Gene Desert Research Articles

Potential Novel Mechanism for Axenfeld-Rieger Syndrome: Deletion of a Distant Region Containing Regulatory Elements ofPITX2

Mutations in PITX2 are associated with Axenfeld-Rieger syndrome (ARS), which involves ocular, dental, and umbilical abnormalities. Identification of cis-regulatory elements of PITX2 is important to better understand the mechanisms of disease. Conserved noncoding elements surrounding PITX2/pitx2 were identified and examined through transgenic analysis in zebrafish; expression pattern was studied by in situ hybridization. Patient samples were screened for deletion/duplication of the PITX2 upstream region using arrays and probes. Zebrafish pitx2 demonstrates conserved expression during ocular and craniofacial development. Thirteen conserved noncoding sequences positioned within a gene desert as far as 1.1 Mb upstream of the human PITX2 gene were identified; 11 have enhancer activities consistent with pitx2 expression. Ten elements mediated expression in the developing brain, four regions were active during eye formation, and two sequences were associated with craniofacial expression. One region, CE4, located approximately 111 kb upstream of PITX2, directed a complex pattern including expression in the developing eye and craniofacial region, the classic sites affected in ARS. Screening of ARS patients identified an approximately 7600-kb deletion that began 106 to 108 kb upstream of the PITX2 gene, leaving PITX2 intact while removing regulatory elements CE4 to CE13. These data suggest the presence of a complex distant regulatory matrix within the gene desert located upstream of PITX2 with an essential role in its activity and provides a possible mechanism for the previous reports of ARS in patients with balanced translocations involving the 4q25 region upstream of PITX2 and the current patient with an upstream deletion.

LOHAS: loss‐of‐heterozygosity analysis suite

Detection of loss of heterozygosity (LOH) plays an important role in genetic, genomic and cancer research. We develop computational methods to estimate the proportion of homozygous SNP calls, identify samples with structural alterations and/or unusual genotypic patterns, cluster samples with close LOH structures and map the genomic segments bearing LOH by analyzing data of genome-wide SNP arrays or customized SNP arrays. In addition to cancer genetics/genomics, we also apply the methods to study long contiguous stretches of homozygosity (LCSH) in general populations. The LCSH analysis aids in the identification of samples with complex LCSH patterns indicative of nonrandom mating and/or meiotic recombination cold spots, separation of samples with different genetic backgrounds and sex, and mapping of regions of LCSH. Affymetrix Human Mapping 500K Set SNP data from an acute lymphoblastic leukemia study containing 304 cancer patients and 50 normal controls and from the HapMap Project containing 30 African trios, 30 Caucasian trios and 90 independent Asian samples were analyzed. We identified common gene regions of LOH, e.g., ETV6 and CDKN1B, and identified frequent regions of LCSH, e.g., the region that encompasses the centromeric gene desert region of chromosome 16. Unsupervised analysis separated cancer subtypes and ethnic subpopulations by patterns of LOH/LCSH. Simulation studies considering LOH width, effect size and heterozygous interference fraction were performed, and the results show that the proposed LOH association test has good test power and controls type 1 error well. The developed algorithms are packaged into LOHAS written in R and R GUI.

9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response

Genome wide association studies (GWAS) have identified SNPs in the 9p21 gene desert associated with coronary artery disease (CAD)1–4 and Type 2 diabetes (T2D)5–7. Despite evidence for a role of the associated interval in neighboring gene regulation8–10, the biological underpinnings of these genetic associations to CAD or T2D have not yet been explained. Here we identify 33 enhancers in 9p21; the interval is the second densest gene-desert for predicted enhancers and 6 times denser than the whole genome (p<6.55 10−33). The CAD risk alleles of SNPs rs10811656/rs10757278 are located in one of these enhancers and disrupt a binding site for STAT1. Lymphoblastoid cell lines (LCL) homozygous for the CAD risk haplotype exhibit no binding of STAT1, and in LCL homozygous for the CAD non-risk haplotype binding of STAT1 inhibits CDKN2BAS expression, which is reversed by siRNA knock-down of STAT1. Using a new, open-ended approach to detect long-distance interactions (3D-DSL), we find that in human vascular endothelium cells (HUVEC) the enhancer interval containing the CAD locus physically interacts with the CDKN2A/B locus, the MTAP gene and an interval downstream of INFA21. In HUVEC, IFNγ activation strongly affects the structure of the chromatin and the transcriptional regulation in the 9p21 locus, including STAT1 binding, long-range enhancer interactions and altered expression of neighboring genes. Our findings establish a link between CAD genetic susceptibility and the response to inflammatory signaling in a vascular cell type and thus demonstrate the utility of GWAS findings to direct studies to novel genomic loci and biological processes important for disease etiology.

Hypertrophy‐Associated Polymorphisms Ascertained in a Founder Cohort Applied to Heart Failure Risk and Mortality

A three-stage approach was undertaken using genome-wide, case-control, and case-only association studies to identify genetic variants associated with heart failure mortality. In an Amish founder population (n = 851), cardiac hypertrophy, a trait integral to the adaptive response to failure, was found to be heritable (h² = 0.28, p = 0.0002) and GWAS revealed 21 candidate hypertrophy SNPs. In a case (n = 1,610)-control (n = 463) study in unrelated Caucasians, one of the SNPs associated with hypertrophy (rs2207418, p = 8 × 10⁻⁶), was associated with heart failure, RR = 1.85(1.25-2.73, p = 0.0019). In heart failure cases rs2207418 was associated with increased mortality, HR = 1.51(1.20-1.97, p = 0.0004). There was consistency between studies, with the GG allele being associated with increased ventricular mass (~13 g/m²) in the Amish, heart failure risk, and heart failure mortality. This SNP is in a gene desert of chromosome 20p12. Five genes are within 2.0 mbp of rs2207418 but with low LD between their SNPs and rs2207418. A region near this SNP is highly conserved in multiple vertebrates (lod score = 1,208). This conservation and the internal consistency across studies suggests that this region has biologic importance in heart failure, potentially acting as an enhancer or repressor element. rs2207418 may be useful for predicting a more progressive form of heart failure that may require aggressive therapy.

Chromatin Reassembly Factors Are Involved in Transcriptional Interference Promoting HIV Latency

The establishment of a stable reservoir of latently infected cells allows HIV to persist in the host. Usually, HIV infection of T cells results in integration of the viral genome, with a preference for regions in the human genome containing active genes, viral expression, and production of new viruses. However, in rare cases T cells become latently infected, and this is presumed to be due to a combination of two factors: integrated viruses are not efficiently transcribed and infected T cells revert to a resting memory state. HIV latency has been associated with provirus integration in regions of constitutive heterochromatin, gene deserts, or very highly expressed genes. We have investigated the transcriptional consequences of latent HIV integration into cellular genes and the involvement of chromatin reassembly factors (CRFs) in the transcriptional interference that a host gene exerts on the integrated cryptic HIV promoter. Chimeric transcripts containing sequences from the host gene and HIV can be detected, having been initiated at promoters of either the cell or the virus. Reactivation of HIV downregulates host gene expression. Cryptic promoters might remain inactive due to the repressive chromatin configuration established by CRFs during transcription elongation. Depletion of CRFs such as Spt6, Chd1, and FACT, or the histone chaperones ASF1a and HIRA, promoted HIV reactivation, concomitantly with chromatin relaxation and a decrease in general RNA polymerase activity. Overall, our results indicate that CRFs play a role in maintaining HIV latency by transcriptional interference when the provirus is integrated into an intron of a highly active gene.

Novel Breast Cancer Susceptibility Locus at 9q31.2: Results of a Genome-Wide Association Study

Genome-wide association studies have identified several common genetic variants associated with breast cancer risk. It is likely, however, that a substantial proportion of such loci have not yet been discovered. We compared 296,114 tagging single-nucleotide polymorphisms in 1694 breast cancer case subjects (92% with two primary cancers or at least two affected first-degree relatives) and 2365 control subjects, with validation in three independent series totaling 11,880 case subjects and 12,487 control subjects. Odds ratios (ORs) and associated 95% confidence intervals (CIs) in each stage and all stages combined were calculated using unconditional logistic regression. Heterogeneity was evaluated with Cochran Q and I(2) statistics. All statistical tests were two-sided. We identified a novel risk locus for breast cancer at 9q31.2 (rs865686: OR = 0.89, 95% CI = 0.85 to 0.92, P = 1.75 × 10(-10)). This single-nucleotide polymorphism maps to a gene desert, the nearest genes being Kruppel-like factor 4 (KLF4, 636 kb centromeric), RAD23 homolog B (RAD23B, 794 kb centromeric), and actin-like 7A (ACTL7A, 736 kb telomeric). We also identified two variants (rs3734805 and rs9383938) mapping to 6q25.1 estrogen receptor 1 (ESR1), which were associated with breast cancer in subjects of northern European ancestry (rs3734805: OR = 1.19, 95% CI = 1.11 to 1.27, P = 1.35 × 10(-7); rs9383938: OR = 1.18, 95% CI = 1.11 to 1.26, P = 1.41 × 10(-7)). A variant mapping to 10q26.13, approximately 300 kb telomeric to the established risk locus within the second intron of FGFR2, was also associated with breast cancer risk, although not at genome-wide statistical significance (rs10510102: OR = 1.12, 95% CI = 1.07 to 1.17, P = 1.58 × 10(-6)). These findings provide further evidence on the role of genetic variation in the etiology of breast cancer. Fine mapping will be needed to identify causal variants and to determine their functional effects.

Mcs5c: A Mammary Carcinoma Susceptibility Locus Located in a Gene Desert that Associates withTenascin CExpression

Genetic factors have been estimated to account for at least 30% of a woman's risk to develop breast cancer. We have developed a rat model using Wistar Furth (WF) and Wistar Kyoto (WKy) strains to genetically identify mammary cancer susceptibility loci. The WKy allele of the mammary carcinogenesis susceptibility locus Mcs5c, was previously shown to reduce carcinoma multiplicity after 7,12-dimethylbenz-[a]anthracene (DMBA) exposure. In this study, Mcs5c was fine-mapped using WF.WKy congenic lines. Mcs5c was located to a region of approximately 176 kb on rat chromosome 5. One of the Mcs5c congenic lines containing a narrow Mcs5c WKy interval displayed a 40% decrease in average carcinoma number compared with WF-homozygous congenic controls after mammary carcinogenesis induction using two different models. As genetically mapped, the Mcs5c locus is located in a gene desert and thus is devoid of genes and annotated RNAs; thus, a genetic element in Mcs5c was hypothesized to regulate the expression of genes outside the locus. Tenascin c (Tnc) was identified as a candidate gene due to its reduced expression in thymus and ovarian tissues of Mcs5c WKy-homozygous congenic females compared with WF-homozygous congenic controls. This allele-specific differential expression is environmentally controlled.

Cis-ruptions d’éléments génomiques hautement conservés non codants à distance du gèneSOX9dans la séquence de Pierre Robin

Major developmental genes, exhibiting complex expression patterns, are often embedded within a genic desert particularly rich in regions, which though non-coding are highly conserved. The developmental expression of these genes in many areas requires coordinated regulation in time and space, which is orchestrated by some of these conserved non-coding regions, acting as transcriptional regulators. SOX9 is an essential gene for many developmental processes, such as chondrogenesis, migration and differentiation of neural crest cells and testis development. In agreement with these major expression areas, SOX9 haploinsufficiency, linked to alterations in coding sequence, leads to a polymorphic malformation syndrome - campomelic dysplasia - whose major symptoms are a bone anomaly, a Pierre Robin sequence, and a sexual differentiation anomaly (Disorder of Sex Development, DSD). SOX9 is located in a ~2.5 Mb gene desert extremely rich in conserved sequences. We have used the SOX9 locus and campomelic dysplasia as a model to show that one or several endophenotypes within a complex syndrome may arise from a tissue-specific deregulation of a major developmental gene transcription. Our work has focused on one of these endophenotypes, SPR, characterized by the triad micro- and/or retrognathy, glossoptosis and cleft palate. Here we report in detail how we identified alterations (translocations, deletions, point mutations) in non-coding regions, located far away (more than 1.2 Mb) upstream and downstream of SOX9, in clustered or sporadic SPR cases.

Acetaminophen-NAPQI Hepatotoxicity: A Cell Line Model System Genome-Wide Association Study

Acetaminophen is the leading cause of acute hepatic failure in many developed nations. Acetaminophen hepatotoxicity is mediated by the reactive metabolite N-acetyl-p-benzoquinonimine (NAPQI). We performed a "discovery" genome-wide association study using a cell line-based model system to study the possible contribution of genomics to NAPQI-induced cytotoxicity. A total of 176 lymphoblastoid cell lines from healthy subjects were treated with increasing concentrations of NAPQI. Inhibiting concentration 50 values were determined and were associated with "glutathione pathway" gene single nucleotide polymorphisms (SNPs) and genome-wide basal messenger RNA expression, as well as with 1.3 million genome-wide SNPs. A group of SNPs in linkage disequilibrium on chromosome 3 was highly associated with NAPQI toxicity. The p value for rs2880961, the SNP with the lowest p value, was 1.88 × 10(-7). This group of SNPs mapped to a "gene desert," but chromatin immunoprecipitation assays demonstrated binding of several transcription factor proteins including heat shock factor 1 (HSF1) and HSF2, at or near rs2880961. These chromosome 3 SNPs were not significantly associated with variation in basal expression for any of the genome-wide genes represented on the Affymetrix U133 Plus 2.0 GeneChip. We have used a cell line-based model system to identify a SNP signal associated with NAPQI cytotoxicity. If these observations are validated in future clinical studies, this SNP signal might represent a potential biomarker for risk of acetaminophen hepatotoxicity. The mechanisms responsible for this association remain unclear.

High resolution mapping and positional cloning of ENU-induced mutations in the Rw region of mouse chromosome 5

BackgroundForward genetic screens in mice provide an unbiased means to identify genes and other functional genetic elements in the genome. Previously, a large scale ENU mutagenesis screen was conducted to query the functional content of a ~50 Mb region of the mouse genome on proximal Chr 5. The majority of phenotypic mutants recovered were embryonic lethals.ResultsWe report the high resolution genetic mapping, complementation analyses, and positional cloning of mutations in the target region. The collection of identified alleles include several with known or presumed functions for which no mutant models have been reported (Tbc1d14, Nol14, Tyms, Cad, Fbxl5, Haus3), and mutations in genes we or others previously reported (Tapt1, Rest, Ugdh, Paxip1, Hmx1, Otoe, Nsun7). We also confirmed the causative nature of a homeotic mutation with a targeted allele, mapped a lethal mutation to a large gene desert, and localized a spermiogenesis mutation to a region in which no annotated genes have coding mutations. The mutation in Tbc1d14 provides the first implication of a critical developmental role for RAB-GAP-mediated protein transport in early embryogenesis.ConclusionThis collection of alleles contributes to the goal of assigning biological functions to all known genes, as well as identifying novel functional elements that would be missed by reverse genetic approaches.

High Resolution Genomic Analysis In CLL Demonstrates Genomic Stability In Untreated Patients and Novel Markers of Progression In Treated Patients

AbstractAbstract 2426Chronic lymphocytic leukemia is the most common leukemia of adults but still incurable. Prognosis at diagnosis is widely variable, and the key cytogenetic abnormalities determined by FISH remain one of the best predictors of prognosis and treatment response. We therefore undertook very high resolution genomic analysis of 161 CLLs with matched germline samples using Affymetrix 6.0 SNP arrays, in an effort to identify additional predictors of prognosis, and have also performed gene expression profiling on most of this patient cohort. The median age at diagnosis for the cohort was 55 (31–79), and the median time to sampling was 4.6 months (0.5–291). 22% of the cohort was previously treated, with an additional 21% of patients receiving treatment during the follow-up period, for a total of 43% treated, with a median time from diagnosis to treatment of 41 months (0.4-161.2 months). The genomic data were analyzed both by GISTIC, which identifies significant deletions and amplifications based on analysis of the frequency and amplitude of each aberration in the tumor samples alone, as well as by paired copy number analysis of each tumor and its cognate germline, using Birdseed, PLINK and PennCNV. Our results show that the CLL genome is overall quite stable, with a median of only one acquired copy number aberration per sample, excluding rearrangements at the immunoglobulin gene loci. GISTIC analysis on the entire population identified the known common CLL abnormalities at frequencies that would be expected in a largely untreated cohort: 57% del 13q, 6.2% deletion 11q, 5.0% deletion 17p, and 12% trisomy 12. The presence of two or more acquired copy number aberrations (CNAs) of any type was associated with a significantly shorter time to first therapy (p<0.0001). A higher number of CNAs was strongly associated with deletions of 11q or 17p, but the predictive power of a higher number of CNAs was still present in those CLLs without deletions 11q or 17p. Detailed analysis of 13q deletion revealed no association of longer deletions or homozygous deletions with time to first therapy. However, any additional somatic copy number aberration in addition to 13q deletion significantly reduced the time to first therapy, making it comparable to non-13q patients. In order to identify genetic markers of progression, we compared treated to untreated patients using GISTIC. This analysis revealed that untreated patients showed peaks largely limited to deletion 13q and trisomy 12. Treated patients however showed three additional significant peaks: a deletion peak at 8p, as well as significant amplification peaks at 3q26.32 and 8q24.21. The deletion peak at 8p was observed in 8 of 161 samples tested (5.0%), and was large, with a common region of deletion spanning 11.0–29.6 Mb. Six of eight of these patients were untreated at the time of sampling but had a very short time to treatment thereafter, independent of whether they had coexistent deletions of 17p or 11q, suggesting that this deletion carries a very poor prognosis in itself. Another notable region of amplification was found on 3q26.32 in nine patients (9/161 or 5.6%). Although many of these amplified regions were large, three of the nine patients carrying this amplification demonstrated focal somatic amplification of the final exon of PIK3CA, the alpha catalytic subunit of PI3K. Finally the amplification on 8q24 was present in 6 of 161 CLLs (3.7%), two of which were focal and amplified only the gene desert region previously implicated in CLL risk by genome-wide association study and located approximately 335 kb centromeric to MYC. Analysis of gene expression profiling comparing patients with and without amplifications demonstrated upregulation of MYC mRNA expression and alteration of downstream targets of MYC in samples with amplification. We conclude that very high resolution copy number analysis with matched germline comparison in CLL reveals a quite stable genome in untreated patients, and identifies amplifications of 3q26 and MYC at 8q24 as progression events. Disclosures:No relevant conflicts of interest to declare.

Histone Depletion Facilitates Chromatin Loops on the Kilobasepair Scale

The packing of eukaryotic DNA in the nucleus is decisive for its function; for instance, contact between remote genome sites constitutes a basic feature of gene regulation. Interactions among regulatory proteins, DNA binding, and transcription activation are facilitated by looping of the intervening chromatin. Such long-range interactions depend on the bending flexibility of chromatin, i.e., the ring-closure probability is a directly measurable indicator of polymer flexibility. The applicability of a wormlike chain model to naked DNA has been widely accepted. However, whether this model also suffices to describe the flexibility of eukaryotic interphase chromatin is still a matter of discussion. Here we compare both 5C data from a gene desert and data from fluorescence in situ hybridization with the results of a Monte Carlo simulation of chromatin fibers with and without histone depletion. We then estimate the ring-closure probabilities of simulated fibers with estimates from analytical calculations and show that the wormlike chain model grossly underestimates chromatin flexibility for sharp bends. Most importantly, we find that only fibers with random depletion of linker histones or nucleosomes can explain the probability of random chromatin contacts on small length scales that play an important role in gene regulation. It is possible that missing linker histones and nucleosomes are not just simple, unavoidable, randomly occurring defects, but instead play a regulatory role in gene expression.

Genetic Studies of Ankylosing Spondylitis in Koreans Confirm Associations with ERAP1 and 2p15 Reported in White Patients

Investigators from the Australo-Anglo-American Spondyloarthritis Consortium have reported additional genes associated with ankylosing spondylitis (AS) susceptibility including IL1R2, ANTXR2, and gene deserts at 2p15 and 21q22. We evaluated these new candidate genes in a large cohort of Korean patients with AS. A group of 1164 patients with AS and 752 healthy controls were enrolled for our study. Eight single-nucleotide polymorphisms (SNP) were analyzed to define genetic association with AS by MassARRAY system. Significant positive associations of AS with endoplasmic reticulum aminopeptidase 1 SNP, rs27037 (p = 1.31 × 10(-4)), and rs27434 (p = 4.59 × 10(-6)), were observed. The rs10865331 of gene desert at 2p15 also showed a significant association with AS (p = 4.63 × 10(-5)). This is the first confirmation in a nonwhite population that genetic polymorphisms of rs27037, rs27434, and rs10865331 are associated with AS, implicating common pathogenetic mechanisms in Korean and white patients with AS.

ANRIL , a long, noncoding RNA, is an unexpected major hotspot in GWAS

A large noncoding RNA called ANRIL (for antisense noncoding RNA in the INK4 locus) has been identified within the p15/CDKN2B-p16/CDKN2A-p14/ARF gene cluster. While the exact role of ANRIL awaited further elucidation, common disease genomewide association studies (GWAS) have surprisingly identified the ANRIL gene as a genetic susceptibility locus shared associated by coronary disease, intracranial aneurysm and also type 2 diabetes. Expression studies have confirmed the coregulation of p15/CDKN2B, p16/CDKN2A, p14/ARF, and ANRIL. Among the cluster, ANRIL expression showed the strongest association with the multiple phenotypes linked to the 9p21.3 region. More recent GWAS also identified ANRIL as a risk locus for gliomas and basal cell carcinomas in accordance with the princeps observation. Moreover, a mouse model has confirmed the pivotal role of ANRIL in regulation of CDKN2A/B expression through a cis-acting mechanism and its implication in proliferation and senescence. The implication of ANRIL in cellular aging has provided an attractive unifying hypothesis to explain its association with various susceptibility risk factors. ANRIL identification emphasizes the underestimated role of long noncoding RNAs. Many GWAS have identified trait-associated SNPs that felt in noncoding genomic regions. It is conceivable to anticipate that long, noncoding RNAs will map to many of these "gene deserts."

Deciphering the genetic basis of common diseases by integrated functional annotation of common and rare variants

Genome-wide associations studies (GWAS) have identified >400 loci associated with common human diseases. Despite the extraordinary achievement that these results represent, several questions remain unanswered: (i) What is the contribution of rare variants to common diseases not addressed by GWAS? (ii) What are the functional variants underlying the GWAS associations? To answer these questions, we first explored the role of common and rare variants in morbid obesity (BMI>40) by identifying all the variants in the intervals of two endocannabinoid metabolic genes (MGLL and FAAH) using targeted sequencing. We used two different statistical approaches (single marker tests and collapsed markers tests) to identify variants in four intervals associated with high BMI. The majority of the associated variants are located in promoter sequences or in predicted transcriptional enhancers, suggesting their regulatory role. Additionally, we demonstrate that the set of rare variants in the FAAH promoter associated with BMI are also associated with an increased level of anandamide, a FAAH substrate, further suggesting a functional role in obesity. In a second study, we examined one of the most compelling GWAS that had identified SNPs in the 9p21 gene desert associated with coronary artery disease (CAD) and Type 2 diabetes (T2D). We identified 33 enhancers in 9p21; the interval is the second most dense gene-desert for predicted enhancers and is six times denser than the whole genome. The activity of three of these enhancers is affected by regulatory variants that show allelic differences in DNA-protein affinity and are strongly associated with either CAD or T2D. Some of these variants are predicted to disrupt the transcription-binding site relevant to CAD biology. Our study shows that the 9p21 gene desert is significantly enriched in enhancer elements and suggests the associations with CAD and T2D likely result from the cumulative contributions of multiple regulatory variants. Taken together, our studies show that a comprehensive approach of human genetics that integrates rare variants and functional knowledge, such as regulatory elements or metabolic and cell-specific effects, can leverage the findings of GWAS and lead to a deeper functional understanding of the role of genetic variation in human diseases.

Establishment of an International Radiogenomics Consortium

It has been known for many years that patients vary in their sensitivity to radiation and that genetics plays an important role influencing this variation. Numerous small-scale candidate gene studies have attempted to demonstrate an association between common genetic variation, identified by single nucleotide polymorphisms (SNPs), and radiation toxicity. However, results have been contradictory. With the increasing affordability of high-throughput genotyping technologies it is now feasible to embark on genome-wide association studies (GWAS). Such studies have been used to great effect to identify novel loci associated with disease susceptibility e.g. in breast cancer, and even locate important loci in “gene deserts” nowhere near recognizable genes. These loci could not even have been considered using a candidate gene approach. A challenge in the performance of GWAS is the issue of “multiple hypothesis testing” since roughly one million SNPs are screened in each subject. This necessitates the collection of many thousands of samples to ensure adequate statistical power. To achieve the sample sizes required, it is essential that groups collaborate and share data at an international level. A group of researchers with a mutual interest in radiogenomics have come together to establish a Radiogenomics Consortium. Investigators from across the world have joined this consortium, which includes representation from the major collaborative groups performing genotyping studies in the UK (RAPPER), USA (GenePARE) and Japan (RadGenomics). The two overall goals of the consortium are to develop an assay based on SNP profiling to predict which cancer patients are most likely to develop toxicity following standard radiotherapy, and to increase our understanding of the molecular pathways responsible for radiation-induced normal tissue toxicities. Specifically, the members of this consortium have agreed to provide a forum for sharing best practice in terms of collecting toxicity and confounding variable data (particularly dose volume histogram data), in genotyping and for the analysis of genetic associations with toxicity. This collaborative effort should raise the quality of SNP association studies and facilitate the eventual pooling of data for an adequately powered GWAS to identify SNPs associated with the development of adverse effects resulting from radiotherapy. Groups who are active in this field and are interested in being involved are welcome to join the consortium.

An 8q24 gene desert variant associated with prostate cancer risk confers differential in vivo activity to a MYC enhancer

Genome-wide association studies (GWAS) routinely identify risk variants in noncoding DNA, as exemplified by reports of multiple single nucleotide polymorphisms (SNPs) associated with prostate cancer in five independent regions in a gene desert on 8q24. Two of these regions also have been associated with breast and colorectal cancer. These findings implicate functional variation within long-range cis-regulatory elements in disease etiology. We used an in vivo bacterial artificial chromosome (BAC) enhancer-trapping strategy in mice to scan a half-megabase of the 8q24 gene desert encompassing the prostate cancer-associated regions for long-range cis-regulatory elements. These BAC assays identified both prostate and mammary gland enhancer activities within the region. We demonstrate that the 8q24 cancer-associated variant rs6983267 lies within an in vivo prostate enhancer whose expression mimics that of the nearby MYC proto-oncogene. Additionally, we show that the cancer risk allele increases prostate enhancer activity in vivo relative to the non-risk allele. This allele-specific enhancer activity is detectable during early prostate development and throughout prostate maturation, raising the possibility that this SNP could assert its influence on prostate cancer risk before tumorigenesis occurs. Our study represents an efficient strategy to build experimentally on GWAS findings with an in vivo method for rapidly scanning large regions of noncoding DNA for functional cis-regulatory sequences harboring variation implicated in complex diseases.

Association between genetic variants of reported candidate genes or regions and risk of cleft lip with or without cleft palate in the polish population

Cleft lip with or without cleft palate (CL/P) is one of the most common craniofacial malformations, with a complex and multifactorial etiology. Because of the genetic heterogeneity of facial clefts, the aim of this study was to investigate the contribution of previously reported candidate genes and chromosomal loci to the risk of CL/P in the Polish population. We performed an analysis of 18 polymorphisms of FOXE1, IRF6, MSX1, PAX9, TBX10, FGF10, FGFR1, TGFalpha, TGFbeta3, SUMO1, and the chromosomal region 8q24 in a group of 175 patients with CL/P and a properly matched control group. Highly significant results were observed for the IRF6 rs642961 variant and the 8q24 region's rs987525 (odds ratio [OR](AG+AAvsGG), 1.635; 95% confidence interval [CI], 1.153-2.319; p = 0.005; and OR(AC+AAvsCC), 1.962; 95% CI, 1.382-2.785; p = 1.4 x 10(-4), respectively). For rs987525, the results were also significant after correction for multiple comparisons. Borderline association with an increased risk of CL/P was also identified for the SUMO1 locus (rs2350350; OR(CGvsGG), 1.580; 95% CI, 1.056-2.363; p = 0.025). Our findings confirmed that genetic variants of IRF6 and the polymorphism located in the 8q24 gene desert are strongly involved in the etiology of facial clefts in the Polish population sample.

Monte Carlo Simulations indicate that Chromati: Nanostructure is accessible by Light Microscopy.

A long controversy exists about the structure of chromatin. Theoretically, this structure could be resolved by scattering experiments if one determines the scattering function - or equivalently the pair distribution function - of the nucleosomes. Unfortunately, scattering experiments with live cells are very difficult and limited to only a couple of nucleosomes.Nevertheless, new techniques like the high-resolution light microscopy supply a new approach to this problem. In this work we determine the radial pair distribution function of chromatin described by our E2A model and find that the dominant peaks which characterize the chromatin structure are very robust in several ways: They can still be identified in the case of chromatin fibers with reasonable linker histone and nucleosome defect rates as well as in the 2D case after a projection like in most high-res light microscopy experiments. This might initiate new experimental approaches like optical microscopy to finally determine the nanostructure of chromatin.Furthermore, we examine the statistics of random chromatin collisions and compare it with 5C data of a gene desert. We find that only chromatin fibers with histone depletion show a significant amount of contacts on the kbp-scale which play a important role in gene regulation. Therefore, linker histone and nucleosome depletion might not only be chromatin defects but even be necessary to facilitate transcription.PACS codes: 82.35.Pq, 87.16.A-, 87.16.af

Chromosome 8q24-Associated Cancers and MYC

Genome-wide association studies (GWAS) have successfully identified common polymorphisms that are strongly associated with many traits, including cancer. A gene desert located on chromosome 8q24 is associated with multiple cancer types. One of the closest genes is the MYC proto-oncogene. Investigations are now turning toward a mechanistic understanding of these (and other) risk loci. Recent studies demonstrate that the 8q24 loci are enhancers and that they physically interact with MYC. A still unresolved issue is the absence of a consistent association between genotype status at the risk loci and steady-state MYC expression levels in adult human tissues. Clarifying the function of the 8q24 variants and their link to MYC regulation by further in vivo and in vitro functional studies will allow a deeper understanding of the mechanisms underlying human cancer development.