89 research outputs found
Estimation of a significance threshold for epigenome-wide association studies.
No full textEpigenome-wide association studies (EWAS) are designed to characterise population-level epigenetic differences across the genome and link them to disease. Most commonly, they assess DNA-methylation status at cytosine-guanine dinucleotide (CpG) sites, using platforms such as the Illumina 450k array that profile a subset of CpGs genome wide. An important challenge in the context of EWAS is determining a significance threshold for declaring a CpG site as differentially methylated, taking multiple testing into account. We used a permutation method to estimate a significance threshold specifically for the 450k array and a simulation extrapolation approach to estimate a genome-wide threshold. These methods were applied to five different EWAS datasets derived from a variety of populations and tissue types. We obtained an estimate of α=2.4×10-7 for the 450k array, and a genome-wide estimate of α=3.6×10-8. We further demonstrate the importance of these results by showing that previously recommended sample sizes for EWAS should be adjusted upwards, requiring samples between ∼10% and ∼20% larger in order to maintain type-1 errors at the desired level
Genotyping pooled DNA using 100K SNP microarrays: a step towards genomewide association scans
No full textThe identification of quantitative trait loci (QTLs) of small effect size that underlie complex traits poses a particular challenge for geneticists due to the large sample sizes and large numbers of genetic markers required for genomewide association scans. An efficient solution for screening purposes is to combine single nucleotide polymorphism (SNP) microarrays and DNA pooling (SNP-MaP), an approach that has been shown to be valid, reliable and accurate in deriving relative allele frequency estimates from pooled DNA for groups such as cases and controls for 10K SNP microarrays. However, in order to conduct a genomewide association study many more SNP markers are needed. To this end, we assessed the validity and reliability of the SNP-MaP method using Affymetrix GeneChip Mapping 100K Array set. Interpretable results emerged for 95% of the SNPs (nearly 110,000 SNPs). We found that SNP-MaP allele frequency estimates correlated 0.939 with allele frequencies for 97 605 SNPs that were genotyped individually in an independent population; the correlation was 0.971 for 26 SNPs that were genotyped individually for the 1028 individuals used to construct the DNA pools. We conclude that extending the SNP-MaP method to the Affymetrix GeneChip Mapping 100K Array set provides a useful screen of >100,000 SNP markers for QTL association scans
Next generation sequencing in epigenetics: insights and challenges
No full textThe epigenetics community was an early adopter of next generation sequencing (NGS). NGS-based studies have provided detailed and comprehensive views of epigenetic modifications for the genomes of many species and cell types. Recently, DNA methylation has attracted much attention due to the discovery of 5-hydroxymethyl-cytosine and its role in epigenetic reprogramming and pluripotency. This renewed interest has been concomitant with methodological progress enabling, for example, high coverage and single base resolution profiling of the mammalian methylome in small numbers of cells. We summarise this progress and highlight resulting key findings about the complexity of eukaryotic DNA methylation, its role in metazoan genome evolution, epigenetic reprogramming, and its close ties with histone modifications in the context of transcription. Finally, we discuss how fundamental insights gained by NGS, particularly the discovery of widespread allele-specific epigenetic variation in the human genome, have the potential to significantly contribute to the understanding of human common complex diseases
What Has Behavioural Genetic Research Told Us About the Origins of Individual Differences in Educational Abilities and Achievements?
No full textAssessing individual differences in genome-wide gene expression in human whole blood: reliability over four hours and stability over 10 months.
No full textStudying the causes and correlates of natural variation in gene expression in healthy populations assumes that individual differences in gene expression can be reliably and stably assessed across time. However, this is yet to be established. We examined 4-hour test-retest reliability and 10 month test-retest stability of individual differences in gene expression in ten 12-year-old children. Blood was collected on four occasions: 10 a.m. and 2 p.m. on Day 1 and 10 months later at 10 a.m. and 2 p.m. Total RNA was hybridized to Affymetrix-U133 plus 2.0 arrays. For each probeset, the correlation across individuals between 10 a.m. and 2 p.m. on Day 1 estimates test-retest reliability. We identified 3,414 variable and abundantly expressed probesets whose 4-hour test-retest reliability exceeded .70, a conventionally accepted level of reliability, which we had 80% power to detect. Of the 3,414 reliable probesets, 1,752 were also significantly reliable 10 months later. We assessed the long-term stability of individual differences in gene expression by correlating the average expression level for each probe-set across the two 4-hour assessments on Day 1 with the average level of each probe-set across the two 4-hour assessments 10 months later. 1,291 (73.7%) of the 1,752 probe-sets that reliably detected individual differences across 4 hours on two occasions, 10 months apart, also stably detected individual differences across 10 months. Heritability, as estimated from the MZ twin intraclass correlations, is twice as high for the 1,752 reliable probesets versus all present probesets on the array (0.68 vs 0.34), and is even higher (0.76) for the 1,291 reliable probesets that are also stable across 10 months. The 1,291 probesets that reliably detect individual differences from a single peripheral blood collection and stably detect individual differences over 10 months are promising targets for research on the causes (e.g., eQTLs) and correlates (e.g., psychopathology) of individual differences in gene expression
The search for quantitative trait loci associated with language and reading impairment in children using DNA pooling and SNP microarrays
No full textEThOS - Electronic Theses Online ServiceGBUnited Kingdo
Hyperfine splitting of [Al VI] 3.66 mu m and the Al isotopic ratio in NGC 6302
No full textThe core of planetary nebula NGC 6302 is filled with high-excitation photoionized gas at low expansion velocities. It represents a unique astrophysical situation in which to search for hyperfine structure (HFS) in coronal emission lines from highly ionized species. HFS is otherwise blended by thermal or velocity broadening. Spectra containing [Al vr] 3.66 mu m P-3(2) <- P-3(1), obtained with Phoenix on Gemini South at resolving powers of up to 75000, resolve the line into five hyperfine components separated by 20-60 km s(-1) as a result of the coupling of the I = 5/2 nuclear spin of Al-27 with the total electronic angular momentum J. The isotope Al-26 has a different nuclear spin of I = 5, and a different HFS, which allows us to place a 3 sigma upper limit on the Al-26/Al-27 abundance ratio of 1/33. We measure the HFS magnetic dipole coupling constants for [Al vr], and provide the first estimates of the electric quadrupole HFS coupling constants obtained through astronomical observations of an atomic transition
Utility of the pooling approach as applied to whole genome association scans with high-density Affymetrix microarrays.
No full textBackground: We report an attempt to extend the previously successful approach of combining SNP (single nucleotide polymorphism) microarrays and DNA pooling (SNP-MaP) employing high-density microarrays. Whereas earlier studies employed a range of Affymetrix SNP microarrays comprising from 10 K to 500 K SNPs, this most recent investigation used the 6.0 chip which displays 906,600 SNP probes and 946,000 probes for the interrogation of CNVs (copy number variations). The genotyping assay using the Affymetrix SNP 6.0 array is highly demanding on sample quality due to the small feature size, low redundancy, and lack of mismatch probes.
Findings: In the first study published so far using this microarray on pooled DNA, we found that pooled cheek swab DNA could not accurately predict real allele frequencies of the samples that comprised the pools. In contrast, the allele frequency estimates using blood DNA pools were reasonable, although inferior compared to those obtained with previously employed Affymetrix microarrays. However, it might be possible to improve performance by developing improved analysis methods.
Conclusions: Despite the decreasing costs of genome-wide individual genotyping, the pooling approach may have applications in very large-scale case-control association studies. In such cases, our study suggests that high-quality DNA preparations and lower density platforms should be preferred
Genome-wide association study of latent cognitive measures in adolescence: genetic overlap with intelligence and education
No full textIndividual differences in executive functions (EF) are heritable and predictive of academic attainment (AA). However, little is known about genetic contributions to EFs or their genetic relationship with AA and intelligence. We conducted genome-wide association analyses for processing speed (PS) and the latent EF measures of working memory (WM) and inhibitory control (IC) in 4,611 adolescents from ALSPAC. Whilst no loci reached genome-wide significance, common genetic variants explained 30% of the variance in WM and 19% in PS. In contrast, we failed to find common genetic contributions to IC. Finally, we examined shared genetic effects between EFs, and general intelligence, AA and ADHD. We identified significant genetic correlations between WM, intelligence and AA. A more specific pattern was observed for PS, with modest genetic overlap with intelligence. Together these findings highlight diversity in the genetic contributions to specific cognitive functions and their genetic relationship with educational and psychiatric outcome
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