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At least 937 records · Page 52Linked to original sources
PubMed2005

The French Congenital Central Hypoventilation Syndrome Registry: general data, phenotype, and genotype.

OBJECTIVE: To analyze the main clinical features, genetic mutations, and outcomes of patients of the French Congenital Central Hypoventilation Syndrome (CCHS) Registry. DESIGN: A country-wide cohort established throughout a long-term multicenter effort. PATIENTS: Seventy French patients with CCHS (29 male patients and 41 female patients). METHODS: The following items were analyzed: the most important moments of the disease course; the main clinical characteristics; associated pathologic conditions; management; clinical outcome; and genetic mutations. RESULTS: An average of four new cases of CCHS per year was observed in the last 5 years. Thus, the incidence may be estimated to be 1 per 200,000 live births in France. The median age at diagnosis was 3.5 months (range, 0.5 to 15 months) before 1995 and < 2 weeks in the last 5 years (p = 0.01). CCHS occurred in isolation in 58 of 70 patients. In the remainder, it was associated with Hirschsprung disease (HSCR) [nine patients], Hirschsprung and neural crest tumor (two patients), and growth hormone deficiency (one patient). Among the 50 patients who lived beyond 1 year of age, all but one received nighttime ventilation, with 10 of them (20%) receiving it noninvasively. Three patients (6%) required daytime ventilatory support in addition to nighttime ventilation. The overall mortality rate was 38% (95% confidence interval [CI], 27 to 49%). The median age at death was 3 months (range, 0.4 months to 21 years). The 2-year mortality rate was greater in male patients than in female patients (p = 0.02; relative risk [RR], 2.71; 95% CI, 1.14 to 6.47) but was not affected by HSCR (p = 0.93; RR, 0.95; 95% CI, 0.28 to 3.2). The 43 patients who are currently alive (11 men; sex ratio, 0.4) have a mean age of 9 years (range, 2 months to 27 years). Among the 34 patients tested thus far, heterozygous mutations of the paired-like homeobox gene 2B (PHOX2B) gene were found in 31 patients (91%). CONCLUSION: Our four major findings are the extreme rarity of CCHS, the improved recognition over time, the lack of effect of HSCR on the mortality rate, and the high frequency of PHOX2B mutations.

Female↗
PubMed2005

Inference and analysis of haplotypes from combined genotyping studies deposited in dbSNP.

In the attempt to understand human variation and the genetic basis of complex disease, a tremendous number of single nucleotide polymorphisms (SNPs) have been discovered and deposited into NCBI's dbSNP public database. More than 2.7 million SNPs in the database have genotype information. This data provides an invaluable resource for understanding the structure of human variation and the design of genetic association studies. The genotypes deposited to dbSNP are unphased, and thus, the haplotype information is unknown. We applied the phasing method HAP to obtain the haplotype information, block partitions, and tag SNPs for all publicly available genotype data and deposited this information into the dbSNP database. We also deposited the orthologous chimpanzee reference sequence for each predicted haplotype block computed using the UCSC BLASTZ alignments of human and chimpanzee. Using dbSNP, researchers can now easily perform analyses using multiple genotype data sets from the same genomic regions. Dense and sparse genotype data sets from the same region were combined to show that the number of common haplotypes is significantly underestimated in whole genome data sets, while the predicted haplotypes over the common SNPs are consistent between studies. To validate the accuracy of the predictions, we bench-marked HAP's running time and phasing accuracy against PHASE. Although HAP is slightly less accurate than PHASE, HAP is over 1000 times faster than PHASE, making it suitable for application to the entire set of genotypes in dbSNP.

Animals↗
PubMed2006

Optimal genotype determination in highly multiplexed SNP data.

High-throughput genotyping technologies that enable large association studies are already available. Tools for genotype determination starting from raw signal intensities need to be automated, robust, and flexible to provide optimal genotype determination given the specific requirements of a study. The key metrics describing the performance of a custom genotyping study are assay conversion, call rate, and genotype accuracy. These three metrics can be traded off against each other. Using the highly multiplexed Molecular Inversion Probe technology as an example, we describe a methodology for identifying the optimal trade-off. The methodology comprises: a robust clustering algorithm and assessment of a large number of data filter sets. The clustering algorithm allows for automatic genotype determination. Many different sets of filters are then applied to the clustered data, and performance metrics resulting from each filter set are calculated. These performance metrics relate to the power of a study and provide a framework to choose the most suitable filter set to the particular study.

Algorithms↗
PubMed2001

A new statistical method for haplotype reconstruction from population data.

Current routine genotyping methods typically do not provide haplotype information, which is essential for many analyses of fine-scale molecular-genetics data. Haplotypes can be obtained, at considerable cost, experimentally or (partially) through genotyping of additional family members. Alternatively, a statistical method can be used to infer phase and to reconstruct haplotypes. We present a new statistical method, applicable to genotype data at linked loci from a population sample, that improves substantially on current algorithms; often, error rates are reduced by > 50%, relative to its nearest competitor. Furthermore, our algorithm performs well in absolute terms, suggesting that reconstructing haplotypes experimentally or by genotyping additional family members may be an inefficient use of resources.

Algorithms↗
PubMed2003

Summary report: Missing data and pedigree and genotyping errors.

Genetic epidemiology is faced with mapping complex traits to genes with relatively small effects whose phenotypes may be modulated by temporal factors. To do this, detailed and accurate data must be available on families, perhaps collected over time. The Framingham Heart Study data supplied to Genetic Analysis Workshop 13 (GAW13), along with its simulated counterpart, contain longitudinal measurements and genomic scan data on 2,885 individuals in 330 families, and offer an opportunity to examine data quality and completeness issues as they affect analytical conclusions. Six GAW13 contributions applied methods to deal with missing data, both phenotypic and genotypic, at a single time point and longitudinally, and with possible errors in pedigree structure and genotypes. The methods included missing phenotypic data imputation by Markov chain Monte Carlo sampling, propensity scoring, regression, and adjusted mean values, as well as the assessment of transmission-disequilibrium tests when missing marker data may be allele-specific. Pedigree structural errors were found by genome-wide allele-sharing probabilities, while Mendelian consistent genotype errors were evaluated through likelihoods of double-recombination events. Each of the methods reviewed here offered insights into how to better take advantage of large, time-dependent, familial data sets. However, no one of them dealt with the longitudinal and familial aspects simultaneously. Overall, more consideration needs to be given to the effects that missing data and data errors have on our ability to map complex traits efficiently and accurately.

Cardiovascular Diseases↗
PubMed2006

High-density haplotyping with microarray-based expression and single feature polymorphism markers in Arabidopsis.

Expression microarrays hybridized with RNA can simultaneously provide both phenotypic (gene expression) and genotypic (marker) data. We developed two types of genetic markers from Affymetrix GeneChip expression data to generate detailed haplotypes for 148 recombinant inbred lines (RILs) derived from Arabidopsis thaliana accessions Bayreuth and Shahdara. Gene expression markers (GEMs) are based on differences in transcript levels that exhibit bimodal distributions in segregating progeny, while single feature polymorphism (SFP) markers rely on differences in hybridization to individual oligonucleotide probes. Unlike SFPs, GEMs can be derived from any type of DNA-based expression microarray. Our method identifies SFPs independent of a gene's expression level. Alleles for each GEM and SFP marker were ascertained with GeneChip data from parental accessions as well as RILs; a novel algorithm for allele determination using RIL distributions capitalized on the high level of genetic replication per locus. GEMs and SFP markers provided robust markers in 187 and 968 genes, respectively, which allowed estimation of gene order consistent with that predicted from the Col-0 genomic sequence. Using microarrays on a population to simultaneously measure gene expression variation and obtain genotypic data for a linkage map will facilitate expression QTL analyses without the need for separate genotyping. We have demonstrated that gene expression measurements from microarrays can be leveraged to identify polymorphisms across the genome and can be efficiently developed into genetic markers that are verifiable in a large segregating RIL population. Both marker types also offer opportunities for massively parallel mapping in unsequenced and less studied species.

Arabidopsis↗
PubMed2003

Genetic association tests for family data with missing parental genotypes: a comparison.

We consider three tests for genetic association in data from nuclear families (the Family-Based Association Test (FBAT) test proposed by Rabinowitz and Laird ([2000] Hum. Hered. 50:211-223), a second test proposed by Rabinowitz ([2002] J. Am. Stat. Assoc. 97:742-758), and the Family Genotype Analysis Program (FGAP) nonfounder or partial score test proposed by Clayton ([1999] Am. J. Hum. Genet. 65:1170-1177) and Whittemore and Tu ([2000] Am. J. Hum. Genet. 66:1329-1340)). We show that each test statistic arises from the efficient score of the family data as the solution to a set of constraints on its null expectation. Moreover, the FBAT and Rabinowitz tests (but not the FGAP test) are locally the most powerful among all tests satisfying their constraints. We used simulations to examine how the three tests perform in situations when their assumptions are violated and the number of families is not huge. We found that the FBAT test tended to have less power than the other two tests, particularly when applied to families in whom all offspring were affected. The Rabinowitz and FGAP tests performed similarly, although the latter tended to extract more information from families containing one typed parent. While none of the tests showed good power to detect rare, recessively acting genes, the Rabinowitz test with a sample variance estimate performed particularly poorly in this case. However, the Rabinowitz test with a model-based variance had power comparable to that of the FGAP test, and more accurate type I error rates. We conclude that for the situations we considered, the Rabinowitz test with model-based variance has good power without forfeiting robustness against misspecification of parental genotype probabilities. However, its utility is limited by the lack of a simple algorithm to apply it to families with varying structures and phenotypes.

Family↗
PubMed2005

Genotyping errors, pedigree errors, and missing data.

Our group studied the effects of genotyping errors, pedigree errors, and missing data on a wide range of techniques, with a focus on the role of single-nucleotide polymorphisms (SNPs). Half of our group used simulated data, and half of our group used data from the Collaborative Study on the Genetics of Alcoholism (COGA). The simulated data had no missing genotypes and no genotyping errors, so our group, as a whole, removed data and introduced artificial errors to study the robustness of various techniques. Our teams showed that genotyping errors are less detectable and may have a greater impact on SNPs than on microsatellites, but recently developed methods that account for genotyping errors help reduce false positives, and the assumptions of these methods appear to be supported by observations from repeated genotyping. The ability to detect linkage disequilibrium (LD) was also substantially reduced by missing data; this in turn could affect tagging SNPs chosen to generate haplotypes. In the COGA sample, genotyping measurements were repeated in three ways. First, full-genome screens were performed on three sets of markers: 328 microsatellites, 11,560 SNPs from the Affymetrix GeneChip Mapping 10 K Array marker set, and 4,720 SNPs from the Illumina Linkage III panel. Second, the entire Affymetrix marker set was typed on the same 184 individuals by two different laboratories. Finally, the Affymetrix and Illumina marker panels had 94 SNPs in common. Our teams showed that both SNPs and microsatellites can be readily used to identify pedigree errors, and that SNPs have fewer genotyping errors and a low inconsistency rate. However, a fairly high rate of no-calls, especially for the Affymetrix platform, suggests that the inconsistency rate may be higher than observed.

Alcoholism↗
PubMed2002

The M235T variant of the angiotensinogen gene and the body mass index are useful markers for prevention of hypertension in pregnancy: a tree-based analysis of gene-environment interaction.

We sought to perform a tree-based analysis of lifestyle risk factors for hypertension in pregnancy (HP) with univariate and multivariate analyses. Seventy-eight HP patients and 199 normal controls were recruited from primiparous women 20 to 34 years of age. Data from angiotensinogen (AGT) genotyping and data from a self-administered questionnaire about lifestyle were subjected to univariate and multivariate analyses. By dividing the subjects into two subgroups--those who possessed "the TT genotype of AGT" and "body mass index (BMI) < 24" and those who did not--we were able to examine the acquired risk factors for HP during pregnancy in these two groups. Multivariate analysis selected "mentally stressful condition" and "no antenatal training during pregnancy" in the former group, and "poorly balanced diet" in the latter group. Determination of factors obvious before pregnancy, such as genotype or prepregnancy BMI, may be useful for devising effective individualized strategies for preventing HP.

Adult↗
PubMed1998

Quantitation of hepatitis C virus in liver and peripheral blood mononuclear cells from patients with chronic hepatitis C virus infection.

Since the natural history of hepatitis C virus-associated liver disease and the therapeutic responsiveness might vary according to liver and blood mononuclear cells viral levels, it may be important to quantitate viral RNA in liver, blood mononuclear cells and serum, and to compare these data with genotype, biochemical and histologic data. A polymerase chain reaction-based assay available for serum hepatitis C virus RNA quantitation has been optimized to quantitate viral genomes in liver and peripheral blood mononuclear cells from 47 chronic hepatitis C patients. The procedure permitted hepatitis C virus RNA quantitation in freshly isolated mononuclear cells and in total RNA extracted from frozen mononuclear cells and liver tissue. The intrahepatic viral amount (median: 2.6 x 10(3) copies/microgram RNA; range: 0 to 3.6 x 10(4) copies/microgram RNA) correlated significantly with the hepatitis C virus RNA concentration in serum (r = 0.76, P < .001), but not in mononuclear cells. Viral RNA concentrations in liver (P < .001), serum (P < 0.01) and PBMC (P < 0.05) were significantly higher in hepatitis C virus genotype 1 patients (essentially type 1b) than in non-1 type cases, but were unrelated to biochemical or histologic indexes of disease activity. In conclusion, the optimized assay permit HCV RNA quantitation in liver and peripheral blood mononuclear cells, suggesting that serum viral level is an accurate measurement of intrahepatic viral burden.

Adult↗
PubMed2006

Linkage disequilibrium in cultivated grapevine, Vitis vinifera L.

We present here the first study of linkage disequilibrium (LD) in cultivated grapevine, Vitis vinifera L. subsp. vinifera (sativa), an outcrossing highly heterozygous perennial species. Our goal was to characterize the amount and pattern of LD at the scale of a few centiMorgans (cM) between 38 microsatellite loci located on five linkage groups, in order to assess its origin and potential applications. We used a core collection of 141 cultivars representing the diversity of the cultivated compartment. LD was evaluated with both independence tests and multilocus r2, both on raw genotypic and reconstructed haplotypic data. Significant genotypic LD was found only within linkage groups, extending up to 16.8 cM. It appeared not to be influenced by the weak structure of the sample and seemed to be mainly of haplotypic origin. Significant haplotypic LD was found over 30 cM. Both genotypic and haplotypic r2 values declined to around 0.1 within 5-10 cM, suggesting a rather narrow genetic base of the cultivated compartment and limited recombination since domestication events. These first results open up a few application opportunities for association mapping of QTLs and marker assisted selection.

Chromosome Mapping↗
PubMed2005

Stromal cell-derived factor-1 (SDF-1) gene and susceptibility of Iranian patients with lung cancer.

Stromal cell derived factor-1 (SDF-1), a CXC chemokine that play important roles in tumor growth, angiogenesis and metastasis of tumor cells, has a polymorphism at position 801 of its 3'-untranslated region, known as SDF1-3'A. This polymorphism has been investigated in HIV-1 infection and the susceptibility to breast cancer. In this investigation 72 lung cancer patients and 262 cases of normal healthy control were investigated for the genotype frequency of SDF-1 gene. Genotype frequency was carried out by PCR-RFLP method. Of 72 cancer patients 9 (12.5%) cases were emerged with AA genotype, 38 (52.8%) patients with AG and 25 (34.7%) with GG genotype. Comparison of these data with genotype frequency of SDF-1 gene of 262 normal healthy controls indicates a significant difference among patient and control groups (P=0.008). Results also showed that the frequency of AA and AG genotypes was higher among patients, while the frequency of GG genotype was lower compared to the controls. By considering the importance of SDF-1 in several physiological processes and also its significant biological behavior in cancer metastasis and on the basis of the results of this study we conclude that AA and AG genotypes of SDF-1 may be considered as factors increasing the susceptibility of Iranian patients to lung cancer.

3' Untranslated Regions↗
PubMed2006

Effects of glutathione S-transferase A1 (GSTA1) genotype and potential modifiers on breast cancer risk.

Glutathione S-transferases (GSTs) are phase II enzymes that are involved in the detoxification of a wide range of carcinogens. The novel GSTA1*A and GSTA1*B genetic polymorphism results in differential expression, with lower transcriptional activation of GSTA1*B (variant) than that of GSTA1*A (common) allele. Considering that cruciferous vegetables induce GSTs, which metabolize tobacco smoke carcinogens, we hypothesized that the variant GSTA1*B genotype may predispose women to breast cancer, particularly among low cruciferous vegetable consumers and among smokers. Thus, we evaluated potential relationships between GSTA1 polymorphisms and breast cancer risk, in relation to vegetable consumption and smoking status in the Long Island Breast Cancer Study Project (1996-1997), a population-based case-control study. Genotyping (1036 cases and 1089 controls) was performed, and putative breast cancer risk factors and usual dietary intakes were assessed. Having GSTA1*A/*B or *B/*B genotypes was not associated with increased breast cancer risk, compared to having the common *A/*A genotype. However, among women in the lowest two tertiles of cruciferous vegetable consumption, *B/*B genotypes were associated with increased risk (OR (95% CI)=1.73 (1.10-2.72) for 0-1 servings/week), compared to women with *A/*A genotypes. Among women with *B/*B genotypes, a significant inverse trend between cruciferous vegetable consumption and breast cancer risk was observed (P for trend=0.05), and higher consumption (4+ servings/week) ameliorated the increased risk associated with the genotype. Current smokers with *B/*B genotypes had a 1.89-fold increase in risk (OR (95% CI)=1.89 (1.09-3.25)), compared with never smokers with *A/*A genotypes. These data indicate that GSTA1 genotypes related to reduced GSTA1 expression are associated with increased breast cancer primarily among women with lower consumption of cruciferous vegetables and among current smokers.

Alleles↗
PubMed2006

Comparative analysis of haplotype association mapping algorithms.

BACKGROUND: Finding the genetic causes of quantitative traits is a complex and difficult task. Classical methods for mapping quantitative trail loci (QTL) in miceuse an F2 cross between two strains with substantially different phenotype and an interval mapping method to compute confidence intervals at each position in the genome. This process requires significant resources for breeding and genotyping, and the data generated are usually only applicable to one phenotype of interest. Recently, we reported the application of a haplotype association mapping method which utilizes dense genotyping data across a diverse panel of inbred mouse strains and a marker association algorithm that is independent of any specific phenotype. As the availability of genotyping data grows in size and density, analysis of these haplotype association mapping methods should be of increasing value to the statistical genetics community. RESULTS: We describe a detailed comparative analysis of variations on our marker association method. In particular, we describe the use of inferred haplotypes from adjacent SNPs, parametric and nonparametric statistics, and control of multiple testing error. These results show that nonparametric methods are slightly better in the test cases we study, although the choice of test statistic may often be dependent on the specific phenotype and haplotype structure being studied. The use of multi-SNP windows to infer local haplotype structure is critical to the use of a diverse panel of inbred strains for QTL mapping. Finally, because the marginal effect of any single gene in a complex disease is often relatively small, these methods require the use of sensitive methods for controlling family-wise error. We also report our initial application of this method to phenotypes cataloged in the Mouse Phenome Database. CONCLUSION: The use of inbred strains of mice for QTL mapping has many advantages over traditional methods. However, there are also limitations in comparison to the traditional linkage analysis from F2 and RI lines. Application of these methods requires careful consideration of algorithmic choices based on both theoretical and practical factors. Our findings suggest general guidelines, though a complete evaluation of these methods can only be performed as more genetic data in complex diseases becomes available.

Algorithms↗
PubMed2000

Pharmacogenetic screening for susceptibility to fetal malformations in women.

OBJECTIVE: To present a review of the literature and research on the pharmacogenetics of congenital defects, with a focus on the need for predictive maternal genotype assays. DATA SOURCE: MEDLINE searches (January 1985-January 1999), past reference reviews, and unpublished research. STUDY SELECTION: Review of relevant human, animal, and basic science studies. DATA EXTRACTION: Data on research on polymorphisms, genotyping, cytochrome P450 enzyme systems, epoxide hydrolase, folate metabolism, metabolism of anticonvulsant medications, molecular genetics of neural tube defects, variations in drug metabolism, and environmental exposures were evaluated. DATA SYNTHESIS: Data synthesis includes not only a review of the literature but suggests ways such data might be used to facilitate the development of maternal genotype assays, with the goal of preventing birth defects. CONCLUSIONS: Individuals vary in how they metabolize drugs and handle toxic environmental exposures. In an ideal pregnancy, there is no or limited exposure to medications and environmental agents. However, in women with chronic medical conditions such as heart disease and seizures, this is often not possible. Unfortunately, no techniques have been available to identify those at risk in this population. Gene polymorphisms for a specific enzyme may result in an absence or reduction in the level of enzyme activity or in no change at all, with little effect on the structure/function of the gene product(s); they are not associated with clinical phenotypes in either the mother or the fetus. Other polymorphisms may be only markers. Thus, developing genotyping assays for women that are predictive of phenotype expression in the fetus is the key to screening for polymorphisms. As more mutations are identified and clinical, pharmacologic, biologic, and pharmacokinetic relationships are established, using these polymorphisms to develop a genotyping assay for women may become a clinical reality, possibly leading to preventive prepregnancy or prenatal treatment that may play an increasingly effective role in maternal care.

Congenital Abnormalities↗
PubMed1996

[A study on angiotensin-I converting enzyme polymorphism in CAPD patients].

To clarify the role of genes related to angiotensin-I converting enzyme (ACE), the author investigated polymorphism of the ACE gene in 60 patients undergoing chronic ambulatory peritoneal dialysis (CAPD) and 50 patients undergoing hemodialysis (HD). One hundred healthy subjects were used as controls. The polymorphism was classified into three genotypes, II, ID and DD, according to insertion (I) and deletion (D) using the polymerase chain reaction method. In dialysis patients (CAPD or HD, n = 110), 21.8% had the II genotype, 48.2% the ID genotype, and 30.0% the DD genotype. There was a significant difference in allele frequency between normal subjects (n = 100) (J = 0.63, D = 0.37) and dialysis patients (I = 0.46, D = 0.54) (chi 2 = 12.321, p < 0.001). The mean plasma ACE activity was 9.9 +/- 1.6 IU/l in CAPD patients with the II genotype, 11.6 +/- 4.7 IU/l in CAPD patients with the ID genotype, and 14.5 +/- 3.5 IU/l in CAPD patients with the DD genotype. The mean rate of decrease in residual urinary volume was 0.8 +/- 0.7% per month in CAPD patients with the II genotype 1.4 +/- 1.3% per month in CAPD patients with the ID genotype, and 2.5 +/- 2.0% per month in CAPD patients with the DD genotype. These data showed a significant decrease in urinary volume in CAPD patients with the DD genotype (p < 0.05). The mean rate of decrease in residual urinary volume was positively correlated with the plasma ACE activity (r = 0.13389, p < 0.02). In CAPD patients, the mean cardiothoracic ratio was 46.6 +/- 3.5% in cases with the II genotype, 47.6 +/- 5.5% in cases with the ID genotype, and 52.9 +/- 8.4% in cases with the DD genotype. These data indicated significant cardiac enlargement in DD genotype cases. It can be concluded that CAPD patients with the DD genotype lost their residual renal function more rapidly and had a larger heart, than patients with the other genotypes.

Adult↗
PubMed1998

Structure and functions of human cerebrospinal fluid lipoproteins from individuals of different APOE genotypes.

Recent data have implicated apolipoprotein E (apoE) in neuritic outgrowth, synaptic stability, and Alzheimer's disease; these data led us to examine the normal role of apoE-containing lipoproteins in the central nervous system (CNS). We isolated lipoproteins from human cerebrospinal fluid (CSF) in order to examine their composition and potential functions. CSF particles were composed of approximately one-third protein, one-third phospholipid, and one-third cholesterol. ApoE3 formed homodimers and heterodimers with apoA-II, while apoE4, as expected, was monomeric. We addressed the function of CSF lipoproteins with assays of cholesterol efflux and cholesterol influx. CSF lipoproteins decreased intracellular levels of cholesterol in cholesterol-loaded fibroblasts, suggesting these particles can act to remove excess lipids from cells. CSF lipoproteins competed for 125I-labeled LDL degradation by fibroblasts, suggesting they can also interact with the LDL receptor. Furthermore, CSF lipoproteins labeled with the fluorescent dye Dil were internalized by neuroglioma cells and primary neurons and astrocytes in culture. Together, these data support a model of CSF lipoproteins acting to remove lipids from degenerating cells and delivering lipids to cells for new membrane synthesis or storage.

Aged↗
PubMed2006

Maximum-likelihood estimation of allelic dropout and false allele error rates from microsatellite genotypes in the absence of reference data.

The importance of quantifying and accounting for stochastic genotyping errors when analyzing microsatellite data is increasingly being recognized. This awareness is motivating the development of data analysis methods that not only take errors into consideration but also recognize the difference between two distinct classes of error, allelic dropout and false alleles. Currently methods to estimate rates of allelic dropout and false alleles depend upon the availability of error-free reference genotypes or reliable pedigree data, which are often not available. We have developed a maximum-likelihood-based method for estimating these error rates from a single replication of a sample of genotypes. Simulations show it to be both accurate and robust to modest violations of its underlying assumptions. We have applied the method to estimating error rates in two microsatellite data sets. It is implemented in a computer program, Pedant, which estimates allelic dropout and false allele error rates with 95% confidence regions from microsatellite genotype data and performs power analysis. Pedant is freely available at http://www.stats.gla.ac.uk/ approximately paulj/pedant.html.

Alleles↗