Fine-scale Mapping Research Articles

The biomarker revolution: a step toward personalized medicine.

Any drug-based treatment, be it prophylactic or therapeutic, is bound to suffer from two limitations. The fi rst one is that the drug will never be active in 100% of individuals. In fact, even in classes of drugs such as prophylactic vaccines, which exhibit very high levels of effi cacy, a full effi cacy rate is very rarely obtained. In the case of small chemical drugs, the range of effi cacy is approximately 50‐70% and overall, 30% of patients do not benefi t from current medicines. The second limitation of any drug is its safety profi le. An ‘active’ drug is likely to induce side effects that will vary in severity from one individual to another. It is noteworthy in this context that the number of reported serious adverse

A novel 2-oxoacid-dependent dioxygenase involved in the formation of the goiterogenic 2-hydroxybut-3-enyl glucosinolate and generalist insect resistance in Arabidopsis,.

Glucosinolates are secondary metabolites found almost exclusively in the order Brassicales. They are synthesized from a variety of amino acids and can have numerous side chain modifications that control biological function. We investigated the biosynthesis of 2-hydroxybut-3-enyl glucosinolate, which has biological activities including toxicity to Caenorhabditis elegans, inhibition of seed germination, induction of goiter disease in mammals, and production of bitter flavors in Brassica vegetable crops. Arabidopsis (Arabidopsis thaliana) accessions contain three different patterns of 2-hydroxybut-3-enyl glucosinolate accumulation (present in leaves and seeds, seeds only, or absent) corresponding to three different alleles at a single locus, GSL-OH. Fine-scale mapping of the GSL-OH locus identified a 2-oxoacid-dependent dioxygenase encoded by At2g25450 required for the formation of both 2R- and 2S-2-hydroxybut-3-enyl glucosinolate from the precursor 3-butenyl glucosinolate precursor. Naturally occurring null mutations and T-DNA insertional mutations in At2g25450 exhibit a complete absence of 2-hydroxybut-3-enyl glucosinolate accumulation. Analysis of herbivory by the generalist lepidopteran Trichoplusia ni showed that production of 2-hydroxybut-3-enyl glucosinolate provides increased resistance. These results show that At2g25450 is necessary for the hydroxylation of but-3-enyl glucosinolate to 2-hydroxybut-3-enyl glucosinolate in planta and that this metabolite increases resistance to generalist herbivory.

Identification and Replication of Three Novel Myopia Common Susceptibility Gene Loci on Chromosome 3q26 using Linkage and Linkage Disequilibrium Mapping

Refractive error is a highly heritable quantitative trait responsible for considerable morbidity. Following an initial genome-wide linkage study using microsatellite markers, we confirmed evidence for linkage to chromosome 3q26 and then conducted fine-scale association mapping using high-resolution linkage disequilibrium unit (LDU) maps. We used a preliminary discovery marker set across the 30-Mb region with an average SNP density of 1 SNP/15 kb (Map 1). Map 1 was divided into 51 LDU windows and additional SNPs were genotyped for six regions (Map 2) that showed preliminary evidence of multi-marker association using composite likelihood. A total of 575 cases and controls selected from the tails of the trait distribution were genotyped for the discovery sample. Malecot model estimates indicate three loci with putative common functional variants centred on MFN1 (180,566 kb; 95% confidence interval 180,505–180, 655 kb), approximately 156 kb upstream from alternate-splicing SOX2OT (182,595 kb; 95% CI 182,533–182,688 kb) and PSARL (184,386 kb; 95% CI 184,356–184,411 kb), with the loci showing modest to strong evidence of association for the Map 2 discovery samples (p<10−7, p<10−10, and p = 0.01, respectively). Using an unselected independent sample of 1,430 individuals, results replicated for the MFN1 (p = 0.006), SOX2OT (p = 0.0002), and PSARL (p = 0.0005) gene regions. MFN1 and PSARL both interact with OPA1 to regulate mitochondrial fusion and the inhibition of mitochondrial-led apoptosis, respectively. That two mitochondrial regulatory processes in the retina are implicated in the aetiology of myopia is surprising and is likely to provide novel insight into the molecular genetic basis of common myopia.

Patch dynamics of a native grass in relation to the spread of invasive smooth brome (Bromus inermis)

The effects of invasive species on the patch dynamics (establishment, growth, and local extinction) of native species are not well studied, owing to the need for relatively fine-scale data on the distribution of species. Within the prairie pothole region of the United States and Canada, the grass, Bromus inermis (smooth brome) has become established by invading disturbed prairies, and through repeated introductions for soil retention and animal graze. In this study, the impact of smooth brome on the patch dynamics of a dominant native grass species, Spartina pectinata (prairie cordgrass), was assessed using fine-scale (sub-meter) mapping of the distribution of cordgrass and brome in three prairie fragments from 2000 to 2006. Using GIS spatial analyses, we determined that cordgrass patch growth was two times greater in areas not invaded by smooth brome versus areas that were heavily infested with smooth brome. Among sites and time periods, there was a consistent significant negative relationship between the amount of smooth brome surrounding a patch of cordgrass and the growth of that cordgrass patch. The probability of establishment of a new patch of cordgrass averaged 1.3 times higher in areas of low brome coverage ( 75%). Conversely, existing cordgrass patches were 7.8 times more likely to go extinct in areas of high than low brome coverage. This is one of only a few field studies to provide evidence of the negative impact of smooth brome on native flora and hopefully will serve as justification for the development of a formal management plan to limit the distribution of this species in tallgrass prairie ecosystems.

Senescence of Manilkara zapota trees and implications for large frugivorous birds in the Southern Yucatan Peninsula, Mexico

It has long been established that mature forests are mosaics of patches in different development phases but it has seldom explicitly been taken into account in ecological studies. We demonstrate here that these development phases, which are related to the population dynamics of trees, play an important role in the distribution of fauna based on observations on frugivorous birds. In an area close to the Calakmul Biosphere Reserve in Mexico, we studied the abundance of large forest bird species in relation to forest development phases, with a methodology that seems promising for ecological diagnosis and prognosis in forest management planning. Fine-scale forest mapping and bird counts were carried out in two block-transects of 40 m × 3000 m. Tree sampling in a sub-transect was used to generate population characteristics of trees. Large bird species preferred mature or senescent forest patches, whereas relatively young, growing forest patches were avoided. Important large tree species such as Manilkara zapota, Thouinia paucidentata, Guaiacum sanctum and Esenbeckia pentaphylla, characteristic of older forest patches, showed skewed size distributions indicating stress or overexploitation. The population of M. zapota, a key fruiting species that accounted for 26.5% of the total woody biomass, was most heavily affected by stress. A future collapse in the population of M. zapota, a decrease of the total area of older forest, and a decline in the abundance of large birds is likely if stress on the system continues at this level.

Fine-scale mapping of recombination rate in Drosophila refines its correlation to diversity and divergence

Regional rates of recombination often correlate with levels of nucleotide diversity, and either selective or neutral hypotheses can explain this relationship. Regional recombination rates also correlate with nucleotide differences between human and chimpanzee, consistent with models where recombination is mutagenic; however, a lack of correlation is observed in the Drosophila melanogaster group, consistent with models invoking natural selection. Here, we revisit the relationship among recombination, diversity, and interspecies difference by generating empirical estimates of these parameters in Drosophila pseudoobscura. To measure recombination rate, we genotyped 1,294 backcross hybrids at 50 markers across the largest assembled linkage group in this species. Genome-wide diversity was estimated by sequencing a second isolate of D. pseudoobscura at shallow coverage. Alignment to the sequenced genome of the closely related species, Drosophila persimilis, provided nucleotide site orthology. Our findings demonstrate that scale is critical in determining correlates to recombination rate: fine-scale cross-over rate estimates are far stronger predictors of both diversity and interspecies difference than broad-scale estimates. The correlation of fine-scale recombination rate to diversity and interspecies difference appears to be genome-wide, evidenced by examination of an X-linked region in greater detail. Because we observe a strong correlation of cross-over rate with interspecies difference, even after correcting for segregating ancestral variation, we suggest that both mutagenic and selective forces generate these correlations, the latter in regions of low crossing over. We propose that it is not cross-overs per se that are mutagenic, but rather repair of DNA double-strand break precursors via crossing over and gene conversion.

Construction of a first genetic map of distylousTurneraand a fine-scale map of theS-locus region

As a prelude to discovery of genes involved in floral dimorphism and incompatibility, a genetic map of distylous Turnera was constructed along with a fine-scale map of the S-locus region. The genetic map consists of 79 PCR-based molecular markers (48 AFLP, 18 RAPD, 9 ISSR, 4 RAMP), 5 isozyme loci, one additional gene, and the S-locus, spanning a total distance of 683.3 cM. The 86 markers are distributed in 5 linkage groups, corresponding to the haploid chromosome number. Molecular markers tightly linked or co-segregating with the S-locus in an initial mapping population of 94 individuals were used to assay an additional 642 progeny to construct a map of the S-locus region. The fine-scale map consists of 2 markers (IS864a and RP45E9) flanking the S-locus at distances of 0.41 and 0.54 cM, respectively, and 3 additional markers (OPK14c, RP45G18, and RP81E18) co-segregating with the S-locus in the total mapping population of 736 individuals. The genetic map constructed will serve as a framework for localization of genes outside the S-locus affecting distyly, while molecular markers of the fine-scale map will be used to initiate chromosome walking to find the genes residing at the S-locus.

Fine-Scale Genetic Mapping Using Independent Component Analysis

The aim of genetic mapping is to locate the loci responsible for specific traits such as complex diseases. These traits are normally caused by mutations at multiple loci of unknown locations and interactions. In this work, we model the biological system that relates DNA polymorphisms with complex traits as a linear mixing process. Given this model, we propose a new fine-scale genetic mapping method based on independent component analysis. The proposed method outputs both independent associated groups of SNPs in addition to specific associated SNPs with the phenotype. It is applied to a clinical data set for the Schizophrenia disease with 368 individuals and 42 SNPs. It is also applied to a simulation study to investigate in more depth its performance. The obtained results demonstrate the novel characteristics of the proposed method compared to other genetic mapping methods. Finally, we study the robustness of the proposed method with missing genotype values and limited sample sizes.

Natural Selection Shapes Genome-Wide Patterns of Copy-Number Polymorphism in Drosophila melanogaster

The role that natural selection plays in governing the locations and early evolution of copy-number mutations remains largely unexplored. We used high-density full-genome tiling arrays to create a fine-scale genomic map of copy-number polymorphisms (CNPs) in Drosophila melanogaster. We inferred a total of 2658 independent CNPs, 56% of which overlap genes. These include CNPs that are likely to be under positive selection, most notably high-frequency duplications encompassing toxin-response genes. The locations and frequencies of CNPs are strongly shaped by purifying selection, with deletions under stronger purifying selection than duplications. Among duplications, those overlapping exons or introns, as well as those falling on the X chromosome, seem to be subject to stronger purifying selection.

Fine-scale genetic mapping of two Pierce’s disease resistance loci and a major segregation distortion region on chromosome 14 of grape

A refined genetic map of chromosome 14, which contains the Pierce's disease (PD) resistance locus, was created from three grape mapping populations. The source of PD resistance in these populations was b43-17, a male form of Vitis arizonica Engelm. that is homozygous resistant. The resistance locus segregated as a single dominant gene and mapped as PdR1a in the F1 selection F8909-17 (9621 population) and as PdR1b in a sibling F1 selection F8909-08 (04190 population). These two full sibs inherited either allele of the Pierce's disease resistance locus from the b43-17 parent, which is homozygous at that locus. The 9621 population consisted of 425 progeny and PdR1a mapped between markers VvCh14-56/VvCh14-02 and UDV095 within a 0.6 cM genetic distance. The 04190 population consisted of 361 progeny and PdR1b mapped between markers VvCh14-02 and UDV095/VvCh14-10 within a 0.4 cM distance. Many of the markers present on chromosome 14 were distorted with an excess of female alleles in the 04190 and 04373 population (developed from a cross of V. vinifera L. F2-35 x b43-17) indicating that potential gametophytic factors are present in this region. Common markers from this region within the 9621 population were not distorted except Scu15. When these markers were compared to V. vinifera-based maps of chromosome 14 they were also distorted suggesting the involvement of gametophytic factors, and prompting the identification of this region as Vitis-segregation distortion region 1 (V-SDR1). The refined genetic maps developed from this study can be used to identify and clone genes that confer resistance to Pierce's disease.

Allele-Specific Up-Regulation of FGFR2 Increases Susceptibility to Breast Cancer

The recent whole-genome scan for breast cancer has revealed the FGFR2 (fibroblast growth factor receptor 2) gene as a locus associated with a small, but highly significant, increase in the risk of developing breast cancer. Using fine-scale genetic mapping of the region, it has been possible to narrow the causative locus to a haplotype of eight strongly linked single nucleotide polymorphisms (SNPs) spanning a region of 7.5 kilobases (kb) in the second intron of the FGFR2 gene. Here we describe a functional analysis to define the causative SNP, and we propose a model for a disease mechanism. Using gene expression microarray data, we observed a trend of increased FGFR2 expression in the rare homozygotes. This trend was confirmed using real-time (RT) PCR, with the difference between the rare and the common homozygotes yielding a Wilcox p-value of 0.028. To elucidate which SNPs might be responsible for this difference, we examined protein–DNA interactions for the eight most strongly disease-associated SNPs in different breast cell lines. We identify two cis-regulatory SNPs that alter binding affinity for transcription factors Oct-1/Runx2 and C/EBPβ, and we demonstrate that both sites are occupied in vivo. In transient transfection experiments, the two SNPs can synergize giving rise to increased FGFR2 expression. We propose a model in which the Oct-1/Runx2 and C/EBPβ binding sites in the disease-associated allele are able to lead to an increase in FGFR2 gene expression, thereby increasing the propensity for tumour formation.

Extent of Linkage Disequilibrium in Holstein Cattle in North America

The success of fine-scale mapping and genomic selection depends mainly on the strength of linkage disequilibrium (LD) between markers and causal mutations. With Lewontin's measure of LD (known as D′), high levels of LD that extend over several million base pairs have been reported in livestock. However, this measure of LD can be strongly biased upward by small samples and by low allele frequencies. The aim of this study was to characterize the level and extent of LD in Holstein cattle in North America (Canada and the United States for purposes of this study) by using the squared correlation of the alleles at 2 loci (r2). The Affymetrix MegAllele GeneChip Bovine Mapping 10K single nucleotide polymorphism (SNP) array was used to genotype 821 bulls, from which 497 were used in the analysis of the extent of LD. A total of 5,564 SNP were used after filtering out SNP with more than 5% of Mendelian inconsistencies, with more than 20% missing genotypes, or with a minor allele frequency of less than 10%. Analysis of syntenic pairs revealed that useful LD (measured as r2>0.3) occurred at distances shorter than 100kb. Linkage disequilibrium decayed very rapidly, within a few hundred kilobase pairs. In addition, no substantial LD between unlinked loci was found. Using a sliding window analysis, we observed an irregular pattern of LD across the genome. These findings suggest that to capture useful LD, which is required for whole-genome fine mapping and genomic selection, a denser SNP map would be needed.

Differential gene expression in incipient species of Anopheles gambiae

A speciation process is ongoing in the primary vector of malaria in Africa, Anopheles gambiae. Assortatively mating incipient species known as the M and S forms differentially exploit larval breeding sites associated with different ecological settings. However, some ongoing gene flow between M and S limits significant genomic differentiation mainly to small centromere-proximal regions on chromosomes X and 2L, termed 'speciation islands' with the expectation that they contain the genes responsible for reproductive isolation. As the speciation islands exhibit reduced recombination and low polymorphism, more detailed genetic analysis using fine-scale mapping is impractical. We measured global gene expression differences between M and S using oligonucleotide microarrays, with the goal of identifying candidate genes that could be involved in this ongoing speciation process. Gene expression profiles were examined in two independent colonies of both forms at each of three developmental periods of interest: fourth instar larvae, virgin females, and gravid females. Patterns were validated on a subset of genes using quantitative real-time reverse transcription polymerase chain reaction of RNA samples from laboratory colonies and wild mosquitoes collected from Cameroon and Burkina Faso. Considered across all three developmental periods, differentially expressed genes represented approximately 1-2% of all expressed genes. Although disproportionately represented in the X speciation island, the vast majority of genes were located outside any speciation island. Compared to samples from the other developmental periods, virgin females were characterized by more than twice as many differentially expressed genes, most notably those implicated in olfaction and potentially, mate recognition.

Development of a high-speed, megapixel benthic imaging system for coastal fisheries research in Alaska

We present a detailed technical description of a new high-speed megapixel benthic imaging system developed by the Alaska Department of Fish and Game with design assistance from Wood's Hole Oceanographic Institution's HabCam project. The towed, bottom tending camera sled features a GigE Vision™ camera with a 1360 × 1024 pixel sensor that streams 16 MB/s of image data to the tow vessel over commercial off-the-shelf Gigabit Ethernet hardware and an armored fiber optic tow cable. The camera images a 1.1 × 0.83 m area of the bottom four times per second under strobe lighting that eliminates blurring in the images (motion artifacts) while towing 5–8.5 km/h. The camera sled was developed for scallop stock assessment but appears to be useful for fine-scale habitat mapping, ground-truthing acoustic data, benthic ecology research, and fishing gear effects studies as well.

A Genome-wide Scan Maps a Novel High Myopia Locus to 5p15

This study was conducted to investigate the genetic component of three Chinese pedigrees originating from Hong Kong with autosomal dominant high myopia. A whole-genome scan was performed by using microsatellite markers spanning the whole genome with an average spacing of 10 cM. Regions containing markers that yielded LOD scores >1.0 were further analyzed by fine mapping with additional microsatellite markers. Fine-scale mapping of the linkage region was performed by genotyping a set of gene-based SNP markers on a cohort of 94 high myopia cases and 94 control subjects. Two-point LOD scores >1 were observed at markers D5S630, D5S416, D7S510, D11S908, and D17S944. Additional microsatellite markers flanking D5S630 revealed a maximum two-point LOD score of 4.81 at D5S2505 at theta = 0.00. Haplotype analysis narrowed the linkage region to 5p15.33-p15.2 with a 17.45-cM interval. The coding sequences of five genes located within this region, IRX2, IRX1, POLS, CCT5, and CTNND2, were screened. No segregation of polymorphism with high myopia was found. Genotyping of 41 SNPs within this region in a Chinese cohort of 94 high myopia cases and 94 control subjects showed that the allele and genotype distributions of one SNP, rs370010, was different between cases and controls (genotype P = 0.01176, allele P = 0.00271 and trend P = 0.00375), but such association did not remain significant after false discovery rate (FDR) correction. This SNP is located within a hypothetical gene LOC442129. A novel autosomal dominant high myopia locus was mapped on chromosome 5p15.33-p15.2 with an interval of 17.45 cM.

Patos Lagoon outflow within the Río de la Plata plume using an airborne salinity mapper: Observing an embedded plume

Major river systems discharging into continental shelf waters frequently form buoyant coastal currents that propagate along the continental shelf in the direction of coastal trapped wave propagation (with the coast on the right/left, in the northern/southern hemisphere). The combined flow of the Uruguay and Paraná Rivers, which discharges freshwater into the Río de la Plata estuary (Lat. ∼36°S), often gives rise to a buoyant coastal current (the ‘Plata plume’) that extends northward along the continental shelf off Uruguay and Southern Brazil. Depending upon the prevailing rainfall, wind and tidal conditions, the Patos/Mirim Lagoon complex (Lat. ∼32°S) may also produce a freshwater outflow plume that expands across the inner continental shelf. Under these circumstances the Patos outflow plume can be embedded in temperature, salinity and current fields that are strongly influenced by the larger Plata plume. The purpose of this paper is to present observations of such an embedded plume structure and to determine the dynamical characteristics of the ambient and embedded plumes. We describe selected results of coincident airborne remote sensing and shipboard in-situ surveys of the salinity distribution and extent of the Plata and Patos/Mirim Lagoon plumes conducted under contrasting winter (2003) and summer (2004) conditions. The surveys were carried out in the context of a comprehensive multi-disciplinary study of the Plata plume and its response to prevailing seasonal weather conditions. The objective was to map the surface salinity distribution of the Plata plume at synoptic scales under representative winter and summer conditions. Additionally, the airborne survey included finer-scale mapping of specific features including the Río de Plata estuarine front and the Patos Lagoon plume, with the objective of determining the distribution and behavior of the plumes in the estuaries and on the continental shelf. The airborne survey was conducted with an aircraft carrying an infrared and microwave radiometer system, the Naval Research Laboratory's (NRL) Salinity, Temperature and Roughness Remote Scanner (STARRS). A series of broad-scale flights over the continental shelf off Argentina, Uruguay and Brazil were made using STARRS to determine the spatial extent of the Plata plume, and detailed mapping flights were undertaken in the vicinity of Río de la Plata Estuary and Patos/Mirim outflows to observe associated frontal features. The results of the airborne surveys were compared with shipboard hydrographic data obtained from a conductivity, temperature and depth (CTD) profiler. The combined ship and aircraft data were used to estimate parameters of dynamical classification schemes. These schemes were used to characterize the gross behavior and dynamics of the ambient Plata plume and embedded Patos plume. The Plata plume was highly asymmetric with along-shelf development towards the north and it behaved dynamically like a buoyant coastal boundary current, with an approximately geostrophic across-shelf momentum balance. The Patos plume, on the other hand, maintained its integrity as a relatively symmetric, ageostrophic, frictionally dominated plume with significant across-shelf, and modest along-shelf, development. The dynamical implications of the embedding of the smaller scale Patos plume within the larger-scale ambient Plata plume were explored, and it was concluded that the ambient plume could exert a significant dynamical influence on the behavior of the embedded plume.

Highly effective SNP-based association mapping and management of recessive defects in livestock

The widespread use of elite sires by means of artificial insemination in livestock breeding leads to the frequent emergence of recessive genetic defects, which cause significant economic and animal welfare concerns. Here we show that the availability of genome-wide, high-density SNP panels, combined with the typical structure of livestock populations, markedly accelerates the positional identification of genes and mutations that cause inherited defects. We report the fine-scale mapping of five recessive disorders in cattle and the molecular basis for three of these: congenital muscular dystony (CMD) types 1 and 2 in Belgian Blue cattle and ichthyosis fetalis in Italian Chianina cattle. Identification of these causative mutations has an immediate translation into breeding practice, allowing marker assisted selection against the defects through avoidance of at-risk matings.

Quantification and site-specification of the support practice factor when mapping soil erosion risk associated with olive plantations in the Mediterranean island of Crete

Due to inappropriate agricultural management practices, soil erosion is becoming one of the most dangerous forms of soil degradation in many olive farming areas in the Mediterranean region, leading to significant decrease of soil fertility and yield. In order to prevent further soil degradation, proper measures are necessary to be locally implemented. In this perspective, an increase in the spatial accuracy of remote sensing datasets and advanced image analysis are significant tools necessary and efficient for mapping soil erosion risk on a fine scale. In this study, the Revised Universal Soil Loss Equation (RUSLE) was implemented in the spatial domain using GIS, while a very high resolution satellite image, namely a QuickBird image, was used for deriving cover management (C) and support practice (P) factors, in order to map the risk of soil erosion in Kolymvari, a typical olive farming area in the island of Crete, Greece. The results comprised a risk map of soil erosion when P factor was taken uniform (conventional approach) and a risk map when P factor was quantified site-specifically using object-oriented image analysis. The results showed that the QuickBird image was necessary in order to achieve site-specificity of the P factor and therefore to support fine scale mapping of soil erosion risk in an olive cultivation area, such as the one of Kolymvari in Crete. Increasing the accuracy of the QB image classification will further improve the resulted soil erosion mapping.

Mapping the World's Intact Forest Landscapes by Remote Sensing

Potapov, P., A. Yaroshenko, S. Turubanova, M. Dubinin, L. Laestadius, C. Thies, D. Aksenov, A. Egorov, Y. Yesipova, I. Glushkov, M. Karpachevskiy, A. Kostikova, A. Manisha, E. Tsybikova, and I. Zhuravleva. 2008. Mapping the world’s intact forest landscapes by remote sensing. Ecology and Society 13(2): 51. https://doi.org/10.5751/ES-02670-130251

Fine-scale linkage disequilibrium mapping: a comparison of coalescent-based and haplotype-clustering-based methods

Among the various linkage-disequilibrium (LD) fine-mapping methods, two broad classes have received considerable development recently: those based on coalescent theory and those based on haplotype clustering. Using Genetic Analysis Workshop 15 Problem 3 simulated data, the ability of these two classes to localize the causal variation were compared. Our results suggest that a haplotype-clustering-based approach performs favorably, while at the same time requires much less computing than coalescent-based approaches. Further, we observe that 1) when marker density is low, a set of equally spaced single-nucleotide polymorphisms (SNPs) provides better localization than a set of tagging SNPs of equal number; 2) denser sets of SNPs generally lead to better localization, but the benefit diminishes beyond a certain density; 3) larger sample size may do more harm than good when poor selection of markers results in biased LD patterns around the disease locus. These results are explained by how well the set of selected markers jointly approximates the expected LD pattern around a disease locus.