first sample than in the second sample.
In another embodiment of the invention an isolated and purified human nucleic acid molecule is provided. The molecule comprises a SAGE tag selected from SEQ ID NOS:1-734.
In yet another aspect of the invention an isolated nucleotide probe is provided. The probe comprises at least 12 nucleotides of a human nucleic acid molecule, wherein the human nucleic acid molecule comprises a SAGE tag selected from SEQ ID NOS: 1-734.
According to another aspect of the invention a method is provided for diagnosing pancreatic cancer in a sample suspected of being neoplastic. The method comprises the steps of:
comparing the level of at least one transcript in a first sample of a tissue to a second sample, wherein the first sample is of a pancreatic tissue suspected of being neoplastic and the second sample is of a normal human colon tissue, wherein said transcript is identified by a tag selected from the group consisting of those shown Table 4;
identifying the first sample as neoplastic when the level of the at least one transcript is found to be higher in the first sample than in the second sample.
According to still another embodiment of the invention a method of diagnosing cancer in a sample suspected of being neoplastic is provided. The method comprises the steps of:
comparing the level of at least one transcript in a first sample of a tissue to a second sample, wherein the first sample is of a tissue suspected of being neoplastic and the second sample is of a normal human tissue, wherein said transcript is identified by a tag selected from the group consisting of those shown Table 5;
identifying the first sample as neoplastic when the level of the at least one transcript is found to be higher in the first sample than in the second sample.
According to another embodiment of the invention a method is provided to aid in the determination of a prognosis for a colon cancer patient. The method comprises the steps of:
comparing the level of at least one transcript in a first sample of a tissue to a second sample, wherein the first sample is of a neoplastic colonic tissue and the second sample is of a normal human colonic tissue, and wherein the transcript is identified by a tag selected from the group consisting of those shown in Table 3;
determining a poorer prognosis if the level of the at least one transcript is found to be lower in the first sample than in the second sample.
According to another aspect of the invention a method to aid in determining a prognosis for a patient with colon cancer is provided. The method comprises the steps of:
comparing the level of at least one transcript in a first tissue sample to a second sample, wherein the first sample is of a colonic cancer tissue and the second sample is of a normal human colonic tissue, and wherein the transcript is identified by a tag selected from the group consisting of those shown in Table 2;
determining a poorer prognosis if the level of the at least one transcript is found to be higher in the first sample than in the second sample.
In yet another embodiment of the invention a method is provided for diagnosing colon cancer in a sample suspected of being neoplastic. The method comprises the steps of:
comparing the level of expression of at least one protein in a first sample of a tissue to a second sample, wherein the first sample is of a colonic tissue suspected of being neoplastic and the second sample is of a normal human colonic tissue, and wherein the protein is encoded by a transcript identified by a tag selected from the group consisting of those shown in Table 3;
identifying the first sample as neoplastic when the level of expression of the protein is found to be lower in the first sample than in the second sample.
In another aspect of the invention a method of diagnosing colon cancer in a sample suspected of being neoplastic is provided. The method comprises the steps of:
comparing the level of expression of at least one protein in a first sample of a tissue to a second sample, wherein the first sample is of a colonic tissue suspected of being neoplastic and the second sample is of a normal human colonic tissue, and wherein the protein is encoded by a transcript identified by a tag selected from the group consisting of those shown in Table 2;
identifying the first sample as neoplastic when expression of the protein is found to be higher in the first sample than in the second sample.
According to another embodiment of the invention a method is provided to aid in determining a prognosis of a patient having pancreatic cancer. The method comprises the steps of:
comparing the level of at least one transcript in a first sample of a tissue to a second sample, wherein the first sample is of a neoplastic pancreatic tissue and the second sample is of a normal human colon tissue, wherein said transcript is identified by a tag selected from the group consisting of those shown Table 4;
determining a poorer prognosis if transcription is found to be higher in the first sample than in the second sample.
In yet another aspect of the invention a method to aid in providing a prognosis for a cancer patient is provided. The method comprises the steps of:
comparing the level of at least one transcript in a first sample of a tissue to a second sample, wherein the first sample is of a neoplastic tissue and the second sample is of a normal human tissue of the same tissue type, wherein said transcript is identified by a tag selected from the group consisting of those shown Table 5;
determining a poorer prognosis if transcription is found to be higher in the first sample than in the second sample.
According to still another aspect of the invention, a method is provided for diagnosing pancreatic cancer in a sample suspected of being neoplastic. The method comprises the ste
Kinzler Kenneth W.
Vogelstein Bert
Zhang Lin
Zhou Wei
Bannee & Witcoff
Fredman Jeffrey
The Johns-Hopkins University
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