Systems and Methods for Expression-Based Classification of Thyroid Tissue

Abstract

A system for classifying thyroid nodule tissue as malignant or benign is provided that is based on the identification of sets of gene transcripts, which are characterized in that changes in expression of each gene transcript within a set of gene transcripts can be correlated to with either malignant or benign thyroid nodule disease. The thyroid classification system provides for sets of “thyroid classifying” target sequences and further provides for combinations of polynucleotide probes and primers derived there from. These combinations of polynucleotide probes can be provided in solution or as an array. The combination of probes and the arrays can be used for diagnosis. The invention further provides further methods of classifying thyroid nodule tissue.

1 .- 35 . (canceled) 
     
     
         36 . A method, comprising:
 (a) assaying by sequencing, array hybridization or nucleic acid amplification an expression level of one or more transcripts in a test sample obtained from a subject, wherein said one or more transcripts correspond to one or more sequences that have at least about 90% sequence identity to a sequence selected from the group consisting of SEQ ID No. 1-12, 261, 283-306, 657, 658, and 659, and wherein said assaying comprises use of probes selected for said one or more sequences; and   (b) in a programmed computer, comparing said expression level of each of said one or more transcripts with a reference expression level of transcripts corresponding to sequences having at least about 90% sequence identity to sequences selected from the group consisting of SEQ ID No. 1-12, 261, 283-306, 657, 658, and 659, to classify said test sample as malignant or benign for a thyroid condition.   
     
     
         37 . The method of  claim 36 , further comprising (i) when said test sample is classified as malignant, treating said subject by surgical removal of at least a portion of a thyroid tissue, radioactive iodine treatment, or a combination thereof, or (ii) when said test sample is classified as benign, monitoring said subject by repeating (a)-(b) on another test sample obtained from said subject at a later time. 
     
     
         38 . The method of  claim 36 , further comprising performing a cytological analysis, an imaging analysis, a measurement of thyroid hormone levels, or any combination thereof to obtain a result, and combining said result with said expression level to determine a classification of said test sample as malignant or benign for said thyroid condition. 
     
     
         39 . The method of  claim 36 , wherein said one or more transcripts comprises a first group of transcripts and a second group of transcripts, wherein said first group of transcripts includes at least one transcript corresponding to one or more sequences having at least about 90% sequence identity to SEQ ID No. 1-4, 8-12 and 261, and said second group of transcripts includes at least one transcript corresponding to one or more sequences having at least about 90% sequence identity to SEQ ID No. 5-7, 283-306, 657, 658, and 659. 
     
     
         40 . The method of  claim 39 , further comprising classifying said test sample as malignant if there is an increase in an expression level corresponding to said first group of transcripts or a decrease in an expression level corresponding to said second group of transcripts. 
     
     
         41 . The method of  claim 39 , further comprising classifying said test sample as benign if there is an increase in an expression level corresponding to said second group of transcripts or a decrease in an expression level corresponding to said first group of transcripts. 
     
     
         42 . The method of  claim 36 , wherein said assaying comprises determining the expression level by RT-PCR, Northern blotting, ligase chain reaction, or any combination thereof. 
     
     
         43 . The method of  claim 36 , further comprising measuring the expression level of at least one control nucleic acid in the test sample. 
     
     
         44 . The method of  claim 36 , wherein the test sample is fresh-frozen or fixed. 
     
     
         45 . The method of  claim 36 , wherein the expression level is measured by pattern recognition. 
     
     
         46 . The method of  claim 36 , wherein said assaying is by nucleic acid amplification using at least two probes that each amplifies a transcript corresponding to a sequence having at least about 90% sequence identity to a sequence as set forth in any one of SEQ ID No. 1-12, 261, 283-306, 657, 658, and 659. 
     
     
         47 . The method of  claim 36 , further comprising generating a report that designates said test sample as malignant or benign for said thyroid condition. 
     
     
         48 . The method of  claim 37 , wherein said treating further comprises thyroid hormone suppression therapy, permanent thyroid hormone replacement therapy, or a combination thereof.