StAMPP: an R package for calculation of genetic differentiation and structure of mixed-ploidy level populations.

Mol Ecol Resour. 2013 Jun 6;

Authors: Pembleton LW, Cogan NO, Forster JW

Abstract
Statistical Analysis of Mixed-Ploidy Populations (StAMPP) is a freely available R package for calculation of population structure and differentiation based on single nucleotide polymorphism (SNP) genotype data from populations of any ploidy level, and/or mixed-ploidy levels. StAMPP provides an advance on previous similar software packages, due to an ability to calculate pairwise FST values along with confidence intervals, Nei's genetic distance and genomic relationship matrixes from data sets of mixed-ploidy level. The software code is designed to efficiently handle analysis of large genotypic data sets that are typically generated by high-throughput genotyping platforms. Population differentiation studies using StAMPP are broadly applicable to studies of molecular ecology and conservation genetics, as well as animal and plant breeding.

PMID: 23738873 [PubMed - as supplied by publisher]

Modelling and visualizing fine-scale linkage disequilibrium structure.

BMC Bioinformatics. 2013 Jun 6;14(1):179

Authors: Edwards D

Abstract
BACKGROUND: Detailed study of genetic variation at the population level in humans and other species is now possible due to the availability of large sets of single nucleotide polymorphism data. Alleles at two or more loci are said to be in linkage disequilibrium (LD) when they are correlated or statistically dependent. Current efforts to understand the genetic basis of complex phenotypes are based on the existence of such associations, making study of the extent and distribution of linkage disequilibrium central to this endeavour. The objective of this paper is to develop methods to study fine-scale patterns of allelic association using probabilistic graphical models. RESULTS: An efficient, linear-time forward-backward algorithm is developed to estimate chromosome-wide LD models by optimizing a penalized likelihood criterion, and a convenient way to display these models is described. To illustrate the methods they are applied to data obtained by genotyping 8341 pigs. It is found that roughly 20% of the porcine genome exhibits complex LD patterns, forming islands of relatively high genetic diversity. CONCLUSIONS: The proposed algorithm is efficient and makes it feasible to estimate and visualize chromosome-wide LD models on a routine basis.

PMID: 23742095 [PubMed - as supplied by publisher]

Single-nucleotide polymorphism array genotyping is equivalent to metaphase cytogenetics for diagnosis of Turner syndrome.

Genet Med. 2013 Jun 6;

Authors: Prakash S, Guo D, Maslen CL, Silberbach M, Milewicz D, Bondy CA

Abstract
Purpose:Turner syndrome is a developmental disorder caused by partial or complete monosomy for the X chromosome in 1 in 2,500 females. We hypothesized that single-nucleotide polymorphism (SNP) array genotyping could provide superior resolution in comparison to metaphase karyotype analysis to facilitate genotype-phenotype correlations.Methods:We genotyped 187 Turner syndrome patients with 733,000 SNP marker arrays. All cases met diagnostic criteria for Turner syndrome based on karyotypes (60%) or characteristic physical features. The SNP array results confirmed the diagnosis of Turner syndrome in 100% of cases.Results:We identified a single X chromosome (45,X) in 113 cases. In 58 additional cases (31%), other mosaic cell lines were present, including isochromosomes (16%), rings (5%), and Xp deletions (8%). The remaining cases were mosaic for monosomy X and normal male or female cell lines. Array-based models of X chromosome structure were compatible with karyotypes in 104 of 116 comparable cases (90%). We found that the SNP array data did not detect X-autosome translocations (three cases) but did identify two derivative Y chromosomes and 13 large copy-number variants that were not detected by karyotyping.Conclusion:Our study is the first systematic comparison between the two methods and supports the utility of SNP array genotyping to address clinical and research questions in Turner syndrome.Genet Med advance online publication 6 June 2013Genetics in Medicine (2013); doi:10.1038/gim.2013.77.

PMID: 23743550 [PubMed - as supplied by publisher]

Linkage disequilibrium and haplotype block structure in six commercial pig lines.

J Anim Sci. 2013 Jun 4;

Authors: Veroneze R, Lopes PS, Guimarães SE, Silva FF, Lopes MS, Harlizius B, Knol EF

Abstract
Linkage disequilibrium (LD) across the genome is critical information for association studies and genomic selection because it determines the number of SNPs (Single Nucleotide Polymorphism) that should be used for a successful association analysis and genomic selection. LD also influences the accuracy of genomic breeding values. Some studies have demonstrated that SNPs in strong LD are organized into discrete blocks of haplotypes which are separated by possibly hot spots of recombination. To reduce the number of markers needed to be genotyped for association mapping, a set of SNPs can be selected that labels all haplotype blocks. We estimated the LD, calculated the average haplotype block size for six pig lines and compared the block size between lines. Six commercial pig lines were genotyped using the Illumina PorcineSNP60 (Number of markers M = 62,163) Genotyping BeadChip (Illumina Inc.); on average, a panel of 37,623 SNPs with an average MAF of 0.283 was included in the analysis. The linkage disequilibrium declined as a function of distance. All pig lines had an average r(2) above 0.3 for markers 100 - 150 apart. The estimated average block size was 394.885 Kb, and blocks between 100 and 400 Kb were most prominent (49.96%) in all lines. These results showed that the extent of LD in pigs is much larger than in the cattle population, in accordance with the genetic map length of pigs, which is much shorter than cattle. The evaluated lines have 2,640 - 3,037 blocks, covering 45% of the pig genome, on average. Differences in haplotype block size between lines were observed for some chromosomes (i.e., 3, 5, 7, 13, 14, and 18), which provide a direction for future studies of haplotype block conservation or divergence across lines.

PMID: 23736062 [PubMed - as supplied by publisher]