Intermarker Distances Research Articles

A linkage map of the Atlantic salmon (Salmo salar) based on EST-derived SNP markers

BackgroundThe Atlantic salmon is a species of commercial and ecological significance. Like other salmonids, the species displays residual tetrasomy and a large difference in recombination rate between sexes. Linkage maps with full genome coverage, containing both type I and type II markers, are needed for progress in genomics. Furthermore, it is important to estimate levels of linkage disequilibrium (LD) in the species. In this study, we developed several hundred single nucleotide polymorphism (SNP) markers for the Atlantic salmon, and constructed male and female linkage maps containing SNP and microsatellite markers. We also investigated further the distribution of male and female recombination events across the genome, and estimated levels of LD between pairs of markers.ResultsThe male map had 29 linkage groups and was 390 cM long. The female map had 30 linkage groups as was 1983 cM long. In total, the maps contained 138 microsatellite markers and 304 SNPs located within genes, most of which were successfully annotated. The ratio of male to female recombination events was either close to zero or very large, indicating that there is little overlap between regions in which male and female crossovers occur. The female map is likely to have close to full genome coverage, while the majority of male linkage groups probably lack markers in telomeric regions where male recombination events occur. Levels of r2 increased with decreasing inter-marker distance in a bimodal fashion; increasing slowly from ~60 cM, and more rapidly more from ~12 cM. Long-ranging LD may be consequence of recent admixture in the population, the population being a 'synthetic' breeding population with contributions from several distinct rivers. Levels of r2 dropped to half its maximum value (above baseline) within 15 cM, and were higher than 0.2 above baseline for unlinked markers ('useful LD') at inter-marker distances less than 5 cM.ConclusionThe linkage map presented here is an important resource for genetic, comparative, and physical mapping of the Atlantic salmon. The female map is likely to have a map coverage that is not far from complete, whereas the male map length is likely to be significantly shorter than the true map, due to suboptimal marker coverage in the apparently small physical regions where male crossovers occur. 'Useful LD' was found at inter-marker distances less than 5 cM.

SU‐FF‐J‐30: Simultaneous Use of An Implanted Fiducial System and An Endorectal Balloon for the Treatment of Prostate Cancer

Purpose: To report on our initial experience of using an on‐line implanted fiducial system simultaneously with an endorectal balloon to treat patients with prostate cancer. Method and Materials: Patients had three fiducial seeds implanted in their prostate prior to radiotherapy treatment planning. Treatment was given in the prone position with an endorectal balloon inflated to 60 cc and a full bladder. Patients were initially positioned with the aid of lasers/tattoos and an immobilization cradle. Open‐field radiation electronic portal images were then taken in the treatment position and compared to reference images prior to each fraction of treatment. The intermarker distances (IMDs) between the three implanted seeds were examined to gain insight on prostate deformation and seed migration for this treatment strategy. The IMDs for the initial three fractions were averaged for each seed pair to serve as our references. For subsequent fractions, the differences in IMDs between measured and reference values were computed. Our data were also compared to similar previously reported studies. Results: We have analyzed the IMDs of 13 patients treated with implanted fiducials and an endorectal balloon. A total of 349 alignments were evaluable and thus, 1047 IMDs were calculated for this set of patients. The mean absolute IMD difference for all samples was 0.86±0.88 mm, while the largest single IMD difference was 8.9 mm. For individual patients, the ranges of mean absolute IMD differences for a given seed pair and corresponding standard deviations were 0.32–1.85 mm and 0.22–1.66 mm, respectively. The maximum absolute IMD difference for individual patients ranged from 1.2–8.9 mm. Conclusions: We have simultaneously implemented an on‐line implanted fiducial system and an endorectal balloon during prostate cancer radiotherapy. The degree of deformation of the prostate gland during treatment has been examined. This study may help predict the potential dosimetric consequences due to prostate motion/deformation.

Association evidence of schizophrenia with distal genomic region of NOTCH4 in Taiwanese families

Evidence for association with schizophrenia has been reported for NOTCH4, although results have been inconsistent. Previous studies have focused on polymorphisms in the 5' promoter region and first exon of NOTCH4. Our aim was to test the association of the entire genomic region of NOTCH4 in 218 families with at least two siblings affected by schizophrenia in Taiwan. We genotyped seven single nucleotide polymorphisms (SNPs) of this gene, with average intermarker distances of 5.3 kb. Intermarker linkage disequilibrium (LD) was calculated using gold software, and single-locus and haplotype association analyses were performed using transmit software. We found that the T allele of SNP rs2071285 (P= 0.035) and the G allele of SNP rs204993 (P= 0.0097) were significantly preferentially transmitted to the affected individuals in the single-locus association analysis. The two SNPs were in high LD (D' > 0.8). Trend for overtransmission was shown for the T-G haplotype of the two SNPs to affected individuals (P= 0.053), with the A-A haplotype significantly undertransmitted (P= 0.034). The associated region distributed across the distal portion of the NOTCH4 gene and overlapped with the genomic region of the G-protein signaling modulator 3 and pre-B-cell leukemia transcription factor 2. In summary, we found modest association evidence between schizophrenia and the distal genomic region of NOTCH4 in this Taiwanese family sample. Further replication for association with the distal genomic region of NOTCH4 is warranted.

On locating multiple interacting quantitative trait loci in intercross designs.

A modified version (mBIC) of the Bayesian Information Criterion (BIC) has been previously proposed for backcross designs to locate multiple interacting quantitative trait loci. In this article, we extend the method to intercross designs. We also propose two modifications of the mBIC. First we investigate a two-stage procedure in the spirit of empirical Bayes methods involving an adaptive (i.e., data-based) choice of the penalty. The purpose of the second modification is to increase the power of detecting epistasis effects at loci where main effects have already been detected. We investigate the proposed methods by computer simulations under a wide range of realistic genetic models, with nonequidistant marker spacings and missing data. In the case of large intermarker distances we use imputations according to Haley and Knott regression to reduce the distance between searched positions to not more than 10 cM. Haley and Knott regression is also used to handle missing data. The simulation study as well as real data analyses demonstrates good properties of the proposed method of QTL detection.

Using sex‐averaged genetic maps in multipoint linkage analysis when identity‐by‐descent status is incompletely known

The ratio of male and female genetic map distances varies dramatically across the human genome. Despite these sex differences in genetic map distances, most multipoint linkage analyses use sex-averaged genetic maps. We investigated the impact of using a sex-averaged genetic map instead of sex-specific maps for multipoint linkage analysis of affected sibling pairs when identity-by-descent states are incompletely known due to missing parental genotypes and incomplete marker heterozygosity. If either all or no parental genotypes were available, for intermarker distances of 10, 5, and 1 cM, we found no important differences in the expected maximum lod score (EMLOD) or location estimates of the disease locus between analyses that used the sex-averaged map and those that used the true sex-specific maps for female:male genetic map distance ratios 1:10 and 10:1. However, when genotypes for only one parent were available and the recombination rate was higher in females, the EMLOD using the sex-averaged map was inflated compared to the sex-specific map analysis if only mothers were genotyped and deflated if only fathers were genotyped. The inflation of the lod score when only mothers were genotyped led to markedly increased false-positive rates in some cases. The opposite was true when the recombination rate was higher in males; the EMLOD was inflated if only fathers were genotyped, and deflated if only mothers were genotyped. While the effects of missing parental genotypes were mitigated for less extreme cases of missingness, our results suggest that when possible, sex-specific maps should be used in linkage analyses.

Inferring Loss-of-Heterozygosity from Unpaired Tumors Using High-Density Oligonucleotide SNP Arrays

Loss of heterozygosity (LOH) of chromosomal regions bearing tumor suppressors is a key event in the evolution of epithelial and mesenchymal tumors. Identification of these regions usually relies on genotyping tumor and counterpart normal DNA and noting regions where heterozygous alleles in the normal DNA become homozygous in the tumor. However, paired normal samples for tumors and cell lines are often not available. With the advent of oligonucleotide arrays that simultaneously assay thousands of single-nucleotide polymorphism (SNP) markers, genotyping can now be done at high enough resolution to allow identification of LOH events by the absence of heterozygous loci, without comparison to normal controls. Here we describe a hidden Markov model-based method to identify LOH from unpaired tumor samples, taking into account SNP intermarker distances, SNP-specific heterozygosity rates, and the haplotype structure of the human genome. When we applied the method to data genotyped on 100 K arrays, we correctly identified 99% of SNP markers as either retention or loss. We also correctly identified 81% of the regions of LOH, including 98% of regions greater than 3 megabases. By integrating copy number analysis into the method, we were able to distinguish LOH from allelic imbalance. Application of this method to data from a set of prostate samples without paired normals identified known regions of prevalent LOH. We have developed a method for analyzing high-density oligonucleotide SNP array data to accurately identify of regions of LOH and retention in tumors without the need for paired normal samples.

Multiple QTLs influencing triglyceride and HDL and total cholesterol levels identified in families with atherogenic dyslipidemia

We conducted a genome-wide scan using variance components linkage analysis to localize quantitative-trait loci (QTLs) influencing triglyceride (TG), high density lipoprotein-cholesterol (HDL-C), low density lipoprotein-cholesterol, and total cholesterol (TC) levels in 3,071 subjects from 459 families with atherogenic dyslipidemia. The most significant evidence for linkage to TG levels was found in a subset of Turkish families at 11q22 [logarithm of the odds ratio (LOD)=3.34] and at 17q12 (LOD=3.44). We performed sequential oligogenic linkage analysis to examine whether multiple QTLs jointly influence TG levels in the Turkish families. These analyses revealed loci at 20q13 that showed strong epistatic effects with 11q22 (conditional LOD=3.15) and at 7q36 that showed strong epistatic effects with 17q12 (conditional LOD=3.21). We also found linkage on the 8p21 region for TG in the entire group of families (LOD=3.08). For HDL-C levels, evidence of linkage was identified on chromosome 15 in the Turkish families (LOD=3.05) and on chromosome 5 in the entire group of families (LOD=2.83). Linkage to QTLs for TC was found at 8p23 in the entire group of families (LOD=4.05) and at 5q13 in a subset of Turkish and Mediterranean families (LOD=3.72). These QTLs provide important clues for the further investigation of genes responsible for these complex lipid phenotypes. These data also indicate that a large proportion of the variance of TG levels in the Turkish population is explained by the interaction of multiple genetic loci.

Intraprostatic Fiducials for Localization of the Prostate Gland: Monitoring Intermarker Distances During Radiation Therapy to Test for Marker Stability

Intraprostatic Fiducials for Localization of the Prostate Gland: Monitoring Intermarker Distances During Radiation Therapy to Test for Marker Stability

Replication of Autism Linkage: Fine-Mapping Peak at 17q21

Autism is a heritable but genetically complex disorder characterized by deficits in language and in reciprocal social interactions, combined with repetitive and stereotypic behaviors. As with many genetically complex disorders, numerous genome scans reveal inconsistent results. A genome scan of 345 families from the Autism Genetic Resource Exchange (AGRE) (AGRE_1), gave the strongest evidence of linkage at 17q11-17q21 in families with no affected females. Here, we report a full-genome scan of an independent sample of 91 AGRE families with 109 affected sibling pairs (AGRE_2) that also shows the strongest evidence of linkage to 17q11-17q21 in families with no affected females. Taken together, these samples provide a replication of linkage to this chromosome region that is, to our knowledge, the first such replication in autism. Fine mapping at 2-centimorgan (cM) intervals in the combined sample of families with no affected females reveals a linkage peak at 66.85 cM, which places this locus at 17q21.

Intraprostatic fiducials for localization of the prostate gland: Monitoring intermarker distances during radiation therapy to test for marker stability

The use of intraprostatic fiducials as surrogates for prostate gland position assumes that the markers are rigidly positioned within the prostate. To test this assumption, the intermarker distances (IMD) of implanted markers was monitored during the full course of radiation therapy to determine marker stability within the prostate gland. The analysis is performed on 56 patients treated with intensity-modulated radiotherapy. A total of 168 markers (3 markers per patient) were implanted. Two high-resolution X-rays were acquired before treatment delivery to visualize the position of the implanted markers. A total of 2,037 daily alignments were performed on the 56 cases (average: 36 alignments per patient). Each pair of X-ray images allows the computation of the 3 IMDs. A total of 6,111 IMDs were available for analysis. To study variations in marker position, daily IMDs were compared with the IMD that was observed during the first alignment. We defined the variation in the IMD as the important measure of intrinsic marker position variation. The standard deviation (SD) of IMD variations was studied as a measure of the extent of marker position variation. Particular attention was given to cases in which significant intermarker variations were observed. The average directional variation of all IMDs (+/- SD) was -0.31 (+/-1.41) mm. The average absolute variation of all IMDs (+/- SD) was 1.01 (+/-1.03) mm. The largest observed variation in IMD was 10.2 mm. Among the individual 56 patients, the SDs of the IMD variations were computed and found to range from 0.4 to 4.2 mm. In 54 of the 56 patients (96%), the variations of all 3 IMDs had SD of 4.0 mm or less, which indicates little variation in the relative position of the markers. Only in 2 patients did any of the IMDs vary, with SD that exceeded 4.0 mm, which indicated noticeable and consistent marker-position variation. The maximum observed SD in the IMD variation was 4.2 mm. In each of the 2 cases, 2 IMDs were found to fluctuate, while the third IMD remained fairly constant. This finding means that 1 of 3 markers varied frequently in its relative position throughout the treatment. Therefore, only 2 of the 168 markers (1%) showed frequent changes in their relative positions. A review of these 2 cases revealed that the observed marker mobility was likely not caused by migration of the marker itself but caused by prostate deformation, secondary to rectal filling. To investigate the frequency of extreme situations, the maximum observed IMD variation was determined for each patient. In 47 of the 56 patients (84%), the maximum difference in IMDs was at least 2 mm. The corresponding numbers for 3, 4, and 5 mm were 23 (41%), 10 (18%), and 5 (9%) patients, respectively. This study is the largest reported series of localized prostate cancer patients with implanted intraprostatic markers used for daily target localization in which individual marker positions were registered and IMDs were computed to test for marker position variation. Only 2 of 168 implanted markers showed a relatively significant and consistent change in their relative position throughout a course of treatment. However, these variations in position were most likely not caused by marker migration but caused by prostate deformation. Typically, the IMDs varied minimally, which indicated relatively little deformation of the gland as well as the absence of significant marker migration. However, during a typical course of treatment, the IMD is likely to vary by several millimeters in some instances, which indicates infrequent but significant deformation. In these instances, an alignment based on the 3 markers' center of mass will still provide a meaningful alignment of the prostate within the radiation field. Intraprostatic implanted fiducials in the prostate allow a reliable and simple localization of the prostate gland, even in the presence of organ deformation.

Ignoring Linkage Disequilibrium among Tightly Linked Markers Induces False-Positive Evidence of Linkage for Affected Sib Pair Analysis

Most multipoint linkage programs assume linkage equilibrium among the markers being studied. The assumption is appropriate for the study of sparsely spaced markers with intermarker distances exceeding a few centimorgans, because linkage equilibrium is expected over these intervals for almost all populations. However, with recent advancements in high-throughput genotyping technology, much denser markers are available, and linkage disequilibrium (LD) may exist among the markers. Applying linkage analyses that assume linkage equilibrium to dense markers may lead to bias. Here, we demonstrated that, when some or all of the parental genotypes are missing, assuming linkage equilibrium among tightly linked markers where strong LD exists can cause apparent oversharing of multipoint identity by descent (IBD) between sib pairs and false-positive evidence for multipoint model-free linkage analysis of affected sib pair data. LD can also mimic linkage between a disease locus and multiple tightly linked markers, thus causing false-positive evidence of linkage using parametric models, particularly when heterogeneity LOD score approaches are applied. Bias can be eliminated by inclusion of parental genotype data and can be reduced when additional unaffected siblings are included in the analysis.

3-D Kinematics Using Moving Cameras. Part 1: Development and Validation of the Mobile Data Acquisition System

Many human activities, particularly sporting skills, occur over large distances. But technical limitations have forced biomechanists to conduct studies only on portions of such skills. In this paper we present the design and validation of a mobile data collection system composed of a camera cart that allows the tracking of athletes along a larger portion of their movements. A key feature of this system is that it requires only a small field of view to record and analyze joint motions. The validation of this method was conducted with three approaches. For all approaches, intermarker distances obtained from real measures were compared to those obtained from digitized video data. In all three experiments, the results proved to be within the accepted error range of 5%. The net differences between measured values and digitized values ranged from 0.8 to 3 mm, while the relative errors ranged from 0.2 to 6%. This first experimentation using a mobile camera array to collect and reconstruct biomechanical data has proven to be valid and worth pursuing for recording and analyzing ice hockey skating.

Genetic maps of microsatellite and single‐nucleotide polymorphism markers: Are the distances accurate?

Genetic maps play an important role in gene mapping. Inaccurate genetic maps can hinder gene mapping by biasing lod scores and reducing the power to map a trait to a particular region. Although sequence-based physical maps can provide a unique order for markers, they do not provide information on genetic map distances. By simulation studies, I investigated how many meioses are necessary to accurately estimate genetic map distances for maps constructed from microsatellite and single-nucleotide polymorphism (SNP) markers for various intermarker distances and marker heterozygosity. To evaluate the accuracy of the generated genetic maps, the length of the 95% confidence interval for intermarker genetic distances was examined. In addition, the power to separate two adjacent markers by a nonzero map distance was investigated. The number of meioses necessary to accurately estimate map distances depends greatly not only on intermarker distances but also on marker heterozygosity. For example, for a genetic map with intermarker distances of 0.5 cM generated with 1,000 meioses, when marker heterozygosity was high (0.90), for 96% of the markers there was a nonzero map distance between adjacent markers. However, when marker heterozygosity was low (0.32), only 48% of the markers mapped to a unique position. For identical numbers of meioses and intermarker distances, genetic maps constructed from microsatellite markers will be more precise than maps assembled from SNP markers, due to the higher levels of heterozygosity for microsatellite markers.

Linkage analysis in schizophrenia using a neurocognitive phenotype

Linkage disequilibrium (LD), the observed correlation between alleles at different loci in the genome, is a determinant parameter in many applications of molecular genetics. With the wider use of genomic technologies in animal breeding and animal genetics, it is worthwhile revising and improving the current knowledge and understanding of cattle LD.This study analyzes levels of LD assessed through the r2 measurement in seven breeds of cattle from both indicine (Bos indicus) and taurine (Bos taurus) (sub)species, genotyped with a high density panel (HD) of over 777,000 single nucleotide polymorphism (SNP) markers. Average levels of LD were assessed for inter-marker distances from 0 kb up to 10 Mb. Two more SNP panels were built in silico from the original genotypes to represent a lower density SNP chip including approximately 50,000 SNPs (50K) and a panel of 249,000 SNPs chosen to comply with specific minor allele frequency (MAF) distributions.The results show higher levels of LD than previously reported, especially at short inter-marker distances of less than 20 kb, assessed through the use of the higher density panel. Negligible impact of MAF changes in the estimation of r2 was observed, supporting the use of the HD panel for LD-based methodologies even when ascertainment bias in the choice of SNPs is suspected. The 50K SNP panel indicated lower levels of LD in the first 100 kb and highly unreliable LD estimates for distances shorter than 50 kb. Overall, lower levels of LD were observed for all indicine breeds as compared to taurine breeds, with larger differences assessed in the first 100 kb, suggesting the need for use of higher SNP densities in this (sub)species when applying LD-dependent methods, as compared to most taurine breeds.

Localization of a Susceptibility Gene for Common Forms of Stroke to 5q12

Stroke is one of the most complex diseases, with several subtypes, as well as secondary risk factors, such as hypertension, hyperlipidemia, and diabetes, which, in turn, have genetic and environmental risk factors of their own. Here, we report the results of a genomewide search for susceptibility genes for the common forms of stroke. We cross-matched a population-based list of patients with stroke in Iceland with an extensive computerized genealogy database clustering 476 patients with stroke within 179 extended pedigrees. Linkage to 5q12 was detected, and the LOD score at this locus meets the criteria for genomewide significance (multipoint allele-sharing LOD score of 4.40, P=3.9 x 10(-6)). A 20-cM region on 5q was physically and genetically mapped to obtain accurate marker order and intermarker distances. This locus on 5q12, which we have designated as "STRK1," does not correspond to known susceptibility loci for stroke or for its risk factors and represents the first mapping of a locus for common stroke.

Peaks of Linkage Are Localized by a BAC/PAC Contig of the 6p Reading Disability Locus

A gene for reading disability has been localized by nonparametric linkage to 6p21.3–p22 in several published reports. However, the lack of an uninterrupted genomic clone contig has made it difficult to determine accurate intermarker distances, precise marker order, and genetic boundaries and hinders direct comparisons of linkage. The search and discovery of the hemochromatosis gene (HFE) led to the creation of a bacterial artificial chromosome (BAC) and P-1 derived artificial chromosome (PAC) contig that extended physical maps 4 Mb from the MHC toward pter and localized new markers in that region [10-12]. Using this contig, we localized 124 sequence tagged sites, expressed sequence tags, and short tandem repeats including most of the markers in linkage with reading disability phenotypes, succinic semialdehyde dehydrogenase, GPLD1, prolactin, and 18 uncharacterized genes. This new contig joins and extends previously published physical maps to span the entire chromosome 6 reading disability genetic locus. Physical mapping data from the complete contig show overlap of the published linkage peaks for reading disability, provide accurate intermarker distances and order, and offer resources for generating additional markers and candidate genes for highresolution genetic studies in this region.

Linkage mapping in populations with karyotypic rearrangements.

A simulation study was used to examine the consequences of karyotypic rearrangements on molecular genetic map construction. Two groups of 50 datasets were created for F2 populations segregating for a reciprocal translocation of chromosomal segments or a reciprocal translocation and inversion. Multiple attempts were made to construct maps for each dataset using MapMaker/EXP. As expected, the markers from segments involved in the translocation formed one linkage group. Maps that corresponded to the known marker order within a segment could be constructed by the following method. The separation of markers distal to the translocation breakpoints into their respective segments could be made by constructing multiple maps, using distinct orders of marker entry, and observing the variances in intermarker distances: variances between pairs of markers from the same segment were an order of magnitude less compared to pairs where markers were from different segments. The order of markers within a segment could be determined from combining the pairwise linkage results from multiple maps, or from maps including all markers from a segment. No bias in map distances was observed. These results indicate that, under conditions similar to those tested, genetic maps corresponding to the segments conserved in translocations can be constructed.

Automated calibration in vascular X-ray images using the accurate localization of catheter marker bands.

To develop a new automated calibration method for vessel measurements in vascular x-ray images. Radiopaque marker bands mounted equidistantly on a small catheter were acquired in vitro at five image intensifier (II) sizes in x-ray projection images. The positions of the marker centers were detected by using a Hough transform and were computed at subpixel precision by using either a novel, iterative center-of-gravity approach (CGA) or a symmetry filter. Curve-fitting procedures were used to reject false-positive marker detections and to calculate intermarker distances. The calibration factor was calculated from the true marker distance and the average of the measured distances in pixels. Results were compared statistically with a grid calibration method, which was taken as the gold standard. A simulation study was performed to assess the influence of image noise on the CGA method. The iterative CGA method was convergent and faster than the symmetry-based technique. For four II sizes (17, 20, 25, and 31 cm), the results from the CGA method were not significantly different from the results obtained with grid calibration. For the II size of 38 cm, a significant difference (0.3% of the grid calibration factor) was found; however, this was caused by the quantification error in the image data and was not clinically relevant. In general, the performance of the CGA method improved with increasing signal-to-noise ratio. A practical new calibration method for small catheter sizes was developed and validated for quantitative vascular arteriography.

A Genomewide Analysis Provides Evidence for Novel Linkages in Inflammatory Bowel Disease in a Large European Cohort

Inflammatory bowel disease (IBD) is characterized by a chronic relapsing intestinal inflammation, typically starting in early adulthood. IBD is subdivided into two subtypes, on the basis of clinical and histologic features: Crohn disease and ulcerative colitis (UC). Previous genomewide searches identified regions harboring susceptibility loci on chromosomes 1, 3, 4, 7, 12, and 16. To expand our understanding of the genetic risk profile, we performed a 9-cM genomewide search for susceptibility loci in 268 families containing 353 affected sibling pairs. Previous linkages on chromosomes 12 and 16 were replicated, and the chromosome 4 linkage was extended in this sample. New suggestive evidence for autosomal linkages was observed on chromosomes 1, 6, 10, and 22, with LOD scores of 2.08, 2.07, 2.30, and 1.52, respectively. A maximum LOD score of 1.76 was observed on the X chromosome, for UC, which is consistent with the clinical association of IBD with Ullrich-Turner syndrome. The linkage finding on chromosome 6p is of interest, given the possible contribution of human leukocyte antigen and tumor necrosis-factor genes in IBD. This genomewide linkage scan, done with a large family cohort, has confirmed three previous IBD linkages and has provided evidence for five additional regions that may harbor IBD predisposition genes.

Multipoint Linkage Analysis

Multipoint linkage analysis is commonly used to evaluate linkage of a disease to multiple markers in a small region. Multipoint analysis is particularly powerful when the IBD relations of family members at the trait locus are ambiguous. The increased power arises because, unlike single-marker analyses, multipoint analysis uses haplotype information from several markers to infer the IBD relations. We wish to temper this advantage with a cautionary note: multipoint analysis is sensitive to power loss due to misspecification of intermarker distances. Such misspecification is especially problematic when dealing with closely spaced markers. We present computer simulations comparing the power of single-point and multipoint analyses, both when IBD relations are ambiguous, and when the intermarker distances are misspecified. We conclude that when evaluating markers in a small region to confirm or refute previous findings, a situation in which p values of modest statistical significance are important, single marker analyses may provide more reliable measures of the strength of support for linkage than multipoint statistics.