Linkage Disequilibrium Mapping Approach Research Articles

Joint linkage and association mapping of complex traits in shrub willow (Salix purpurea L.).

Increasing energy demands and the necessity to reduce greenhouse gas emissions are key motivating factors driving the development of lignocellulosic crops as an alternative to non-renewable energy sources. The effects of global climate change will require a better understanding of the genetic basis of complex adaptive traits to breed more resilient bioenergy feedstocks, like willow (Salix spp.). Shrub willow is a sustainable and dedicated bioenergy crop, bred to be fast-growing and high-yielding on marginal land without competing with food crops. In a rapidly changing climate, genomic advances will be vital for the sustained improvement of willow and other non-model bioenergy crops. Here, joint genetic mapping was used to exploit genetic variation garnered from both recent and historical recombination events in S. purpurea. A panel of North American naturalized S. purpurea accessions and full-sib F2S. purpurea population were genotyped and phenotyped for a suite of morphological, physiological, pest and disease resistance, and wood chemical composition traits, collected from multi-environment and multi-year replicated field trials. Controlling for population stratification and kinship in the association panel and spatial variation in the F2, a comprehensive mixed model analysis was used to dissect the complex genetic architecture and plasticity of these important traits. Individually, genome-wide association (GWAS) models differed in terms of power, but the combined approach, which corrects for yearly and environmental co-factors across datasets, improved the overall detection and resolution of associated loci. Although there were few significant GWAS hits located within support intervals of QTL for corresponding traits in the F2, many large-effect QTL were identified, as well as QTL hotspots. This study provides the first comparison of linkage analysis and linkage disequilibrium mapping approaches in Salix, and highlights the complementarity and limits of these two methods for elucidating the genetic architecture of complex bioenergy-related traits of a woody perennial breeding programme.

Quantitative Trait Loci Mapping of Western Corn Rootworm (Coleoptera: Chrysomelidae) Host Plant Resistance in Two Populations of Doubled Haploid Lines in Maize (Zea mays L.).

Over the last 70 yr, more than 12,000 maize accessions have been screened for their level of resistance to western corn rootworm, Diabrotica virgifera virgifera (LeConte; Coleoptera: Chrysomelidae), larval feeding. Less than 1% of this germplasm was selected for initiating recurrent selection or other breeding programs. Selected genotypes were mostly characterized by large root systems and superior root regrowth after root damage caused by western corn rootworm larvae. However, no hybrids claiming native (i.e., host plant) resistance to western corn rootworm larval feeding are currently commercially available. We investigated the genetic basis of western corn rootworm resistance in maize materials with improved levels of resistance using linkage disequilibrium mapping approaches. Two populations of topcrossed doubled haploid maize lines (DHLs) derived from crosses between resistant and susceptible maize lines were evaluated for their level of resistance in three to four different environments. For each DHL topcross an average root damage score was estimated and used for quantitative trait loci (QTL) analysis. We found genomic regions contributing to western corn rootworm resistance on all maize chromosomes, except for chromosome 4. Models fitting all QTL simultaneously explained about 30 to 50% of the genotypic variance for root damage scores in both mapping populations. Our findings confirm the complex genetic structure of host plant resistance against western corn rootworm larval feeding in maize. Interestingly, three of these QTL regions also carry genes involved in ascorbate biosynthesis, a key compound we hypothesize is involved in the expression of western corn rootworm resistance.

Linkage and Association Mapping for Two Major Traits Used in the Maritime Pine Breeding Program: Height Growth and Stem Straightness.

BackgroundIncreasing our understanding of the genetic architecture of complex traits, through analyses of genotype-phenotype associations and of the genes/polymorphisms accounting for trait variation, is crucial, to improve the integration of molecular markers into forest tree breeding. In this study, two full-sib families and one breeding population of maritime pine were used to identify quantitative trait loci (QTLs) for height growth and stem straightness, through linkage analysis (LA) and linkage disequilibrium (LD) mapping approaches.ResultsThe populations used for LA consisted of two unrelated three-generation full-sib families (n = 197 and n = 477). These populations were assessed for height growth or stem straightness and genotyped for 248 and 217 markers, respectively. The population used for LD mapping consisted of 661 founders of the first and second generations of the breeding program. This population was phenotyped for the same traits and genotyped for 2,498 single-nucleotide polymorphism (SNP) markers corresponding to 1,652 gene loci. The gene-based reference genetic map of maritime pine was used to localize and compare the QTLs detected by the two approaches, for both traits. LA identified three QTLs for stem straightness and two QTLs for height growth. The LD study yielded seven significant associations (P ≤ 0.001): four for stem straightness and three for height growth. No colocalisation was found between QTLs identified by LA and SNPs detected by LD mapping for the same trait.ConclusionsThis study provides the first comparison of LA and LD mapping approaches in maritime pine, highlighting the complementary nature of these two approaches for deciphering the genetic architecture of two mandatory traits of the breeding program.

Multiple Linkage Disequilibrium Mapping Methods to Validate Additive Quantitative Trait Loci in Korean Native Cattle (Hanwoo).

The efficiency of genome-wide association analysis (GWAS) depends on power of detection for quantitative trait loci (QTL) and precision for QTL mapping. In this study, three different strategies for GWAS were applied to detect QTL for carcass quality traits in the Korean cattle, Hanwoo; a linkage disequilibrium single locus regression method (LDRM), a combined linkage and linkage disequilibrium analysis (LDLA) and a BayesCπ approach. The phenotypes of 486 steers were collected for weaning weight (WWT), yearling weight (YWT), carcass weight (CWT), backfat thickness (BFT), longissimus dorsi muscle area, and marbling score (Marb). Also the genotype data for the steers and their sires were scored with the Illumina bovine 50K single nucleotide polymorphism (SNP) chips. For the two former GWAS methods, threshold values were set at false discovery rate <0.01 on a chromosome-wide level, while a cut-off threshold value was set in the latter model, such that the top five windows, each of which comprised 10 adjacent SNPs, were chosen with significant variation for the phenotype. Four major additive QTL from these three methods had high concordance found in 64.1 to 64.9Mb for Bos taurus autosome (BTA) 7 for WWT, 24.3 to 25.4Mb for BTA14 for CWT, 0.5 to 1.5Mb for BTA6 for BFT and 26.3 to 33.4Mb for BTA29 for BFT. Several candidate genes (i.e. glutamate receptor, ionotropic, ampa 1 [GRIA1], family with sequence similarity 110, member B [FAM110B], and thymocyte selection-associated high mobility group box [TOX]) may be identified close to these QTL. Our result suggests that the use of different linkage disequilibrium mapping approaches can provide more reliable chromosome regions to further pinpoint DNA makers or causative genes in these regions.

Detection of QTL for Carcass Quality on Chromosome 6 by Exploiting Linkage and Linkage Disequilibrium in Hanwoo.

The purpose of this study was to improve mapping power and resolution for the QTL influencing carcass quality in Hanwoo, which was previously detected on the bovine chromosome (BTA) 6. A sample of 427 steers were chosen, which were the progeny from 45 Korean proven sires in the Hanwoo Improvement Center, Seosan, Korea. The samples were genotyped with the set of 2,535 SNPs on BTA6 that were imbedded in the Illumina bovine 50 k chip. A linkage disequilibrium variance component mapping (LDVCM) method, which exploited both linkage between sires and their steers and population-wide linkage disequilibrium, was applied to detect QTL for four carcass quality traits. Fifteen QTL were detected at 0.1% comparison-wise level, for which five, three, five, and two QTL were associated with carcass weight (CWT), backfat thickness (BFT), longissimus dorsi muscle area (LMA), and marbling score (Marb), respectively. The number of QTL was greater compared with our previous results, in which twelve QTL for carcass quality were detected on the BTA6 in the same population by applying other linkage disequilibrium mapping approaches. One QTL for LMA was detected on the distal region (110,285,672 to 110,633,096 bp) with the most significant evidence for linkage (p<10−5). Another QTL that was detected on the proximal region (33,596,515 to 33,897,434 bp) was pleiotrophic, i.e. influencing CWT, BFT, and LMA. Our results suggest that the LDVCM is a good alternative method for QTL fine-mapping in detection and characterization of QTL.

Variants in estrogen receptor alpha gene are associated with phenotypical expression of obsessive-compulsive disorder

Compelling data from animal and clinical studies suggest that sex steroids may play a role in the etiopathology of obsessive-compulsive disorder (OCD). The aim of this study was to investigate whether variants in estrogen receptor genes ESR1 and ESR2 may contribute to the genetic susceptibility to OCD, through a case-control association study using an extensive linkage disequilibrium-mapping approach. Twenty tag single-nucleotide polymorphisms (tagSNPs) covering the ESR2 region and nine tagSNPS from regions of ESR1 reported to be related to transcriptional control were genotyped in 229 OCD patients and 279 controls. SNP association and haplotype analysis were performed. The association of these genes and OCD subphenotypes was tested, considering early-onset OCD, comorbid tic and affective disorders, and OCD symptom dimensions. No significant difference in the distribution of alleles or genotypes was detected between controls and OCD subjects. Nevertheless, on analyzing OCD subphenotypes, SNP rs34535804 in ESR1 and a five SNPs haplotype, located at the 5' end of intron 1 of ESR1, were associated with the presence of contamination obsessions and cleaning compulsions. Specifically, carriers of the ACCCG haplotype, a combination of functional alleles related to higher ER alpha expression, showed a reduced risk of suffering from these symptoms. Our results suggest that the ESR1 gene may contribute to the genetic vulnerability to certain OCD manifestations. The dissection of OCD into more homogeneous subphenotypes may well help to identify susceptibility genes for the disorder.

Characterization of new Ashkenazi Jewish founder mutations in MSH6 causing Lynch syndrome.

1514 Background: Founder mutations are an important cause of Lynch syndrome and facilitate genetic testing in specific ethnic populations. Two recently described mutations in MSH6 are putative founder mutations, warranting careful clinical and genetic analysis. Methods: MSH6 exon 9 insertion and deletion mutations were analyzed in 2,660 colorectal cancer (CRC) cases and 3,270 healthy controls of Ashkenazi Jewish (AJ) descent from population-based and hospital-based case-control studies in Israel, Canada and the USA. Microsatellite markers and single nucleotide polymorphisms were analyzed in carriers from case-control studies and clinical series. Age of the mutation was estimated using a Bayesian MCMC linkage disequilibrium mapping approach (DMLE+ software). Results: We characterized two recently described mutations in MSH6 exon 9, c.3984_3987dupGTCA (MSH6 dup) and c.3959_3962delCAAG (MSH6 del). MSH6 dup was found in 8 of 2,660 cases and 1 of 3,270 controls, consistent with a very high risk of CRC (odds ratio [OR] = 9.8, 95% confidence interval [CI] = 1.2-78.7, Fisher's exact p = 0.0136). Of note, the only control carrying MSH6 dup had a remote history of endometrial cancer (age 61) and developed cecal cancer at age 76, several years after being ascertained as a control without CRC. The MSH6 del was less common, identified in 3 of 2660 cases and no controls. Survival analysis indicates a trend of better overall survival among CRC patients with MSH6 dup or del (hazard ratio [HR] = 0.7, 95% CI = 0.5-1.1) compared to CRC patients without MMR mutations. Haplotype analysis demonstrated separate conserved haplotypes for each mutation. Four recombination events in MSH6 dup carriers allowed estimation of the age of the mutation, which arose ∼650 years ago in the fourteenth century. No carriers of either mutation were identified in 450 Sephardi Jewish cases or 490 Sephardi Jewish controls. Conclusions: MSH6 truncating mutations c.3984_3987dupGTCA and c.3959_3962delCAAG are founder mutations in Ashkenazi Jews that cause Lynch syndrome. Although less common than other Jewish founder mutations, these mutations substantially contribute to CRC in this ethnic group and are relevant for the diagnosis and management of AJ Lynch syndrome patients. No significant financial relationships to disclose.

A common variant in DRD3 gene is associated with risperidone-induced extrapyramidal symptoms

We present a pharmacogenetic study of acute antipsychotic (AP)-induced extrapyramidal symptoms (EPS) using an extensive linkage disequilibrium mapping approach in seven-candidate genes with a well-established link to dopamine (DRD2, DRD3, ACE, COMT, DAT, MAO-A, MAO-B). From a cohort of 321 psychiatric inpatients, 81 cases presenting with EPS (Simpson-Angus > 3) and 189 controls presenting without EPS (Simpson-Angus < or = 3) took part. Eighty-four-tag single nucleotide polymorphisms (SNPs) in candidate genes were genotyped. After extensive data cleaning, 70 SNPs were analyzed for association of single markers and haplotypes. AP dosage, AP-DRD2 blockade potency and age were identified as susceptibility factors for AP-induced EPS. One SNP of the DRD3 gene, rs167771, achieved significant association with EPS risk after Bonferroni correction (nominal P-value 1.3 x 10(-4)) in the patients treated with risperidone (132 patients). AP-induced EPS remains a serious public health problem. Our finding of a common SNP (rs167771) in the DRD3 gene provides a strong new candidate gene for risperidone-induced EPS.

Ubiquitin associated protein 1 is a risk factor for frontotemporal lobar degeneration

Frontotemporal lobar degeneration (FTLD) is now recognised as a common form of early onset dementia. Up to 40% of patients have a family history of disease demonstrating a large genetic component to its etiology. Linkage to chromosome 9p21 has recently been reported in families with this disorder. We undertook a large scale two-stage linkage disequilibrium mapping approach of this region in the Manchester FTLD cohort. We identified association of ubiquitin associated protein 1 ( UBAP1; OR 1.42 95% CI 1.08–1.88, P = 0.013) with FTLD in this cohort and we replicated this finding in an additional two independent cohorts from the Netherlands (OR 1.33 95% CI 1.04–1.69, P = 0.022), the USA (OR 1.4 95% CI 1.02–1.92, P = 0.032) and a forth Spanish cohort approached significant association (OR 1.45 95% CI 0.97–2.17, P = 0.064). However, we failed to replicate in a fifth cohort from London (OR 0.99 95% CI 0.72–1.37, P = 0.989). Quantitative analysis of UBAP1 mRNA extracted from tissue from the Manchester cases demonstrated a significant reduction of expression from the disease-associated haplotype. In addition, we identified a case of familial FTLD that demonstrated colocalisation of UBAP1 and TDP-43 in the neuronal cytoplasmic inclusions in the brain of this individual. Our data for the first time identifies UBAP1 as a genetic risk factor for FTLD and suggests a mechanistic relationship between this protein and TDP-43.

Perspectives on genome mapping and marker-assisted breeding of eucalypts

In Eucalyptus and forest tree breeding in general, the generalised application of molecular markers for directional selection is still an unfulfilled promise. In highly heterogeneous eucalypts, while conventional quantitative trait loci (QTL) mapping has revealed useful markers that are currently exploited in within-family selection tactics, only a more direct linkage disequilibrium mapping approach will likely uncover population-wide applicable marker–trait associations. Due to the very low-range linkage disequilibrium seen in Eucalyptus, a whole-genome association approach does not seem immediately feasible. Association studies based on candidate genes have been started in Eucalyptus, but only small proportions of the variation have been accounted for by such genes to be exciting news to breeders. Selection of candidate genes for direct manipulation or association studies based on their presumed biochemical role is not an easy task even for well-defined phenotypes and/or known metabolic pathways. Going from phenotypes to genes by a forward genomics approach based on an integrative expression–QTL mapping route, should prove to be a powerful way to choose target genes for marker-assisted selection. In this context at least two possibilities have recently emerged. The first one is to use high-performance genotyping technologies that would allow sufficient throughput and low cost for association genetic analysis of thousands of genes at a time. The second one would be to have access to a whole genome sequence so that candidate genes in a fine mapping interval delimited by flanking markers could be mined, reannotated and then analysed in association mapping. A fully public draft of the E. grandis genome will be sequenced by the US Department of Energy within the next few years following a proposal submitted by the International Eucalyptus Genome Network (EUCAGEN). As this genome project advances and more powerful tools become accessible, the true challenge for understanding and manipulating the complex nature of important traits in Eucalyptus will depend to a large extent on our ability to accurately phenotype trees, analyse the overwhelming amount of genomic data and translate this into truly useful molecular tools for breeding.

Incorporation of covariates into multipoint linkage disequilibrium mapping in case‐control studies

Case-control designs are commonly adopted in genetic epidemiological studies because they are cost effective and offer powerful tests for genetic and environmental risk factors, as well as their interactions. Previously, we proposed an association mapping approach to estimate the position of an unobserved disease locus as well as measuring its genetic effect on risk. The method provides a confidence interval for the estimated map position to help narrow the chromosomal region potentially harboring a disease locus. However, concerns often rise about case-control designs including possible false positives or bias due to confounders, heterogeneity or interactions among genes and between genes and environments. In the present work, we extended the multipoint linkage disequilibrium mapping approach for case-control studies to incorporate information about factors influencing the effect of causal genes to improve precision and efficiency of the estimated location. The efficiency, bias and coverage probability of this extended approach for locating a disease locus using case-control data with and without additional information on a covariate were compared through simulation. An example of a case-control study for type 2 diabetes was used to illustrate this extended method. In this study, a strong association between diabetes and a candidate gene, SCL2A10, was detected among nonobese subjects, whereas no evidence of association was found for either obese subjects or the whole sample when obesity was ignored. Simulation studies and these diabetes data both demonstrate how the efficiency of the estimated location of a disease gene can be improved substantially by incorporating information on covariates.

Discovery, linkage disequilibrium and association analyses of polymorphisms of the immune complement inhibitor, decay-accelerating factor gene (DAF/CD55) in type 1 diabetes.

BackgroundType 1 diabetes (T1D) is a common autoimmune disease resulting from T-cell mediated destruction of pancreatic beta cells. Decay accelerating factor (DAF, CD55), a glycosylphosphatidylinositol-anchored membrane protein, is a candidate for autoimmune disease susceptibility based on its role in restricting complement activation and evidence that DAF expression modulates the phenotype of mice models for autoimmune disease. In this study, we adopt a linkage disequilibrium (LD) mapping approach to test for an association between the DAF gene and T1D.ResultsInitially, we used HapMap II genotype data to examine LD across the DAF region. Additional resequencing was required, identifying 16 novel polymorphisms. Combining both datasets, a LD mapping approach was adopted to test for association with T1D. Seven tag SNPs were selected and genotyped in case-control (3,523 cases and 3,817 controls) and family (725 families) collections.ConclusionWe obtained no evidence of association between T1D and the DAF region in two independent collections. In addition, we assessed the impact of using only HapMap II genotypes for the selection of tag SNPs and, based on this study, found that HapMap II genotypes may require additional SNP discovery for comprehensive LD mapping of some genes in common disease.

Relative efficiency of the linkage disequilibrium mapping approach in detecting candidate genes for schizophrenia in different European populations

Detection of susceptibility genes in indirect association studies depends not only on the degree of linkage disequilibrium between the disease variant and the SNP marker but also on the difference in their allele frequencies. Little is known about how variations in these parameters may affect the power of indirect association studies among related populations. Toward this goal, we genotyped 40 SNPs at four loci in samples from three European populations, Galician, Greek, and Norwegian. We compared the relative efficiency of all pairs of SNPs in detecting each other in each one of the populations. Our results show that a low percentage of marker SNPs may detect association in some populations but be totally ineffective in others. Therefore, these differences have to be an additional factor to consider when a replication study fails to confirm initial associations, especially if the replication is focused on very few markers.

Localization of Cancer Susceptibility Genes by Genome-wide Single-Nucleotide Polymorphism Linkage-Disequilibrium Mapping

With the large numbers of single nucleotide polymorphisms (SNPs) available and new technologies that permit high throughput genotyping, we have investigated the possibility of the localization of disease genes with genome-wide panels of SNP markers and taking advantage of the linkage-disequilibrium (LD) between the disease gene and closely linked markers. For this purpose, we selected cases from the Ashkenazi Jewish population, in which the mutant alleles are expected to be identical by descent from a common founder and the regions of LD encompassing these mutant alleles are large. As a validation of this approach for localization, we performed two trials: one in autosomal recessive Bloom syndrome, in which a unique mutation of the BLM gene is present at elevated frequencies in cases, and the other in autosomal dominant hereditary nonpolyposis colorectal cancer (HNPCC), in which a unique mutation of MSH2 is present at elevated frequencies. In the Bloom syndrome trial, we genotyped 3,258 SNPs in 10 Jewish Bloom syndrome cases and 31 non-Bloom syndrome Jewish persons as a comparison group. In the HNPCC trial, we genotyped 8,549 SNPS in 13 Jewish HNPCC cases whose colon cancers exhibited microsatellite instability and in 63 healthy Jews as a comparison group. To identify significant associations, we performed (a) Fisher's exact test comparing genotypes at each locus in cases versus controls and (b) a haplotype analysis by estimating the frequency of haplotypes with the expectation-maximization algorithm and comparing haplotype frequencies in cases versus controls by logistic regression and a maximum likelihood ratio method. In the Bloom syndrome trial, by Fisher's exact test, statistically significant association was detected at a single locus, TSC0754862, which is a locus 1.7 million bp from BLM. Two-locus, three-locus, and four-locus haplotypes that included TSC0754862 and flanked BLM were also statistically more frequent in cases versus controls. In the HNPCC trial, although a significant P value was not obtained by the single SNP genotype analysis, significant associations were detected for several multilocus haplotypes in an 11-million-bp region that contained the MSH2 gene. This work demonstrates the power of the LD mapping approach in an isolated population and its general applicability to the identification of novel cancer-causing genes.

Linkage disequilibrium mapping in trisomic populations: analytical approaches and an application to congenital heart defects in Down syndrome.

Many of the birth defects associated with trisomy exhibit both variable expressivity and incomplete penetrance. This variability suggests that it is allelic variation and not simply the presence of an additional chromosome that leads to the development of certain trisomy-associated birth defects. With the proper tools, one may use trisomic populations to identify genes involved in the development of specific birth defects. A trisomic population may be advantageous over a normal population if the defect is over-represented in the trisomic population. Alternatively, one can view the trisomic populations as a "model system" to offer insight into aspects of both normal and abnormal embryonic development. Standard disomic linkage disequilibrium mapping approaches need to be adjusted to account for the presence of the additional genetic material in the trisomic individuals. We present an approach for linkage disequilibrium mapping of variable phenotypes in a trisomic population that adequately accounts for the additional alleles and the pattern of non-independent inheritance. We establish the laboratory methods and statistical tools necessary to conduct an association study in a trisomic population. As an example, we have applied these tools to a pilot study of Down syndrome-associated congenital heart defects.

Genome-wide single nucleotide polymorphism analyses on rheumatoid arthritis

Although the etiology of rheumatoid arthritis (RA) is still unknown, it is generally believed that a combination of multiple polymorphic genetic factors and environmental contributions lead to the pathogenic auto-immune reactions characterized by destructive polyarthritis and various extra-articular inflammatory involvements. A genetic approach to identify RA-associated genes from the whole genome is proposed to be one of the promising methodologies to elucidate the etiology of RA. Although multiple genome-wide linkage studies and many association studies to test an individual gene that is functionally relevant to RA have been performed to identify RA-associated nonhuman leukocyte antigen genes, no region or gene has been conclusively shown to be one of the RA-susceptible loci or genes. Therefore, a linkage disequilibrium approach using single nucleotide polymorphisms (SNPs) as genetic markers to identify disease-associated genes was considered a promising alternative method for RA, as well as other common diseases with complex genetic predispositions. Our RIKEN SNP Research Center has established a high-throughput SNP-genotyping system and has been investigating multiple common diseases using a whole-genome gene-based linkage disequilibrium mapping approach. In 2003, we reported that functional variants of the PADI4 gene were associated with RA. PADI4 is an enzyme that converts arginine residue in proteins to citrulline. The citrullinated proteins are targets of the most specific autoantibodies in RA. We have identified this gene in a whole-genome, hypothesis-free approach. Therefore, this made our methodology strongly reliable in that the RA-associated gene identified by our hypothesis-free approach was functionally strongly relevant to the pathogenesis of RA. Recently we also found that SLC22A4 and RUNX1 are associated with RA. SLC22A4 is an organic cation transporter with unknown physiologic function, and RUNX1 is a hematologic transcriptional regulator that has been shown to be responsible for acute myelogenic leukemia. It is suggested that the association of RUNX1 with RA is due to its regulation of expression of SLC22A4. Because the physiologic function of SLC22A4 is still unclear, further investigation is needed into how SLC22A4 affects RA susceptibility. Although the association of RUNX1 with RA was identified as a regulatory factor of SLC22A4, it is possible that RUNX1 is a key molecule in autoimmunity, as it has been reported to be associated with systemic lupus erythematosus and psoriasis, two other autoimmune diseases.

Multipoint linkage disequilibrium mapping approach: incorporating evidence of linkage and linkage disequilibrium from unlinked region.

Gene mapping for complex diseases is still a challenge in genetic studies. For family-based studies, the single-locus methods for detecting linkage and linkage disequilibrium (LD) one at a time may not capture the assumed interaction between multiple causal genes efficiently. We propose a multipoint LD approach for assessing the evidence of linkage and LD in a targeted chromosomal region by incorporating evidence from an unlinked region using the case-parent trio design. The paternal and maternal preferential transmission statistics defined in Liang et al. ([2001] Am. J. Hum. Genet. 68:937-950) are the primary statistics for this approach. Our generalized estimating equation (GEE) method builds on a model using the expected preferential transmission statistic from the targeted region conditional on this same statistic from the unlinked region. The major assumption is that there is no more than one trait locus in both the targeted region and unlinked region. The map position of an unobserved trait locus and its confidence interval can be calculated. Finally, we apply this approach to the African-American families drawn from the Collaborative Study on the Genetics of Asthma (CSGA). Previous analysis using this GEE approach developed by Liang et al. ([2001] Am. J. Hum. Genet. 68:937-950) suggested strong evidence of linkage and LD on chromosome 11, but only marginal evidence on chromosome 8. While conditioning on marker D11S937 on chromosome 11, a separate trait locus on chromosome 8 was estimated at tau(2) empty set = 11.67 cM, with a 95% confidence interval of (8.75, 14.59), and the test statistic shows significant evidence of linkage and LD (P-value=0.0198) in this region of chromosome 8.

Linkage disequilibrium mapping with genotype data.

Linkage disequilibrium mapping has proven a powerful tool for locating disease genes. Although all existing linkage disequilibrium mapping methods implicitly assume that individual haplotypes can be inferred, only genotypes are directly observable in practice, and haplotypes cannot always be uniquely resolved based on genotype data. In this article, we propose a likelihood-based linkage disequilibrium mapping approach to analyzing multilocus genotype data arising from case-control studies. Results from extensive simulation studies suggest that this approach may be a useful tool to fine map disease genes using case-control data.

Characterizing patterns of genetic variation

The efforts of the Human Genome Project have resulted in, among other things, the identification and mapping of hundreds of thousands of anonymous single nucleotide polymorphisms (SNPs) for use in genome-wide association studies. The successful application of SNP maps to finding genes that underlie common diseases and drug responses depends, in part, on the extent of linkage disequilibrium (LD) in the population under study. Linkage disequilibrium, or correlation between polymorphisms located in close proximity to each other, allows anonymous polymorphisms throughout the entire genome to be tested for their association with disease and/or drug response. Through LD, these anonymous SNPs can pinpoint genomic regions that might harbor the true, causative genetic variants that underlie the association with disease and drug response. Until recently, the extent of LD, or distance over which two genetic variants could be separated and still be correlated, was poorly understood and the feasibility of such LD mapping approaches uncertain.

Linkage Disequilibrium Analysis of Biallelic DNA Markers, Human Quantitative Trait Loci, and Threshold-Defined Case and Control Subjects

Linkage disequilibrium (LD) mapping has been applied to many simple, monogenic, overtly Mendelian human traits, with great success. However, extensions and applications of LD mapping approaches to more complex human quantitative traits have not been straightforward. In this article, we consider the analysis of biallelic DNA marker loci and human quantitative trait loci in settings that involve sampling individuals from opposite ends of the trait distribution. The purpose of this sampling strategy is to enrich samples for individuals likely to possess (and not possess) trait-influencing alleles. Simple statistical models for detecting LD between a trait-influencing allele and neighboring marker alleles are derived that make use of this sampling scheme. The power of the proposed method is investigated analytically for some hypothetical gene-effect scenarios. Our studies indicate that LD mapping of loci influencing human quantitative trait variation should be possible in certain settings. Finally, we consider possible extensions of the proposed methods, as well as areas for further consideration and improvement.