In silico and in vitro comparative analysis to select, validate and test SNPs for human identification

<p>Abstract</p> <p>Background</p> <p>The recent advances in human genetics have recently provided new insights into phenotypic variation and genome variability. Current forensic DNA techniques involve the search for genetic similarities and differences between biological samples. Consequently the selection of ideal genomic biomarkers for human identification is crucial in order to ensure the highest stability and reproducibility of results.</p> <p>Results</p> <p>In the present study, we selected and validated 24 SNPs which are useful in human identification in 1,040 unrelated samples originating from three different populations (Italian, Benin Gulf and Mongolian). A Rigorous <it>in silico </it>selection of these markers provided a list of SNPs with very constant frequencies across the populations tested as demonstrated by the F_stvalues. Furthermore, these SNPs also showed a high specificity for the human genome (only 5 SNPs gave positive results when amplified in non-human DNA).</p> <p>Conclusion</p> <p>Comparison between <it>in silico </it>and <it>in vitro </it>analysis showed that current SNPs databases can efficiently improve and facilitate the selection of markers because most of the analyses performed (F_st, r², heterozigosity) in more than 1,000 samples confirmed available population data.</p

Sex-Specific Parental Effects on Offspring Lipid Levels

Background: Plasma lipid levels are highly heritable traits, but known genetic loci can only explain a small portion of their heritability. Methods and Results: In this study, we analyzed the role of parental levels of total cholesterol (TC), low‐density lipoprotein cholesterol (LDL‐C), high‐density lipoprotein cholesterol (HDL‐C), and triglycerides (TGs) in explaining the values of the corresponding traits in adult offspring. We also evaluated the contribution of nongenetic factors that influence lipid traits (age, body mass index, smoking, medications, and menopause) alone and in combination with variability at the genetic loci known to associate with TC, LDL‐C, HDL‐C, and TG levels. We performed comparisons among different sex‐specific regression models in 416 families from the Framingham Heart Study and 304 from the SardiNIA cohort. Models including parental lipid levels explain significantly more of the trait variation than models without these measures, explaining up to ≈39% of the total trait variation. Of this variation, the parent‐of‐origin effect explains as much as ≈15% and it does so in a sex‐specific way. This observation is not owing to shared environment, given that spouse‐pair correlations were negligible (\u3c1.5% explained variation in all cases) and is distinct from previous genetic and acquired factors that are known to influence serum lipid levels. Conclusions: These findings support the concept that unknown genetic and epigenetic contributors are responsible for most of the heritable component of the plasma lipid phenotype, and that, at present, the clinical utility of knowing age‐matched parental lipid levels in assessing risk of dyslipidemia supersedes individual locus effects. Our results support the clinical utility of knowing parental lipid levels in assessing future risk of dyslipidemia

Fine-mapping of lipid regions in global populations discovers ethnic-specific signals and refines previously identified lipid loci

Genome-wide association studies have identified over 150 loci associated with lipid traits, however, no large-scale studies exist for Hispanics and other minority populations. Additionally, the genetic architecture of lipid-influencing loci remains largely unknown. We performed one of the most racially/ethnically diverse fine-mapping genetic studies of HDL-C, LDL-C, and triglycerides to-date using SNPs on the MetaboChip array on 54,119 individuals: 21,304 African Americans, 19,829 Hispanic Americans, 12,456 Asians, and 530 American Indians. The majority of signals found in these groups generalize to European Americans. While we uncovered signals unique to racial/ethnic populations, we also observed systematically consistent lipid associations across these groups. In African Americans, we identified three novel signals associated with HDL-C (LPL, APOA5, LCAT) and two associated with LDL-C (ABCG8, DHODH). In addition, using this population, we refined the location for 16 out of the 58 known MetaboChip lipid loci. These results can guide tailored screening efforts, reveal population-specific responses to lipid-lowering medications, and aid in the development of new targeted drug therapies

HMOX1 Gene Promoter Alleles and High HO-1 Levels Are Associated with Severe Malaria in Gambian Children

Heme oxygenase 1 (HO-1) is an essential enzyme induced by heme and multiple stimuli associated with critical illness. In humans, polymorphisms in the HMOX1 gene promoter may influence the magnitude of HO-1 expression. In many diseases including murine malaria, HO-1 induction produces protective anti-inflammatory effects, but observations from patients suggest these may be limited to a narrow range of HO-1 induction, prompting us to investigate the role of HO-1 in malaria infection. In 307 Gambian children with either severe or uncomplicated P. falciparum malaria, we characterized the associations of HMOX1 promoter polymorphisms, HMOX1 mRNA inducibility, HO-1 protein levels in leucocytes (flow cytometry), and plasma (ELISA) with disease severity. The (GT)n repeat polymorphism in the HMOX1 promoter was associated with HMOX1 mRNA expression in white blood cells in vitro, and with severe disease and death, while high HO-1 levels were associated with severe disease. Neutrophils were the main HO-1-expressing cells in peripheral blood, and HMOX1 mRNA expression was upregulated by heme-moieties of lysed erythrocytes. We provide mechanistic evidence that induction of HMOX1 expression in neutrophils potentiates the respiratory burst, and propose this may be part of the causal pathway explaining the association between short (GT)n repeats and increased disease severity in malaria and other critical illnesses. Our findings suggest a genetic predisposition to higher levels of HO-1 is associated with severe illness, and enhances the neutrophil burst leading to oxidative damage of endothelial cells. These add important information to the discussion about possible therapeutic manipulation of HO-1 in critically ill patients

<i>OLR1</i> expression in KK, KN and NN in differentiated macrophages.

<p>(<i>Nf-kB</i>: nuclear factor kappa-light-chain-enhancer of activated B cells, <i>ERK1/2</i>: extracellular related kinase 1) (* p<0.05 vs KK).</p

Gene expression levels from Peripheral Mononuclear Cells (PBMCs) of KK, KN and NN carriers.

<p>Expression levels are measured by the log (ΔΔCt) obtained comparing each gene's expression with that of the housekeeping gene, <i>HPRT1</i>. (<i>Nf-kB</i>: nuclear factor kappa-light-chain-enhancer of activated B cells, <i>ERK1/2</i>: extracellular related kinase 1/2, <i>IL-6</i>: Interleukin-6, <i>CD40</i>: cluster of designation 40, <i>CX3CR1</i>: CX3 chemokine receptor 1, <i>TLR-4</i>: Toll-like receptor 4, <i>MMP</i>: metalloproteinase).</p

Statistical observations on the association between <i>OLR1</i> polymorphisms in males.

<p>Statistical observations on the association between <i>OLR1</i> polymorphisms in males.</p