Dataset Information

Genetic association of swine leukocyte antigen class II haplotypes and body weight in Microminipigs.

ABSTRACT: Microminipigs are a novel animal model with extensive applications in laboratory studies owing, in part, to their extremely small body sizes. In this study, the relationship between swine leukocyte antigen (SLA) class II haplotype and body weight was evaluated in the Microminipig population.A total of 1,900 haplotypes, covering SLA class II haplotypes Lr-0.7, Lr-0.23, Lr-0.17, Lr-0.37, Lr-0.16, Lr-0.11, Lr-0.13, and Lr-0.18, were analyzed in 950 piglets. Birth weights and weights on postnatal day 50 were examined in piglets with eight different SLA class II haplotypes.The mean birth weight of piglets with the Lr-0.23 haplotype (0.415 kg, n = 702) was significantly lower than that of piglets with Lr-0.17 (0.445 kg, n = 328) and Lr-0.37 (0.438 kg, n = 383) haplotypes. At postnatal day 50, the mean body weight of piglets with the Lr-0.23 haplotype (3.14 kg) was significantly lower than that of piglets with the Lr-0.13 haplotype (3.46 kg, p<0.01). There were no significant differences in daily gains (DGs) among the eight haplotypes. However, piglets with the Lr-0.11 and -0.18 haplotype combination or any heterozygous haplotype combinations containing Lr-0.23 had significantly lower DGs than those of piglets with the Lr-0.18, 0.37 haplotype combination.Piglets with the Lr-0.23 haplotype had relatively low body weights at birth and on postnatal day 50 and slightly lower DGs than those of piglets with other haplotypes. Therefore, the Lr-0.23 SLA class II haplotype may be a suitable marker for the selective breeding of Microminipigs with small body sizes.

SUBMITTER: Matsubara T

PROVIDER: S-EPMC5767497 | biostudies-other | 2018 Feb

REPOSITORIES: biostudies-other

ACCESS DATA

Publications

Genetic association of swine leukocyte antigen class II haplotypes and body weight in Microminipigs.

Matsubara Tatsuya T Takasu Masaki M Imaeda Noriaki N Nishii Naohito N Takashima Satoshi S Nishimura Takashi T Nishimura Toshiaki T Shiina Takashi T Ando Asako A Kitagawa Hitoshi H

Asian-Australasian journal of animal sciences 20170816 2

<h4>Objective</h4>Microminipigs are a novel animal model with extensive applications in laboratory studies owing, in part, to their extremely small body sizes. In this study, the relationship between swine leukocyte antigen (SLA) class II haplotype and body weight was evaluated in the Microminipig population.<h4>Methods</h4>A total of 1,900 haplotypes, covering SLA class II haplotypes Lr-0.7, Lr-0.23, Lr-0.17, Lr-0.37, Lr-0.16, Lr-0.11, Lr-0.13, and Lr-0.18, were analyzed in 950 piglets. Birth w ...[more]

PMID: 28823133

Similar Datasets

Project description:Class II human leukocyte antigens (HLA II) are proteins involved in the human immunological adaptive response by binding and exposing some pre-processed, non-self peptides in the extracellular domain in order to make them recognizable by the CD4+ T lymphocytes. However, the understanding of HLA-peptide binding interaction is a crucial step for designing a peptide-based vaccine because the high rate of polymorphisms in HLA class II molecules creates a big challenge, even though the HLA II proteins can be grouped into supertypes, where members of different class bind a similar pool of peptides. Hence, first we performed the supertype classification of 27 HLA II proteins using their binding affinities and structural-based linear motifs to create a stable group of supertypes. For this purpose, a well-known clustering method was used, and then, a consensus was built to find the stable groups and to show the functional and structural correlation of HLA II proteins. Thus, the overlap of the binding events was measured, confirming a large promiscuity within the HLA II-peptide interactions. Moreover, a very low rate of locus-specific binding events was observed for the HLA-DP genetic locus, suggesting a different binding selectivity of these proteins with respect to HLA-DR and HLA-DQ proteins. Secondly, a predictor based on a support vector machine (SVM) classifier was designed to recognize HLA II-binding peptides. The efficiency of prediction was estimated using precision, recall (sensitivity), specificity, accuracy, F-measure, and area under the ROC curve values of random subsampled dataset in comparison with other supervised classifiers. Also the leave-one-out cross-validation was performed to establish the efficiency of the predictor. The availability of HLA II-peptide interaction dataset, HLA II-binding motifs, high-quality amino acid indices, peptide dataset for SVM training, and MATLAB code of the predictor is available at http://sysbio.icm.edu.pl/HLA .

Project description:BACKGROUND:Associations between human leukocyte antigens (HLA) alleles and cervical cancer are largely representative of squamous cell carcinoma (SCC), the major histologic subtype. We evaluated the association between HLA class I (A, B, and C) and class II (DRB1 and DQB1) loci and risk of cervical adenocarcinoma (ADC), a less common but aggressive histologic subtype. METHODS:We pooled data from the Eastern and Western US Cervical Cancer studies, and evaluated the association between individual alleles and allele combinations and ADC (n = 630 ADC; n = 775 controls). Risk estimates were calculated for 11 a priori (based on known associations with cervical cancer regardless of histologic type) and 38 non a priori common alleles, as odds ratios (OR) and 95% confidence intervals (CI), adjusted for age and study. In exploratory analysis, we compared the risk associations between subgroups with HPV16 or HPV18 DNA in ADC tumor tissues in the Western US study cases and controls. RESULTS:Three of the a priori alleles were significantly associated with decreased risk of ADC [DRB1*13:01 (OR = 0.61; 95% CI: 0.41-0.93), DRB1*13:02 (OR = 0.49; 95% CI: 0.31-0.77), and DQB1*06:03 (OR = 0.64; 95% CI: 0.42-0.95)]; one was associated with increased risk [B*07:02 (OR = 1.39; 95% CI: 1.07-1.79)]. Among alleles not previously reported, DQB1*06:04 (OR = 0.46; 95% CI: 0.27-0.78) was associated with decreased risk of ADC and remained significant after correction for multiple comparisons, and C*07:02 (OR = 1.41; 95% CI: 1.09-1.81) was associated with increased risk. We did not observe a difference by histologic subtype. ADC was most strongly associated with increased risk with B*07:02/C*07:02 alleles (OR = 1.33; 95% CI: 1.01-1.76) and decreased risk with DRB1*13:02/DQB1*06:04 (OR = 0.41; 95% CI: 0.21-0.80). CONCLUSION:RESULTS suggest that HLA allele associations with cervical ADC are similar to those for cervical SCC. An intriguing finding was the difference in risk associated with several alleles restricted to HPV16 or HPV18-related tumors, consistent with the hypothesis that HLA recognition is HPV type-specific.

Dataset Information

Genetic association of swine leukocyte antigen class II haplotypes and body weight in Microminipigs.

Publications

Genetic association of swine leukocyte antigen class II haplotypes and body weight in Microminipigs.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure