Project description:We performed a comparative study of European and Asian populations using Illumina HM450K. We found that the majority of Infinium probes, which differentiated two examined groups, had SNPs in their target sequence. We investigated the impact of those SNPs on methylation readouts by Illumina HM450K Array. Our study clearly demonstrates that SNP variation existing in the genome, if not accounted for, may lead to false interpretation of the methylation signal differences suggested by some of the Illumina Infinium probes.
Project description:Characterization of ancestry-linked peptide variants in disease-relevant patient tissues represents a foundational step to connect patient ancestry with molecular disease pathogenesis. Nonsynonymous single nucleotide polymorphisms (SNPs) encoding missense substitutions within tryptic peptides exhibiting high allele frequencies in European, African, and East Asian populations, termed peptide ancestry informative markers (pAIMs), were prioritized from 1000 genomes. In silico analysis shows that as few as 20 pAIMs can determine ancestry proportions similarly to >260K SNPs (R2=0.9905). Multiplexed proteomic analysis of >100 human endometrial cancer cell lines and uterine leiomyoma (ULM) tissues combined resulted in the quantitation of 62 pAIMs that correlate with self-described race and genotype-confirmed patient ancestry. Candidates include a D451E substitution in GC vitamin D-binding protein previously associated with altered vitamin D levels in African and European populations. These efforts describe a generalized set of markers for proteoancestry assessment that will further support studies investigating the impact of ancestry on the human proteome and how this relates to the pathogenesis of uterine neoplasms.
Project description:To study the population genetics context of the Saqqaq individual we carried out Illumina Bead-Array-based genotyping on four native North American and twelve north Asian populations.
Project description:Genome-wide age-associated methylation signatures of 485,000 CpG sites were profiled in 192 individuals, age 6-85, of Northern European ancestry were profiled using the Illumina HM450 array.
Project description:Hispanic/Latino populations possess a complex genetic structure that reflects recent admixture among and potentially ancient substructure within Native American, European, and West African source populations. Here, we quantify genome-wide patterns of SNP and haplotype variation among 100 individuals with ancestry from Ecuador, Colombia, Puerto Rico, and the Dominican Republic genotyped using Illumina technology. To investigate variations of continental ancestry between different Hispanic/Latino groups (using self-reported country-specific identification of individual, both parents, and all four grandparents) and within them from healthy controls represented in the New York Health Project Biorepository. Genotyped on the Illumina 610-Quad, which is identical to HumanHap550-v3 SNPs plus an additional ~60,000 SNPs for CNV, no CNV data is provided or was analyzed.
Project description:We wanted to explore the genomic regions 1p13, 1q41, 9p21 and 10q11, which are among the labeled âtop 12 golden lociâ linked to coronary artery disease (CAD) risk, in order to see whether their geographic variation could be explained by demographic effects. To do this, we have genotyped these risk regions in a set of Mediterranean populations. Genomic DNA was extracted from blood cells using a Blood Midi kit (Omega Biotek, USA) according to manufacturer's procedures. DNA samples were genotyped for a combined set of 366 SNPs using an Illumina Custom GoldenGate Panel. SNPs were selected as a representative set of the common variation in the four genomic regions, according to the following criteria: i) average coverage of 1 SNP every 1.5 kb, ii) minor allele frequency (MAF) higher than 0.05 in CEU and TSI HapMap populations, iii) given priority to markers not in linkage disequilibrium (LD) (r2<0.8) in European populations, and iv) prioritizing markers previously associated with CAD. These criteria were applied giving preference to tag SNPs.
Project description:Epigenetic and genetic profiles (N=67) were based on the Illumina Infinium HumanMethylation450 BeadChip. We searched for differentially methylated probes (DMPs) and regions (DMRs). For genetic associations we analyzed the CpG-SNPs present on the array
Project description:Abstract: DNA methylation is an essential epigenetic modification that plays a key role associated with the regulation of gene expression during differentiation but in disease states such as cancer, the DNA methylation landscape is often deregulated. There are now numerous technologies available to interrogate DNA methylation status of CpG sites in a targeted or genome-wide fashion but each method, due to intrinsic biases, potentially interrogates different fractions of the genome. In this study, affinity-purification of methylated DNA using two popular genome-wide techniques: methylated DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain-based capture (MBDCap) were evaluated, highlighting that each technique operates in a different domain of the CpG density landscape. The effect of whole genome amplification was explored, illustrating that it can reduce sensitivity for detecting DNA methylation in GC-rich regions of the genome. Using MBDCap, microarray- and sequencing-based readouts were compared, highlighting the impact that copy number variation (CNV) can make in differential comparisons of methylomes. These studies reveal that the analysis of DNA methylation data and genome coverage is highly dependent on the method employed and consideration must be made in light of GC content, extent of DNA amplification and copy number. Comparison of MeDIP/MBD for DNA methylation profiling, comparison of whole genome amplification techniques, using tiling array for copy number aberration detection and comparisons of tiling array data to sequencing readouts
Project description:ASA-750K is a commercial array developed by Novogene Bioinformatics Technology Co.Ltd. The array contains 738980 sites in total including Illumina Asian Screening Arrary with additional 50k SNP sites (see http://www.novogene.com for more information).
Project description:Epienome-wide DNA methylation profiling of systemic lupus erythematosus (SLE). The Illumina HumanMethylation450K Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in normal human blood samples from females. Samples included 33 non-SLE female patients (control) and 57 SLE female patients. SLE patients:- Ethnicity included 39 African americans and 18 European Americans. SLEDAI score ranged from 2-30. Non-SLE pateients:-Ethnicity indclued 17 African Americans and 16 European Americans, all with a SLEDAI score of zero.
