Correction: SNP Array Analysis Reveals Novel Genomic Abnormalities Including Copy Neutral Loss of Heterozygosity in Anaplastic Oligodendrogliomas.
PLoS One. 2013;8(5)
Authors: Idbaih A, Ducray F, Dehais C, Courdy C, Carpentier C, de Bernard S, Uro-Coste E, Mokhtari K, Jouvet A, Honnorat J, Chinot O, Ramirez C, Beauchesne P, Benouaich-Amiel A, Godard J, Eimer S, Parker F, Lechapt-Zalcman E, Colin P, Loussouarn D, Faillot T, Dam-Hieu P, Elouadhani-Hamdi S, Bauchet L, Langlois O, Le Guerinel C, Fontaine D, Vauleon E, Menei P, Fotso MJ, Desenclos C, Verrelle P, Ghiringhelli F, Noel G, Labrousse F, Carpentier A, Dhermain F, Delattre JY, Figarella-Branger D, POLA Network
[This corrects the article on p. e45950 in vol. 7.].
PMID: 23675404 [PubMed - as supplied by publisher]
Association of the HLA-DQA1 and HLA-DQB1 Alleles in Type 2 Diabetes Mellitus and Diabetic Nephropathy in the Han Ethnicity of China.
J Diabetes Res. 2013;2013:452537
Authors: Ma ZJ, Sun P, Guo G, Zhang R, Chen LM
HLA gene system is one of the most polymorphic regions of the human genome. The association of HLA class II genes in T1DM pathogenesis has been reported for several ethnicities. Associations of HLA class II genes with T2DM have revealed inconsistent results. Moreover, correlations between DN and HLA alleles remain unclear. We carried out DNA typing chip by specific medium resolution typing probes in 310 T2DM subjects (including 210 patients with DN and 100 patients without DN) in addition to 100 healthy controls. Differences were found between patients with T2DM and the control group in the frequencies of the HLA-DQA1∗0301 (15.5% versus 8.0%, P < 0.01) and the HLA-DQA1∗0501 alleles (16.6% versus 8.5%, P < 0.01). Differences were found between patients with DN and without DN in the frequencies of the HLA-DQA1∗0302 (6.9% versus 13.5%, P < 0.01) and HLA-DQB1∗0501 alleles (5.8% versus 14.5%, P < 0.01). Diabetes duration and systolic blood pressure were independent risk factors associated with DN (OR = 2.277 and 1.366, resp., P < 0.05), whereas the HLA-DQB1∗0501 llele had a protective effect on DN (OR = 0.53, P < 0.05). These data suggest the HLA-DQA1∗0301 and HLA-DQA1∗0501 alleles are markers of susceptibility for T2DM, and the HLA-DQB1∗0501 allele is associated with a protective effect on DN in Han ethnicity of China.
PMID: 23671871 [PubMed - in process]
Single nucleotide polymorphism discovery in albacore and Atlantic bluefin tuna provides insights into worldwide population structure.
Anim Genet. 2013 May 14;
Authors: Albaina A, Iriondo M, Velado I, Laconcha U, Zarraonaindia I, Arrizabalaga H, Pardo MA, Lutcavage M, Grant WS, Estonba A
The optimal management of the commercially important, but mostly over-exploited, pelagic tunas, albacore (Thunnus alalunga Bonn., 1788) and Atlantic bluefin tuna (BFT; Thunnus thynnus L., 1758), requires a better understanding of population structure than has been provided by previous molecular methods. Despite numerous studies of both species, their population structures remain controversial. This study reports the development of single nucleotide polymorphisms (SNPs) in albacore and BFT and the application of these SNPs to survey genetic variability across the geographic ranges of these tunas. A total of 616 SNPs were discovered in 35 albacore tuna by comparing sequences of 54 nuclear DNA fragments. A panel of 53 SNPs yielded FST values ranging from 0.0 to 0.050 between samples after genotyping 460 albacore collected throughout the distribution of this species. No significant heterogeneity was detected within oceans, but between-ocean comparisons (Atlantic, Pacific and Indian oceans along with Mediterranean Sea) were significant. Additionally, a 17-SNP panel was developed in Atlantic BFT by cross-species amplification in 107 fish. This limited number of SNPs discriminated between samples from the two major spawning areas of Atlantic BFT (FST = 0.116). The SNP markers developed in this study can be used to genotype large numbers of fish without the need for standardizing alleles among laboratories.
PMID: 23668670 [PubMed - as supplied by publisher]
A note on statistical method for genotype calling of high-throughput SNP arrays.
J Appl Stat. 2013;40(6):1372-1381
Authors: Yang J, Zhang W, Wu B
We study the genotype calling algorithms for the high-throughput single-nucleotide polymorphism (SNP) arrays. Building upon the novel SNP-RMA preprocessing approach and the state-of-the-art CRLMM approach for genotype calling, we propose a simple modification to better model and combine the information across multiple SNPs with empirical Bayes modeling, which could often significantly improve the genotype calling of CRLMM. Through applications to the HapMap Trio data set and a non-HapMap test set of high quality SNP chips, we illustrate the competitive performance of the proposed method.
PMID: 23667285 [PubMed - as supplied by publisher]