The Genomics Research and Innovation Network: creating an interoperable, federated, genomics learning system.

PURPOSE: Clinicians and researchers must contextualize a patient's genetic variants against population-based references with detailed phenotyping. We sought to establish globally scalable technology, policy, and procedures for sharing biosamples and associated genomic and phenotypic data on broadly consented cohorts, across sites of care. METHODS: Three of the nation's leading children's hospitals launched the Genomic Research and Innovation Network (GRIN), with federated information technology infrastructure, harmonized biobanking protocols, and material transfer agreements. Pilot studies in epilepsy and short stature were completed to design and test the collaboration model. RESULTS: Harmonized, broadly consented institutional review board (IRB) protocols were approved and used for biobank enrollment, creating ever-expanding, compatible biobanks. An open source federated query infrastructure was established over genotype-phenotype databases at the three hospitals. Investigators securely access the GRIN platform for prep to research queries, receiving aggregate counts of patients with particular phenotypes or genotypes in each biobank. With proper approvals, de-identified data is exported to a shared analytic workspace. Investigators at all sites enthusiastically collaborated on the pilot studies, resulting in multiple publications. Investigators have also begun to successfully utilize the infrastructure for grant applications. CONCLUSIONS: The GRIN collaboration establishes the technology, policy, and procedures for a scalable genomic research network.

Correction: The Genomics Research and Innovation Network: creating an interoperable, federated, genomics learning system.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

De novo mutations in histone-modifying genes in congenital heart disease.

Congenital heart disease (CHD) is the most frequent birth defect, affecting 0.8% of live births. Many cases occur sporadically and impair reproductive fitness, suggesting a role for de novo mutations. Here we compare the incidence of de novo mutations in 362 severe CHD cases and 264 controls by analysing exome sequencing of parent-offspring trios. CHD cases show a significant excess of protein-altering de novo mutations in genes expressed in the developing heart, with an odds ratio of 7.5 for damaging (premature termination, frameshift, splice site) mutations. Similar odds ratios are seen across the main classes of severe CHD. We find a marked excess of de novo mutations in genes involved in the production, removal or reading of histone 3 lysine 4 (H3K4) methylation, or ubiquitination of H2BK120, which is required for H3K4 methylation. There are also two de novo mutations in SMAD2, which regulates H3K27 methylation in the embryonic left-right organizer. The combination of both activating (H3K4 methylation) and inactivating (H3K27 methylation) chromatin marks characterizes 'poised' promoters and enhancers, which regulate expression of key developmental genes. These findings implicate de novo point mutations in several hundreds of genes that collectively contribute to approximately 10% of severe CHD.

Correction: Novel findings with reassessment of exome data: implications for validation testing and interpretation of genomic data.

In the published version of this article, the degree of author Bo Zhang was incorrectly listed as PhD. The correct degree is BS.

Novel findings with reassessment of exome data: implications for validation testing and interpretation of genomic data.

PurposeThe objective of this study was to assess the ability of our laboratory's exome-sequencing test to detect known and novel sequence variants and identify the critical factors influencing the interpretation of a clinical exome test.MethodsWe developed a two-tiered validation strategy: (i) a method-based approach that assessed the ability of our exome test to detect known variants using a reference HapMap sample, and (ii) an interpretation-based approach that assessed our relative ability to identify and interpret disease-causing variants, by analyzing and comparing the results of 19 randomly selected patients previously tested by external laboratories.ResultsWe demonstrate that this approach is reproducible with >99% analytical sensitivity and specificity for single-nucleotide variants and indels <10 bp. Our findings were concordant with the reference laboratories in 84% of cases. A new molecular diagnosis was applied to three cases, including discovery of two novel candidate genes.ConclusionWe provide an assessment of critical areas that influence interpretation of an exome test, including comprehensive phenotype capture, assessment of clinical overlap, availability of parental data, and the addressing of limitations in database updates. These results can be used to inform improvements in phenotype-driven interpretation of medical exomes in clinical and research settings.

Correction: Novel findings with reassessment of exome data: implications for validation testing and interpretation of genomic data.

In the published version of this article, the name of the 18th author was misspelled as Minjie Lou. The correct name is Minjie Luo. The authors regret the error.

Testing the effects of four urbanization filters on forest plant taxonomic, functional, and phylogenetic diversity.

Ongoing urban development has significant effects on ecosystems, including changes to land cover, environmental conditions, and species' distributions. These various impacts may have opposing or interacting effects on plant communities, making it difficult to predict how plant biodiversity will respond to urban development. A frequently cited conceptual framework predicts how urban development influences plant taxonomic, functional, and phylogenetic diversity by simplifying multiple coincident effects of urbanization into four primary filters of biodiversity: habitat transformation, fragmentation, the urban environment, and human preferences. Each filter prevents some plant species from persisting in urban areas while promoting others, but species introductions according to human preferences are expected to cause a net increase in biodiversity while the other filters limit diversity. In this study, we used structural equation modeling to test these predictions and examine the relative importance of each filter on the taxonomic, functional, and phylogenetic diversity of riparian forest plant species sampled along an urban-to-rural gradient in the Research Triangle area of North Carolina. Most diversity measures declined with urbanization, but some (e.g., functional Rao's Q) increased with urbanization. We found support for some of the predicted relationships between urbanization filters and biodiversity, as well as some unexpected relationships, including positive effects of urban environments. Overall, urban environments and human preferences were stronger predictors than habitat transformation and fragmentation. Our approach could be used to test a general framework predicting the effects of urbanization on plant diversity across multiple cities and contribute to a more synthetic understanding of urban biodiversity.

Investigation of the Use of a Family Health History Application in Genetic Counseling.

The paper-based pedigree is the current standard for family health history (FHH) documentation in genetic counseling. Several tools for electronic capture of family health data have been developed to improve re-use and accessibility, data quality and standardization, ease of updating, and integration with electronic medical records. One such tool, the tablet-based Proband application, provides a flexible approach to data capture in dynamic and diverse clinical settings. This study compared Proband FHH collection to paper-based methods and investigated the usability of Proband in a clinical setting. After one use by 23 genetic counselors and students, Proband had 91% accuracy with a FHH audio scenario, which was significantly less (p < 0.001) than paper's 96% accuracy. These differences were attributed to incorrect or missing ages of grandparents (p < 0.001) and great-aunts/uncles (p = 0.012) and missing documentation of consanguinity (p < 0.001). Possible explanations for these differences include greater experience with paper FHH documentation and pre-populated prompts for consanguinity on the paper template used. Proband's perceived usability increased with use, with individual System Usability Scores increasing between first and last use (p = 0.033). We conclude that tools for dynamic, provider-driven FHH documentation such as Proband show promise for improving risk assessment accuracy and quality patient care.

Catalytic Enantioselective [3 + 2] Cycloaddition of α-Keto Ester Enolates and Nitrile Oxides.

An enantioselective [3 + 2] cycloaddition reaction between nitrile oxides and transiently generated enolates of α-keto esters has been developed. The catalyst system was found to be compatible with in situ nitrile oxide-generation conditions. A versatile array of nitrile oxides and α-keto esters could participate in the cycloaddition, providing novel 5-hydroxy-2-isoxazolines in high chemical yield with high levels of diastereo- and enantioselectivity. Notably, the optimal reaction conditions circumvented concurrent reactions via O-imidoylation and hetero-[3 + 2] pathways.

Ammonia Synthesis from a Pincer Ruthenium Nitride via Metal-Ligand Cooperative Proton-Coupled Electron Transfer.

The conversion of metal nitride complexes to ammonia may be essential to dinitrogen fixation. We report a new reduction pathway that utilizes ligating acids and metal-ligand cooperation to effect this conversion without external reductants. Weak acids such as 4-methoxybenzoic acid and 2-pyridone react with nitride complex [(H-PNP)RuN]+ (H-PNP = HN(CH2CH2PtBu2)2) to generate octahedral ammine complexes that are κ2-chelated by the conjugate base. Experimental and computational mechanistic studies reveal the important role of Lewis basic sites proximal to the acidic proton in facilitating protonation of the nitride. The subsequent reduction to ammonia is enabled by intramolecular 2H+/2e- proton-coupled electron transfer from the saturated pincer ligand backbone.

Mapping the Binding Modes of Hemilabile Pincer-Crown Ether Ligands in Solution Using Diamagnetic Anisotropic Effects on NMR Chemical Shift.

A protocol for identifying ligand binding modes in a series of iridium pincer complexes bearing hemilabile aza-crown ether ligands has been developed using readily accessible NMR methods. The approach was tested on a collection of 13 structurally diverse pincer-crown ether complexes that include several newly characterized species. New synthetic routes enable facile interconversion of coordination modes and supporting ligands. Detailed structural assignments of five complexes reveal that the difference in chemical shift (Δδ) between geminal protons in the crown ether is influenced by diamagnetic anisotropy arising from halides and other ligands in the primary coordination sphere. The average difference in chemical shift between diastereotopic geminal protons in the crown ether macrocycle (Δδavg), as determined through a single 1H-13C HSQC experiment, provides information on the pincer ligand binding mode by establishing whether the macrocycle is in close proximity to the metal center. The Δδavg values for binding modes that involve chelating ether(s) bound to iridium are roughly 2-fold larger than those for tridentate complexes with no Ir-O bonds.

Investigation of a Catenane with a Responsive Noncovalent Network: Mimicking Long-Range Responses in Proteins.

We report a functional synthetic model for studying the noncovalent networks (NCNs) required for complex protein functions. The model [2]-catenane is self-assembled from dipeptide building blocks and contains an extensive network of hydrogen bonds and aromatic interactions. Perturbations to the catenane cause compensating changes in the NCNs structure and dynamics, resulting in long-distance changes reminiscent of a protein. Key findings include the notion that NCNs require regions of negative cooperativity, or "frustrated" noncovalent interactions, as a source of potential energy for driving the response. We refer to this potential energy as latent free energy and describe a mechanistic and energetic model for responsive systems.

Utility and limitations of exome sequencing as a genetic diagnostic tool for conditions associated with pediatric sudden cardiac arrest/sudden cardiac death.

BACKGROUND: Conditions associated with sudden cardiac arrest/death (SCA/D) in youth often have a genetic etiology. While SCA/D is uncommon, a pro-active family screening approach may identify these inherited structural and electrical abnormalities prior to symptomatic events and allow appropriate surveillance and treatment. This study investigated the diagnostic utility of exome sequencing (ES) by evaluating the capture and coverage of genes related to SCA/D. METHODS: Samples from 102 individuals (13 with known molecular etiologies for SCA/D, 30 individuals without known molecular etiologies for SCA/D and 59 with other conditions) were analyzed following exome capture and sequencing at an average read depth of 100X. Reads were mapped to human genome GRCh37 using Novoalign, and post-processing and analysis was done using Picard and GATK. A total of 103 genes (2,190 exons) related to SCA/D were used as a primary filter. An additional 100 random variants within the targeted genes associated with SCA/D were also selected and evaluated for depth of sequencing and coverage. Although the primary objective was to evaluate the adequacy of depth of sequencing and coverage of targeted SCA/D genes and not for primary diagnosis, all patients who had SCA/D (known or unknown molecular etiologies) were evaluated with the project's variant analysis pipeline to determine if the molecular etiologies could be successfully identified. RESULTS: The majority of exons (97.6 %) were captured and fully covered on average at minimum of 20x sequencing depth. The proportion of unique genomic positions reported within poorly covered exons remained small (4 %). Exonic regions with less coverage reflect the need to enrich these areas to improve coverage. Despite limitations in coverage, we identified 100 % of cases with a prior known molecular etiology for SCA/D, and analysis of an additional 30 individuals with SCA/D but no known molecular etiology revealed a diagnostic answer in 5/30 (17 %). We also demonstrated 95 % of 100 randomly selected reported variants within our targeted genes would have been picked up on ES based on our coverage analysis. CONCLUSIONS: ES is a helpful clinical diagnostic tool for SCA/D given its potential to successfully identify a molecular diagnosis, but clinicians should be aware of limitations of available platforms from technical and diagnostic perspectives.

Increased frequency of de novo copy number variants in congenital heart disease by integrative analysis of single nucleotide polymorphism array and exome sequence data.

RATIONALE: Congenital heart disease (CHD) is among the most common birth defects. Most cases are of unknown pathogenesis. OBJECTIVE: To determine the contribution of de novo copy number variants (CNVs) in the pathogenesis of sporadic CHD. METHODS AND RESULTS: We studied 538 CHD trios using genome-wide dense single nucleotide polymorphism arrays and whole exome sequencing. Results were experimentally validated using digital droplet polymerase chain reaction. We compared validated CNVs in CHD cases with CNVs in 1301 healthy control trios. The 2 complementary high-resolution technologies identified 63 validated de novo CNVs in 51 CHD cases. A significant increase in CNV burden was observed when comparing CHD trios with healthy trios, using either single nucleotide polymorphism array (P=7×10(-5); odds ratio, 4.6) or whole exome sequencing data (P=6×10(-4); odds ratio, 3.5) and remained after removing 16% of de novo CNV loci previously reported as pathogenic (P=0.02; odds ratio, 2.7). We observed recurrent de novo CNVs on 15q11.2 encompassing CYFIP1, NIPA1, and NIPA2 and single de novo CNVs encompassing DUSP1, JUN, JUP, MED15, MED9, PTPRE SREBF1, TOP2A, and ZEB2, genes that interact with established CHD proteins NKX2-5 and GATA4. Integrating de novo variants in whole exome sequencing and CNV data suggests that ETS1 is the pathogenic gene altered by 11q24.2-q25 deletions in Jacobsen syndrome and that CTBP2 is the pathogenic gene in 10q subtelomeric deletions. CONCLUSIONS: We demonstrate a significantly increased frequency of rare de novo CNVs in CHD patients compared with healthy controls and suggest several novel genetic loci for CHD.

Ligand exchanges and selective catalytic hydrogenation in molecular single crystals.

Chemical reactions inside single crystals are likely to be highly selective, but examples of single crystal to single crystal (SC-SC) transformations are uncommon, because crystallinity is difficult to retain following the rearrangement of atoms in the solid state. The most widely studied SC-SC transformations involve solvent exchange reactions in porous coordination polymers or metal-organic frameworks, which take advantage of the robust polymeric networks of the hosts. Examples of reactions occurring within molecular organic crystals generally involve photo-induced reactions, such as the coupling of alkenes or alkynes within the crystal. For nonporous molecular inorganic or organometallic crystals, single-crystal transformations involving the formation or cleavage of metal-ligand bonds are rare; known examples usually involve ligand loss from the single crystal and reversible religation, a process sometimes accompanied by decay of the single crystal to a microcrystalline powder. Here we report a series of SC-SC transformations that involve the interchange of multiple small gaseous ligands (N(2), CO, NH(3), C(2)H(4), H(2) and O(2)) at an iridium centre in molecular single crystals of a pincer Ir(I) complex. The single crystal remains intact during these ligand-exchange reactions, which occur within the crystal and do not require prior ligand extrusion. We reveal a selective catalytic transformation within a nonporous molecular crystal: pincer iridium single crystals ligated with nitrogen, ethylene or hydrogen show selective hydrogenation of ethylene relative to propylene (25:1) when surface sites are passified by CO.

Microclimate moderates plant responses to macroclimate warming.

Recent global warming is acting across marine, freshwater, and terrestrial ecosystems to favor species adapted to warmer conditions and/or reduce the abundance of cold-adapted organisms (i.e., "thermophilization" of communities). Lack of community responses to increased temperature, however, has also been reported for several taxa and regions, suggesting that "climatic lags" may be frequent. Here we show that microclimatic effects brought about by forest canopy closure can buffer biotic responses to macroclimate warming, thus explaining an apparent climatic lag. Using data from 1,409 vegetation plots in European and North American temperate forests, each surveyed at least twice over an interval of 12-67 y, we document significant thermophilization of ground-layer plant communities. These changes reflect concurrent declines in species adapted to cooler conditions and increases in species adapted to warmer conditions. However, thermophilization, particularly the increase of warm-adapted species, is attenuated in forests whose canopies have become denser, probably reflecting cooler growing-season ground temperatures via increased shading. As standing stocks of trees have increased in many temperate forests in recent decades, local microclimatic effects may commonly be moderating the impacts of macroclimate warming on forest understories. Conversely, increases in harvesting woody biomass--e.g., for bioenergy--may open forest canopies and accelerate thermophilization of temperate forest biodiversity.

Clinical phenotype-based gene prioritization: an initial study using semantic similarity and the human phenotype ontology.

BACKGROUND: Exome sequencing is a promising method for diagnosing patients with a complex phenotype. However, variant interpretation relative to patient phenotype can be challenging in some scenarios, particularly clinical assessment of rare complex phenotypes. Each patient's sequence reveals many possibly damaging variants that must be individually assessed to establish clear association with patient phenotype. To assist interpretation, we implemented an algorithm that ranks a given set of genes relative to patient phenotype. The algorithm orders genes by the semantic similarity computed between phenotypic descriptors associated with each gene and those describing the patient. Phenotypic descriptor terms are taken from the Human Phenotype Ontology (HPO) and semantic similarity is derived from each term's information content. RESULTS: Model validation was performed via simulation and with clinical data. We simulated 33 Mendelian diseases with 100 patients per disease. We modeled clinical conditions by adding noise and imprecision, i.e. phenotypic terms unrelated to the disease and terms less specific than the actual disease terms. We ranked the causative gene against all 2488 HPO annotated genes. The median causative gene rank was 1 for the optimal and noise cases, 12 for the imprecision case, and 60 for the imprecision with noise case. Additionally, we examined a clinical cohort of subjects with hearing impairment. The disease gene median rank was 22. However, when also considering the patient's exome data and filtering non-exomic and common variants, the median rank improved to 3. CONCLUSIONS: Semantic similarity can rank a causative gene highly within a gene list relative to patient phenotype characteristics, provided that imprecision is mitigated. The clinical case results suggest that phenotype rank combined with variant analysis provides significant improvement over the individual approaches. We expect that this combined prioritization approach may increase accuracy and decrease effort for clinical genetic diagnosis.

Oxygen atom transfer to a half-sandwich iridium complex: clean oxidation yielding a molecular product.

The oxidation of [Ir(Cp*)(phpy)(NCAr(F))][B(Ar(F))4] (1; Cp* = η(5)-pentamethylcyclopentadienyl, phpy = 2-phenylene-κC(1')-pyridine-κN, NCAr(F) = 3,5-bis(trifluoromethyl)benzonitrile, B(Ar(F))4 = tetrakis[3,5-bis(trifluoromethyl)phenyl]borate) with the oxygen atom transfer (OAT) reagent 2-tert-butylsulfonyliodosobenzene (sPhIO) yielded a single, molecular product at -40 °C. New Ir(Cp*) complexes with bidentate ligands derived by oxidation of phpy were synthesized to model possible products resulting from oxygen atom insertion into the iridium-carbon and/or iridium-nitrogen bonds of phpy. These new ligands were either cleaved from iridium by water or formed unreactive, phenoxide-bridged iridium dimers. The reactivity of these molecules suggested possible decomposition pathways of Ir(Cp*)-based water oxidation catalysts with bidentate ligands that are susceptible to oxidation. Monitoring the [Ir(Cp*)(phpy)(NCAr(F))](+) oxidation reaction by low-temperature NMR techniques revealed that the reaction involved two separate OAT events. An intermediate was detected, synthesized independently with trapping ligands, and characterized. The first oxidation step involves direct attack of the sPhIO oxidant on the carbon of the coordinated nitrile ligand. Oxygen atom transfer to carbon, followed by insertion into the iridium-carbon bond of phpy, formed a coordinated organic amide. A second oxygen atom transfer generated an unidentified iridium species (the "oxidized complex"). In the presence of triphenylphosphine, the "oxidized complex" proved capable of transferring one oxygen atom to phosphine, generating phosphine oxide and forming an Ir-PPh3 adduct in 92% yield. The final Ir-PPh3 product was fully characterized.

Analysis of chromosomal structural variation in patients with congenital left-sided cardiac lesions.

BACKGROUND: We sought to characterize the landscape of structural variation associated with the subset of congenital cardiac defects characterized by left-sided obstruction. METHODS: Cases with left-sided cardiac defects (LSCD) and pediatric controls were uniformly genotyped and assessed for copy number variant (CNV) calls. Significance testing was performed to ascertain differences in overall CNV incidence, and for CNV enrichment of specific genes and gene functions in LSCD cases relative to controls. RESULTS: A total of 257 cases of European descent and 962 ethnically matched, disease-free pediatric controls were included. Although there was no difference in CNV rate between cases and controls, a significant enrichment in rare LSCD CNVs was detected overall (p=7.30 × 10(-3) , case/control ratio=1.26) and when restricted either to deletions (p=7.58 × 10(-3) , case/control ratio=1.20) or duplications (3.02 × 10(-3) , case/control ratio=1.43). Neither gene-based, functional nor knowledge-based analyses identified genes, loci or pathways that were significantly enriched in cases as compared to controls when appropriate corrections for multiple tests were applied. However, several genes of interest were identified by virtue of their association with cardiac development, known human conditions, or reported disruption by CNVs in other patient cohorts. CONCLUSION: This study examines the largest cohort to date with LSCD for structural variation. These data suggest that CNVs play a role in disease risk and identify numerous genes disrupted by CNVs of potential disease relevance. These findings further highlight the genetic heterogeneity and complexity of these disorders.

Efficient digest of high-throughput sequencing data in a reproducible report.

BACKGROUND: High-throughput sequencing (HTS) technologies are spearheading the accelerated development of biomedical research. Processing and summarizing the large amount of data generated by HTS presents a non-trivial challenge to bioinformatics. A commonly adopted standard is to store sequencing reads aligned to a reference genome in SAM (Sequence Alignment/Map) or BAM (Binary Alignment/Map) files. Quality control of SAM/BAM files is a critical checkpoint before downstream analysis. The goal of the current project is to facilitate and standardize this process. RESULTS: We developed bamchop, a robust program to efficiently summarize key statistical metrics of HTS data stored in BAM files, and to visually present the results in a formatted report. The report documents information about various aspects of HTS data, such as sequencing quality, mapping to a reference genome, sequencing coverage, and base frequency. Bamchop uses the R language and Bioconductor packages to calculate statistical matrices and the Sweave utility and associated LaTeX markup for documentation. Bamchop's efficiency and robustness were tested on BAM files generated by local sequencing facilities and the 1000 Genomes Project. Source code, instruction and example reports of bamchop are freely available from https://github.com/CBMi-BiG/bamchop. CONCLUSIONS: Bamchop enables biomedical researchers to quickly and rigorously evaluate HTS data by providing a convenient synopsis and user-friendly reports.