A novel Alzheimer disease locus located near the gene encoding tau protein.

APOE ɛ4, the most significant genetic risk factor for Alzheimer disease (AD), may mask effects of other loci. We re-analyzed genome-wide association study (GWAS) data from the International Genomics of Alzheimer's Project (IGAP) Consortium in APOE ɛ4+ (10 352 cases and 9207 controls) and APOE ɛ4- (7184 cases and 26 968 controls) subgroups as well as in the total sample testing for interaction between a single-nucleotide polymorphism (SNP) and APOE ɛ4 status. Suggestive associations (P<1 × 10(-4)) in stage 1 were evaluated in an independent sample (stage 2) containing 4203 subjects (APOE ɛ4+: 1250 cases and 536 controls; APOE ɛ4-: 718 cases and 1699 controls). Among APOE ɛ4- subjects, novel genome-wide significant (GWS) association was observed with 17 SNPs (all between KANSL1 and LRRC37A on chromosome 17 near MAPT) in a meta-analysis of the stage 1 and stage 2 data sets (best SNP, rs2732703, P=5·8 × 10(-9)). Conditional analysis revealed that rs2732703 accounted for association signals in the entire 100-kilobase region that includes MAPT. Except for previously identified AD loci showing stronger association in APOE ɛ4+ subjects (CR1 and CLU) or APOE ɛ4- subjects (MS4A6A/MS4A4A/MS4A6E), no other SNPs were significantly associated with AD in a specific APOE genotype subgroup. In addition, the finding in the stage 1 sample that AD risk is significantly influenced by the interaction of APOE with rs1595014 in TMEM106B (P=1·6 × 10(-7)) is noteworthy, because TMEM106B variants have previously been associated with risk of frontotemporal dementia. Expression quantitative trait locus analysis revealed that rs113986870, one of the GWS SNPs near rs2732703, is significantly associated with four KANSL1 probes that target transcription of the first translated exon and an untranslated exon in hippocampus (P ⩽ 1.3 × 10(-8)), frontal cortex (P ⩽ 1.3 × 10(-9)) and temporal cortex (P⩽1.2 × 10(-11)). Rs113986870 is also strongly associated with a MAPT probe that targets transcription of alternatively spliced exon 3 in frontal cortex (P=9.2 × 10(-6)) and temporal cortex (P=2.6 × 10(-6)). Our APOE-stratified GWAS is the first to show GWS association for AD with SNPs in the chromosome 17q21.31 region. Replication of this finding in independent samples is needed to verify that SNPs in this region have significantly stronger effects on AD risk in persons lacking APOE ɛ4 compared with persons carrying this allele, and if this is found to hold, further examination of this region and studies aimed at deciphering the mechanism(s) are warranted.

GWAS analysis implicates NF-κB-mediated induction of inflammatory T cells in multiple sclerosis.

To identify genes and biologically relevant pathways associated with risk to develop multiple sclerosis (MS), the Genome-Wide Association Studies noise reduction method (GWAS-NR) was applied to MS genotyping data. Regions of association were defined based on the significance of linkage disequilibrium blocks. Candidate genes were cross-referenced based on a review of current literature, with attention to molecular function and directly interacting proteins. Supplementary annotations and pathway enrichment scores were generated using The Database for Annotation, Visualization and Integrated Discovery. The candidate set of 220 MS susceptibility genes prioritized by GWAS-NR was highly enriched with genes involved in biological pathways related to positive regulation of cell, lymphocyte and leukocyte activation (P=6.1E-15, 1.2E-14 and 5.0E-14, respectively). Novel gene candidates include key regulators of NF-κB signaling and CD4+ T helper type 1 (Th1) and T helper type 17 (Th17) lineages. A large subset of MS candidate genes prioritized by GWAS-NR were found to interact in a tractable pathway regulating the NF-κB-mediated induction and infiltration of pro-inflammatory Th1/Th17 T-cell lineages, and maintenance of immune tolerance by T-regulatory cells. This mechanism provides a biological context that potentially links clinical observations in MS to the underlying genetic landscape that may confer susceptibility.

Kinetics of Evaporation of Pinned Nanofluid Volatile Droplets at Subatmospheric Pressures.

We examine the effects of nanoparticle addition at low concentration on the evaporation kinetics of droplets in the constant radius mode. The evaporative behavior of deionized water and Al2O3 nanoparticle laden water on an aluminum substrate was observed at atmospheric and at different subatmospheric pressures. The two fluids exhibit the same evaporative behavior, independent of the droplet volume or the subatmospheric pressure. Moreover, the linear relationship between evaporation rate and droplet radius, initially proposed by Picknett and Bexon nearly four decades ago for droplets evaporating in the constant radius mode, is satisfied for both liquids. In addition, we have established a unified correlation solely function of fluid properties that extends this relationship to any subatmospheric pressure and fluid tested. We conclude that the addition of a small quantity of nanoparticles to the base fluid does not modify the kinetics of evaporation for pinned volatile droplets.

"Biodrop" Evaporation and Ring-Stain Deposits: The Significance of DNA Length.

Small sessile drops of water containing either long or short strands of DNA ("biodrops") were deposited on silicon substrates and allowed to evaporate. Initially, the triple line (TL) of both types of droplet remained pinned but later receded. The TL recession mode continued at constant speed until almost the end of drop lifetime for the biodrops with short DNA strands, whereas those containing long DNA strands entered a regime of significantly lower TL recession. We propose a tentative explanation of our observations based on free energy barriers to unpinning and increases in the viscosity of the base liquid due to the presence of DNA molecules. In addition, the structure of DNA deposits after evaporation was investigated by AFM. DNA self-assembly in a series of perpendicular and parallel orientations was observed near the contact line for the long-strand DNA, while, with the short-stranded DNA, smoother ring-stains with some nanostructuring but no striations were evident. At the interior of the deposits, dendritic and faceted crystals were formed from short and long strands, respectively, due to diffusion and nucleation limited processes, respectively. We suggest that the above results related to the biodrop drying and nanostructuring are indicative of the importance of DNA length, i.e., longer DNA chains consisting of linearly bonded shorter, rod-like DNA strands.

Genome-wide scan demonstrates significant linkage for male sexual orientation.

BACKGROUND: Findings from family and twin studies support a genetic contribution to the development of sexual orientation in men. However, previous studies have yielded conflicting evidence for linkage to chromosome Xq28. METHOD: We conducted a genome-wide linkage scan on 409 independent pairs of homosexual brothers (908 analyzed individuals in 384 families), by far the largest study of its kind to date. RESULTS: We identified two regions of linkage: the pericentromeric region on chromosome 8 (maximum two-point LOD = 4.08, maximum multipoint LOD = 2.59), which overlaps with the second strongest region from a previous separate linkage scan of 155 brother pairs; and Xq28 (maximum two-point LOD = 2.99, maximum multipoint LOD = 2.76), which was also implicated in prior research. CONCLUSIONS: Results, especially in the context of past studies, support the existence of genes on pericentromeric chromosome 8 and chromosome Xq28 influencing development of male sexual orientation.

Effect of Poly(ethylene oxide) Molecular Weight on the Pinning and Pillar Formation of Evaporating Sessile Droplets: The Role of the Interface.

We report on the drying process of sessile droplets of aqueous poly(ethylene oxide) (PEO) solutions studied by contact angle analysis. Liquid samples were prepared with the same initial concentration of four different molecular weights, Mw, of PEO. Droplets with initial volumes of between 1 and 5 µL were left to evaporate while temperature, pressure, and relative humidity were kept constant. Residues were formed with either a disklike puddle or a distinctive tall conical pillar shape. The latter occurred following a four-stage deposition process: pinned drying, during which the contact line is stationary; pseudodewetting, where the receding contact line is induced by precipitation; bootstrap building, during which the liquid droplet is lifted on freshly precipitated solid; and late drying. Contact angle analysis allowed us to monitor all stages during drying and consider transitions between stages for different molecular weights. We illustrate the mechanisms taking place during the crucial stages of pinning and depinning, revealing the effect of adhesion and contact line friction for high molecular weights and its influence on the final morphology of the dried PEO solute. To this end, we performed PEO solution droplet evaporation on PEO and PTFE films demonstrating the importance of interfacial interaction phenomena. We show that the formation of disklike puddles for high molecular weights on glass is associated with continuous droplet contact line pinning. This results from the strong adhesion due to the interdigitation of the loops and tails of a polymer layer (adsorbed on glass during evaporation) with the polymer gel network inside the droplet that forms as water evaporates.

Inertial to viscoelastic transition in early drop spreading on soft surfaces.

It has been known for many years that a spreading liquid droplet can be appreciably slowed on a soft, viscoelastic substrate by the appearance of a "wetting ridge" or protuberance of the solid near the triple phase contact line because of capillary forces. Viscoelastic dissipation in the solid surface can outweigh that of liquid viscosity and, therefore, dominate wetting dynamics. In this paper, we show that a short, rapid spreading stage exists after initial contact. The requisite balance determining the speed of motion is between capillary forces and inertial effects. As spreading proceeds, however, inertia lessens and the lower spreading speed allow for viscoelastic effects in the solid to increase. The transition between early inertial and viscoelastic regimes is studied with high-speed photography and explained by a simple theory.

SeqEM: an adaptive genotype-calling approach for next-generation sequencing studies.

MOTIVATION: Next-generation sequencing presents several statistical challenges, with one of the most fundamental being determining an individual's genotype from multiple aligned short read sequences at a position. Some simple approaches for genotype calling apply fixed filters, such as calling a heterozygote if more than a specified percentage of the reads have variant nucleotide calls. Other genotype-calling methods, such as MAQ and SOAPsnp, are implementations of Bayes classifiers in that they classify genotypes using posterior genotype probabilities. RESULTS: Here, we propose a novel genotype-calling algorithm that, in contrast to the other methods, estimates parameters underlying the posterior probabilities in an adaptive way rather than arbitrarily specifying them a priori. The algorithm, which we call SeqEM, applies the well-known Expectation-Maximization algorithm to an appropriate likelihood for a sample of unrelated individuals with next-generation sequence data, leveraging information from the sample to estimate genotype probabilities and the nucleotide-read error rate. We demonstrate using analytic calculations and simulations that SeqEM results in genotype-call error rates as small as or smaller than filtering approaches and MAQ. We also apply SeqEM to exome sequence data in eight related individuals and compare the results to genotypes from an Illumina SNP array, showing that SeqEM behaves well in real data that deviates from idealized assumptions. CONCLUSION: SeqEM offers an improved, robust and flexible genotype-calling approach that can be widely applied in the next-generation sequencing studies. AVAILABILITY AND IMPLEMENTATION: Software for SeqEM is freely available from our website: www.hihg.org under Software Download.

On the behavior of dew drops.

It may be observed that, when dew drops form, although they may be positioned randomly on flat leaves, they tend to accumulate at the pointed ends of thin, slightly conical growths. We discuss here the basic physics leading to this phenomenon.

Stick-slip of evaporating droplets: substrate hydrophobicity and nanoparticle concentration.

The dynamics of the three-phase contact line for water and ethanol is experimentally investigated using substrates of various hydrophobicities. Different evolutions of the droplet profile (contact line, R, and contact angle, θ) are found to be dependent on the hydrophobicity of the substrate. A simple theoretical approach based on the unbalanced Young force is used to explain the depinning of the contact line on hydrophilic surfaces or the monotonic slip on hydrophobic substrates. The second part of the article involves the addition of different quantities of titanium oxide nanoparticles to water, and a comparison of the evaporative behavior of these novel fluids with the base liquid (water) on substrates varying in hydrophobicity (i.e., silicon, Cytop, and PTFE) is presented. The observed stick-slip behavior is found to be dependent on the nanoparticle concentration. The evaporation rate is closely related to the dynamics of the contact line. These findings may have an important impact when considering the evaporation of droplets on different substrates and/or those containing nanoparticles.

Multifactor dimensionality reduction-phenomics: a novel method to capture genetic heterogeneity with use of phenotypic variables.

Complex human diseases do not have a clear inheritance pattern, and it is expected that risk involves multiple genes with modest effects acting independently or interacting. Major challenges for the identification of genetic effects are genetic heterogeneity and difficulty in analyzing high-order interactions. To address these challenges, we present MDR-Phenomics, a novel approach based on the multifactor dimensionality reduction (MDR) method, to detect genetic effects in pedigree data by integration of phenotypic covariates (PCs) that may reflect genetic heterogeneity. The P value of the test is calculated using a permutation test adjusted for multiple tests. To validate MDR-Phenomics, we compared it with two MDR-based methods: (1) traditional MDR pedigree disequilibrium test (PDT) without consideration of PCs (MDR-PDT) and (2) stratified phenotype (SP) analysis based on PCs, with use of MDR-PDT with a Bonferroni adjustment (SP-MDR). Using computer simulations, we examined the statistical power and type I error of the different approaches under several genetic models and sampling scenarios. We conclude that MDR-Phenomics is more powerful than MDR-PDT and SP-MDR when there is genetic heterogeneity, and the statistical power is affected by sample size and the number of PC levels. We further compared MDR-Phenomics with conditional logistic regression (CLR) for testing interactions across single or multiple loci with consideration of PC. The results show that CLR with PC has only slightly smaller power than does MDR-Phenomics for single-locus analysis but has considerably smaller power for multiple loci. Finally, by applying MDR-Phenomics to autism, a complex disease in which multiple genes are believed to confer risk, we attempted to identify multiple gene effects in two candidate genes of interest--the serotonin transporter gene (SLC6A4) and the integrin beta 3 gene (ITGB3) on chromosome 17. Analyzing four markers in SLC6A4 and four markers in ITGB3 in 117 white family triads with autism and using sex of the proband as a PC, we found significant interaction between two markers--rs1042173 in SLC6A4 and rs3809865 in ITGB3.

Association and gene-gene interaction of SLC6A4 and ITGB3 in autism.

Autism is a heritable neurodevelopmental disorder with substantial genetic heterogeneity. Studies point to possible links between autism and two serotonin related genes: SLC6A4 and ITGB3 with a sex-specific genetic effect and interaction between the genes. Despite positive findings, inconsistent results have complicated interpretation. This study seeks to validate and clarify previous findings in an independent dataset taking into account sex, family-history (FH) and gene-gene effects. Family-based association analysis was performed within each gene. Gene-gene interactions were tested using extended multifactor dimensionality reduction (EMDR) and MDR-phenomics (MDR-P) using sex of affecteds and FH as covariates. No significant associations with individual SNPs were found in the datasets stratified by sex, but associations did emerge when we stratified by family history. While not significant in the overall dataset, nominally significant association was identified at RS2066713 (P = 0.006) within SLC6A4 in family-history negative (FH-) families, at RS2066713 (P = 0.038) in family-history positive (FH+) families but with the opposite risk allele as in the FH- families. For ITGB3, nominally significant association was identified at RS3809865 overall (P = 0.040) and within FH+ families (P = 0.031). However, none of the associations survived the multiple testing correction. MDR-P confirmed gene-gene effects using sex of affecteds (P = 0.023) and family history (P = 0.014, survived the multiple testing corrections) as covariates. Our results indicate the extensive heterogeneity within these two genes among families. The potential interaction between SLC6A4 and ITGB3 may be clarified using family history as an indicator of genetic architecture, illustrating the importance of covariates as markers of heterogeneity in genetic analyses.

Effect of TiO2 nanoparticles on contact line stick-slip behavior of volatile drops.

We describe an experimental investigation of the concomitant evaporation and (de)wetting behavior of sessile drops of ethanol, either pure, or containing small amounts of titanium oxide nanoparticles. Pure ethanol behaved in a more or less "ideal" manner, with constantly decreasing contact radius, at essentially constant contact angle. However, distinct "stick-slip" pinning behavior of the triple line occurred when nanoparticles were added to the base liquid. Increased nanoparticle concentration enhanced the "stick-slip" behavior. The observed behavior is attributed to the effects of particle accumulation near the contact line, caused by the now-established advective flow during evaporation. "Slip" behavior can be explained by hysteretic energy barriers, somewhat akin to line tension. The "stick" behavior was not complete: some triple line drift occurred ("pseudo-pinning"). It is postulated that this may be due to small-scale pinning of the triple line by deposited particles, or to increased effective viscosity due to high, local nanoparticle concentrations.

The future is now - will the real disease gene please stand up?

The transmission/disequilibrium test (TDT) [Spielman et al.: Am J Hum Genet 1993;52:506-516] has been postulated as the future of gene mapping for complex diseases, provided one is able to genotype a dense enough map of markers across the genome. Risch and Merikangas [Science 1996;273:1516-1517] suggested a million-marker screen in affected sibpair (ASP) families, demonstrating that the TDT is a more powerful test of linkage than traditional linkage tests based on allele-sharing when there is also association between marker and disease alleles. While the future of genotyping has arrived, successes in family-based association studies have been modest. This is often attributed to excessive false positives in candidate gene studies. This problem is only exacerbated by the increasing numbers of whole genome association (WGA) screens. When applied in ASPs, the TDT statistic, which assumes transmissions to siblings are independent, is not expected to have a constant variance in the presence of variable linkage. This results in generally more extreme statistics, hence will further aggravate the problem of having a large number of positive results to sort through. So an important question is how many positive TDT results will show up on a chromosome containing a disease gene due only to linkage, and will they obfuscate the true disease gene location. To answer this question we combined theory and computer simulations. These studies show that in ASPs the normal version of the TDT statistic has a mean of 0 and a variance of 1 in unlinked regions, but has a variance larger than 1 in linked regions. In contrast, the pedigree disequilibrium test (PDT) statistic adjusts for correlation between siblings due to linkage and maintains a constant variance of 1 at unassociated markers irrespective of linkage. The TDT statistic is generally larger than the PDT statistic across linked regions. This is true for unassociated as well as associated markers. To compare the two tests we ranked both statistics at the disease locus, or an associated marker, among statistics at all other markers. The TDT did better job than PDT placing the score of the associated marker near the top. Though, strictly speaking, the TDT in ASPs should be interpreted as a test of linkage and not a test of association, there is a good chance that if a marker stands out, the marker is associated as well as linked. In conclusion, our results suggest that TDT is an effective screening tool for WGA studies, especially in multiplex families.

Linkage and association study of late-onset Alzheimer disease families linked to 9p21.3.

A chromosomal locus for late-onset Alzheimer disease (LOAD) has previously been mapped to 9p21.3. The most significant results were reported in a sample of autopsy-confirmed families. Linkage to this locus has been independently confirmed in AD families from a consanguineous Israeli-Arab community. In the present study we analyzed an expanded clinical sample of 674 late-onset AD families, independently ascertained by three different consortia. Sample subsets were stratified by site and autopsy-confirmation. Linkage analysis of a dense array of SNPs across the chromosomal locus revealed the most significant results in the 166 autopsy-confirmed families of the NIMH sample. Peak HLOD scores of 4.95 at D9S741 and 2.81 at the nearby SNP rs2772677 were obtained in a dominant model. The linked region included the cyclin-dependent kinase inhibitor 2A gene (CDKN2A), which has been suggested as an AD candidate gene. By re-sequencing all exons in the vicinity of CDKN2A in 48 AD cases, we identified and genotyped four novel SNPs, including a non-synonymous, a synonymous, and two variations located in untranslated RNA sequences. Family-based allelic and genotypic association analysis yielded significant results in CDKN2A (rs11515: PDT p = 0.003, genotype-PDT p = 0.014). We conclude that CDKN2A is a promising new candidate gene potentially contributing to AD susceptibility on chromosome 9p.

Wetting and evaporation of binary mixture drops.

Experimental results on the wetting behavior of water, methanol, and binary mixture sessile drops on a smooth, polymer-coated substrate are reported. The wetting behavior of evaporating water/methanol drops was also studied in a water-saturated environment. Drop parameters (contact angle, shape, and volume) were monitored in time. The effects of the initial relative concentrations on subsequent evaporation and wetting dynamics were investigated. Physical mechanisms responsible for the various types of wetting behavior during different stages are proposed and discussed. Competition between evaporation and hydrodynamic flow are evoked. Using an environment saturated with water vapor allowed further exploration of the controlling mechanisms and underlying processes. Wetting stages attributed to differential evaporation of methanol were identified. Methanol, the more volatile component, evaporates predominantly in the initial stage. The data, however, suggest that a small proportion of methanol remained in the drop after the first stage of evaporation. This residual methanol within the drop seems to influence subsequent wetting behavior strongly.

Exome Sequencing of Extended Families with Alzheimer's Disease Identifies Novel Genes Implicated in Cell Immunity and Neuronal Function.

OBJECTIVE: Alzheimer's disease (AD) is a neurodegenerative disorder for which more than 20 genetic loci have been implicated to date. However, studies demonstrate not all genetic factors have been identified. Therefore, in this study we seek to identify additional rare variants and novel genes potentially contributing to AD. METHODS: Whole exome sequencing was performed on 23 multi-generational families with an average of eight affected subjects. Exome sequencing was filtered for rare, nonsynonymous and loss-of-function variants. Alterations predicted to have a functional consequence and located within either a previously reported AD gene, a linkage peak (LOD>2), or clustering in the same gene across multiple families, were prioritized. RESULTS: Rare variants were found in known AD risk genes including AKAP9, CD33, CR1, EPHA1, INPP5D, NME8, PSEN1, SORL1, TREM2 and UNC5C. Three families had five variants of interest in linkage regions with LOD>2. Genes with segregating alterations in these peaks include CD163L1 and CLECL1, two genes that have both been implicated in immunity, CTNNA1, which encodes a catenin in the cerebral cortex and MIEF1, a gene that may induce mitochondrial dysfunction and has the potential to damage neurons. Four genes were identified with alterations in more than one family include PLEKHG5, a gene that causes Charcot-Marie-Tooth disease and THBS2, which promotes synaptogenesis. CONCLUSION: Utilizing large families with a heavy burden of disease allowed for the identification of rare variants co-segregating with disease. Variants were identified in both known AD risk genes and in novel genes.

Targeted sequencing of ABCA7 identifies splicing, stop-gain and intronic risk variants for Alzheimer disease.

Several variants in the gene ABCA7 have been identified as potential causal variants for late-onset Alzheimer's disease (LOAD). In order to replicate these findings, and search for novel causal variants, we performed targeted sequencing of this gene in cohorts of non-Hispanic White (NHW) and African-American (AA) LOAD cases and controls. We sequenced the gene ABCA7 in 291 NHW LOAD cases and 103 controls. Variants were prioritized for rare, damaging variants and previously reported variants associated with LOAD, and were follow-up genotyped in 4076 NHW and 1157 AA cases and controls. We confirm three previously associated ABCA7 risk variants and extend two of these associations to other populations, an intronic variant in NHW (P=3.0×10-3) (originally reported in a Belgian population), and a splice variant originally associated in the Icelandic population, which was significantly associated in the NHW cohort (P=1.2×10-6) and nominally associated in the AA cohort (P=0.017). We also identify a 3'-UTR splice variant that segregates in four siblings of one family and is nominally associated with LOAD (P=0.040). Multiple variants in ABCA7 contribute to LOAD risk.

Interaction between the alpha-T catenin gene (VR22) and APOE in Alzheimer's disease.

BACKGROUND: APOE is the only gene that has been consistently replicated as a risk factor for late onset Alzheimer's disease. Several recent studies have identified linkage to chromosome 10 for both risk and age of onset, suggesting that this region harbours genes that influence the development of the disease. A recent study reported association between single nucleotide polymorphisms (SNPs) in the VR22 gene (CTNNA3) on chromosome 10 and plasma levels of Abeta42, an endophenotype related to Alzheimer's disease. OBJECTIVE: To assess whether polymorphisms in the VR22 gene are associated with Alzheimer's disease in a large sample of Alzheimer's disease families and an independent set of unrelated cases and controls. RESULTS: Several SNPs showed association in either the family based or case-control analyses (p<0.05). The most consistent findings were with SNP6, for which there was significant evidence of association in both the families and the unrelated cases and controls. Furthermore, there was evidence of significant interaction between APOE-4 and two of the VR22 SNPs, with the strongest evidence of association being concentrated in individuals carrying APOE-4. CONCLUSIONS: This study suggests that VR22 or a nearby gene influences susceptibility to Alzheimer's disease, and the effect is dependent on APOE status.