Reliability of genomic predictions of complex human phenotypes

Genome-wide association studies have helped us identify a wealth of genetic variants associated with complex human phenotypes. Because most variants explain a small portion of the total phenotypic variation, however, marker-based studies remain limited in their ability to predict such phenotypes. Here, we show how modern statistical genetic techniques borrowed from animal breeding can be employed to increase the accuracy of genomic prediction of complex phenotypes and the power of genetic mapping studies. Specifically, using the triglyceride data of the GAW20 data set, we apply genomic-best linear unbiased prediction (G-BLUP) methods to obtain empirical genetic values (EGVs) for each triglyceride phenotype and each individual. We then study 2 different factors that influence the prediction accuracy of G-BLUP for the analysis of human data: (a) the choice of kinship matrix, and (b) the overall level of relatedness. The resulting genetic values represent the total genetic component for the phenotype of interest and can be used to represent a trait without its environmental component. Finally, using empirical data, we demonstrate how this method can be used to increase the power of genetic mapping studies. In sum, our results show that dense genome-wide data can be used in a wider scope than previously anticipated

Heritability and genetic associations of triglyceride and HDL-C levels using pedigree-based and empirical kinships

The heritability of a phenotype is an estimation of the percent of variance in that phenotype that is attributable to additive genetic factors. Heritability is optimally estimated in family-based sample populations. Traditionally, this involves use of a pedigree-based kinship coefficient generated from the collected genealogical relationships between family members. An alternative, when dense genotype data are available, is to directly measure the empirical kinship between samples. This study compares the use of pedigree and empirical kinships in the GAW20 data set. Two phenotypes were assessed: triglyceride levels and high-density lipoprotein cholesterol (HDL-C) levels pre- and postintervention with the cholesterol-reducing drug fenofibrate. Using SOLAR (Sequential Oligogenic Linkage Analysis Routines), pedigree-based kinships and empirically calculated kinships (using IBDLD and LDAK) were used to calculate phenotype heritability. In addition, a genome-wide association study was conducted using each kinship model for each phenotype to identify genetic variants significantly associated with phenotypic variation. The variant rs247617 was significantly associated with HDL-C levels both pre- and post-fenofibrate intervention. Overall, the phenotype heritabilities calculated using pedigree based kinships or either of the empirical kinships generated using IBDLD or LDAK were comparable. Phenotype heritabilities estimated from empirical kinships generated using IBDLD were closest to the pedigree-based estimations. Given that there was not an appreciable amount of unknown relatedness between the pedigrees in this data set, a large increase in heritability in using empirical kinship was not expected, and our calculations support this. Importantly, these results demonstrate that when sufficient genotypic data are available, empirical kinship estimation is a practical alternative to using pedigree-based kinships

Genome-wide linkage scan for loci influencing plasma triglyceride levels

We conducted a genome-wide linkage scan to detect loci that influence the levels of fasting triglycerides in plasma. Fasting triglyceride levels were available at 4 time points (visits), 2 pre- and 2 post-fenofibrate intervention. Multipoint identity-by-descent (MIBD) matrices were derived from genotypes using IBDLD. Variance-component linkage analyses were then conducted using SOLAR (Sequential Oligogenic Linkage Analysis Routines). We found evidence of linkage (logarithm of odds [LOD] ≥3) at 5 chromosomal regions with triglyceride levels in plasma. The highest LOD scores were observed for linkage to the estimated genetic value (additive genetic component) of the log-normalized triglyceride levels in plasma. Our results suggest that a chromosome 10 locus at 37 cM (LODpre = 3.01, LODpost = 3.72) influences fasting triglyceride levels in plasma regardless of the fenofibrate intervention, and that loci in chromosomes 1 at 170 cM and 4 at 24 cM ceases to affect the triglyceride levels when fenofibrate is present, while the regions in chromosomes 6 at 136 to 162 cM and 11 at 39 to 40 cM appear to influence triglyceride levels in response to fenofibrate

Mid-T Heat Treatments on BCPed Coaxial Cavities at TRIUMF

Mid-T heat treatments in the range from 250 to 400 C on superconducting radio-frequency (SRF) cavities have been shown to provide high quality factors that rise with applied rf field strength in high frequency, electro-polished (EP), elliptical cavities operating at 2K, similar to nitrogen doped cavities. The rise in quality factor is attributed to a decrease in the temperature dependent part of the surface resistance $R_{BCS}$. Until now, no results have been reported for these new treatments on quarter-wave resonators (QWR) and half-wave resonators (HWR). The TRIUMF multi-mode coaxial cavities are dedicated test cavities that allow frequency and temperature resolved performance characterization of treatments without changing environments, therefore providing an excellent test vehicle to test these new treatments with rf frequencies ranging from 200 to 1200 MHz. In this paper, performance measurements from both QWR and HWR cavities are reported and their performance compared with four different treatments: baseline, a conventional 120C low temperature bake for 48 hours, and two mid-T bakes at 300 and 400C for 3 hours. In addition, sample analysis using SEM, EDX and SIMS of witness samples is also shown. It is found that the mid-T bakes are not directly transferable to low frequency cavities. In the fundamental modes of the two test cavities, no performance gain over the baseline treatment nor a decreasing temperature dependent component with rising rf amplitude was observed. At frequencies above 1GHz and low temperatures, the mid-T bakes show a reduced field dependence of $R_{BCS}$ compared to both the baseline and 120C treatments

Local extinction and colonisation in native and exotic fish in relation to changes in land use

Distribution patterns of many native and exotic fish species are well documented, yet little is known about the temporal dynamics of native and exotic diversity in relation to changes in land use. We hypothesised that colonisation rates would be higher for exotic fish species and that extinction rates would be higher for native species in large stream systems. We also predicted that cold-water species would be more impacted than thermally tolerant species. To test these hypotheses, we used generalised linear mixed models to compare changes in native and exotic fish species richness over 10 years in a French drainage basin subjected to landscape alterations. Exotic fish were more susceptible to local extinction than the native ones. Extinction was greater among cold-tolerant species and at higher elevations. Colonisation by exotic species was higher at lower elevations. Although a decade of expanding urbanisation affected fish colonisation, agricultural lands experienced higher extinction rates. In the context of global changes in land use and population pressure, our study suggests that the temporal dynamics of fish diversity are driven by landscape alterations as well as by the thermal tolerance of species

The Small Subunit of the Mammalian Mitochondrial Ribosome: IDENTIFICATION OF THE FULL COMPLEMENT OF RIBOSOMAL PROTEINS PRESENT

Identification of all the protein components of the small subunit (28 S) of the mammalian mitochondrial ribosome has been achieved by carrying out proteolytic digestions of whole 28 S subunits followed by analysis of the resultant peptides by liquid chromatography and tandem mass spectrometry (LC/MS/MS). Peptide sequence information was used to search the human EST data bases and complete coding sequences of the proteins were assembled. The human mitochondrial ribosome has 29 distinct proteins in the small subunit. Fourteen of this group of proteins are homologs of the Escherichia coli 30 S ribosomal proteins S2, S5, S6, S7, S9, S10, S11, S12, S14, S15, S16, S17, S18, and S21. All of these proteins have homologs in Drosophila melanogaster, Caenorhabditis elegans, and Saccharomyces cerevisiae mitochondrial ribosomes. Surprisingly, three variants of ribosomal protein S18 are found in the mammalian and D. melanogaster mitochondrial ribosomes while C. elegans has two S18 homologs. The S18 homologs tend to be more closely related to chloroplast S18s than to prokaryotic S18s. No mitochondrial homologs to prokaryotic ribosomal proteins S1, S3, S4, S8, S13, S19, and S20 could be found in the peptides obtained from the whole 28 S subunit digests or by analysis of the available data bases. The remaining 15 proteins present in mammalian mitochondrial 28 S subunits (MRP-S22 through MRP-S36) are specific to mitochondrial ribosomes. Proteins in this group have no apparent homologs in bacterial, chloroplast, archaebacterial, or cytosolic ribosomes. All but two of these proteins have a clear homolog in D. melanogaster while all but three can be found in the genome of C. elegans. Five of the mitochondrial specific ribosomal proteins have homologs in S. cerevisiae

Endovascular thrombectomy in patients with large core ischemic stroke: a cost-effectiveness analysis from the SELECT study

Background It is unknown whether endovascular thrombectomy (EVT) is cost effective in large ischemic core infarcts. Methods In the prospective, multicenter, cohort study of imaging selection study (SELECT), large core was defined as computed tomography (CT) ASPECTS(CTP) ischemic core volume (rCBF Results From 361 patients enrolled in SELECT, 105 had large core on CT or CTP (EVT 62, MM 43). 19 (31%) EVT vs 6 (14%) MM patients achieved modified Rankin Scale (mRS) score 0–2 (OR 3.27, 95% CI 1.11 to 9.62, P=0.03) with a shift towards better mRS (cOR 2.12, 95% CI 1.05 to 4.31, P=0.04). Over the projected lifetime of patients presenting with large core, EVT led to incremental costs of $33 094 and a gain of 1.34 QALYs per patient, resulting in ICER of$24 665 per QALY. EVT has a higher NMB compared with MM at lower (EVT -$42 747, MM -$76 740) and upper (EVT $155 041, MM$57 134) WTP thresholds. PSA confirmed the results and CEAC showed 77% and 92% acceptability of EVT at the WTP of $50 000 and$100 000, respectively. EVT was associated with an increment of $29 225 in societal costs. The pivotal EVT trials (HERMES, DAWN, DEFUSE 3) were dominant in a sensitivity analysis at the same inputs, with societal cost-savings of$37 901, $86 164 and$22 501 and a gain of 1.62, 2.36 and 2.21 QALYs, respectively. Conclusions In a non-randomized prospective cohort study, EVT resulted in better outcomes in large core patients with higher QALYs, NMB and high cost-effectiveness acceptability rates at current WTP thresholds. Randomized trials are needed to confirm these results. Clinical trial registration NCT0244658

The Large Subunit of the Mammalian Mitochondrial Ribosome: ANALYSIS OF THE COMPLEMENT OF RIBOSOMAL PROTEINS PRESENT

Identification of all the protein components of the large subunit (39 S) of the mammalian mitochondrial ribosome has been achieved by carrying out proteolytic digestions of whole 39 S subunits followed by analysis of the resultant peptides by liquid chromatography and mass spectrometry. Peptide sequence information was used to search the human EST data bases and complete coding sequences were assembled. The human mitochondrial 39 S subunit has 48 distinct proteins. Twenty eight of these are homologs of the Escherichia coli 50 S ribosomal proteins L1, L2, L3, L4, L7/L12, L9, L10, L11, L13, L14, L15, L16, L17, L18, L19, L20, L21, L22, L23, L24, L27, L28, L30, L32, L33, L34, L35, and L36. Almost all of these proteins have homologs in Drosophila melanogaster, Caenorhabditis elegans, and Saccharomyces cerevisiae mitochondrial ribosomes. No mitochondrial homologs to prokaryotic ribosomal proteins L5, L6, L25, L29, and L31 could be found either in the peptides obtained or by analysis of the available data bases. The remaining 20 proteins present in the 39 S subunits are specific to mitochondrial ribosomes. Proteins in this group have no apparent homologs in bacterial, chloroplast, archaebacterial, or cytosolic ribosomes. All but two of the proteins has a clear homolog in D. melanogaster while all can be found in the genome of C. elegans. Ten of the 20 mitochondrial specific 39 S proteins have homologs in S. cerevisiae. Homologs of 2 of these new classes of ribosomal proteins could be identified in the Arabidopsis thaliana genome

A Proteomic Analysis of Human Cilia: Identification of Novel Components

Cilia play an essential role in protecting the respiratory tract by providing the force necessary for mucociliary clearance. Although the major structural components of human cilia have been described, a complete understanding of cilia function and regulation will require identification and characterization of all ciliary components. Estimates from studies o