Newborn metabolomic signatures of maternal per- and polyfluoroalkyl substance exposure and reduced length of gestation

Marginalized populations experience disproportionate rates of preterm birth and early term birth. Exposure to per- and polyfluoroalkyl substances (PFAS) has been reported to reduce length of gestation, but the underlying mechanisms are unknown. In the present study, we characterized the molecular signatures of prenatal PFAS exposure and gestational age at birth outcomes in the newborn dried blood spot metabolome among 267 African American dyads in Atlanta, Georgia between 2016 and 2020. Pregnant people with higher serum perfluorooctanoic acid and perfluorohexane sulfonic acid concentrations had increased odds of an early birth. After false discovery rate correction, the effect of prenatal PFAS exposure on reduced length of gestation was associated with 8 metabolomic pathways and 52 metabolites in newborn dried blood spots, which suggested perturbed tissue neogenesis, neuroendocrine function, and redox homeostasis. These mechanisms explain how prenatal PFAS exposure gives rise to the leading cause of infant death in the United States.

Thermal Evolution of Dirac Magnons in the Honeycomb Ferromagnet CrBr_{3}

CrBr_{3} is an excellent realization of the two-dimensional honeycomb ferromagnet, which offers a bosonic equivalent of graphene with Dirac magnons and topological character. We perform inelastic neutron scattering measurements using state-of-the-art instrumentation to update 50-year-old data, thereby enabling a definitive comparison both with recent experimental claims of a significant gap at the Dirac point and with theoretical predictions for thermal magnon renormalization. We demonstrate that CrBr_{3} has next-neighbor J_{2} and J_{3} interactions approximately 5% of J_{1}, an ideal Dirac magnon dispersion at the K point, and the associated signature of isospin winding. The magnon lifetime and the thermal band renormalization show the universal T^{2} evolution expected from an interacting spin-wave treatment, but the measured dispersion lacks the predicted van Hove features, pointing to the need for more sophisticated theoretical analysis.

Quantitative methods for metabolomic analyses evaluated in the Children's Health Exposure Analysis Resource (CHEAR)

With advances in technologies that facilitate metabolome-wide analyses, the incorporation of metabolomics in the pursuit of biomarkers of exposure and effect is rapidly evolving in population health studies. However, many analytic approaches are limited in their capacity to address high-dimensional metabolomics data within an epidemiologic framework, including the highly collinear nature of the metabolites and consideration of confounding variables. In this Children's Health Exposure Analysis Resource (CHEAR) network study, we showcase various analytic approaches that are established as well as novel in the field of metabolomics, including univariate single metabolite models, least absolute shrinkage and selection operator (LASSO), random forest, weighted quantile sum (WQS_RS) regression, exploratory factor analysis (EFA), and latent class analysis (LCA). Here, in a Bangladeshi birth cohort (n = 199), we illustrate research questions that can be addressed by each analytic method in the assessment of associations between cord blood metabolites (¹H NMR measurements) and birth anthropometric measurements (birth weight and head circumference).

Pauling Entropy, Metastability, and Equilibrium in Dy_{2}Ti_{2}O_{7} Spin Ice

Determining the fate of the Pauling entropy in the classical spin ice material Dy_{2}Ti_{2}O_{7} with respect to the third law of thermodynamics has become an important test case for understanding the existence and stability of ice-rule states in general. The standard model of spin ice-the dipolar spin ice model-predicts an ordering transition at T≈0.15  K, but recent experiments by Pomaranski et al. suggest an entropy recovery over long timescales at temperatures as high as 0.5 K, much too high to be compatible with the theory. Using neutron scattering and specific heat measurements at low temperatures and with long timescales (0.35  K/10^{6}  s and 0.5  K/10^{5}  s, respectively) on several isotopically enriched samples, we find no evidence of a reduction of ice-rule correlations or spin entropy. High-resolution simulations of the neutron structure factor show that the spin correlations remain well described by the dipolar spin ice model at all temperatures. Furthermore, by careful consideration of hyperfine contributions, we conclude that the original entropy measurements of Ramirez et al. are, after all, essentially correct: The short-time relaxation method used in that study gives a reasonably accurate estimate of the equilibrium spin ice entropy due to a cancellation of contributions.

Special temperatures in frustrated ferromagnets

The description and detection of unconventional magnetic states, such as spin liquids, is a recurring topic in condensed matter physics. While much of the efforts have traditionally been directed at geometrically frustrated antiferromagnets, recent studies reveal that systems featuring competing antiferromagnetic and ferromagnetic interactions are also promising candidate materials. We find that this competition leads to the notion of special temperatures, analogous to those of gases, at which the competing interactions balance, and the system is quasi-ideal. Although induced by weak perturbing interactions, these special temperatures are surprisingly high and constitute an accessible experimental diagnostic of eventual order or spin-liquid properties. The well characterised Hamiltonian and extended low-temperature susceptibility measurement of the canonical frustrated ferromagnet Dy₂Ti₂O₇ enables us to formulate both a phenomenological and microscopic theory of special temperatures for magnets. Other members of this class of magnets include kapellasite Cu₃Zn(OH)₆Cl₂ and the spinel GeCo₂O₄.

Competing interactions in frustrated magnets give rise to complex emergent phenomena, which challenge a full microscopic understanding but invite comparison to other systems. Bovo et al. find an analogy to classical gases and identify special temperatures that reveal fine details of the microscopic Hamiltonian.

Dipolar Spin Ice States with a Fast Monopole Hopping Rate in CdEr_{2}X_{4} (X=Se, S)

Excitations in a spin ice behave as magnetic monopoles, and their population and mobility control the dynamics of a spin ice at low temperature. CdEr_{2}Se_{4} is reported to have the Pauling entropy characteristic of a spin ice, but its dynamics are three orders of magnitude faster than the canonical spin ice Dy_{2}Ti_{2}O_{7}. In this Letter we use diffuse neutron scattering to show that both CdEr_{2}Se_{4} and CdEr_{2}S_{4} support a dipolar spin ice state-the host phase for a Coulomb gas of emergent magnetic monopoles. These Coulomb gases have similar parameters to those in Dy_{2}Ti_{2}O_{7}, i.e., dilute and uncorrelated, and so cannot provide three orders faster dynamics through a larger monopole population alone. We investigate the monopole dynamics using ac susceptometry and neutron spin echo spectroscopy, and verify the crystal electric field Hamiltonian of the Er^{3+} ions using inelastic neutron scattering. A quantitative calculation of the monopole hopping rate using our Coulomb gas and crystal electric field parameters shows that the fast dynamics in CdEr_{2}X_{4} (X=Se, S) are primarily due to much faster monopole hopping. Our work suggests that CdEr_{2}X_{4} offer the possibility to study alternative spin ice ground states and dynamics, with equilibration possible at much lower temperatures than the rare earth pyrochlore examples.

Erratum: Sequence data and association statistics from 12,940 type 2 diabetes cases and controls

This corrects the article DOI: 10.1038/sdata.2017.179.

Sequence data and association statistics from 12,940 type 2 diabetes cases and controls

To investigate the genetic basis of type 2 diabetes (T2D) to high resolution, the GoT2D and T2D-GENES consortia catalogued variation from whole-genome sequencing of 2,657 European individuals and exome sequencing of 12,940 individuals of multiple ancestries. Over 27M SNPs, indels, and structural variants were identified, including 99% of low-frequency (minor allele frequency [MAF] 0.1-5%) non-coding variants in the whole-genome sequenced individuals and 99.7% of low-frequency coding variants in the whole-exome sequenced individuals. Each variant was tested for association with T2D in the sequenced individuals, and, to increase power, most were tested in larger numbers of individuals (>80% of low-frequency coding variants in ~82 K Europeans via the exome chip, and ~90% of low-frequency non-coding variants in ~44 K Europeans via genotype imputation). The variants, genotypes, and association statistics from these analyses provide the largest reference to date of human genetic information relevant to T2D, for use in activities such as T2D-focused genotype imputation, functional characterization of variants or genes, and other novel analyses to detect associations between sequence variation and T2D.

A Low-Frequency Inactivating AKT2 Variant Enriched in the Finnish Population Is Associated With Fasting Insulin Levels and Type 2 Diabetes Risk

To identify novel coding association signals and facilitate characterization of mechanisms influencing glycemic traits and type 2 diabetes risk, we analyzed 109,215 variants derived from exome array genotyping together with an additional 390,225 variants from exome sequence in up to 39,339 normoglycemic individuals from five ancestry groups. We identified a novel association between the coding variant (p.Pro50Thr) in AKT2 and fasting plasma insulin (FI), a gene in which rare fully penetrant mutations are causal for monogenic glycemic disorders. The low-frequency allele is associated with a 12% increase in FI levels. This variant is present at 1.1% frequency in Finns but virtually absent in individuals from other ancestries. Carriers of the FI-increasing allele had increased 2-h insulin values, decreased insulin sensitivity, and increased risk of type 2 diabetes (odds ratio 1.05). In cellular studies, the AKT2-Thr50 protein exhibited a partial loss of function. We extend the allelic spectrum for coding variants in AKT2 associated with disorders of glucose homeostasis and demonstrate bidirectional effects of variants within the pleckstrin homology domain of AKT2.

Magnetic Excitations and Electronic Interactions in Sr_{2}CuTeO_{6}: A Spin-1/2 Square Lattice Heisenberg Antiferromagnet

Sr_{2}CuTeO_{6} presents an opportunity for exploring low-dimensional magnetism on a square lattice of S=1/2  Cu^{2+} ions. We employ ab initio multireference configuration interaction calculations to unravel the Cu^{2+} electronic structure and to evaluate exchange interactions in Sr_{2}CuTeO_{6}. The latter results are validated by inelastic neutron scattering using linear spin-wave theory and series-expansion corrections for quantum effects to extract true coupling parameters. Using this methodology, which is quite general, we demonstrate that Sr_{2}CuTeO_{6} is an almost ideal realization of a nearest-neighbor Heisenberg antiferromagnet but with relatively weak coupling of 7.18(5) meV.

Analysis of protein-coding genetic variation in 60,706 humans

Large-scale reference data sets of human genetic variation are critical for the medical and functional interpretation of DNA sequence changes. Here we describe the aggregation and analysis of high-quality exome (protein-coding region) DNA sequence data for 60,706 individuals of diverse ancestries generated as part of the Exome Aggregation Consortium (ExAC). This catalogue of human genetic diversity contains an average of one variant every eight bases of the exome, and provides direct evidence for the presence of widespread mutational recurrence. We have used this catalogue to calculate objective metrics of pathogenicity for sequence variants, and to identify genes subject to strong selection against various classes of mutation; identifying 3,230 genes with near-complete depletion of predicted protein-truncating variants, with 72% of these genes having no currently established human disease phenotype. Finally, we demonstrate that these data can be used for the efficient filtering of candidate disease-causing variants, and for the discovery of human 'knockout' variants in protein-coding genes.

Identification of neuropeptide S antagonists: structure-activity relationship studies, X-ray crystallography, and in vivo evaluation

Modulation of the neuropeptide S (NPS) system has been linked to a variety of CNS disorders such as panic disorder, anxiety, sleeping disorders, asthma, obesity, PTSD, and substance abuse. In this study, a series of diphenyltetrahydro-1H-oxazolo[3,4-α]pyrazin-3(5H)-ones were synthesized and evaluated for antagonist activity at the neuropeptide S receptor. The absolute configuration was determined by chiral resolution of the key synthetic intermediate, followed by analysis of one of the individual enantiomers by X-ray crystallography. The R isomer was then converted to a biologically active compound (34) that had a Ke of 36 nM. The most potent compound displayed enhanced aqueous solubility compared with the prototypical antagonist SHA-68 and demonstrated favorable pharmacokinetic properties for behavioral assessment. In vivo analysis in mice indicated a significant blockade of NPS induced locomotor activity at an ip dose of 50 mg/kg. This suggests that analogs having improved drug-like properties will facilitate more detailed studies of the neuropeptide S receptor system.

Association of a low-frequency variant in HNF1A with type 2 diabetes in a Latino population

IMPORTANCE

Latino populations have one of the highest prevalences of type 2 diabetes worldwide.

OBJECTIVES

To investigate the association between rare protein-coding genetic variants and prevalence of type 2 diabetes in a large Latino population and to explore potential molecular and physiological mechanisms for the observed relationships.

DESIGN, SETTING, AND PARTICIPANTS

Whole-exome sequencing was performed on DNA samples from 3756 Mexican and US Latino individuals (1794 with type 2 diabetes and 1962 without diabetes) recruited from 1993 to 2013. One variant was further tested for allele frequency and association with type 2 diabetes in large multiethnic data sets of 14,276 participants and characterized in experimental assays.

MAIN OUTCOME AND MEASURES

Prevalence of type 2 diabetes. Secondary outcomes included age of onset, body mass index, and effect on protein function.

RESULTS

A single rare missense variant (c.1522G>A [p.E508K]) was associated with type 2 diabetes prevalence (odds ratio [OR], 5.48; 95% CI, 2.83-10.61; P = 4.4 × 10(-7)) in hepatocyte nuclear factor 1-α (HNF1A), the gene responsible for maturity onset diabetes of the young type 3 (MODY3). This variant was observed in 0.36% of participants without type 2 diabetes and 2.1% of participants with it. In multiethnic replication data sets, the p.E508K variant was seen only in Latino patients (n = 1443 with type 2 diabetes and 1673 without it) and was associated with type 2 diabetes (OR, 4.16; 95% CI, 1.75-9.92; P = .0013). In experimental assays, HNF-1A protein encoding the p.E508K mutant demonstrated reduced transactivation activity of its target promoter compared with a wild-type protein. In our data, carriers and noncarriers of the p.E508K mutation with type 2 diabetes had no significant differences in compared clinical characteristics, including age at onset. The mean (SD) age for carriers was 45.3 years (11.2) vs 47.5 years (11.5) for noncarriers (P = .49) and the mean (SD) BMI for carriers was 28.2 (5.5) vs 29.3 (5.3) for noncarriers (P = .19).

CONCLUSIONS AND RELEVANCE

Using whole-exome sequencing, we identified a single low-frequency variant in the MODY3-causing gene HNF1A that is associated with type 2 diabetes in Latino populations and may affect protein function. This finding may have implications for screening and therapeutic modification in this population, but additional studies are required.

Loss-of-function mutations in SLC30A8 protect against type 2 diabetes

Loss-of-function mutations protective against human disease provide in vivo validation of therapeutic targets, but none have yet been described for type 2 diabetes (T2D). Through sequencing or genotyping of ~150,000 individuals across 5 ancestry groups, we identified 12 rare protein-truncating variants in SLC30A8, which encodes an islet zinc transporter (ZnT8) and harbors a common variant (p.Trp325Arg) associated with T2D risk and glucose and proinsulin levels. Collectively, carriers of protein-truncating variants had 65% reduced T2D risk (P = 1.7 × 10(-6)), and non-diabetic Icelandic carriers of a frameshift variant (p.Lys34Serfs*50) demonstrated reduced glucose levels (-0.17 s.d., P = 4.6 × 10(-4)). The two most common protein-truncating variants (p.Arg138* and p.Lys34Serfs*50) individually associate with T2D protection and encode unstable ZnT8 proteins. Previous functional study of SLC30A8 suggested that reduced zinc transport increases T2D risk, and phenotypic heterogeneity was observed in mouse Slc30a8 knockouts. In contrast, loss-of-function mutations in humans provide strong evidence that SLC30A8 haploinsufficiency protects against T2D, suggesting ZnT8 inhibition as a therapeutic strategy in T2D prevention.

Magnetoelastic excitations in the pyrochlore spin liquid Tb2Ti2O7

At low temperatures, Tb2Ti2O7 enters a spin liquid state, despite expectations of magnetic order and/or a structural distortion. Using neutron scattering, we have discovered that in this spin liquid state an excited crystal field level is coupled to a transverse acoustic phonon, forming a hybrid excitation. Magnetic and phononlike branches with identical dispersion relations can be identified, and the hybridization vanishes in the paramagnetic state. We suggest that Tb2Ti2O7 is aptly named a "magnetoelastic spin liquid" and that the hybridization of the excitations suppresses both magnetic ordering and the structural distortion. The spin liquid phase of Tb2Ti2O7 can now be regarded as a Coulomb phase with propagating bosonic spin excitations.

Neutron scattering and μSR investigations of the low temperature state of LuCuGaO₄

LuCuGaO₄ has magnetic Cu(2+) and diamagnetic Ga(3+) ions distributed on a triangular bilayer and is suggested to undergo a spin glass transition at Tg ∼ 0.4 K. Using μSR (muon spin rotation) and neutron scattering measurements, we show that at low temperature the spins form a short range correlated state with spin fluctuations detectable over a wide range of timescales: at 0.05 K magnetic fluctuations can be detected in both the μSR time window and also extending beyond 7 meV in the inelastic neutron scattering response, indicating magnetic fluctuations spanning timescales between ∼10(-5) and ∼10(-10) s. The dynamical susceptibility scales according to the form χ″(ω)T(α), with α = 1, throughout the measured temperature range (0.05-50 K). These effects are associated with quantum fluctuations and some degree of structural disorder in ostensibly quite different materials, including certain heavy fermion alloys, kagome spin liquids, quantum spin glasses, and valence bond glasses. We therefore suggest that LuCuGaO₄ is an interesting model compound for the further examination of disorder and quantum magnetism.

Mutational heterogeneity in cancer and the search for new cancer-associated genes

Major international projects are underway that are aimed at creating a comprehensive catalogue of all the genes responsible for the initiation and progression of cancer. These studies involve the sequencing of matched tumour-normal samples followed by mathematical analysis to identify those genes in which mutations occur more frequently than expected by random chance. Here we describe a fundamental problem with cancer genome studies: as the sample size increases, the list of putatively significant genes produced by current analytical methods burgeons into the hundreds. The list includes many implausible genes (such as those encoding olfactory receptors and the muscle protein titin), suggesting extensive false-positive findings that overshadow true driver events. We show that this problem stems largely from mutational heterogeneity and provide a novel analytical methodology, MutSigCV, for resolving the problem. We apply MutSigCV to exome sequences from 3,083 tumour-normal pairs and discover extraordinary variation in mutation frequency and spectrum within cancer types, which sheds light on mutational processes and disease aetiology, and in mutation frequency across the genome, which is strongly correlated with DNA replication timing and also with transcriptional activity. By incorporating mutational heterogeneity into the analyses, MutSigCV is able to eliminate most of the apparent artefactual findings and enable the identification of genes truly associated with cancer.

Comparative analysis of RNA sequencing methods for degraded or low-input samples

RNA-seq is an effective method for studying the transcriptome, but it can be difficult to apply to scarce or degraded RNA from fixed clinical samples, rare cell populations or cadavers. Recent studies have proposed several methods for RNA-seq of low-quality and/or low-quantity samples, but the relative merits of these methods have not been systematically analyzed. Here we compare five such methods using metrics relevant to transcriptome annotation, transcript discovery and gene expression. Using a single human RNA sample, we constructed and sequenced ten libraries with these methods and compared them against two control libraries. We found that the RNase H method performed best for chemically fragmented, low-quality RNA, and we confirmed this through analysis of actual degraded samples. RNase H can even effectively replace oligo(dT)-based methods for standard RNA-seq. SMART and NuGEN had distinct strengths for measuring low-quantity RNA. Our analysis allows biologists to select the most suitable methods and provides a benchmark for future method development.

Power-law spin correlations in the pyrochlore antiferromagnet Tb(2)Ti(2)O(7)

We investigate the low-temperature state of the rare-earth pyrochlore Tb(2)Ti(2)O(7) using polarized neutron scattering. Tb(2)Ti(2)O(7) is often described as an antiferromagnetic spin liquid with spin correlations extending over lengths comparable to individual tetrahedra of the pyrochlore lattice. We confirm this picture at 20 K but find that at 0.05 K the data contain evidence of pinch-point scattering, suggesting that the low temperature state of Tb(2)Ti(2)O(7) has power-law spin correlations.

Melanoma genome sequencing reveals frequent PREX2 mutations

Melanoma is notable for its metastatic propensity, lethality in the advanced setting, and association with ultraviolet (UV) exposure early in life¹. To obtain a comprehensive genomic view of melanoma, we sequenced the genomes of 25 metastatic melanomas and matched germline DNA. A wide range of point mutation rates was observed: lowest in melanomas whose primaries arose on non-UV exposed hairless skin of the extremities (3 and 14 per Mb genome), intermediate in those originating from hair-bearing skin of the trunk (range = 5 to 55 per Mb), and highest in a patient with a documented history of chronic sun exposure (111 per Mb). Analysis of whole-genome sequence data identified PREX2 - a PTEN-interacting protein and negative regulator of PTEN in breast cancer² - as a significantly mutated gene with a mutation frequency of approximately 14% in an independent extension cohort of 107 human melanomas. PREX2 mutations are biologically relevant, as ectopic expression of mutant PREX2 accelerated tumor formation of immortalized human melanocytes in vivo. Thus, whole-genome sequencing of human melanoma tumors revealed genomic evidence of UV pathogenesis and discovered a new recurrently mutated gene in melanoma.

RNA-SeQC: RNA-seq metrics for quality control and process optimization

RNA-seq, the application of next-generation sequencing to RNA, provides transcriptome-wide characterization of cellular activity. Assessment of sequencing performance and library quality is critical to the interpretation of RNA-seq data, yet few tools exist to address this issue. We introduce RNA-SeQC, a program which provides key measures of data quality. These metrics include yield, alignment and duplication rates; GC bias, rRNA content, regions of alignment (exon, intron and intragenic), continuity of coverage, 3'/5' bias and count of detectable transcripts, among others. The software provides multi-sample evaluation of library construction protocols, input materials and other experimental parameters. The modularity of the software enables pipeline integration and the routine monitoring of key measures of data quality such as the number of alignable reads, duplication rates and rRNA contamination. RNA-SeQC allows investigators to make informed decisions about sample inclusion in downstream analysis. In summary, RNA-SeQC provides quality control measures critical to experiment design, process optimization and downstream computational analysis.

AVAILABILITY AND IMPLEMENTATION

See www.genepattern.org to run online, or www.broadinstitute.org/rna-seqc/ for a command line tool.

Abstract 5056: A glimpse into the somatic mutation landscape of melanoma through exome sequencing of 121 tumor-normal pairs

Melanoma is an aggressive skin cancer of melanocytic origin characterized by high metastatic potential and mutation rate. Affording a survey of the wide breadth of genomic lesions found in melanoma, we present here an analysis of the somatic mutations discovered in the sequenced exomes of 121 melanoma tumor-normal pairs. We identify frequent genomic alterations both in genes previously implicated in melanoma (BRAF, NRAS, TP53, CDKN2A, PTEN) as well as in several genes whose role in melanoma tumorigenesis has not yet been established and thus are of particular interest. To do so we implement a novel method to increase the identification of genes that are significantly recurrently mutated in melanoma in the setting of its exceptionally high mutation rate. A preponderance of C>T transitions (∼85%) in the observed mutational profile reflects a history of DNA damage due to UV radiation, though the majority of somatic mutations in known melanoma genes are not C>T events. Our study broadens understanding of the genomic lesions involved in melanoma tumorigenesis, and we expect our analysis approach to inform future genomic studies of cancer lineages with similarly high mutation rates.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5056. doi:1538-7445.AM2012-5056

Disposition and metabolism of N,N-dimethylacetoacetamide in male F344 and Wistar-Han rats and female B6C3F1 mice

N,N-dimethylacetoacetamide (DMAAm) is a β-dicarbonyl compound used as an industrial intermediate. This study investigated the disposition and metabolism of [¹⁴C]DMAAm in male rats and female mice. A single oral dose of [¹⁴C]DMAAm (target dose of 10 or 130 mg/kg) was administered to male F344 and Wistar-Han rats. [¹⁴C]DMAAm was almost completely absorbed and excreted in urine, with ca. 80-90% of the dose recovered within 24 h for both rat strains. Fecal excretion and CO₂ exhalation were minimal (1 and 2%, respectively). Less than 3% of the dose remained in tissues at 24 h. There was no apparent dose- or strain-related difference in the disposition of [¹⁴C]DMAAm in rats. In female B6C3F1 mice administered 8 mg/kg [¹⁴C]DMAAm, 80% of the administered radioactivity was recovered in urine and cage rinse in 24 h. Urinary metabolites were isolated and characterized by liquid chromatography /mass spectrometry following oral administration of 435 mg/kg [(¹⁴C]DMAAm in male F344 rats. Metabolism occurred via reduction of the 3-keto group and oxidation of the N-methyl groups, to give N,N-dimethyl-3-hydroxybutanamide, N-methyl-N-hydroxymethyl-3-hydroxybutanamide, and N-hydroxymethyl-3-hydroxybutanamide, and N-demethylation to give N-monomethylacetoacetamide (MMAAm).

Hybrid selection for sequencing pathogen genomes from clinical samples

We have adapted a solution hybrid selection protocol to enrich pathogen DNA in clinical samples dominated by human genetic material. Using mock mixtures of human and Plasmodium falciparum malaria parasite DNA as well as clinical samples from infected patients, we demonstrate an average of approximately 40-fold enrichment of parasite DNA after hybrid selection. This approach will enable efficient genome sequencing of pathogens from clinical samples, as well as sequencing of endosymbiotic organisms such as Wolbachia that live inside diverse metazoan phyla.

Spangolite: an s = 1/2 maple leaf lattice antiferromagnet?

Spangolite, Cu(6)Al(SO(4))(OH)(12)Cl·3H(2)O, is a hydrated layered copper sulfate mineral. The Cu(2+) ions of each layer form a systematically depleted triangular lattice which approximates a maple leaf lattice. We present details of the crystal structure, which suggest that in spangolite this lattice actually comprises two species of edge linked trimers with different exchange parameters. However, magnetic susceptibility measurements show that despite the structural trimers, the magnetic properties are dominated by dimerization. The high temperature magnetic moment is strongly reduced below that expected for the six s = 1/2 in the unit cell.

The genomic complexity of primary human prostate cancer

Prostate cancer is the second most common cause of male cancer deaths in the United States. However, the full range of prostate cancer genomic alterations is incompletely characterized. Here we present the complete sequence of seven primary human prostate cancers and their paired normal counterparts. Several tumours contained complex chains of balanced (that is, 'copy-neutral') rearrangements that occurred within or adjacent to known cancer genes. Rearrangement breakpoints were enriched near open chromatin, androgen receptor and ERG DNA binding sites in the setting of the ETS gene fusion TMPRSS2-ERG, but inversely correlated with these regions in tumours lacking ETS fusions. This observation suggests a link between chromatin or transcriptional regulation and the genesis of genomic aberrations. Three tumours contained rearrangements that disrupted CADM2, and four harboured events disrupting either PTEN (unbalanced events), a prostate tumour suppressor, or MAGI2 (balanced events), a PTEN interacting protein not previously implicated in prostate tumorigenesis. Thus, genomic rearrangements may arise from transcriptional or chromatin aberrancies and engage prostate tumorigenic mechanisms.

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

Despite the ever-increasing output of Illumina sequencing data, loci with extreme base compositions are often under-represented or absent. To evaluate sources of base-composition bias, we traced genomic sequences ranging from 6% to 90% GC through the process by quantitative PCR. We identified PCR during library preparation as a principal source of bias and optimized the conditions. Our improved protocol significantly reduces amplification bias and minimizes the previously severe effects of PCR instrument and temperature ramp rate.

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

Despite the ever-increasing output of Illumina sequencing data, loci with extreme base compositions are often under-represented or absent. To evaluate sources of base-composition bias, we traced genomic sequences ranging from 6% to 90% GC through the process by quantitative PCR. We identified PCR during library preparation as a principal source of bias and optimized the conditions. Our improved protocol significantly reduces amplification bias and minimizes the previously severe effects of PCR instrument and temperature ramp rate.

Abstract 1139: Complete characterization of prostate cancer genomes by massively parallel sequencing

Prostate cancer is the most common type of cancer diagnosed among men in the United States, accounting for 200,000 new cases and 27,000 deaths per year. Prior genetic studies have shown that chromosomal rearrangements comprise a major mechanism of oncogene activation in prostate cancer. For example, androgen-regulated gene fusions involving ETS family transcription factors are present in the majority of prostate cancers, yet the full repertoire of genomic alterations driving prostate carcinogenesis and progression remains unknown. Toward this end, recent technological advances have made it possible to characterize the full complement of somatic mutations in a single tumor through whole genome sequencing.

We are using massively parallel sequencing technology to characterize the complete genomes of several primary prostate adenocarcinomas at >30x coverage. All samples are high-grade primary tumors (Gleason grade 7 to 9) and include cases with and without known ETS family translocations. For each tumor, we are also obtaining >30x sequence coverage of matched normal DNA from blood of these same patients in order to determine the somatic component of the overall variation we observe. Our results indicate that translocations and other chromosomal rearrangements occur frequently in prostate cancer, at a rate of >100 per genome. Further, we have discovered many nonsynonymous sequence mutations (point mutations and indels) in each tumor, some of which may represent novel candidate drivers of tumor progression. The overall rate of somatic point mutations is approximately 1 per Megabase. Integrated analysis of all genomes reveals both recurrent and private alterations. Together, these results illuminate potential avenues for target discovery and demonstrate the unparalleled value in performing complete genome sequencing in this malignancy.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1139.

Neutron scattering and crystal field studies of the rare earth double perovskite Ba2ErSbO6

The rare earth double perovskite Ba(2)ErSbO(6) contains an ordered face-centred cubic lattice of Er(3+) ions, suggesting that this material is a candidate for showing the effects of geometric magnetic frustration. Crystal field effects have also been shown to be important in this series. We report a systematic experimental study involving neutron scattering and bulk measurements that show no evidence of long ranged magnetic order or spin glass freezing down to 70 mK. A description of the system in terms of a crystal field scheme is established from inelastic neutron scattering. These measurements rule out significant magnetic coupling and show that all observed properties are fully explained by a model of uncoupled magnetic Er(3+) ions.

Metabolomics in the assessment of chemical-induced reproductive and developmental outcomes using non-invasive biological fluids: application to the study of butylbenzyl phthalate

This study was conducted to evaluate the use of metabolomics for improving our ability to draw correlations between early life exposures and reproductive and/or developmental outcomes. Pregnant CD rats were exposed by gavage daily during gestation to vehicle or to butylbenzyl phthalate (BBP) in vehicle at a level known to induce effects in the offspring and at a level previously not shown to induce effects. Urine was collected for 24 h (on dry ice using all glass metabolism chambers) from dams on gestational day 18 (during exposure) and on post natal day (pnd) 21, and from pnd 25 pups. Traditional phenotypic anchors were measured in pups (between pnd 0 and pnd 26). Metabolomics of urine collected from dams exposed to vehicle or BBP exhibited different patterns for endogenous metabolites. Even three weeks after gestational exposure, metabolic profiles of endogenous compounds in urine could differentiate dams that received the vehicle, low dose or high dose of BBP. Metabolic profiles could differentiate male from female pups, pups born to dams receiving the vehicle, low or high BBP dose, and pups with observable adverse reproductive effects from pups with no observed effects. Metabolites significant to the separation of dose groups and their relationship with effects measured in the study were mapped to biochemical pathways for determining mechanistic relevance. The application of metabolomics to understanding the mechanistic link between low levels of environmental exposure and disease/dysfunction holds huge promise, because this technology is ideal for the analysis of biological fluids in human populations.

Consequence of excess configurational entropy on fragility: the case of a polymer-oligomer blend

By taking advantage of the molecular weight dependence of the glass transition of polymers and their ability to form perfectly miscible blends, we propose a way to modify the fragility of a system, from fragile to strong, keeping the same glass properties, i.e., vibrational density of states, mean-square displacement, and local structure. Both slow and fast dynamics are investigated by calorimetry and neutron scattering in an athermal polystyrene-oligomer blend, and compared to those of a pure 17-mer polystyrene considered to be a reference, of the same Tg. Whereas the blend and the pure 17-mer have the same heat capacity in the glass and in the liquid, their fragilities differ strongly. Thus, the difference in fragility is related to an extra configurational entropy created by the mixing process and acting at a scale much larger than the interchain distance, without affecting the fast dynamics and the structure of the glass.

Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts

Targeted RNA-Seq combines next-generation sequencing with capture of sequences from a relevant subset of a transcriptome. When testing by capturing sequences from a tumor cDNA library by hybridization to oligonucleotide probes specific for 467 cancer-related genes, this method showed high selectivity, improved mutation detection enabling discovery of novel chimeric transcripts, and provided RNA expression data. Thus, targeted RNA-Seq produces an enhanced view of the molecular state of a set of "high interest" genes.

Magnetic Coulomb phase in the spin ice Ho2Ti2O7

Spin-ice materials are magnetic substances in which the spin directions map onto hydrogen positions in water ice. Their low-temperature magnetic state has been predicted to be a phase that obeys a Gauss' law and supports magnetic monopole excitations: in short, a Coulomb phase. We used polarized neutron scattering to show that the spin-ice material Ho2Ti2O7 exhibits an almost perfect Coulomb phase. Our result proves the existence of such phases in magnetic materials and strongly supports the magnetic monopole theory of spin ice.

Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing

Targeting genomic loci by massively parallel sequencing requires new methods to enrich templates to be sequenced. We developed a capture method that uses biotinylated RNA “baits” to “fish” targets out of a “pond” of DNA fragments. The RNA is transcribed from PCR-amplified oligodeoxynucleotides originally synthesized on a microarray, generating sufficient bait for multiple captures at concentrations high enough to drive the hybridization. We tested this method with 170-mer baits that target >15,000 coding exons (2.5 Mb) and four regions (1.7 Mb total) using Illumina sequencing as read-out. About 90% of uniquely aligning bases fell on or near bait sequence; up to 50% lay on exons proper. The uniformity was such that ~60% of target bases in the exonic “catch”, and ~80% in the regional catch, had at least half the mean coverage. One lane of Illumina sequence was sufficient to call high-confidence genotypes for 89% of the targeted exon space.

Static magnetic order in Tb2Sn2O7 revealed by muon spin relaxation with exterior muon implantation

Tb2Sn2O7 has been proposed as an ordered spin ice, but the precise nature of the low temperature magnetic state remains uncertain. Recent independent muon spin relaxation (microSR) investigations suggest the possibility of exotic ground states with static order precluded on time scales longer than 10(-6) s. Here the more conventional hypothesis of canted ferromagnetism is tested by means of microSR with the muons stopped outside the sample, as well as ultralow field bulk magnetization measurements. The field cooled state shows conventional static order, while the zero field cooled state may be interpreted in terms of conventional closed domains. These results rule out purely dynamical ground states and illustrate the value of exterior muon implantation as a complement to the conventional technique.

The implementation of a nurse-provided, ward-based bilevel non-invasive ventilation service

Bilevel non-invasive ventilation (NIV) is now standard of care for patients with acute hypercapnic respiratory failure (AHRF), and has an increasing role to play in patients with stable chronic hypercapnic respiratory failure (CHRF). The institution of an NIV service in a hospital setting requires major infrastructural and multidisciplinary input to be effective. This paper describes our experiences in setting up a 24-hour, nurse-provided, ward-based NIV service in a new acute teaching hospital in Dublin over a 39-month period. In addition, we provide audit data on 78 patients with AHRF treated with NIV by this service over this time period. The majority of patients (65) had their respiratory acidosis corrected and were discharged home; 11 patients failed NIV and were intubated and mechanically ventilated in the ITU; 13 patients died, 8 from respiratory causes and 5 from non-respiratory causes, indicating the critical nature of this condition.

Spin correlations in Ho2Ti2O7: a dipolar spin ice system

The pyrochlore material Ho2Ti2O7 has been suggested to show "spin ice" behavior. We present neutron scattering and specific heat results that establish unambiguously that Ho2Ti2O7 exhibits spin ice correlations at low temperature. Diffuse magnetic neutron scattering is quite well described by a nearest neighbor spin ice model and very accurately described by a dipolar spin ice model. The heat capacity is well accounted for by the sum of a dipolar spin ice contribution and an expected nuclear spin contribution, known to exist in other Ho3+ salts. These results settle the question of the nature of the low temperature spin correlations in Ho2Ti2O7 for which contradictory claims have been made.

Relationships between biomarkers of exposure and neurological effects in a group of workers exposed to acrylamide

A study was performed among 41 workers heavily exposed to a mixture of acrylamide and acrylonitrile in the city of Xinxiang, Henan province, People's Republic of China. The workers underwent a complete medical and neurological examination and provided blood and urine for the determination of several biomarkers of exposure. Among the exposed workers, signs and symptoms indicating peripheral neuropathy were found with statistically significant increased frequencies compared to a group of controls from the same city. Based on neuropathic signs and symptoms and quantifiable indicators of peripheral nervous dysfunction, such as vibration thresholds and electroneuromyography measurements, a neurotoxicity index (NIn) specific for acrylamide-induced peripheral neuropathy was designed. The NIn, which adequately predicted the clinical diagnosis of peripheral neuropathy, was significantly correlated with the levels of mercapturic acids in 24-hr urine, hemoglobin adducts of acrylamide, accumulated in vivo doses of acrylamide, employment time, and vibration sensitivity. The NIn was correlated also with hemoglobin adducts of acrylonitrile, which was explained primarily by a correlation between acrylamide and acrylonitrile exposure in this workshop. However, it was not significantly correlated with momentary measures of exposure such as concentrations of acrylamide in the air or in the plasma of exposed workers. This study is the first in which adduct monitoring has been applied to the same group of individuals in which adverse health effects have been observed. The results seem to indicate that hemoglobin adducts are useful as predictors of acrylamide-induced peripheral neuropathy and that measurements of vibration thresholds are useful for identifying early neurotoxic effects in workplaces with hazardous exposures to acrylamide.