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Key Message: We show the application of association mapping and genomic selection for key breeding targets using a large panel of elite winter wheat varieties and a large volume of agronomic data. The heightening urgency to increase wheat production in line with the needs of a growing population, and in the face of climatic uncertainty, mean new approaches, including association mapping (AM) and genomic selection (GS) need to be validated and applied in wheat breeding. Key adaptive responses are the cornerstone of regional breeding. There is evidence that new ideotypes for long-standing traits such as flowering time may be required. In order to detect targets for future marker-assisted improvement and validate the practical application of GS for wheat breeding we genotyped 376 elite wheat varieties with 3,046 DArT, single nucleotide polymorphism and gene markers and measured seven traits in replicated yield trials over 2 years in France, Germany and the UK. The scale of the phenotyping exceeds the breadth of previous AM and GS studies in these key economic wheat production regions of Northern Europe. Mixed-linear modelling (MLM) detected significant marker-trait associations across and within regions. Genomic prediction using elastic net gave low to high prediction accuracies depending on the trait, and could be experimentally increased by modifying the constituents of the training population (TP). We also tested the use of differentially penalised regression to integrate candidate gene and genome-wide markers to predict traits, demonstrating the validity and simplicity of this approach. Overall, our results suggest that whilst AM offers potential for application in both research and breeding, GS represents an exciting opportunity to select key traits, and that optimisation of the TP is crucial to its successful implementation.

Purpose: Fine-needle aspiration (FNA) with cytologic evaluation is the most reliable tool for malignancy prediction in thyroid nodules, but cytologic diagnosis remains indeterminate for 12-18 % of nodules. BRAF V600E mutation has been reported to show a high specificity for malignant thyroid nodules and the use of this marker to refine indeterminate FNA cytology results may be a useful diagnostic adjunctive tool in the pre-operative evaluation of thyroid nodules. The aim of this study was to estimate the prevalence of BRAF exon 15 mutation (V600E) and its clinical value as a diagnostic tool in a series of thyroid nodules with indeterminate cytology from an area of borderline iodine deficiency., Subjects and Methods: One hundred and fifty-three thyroid samples obtained by FNA of thyroid nodules from 151 patients were subjected to the analysis of BRAF V600E mutation by direct sequencing. In the study 54 nodules with indeterminate cytology, 56 benign and 43 malignant thyroid nodules were included., Results: V600E BRAF gene mutation was demonstrated in 19/43 malignant nodules, in 0/56 benign nodules and in only 1/54 indeterminate nodules that, after histology, turned out to be at a papillary thyroid carcinoma., Conclusions: The application of BRAF exon 15 analysis showed limitations when applied to discriminate thyroid nodules with indeterminate cytology if wild-type BRAF is found, and there is no role for avoiding diagnostic thyroid surgery.

Background: Fine needle aspiration (FNA) with cytologic evaluation is the most reliable tool for malignancy prediction in thyroid nodules, but cytologic diagnosis remains undetermined for 20% of nodules., Aim: We investigated the diagnostic potential of a set of 6 marker genes to distinguish benign and malignant thyroid nodules., Subjects and Methods: The prospective study included 153 thyroid samples obtained by FNA of thyroid nodules from 151 patients (56 benign, 43 malignant, and 54 nodules with undetermined cytology). Gene expression was evaluated by quantitative realtime PCR and statistical analysis of data was performed. All samples were analyzed for V600E BRAF mutation., Results: A decrease in TTF3 and HGD1 expression was observed in malignant nodules with respect to benign ones, while an increase in PLAB expression was demonstrated in these nodules. The decision model was valid for 88 of 99 cases of benign and malignant nodules, with a total of 11 false positive or negative predictions. The obtained malignant/benign phenotype prediction was also valid for 37 of 54 cases of nodules with undetermined cytology with a total of 8 false positive and 9 false negative predictions. V600E BRAF gene mutation was demonstrated in 19/43 malignant nodules, in 0/56 benign nodules, and in 1/54 undetermined nodules., Conclusions: The expression profiles of genes (TFF3, HGD1, and PLAB) allowed a good prediction for the differentiation of benign thyroid lesions and thyroid cancer starting from cells of FNA; however, this assay showed limitations when applied to discriminate thyroid nodules with undetermined cytology.

Objective: We evaluated the association between thyroid autoimmunity and thyroid cancer in a retrospective series of unselected thyroid nodules submitted to fine-needle aspiration (FNA) cytology., Design: Anti-thyroid antibodies (TAb) were measured in patients with multinodular goiter (MNG) and single/isolated thyroid nodule (S/I) submitted to FNA. Thyroid lymphocytic infiltration (LI) on histology was studied in a subgroup of patients submitted to thyroidectomy; 13,021 patients were included: on cytology 622 had papillary thyroid cancer (c- PTC) and 12,399 benign thyroid nodular diseases (c-BTN). LI was evaluated in histological samples of 688 patients: 304 with PTC (h-PTC) and 384 with BTN (h-BTN)., Results: TAb prevalence was not different in c-BTN and c-PTC (38.7% vs 35.6%). TAb were more frequent in c-BTN than c-PTC in females with MNG (40.1% vs 32.5%, p=0.02), and in c-PTC than in c-BTN in males with S/I (31.2% vs 20.4%, p=0.02) and, although not significantly, in females younger than 30 yr (35.1% vs 30.7%). The frequency and severity of LI was significantly higher in h-PTC than h-BTN, both in MNG (82.5% vs 45.0%, p<0.001) and S/I (85.6% vs 71.0%, p<0.001), but a higher number of patients with h-PTC had negative circulating TAb, despite the presence of moderate/severe LI., Conclusions: TAb are weakly associated to PTC in males and young females, while they are more frequent in older females with BTN. The frequency and severity of LI is significantly higher in PTC than in BTN, but in cancer patients TAb are frequently negative, despite the evidence of histological thyroiditis. These data suggest that different kinds of immune response may be involved in PTC and BTN.

The newly developed three-dimensional (3D) and two-dimensional (2D) thyroid ultrasound (US) were compared in assessing thyroid volume (TV) in 104 patients: 53 had an isolated thyroid nodule, 32 toxic diffuse goiter, 17 non-toxic multinodular goiter, 1 toxic multinodular goiter and 1 a toxic adenoma. A real-time Technos apparatus (Esaote SpA, Italy) with a 7,5 MHz linear transducer was used. The volume of thyroid lobes by 2D was calculated according to the ellipsoid formula. In the same session, TV by 3D US was calculated using a probe tracking system (in vivo ScanNT Esaote 3.4 MedCom. Darmasdt) and software to reconstruct 3D images, directly giving the lobe volume. There was a very good agreement between 2D and 3D, but in 94/208 lobes with nodular lesions 2D showed a 10% systematic overestimation compared to 3D, the percentage error being higher in lobes with lower volumes. A possible explanation for this result is the inadequacy of the ellipsoid formula in forecasting the correct lobe profile in the presence of nodules. This intrinsic defect of 2D US should be taken into account when evaluating TV in patients with nodular goiter.