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]
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]
A Familial Deletion of 16q21 Characterized by an SNP Array and Associated With a Normal Phenotype.
Am J Med Genet A. 2013 Apr 30;:0
Authors: Kowalczyk M, Tomaszewska A, Podbiol-Palenta A, Remiszewska B, Galjaard RJ, Zajaczek S, Srebniak MI
PMID: 23633153 [PubMed - as supplied by publisher]
Analysis of copy number variations in the sheep genome using 50K SNP BeadChip array.
BMC Genomics. 2013 Apr 8;14(1):229
Authors: Liu J, Zhang L, Xu L, Ren H, Lu J, Zhang X, Zhang S, Zhou X, Wei C, Zhao F, Du L
BACKGROUND: In recent years, genome-wide association studies have successfully uncovered single-nucleotide polymorphisms (SNPs) associated with complex traits such as diseases and quantitative phenotypes. These variations account for a small proportion of heritability. With the development of high throughput techniques, abundant submicroscopic structural variations have been found in organisms, of which the main variations are copy number variations (CNVs). Therefore, CNVs are increasingly recognized as an important and abundant source of genetic variation and phenotypic diversity. RESULTS: Analyses of CNVs in the genomes of three sheep breeds were performed using the Ovine SNP50 BeadChip array. A total of 238 CNV regions (CNVRs) were identified, including 219 losses, 13 gains, and six with both events (losses and gains), which cover 60.35 Mb of the sheep genomic sequence and correspond to 2.27% of the autosomal genome sequence. The length of the CNVRs on autosomes range from 13.66 kb to 1.30 Mb with a mean size of 253.57 kb, and 75 CNVRs events had a frequency > 3%. Among these CNVRs, 47 CNVRs identified by the PennCNV overlapped with the CNVpartition. Functional analysis indicated that most genes in the CNVRs were significantly enriched for involvement in the environmental response. Furthermore, 10 CNVRs were selected for validation and 6 CNVRs were further experimentally confirmed by qPCR. In addition, there were 57 CNVRs overlapped in our new dataset and other published ruminant CNV studies. CONCLUSIONS: In this study, we firstly constructed a sheep CNV map based on the Ovine SNP50 array. Our results demonstrated the differences of two detection tools and integration of multiple algorithms can enhance the detection of sheep genomic structure variations. Furthermore, our findings would be of help for understanding the sheep genome and provide preliminary foundation for carrying out the CNVs association studies with economically important phenotypes of sheep in the future.
PMID: 23565757 [PubMed - as supplied by publisher]
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