Analysis of transcriptome in ectopic versus orthotopic thyroid tissue.

Congenital hypothyroidism from thyroid dysgenesis (CHTD) is a sporadic disease characterized by defects in the differentiation, migration or growth of thyroid tissue. Of these defects, incomplete migration resulting in ectopic thyroid tissue is the most common (up to 80%). We obtained flashfrozen samples of ectopic thyroid tissue removed from 3 girls aged 8, 10 and 15 yr, because it caused local symptoms. For comparison, we used orthotopic thyroid tissue from a Caucasian female, age 68 with gall bladder cancer. Analysis of transcriptome revealed up to 1011 genes more than twofold induced or repressed. Microarray hybridization was performed on three independent pairs of ectopic thyroids (one pair performed in duplicate) compared to control thyroid tissue. After amplification and labelling, sample pairs were hybridized onto Human Exonic Evidence Based Oligonucleotide HEEBO slides (Stanford Functional Genomics Facility, CA). The oligonucleotide set consists of 44544 70-mer probes that were designed using a transcriptome-based annotation of exonic structure for genomic loci. Hybridizations were replicated with dye swap.