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]

Single nucleotide polymorphism typing with massively parallel sequencing for human identification.

Int J Legal Med. 2013 Jun 5;

Authors: Seo SB, King JL, Warshauer DH, Davis CP, Ge J, Budowle B

Abstract
The Ion AmpliSeq™ HID single nucleotide polymorphism (SNP) panel, a primer pool of 103 autosomal SNPs and 33 Y-SNPs, was evaluated using the Ion 314™ Chip on the Ion PGM™ Sequencer with four DNA samples. The study focused on the sequencing of DNA at three different initial target quantities, related interpretation issues, and concordance of results with another sequencing platform, i.e., Genome Analyzer IIx. With 10 ng of template DNA, all genotypes at the 136 SNPs were detected. With 1 ng of DNA, all SNPs were detected and one SNP locus in one sample showed extreme heterozygote imbalance on allele coverage. With 100 pg of DNA, an average of 1.6 SNP loci were not detected, and an average of 4.3 SNPs showed heterozygote imbalance. The average sequence coverage was 945-600× at autosomal SNPs and 465-209× at Y-SNPs for 10 ng-100 pg of DNA. The average heterozygote allele coverage ratio was 89.6-61.8 % for 10 ng-100 pg of DNA. At 10 ng of DNA, all genotypes of the 95 SNPs shared between the two different sequencing platforms were concordant except for one SNP, rs1029047. The error was due to the misalignment of a flanking homopolymer. Overall, the data support that genotyping a large battery of SNPs is feasible with massively parallel sequencing. With barcode systems, better allele balance, and specifically designed alignment software, a more comprehensive rapid genotyping and more cost-effective results may be obtained from multiple samples in one analysis than are possible with current typing and capillary electrophoresis systems.

PMID: 23736940 [PubMed - as supplied by publisher]

IFNG polymorphisms are associated with tuberculosis in Han Chinese pediatric female population.

Mol Biol Rep. 2013 Jun 5;

Authors: Shen C, Jiao WW, Feng WX, Wu XR, Xiao J, Miao Q, Sun L, Wang BB, Wang J, Liu F, Shen D, Shen AD

Abstract
Host genetic factors play a major role in determining differential susceptibility to human tuberculosis (TB), a re-emerging infectious disease throughout the world. Genetic variations in the IFNG gene coding for interferon gamma (IFN-γ), have been identified in TB patients. To investigate the association of the IFNG polymorphisms with TB susceptibility in Chinese pediatric population. A case-control study of 189 TB patients and 164 controls was performed using single-nucleotide polymorphism (SNP) analysis. Genomic DNA was extracted from leukocytes in peripheral blood. Three SNPs of IFNG, including -1616C/T (rs2069705), +874A/T (rs2430561), and +3234C/T (rs2069718), were selected for genotyping and analysis. The +874A and +3234C alleles were more frequent among TB patients (P = 0.108 and P = 0.088), especially in females (both P = 0.029), although this difference was not significant since Bonferroni corrected significance threshold was 0.025 (two of three SNPs were found to be in linkage disequilibrium). More pronounced differences for the +874 and +3234 polymorphisms were found under the genotype comparison between TB cases and controls in the total population [P = 0.026 (borderline non-significance) and P = 0.020, respectively], and in the female subgroup (P = 0.020 and P = 0.020). The dominant model of inheritance was shown to be significant for +874A and +3234C alleles (both P = 0.019) in the female subgroup. The +874A and +3234C alleles were more frequently found in extrapulmonary TB patients than in controls (P = 0.039). Haplotype analysis carried out on these three SNPs showed the TTT haplotype to be more frequent in controls than in TB cases, and this difference showed a strong significance (P = 0.005). The +874A and +3234C alleles may be related to TB susceptibility in the female subgroup in the Chinese pediatric population of North China. The higher rate of +874A (known to correlate with lower IFN-γ expression) in the extrapulmonary TB subgroup suggests a sufficient IFN-γ expression to be not only an important factor for the onset of TB disease but also for limiting its dissemination to lungs.

PMID: 23737189 [PubMed - as supplied by publisher]

High Quality Genome-Wide Genotyping from Archived Dried Blood Spots without DNA Amplification.

PLoS One. 2013;8(5):e64710

Authors: St Julien KR, Jelliffe-Pawlowski LL, Shaw GM, Stevenson DK, O'Brodovich HM, Krasnow MA, Stanford BPD Study Group

Abstract
Spots of blood are routinely collected from newborn babies onto filter paper called Guthrie cards and used to screen for metabolic and genetic disorders. The archived dried blood spots are an important and precious resource for genomic research. Whole genome amplification of dried blood spot DNA has been used to provide DNA for genome-wide SNP genotyping. Here we describe a 96 well format procedure to extract DNA from a portion of a dried blood spot that provides sufficient unamplified genomic DNA for genome-wide single nucleotide polymorphism (SNP) genotyping. We show that SNP genotyping of the unamplified DNA is more robust than genotyping amplified dried blood spot DNA, is comparable in cost, and can be done with thousands of samples. This procedure can be used for genome-wide association studies and other large-scale genomic analyses that require robust, high-accuracy genotyping of dried blood spot DNA.

PMID: 23737996 [PubMed - in process]