Thyroid fine needle aspiration molecular assay

Abstract

The present invention relates to methods, compositions and articles directed to diagnosing thyroid carcinoma, differentiating between thyroid carcinoma and benign thyroid diseases, testing indeterminate thyroid fine needle aspirate samples of thyroid nodules, and determining patient protocols and outcomes.

Description

Background of the invention

[0001] In the United States, approximately 25,600 new cases of thyroid cancer are diagnosed each year, and 1,400 patients will die from the disease. About 75% of all thyroid cancers are of the papillary thyroid cancer type. The remainder consists of 10% of follicular carcinomas, 5%-9% of medullary thyroid carcinomas, 1%-2% of anaplastic carcinomas, 1%-3% of lymphomas and less than 1% of sarcomas and other rare Tumor composition. Often, lumps (nodules) in the thyroid gland are the first sign of thyroid cancer. In the United States, 10-18 million people have a single thyroid nodule, and approximately 490,000 become clinically apparent each year. Fortunately, only about 5% of these nodules are cancerous.

[0002] A common method for diagnosing thyroid cancer is a fine-needle aspiration (FNA) biopsy. The FNA sample is examined cytologically to determine whether the nodule is benign or cancerous. The sensitivity and specificity of FNA range from 68...

Examples

Embodiment 1

[0089] Materials and methods

[0090] tissue sample

[0091] Fresh-frozen samples of benign thyroid disease, follicular adenoma, follicular carcinoma, and papillary carcinoma were obtained from various commercial suppliers, including Genomics Collaborative, Inc. (Cambridge, MA), Asterand (Detroit, MI), and Proteogenex ( Los Angeles, CA). All samples were collected according to Institutional Review Board approved protocols. Patient demographic and pathological information was also collected. Review histopathological features of each sample to confirm diagnosis, estimate sample preservation, and tumor content.

[0092] RNA isolation

[0093] All RNA isolations were performed using standard TriZol protocols. Tissues were homogenized in TriZol reagent (Invitrogen, Carlsbad, CA). Total RNA was isolated from TriZol and precipitated with isopropanol at -20°C. The RNA pellet was washed with 75% ethanol, dissolved in water, and stored at -80°C for future use. RNA integrity was ...

Embodiment 2

[0114] microarray analysis

[0115] Labeled cRNA was prepared and hybridized to the High Density Oligonucleotide Array Hu133A Gene Chip (Affymetrix, Santa Clara, CA) containing a total of 22,000 probe sets. Hybridization was performed according to standard protocols provided by the manufacturer. Arrays were scanned using the Affymetrix protocol and scanner. For subsequent analyses, each probe set was considered an independent gene. The expression value of each gene was calculated using Affymetrix gene chip analysis software MAS 5.0. All chips met the following quality control criteria: percentage of "presence" calls, scaling factors, background levels and noise levels must be within + or -3 standard deviations of the mean. All chips used for subsequent analysis have passed these quality control standards. Sample collection for marker selection and independent validation is summarized in Table 1.

[0116] Table 1. Sample collection for labeled training and validation

[0...

Embodiment 3

[0120] Result marker identification

[0121] A. Gene selection

[0122] A total of 98 samples, including 31 primary papillary thyroid tumors, 21 follicular thyroid carcinomas, 33 follicular adenomas, and 13 benign thyroid tissues, were analyzed using the Affymetrix human U133A gene chip. Five gene selection criteria were applied to the entire data set to obtain a limited number of genes for subsequent gene signature or marker identification:

[0123] 1. Consider genes with at least one "Present Call" in the sample set.

[0124] 2. Exclude genes with more than one "present request" in 12 PBL samples.

[0125] 3. Only genes with chip intensities greater than 200 in all samples were selected.

[0126] 4. Using genes that passed the above 3 criteria, we performed a number of analyzes listed in Table 2 to identify genes that were up- or down-regulated in thyroid tumors.

[0127] 5. Finally, genes with a greater than 1.4-fold change in expression were selected.

[0128] Table 2...

Background of the invention

[0001] In the United States, approximately 25,600 new cases of thyroid cancer are diagnosed each year, and 1,400 patients will die from the disease. About 75% of all thyroid cancers are of the papillary thyroid cancer type. The remainder consists of 10% of follicular carcinomas, 5%-9% of medullary thyroid carcinomas, 1%-2% of anaplastic carcinomas, 1%-3% of lymphomas and less than 1% of sarcomas and other rare Tumor composition. Often, lumps (nodules) in the thyroid gland are the first sign of thyroid cancer. In the United States, 10-18 million people have a single thyroid nodule, and approximately 490,000 become clinically apparent each year. Fortunately, only about 5% of these nodules are cancerous.

[0002] A common method for diagnosing thyroid cancer is a fine-needle aspiration (FNA) biopsy. The FNA sample is examined cytologically to determine whether the nodule is benign or cancerous. The sensitivity and specificity of FNA range from 68...

Examples

Embodiment 1

[0089] Materials and methods

[0090] tissue sample

[0091] Fresh-frozen samples of benign thyroid disease, follicular adenoma, follicular carcinoma, and papillary carcinoma were obtained from various commercial suppliers, including Genomics Collaborative, Inc. (Cambridge, MA), Asterand (Detroit, MI), and Proteogenex ( Los Angeles, CA). All samples were collected according to Institutional Review Board approved protocols. Patient demographic and pathological information was also collected. Review histopathological features of each sample to confirm diagnosis, estimate sample preservation, and tumor content.

[0092] RNA isolation

[0093] All RNA isolations were performed using standard TriZol protocols. Tissues were homogenized in TriZol reagent (Invitrogen, Carlsbad, CA). Total RNA was isolated from TriZol and precipitated with isopropanol at -20°C. The RNA pellet was washed with 75% ethanol, dissolved in water, and stored at -80°C for future use. RNA integrity was ...

Embodiment 2

[0114] microarray analysis

[0115] Labeled cRNA was prepared and hybridized to the High Density Oligonucleotide Array Hu133A Gene Chip (Affymetrix, Santa Clara, CA) containing a total of 22,000 probe sets. Hybridization was performed according to standard protocols provided by the manufacturer. Arrays were scanned using the Affymetrix protocol and scanner. For subsequent analyses, each probe set was considered an independent gene. The expression value of each gene was calculated using Affymetrix gene chip analysis software MAS 5.0. All chips met the following quality control criteria: percentage of "presence" calls, scaling factors, background levels and noise levels must be within + or -3 standard deviations of the mean. All chips used for subsequent analysis have passed these quality control standards. Sample collection for marker selection and independent validation is summarized in Table 1.

[0116] Table 1. Sample collection for labeled training and validation

[0...

Embodiment 3

[0120] Result marker identification

[0121] A. Gene selection

[0122] A total of 98 samples, including 31 primary papillary thyroid tumors, 21 follicular thyroid carcinomas, 33 follicular adenomas, and 13 benign thyroid tissues, were analyzed using the Affymetrix human U133A gene chip. Five gene selection criteria were applied to the entire data set to obtain a limited number of genes for subsequent gene signature or marker identification:

[0123] 1. Consider genes with at least one "Present Call" in the sample set.

[0124] 2. Exclude genes with more than one "present request" in 12 PBL samples.

[0125] 3. Only genes with chip intensities greater than 200 in all samples were selected.

[0126] 4. Using genes that passed the above 3 criteria, we performed a number of analyzes listed in Table 2 to identify genes that were up- or down-regulated in thyroid tumors.

[0127] 5. Finally, genes with a greater than 1.4-fold change in expression were selected.

[0128] Table 2...

Images