Genetic mapping and exome sequencing identify variants associated with five novel diseases

The Clinic for Special Children (CSC) has integrated biochemical and molecular methods into a rural pediatric practice serving Old Order Amish and Mennonite (Plain) children. Among the Plain people, we have used single nucleotide polymorphism (SNP) microarrays to genetically map recessive disorders to large autozygous haplotype blocks (mean = 4.4 Mb) that contain many genes (mean = 79). For some, uninformative mapping or large gene lists preclude disease-gene identification by Sanger sequencing. Seven such conditions were selected for exome sequencing at the Broad Institute; all had been previously mapped at the CSC using low density SNP microarrays coupled with autozygosity and linkage analyses. Using between 1 and 5 patient samples per disorder, we identified sequence variants in the known disease-causing genes SLC6A3 and FLVCR1, and present evidence to strongly support the pathogenicity of variants identified in TUBGCP6, BRAT1, SNIP1, CRADD, and HARS. Our results reveal the power of coupling new genotyping technologies to population-specific genetic knowledge and robust clinical data.     

A Common variant near the melanocortin 4 receptor is associated with low-density lipoprotein cholesterol and total cholesterol in the Chinese Han population

A number of recent genome-wide association studies in European populations have reported that variant rs17782313 is significantly associated with obesity and body mass index (BMI). The purpose of the present study was to evaluate the association of rs17782313 with obesity and BMI in the Chinese Han population. We also sought to extend previous studies by determining whether this SNP is associated with plasma lipid levels in the Chinese Han population. Rs17782313 was genotyped in two independent Chinese Han cohorts (Cohort1: n = 2533; Cohort2: n = 2105). In our study, rs17782313 did not show significant association with either obesity or BMI in the Chinese Han population, but showed evidence for association with LDL-C (P ~ 0.003) and TC (P ~ 0.001). Our findings indicate that the variant rs17782313 near MC4R is likely to have an impact on plasma lipid levels of LDL-C and TC in the Chinese Han population.     

Fine mapping of quantitative trait loci using linkage disequilibria with closely linked marker loci

A multimarker linkage disequilibrium mapping method was developed for the fine mapping of quantitative trait loci (QTL) using a dense marker map. The method compares the expected covariances between haplotype effects given a postulated QTL position to the covariances that are found in the data. The expected covariances between the haplotype effects are proportional to the probability that the QTL position is identical by descent (IBD) given the marker haplotype information, which is calculated using the genedropping method. Simulation results showed that a QTL was correctly positioned within a region of 3, 1.5, or 0.75 cM in 70, 62, and 68%, respectively, of the replicates using markers spaced at intervals of 1, 0.5, and 0.25 cM, respectively. These results were rather insensitive to the number of generations since the QTL occurred and to the effective population size, except that 10 generations yielded rather poor estimates of the QTL position. The position estimates of this multimarker disequilibrium mapping method were more accurate than those from a single marker transmission disequilibrium test. A general approach for identifying QTL is suggested, where several stages of disequilibrium mapping are used with increasingly dense marker spacing.     

Incubation of acetylated low-density lipoprotein with cholesterol-rich dispersions enhances cholesterol uptake by macrophages

Incubation of J774 macrophages with mixtures of acetylated low-density lipoprotein (acLDL) and free cholesterol-rich phospholipid dispersions increases cellular cholesterol deposition 2-4-fold over that achieved with either acLDL or dispersions alone. Both free and esterified cholesterol accumulate in cells incubated with the mixture of acLDL and dispersions. A similar result is observed when acLDL is replaced by malondialdehyde-LDL. The enhanced deposition of cholesterol is not unique to J774 macrophages, as P388D1 macrophages also accumulate more cholesterol when incubated with the mixture of acLDL and dispersions than either particle alone. A preincubation of the particles for at least 6 h prior to incubation with cells is required in order to observe maximal cholesterol delivery. Both dispersion free cholesterol and phospholipid accumulate in J774 cells, suggesting that a complex is formed between acLDL and dispersions which results in a cholesterol-rich acLDL/dispersion particle. Partial purification of the acLDL-dispersion complex revealed increases in the size distribution of the particles compared to acLDL and increases in free cholesterol and phospholipid contents. Cholesterol uptake from the mixture of acLDL and dispersions was saturable and the enhanced cellular uptake of both cholesterol and phospholipid from the complex could be abolished by inhibitors of the scavenger receptor pathway. In addition to the receptor-mediated uptake of cholesterol from the acLDL-dispersion complex, it was observed that approx. 30% of the total cholesterol uptake from the complex was via non-specific components, including surface transfer.     

A unifying framework for evaluating the predictive power of genetic variants based on the level of heritability explained

An increasing number of genetic variants have been identified for many complex diseases. However, it is controversial whether risk prediction based on genomic profiles will be useful clinically. Appropriate statistical measures to evaluate the performance of genetic risk prediction models are required. Previous studies have mainly focused on the use of the area under the receiver operating characteristic (ROC) curve, or AUC, to judge the predictive value of genetic tests. However, AUC has its limitations and should be complemented by other measures. In this study, we develop a novel unifying statistical framework that connects a large variety of predictive indices together. We showed that, given the overall disease probability and the level of variance in total liability (or heritability) explained by the genetic variants, we can estimate analytically a large variety of prediction metrics, for example the AUC, the mean risk difference between cases and non-cases, the net reclassification improvement (ability to reclassify people into high- and low-risk categories), the proportion of cases explained by a specific percentile of population at the highest risk, the variance of predicted risks, and the risk at any percentile. We also demonstrate how to construct graphs to visualize the performance of risk models, such as the ROC curve, the density of risks, and the predictiveness curve (disease risk plotted against risk percentile). The results from simulations match very well with our theoretical estimates. Finally we apply the methodology to nine complex diseases, evaluating the predictive power of genetic tests based on known susceptibility variants for each trait.     

Functional mapping of quantitative trait loci associated with rice tillering

Several biologically significant parameters that are related to rice tillering are closely associated with rice grain yield. Although identification of the genes that control rice tillering and therefore influence crop yield would be valuable for rice production management and genetic improvement, these genes remain largely unidentified. In this study, we carried out functional mapping of quantitative trait loci (QTLs) for rice tillering in 129 doubled haploid lines, which were derived from a cross between IR64 and Azucena. We measured the average number of tillers in each plot at seven developmental stages and fit the growth trajectory of rice tillering with the Wang–Lan–Ding mathematical model. Four biologically meaningful parameters in this model––the potential maximum for tiller number (K), the optimum tiller time (t ₀), and the increased rate (r), or the reduced rate (c) at the time of deviation from t ₀––were our defined variables for multi-marker joint analysis under the framework of penalized maximum likelihood, as well as composite interval mapping. We detected a total of 27 QTLs that accounted for 2.49–8.54% of the total phenotypic variance. Nine common QTLs across multi-marker joint analysis and composite interval mapping showed high stability, while one QTL was environment-specific and three were epistatic. We also identified several genomic segments that are associated with multiple traits. Our results describe the genetic basis of rice tiller development, enable further marker-assisted selection in rice cultivar development, and provide useful information for rice production management.     

An investigation of five genetic loci controlling polymorphic variants in the red cells of goats

Results of a joint study carried out in South Africa and England to search for new genetic markers in the blood of goats are presented. Haemoglobin (Hb) phenotypes were reinvestigated with the technique of isoelectric focusing; frequencies in different goat breeds are given. Anaemic Hb type A, AB and B goats all produced a Hb C with an identical electrophoretic pattern. All goats tested had identical carbonic anhydrase (CA) types, but showed polymorphism of 'X' protein. Preliminary results indicated that nucleoside phosphorylase (NP) may be polymorphic.     

Fine mapping of the human biotinidase gene and haplotype analysis of five common mutations

Biotinidase deficiency is an autosomal recessive defect in the recycling of biotin that can lead to a variety of neurologic and cutaneous symptoms. The disease can be prevented or effectively treated with exogenous biotin. The biotinidase locus (BTD) has been maped to 3p25 by in situ hybridization. The gene has been cloned, the coding region sequenced, the genomic organization determined, and a spectrum of mutations has been characterized in more than 90 individuals with profound or partial biotinidase deficiency. We have conducted haplotype analysis of 10 consanguineous and 39 nonconsanguineous probands from the United States and 8 consanguineous probands from Turkey to localize BTD with respect to polymorphic markers on 3p and to investigate the origins of five common mutations. The inbred probands were homozygous for overlapping regions of 3p ranging in size from 1.1 to 80 cM which were flanked most narrowly by D3S1259 and D3S1293. Radiation hybrids and haplotype analysis of markers within this region suggest that BTD is located within a 0.1-cM region flanked by D3S3510 and D3S1286. The radiation hybrid data suggest that the BTD gene is oriented 5' to 3' between the centromere and the 3p telomere. Association studies indicate that the gene is closer to a third locus D3S3613 than D3S3510, two markers which cannot be resolved by existing linkage data. The BTD locus and D3S3613 must therefore lie between D3S3510 and D3S1286. Comparison of haplotypes reveals evidence for possible founder effects for four of the five common mutations.     

Lecithin:cholesterol acyltransferase reduces the adverse effects of oxidized low-density lipoprotein while incurring damage itself.

In this study, we tried to determine (a) whether there is any permanent effect of oxLDL on the LCAT molecule and its activator lipoprotein apoA-I, and (b) the fate of oxLDL after its exposure to LCAT and apoA-I. Purified LCAT and LDL/oxLDL was incubated at 37 degrees C for 1 h, and separated by gel-permeation chromatography. Its activity was significantly less (30% less) after separating from oxLDL compared to that of LDL. Cofactor activity of isolated apoA-I (incubated with LDL/oxLDL) was found affected by oxLDL. These results indicate modification of the LCAT and apoA-I molecule. But LCAT was found more affected compared to apoA-I in terms of LCAT activity. We are also reporting a novel function of LCAT. It was found to reduce the adverse effects of oxLDL, for example, ability to affect the LCAT activity and TBARS value. This ability of LCAT to repair oxLDL was dose-dependent. But there was no change in its REM values or fluorescence intensity.     

An investigation of five genetic loci controlling polymorphic variants in the red cells of goats*

Results of a joint study carried out in South Africa and England to search for new genetic markers in the blood of goats are presented. Haemoglobin (Hb) phenotypes were reinvestigated with the technique of isoelectric focusing; frequencies in different goat breeds are given. Anaemic Hb type A, AB and B goats all produced a Hb C with an identical electrophoretic pattern. All goats tested had identical carbonic anhydrase (CA) types, but showed polymorphism of ‘X’ protein. Preliminary results indicated that nucleoside phosphorylase (NP) may be polymorphic.     

Recycling of apoprotein E is associated with cholesterol efflux and high density lipoprotein internalization

After receptor-mediated endocytosis of triglyceride-rich lipoproteins (TRL) into the liver, TRL particles are immediately disintegrated in peripheral endosomal compartments. Whereas core lipids and apoprotein B are delivered for degradation into lysosomes, TRL-derived apoE is efficiently recycled back to the plasma membrane. This is followed by apoE re-secretion and association of apoE with high density lipoproteins (HDL). Because HDL and apoE can independently promote cholesterol efflux, we investigated whether recycling of TRL-derived apoE in human hepatoma cells and fibroblasts could be linked to intracellular cholesterol transport. In this study we demonstrate that HDL(3) does not only act as an extracellular acceptor for recycled apoE but also stimulates the recycling of internalized TRL-derived apoE. Furthermore, radioactive pulse-chase experiments indicate that apoE recycling is accompanied by cholesterol efflux. Confocal imaging reveals co-localization of apoE and cholesterol in early endosome antigen 1-positive endosomes. During apoE re-secretion, HDL(3)-derived apoA-I is found in these early endosome antigen 1, cholesterol-containing endosomes. As shown by time-lapse fluorescence microscopy, apoE recycling involves the intracellular trafficking of apoA-I to pre-existing and TRL-derived apoE/cholesterol-containing endosomes in the periphery. Thus, these studies provide evidence for a new intracellular link between TRL-derived apoE, cellular cholesterol transport, and HDL metabolism.     

Mouse centromere mapping using oligonucleotide probes that detect variants of the minor satellite

Cytologically, the centromere is found at the very end of most Mus musculus chromosomes, co-localizing with an array of minor satellite sequences. It is separated from the euchromatin of the long arm by a large domain of heterochromatin, composed in part of arrays of major satellite sequences. We used oligonucleotide probes that specifically detect regions of sequence variation found in certain cloned minor satellite sequences. They detect a limited subset of the minor satellite arrays in the mouse genome, based on both pulsed-field gel electrophoresis and in situ hybridization data, and provide direct molecular genetic markers for individual centromeres in some inbred mouse strains. Array size polymorphisms detected by these probes map to positions consisten with the centromeres of chromosomes 1 and 14 in the BXD recombinant inbred (RI) strains. The genetic distances between these minor satellite arrays and loci on the long arms of chromosomes 1 and 14 are consistent with repression of meiotic recombination in the heterochromatic domains separating them. The existence of chromosome-specific minor satellite sequences implies that the rate of sequence exchange between non-homologous chromosomes relative to the rate between homologous chromosomes is much lower than has previously been postulated. We suggest that the high degree of sequence homogeneity of mouse satellite sequences may instead reflect recent common ancestry.     

Molecular studies of pH-dependent ligand interactions with the low-density lipoprotein receptor

The release of ligand from the low-density lipoprotein receptor (LDLR) has been postulated to involve a "histidine switch"-induced intramolecular rearrangement that discharges bound ligand. A recombinant soluble low-density lipoprotein receptor (sLDLR) was employed in ligand binding experiments with a fluorescently tagged variant apolipoprotein E N-terminal domain (apoE-NT). Binding was monitored as a function of fluorescence resonance energy transfer (FRET) from excited Trp residues in sLDLR to an extrinsic fluorophore covalently attached to Trp-null apoE3-NT. In binding experiments with wild-type (WT) sLDLR, FRET-dependent AEDANS fluorescence decreased as the pH was lowered. To investigate the role of His190, His562, and His586 in sLDLR in pH-dependent ligand binding and discharge, site-directed mutagenesis studies were performed. Compared to WT sLDLR, triple His --> Ala mutant sLDLR displayed attenuated pH-dependent ligand binding and a decreased level of ligand release as a function of low pH. When these His residues were substituted for Lys, the positively charged side chain of which does not ionize over this pH range, ligand binding was nearly abolished at all pH values. When sequential His to Lys mutants were examined, the evidence suggested that His562 and His586 function cooperatively. Whereas the sedimentation coefficient for WT sLDLR increased when the pH was reduced from 7 to 5, no such change occurred in the case of the triple Lys mutant receptor or a His562Lys/His586Lys double mutant receptor. The data support the existence of a cryptic, histidine side chain ionization-dependent alternative ligand that modulates ligand discharge via conformational reorganization.     

Association of low-density lipoprotein with particulate connective tissue matrix components enhances cholesterol accumulation in cultured subendothelial cells of human aorta

Low-density lipoproteins (LDL) were incubated with elastin particles, collagenase-resistant debris isolated from human aorta, and latex beads of 1.13 microns in diameter. As a result of incubation, insoluble LDL-associates were formed. These associates, as well as LDL-heparin-fibronectin-gelatin complexes described by other workers, were added to a 7-day primary culture of enzyme-isolated cells of human aortic subendothelial intima. The culture contained a mixed cell population made up mostly of typical and modified smooth muscle cells. 24 h later, total cholesterol, phospholipid, triacylglycerol, free cholesterol and cholesteryl ester levels were measured. Addition of insoluble LDL-complexes as well as LDL-associates to culture brought about a substantial accumulation of intracellular lipids; primarily, cholesteryl esters. The total cholesterol level in cultured cells was raised 3- to 8-fold. Addition of free LDL or LDL-free particles had no effect on the content of intracellular lipids. The results obtained allow the assumption that the occurrence of the LDL-mediated accumulation of intracellular lipids is due mainly to the LDL penetration inside the cell via 'nonspecific' phagocytosis and not through a regulated receptor-dependent pathway.