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PubMed2004

The genomes of recombinant inbred lines.

Recombinant inbred lines (RILs) can serve as powerful tools for genetic mapping. Recently, members of the Complex Trait Consortium proposed the development of a large panel of eight-way RILs in the mouse, derived from eight genetically diverse parental strains. Such a panel would be a valuable community resource. The use of such eight-way RILs will require a detailed understanding of the relationship between alleles at linked loci on an RI chromosome. We extend the work of Haldane and Waddington on two-way RILs and describe the map expansion, clustering of breakpoints, and other features of the genomes of multiple-strain RILs as a function of the level of crossover interference in meiosis.

Alleles↗
PubMed2005

DNA sequence variation and selection of tag single-nucleotide polymorphisms at candidate genes for drought-stress response in Pinus taeda L.

Genetic association studies are rapidly becoming the experimental approach of choice to dissect complex traits, including tolerance to drought stress, which is the most common cause of mortality and yield losses in forest trees. Optimization of association mapping requires knowledge of the patterns of nucleotide diversity and linkage disequilibrium and the selection of suitable polymorphisms for genotyping. Moreover, standard neutrality tests applied to DNA sequence variation data can be used to select candidate genes or amino acid sites that are putatively under selection for association mapping. In this article, we study the pattern of polymorphism of 18 candidate genes for drought-stress response in Pinus taeda L., an important tree crop. Data analyses based on a set of 21 putatively neutral nuclear microsatellites did not show population genetic structure or genomewide departures from neutrality. Candidate genes had moderate average nucleotide diversity at silent sites (pi(sil) = 0.00853), varying 100-fold among single genes. The level of within-gene LD was low, with an average pairwise r2 of 0.30, decaying rapidly from approximately 0.50 to approximately 0.20 at 800 bp. No apparent LD among genes was found. A selective sweep may have occurred at the early-response-to-drought-3 (erd3) gene, although population expansion can also explain our results and evidence for selection was not conclusive. One other gene, ccoaomt-1, a methylating enzyme involved in lignification, showed dimorphism (i.e., two highly divergent haplotype lineages at equal frequency), which is commonly associated with the long-term action of balancing selection. Finally, a set of haplotype-tagging SNPs (htSNPs) was selected. Using htSNPs, a reduction of genotyping effort of approximately 30-40%, while sampling most common allelic variants, can be gained in our ongoing association studies for drought tolerance in pine.

Base Sequence↗
PubMed2005

Patterns of nucleotide diversity in wild and cultivated sunflower.

Interest in the level and organization of nucleotide diversity in domesticated plant lineages has recently been motivated by the potential for using association-based mapping techniques as a means for identifying the genes underlying complex traits. To date, however, such data have been available only for a relatively small number of well-characterized plant taxa. Here we provide the first detailed description of patterns of nucleotide polymorphism in wild and cultivated sunflower (Helianthus annuus), using sequence data from nine nuclear genes. The results of this study indicate that wild sunflower harbors at least as much nucleotide diversity as has been reported in other wild plant taxa, with randomly selected sequence pairs being expected to differ at 1 of every 70 bp. In contrast, cultivated sunflower has retained only 40-50% of the diversity present in the wild. Consistent with this dramatic reduction in polymorphism, a phylogenetic analysis of our data revealed that the cultivars form a monophyletic clade, adding to the growing body of evidence that sunflower is the product of a single domestication. Eight of the nine loci surveyed appeared to be evolving primarily under purifying selection, while the remaining locus may have been the subject of positive selection. Linkage disequilibrium (LD) decayed very rapidly in the self-incompatible wild sunflower, with the expected LD falling to negligible levels within 200 bp. The cultivars, on the other hand, exhibited somewhat higher levels of LD, with nonrandom associations persisting up to approximately 1100 bp. Taken together, these results suggest that association-based approaches will provide a high degree of resolution for the mapping of functional variation in sunflower.

Base Pairing↗
PubMed2006

Segregating variation in the transcriptome: cis regulation and additivity of effects.

Properties of genes underlying variation in complex traits are largely unknown, especially for variation that segregates within populations. Here, we evaluate allelic effects, cis and trans regulation, and dominance patterns of transcripts that are genetically variable in a natural population of Drosophila melanogaster. Our results indicate that genetic variation due to the third chromosome causes mainly additive and nearly additive effects on gene expression, that cis and trans effects on gene expression are numerically about equal, and that cis effects account for more genetic variation than do trans effects. We also evaluated patterns of variation in different functional categories and determined that genes involved in metabolic processes are overrepresented among variable transcripts, but those involved in development, transcription regulation, and signal transduction are underrepresented. However, transcripts for proteins known to be involved in protein-protein interactions are proportionally represented among variable transcripts.

Animals↗
PubMed2006

Fine-scale map of encyclopedia of DNA elements regions in the Korean population.

The International HapMap Project aims to generate detailed human genome variation maps by densely genotyping single-nucleotide polymorphisms (SNPs) in CEPH, Chinese, Japanese, and Yoruba samples. This will undoubtedly become an important facility for genetic studies of diseases and complex traits in the four populations. To address how the genetic information contained in such variation maps is transferable to other populations, the Korean government, industries, and academics have launched the Korean HapMap project to genotype high-density Encyclopedia of DNA Elements (ENCODE) regions in 90 Korean individuals. Here we show that the LD pattern, block structure, haplotype diversity, and recombination rate are highly concordant between Korean and the two HapMap Asian samples, particularly Japanese. The availability of information from both Chinese and Japanese samples helps to predict more accurately the possible performance of HapMap markers in Korean disease-gene studies. Tagging SNPs selected from the two HapMap Asian maps, especially the Japanese map, were shown to be very effective for Korean samples. These results demonstrate that the HapMap variation maps are robust in related populations and will serve as an important resource for the studies of the Korean population in particular.

Asian People↗
PubMed2006

Relaxed significance criteria for linkage analysis.

Linkage analysis involves performing significance tests at many loci located throughout the genome. Traditional criteria for declaring a linkage statistically significant have been formulated with the goal of controlling the rate at which any single false positive occurs, called the genomewise error rate (GWER). As complex traits have become the focus of linkage analysis, it is increasingly common to expect that a number of loci are truly linked to the trait. This is especially true in mapping quantitative trait loci (QTL), where sometimes dozens of QTL may exist. Therefore, alternatives to the strict goal of preventing any single false positive have recently been explored, such as the false discovery rate (FDR) criterion. Here, we characterize some of the challenges that arise when defining relaxed significance criteria that allow for at least one false positive linkage to occur. In particular, we show that the FDR suffers from several problems when applied to linkage analysis of a single trait. We therefore conclude that the general applicability of FDR for declaring significant linkages in the analysis of a single trait is dubious. Instead, we propose a significance criterion that is more relaxed than the traditional GWER, but does not appear to suffer from the problems of the FDR. A generalized version of the GWER is proposed, called GWERk, that allows one to provide a more liberal balance between true positives and false positives at no additional cost in computation or assumptions.

Algorithms↗
PubMed2006

Haplotype probabilities for multiple-strain recombinant inbred lines.

Recombinant inbred lines (RIL) derived from multiple inbred strains can serve as a powerful resource for the genetic dissection of complex traits. The use of such multiple-strain RIL requires a detailed knowledge of the haplotype structure in such lines. Broman (2005) derived the two- and three-point haplotype probabilities for 2(n)-way RIL; the former required hefty computation to infer the symbolic results, and the latter were strictly numerical. We describe a simpler approach for the calculation of these probabilities, which allowed us to derive the symbolic form of the three-point haplotype probabilities. We also extend the two-point results for the case of additional generations of intermating, including the case of 2(n)-way intermated recombinant inbred populations (IRIP).

Animals↗
PubMed2006

An integrated in silico gene mapping strategy in inbred mice.

In recent years in silico analysis of common laboratory mice has been introduced and subsequently applied, in slightly different ways, as a methodology for gene mapping. Previously we have demonstrated some limitation of the methodology due to sporadic genetic correlations across the genome. Here, we revisit the three main aspects that affect in silico analysis. First, we report on the use of marker maps: we compared our existing 20,000 SNP map to the newly released 140,000 SNP map. Second, we investigated the effect of varying strain numbers on power to map QTL. Third, we introduced a novel statistical approach: a cladistic analysis, which is well suited for mouse genetics and has increased flexibility over existing in silico approaches. We have found that in our examples of complex traits, in silico analysis by itself does fail to uniquely identify quantitative trait gene (QTG)-containing regions. However, when combined with additional information, it may significantly help to prioritize candidate genes. We therefore recommend using an integrated work flow that uses other genomic information such as linkage regions, regions of shared ancestry, and gene expression information to obtain a list of candidate genes from the genome.

Algorithms↗
PubMed2006

Identification of atherosclerosis-modifying genes: pathogenic insights and therapeutic potential.

Atherosclerosis is a common, complex trait, with genetic variation in many genes and the environment contributing to risk for this condition, which has multiple and highly variable phenotypic manifestations. Progress has been made in the identification of atherosclerosis-modifying genes in both human studies and through the use of animal models. In the future, it may be possible to administer a genetic test for variation in a handful of the most common atherosclerosis-modifier genes, and thus predict if a patient is likely to develop atherosclerosis and ischemic heart disease. These patients could then be treated aggressively to lower their low-density lipoprotein cholesterol levels and other risk factors, including counseling to make adjustments in their lifestyle. This review will summarize the methods and results thus far in the identification of atherosclerosis-modifier genes.

Animals↗
PubMed2005

Genetic hypercalciuria.

Hypercalciuria is an important, identifiable, and reversible risk factor in stone formation. The foremost and most fundamental step in dissecting the genetics of hypercalciuria is understanding its pathophysiology. Hypercalciuria is a complex trait. This article outlines the various factors that compromise the attempt to dissect the genetics of hypercalciuria, summarizes the clinical and experimental monogenic causes of hypercalciuria, and outlines the initial results from attempts in studying polygenic hypercalciuria. Finally, the problem is set in perspective of the current database, technologic advances and limitations are highlighted, and prospects of further advances in the field are speculated upon.

Animals↗
PubMed1991

Assessing the role of APNH, a gene encoding for a human amiloride-sensitive Na+/H+ antiporter, on the interindividual variation in red cell Na+/Li+ countertransport.

The "reverse genetic" approach to essential hypertension is complicated by the fact that blood pressure is a heterogeneous, quantitative, complex trait. One strategy is to use "intermediate phenotypes" that are not only associated with hypertension but that also have a simple mode of inheritance, compatible with the action of a single gene. Red cell sodium-lithium countertransport (SLC) is one of the best characterized intermediate phenotypes for hypertension. The similarity in stoichiometry and kinetics between SLC and Na+/H+ exchange has led to the proposal that the gene encoding the Na+/H+ antiporter (APNH) may be responsible for the individual variance in SLC. We have tested this hypothesis by both an association study and Haseman and Elston's sib pair method of linkage analysis, by using a polymorphism at the APNH locus detected by denaturing gradient gel electrophoresis. Both analytical techniques were performed before and after correction of SLC values for known covariates. There was no significant association between mean SLC values and any of the three possible genotypes of the APNH locus either before or after regressing out covariates (F = 0.64 and P greater than 0.52; F = 0.63 and P greater than 0.53, respectively). Linkage analysis similarly failed to demonstrate a relationship between the squared difference in SLC values and the identity by descent status for APNH as well as other loci that map close to APNH (D1S57, RH, and ALPL). Taking these results together, we conclude that mutations at the APNH locus are not responsible for the observed variation in SLC values.

Amiloride↗
PubMed2026

Partitioned blood pressure polygenic risk reveals differential genetic effects of tissue-specific enhancers and their interactions on cardiovascular disease.

Polygenic risk scores (PRS) compress genome-wide associations into a single predictor, but this aggregation obscures the distinct biological mechanisms through which genetic variation shapes complex traits. Here we introduce a framework that additively decomposes a trait's PRS, without loss of SNP heritability, into independent components defined by the tissue-specific and tissue-agnostic cis-regulatory elements (CREs) in which its variants act. Applied to blood pressure (BP) using ~0.5 million CREs across four BP-relevant tissues (adrenal gland, artery, heart, kidney), the framework reveals that regulatory effects are globally additive across tissues yet locally non-additive, and that the resulting partitioned scores carry pronounced, reproducible heterogeneity in their effects on BP and cardiovascular outcomes. We show this heterogeneity reflects gene-environment interactions, and trace one example to its mechanism: a kidney-CRE-partitioned score is protective against coronary artery disease and myocardial infarction through an interaction between ATP2B1 and antihypertensive medication. Explicitly modeling these interactions improves prediction and transferability, and tissue-focused partitioning increases power to resolve causal genes and reveals genes such as ADAMTS8 with antagonistic effects across BP components. Validated in an independent All of Us cohort, these findings recast the PRS from a blunt aggregate predictor into a mechanistic probe of context-dependent genetic architecture.

Journal Article↗
PubMed2002

fRFLP and fAFLP: medium-throughput genotyping by fluorescently post-labeling restriction digestion.

Genome-scale studies of population structure and high-resolution mapping of genetically complex traits both require techniques for accurately and efficiently genotyping large numbers of polymorphic sites in multiple individuals. Many high-throughput genotyping technologies require the purchase of expensive equipment or consumables and are therefore out of reach of some individual research laboratories. Conversely, less expensive technologies are often labor intensive so that the effort involved in typing large numbers of samples or polymorphic sites is prohibitive. Here we present a method of fluorescently post-labeling restriction digestion using standard dye-terminator sequencing chemistry so that RFLP and AFLP products can be visualized on an automated sequencer This labeling method is efficient, inexpensive, easily multiplexed, and requires no unusual equipment or reagents, thus striking a balance between cost and throughput that should be appropriate for many research groups and core facilities.

Animals↗
PubMed2004

An obesity-related locus in chromosome region 12q23-24.

Obesity is a growing health problem in the U.S. As a complex trait, obesity involves multiple genes and gene-gene and gene-environment interactions that contribute to its pathogenesis. Here we report significant linkage from a scan of a large sample segregating extreme obesity and normal weight. We have used 382 microsatellite markers in 1,297 individuals from 260 European-American families. We conducted nonparametric linkage (NPL) analyses for dichotomous BMI (using BMI >/=27, >/=30, >/=35, and >/=40 kg/m(2)) using Genehunter. We also analyzed quantitative traits (BMI, percentage of fat, and waist circumference) by the family regression method using Merlin_regress. We found evidence for linkage on chromosome 12 (125 cM, D12S2070, logarithm of odds [LOD] 3.79, P = 0.00001 for percentage of fat; LOD 2.98, P = 0.0001 for BMI; and LOD 2.86, P = 0.00014 for waist circumference) by family regression analyses. Adding three additional markers to the intervals flanking the chromosome 12 peak yielded an LOD score of 4.08 (P = 0.00001) for percentage of fat at 116 cM and LOD scores of 3.57 (P = 0.00003) and 3.05 (P = 0.00009) for BMI and waist circumference, respectively, at 125 cM. We also obtained other suggestive linkages on chromosomes 2, 3, 7, 8, 9, 12, 13, and 21. Our results suggest multiple loci that could influence obesity, particularly a locus in chromosome region 12q23-24.

Adolescent↗
PubMed1996

Candidate genes for insulin resistance.

Insulin resistance confers increased susceptibility to NIDDM, atherosclerotic cardiovascular disease, ovarian hyperandrogenism, and possibly hypertension. Insulin resistance is largely inherited, in rare cases as a monogenic disorder or more commonly as a complex trait. The search for insulin resistance genes relies mainly on two complementary approaches: 1) positional cloning using random DNA markers present throughout the genome; and 2) the analysis of specific candidate genes. This report briefly summarizes the candidate gene approach to insulin resistance. Progress related to the analysis of genes encoding molecules that participate in insulin action is reviewed. In addition, the spectrum of potential genetic defects that might contribute to insulin resistance, both at the level of the target cell and secondarily (e.g., obesity genes), is discussed.

Animals↗
PubMed1992

Twin studies in metabolic diseases.

The traditional role of twin studies has been to assess the relative role of genetic factors as a first step in defining the genetic architecture of complex traits. This has been based on the realization that monozygotic pairs (MZ) share all their genes, while dizygotic pairs (DZ) share 50% of their genes on average. Thus, greater similarity of MZ pairs compared to DZ pairs has been taken as prima facie evidence of the role of genetic factors. This is true provided the environmental similarity of MZ pairs is not greater than for DZ pairs for effects relevant to the trait in question. This first step in genetic studies was carried out long ago in many research areas, but not in others. More detailed knowledge of the genetic architecture of traits is then obtained by other means. In this paper, we give a brief overview of some results for metabolic diseases (ischaemic heart disease, hypertension, subarachnoid haemorrhage, NIDDM and IDDM) using the classical twin approach in a large, unselected population-based twin cohort. We also outline approaches to using twins that we believe will continue to be useful, particularly for the study of environmental effects.

Cohort Studies↗
PubMed1999

Transmission ratio distortion in females on chromosome 10p11-p15.

A number of recent reports of linkage of markers on chromosome 10p to schizophrenia, and evidence for linkage in one study to bipolar affective disorder, provide encouragement for psychiatric genetics, after nonreplication of linkage findings at other chromosomal regions. The same region on chromosome 10 also demonstrates evidence for linkage to obesity, female alcoholism, and female type 1 diabetes. However, evidence for linkage can be confounded by the biological phenomenon of transmission ratio distortion. Transmission ratio distortion (also termed segregation distortion or meiotic drive) results in non-Mendelian segregation of alleles to live born offspring, and has not been investigated at the majority of loci for complex traits. We examined evidence for transmission ratio distortion using 40 Centre d'Etude du Polymorphisme Humain (CEPH) pedigrees across chromosome 10 using CEPH genotype data. Evidence for linkage of females to D10S211 was found (multipoint non-parametric linkage Z score [NPL] = 1.84, P = 0.040), while there was no linkage of this marker to male sex. The observation of possible transmission ratio distortion in females on chromosome 10p requires additional study, and may impact on the interpretation of positive linkage findings in this region. Am. J. Med. Genet. (Neuropsychiatr. Genet.) 88:657-661, 1999.

Alcoholism↗
PubMed1999

The new genetics. What are the everyday clinical applications?

BACKGROUND: Our understanding of human genetics has changed exponentially in recent years, but genetic research is sometimes perceived as an esoteric and expensive pursuit with few practical implications for the majority of the population. As the human genome project nears completion, we need to assess how we can use this vast knowledge effectively. OBJECTIVE: To focus on the role of new genetics in the understanding of both single gene disorders and the inheritance of complex traits (which have genetic and environmental components) and to discuss the role of the general practitioner (GP) utilising this knowledge in daily practice. DISCUSSION: Genetic data is often best used to understand and modify environmental causes of disease in regard to the susceptibility of an individual or family. This article discusses the role of GPs in identifying those at high risk of disease by history, prenatal diagnostic techniques and appropriate genetic testing and providing practical, cost effective strategies for individuals and the community to minimise risk of illness.

Family Practice↗