Common DNA Sequence Research Articles

Haplotype variability in mitochondrial rRNA predisposes to metabolic syndrome

Metabolic syndrome is a growing concern in developed societies and due to its polygenic nature, the genetic component is only slowly being elucidated. Common mitochondrial DNA sequence variants have been associated with symptoms of metabolic syndrome and may, therefore, be relevant players in the genetics of metabolic syndrome. We investigate the effect of mitochondrial sequence variation on the metabolic phenotype in conplastic rat strains with identical nuclear but unique mitochondrial genomes, challenged by high-fat diet. We find that the variation in mitochondrial rRNA sequence represents risk factor in the insulin resistance development, which is associated with diacylglycerols accumulation, induced by tissue-specific reduction of the oxidative capacity. These metabolic perturbations stem from the 12S rRNA sequence variation affecting mitochondrial ribosome assembly and translation. Our work demonstrates that physiological variation in mitochondrial rRNA might represent a relevant underlying factor in the progression of metabolic syndrome.

Common DNA sequence variation influences epigenetic aging in African populations.

Aging is associated with genome-wide changes in DNA methylation in humans, facilitating the development of epigenetic age prediction models. However, most of these models have been trained primarily on European-ancestry individuals, and none account for the impact of methylation quantitative trait loci (meQTL). To address these gaps, we analyzed the relationships between age, genotype, and CpG methylation in 3 understudied populations: central African Baka (n = 35), southern African ‡Khomani San (n = 52), and southern African Himba (n = 51). We find that published prediction methods yield higher mean errors in these cohorts compared to European-ancestry individuals, and find that unaccounted-for DNA sequence variation may be a significant factor underlying this loss of accuracy. We leverage information about the associations between DNA genotype and CpG methylation to develop an age predictor that is minimally influenced by meQTL, and show that this model remains accurate across a broad range of genetic backgrounds. Intriguingly, we also find that the older individuals and those exhibiting relatively lower epigenetic age acceleration in our cohorts tend to carry more epigenetic age-reducing genetic variants, suggesting a novel mechanism by which heritable factors can influence longevity.

Effectiveness of multigene analysis for associating dimorphic partners in flat wasps (Hymenoptera, Bethylidae, Dissomphalus).

DNA sequences have proved valuable for associating males and females of the same dimorphic species in Hymenoptera. These molecular associations, however, depend on the used DNA sequences and the analysis methods. In the present study, we evaluated the molecular associations on 23 species of Dissomphalus (Hymenoptera, Bethylidae) using the three most common DNA sequences in molecular studies of Hymenoptera (28S rRNA, COI and ITS2). Our results indicated the male-female association with these three markers. COI, however, showed to be more suitable than the other markers because there was no overlap of genetic variation among species. In contrast, the 28S rRNA showed overlapping of genetic distance limits, indicating that the distance matrix is not enough to assign a sexual conspecificity. We were able to perform female association to the described species D. verus Mugrabi & Azevedo, demonstrating that phylogenetic analysis is a valuable tool for associating the sexes of dimorphic species.

An Efficient Technique for Finding Longest Common Subsequence of DNA Sequences

Molecular biologists rely very heavily on computer science algorithms as research tools. The process of finding the longest common subsequence of two DNA sequences has a wide range of applications in modern bioinformatics. Genetics databases can hold enormous amounts of raw data, for example the human genome consists of approximately three billion DNA base pairs. The processing of this gigantic volume of data necessitates the use of extremely efficient string algorithms. This paper introduces a space and time effective technique for retrieving the longest common subsequence of DNA sequences.

Common DNA sequence variation influences 3-dimensional conformation of the human genome

BackgroundThe 3-dimensional (3D) conformation of chromatin inside the nucleus is integral to a variety of nuclear processes including transcriptional regulation, DNA replication, and DNA damage repair. Aberrations in 3D chromatin conformation have been implicated in developmental abnormalities and cancer. Despite the importance of 3D chromatin conformation to cellular function and human health, little is known about how 3D chromatin conformation varies in the human population, or whether DNA sequence variation between individuals influences 3D chromatin conformation.ResultsTo address these questions, we perform Hi-C on lymphoblastoid cell lines from 20 individuals. We identify thousands of regions across the genome where 3D chromatin conformation varies between individuals and find that this variation is often accompanied by variation in gene expression, histone modifications, and transcription factor binding. Moreover, we find that DNA sequence variation influences several features of 3D chromatin conformation including loop strength, contact insulation, contact directionality, and density of local cis contacts. We map hundreds of quantitative trait loci associated with 3D chromatin features and find evidence that some of these same variants are associated at modest levels with other molecular phenotypes as well as complex disease risk.ConclusionOur results demonstrate that common DNA sequence variants can influence 3D chromatin conformation, pointing to a more pervasive role for 3D chromatin conformation in human phenotypic variation than previously recognized.

A 3-SNP gene risk score and a metabolic risk score both predict hypertriglyceridemia and cardiovascular disease risk

Evidence on the causal link between plasma triglyceride (TG) levels and risk for cardiovascular disease (CVD) has recently emerged. Individuals with the metabolic syndrome have an increased risk for acquiring elevated TG levels later in life. Moreover, common DNA sequence variations in genes affecting TG levels identify individuals at risk for elevated plasma TG levels. We evaluated whether a 3-single nucleotide polymorphism (SNP) TG gene risk score (GRS) and a metabolic risk score (MetRS) both improved CVD risk prediction. A 3-SNP GRS and MetRS were generated in the EPIC-Norfolk cohort (n=20,074) based on 3 SNPs in LPL and APOA5 or the number of Metabolic Syndrome criteria present (maximum 5), respectively. The associations between the 3-SNP GRS, MetRS, TG levels, and CVD risk were evaluated. The 3-SNP GRS and MetRS were both linearly associated with plasma TG levels, that is,+0.25mmol/L [95% CI 0.22-0.27] per allele change (P<.001) and+0.72mmol/L [95% CI 0.70-0.73] per increase of number of metabolic syndrome risk score points (P<.001), respectively. We observed a positive association between the 3-SNP GRS and the risk of CVD with an adjusted hazard ratio (HR) of 1.35 [95% CI 1.04-1.74] for the highest versus the lowest GRS, which was independent of the MetRS. For the MetRS, the adjusted HR was 2.03 [95% CI 1.73-2.40] for the highest versus the lowest MetRS. Both the 3-SNP GRS and the MetRS are associated with increased plasma TG levels and increased risk for CVD.

Ethics of Human Genome Editing.

Advances in human genome editing, in particular the development of the clustered regularly interspaced palindromic repeats (CRISPR)/Cas9 method, have led to increasing concerns about the ethics of editing the human genome. In response, the US National Academy of Sciences and the National Academy of Medicine constituted a multidisciplinary, international committee to review the current status and make recommendations. I was a member of that committee, and the core of this review reflects the committee's conclusions. The committee's report, issued in February 2017, recommends the application of current ethical and regulatory standards for gene therapy to somatic (nonheritable) human genome editing. It also recommends allowing experimental germline genome editing to proceed if ( a) it is restricted to preventing transmission of a serious disease or condition, ( b) the edit is a modification to a common DNA sequence known not to be associated with disease, and ( c) the research is conducted under a stringent set of ethical and regulatory requirements. Crossing the so-called red line of germline genome editing raises important bioethical issues, most importantly, serious concern about the potential negative impact on individuals with disabilities. This review highlights some of the major ethical considerations in human genome editing in light of the report's recommendations.

EMBL2checklists: A Python package to facilitate the user-friendly submission of plant and fungal DNA barcoding sequences to ENA

BackgroundThe submission of DNA sequences to public sequence databases is an essential, but insufficiently automated step in the process of generating and disseminating novel DNA sequence data. Despite the centrality of database submissions to biological research, the range of available software tools that facilitate the preparation of sequence data for database submissions is low, especially for sequences generated via plant and fungal DNA barcoding. Current submission procedures can be complex and prohibitively time expensive for any but a small number of input sequences. A user-friendly software tool is needed that streamlines the file preparation for database submissions of DNA sequences that are commonly generated in plant and fungal DNA barcoding.MethodsA Python package was developed that converts DNA sequences from the common EMBL and GenBank flat file formats to submission-ready, tab-delimited spreadsheets (so-called ‘checklists’) for a subsequent upload to the annotated sequence section of the European Nucleotide Archive (ENA). The software tool, titled ‘EMBL2checklists’, automatically converts DNA sequences, their annotation features, and associated metadata into the idiosyncratic format of marker-specific ENA checklists and, thus, generates files that can be uploaded via the interactive Webin submission system of ENA.ResultsEMBL2checklists provides a simple, platform-independent tool that automates the conversion of common DNA barcoding sequences into easily editable spreadsheets that require no further processing but their upload to ENA via the interactive Webin submission system. The software is equipped with an intuitive graphical as well as an efficient command-line interface for its operation. The utility of the software is illustrated by its application in four recent investigations, including plant phylogenetic and fungal metagenomic studies.DiscussionEMBL2checklists bridges the gap between common software suites for DNA sequence assembly and annotation and the interactive data submission process of ENA. It represents an easy-to-use solution for plant and fungal biologists without bioinformatics expertise to generate submission-ready checklists from common DNA sequence data. It allows the post-processing of checklists as well as work-sharing during the submission process and solves a critical bottleneck in the effort to increase participation in public data sharing.

Variants at the APOE /C1/C2/C4 Locus Modulate Cholesterol Efflux Capacity Independently of High-Density Lipoprotein Cholesterol.

BackgroundMacrophage cholesterol efflux to high‐density lipoproteins (HDLs) is the first step of reverse cholesterol transport. The cholesterol efflux capacity (CEC) of HDL particles is a protective risk factor for coronary artery disease independent of HDL cholesterol levels. Using a genome‐wide association study approach, we aimed to identify pathways that regulate CEC in humans.Methods and ResultsWe measured CEC in 5293 French Canadians. We tested the genetic association between 4 CEC measures and genotypes at >9 million common autosomal DNA sequence variants. These analyses yielded 10 genome‐wide significant signals (P<6.25×10−9) representing 7 loci. Five of these loci harbor genes with important roles in lipid biology (CETP,LIPC,LPL,APOA1/C3/A4/A5, and APOE /C1/C2/C4). Except for the APOE/C1/C2/C4 variant (rs141622900, P nonadjusted=1.0×10−11; P adjusted=8.8×10−9), the association signals disappear when correcting for HDL cholesterol and triglyceride levels. The additional 2 significant signals were near the PPP1CB/PLB1 and RBFOX3/ENPP7 genes. In secondary analyses, we considered candidate functional variants for 58 genes implicated in HDL biology, as well as 239 variants associated with blood lipid levels and/or coronary artery disease risk by genome‐wide association study. These analyses identified 27 significant CEC associations, implicating 5 additional loci (GCKR,LIPG,PLTP,PPARA, and TRIB1).ConclusionsOur genome‐wide association study identified common genetic variation at the APOE/C1/C2/C4 locus as a major determinant of CEC that acts largely independently of HDL cholesterol. We predict that HDL‐based therapies aiming at increasing CEC will be modulated by changes in the expression of apolipoproteins in this gene cluster.

Sharing of Genes and Pathways Across Complex Phenotypes: A Multilevel Genome-Wide Analysis.

Evidence from genome-wide association studies (GWAS) suggest that pleiotropic effects on human complex phenotypes are very common. Recently, an atlas of genetic correlations among complex phenotypes has broadened our understanding of human diseases and traits. Here, we examine genetic overlap, from a gene-centric perspective, among the same 24 phenotypes previously investigated for genetic correlations. After adopting the multilevel pipeline (freely available at http://grass.cgs.hku.hk/limx/kgg/), which includes intragenic single nucleotide polymorphisms (SNPs), genes, and gene-sets, to estimate genetic similarities across phenotypes, a large amount of sharing of several biologically related phenotypes was confirmed. In addition, significant genetic overlaps were also found among phenotype pairs that were previously unidentified by SNP-level approaches. All these pairs with new genetic links are supported by earlier epidemiological evidence, although only a few of them have pleiotropic genes in the GWAS Catalog. Hence, our gene and gene-set analyses are able to provide new insights into cross-phenotype connections. The investigation on genetic sharing at three different levels presents a complementary picture of how common DNA sequence variations contribute to disease comorbidities and trait manifestations.

Polygenic Risk Score Identifies Subgroup With Higher Burden of Atherosclerosis and Greater Relative Benefit From Statin Therapy in the Primary Prevention Setting.

Relative risk reduction with statin therapy has been consistent across nearly all subgroups studied to date. However, in analyses of 2 randomized controlled primary prevention trials (ASCOT [Anglo-Scandinavian Cardiac Outcomes Trial-Lipid-Lowering Arm] and JUPITER [Justification for the Use of Statins in Prevention: An Intervention Trial Evaluating Rosuvastatin]), statin therapy led to a greater relative risk reduction among a subgroup at high genetic risk. Here, we aimed to confirm this observation in a third primary prevention randomized controlled trial. In addition, we assessed whether those at high genetic risk had a greater burden of subclinical coronary atherosclerosis. We studied participants from a randomized controlled trial of primary prevention with statin therapy (WOSCOPS [West of Scotland Coronary Prevention Study]; n=4910) and 2 observational cohort studies (CARDIA [Coronary Artery Risk Development in Young Adults] and BioImage; n=1154 and 4392, respectively). For each participant, we calculated a polygenic risk score derived from up to 57 common DNA sequence variants previously associated with coronary heart disease. We compared the relative efficacy of statin therapy in those at high genetic risk (top quintile of polygenic risk score) versus all others (WOSCOPS), as well as the association between the polygenic risk score and coronary artery calcification (CARDIA) and carotid artery plaque burden (BioImage). Among WOSCOPS trial participants at high genetic risk, statin therapy was associated with a relative risk reduction of 44% (95% confidence interval [CI], 22-60; P<0.001), whereas in all others, the relative risk reduction was 24% (95% CI, 8-37; P=0.004) despite similar low-density lipoprotein cholesterol lowering. In a study-level meta-analysis across the WOSCOPS, ASCOT, and JUPITER primary prevention, relative risk reduction in those at high genetic risk was 46% versus 26% in all others (P for heterogeneity=0.05). Across all 3 studies, the absolute risk reduction with statin therapy was 3.6% (95% CI, 2.0-5.1) among those in the high genetic risk group and 1.3% (95% CI, 0.6-1.9) in all others. Each 1-SD increase in the polygenic risk score was associated with 1.32-fold (95% CI, 1.04-1.68) greater likelihood of having coronary artery calcification and 9.7% higher (95% CI, 2.2-17.8) burden of carotid plaque. Those at high genetic risk have a greater burden of subclinical atherosclerosis and derive greater relative and absolute benefit from statin therapy to prevent a first coronary heart disease event. URL: http://www.clinicaltrials.gov. Unique identifiers: NCT00738725 (BioImage) and NCT00005130 (CARDIA). WOSCOPS was carried out and completed before the requirement for clinical trial registration.

Abstract 154: Genetic Variants in CETP That Increase HDL Levels also Increase Risk of Intracerebral Hemorrhage

Introduction: In observational studies, higher plasma high-density lipoprotein cholesterol (HDL-C) has been associated with increased risk of spontaneous intracerebral hemorrhage (ICH). Common DNA sequence variants within the cholesteryl ester transfer protein ( CETP ) gene decrease CETP protein activity and increase plasma HDL-C; as such, medicines that inhibit CETP and raise HDL-C are in clinical development to combat coronary artery disease. Hypothesis: Common CETP DNA sequence variants associated with higher HDL-C also increase risk for ICH. Methods: We performed a two-stage case-control genetic association study in Caucasians. The discovery phase utilized data on 12 independent loci within CETP (+/- 50 kilobases) from 3 genome-wide association studies of ICH. Replication involved direct genotyping in 5 additional studies. We also constructed a genetic risk score with 7 independent CETP variants and tested it for association with HDL-C and ICH risk. We used principal component analysis to account for population structure and a Bonferroni-adjusted p&lt;0.004 (12 tests) to declare statistical significance. Results: The discovery phase included 1149 ICH cases (43% lobar hemorrhages) and 1238 controls. Twelve variants were nominally associated (p&lt;0.05) with ICH, with the strongest association at the rs173539 locus (Figure 1: OR 1.25, 95%CI 1.11-1.41; p=6.0x10 -4 ) and no heterogeneity across studies (I 2 =0%). This association was replicated in 1625 cases (43% lobar hemorrhages) and 1845 controls (OR 1.12, 95%CI 1.02-1.24; p=0.03). A genetic score of independent CETP variants known to increase HDL-C by ~2.85 mg/dL was strongly associated with ICH risk (OR 1.86, 95%CI 1.44-2.40; p=1.4x10 -6 ). Conclusion: Genetic variants in CETP associated with increased HDL-C raise the risk of ICH. Given ongoing therapeutic development in CETP inhibition and other HDL-raising strategies, further exploration of potential adverse cerebrovascular outcomes is warranted.

Interactions of CCAAT/enhancer-binding protein β with transcriptional coregulators

CCAAT/enhancer-binding proteins (C/EBPs) are key regulators of numerous cellular processes, including cell proliferation, differentiation, and tumorigenesis. Their biological activities require interactions with several protein partners and the formation of functional multiprotein complexes involved in DNA repair and cell cycle control. Members of the family (C/EBPα, β, δ, ε, and γ) bind to common DNA sequence motifs as homo- or hetero-dimers and interact with other transcription factors to control transcription of a number of eukaryotic genes. Of particular interest is C/EBPβ, which binds to closed chromatin and acts as a pioneering factor for initiating tissue-specific gene expression at several promoters. This review focuses on intermolecular interactions that underlie C/EBPβ's ability to regulate chromatin accessibility and directs readers to general reviews describing transcription regulation in eukaryotes.

Whole-genome sequencing in French Canadians from Quebec.

Genome-wide association studies (GWAS) have had a tremendous success in the identification of common DNA sequence variants associated with complex human diseases and traits. However, because of their design, GWAS are largely inappropriate to characterize the role of rare and low-frequency DNA variants on human phenotypic variation. Rarer genetic variation is geographically more restricted, supporting the need for local whole-genome sequencing (WGS) efforts to study these variants in specific populations. Here, we present the first large-scale low-pass WGS of the French-Canadian population. Specifically, we sequenced at ~5.6× coverage the whole genome of 1970 French Canadians recruited by the Montreal Heart Institute Biobank and identified 29 million bi-allelic variants (31% novel), including 19 million variants with a minor allele frequency (MAF) <0.5%. Genotypes from the WGS data are highly concordant with genotypes obtained by exome array on the same individuals (99.8%), even when restricting this analysis to rare variants (MAF <0.5, 99.9%) or heterozygous sites (98.9%). To further validate our data set, we showed that we can effectively use it to replicate several genetic associations with myocardial infarction risk and blood lipid levels. Furthermore, we analyze the utility of our WGS data set to generate a French-Canadian-specific imputation reference panel and to infer population structure in the Province of Quebec. Our results illustrate the value of low-pass WGS to study the genetics of human diseases in the founder French-Canadian population.

Progress in genetic research of human height

It is well known that both environmental and genetic factors contribute to adult height variation in general population. However, heritability studies have shown that the variation in height is more affected by genetic factors. Height is a typical polygenic trait which has been studied by traditional linkage analysis and association analysis to identify common DNA sequence variation associated with height, but progress has been slow. More recently, with the development of genotyping and DNA sequencing technologies, tremendous achievements have been made in genetic research of human height. Hundreds of single nucleotide polymorphisms (SNPs) associated with human height have been identified and validated with the application of genome-wide association studies (GWAS) methodology, which deepens our understanding of the genetics of human growth and development and also provides theoretic basis and reference for studying other complex human traits. In this review, we summarize recent progress in genetic research of human height and discuss problems and prospects in this research area which may provide some insights into future genetic studies of human height.

GESPA: classifying nsSNPs to predict disease association.

BackgroundNon-synonymous single nucleotide polymorphisms (nsSNPs) are the most common DNA sequence variation associated with disease in humans. Thus determining the clinical significance of each nsSNP is of great importance. Potential detrimental nsSNPs may be identified by genetic association studies or by functional analysis in the laboratory, both of which are expensive and time consuming. Existing computational methods lack accuracy and features to facilitate nsSNP classification for clinical use. We developed the GESPA (GEnomic Single nucleotide Polymorphism Analyzer) program to predict the pathogenicity and disease phenotype of nsSNPs.ResultsGESPA is a user-friendly software package for classifying disease association of nsSNPs. It allows flexibility in acceptable input formats and predicts the pathogenicity of a given nsSNP by assessing the conservation of amino acids in orthologs and paralogs and supplementing this information with data from medical literature. The development and testing of GESPA was performed using the humsavar, ClinVar and humvar datasets. Additionally, GESPA also predicts the disease phenotype associated with a nsSNP with high accuracy, a feature unavailable in existing software. GESPA’s overall accuracy exceeds existing computational methods for predicting nsSNP pathogenicity. The usability of GESPA is enhanced by fast SQL-based cloud storage and retrieval of data.ConclusionsGESPA is a novel bioinformatics tool to determine the pathogenicity and phenotypes of nsSNPs. We anticipate that GESPA will become a useful clinical framework for predicting the disease association of nsSNPs. The program, executable jar file, source code, GPL 3.0 license, user guide, and test data with instructions are available at http://sourceforge.net/projects/gespa. Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0673-2) contains supplementary material, which is available to authorized users.

Variation in a molecular marker for resistance of Saudi date palm germplasm to Fusarium oxysporum f. sp. albedinis the causal agent of Bayoud disease

Fusarium oxysporum f. sp. albedinis (FOA) is a seed- and soil-borne vascular wilt pathogen that causes a very serious and destructive disease of date palm (Bayoud disease). FOA is not currently known to occur in Saudi Arabia, but the disease has been moving eastward from its origin in Morocco and Algeria. The main objective of this study was to evaluate Saudi Arabian date palm germplasm at the molecular level to assess the presence of R or S plasmid. We evaluated 711 trees representing 42 date palm varieties in Saudi Arabia with a mitochondrial molecular marker and sequenced 64 of the diagnostic PCR amplicons. Most of the trees (628/711) carried the R-plasmid which is associated with Bayoud resistance against FOA fungus. The other 83 trees carried the S-plasmid and are predicted to be susceptible. All amplifications from putatively resistant trees had the same DNA sequence. Moreover, the sequence of the Saudi resistance amplicon was identical to the sequence of Moroccan resistance DNA publically available in NCBI-GenBank database. All the sensitive trees from Saudi Arabia shared a common DNA sequence. This sequence differed from the Moroccan susceptible one at seven unique mutations including five single nucleotide polymorphisms (SNPs) and two insertion/deletion (indels) regions. The uniformity of the sequences means that the introduction of new germplasm to Saudi Arabia will be easily detected. The relatively high frequency of putative resistance means that if/when this disease enters the Kingdom that most trees should be resistant.

Mitochondrial DNA sequence variation in multiple sclerosis.

To assess the influence of common mitochondrial DNA (mtDNA) sequence variation on multiple sclerosis (MS) risk in cases and controls part of an international consortium. We analyzed 115 high-quality mtDNA variants and common haplogroups from a previously published genome-wide association study among 7,391 cases from the International Multiple Sclerosis Genetics Consortium and 14,568 controls from the Wellcome Trust Case Control Consortium 2 project from 7 countries. Significant single nucleotide polymorphism and haplogroup associations were replicated in 3,720 cases and 879 controls from the University of California, San Francisco. An elevated risk of MS was detected among haplogroup JT carriers from 7 pooled clinic sites (odds ratio [OR] = 1.15, 95% confidence interval [CI] = 1.07-1.24, p = 0.0002) included in the discovery study. The increased risk of MS was observed for both haplogroup T (OR = 1.17, 95% CI = 1.06-1.29, p = 0.002) and haplogroup J carriers (OR = 1.11, 95% CI = 1.01-1.22, p = 0.03). These haplogroup associations with MS were not replicated in the independent sample set. An elevated risk of primary progressive (PP) MS was detected for haplogroup J participants from 3 European discovery populations (OR = 1.49, 95% CI = 1.10-2.01, p = 0.009). This elevated risk was borderline significant in the US replication population (OR = 1.43, 95% CI = 0.99-2.08, p = 0.058) and remained significant in pooled analysis of discovery and replication studies (OR = 1.43, 95% CI = 1.14-1.81, p = 0.002). No common individual mtDNA variants were associated with MS risk. Identification and validation of mitochondrial genetic variants associated with MS and PPMS may lead to new targets for treatment and diagnostic tests for identifying potential responders to interventions that target mitochondria.

The association of 5-alpha reductase type 2 (SRD5A2) gene polymorphisms with prostate cancer in a Korean population

PurposeSteroid 5-alpha reductase type 2 (SRD5A2) modifies testosterone to dihydrotestosterone (DHT) in the prostate. Single-nucleotide polymorphisms (SNPs) of the SRD5A2 gene might affect DHT. We sought to understand the relationship of SRD5A2 SNPs to prostate cancer in the Korean population.Materials and MethodsTwenty-six common SNPs in the SRD5A2 gene were assessed in 272 prostate cancer cases and 173 controls. Single-locus analyses were conducted by using conditional logistic regression. Additionally, we performed a haplotype analysis for the SRD5A2 SNPs tested.ResultsAmong the 20 SNPs and 4 haplotypes, there were no statistically significant results in the prostate cancer patients and the controls. In the logistic analysis of SRD5A2 polymorphisms with prostate-specific antigen (PSA) criteria, two SNPs (rs508562, rs11675297) and haplotype 1 displayed significant results (odds ratio [OR], 1.76; p=0.05; OR, 1.88-2.02; p=0.01-0.04; OR, 0.59; p=0.02, respectively). rs508562, rs11675297, rs2208532, and haplotype 1 (OR, 1.49; p=0.05; OR, 2.02; p=0.05; OR, 2.01; p=0.04; OR, 0.56-0.64, p=0.03-0.04, respectively) had significant associations with Gleason score. rs508562, rs11675297, and haplotype 1 (OR, 1.41-2.34; p=0.004-0.05; OR, 1.74-1.82; p=0.03-0.05; OR, 0.42-0.67; p=0.0005-0.03, respectively) were significantly associated with clinical stage.ConclusionsWe conclude that there was no significant association between SRD5A2 SNPs and the risk of prostate cancer in the Korean population. However, we found that some SNPs and 1 haplotype influenced PSA level, Gleason score, and clinical stage.

Abstract 3426: A novel approach to copy number assessment by whole genome sequencing reveals extensive spatial heterogeneity in diffuse low-grade glioma

Abstract Introduction: The disease course of patients with diffuse low-grade gliomas (LGGs) is notoriously unpredictable. Detailed analysis of the genetic make-up is therefore key to understand this wide variety in overall survival of patients diagnosed with LGGs. Reports on the prognostic value of CNAs other than 1p/19q co-deletion are conflicting, which may be explained by spatial copy number heterogeneity. Aim: Prognostic implications of spatial and temporal copy number aberrations in LGGs by whole genome sequencing. Methods: Approximately 25% of LGG patients have a life expectation of more than 20 years following diagnosis, which necessitates collection of samples with long clinical follow up information. Therefore archival material was selected for this project and WGS was developed to access these samples without the requirement for a normal reference. We collected 156 formalin-fixed and paraffin-embedded (FFPE) samples in a discovery cohort of 98 LGG patients with extensive clinical follow-up data, which included recurrent tumours and spatially distinct regions. An independent cohort of 126 samples was obtained from a recently published study (Alentorn et al, Neuro-oncology 2014). Technical challenges for genome-wide inference of copy number aberrations include repetitive and common DNA sequences in the genome and sequence variation across the general population, as well as the compromised and variable quality of DNA obtained from archived tissues. We developed a robust and cost effective method that infers copy number aberrations from WGS data of approximately 0.1x coverage, without the need for a reference signal. This method implements (1) a combined LOESS correction for mappability and GC content, and improves on previous methods by (2) comprehensive filtering based on public genome project data, 1000-Genomes project and ENCODE blacklists. Results: Both prognostic value, temporal evolution and spatial heterogeneity of CNA were assessed by WGS. We confirmed prognostic favourable value of 1p/19q co-deletion, and demonstrated loss of 10q to be an unfavourable marker. In paired recurrences 10q loss was invariably maintained and surfaced in 4 additional recurrences of the discovery cohort. In spatial regions of LGGs we recognized extensive copy number heterogeneity; 15 of 17 LGGs show spatial variability of CNAs. 1p/19q co-deletion is homogeneous, while loss of 10q is heterogeneously present. Conclusions: we present clinically relevant CNAs, but also demonstrate extensive spatial copy number heterogeneity in diffuse LGGs that might complicate unequivocal biomarker discovery. Citation Format: Ilari Scheinin, Hinke F. van Thuijl, Daoud Sie, Hendrik F. van Essen, Paul P. Eijk, Francois Rustenburg, Ahmed Idbaih, Agusti Alentorn, Gerrit A. Meijer, Mark A. van der Wiel, Henrik Bengtsson, Adam Olshen, Eleonora Aronica, Jan J. Heimans, Jaap C. Reijneveld, Pieter Wesseling, Donna G. Albertson, Dan Pinkel, Bauke Ylstra. A novel approach to copy number assessment by whole genome sequencing reveals extensive spatial heterogeneity in diffuse low-grade glioma. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3426. doi:10.1158/1538-7445.AM2014-3426