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Across a variety of Mendelian disorders, ∼50–75% of patients do not receive a genetic diagnosis by exome sequencing indicating disease-causing variants in non-coding regions. Although genome sequencing in principle reveals all genetic variants, their sizeable number and poorer annotation make prioritization challenging. Here, we demonstrate the power of transcriptome sequencing to molecularly diagnose 10% (5 of 48) of mitochondriopathy patients and identify candidate genes for the remainder. We find a median of one aberrantly expressed gene, five aberrant splicing events and six mono-allelically expressed rare variants in patient-derived fibroblasts and establish disease-causing roles for each kind. Private exons often arise from cryptic splice sites providing an important clue for variant prioritization. One such event is found in the complex I assembly factor TIMMDC1 establishing a novel disease-associated gene. In conclusion, our study expands the diagnostic tools for detecting non-exonic variants and provides examples of intronic loss-of-function variants with pathological relevance. Genome sequencing alone fails to provide a genetic diagnosis for many Mendelian disorder patients. Here, the authors utilize RNA sequencing to complement genotyping of patients with a rare mitochondrial disease by detecting aberrant RNA expression, splicing and allele-specific expression.

The authors show that haploinsufficiency of TBK1 causes familial forms of the neurodegenerative diseases ALS and FTD. Loss of binding of a TBK1 protein interaction domain to optineurin, a protein previously linked to ALS, is sufficient to cause the disease. Both proteins regulate autophagy and inflammation. Amyotrophic lateral sclerosis (ALS) is a genetically heterogeneous neurodegenerative syndrome hallmarked by adult-onset loss of motor neurons. We performed exome sequencing of 252 familial ALS (fALS) and 827 control individuals. Gene-based rare variant analysis identified an exome-wide significant enrichment of eight loss-of-function (LoF) mutations in TBK1 (encoding TANK-binding kinase 1) in 13 fALS pedigrees. No enrichment of LoF mutations was observed in a targeted mutation screen of 1,010 sporadic ALS and 650 additional control individuals. Linkage analysis in four families gave an aggregate LOD score of 4.6. In vitro experiments confirmed the loss of expression of TBK1 LoF mutant alleles, or loss of interaction of the C-terminal TBK1 coiled-coil domain (CCD2) mutants with the TBK1 adaptor protein optineurin, which has been shown to be involved in ALS pathogenesis. We conclude that haploinsufficiency of TBK1 causes ALS and fronto-temporal dementia.

High‐resolution, three‐dimensional, reactive flow and transport simulations are carried out to describe the migration of hexavalent uranium [U(VI)] at the Hanford 300 Area bordering the Columbia River and to better understand the persistence of the uranium plume at the site. The computer code PFLOTRAN developed under a DOE SciDAC‐2 project is employed in the simulations that are executed on ORNL's Cray XT4/XT5 supercomputer Jaguar. The conceptual model used in the simulations is based on the recognition of three distinct phases or time periods in the evolution of the U(VI) plume. These correspond to (1) initial waste emplacement; (2) initial presence of both labile and nonlabile U(VI) with an evolved U(VI) plume extending from the source region to the river boundary, representing present‐day conditions; and (3) the complete removal of all nonlabile U(VI) and labile U(VI) in the vadose zone. This work focuses primarily on modeling Phase II using equilibrium and multirate sorption models for labile U(VI) and a continuous source release of nonlabile U(VI) in the South Process Pond through dissolution of metatorbernite as a surrogate mineral. For this case, rapid fluctuations in the Columbia River stage combined with the slow release of nonlabile U(VI) from contaminated sediment are found to play a predominant role in determining the migration behavior of U(VI) with sorption only a second‐order effect. Nevertheless, a multirate model was essential in explaining breakthrough curves obtained from laboratory column experiments using the same sediment and is demonstrated to be important in Phase III. The calculations demonstrate that U(VI) is discharged to the river at a highly fluctuating rate in a ratchet‐like behavior as the river stage rises and falls. The high‐frequency fluctuations must be resolved in the model to calculate the flux of U(VI) at the river boundary. By time averaging the instantaneous flux to average out noise superimposed on the river stage fluctuations, the cumulative U(VI) flux to the river is found to increase approximately linearly with time. The flow rate and U(VI) flux are highly sensitive to the conductance boundary condition that describes the river‐sediment interface. By adjusting the conductance coefficient to give a better match to the measured piezometric head, good agreement was obtained with field studies for both the mean flux of water of 109 kg/yr and U(VI) of 25 kg/yr at the river‐aquifer boundary for a computational domain encompassing the South Process Pond. Finally, it is demonstrated that, through global mass conservation, the U(VI) leach rate from the source region is related to the U(VI) flux at the river boundary.

BACKGROUND: The impact of additive-genetic relationships captured by single nucleotide polymorphisms (SNPs) on the accuracy of genomic breeding values (GEBVs) has been demonstrated, but recent studies on data obtained from Holstein populations have ignored this fact. However, this impact and the accuracy of GEBVs due to linkage disequilibrium (LD), which is fairly persistent over generations, must be known to implement future breeding programs. MATERIALS AND METHODS: The data set used to investigate these questions consisted of 3,863 German Holstein bulls genotyped for 54,001 SNPs, their pedigree and daughter yield deviations for milk yield, fat yield, protein yield and somatic cell score. A cross-validation methodology was applied, where the maximum additive-genetic relationship (a max) between bulls in training and validation was controlled. GEBVs were estimated by a Bayesian model averaging approach (BayesB) and an animal model using the genomic relationship matrix (G-BLUP). The accuracy of GEBVs due to LD was estimated by a regression approach using accuracy of GEBVs and accuracy of pedigree-based BLUP-EBVs. RESULTS: Accuracy of GEBVs obtained by both BayesB and G-BLUP decreased with decreasing a max for all traits analyzed. The decay of accuracy tended to be larger for G-BLUP and with smaller training size. Differences between BayesB and G-BLUP became evident for the accuracy due to LD, where BayesB clearly outperformed G-BLUP with increasing training size. CONCLUSIONS: GEBV accuracy of current selection candidates varies due to different additive-genetic relationships relative to the training data. Accuracy of future candidates can be lower than reported in previous studies because information from close relatives will not be available when selection on GEBVs is applied. A Bayesian model averaging approach exploits LD information considerably better than G-BLUP and thus is the most promising method. Cross-validations should account for family structure in the data to allow for long-lasting genomic based breeding plans in animal and plant breeding.

Genetic factors undoubtedly affect the development of congenital heart disease (CHD) but still remain ill defined. We sought to identify genetic risk factors associated with CHD and to accomplish a functional analysis of SNP-carrying genes. We performed a genome-wide association study (GWAS) of 4034 White patients with CHD and 8486 healthy controls. One SNP on chromosome 5q22.2 reached genome-wide significance across all CHD phenotypes and was also indicative for septal defects. One region on chromosome 20p12.1 pointing to the MACROD2 locus identified 4 highly significant SNPs in patients with transposition of the great arteries (TGA). Three highly significant risk variants on chromosome 17q21.32 within the GOSR2 locus were detected in patients with anomalies of thoracic arteries and veins (ATAV). Genetic variants associated with ATAV are suggested to influence the expression of WNT3, and the variant rs870142 related to septal defects is proposed to influence the expression of MSX1. We analyzed the expression of all 4 genes during cardiac differentiation of human and murine induced pluripotent stem cells in vitro and by single-cell RNA-Seq analyses of developing murine and human hearts. Our data show that MACROD2, GOSR2, WNT3, and MSX1 play an essential functional role in heart development at the embryonic and newborn stages.

We apply a multi-component reactive transport lattice Boltzmann model developed in previous studies for modeling the injection of a CO 2 -saturated brine into various porous media structures at temperatures T  = 25 and 80°C. In the various cases considered the porous medium consists initially of calcite with varying grain size and shape. A chemical system consisting of Na + , Ca 2+ , Mg 2+ , H + , , and Cl − is considered. Flow and transport by advection and diffusion of aqueous species, combined with homogeneous reactions occurring in the bulk fluid, as well as the dissolution of calcite and precipitation of dolomite are simulated at the pore scale. The effects of the structure of the porous media on reactive transport are investigated. The results are compared with a continuum-scale model and the discrepancies between the pore- and continuum-scale models are discussed. This study sheds some light on the fundamental physics occurring at the pore scale for reactive transport involved in geologic CO 2 sequestration.

Understanding the flow and reactivity of CO2 injected into geological reservoirs is important for many subsurface applications including secure geologic carbon storage (GCS), critical mineral extraction, enhanced geothermal systems (EGS), and enhanced oil recovery (EOR). Traditionally, subsurface CO2 injection for GCS applications has focused on geologic formations with favorable subsurface configurations for CO2 migration and trapping through non-reactive mechanisms such as structural, solubility, and petrophysical trapping. Recently, CO2-reactive rocks such as mafic and ultramafic basalts have been investigated for their potential to react with injected CO2 in situ to simultaneously dissolve host rock minerals and mineralize CO2 as carbonates. Engineering rapid CO2 mineralization in the subsurface is attractive because of the increased density of stored CO2, the additional safety factors associated with solidification, and the potential to extract valuable critical minerals. Here we present recent developments in the parallel flow and reactive transport simulator PFLOTRAN to model coupled CO2-brine flow and reactive transport for a wide range of injection and production applications involving reactive CO2-brine systems. These developments are based on the well established and trusted CO2 flow capabilities in the STOMP-CO2 simulator. New capabilities added to PFLOTRAN include new CO2-brine equations of state with optional thermal coupling, several new constitutive relationships like capillary pressure smoothing and scanning path hysteresis, a fully implicit well model, and native linkage with PFLOTRAN's well-established reactive transport libraries. A series of benchmarks between PFLOTRAN and STOMP-CO2 verify the newly developed CO2-brine flow capabilities. Demonstrations of coupled CO2-brine flow modeling and reactive transport show how CO2 mineralization can be engineered in reactive host rocks. Finally, an example use case involving copper leaching by CO2 and critical mineral extraction is presented to showcase the strengths of this new implementation. Several limitations still remain, including limited availability of field data to parameterize models. Future work should constrain the evolution of mineral surface area during mineralization and the temperature and/or pH dependence of geochemical reactions for specific systems of interest.

The recent CRISPR revolution has provided researchers with powerful tools to perform genome editing in a variety of organisms. However, recent reports indicate widespread occurrence of unintended CRISPR-induced on-target effects (OnTEs) at the edited site in mice and human induced pluripotent stem cells (iPSCs) that escape standard quality controls. By altering gene expression of targeted or neighbouring genes, OnTEs can severely affect phenotypes of CRISPR-edited cells and organisms and thus lead to data misinterpretation, which can undermine the reliability of CRISPR-based studies. Here we describe a broadly applicable framework for detecting OnTEs in genome-edited cells and organisms after non-homologous end joining-mediated and homology-directed repair-mediated editing. Our protocol enables identification of OnTEs such as large deletions, large insertions, rearrangements or loss of heterozygosity (LOH). This is achieved by subjecting genomic DNA first to quantitative genotyping PCR (qgPCR), which determines the number of intact alleles at the target site using the same PCR amplicon that has been optimized for genotyping. This combination of genotyping and quantitation makes it possible to exclude clones with monoallelic OnTEs and hemizygous editing, which are often mischaracterized as correctly edited in standard Sanger sequencing. Second, occurrence of LOH around the edited locus is detected by genotyping neighbouring single-nucleotide polymorphisms (SNPs), using either a Sanger sequencing-based method or SNP microarrays. All steps are optimized to maximize simplicity and minimize cost to promote wide dissemination and applicability across the field. The entire protocol from genomic DNA extraction to OnTE exclusion can be performed in 6–9 d. CRISPR-induced on-target effects (large deletions, large insertions, rearrangements or loss of heterozygosity) occur frequently at the edited site. This protocol describes how to identify these effects using quantitative genotyping PCR and SNP genotyping.

Alfons Meindl and colleagues report heterozygous germline mutations in RAD51C in families with breast and ovarian cancer. Mutations were found in 1.3% of 480 pedigrees with breast and ovarian cancer, but not in 620 pedigrees with breast cancer only. Germline mutations in a number of genes involved in the recombinational repair of DNA double-strand breaks are associated with predisposition to breast and ovarian cancer. RAD51C is essential for homologous recombination repair, and a biallelic missense mutation can cause a Fanconi anemia–like phenotype. In index cases from 1,100 German families with gynecological malignancies, we identified six monoallelic pathogenic mutations in RAD51C that confer an increased risk for breast and ovarian cancer. These include two frameshift-causing insertions, two splice-site mutations and two nonfunctional missense mutations. The mutations were found exclusively within 480 pedigrees with the occurrence of both breast and ovarian tumors (BC/OC; 1.3%) and not in 620 pedigrees with breast cancer only or in 2,912 healthy German controls. These results provide the first unambiguous evidence of highly penetrant mutations associated with human cancer in a RAD51 paralog and support the 'common disease, rare allele' hypothesis.

Recent advances in the identification of susceptibility genes and environmental exposures provide broad support for a post-infectious autoimmune basis for narcolepsy/hypocretin (orexin) deficiency. We genotyped loci associated with other autoimmune and inflammatory diseases in 1,886 individuals with hypocretin-deficient narcolepsy and 10,421 controls, all of European ancestry, using a custom genotyping array (ImmunoChip). Three loci located outside the Human Leukocyte Antigen (HLA) region on chromosome 6 were significantly associated with disease risk. In addition to a strong signal in the T cell receptor alpha (TRA@), variants in two additional narcolepsy loci, Cathepsin H (CTSH) and Tumor necrosis factor (ligand) superfamily member 4 (TNFSF4, also called OX40L), attained genome-wide significance. These findings underline the importance of antigen presentation by HLA Class II to T cells in the pathophysiology of this autoimmune disease.