Genetics of congenital heart defects: a candidate gene approach

By using a candidate gene approach, we have identified novel single-nucleotide polymorphisms specific to patients diagnosed with atrioventricular valve and septum defects. Here we discuss how the gene products, in which these polymorphisms were found, functionally interact to regulate endocardial cushion formation during embryo development. These findings support a model in which mutations in different genes but regulating the same process can cause or make one more susceptible to developing atrioventricular valve and septum defects.     

Genetic and physical mapping of the Lps locus: identification of the toll-4 receptor as a candidate gene in the critical region

On the basis of 2093 meioses analyzed in two separate intraspecific backcrosses, the location of the mouse Lpsd mutation was circumscribed to a genetic interval 0.9 cM in size. A total of 19 genetic markers that lie in close proximity to the mutation were examined in mapping. Most of these were previously unpublished polymorphic microsatellites, identified by fragmentation of YAC and BAC clones spanning the region of interest. Lpsd was found to be inseparable from the microsatellite marker D4MIT178, and from three novel polymorphic microsatellites identified near D4MIT178. The mutation was confined between two novel microsatellite markers, herein designated "B" and "83.3." B lies centromeric to the mutation, and was separated by four crossovers in a panel of 1600 mice; 83.3 lies distal to the mutation and was separated by three crossovers in a panel of 493 mice. 66 BAC clones and one YAC clone were assembled to cover > 95% of the critical region. Estimates based on pulsed field gel electrophoresis and fluorescence in situ hybridization indicate that the The B-->83.3 interval is about 3.2 Mb in length. A minimal area of zero recombinational distance from Lpsd was also assigned, and found to occupy approximately 1.2 Mb of physical size. To identify gene candidates, nearly 40,000 sequencing runs were performed across the critical region. Selective hybridization and exon trapping were also employed to identify genes throughout the "zero" region. Only a single intact gene was identified within the entire critical region. This gene encodes the Toll-4 receptor, a member of the IL-1 receptor family.     

cDNA cloning and gene mapping of a candidate human cell cycle checkpoint protein.

A family of proteins involved in cell cycle progression, DNA recombination, and the detection of DNA damage has been recently identified. One of the members of this family, human ATM, is defective in the cells of patients with ataxia telangiectasia and is involved in detection and response of cells to damaged DNA. Other members include Mei-41 (Drosophila melanogaster), Mec1p (Saccharomyces cerevisiae), and Rad3 (Schizosaccharomyces pombe), which are required for the S and G2/M checkpoints, as well as FRAP (Homo sapiens) and Torl/2p (S. cerevisiae), which are involved in a rapamycin-sensitive pathway leading to G1 cell cycle progression. We report here the cloning of a human cDNA encoding a protein with significant homology to members of this family. Three overlapping clones isolated from a Jurkat T-cell cDNA library revealed a 7.9-kb open reading frame encoding a protein that we have named FRP1 (FRAP-related protein) with 2644 amino acids and a predicted molecular mass of 301 kDa. Using fluorescence in situ hybridization and a full-length cDNA FRP1 clone, the FRP1 gene has been mapped to the chromosomal locus 3q22-q24. FRP1 is most closely related to three of the PIK-related kinase family members involved in checkpoint function--Mei-41, Mec1p, and Rad3--and as such may be the functional human counterpart of these proteins.     

Structural gene identification and mapping by DNA-mRNA hybrid-arrested cell-free translation.

We present a simple method for directly correlating structural gene sequences in DNA with their corresponding mRNAs. This is based upon the fact that mRNA hybridized with its complementary DNA will not direct the cell-free synthesis of a complete polypeptide. Full translational activity of the mRNA is recovered upon the heat melting of the hybrid. Utilizing the rabbit beta globin clone PbetaG1, we demonstrate the application of hybrid-arrested translation for the identification of structural gene sequences within recombinant DNA molecules. In addition, the method is used to locate and order precisely several adenovirus 2 polypeptides within the viral genome.     

An antisense approach to phenotype-based gene cloning in Tetrahymena

We report a pioneering approach using Tetrahymena thermophila that permits rapid identification of genes based on their null or hypomorphic phenotypes. This technique involves cell transformation with a library of plasmids that encode 26S ribosomal subunits containing short insertions. The insertions correspond to antisense sequences for a large number of genes. The majority of cells each acquires a single antisense sequence, which silences a single genomic locus. Because the insertion site within the ribosomal sequence is known, the silenced gene is easily amplified. We demonstrate that this approach can be used to identify genes required for dense core granule exocytosis.     

An alternative approach to somatic cell gene therapy.

Mouse primary skin fibroblasts were infected with a recombinant retrovirus containing human factor IX cDNA. Bulk infected cells capable of synthesizing and secreting biologically active human factor IX protein were embedded in collagen, and the implant was grafted under the epidermis. Sera from the transplanted mice contain human factor IX protein for at least 10-12 days. Loss of immunoreactive human factor IX protein in the mouse serum is not due to graft rejection. Instead, the mouse serum contains anti-human factor IX antibodies, which react with the protein. We suggest that retroviral-infected primary skin fibroblasts offer an alternative approach to somatic cell gene therapy.     

An integrated approach for identifying and mapping human genes.

We have developed a method for generating expressed-sequence maps of human chromosomes. The method involves several steps that begin with libraries of highly representative short cDNAs prepared by using random oligomers as primers. The cDNA inserts are amplified by PCR with flanking vector primers. Chromosomal region-specific cDNA packets are prepared by hybridization of the cDNA inserts to DNA derived from yeast artificial chromosomes (YACs) assigned to defined regions of human chromosomes. The cDNA packets are cloned into yeast chromosome fragmentation vectors and used for transformation of yeast bearing the YAC used for affinity purification. Sequences in the cDNAs undergo homologous recombination with the corresponding exons in the genomic DNA yielding a set of truncated YACs. Each unique truncation specifies the location of an exon in the YAC. Since all of the truncation events end with the same vector sequence, it is possible to rescue and sequence these ends to generate expressed sequence tags. The method couples rapid purification of region-specific cDNAs with precise mapping of their genes on YACs. Appropriately truncated YACs also provide easy access to gene regulatory sequences. We describe the feasibility of individual steps of the method using the factor IX (F9) gene as a model system and we present the mapping of several expressed sequences corresponding to a 330-kb YAC containing DNA from human chromosome 6p21. In addition, we obtained the sequence, including an intron-exon junction, flanking a particular truncation event.     

Genetics of inflammatory bowel disease. The candidate gene approach: susceptibility versus disease heterogeneity

Ulcerative colitis and Crohn's disease are complex diseases of unknown etiology. Several genes are involved in the susceptibility. These genes are necessary to suffer from these diseases but not sufficient. Environmental factors trigger the inflammatory response. Evidence is accumulating that this response is abnormal in these patients. Therefore, the study of genes that are involved in the regulation of the inflammation may help to clarify the pathogenesis of the disease. The working hypothesis is that HLA and cytokine gene polymorphisms, of extreme importance in the regulation of inflammation, contribute to determining the heterogeneity of the disease and the prognosis. In this case, the candidate genes are those involved in the regulation of the immune response of the host. These studies may be of great importance in the tailoring of an appropriate treatment for particular subgroups of patients. A premise for the success of these studies is to use a solid classification, which should take into account the dynamic process and the natural evolution of the disease; to use a carefully selected and ethnically matched group of healthy controls, and to use the advanced molecular biological typing techniques. In the present article, this concept is explored by taking into account some of the recent findings obtained with the HLA and cytokine gene polymorphisms in inflammatory bowel diseases. The results support the concept that these gene polymorphisms are of greater importance in determining the severity of the disease than in determining the susceptibility to suffer from the disease. From this point of view, these studies are complementary and a necessary addition to studies using the whole genome approach in the effort to understand the genetics of these chronic multifactorial diseases.     

Genetic factors in addiction: QTL mapping and candidate gene studies implicate GABAergic genes in alcohol and barbiturate withdrawal in mice

Quantitative trait locus (QTL) mapping has allowed dramatic progress toward the detection and chromosome mapping of minor and major gene loci involved in murine responses to alcohol and other drugs of abuse. Here we focus on the identification of QTLs for one particular trait relevant to addiction, drug withdrawal following acute or chronic drug administration. To date, five significant QTLs ( p < 5 × 10 ^-5) and six suggestive QTLs ( p < 0.001) have been mapped to specific murine chromosomes for alcohol and pentobarbital withdrawal, indicating the presence of a relevant gene or genes at each location. Overlapping QTLs for alcohol withdrawal and pentobarbital withdrawal are identified on murine chromosomes 1, 4, and 11, and may detect the influence of common genes. For many QTLs, candidate genes with relevant neurobiological function lie within the mapped region. Notably, several QTLs for alcohol and pentobarbital withdrawal are in proximity to genes that directly or indirectly affect GABA _A receptor-mediated transmission, which has been implicated in some of the actions of alcohol and other drugs. These include a cluster of GABA _A receptor genes and genes encoding the enzymes steroid 5α-reductase-1 (involved in biosynthesis of the neuroactive steroid allopregnanolone) and glutamic acid decarboxylase-1 (involved in GABA biosynthesis). This paper will discuss data that examines the involvement of GABAergic genes in withdrawal and other drug responses, including genetic variation in gene sequence, expression and function.     

Genetic determinants of hypertension: identification of candidate phenotypes

Our long-term objective is to identify genes whose expression results in hypertension and in phenotypic changes that may contribute to hypertension. The purpose of the present study was to describe evidence for the heritability of hypertension-related phenotypes in hypertensive, hyperlipidemic black sib pairs. Outpatient anthropomorphic measurements were obtained in >200 affected sib pairs. In addition, 68 of these sib pairs were studied under controlled, standardized conditions at an inpatient clinical research center while off both antihypertensive and lipid-lowering medications. Heritability was estimated on the basis of sib-sib correlations and with an association model. Higher heritability estimates for blood pressure were observed with multiple measurements averaged over 24 hours than with measurements at a single time point, and heritability estimates for nighttime blood pressures were higher than those for daytime blood pressures. Heritability estimates for several of the phenotypes were augmented by obtaining measurements in response to a standardized stimulus, including (1) blood pressure responses to the assumption of upright posture, standardized psychological stress, and norepinephrine infusion; (2) plasma renin, aldosterone, epinephrine, and cAMP and cGMP responses to the assumption of upright posture; (3) para-aminohippurate and inulin clearances in response to norepinephrine infusion; and (4) plasma arginine vasopressin in response to NaCl infusion. High heritability estimates were also observed for various measures of body size and body fat, left ventricular size, cardiac index, stroke volume, total peripheral resistance, and serum concentrations of LDL and HDL cholesterol and leptin. These heritability estimates identify the hypertension-related phenotypes that may facilitate the identification of specific genetic determinants of hypertension in blacks with hyperlipidemia.     

Brachial approach to NOGA-guided procedures: electromechanical mapping and transendocardial stem-cell injections

Several methods are available for delivering stem cells to the heart. Recent studies have highlighted the advantages of injecting the cells directly into the myocardium in order to increase myocardial retention of cells. A particular focus has been on percutaneous transendocardial injection, facilitated by electromechanical mapping.The NOGA XP Cardiac Navigation System has a multicomponent catheter that is designed to guide and deliver transendocardial injections via a transfemoral approach, without a guidewire. However, this method may not be feasible in some patients who have peripheral vascular disease. Herein, we describe the case of a 68-year-old man whose tortuous, sharply angled iliac arteries precluded a femoral approach to transendocardial injection. To overcome the anatomic and mechanical challenges, we used a brachial approach. We believe that this is the 1st report of using the brachial route for transendocardial injection, and that it can be a viable alternative to the transfemoral approach in selected patients.     

Genome-wide association mapping to candidate polymorphism resolution in the unsequenced barley genome

Although commonplace in human disease genetics, genome-wide association (GWA) studies have only relatively recently been applied to plants. Using 32 phenotypes in the inbreeding crop barley, we report GWA mapping of 15 morphological traits across ～500 cultivars genotyped with 1,536 SNPs. In contrast to the majority of human GWA studies, we observe high levels of linkage disequilibrium within and between chromosomes. Despite this, GWA analysis readily detected common alleles of high penetrance. To investigate the potential of combining GWA mapping with comparative analysis to resolve traits to candidate polymorphism level in unsequenced genomes, we fine-mapped a selected phenotype (anthocyanin pigmentation) within a 140-kb interval containing three genes. Of these, resequencing the putative anthocyanin pathway gene HvbHLH1 identified a deletion resulting in a premature stop codon upstream of the basic helix-loop-helix domain, which was diagnostic for lack of anthocyanin in our association and biparental mapping populations. The methodology described here is transferable to species with limited genomic resources, providing a paradigm for reducing the threshold of map-based cloning in unsequenced crops.     

Combining linkage and association mapping identifies RECEPTOR-LIKE PROTEIN KINASE1 as an essential Arabidopsis shoot regeneration gene

De novo shoot organogenesis (i.e., the regeneration of shoots on nonmeristematic tissue) is widely applied in plant biotechnology. However, the capacity to regenerate shoots varies highly among plant species and cultivars, and the factors underlying it are still poorly understood. Here, we evaluated the shoot regeneration capacity of 88 Arabidopsis thaliana accessions and found that the process is blocked at different stages in different accessions. We show that the variation in regeneration capacity between the Arabidopsis accessions Nok-3 and Ga-0 is determined by five quantitative trait loci (QTL): REG-1 to REG-5. Fine mapping by local association analysis identified RECEPTOR-LIKE PROTEIN KINASE1 (RPK1), an abscisic acid-related receptor, as the most likely gene underlying REG-1, which was confirmed by quantitative failure of an RPK1 mutation to complement the high and low REG-1 QTL alleles. The importance of RPK1 in regeneration was further corroborated by mutant and expression analysis. Altogether, our results show that association mapping combined with linkage mapping is a powerful method to discover important genes implicated in a biological process as complex as shoot regeneration.The capacity to regenerate in vitro adventitious shoots is of major importance for biotechnological breeding and commercial in vitro initiation and propagation of plants. Unfortunately, shoot regeneration is not always easy to achieve: among plant species, varieties, and cultivars, it is highly variable and currently unpredictable. The impact of shoot regeneration for horticulture and agriculture is illustrated by the numerous studies that assess the natural allelic variation and map quantitative trait loci (QTL) for the regeneration capacity in diverse crops, such as tomato (Solanum lycopersicum), wheat (Triticum aestivum), rice (Oryza sativa), barley (Hordeum vulgare), sunflower (Helianthus annuus), cabbage (Brassica oleracea), and potato (Solanum tuberosum) (1–12). However, it is difficult to draw general conclusions from these studies because of the low-resolution linkage maps and little detailed knowledge about gene functions in these crops.Therefore, the use of the model plant Arabidopsis thaliana is more appropriate. In a widely applied two-step regeneration procedure, root explants are first incubated on an auxin-rich callus-inducing medium (CIM) and subsequently transferred to a cytokinin-rich shoot-inducing medium (SIM) (13). Genome-wide analyses of the gene expression profiles accompanying the successive steps in the regeneration process revealed multiple key regulators and genes implicated in phytohormonal signaling during shoot regeneration (14–18). Reporter gene fusions with marker genes allowed visualization of their spatiotemporal expression patterns during regeneration, contributing to the elucidation of the function of important shoot-related genes, such as CUP SHAPED COTYLEDON1, CUP SHAPED COTYLEDON2, SHOOT MERISTEMLESS, WUSCHEL (WUS), and CLAVATA3 (14, 19–22). By means of classical forward and reverse genetics approaches, additional genes involved in shoot regeneration have been identified (23).Shoot regeneration in Arabidopsis has also been studied by QTL mapping with recombinant inbred lines (RILs) of Ler × Col (24, 25) or Ler × Cvi (26). These studies revealed multiple QTL, but thus far, no quantitative trait gene (QTG) or quantitative trait nucleotide (QTN) responsible for any of these QTL has been reported. Indeed, linkage mapping studies often fail to identify the causal gene because of their limiting mapping resolution (27).Recently, genome-wide association studies with an increased mapping resolution have received much attention for the identification of QTL in plants, particularly in Arabidopsis, as an alternative to or combined with linkage mapping approaches (28–31). Here, we aimed at identifying QTGs underlying the natural shoot regeneration variation in Arabidopsis by using linkage mapping complemented with association mapping. Furthermore, early parameters, such as callus and root formation, explant greenness, and shoot primordia development, were examined in a set of 88 Arabidopsis accessions. We calculated pairwise correlations between the different parameters and shoot formation to assess whether the early observations could predict regeneration. We phenotyped 86 RILs derived from a cross of Nok-3 and Ga-0, accessions with high- and low-regeneration abilities, respectively, and mapped five regeneration QTL. A local association mapping revealed that RECEPTOR-LIKE PROTEIN KINASE1 (RPK1) is the most likely gene underlying the major QTL REG-1, which was supported by mutant analysis and a quantitative complementation test.     

Admixture mapping as a gene discovery approach for complex human traits and diseases

Admixture mapping (AM) is a special form of conventional meiotic or recombination mapping for disease gene discovery in humans that exploits naturally occurring genetic and phenotypic differences existing in populations between which recent gene flow has occurred. Essentially, mates from two different "parental" populations with different allelic and disease-predisposing mutation profiles will produce "admixed" offspring whose genomes will be mixtures of the genomes associated with the parental populations. Strong linkage disequilibrium (LD) will exist for several generations between neighboring loci of admixed individuals and can be exploited for identifying the genomic location of trait-influencing loci. Although it may be a very clever strategy for identifying genes that influence human traits and diseases, AM can be problematic. We review the foundations, basic strategies, resources, and settings necessary for AM. We conclude that AM has potential in the identification of disease-predisposing loci, but this potential may only exist in a limited number of realistic settings.     

Conserved sequence-tagged sites: a phylogenetic approach to genome mapping.

Cognate sites in genomes that diverged approximately 100 million years ago can be detected by PCR assays based on primer pairs from unique sequences. The great majority of such syntenically equivalent sequence-tagged sites (STSs) from human DNA can be used to assemble and format corresponding maps for other primates, and some based on gene sequences are shown to be useful for mouse and rat as well. Universal genomic mapping strategies may be possible by using sets of STSs common to many mammalian species.