SUMMARY Total lamb weights weaned (TLW), total milk yield (TMY) and wool production (WP) of Hamdani ewes were investigated in a random sample of Karadi breed (Hamdani) in Kurdistan. Best Linear Unbiased Prediction (BLUP) of ewes at Agricultural College and Commercial flocks for the traits studied was calculated using SAS (2002). Genetic-economic index (based on BLUP and the market prices of the traits) was calculated for the ewes under investigation (pooled ewes sampled). The ewes were divided into two categorized groups (low and high genetic-economic index). Furthermore, molecular characterization of the ewes under investigation was carried out using microsatellite markers. A total of sixty four blood samples were collected from ewes of the two flocks. DNA was extracted from each of the blood sample using Magic Buffer methods. Quality check and quantification was done by UV Spectrophotometry and electrophoresis on 1% agarose gel. The DNA concentration was determined. Genetic analyzer 3100 was used to determine the fragment length (Allele) for each microsatellite. A total of 35 microsatellite markers (fluorescently labeled primers) were used. Only forward primers of each pair were labeled with one of the three fluorophore i.e. FAM, NED and VIC. Genetic parameters of observed alleles, alleles frequency, number and frequency of genotypes, heterozygosity, Hardy-Weinberg equilibrium and Linkage disequilibrium were calculated using software GENEPOP version 3.3. Polymorphic information content (PIC), inbreeding coefficient, Genetic Distance Estimations, Tree Construction and Molecular markers affecting quantitative traits were investigated using Power Marker version 3.25. Statistical as well as genetic analyses of field and lab data collected were performed to figure out and identified molecular markers which can be used for selection at early age to speed up genetic improvement of quantitative traits in Hamdani sheep. Over pooled ewes (ewes at Agricultural and Commercial flocks) means of TLW, TMY and WP were 22.819, 83.998 kg/ewe and 2.047 kg/ewe, respectively. Ewes in Commercial flock produced more TLW, TMY and WP than ewes in Agricultural College flock. BLUP value for TLW, TMY and WP ranged from -12.338 to 11.6023, -68.160 to 139.951 kg and -0.2368 to 0.38531 kg, respectively. Furthermore, genetic-economic index values of pooled ewes ranged from -126613 to 213204.1 Iraqi Dinars. Out of 35 microsatellites investigated, result revealed that a total of 496, 395 and 356 alleles, 820, 549 and 489 genotypes and 14.171, 11.286 and 10.171 mean number of alleles was observed in pooled ewes, Agricultural College and Commercial flocks, respectively. Moreover, groups of low and high genetic-economic index showed to have a total of 164, 169 alleles and 160, 165 genotypes and 4.686, 4.829 mean number of alleles, respectively. The mean number observed and expected heterozygosity values at these microsatellites for pooled ewes, Agricultural College flock, Commercial flock, low and high genetic-economic index groups were (0.407 and 0.764), (0.393 and 0.742) and (0.425 and 0.745), (0.428 and 0.658) and (0.429 and 0.644), respectively. The sample of pooled ewes studied was significantly deviated from Hardy-Weinberg equilibrium for all markers. Allelic frequency at microsatellites BM1818, ILSTS019 and SPS113 in Agricultural College flock and BMS1494 and MAF035 in Commercial flock found to be in Hardy-Weinberg equilibrium. Furthermore, the low and high genetic-economic groups deviated from Hardy-Weinberg Equilibrium at 17 and 14 microsatellite markers, respectively. Highest correlation (0.5) was found between McM527 and OarAE129 on chromosome 5 and the lowest correlation (0.246) was found between INRA023 and SRCRSP15 on chromosome 1 and that between OarFCB048 and MAF209 on chromosome 17. Average PIC values of pooled ewes, Agricultural College flock, Commercial flock, low and high genetic-economic index groups were (0.744, 0.719, 0.721, 0.617 and 0.656) respectively, while corresponding inbreeding coefficient values were (0.467, 0.479, 0.438, 0.418 and 0.410), respectively. Neis genetic distance between two flocks of Hamdani sheep for 35 markers investigated in this study was 0.2304. Furthermore, the higher genetic distance of pooled ewes was observed between high and low genetic-economic index groups being 0.4529. Whereas, higher genetic distance between genetic-economic indexes groups in Agricultural College and Commercial flocks observed being 0.5729 and 0.6024, respectively. Out of 35 markers over all animals, four markers (MAF065, ILSTS011, MAF209 and ILSTS005), six markers (ILSTS087, MAF209, MAF070, BM6444, OARFCB304 and SRCRSP15) and four markers (ILSTS087, MAF209, TCRVB6 and OARFCB304) on different chromosomes have significant effects on TLW, TMY and WP, respectively. It is concluded that high degree of genetic variability in Hamdani sheep breed was observed. Furthermore, result indicated the possibility of early selection of animals based on identifying specific microsatellites can improve quantitative trait(s).

Abstract : The genetic variation in Hamdani sheep in the Kurdistan region of Iraq was studied using 35 microsatellite markers. All 35 markers were found to be highly polymorphic. The mean number of observed alleles ranged from four at BMS1494 to twenty five at BM6444 and INRABERN185 loci. The polymorphic information content (PIC) values ranged from 0.208 for BMS1494 loci to 0.935 for INRABERN185 with an average value of 0.744. The overall observed and expected heterozygosity values were 0.407 and 0.764, respectively. Test of genotype frequencies for deviation from the Hardy-Weinberg equilibrium (HWE) at each locus, revealed a significant departure from HWE due to loss in heterozygotes by high level of inbreeding. The average inbreeding value for the 35 markers investigated was 0.469. The high observed heterozygosity is an indication of genetic variability that could be used for developing efficient utilization and genetic improvement strategies for Hamdani sheep. Key words: Hamdani sheep, microsatellites, polymorphism, genetic diversity, inbreeding, heterozygosity.

To combine clinical and molecular markers into an algorithm for predicting outcome for individual patients with human papillomavirus (HPV) DNA/p16(INK4a) positive tonsillar and base of tongue squamous cell carcinoma (TSCC and BOTSCC). Head-neck cancer treatment has become more intensified, comprising not only surgery and radiotherapy, but also induction/concomitant chemotherapy and targeted therapy. With less treatment, 3-year disease free survival (DFS) is 80% for HPV-positive TSCC and BOTSCC. An 85-100% 3-year DFS is observed for HPV(+) TSCC and BOTSCC with absence of HLA class I, or CD44 expression, or high CD8(+) tumour-infiltrating lymphocyte (TIL) counts suggesting that therapy could be tapered for many if patients could be identified individually. Patients treated curatively, with HPV DNA/p16(INK4a) positive tumours examined for HLA class I and II, CD44 and CD8(+)TILs, were included. An L1-regularised logistic regression was used to evaluate the effect of the biomarker data, age, stage, diagnosis, smoking and treatment on 3-year risk of death or relapse on a training cohort of 197 patients diagnosed 2000-2007 and validated on a cohort of 118 patients diagnosed 2008-2011. The variables finally included in the model were HLA class I, CD8(+) TILs, age, stage and diagnosis (TSCC or BOTSCC). The model showed acceptable discrimination and calibration. The discriminative ability of the model did not diminish after validation (AUC=0.77). To our knowledge, this is the first model to utilise information from several markers to predict an individual probability of clinical outcome for patients with HPV DNA/p16(INK4a) positive tumours. Copyright © 2015 Elsevier Ltd. All rights reserved.