An incomplete enumeration algorithm for an exact test of Hardy-Weinberg proportions with multiple alleles

Testing of Hardy-Weinberg proportions (HWP) with asymptotic goodness-of-fit tests is problematic when the contingency table of observed genotype counts has sparse cells or the sample size is low, and exact procedures are to be preferred. Exact p-values can be (1) calculated via computational demanding enumeration methods or (2) approximated via simulation methods. Our objective was to develop a new algorithm for exact tests of HWP with multiple alleles on the basis of conditional probabilities of genotype arrays, which is faster than existing algorithms. We derived an algorithm for calculating the exact permutation significance value without enumerating all genotype arrays having the same allele counts as the observed one. The algorithm can be used for testing HWP by (1) summation of the conditional probabilities of occurrence of genotype arrays with smaller probability than the observed one, and (2) comparison of the sum with a nominal Type I error rate alpha. Application to published experimental data from seven maize populations showed that the exact test is computationally feasible and reduces the number of enumerated genotype count matrices about 30% compared with previously published algorithms.

Cytokines, autoantibodies and viral antibodies in premorbid and postdiagnostic sera from patients with rheumatoid arthritis: case-control study nested in a cohort of Norwegian blood donors

OBJECTIVE

To assess the timing of changes in cytokines, cytokine-related markers, autoantibodies and viral antibodies in the pathogenesis of rheumatoid arthritis (RA).

METHODS

Case-control study nested in a prospective cohort of 31 330 blood donors in Oslo, Norway. Forty-nine donors developed RA up to 23 years after their most recent blood donation. Stored sera from these donors (case sera) and a sex- and age-matched sample of 245 healthy donors (control sera), and postdiagnostic sera from 33 of the 49 RA cases, were analysed for a panel of cytokines and cytokine-related markers, autoantibodies and antibodies against Epstein-Barr virus and parvovirus B19.

RESULTS

Cytokines and cytokine-related markers were generally negative in case sera from >5 years before the diagnosis of RA. In the 5-year interval immediately before the diagnosis of RA, more case than control sera were positive (odds ratios >2) for interleukin (IL)-1 alpha, IL-1 beta, IL-1 receptor antagonist, IL-4, IL-10, tumour necrosis factor-alpha and soluble tumour necrosis factor receptor I. In postdiagnostic sera, however, 11 of 16 examined cytokines and cytokine-related markers were statistically significantly elevated compared with control sera. Seropositivity for IgG antibodies against cyclic citrullinated peptides and for IgM and IgA rheumatoid factors were seen in case sera from up to 18 years before the diagnosis of RA. IgG antibodies against Epstein-Barr virus and parvovirus B19 did not differ significantly between case and control sera.

CONCLUSIONS

Cytokines and cytokine-related markers appear to be upregulated rather late in RA pathogenesis. In contrast, IgM rheumatoid factor and IgG anti-cyclic citrullinated peptide autoantibodies may precede the diagnosis of RA by up to two decades.

Linkage disequilibrium in two European F(2) flint maize populations under modified recurrent full-sib selection

According to quantitative genetic theory, linkage disequilibrium (LD) can hamper the short- and long-term selection response in recurrent selection (RS) programs. We analyzed LD in two European flint maize populations, KW1265 x D146 (A x B) and D145 x KW1292 (C x D), under modified recurrent full-sib selection. Our objectives were to investigate (1) the decay of initial parental LD present in F(2) populations by three generations of intermating, (2) the generation of new LD in four (A x B) and seven (C x D) selection cycles, and (3) the relationship between LD changes and estimates of the additive genetic variance. We analyzed the F(2) and the intermated populations as well as all selection cycles with 104 (A x B) and 101 (C x D) simple sequence repeat (SSR) markers with a uniform coverage of the entire maize genome. The LD coefficient D and the composite LD measure Delta were estimated and significance tests for LD were performed. LD was reduced by intermating as expected from theory. A directional generation of negative LD between favorable alleles could not be observed during the selection cycles. However, considerable undirectional changes in D were observed, which we attributed to genetic sampling due to the finite population size used for recombination. Consequently, a long-term reduction of the additive genetic variance due to negative LD was not observed. Our experimental results support the hypothesis that in practical RS programs with maize, LD generated by selection is not a limiting factor for obtaining a high selection response.

Temporal changes in allele frequencies in two European F(2) flint maize populations under modified recurrent full-sib selection

Selection and random genetic drift are the two main forces affecting the selection response of recurrent selection (RS) programs by changes in allele frequencies. Therefore, detailed knowledge on allele frequency changes attributable to these forces is of fundamental importance for assessing RS programs. The objectives of our study were to (1) estimate the number, position, and genetic effect of quantitative trait loci (QTL) for selection index and its components in the base populations, (2) determine changes in allele frequencies of QTL regions due to the effects of random genetic drift and selection, and (3) predict allele frequency changes by using QTL results and compare these predictions with observed values. We performed QTL analyses, based on restriction fragment length polymorphisms (RFLPs) and simple sequence repeats (SSRs), in 274 F(2:3) lines of cross KW1265 x D146 (A x B) and 133 F(3:4) lines of cross D145 x KW1292 (C x D) originating from two European flint maize populations. Four (A x B) and seven (C x D) cycles of RS were analyzed with SSRs for significant allele frequency changes due to selection. Several QTL regions for selection index were detected with simple and composite interval mapping. In some of them, flanking markers showed a significant allele frequency change after the first and the final selection cycles. The correlation between observed and predicted allele frequencies was significant only in A x B. We attribute these observations mainly to (1) the high dependence of the power of QTL detection on the population size and (2) the occurrence of undetectable QTL in repulsion phase. Assessment of allele frequency changes in RS programs can be used to detect marker alleles linked to QTL regions under selection pressure.

Correlations between Epstein-Barr virus antibody levels and risk factors for multiple sclerosis in healthy individuals

BACKGROUND

Female gender, human leukocyte antigen (HLA) DR2, tobacco smoking and Epstein-Barr virus (EBV) are established risk factors for multiple sclerosis (MS). Their possible interaction however, has been sparsely studied.

OBJECTIVES

To investigate possible associations between EBV antibody levels and a range of other recognized MS risk factors. DESIGN, SETTING AND STUDY POPULATION: Cross-sectional study undertaken in Denmark based on 517 healthy individuals selected from the Danish population.

METHODS

We measured change in mean log (anti-Epstein-Barr viral capsid antigen (VCA) immune globulin G) using linear regression.

RESULTS

Anti-Epstein-Barr VCA immune globulin G levels were positively correlated with female gender and HLA DR2. Furthermore, current smoking and cumulative tobacco consumption were positively associated with EBV antibody levels.

CONCLUSION

The association between Epstein-Barr VCA antibody levels and non-viral MS risk factors support the view that EBV is critically involved in the etiology of MS. These non-viral MS risk factors may be linked with MS risk through EBV-specific immune responses.

Prediction of single-cross hybrid performance for grain yield and grain dry matter content in maize using AFLP markers associated with QTL

Prediction methods to identify single-cross hybrids with superior yield performance have the potential to greatly improve the efficiency of commercial maize (Zea mays L.) hybrid breeding programs. Our objectives were to (1) identify marker loci associated with quantitative trait loci for hybrid performance or specific combining ability (SCA) in maize, (2) compare hybrid performance prediction by genotypic value estimates with that based on general combining ability (GCA) estimates, and (3) investigate a newly proposed combination of the GCA model with SCA predictions from genotypic value estimates. A total of 270 hybrids was evaluated for grain yield and grain dry matter content in four Dent x Flint factorial mating experiments, their parental inbred lines were genotyped with 20 AFLP primer-enzyme combinations. Markers associated significantly with hybrid performance and SCA were identified, genotypic values and SCA effects were estimated, and four hybrid performance prediction approaches were evaluated. For grain yield, between 38 and 98 significant markers were identified for hybrid performance and between zero and five for SCA. Estimates of prediction efficiency (R (2)) ranged from 0.46 to 0.86 for grain yield and from 0.59 to 0.96 for grain dry matter content. Models enhancing the GCA approach with SCA estimates resulted in the highest prediction efficiency if the SCA to GCA ratio was high. We conclude that it is advantageous for prediction of single-cross hybrids to enhance a GCA-based model with SCA effects estimated from molecular marker data, if SCA variances are of similar or larger importance as GCA variances.

Genetic drift and selection effects of modified recurrent full-sib selection programs in two F2 populations of European flint maize

Selection response of a modified recurrent full-sib (FS) selection scheme conducted in two European flint F(2) maize (Zea mays L.) populations was re-evaluated. Our objectives were to (1) determine the selection response for per se and testcross performance in both populations and (2) separate genetic effects due to selection from those due to random genetic drift. Modified recurrent FS selection was conducted at three locations using an effective population size N(e) = 32 and a selection rate of 25% for a selection index, based on grain yield and grain moisture. Recombination was performed according to a pseudo-factorial mating scheme. Selection response was assessed using a population diallel including the source population and advanced selection cycles, as well as testcrosses with unrelated inbred line testers and the parental F(1) generation. Selection response per cycle was significant for grain yield and grain moisture in both populations. Effects of random genetic drift caused only a small reduction in the selection response. No significant selection response was observed for testcrosses, suggesting that for heterotic traits, such as grain yield, a high frequency of favorable alleles in the elite tester masked the effects of genes segregating in the populations. We conclude that our modified recurrent FS selection is an alternative to other commonly applied intrapopulation recurrent selection schemes, and some of its features may also be useful for increasing the efficiency of interpopulation recurrent selection programs.

Comparison of linkage maps from F2 and three times intermated generations in two populations of European flint maize (Zea mays L.)

Intermated mapping populations are expected to result in high mapping resolution for tightly linked loci. The objectives of our study were to (1) investigate the consequences of constructing linkage maps from intermated populations using mapping methods developed for F(2) populations, (2) compare linkage maps constructed from intermated populations (F(2)Syn3) with maps generated from corresponding F(2) and F(3) base populations, and (3) investigate the advantages of intermated mapping populations for applications in plant breeding programs. We constructed linkage maps for two European flint maize populations (A x B, C x D) by mapping 105 SSR markers in generations F(2) and F(2)Syn3 of population A x B, and 102 SSR markers in generations F(3) and F(2)Syn3 of population C x D. Maps for F(2)Syn3 were constructed with mapping methods for F(2) populations (Map A) as well as with those specifically developed for intermated populations (Map B). Both methods relate map distances to recombination frequencies in a single meiosis and, therefore, did not show a map expansion in F(2)Syn3 compared with maps constructed from the respective F(2) or F(3) base populations. Map A and B differed considerably, presumably because of theoretical shortcomings of Map A. Since loosely linked markers could not unambiguously be mapped in the F(2)Syn3 populations, they may hamper the construction of linkage maps from intermated populations.

Grouping of accessions of Mexican races of maize revisited with SSR markers

Mexican races of maize (Zea mays L.) represent a valuable genetic resource for breeding and genetic surveys. We applied simple sequence repeat (SSR) markers to characterize 25 accessions of races of maize from Mexico. Our objectives were to (1) study the molecular genetic diversity within and among these accessions and (2) examine their relationships as assumed previously on the basis of morphological data. A total of 497 individuals were fingerprinted with 25 SSR markers. We observed a high total number of alleles (7.84 alleles per locus) and total gene diversity (0.61), confirming the broad genetic base of the maize races from Mexico. In addition, the accessions were grouped into distinct racial complexes on the basis of a model-based clustering approach. The principal coordinate analyses of the four Modern Incipient hybrids corroborated the proposed parental races of Chalqueño, Cónico Norteño, Celaya, and Bolita on the basis of the morphological data. Consequently, for some of the accessions, hybridizations provide a clue that can further be used to explain the associations among the Mexican races of maize.

Trends in population parameters and best linear unbiased prediction of progeny performance in a European F(2) maize population under modified recurrent full-sib selection

Recurrent selection is a cyclic breeding procedure designed to improve the mean of a population for the trait(s) under selection. Starting from an F(2) population of European flint maize (Zea mays L.) intermated for three generations, we conducted seven cycles of a modified recurrent full-sib (FS) selection scheme. The objectives of our study were to (1) monitor trends across selection cycles in the estimates of the population mean, additive and dominance variances, (2) compare predicted and realized selection responses, and (3) investigate the usefulness of best linear unbiased prediction (BLUP) of progeny performance under the recurrent FS selection scheme applied. Recurrent FS selection was conducted at three locations using a selection rate of 25% for a selection index, based on grain yield and grain moisture. Recombination was performed according to a pseudo-factorial mating scheme, where the selected FS families were divided into an upper-ranking group of parents mated to the lower-ranking group. Variance components were estimated with restricted maximum likelihood. Average grain yield increased 9.1% per cycle, average grain moisture decreased 1.1% per cycle, and the selection index increased 11.2% per cycle. For the three traits we observed, no significant changes in additive and dominance variances occurred, suggesting future selection response at or near current rates of progress. Predictions of FS family performance in Cn+1 based on mean performance of parental FS families in Cn were of equal or higher precision as those based on the mean additive genetic BLUP of their parents, and corresponding correlations were of moderate size only for grain moisture. The significant increase in grain yield combined with the decrease in grain moisture suggest that the F(2) source population with use of a pseudo-factorial mating scheme is an appealing alternative to other types of source materials and random mating schemes commonly used in recurrent selection.

Identification of essentially derived varieties with molecular markers: an approach based on statistical test theory and computer simulations

Genetic similarities (GS) based on molecular markers have been proposed as a tool for identification of essentially derived varieties (EDVs). Nevertheless, scientifically reliable criteria for discrimination of EDVs and independently derived varieties with GS estimates are scanty, and implementation into practical breeding has not yet taken place. Our objectives were to (1) assess the influence of chromosome number and length, marker density, and distribution, as well as the degree of polymorphism between the parental inbreds on the distribution of GS between parental inbreds and their progenies [GS(P1,O)] derived from F2 and different backcross populations and (2) evaluate these factors with regard to the power for distinguishing F2- versus BC1- and BC1- versus BC2-derived lines with molecular markers. We developed an approach based on statistical test theory for the identification of EDVs with molecular markers. Standard deviations and overlaps of distributions of GS(P1,O) of F2-, BC1-, and BC2-derived lines were smaller with (1) increasing chromosome number and length, (2) increasing marker density, and (3) uniformly instead of randomly distributed markers, approaching a lower boundary determined by the genetic parameters. The degree of polymorphism between the parental inbreds influenced the power only if the remaining number of polymorphic markers was low. Furthermore, suggestions are made for (1) determining the number of markers required to ascertain a given power and (2) EDV identification procedures.

MatInspector and beyond: promoter analysis based on transcription factor binding sites

MOTIVATION

Promoter analysis is an essential step on the way to identify regulatory networks. A prerequisite for successful promoter analysis is the prediction of potential transcription factor binding sites (TFBS) with reasonable accuracy. The next steps in promoter analysis can be tackled only with reliable predictions, e.g. finding phylogenetically conserved patterns or identifying higher order combinations of sites in promoters of co-regulated genes.

RESULTS

We present a new version of the program MatInspector that identifies TFBS in nucleotide sequences using a large library of weight matrices. By introducing a matrix family concept, optimized thresholds, and comparative analysis, the enhanced program produces concise results avoiding redundant and false-positive matches. We describe a number of programs based on MatInspector allowing in-depth promoter analysis (DiAlignTF, FrameWorker) and targeted design of regulatory sequences (SequenceShaper).

Duplicate marker loci can result in incorrect locus orders on linkage maps

Genetic linkage maps, constructed from multi-locus recombination data, are the basis for many applications of molecular markers. For the successful employment of a linkage map, it is essential that the linear order of loci on a chromosome is correct. The objectives of this theoretical study were to (1) investigate the occurrence of incorrect locus orders caused by duplicate marker loci, (2) develop a statistical test for the detection of duplicate markers, and (3) discuss the implications for practical applications of linkage maps. We derived conditions, under which incorrect locus orders do or do not occur with duplicate marker loci for the general case of n markers on a chromosome in a BC(1) mapping population. We further illustrated these conditions numerically for the special case of four markers. On the basis of the extent of segregation distortion, an exact test for the presence of duplicate marker loci was suggested and its power was investigated numerically. Incorrect locus orders caused by duplicate marker loci can (1) negatively affect the assignment of target genes to chromosome regions in a map-based cloning experiment, (2) hinder indirect selection for a favorable allele at a quantitative trait locus, and (3) decrease the efficiency of reducing the length of the chromosome segment attached to a target gene in marker-assisted backcrossing.

Use of SSRs for establishing heterotic groups in subtropical maize

Heterotic groups and patterns are of fundamental importance in hybrid breeding. The objectives of our research were to: (1) investigate the relationship of simple sequence repeats (SSR) based genetic distances between populations and panmictic midparent heterosis (PMPH) in a broad range of CIMMYT maize germplasm, (2) evaluate the usefulness of SSR markers for defining heterotic groups and patterns in subtropical germplasm, and (3) examine applications of SSR markers for broadening heterotic groups by systematic introgression of other germplasm. Published data of two diallels and one factorial evaluated for grain yield were re-analyzed to calculate the PMPH in population hybrids. Additionally, 20 pools and populations widely used in CIMMYT's breeding program were assayed with 83 SSR markers covering the entire maize genome. Correlations of squared modified Roger's distance (MRD(2)) and PMPH were mostly positive and significant, but adaption problems caused deviations in some cases. For intermediate- and early-maturity subtropical germplasm, two heterotic groups could be suggested consisting of a flint and dent composite. We concluded that the relationships between the populations obtained by SSR analyses are in excellent agreement with pedigree information. SSR markers are a valuable complementation to field trials for identifying heterotic groups and can be used to introgress exotic germplasm systematically.

Appendectomy in adulthood and the risk of inflammatory bowel diseases

BACKGROUND

There is controversy as to whether appendectomy protects against the development of ulcerative colitis, but the possible impact of appendectomies performed in adulthood has not been systematically investigated.

METHODS

We conducted a large case-control study based on inpatient records from Veterans Affairs hospitals in the United States for the period 1969-96. We identified 6,172 male patients with ulcerative colitis (age range 19-101 years, mean 57.4 years) and 4,498 male patients with Crohn disease (age range 18-99 years, mean 52.9 years). Each of these case patients was individually age- and race-matched to five other male veterans without recorded history of inflammatory bowel disease. We compared records of prior appendectomies in adulthood for the matched case-control sets using conditional logistic regression.

RESULTS

Overall, both ulcerative colitis (odds ratio (OR) = 1.6, 95% confidence interval (CI): 1.3-2.1) and Crohn disease (OR = 2.5, 95% CI: 2.0-3.3) were significantly and positively associated with history of appendectomy in adulthood. However, risks were not increased at intervals of 15 years or more between appendectomy and inflammatory bowel disease (ulcerative colitis: OR = 0.9, 95% CI: 0.4-2.1; Crohn disease: OR = 1.2. 95% CI: 0.5-2.5).

CONCLUSIONS

The elevated risk of inflammatory bowel disease, notably Crohn disease, after appendectomy probably reflects differential diagnostic difficulties in patients with abdominal pain. Appendectomy carried out during adulthood seems not to confer protection against ulcerative colitis.

Cancers associated with Kaposi's sarcoma (KS) in AIDS: a link between KS herpesvirus and immunoblastic lymphoma

Kaposi's sarcoma (KS), common among persons with acquired immunodeficiency syndrome (AIDS), is caused by KS herpesvirus (KSHV) but whether KSHV causes other malignancies is uncertain. Using linked United States AIDS and cancer registries, we measured the incidence of specific malignancies in persons with AIDS (4-27 months after AIDS onset). We identified associations with KSHV by calculating a relative risk: cancer incidence in persons with KS (all were KSHV-infected) divided by incidence in persons without KS. Using Poisson regression, relative risks were adjusted for human immunodeficiency virus risk group, gender, age, race, and calendar year. We included 189 159 subjects (26 972 with KS). Immunoblastic lymphoma was significantly associated with KS (506 cases; relative risks: unadjusted 2.44, 95%CI 2.00-2.96, adjusted 1.58, 95%CI 1.29-1.93). Only one immunoblastic lymphoma had pleura as primary site. None of 37 other specified malignancies (other non-Hodgkin lymphomas, haematological malignancies, solid tumours) was significantly associated with KS. In summary, the association of immunoblastic lymphoma with KS was specific among examined malignancies and remained significant after statistical adjustment. Our findings, and the previously demonstrated presence of KSHV in the histologically related primary effusion lymphoma, suggest that KSHV is involved in the pathogenesis of some immunoblastic lymphomas.

Risk for anogenital cancer and other cancer among women hospitalized with gonorrhea

BACKGROUND

We investigated the relationship between infections with Neisseria gonorrhoeae and anogenital and other cancers.

METHODS

Nationwide and population based register linkage study utilizing prospectively notified information. The observed numbers of cancers among the women were compared with those expected on the basis of national incidence rates.

RESULTS

In a cohort of 4440 women hospitalized for gonorrhea we observed a total of 227 cases of cervical intraepithelial neoplasia grade III (CIN III), with 103 expected (standardized incidence ratio (SIR), 2.2; 95% confidence interval (CI), 1.9-2.5). No significantly increased risk for other anogenital cancers or cancer at other sites was seen.

CONCLUSIONS

These results support the view that the observed association between gonorrheal infection and subsequent cervical preneoplasia is due mainly to surveillance bias. However, our results also indicate that women hospitalized with a N. gonorrhoeae infection will benefit from the compliance with the regular Pap smear screening programs.

Incidence of Hodgkin's disease in Nordic countries

We analysed age and sex-specific trends in the incidence of Hodgkin's lymphoma in Denmark, Sweden, Norway, and Finland during 1978-97. The incidence of Hodgkin's lymphoma decreased significantly in all age groups above 40 years; there was a significant increase in incidence among adolescents and young adults. This increase occurred primarily for Hodgkin's lymphoma of the nodular sclerosis subtype. These observations emphasise the need to identify risk factors for Hodgkin's lymphoma in the young.

Central activation by histamine-induced itch: analogies to pain processing: a correlational analysis of O-15 H2O positron emission tomography studies

The aim of this study was to identify the functional cerebral network involved in the central processing of itch and to detect analogies and differences to previously identified cerebral activation patterns triggered by painful noxious stimuli. Repeated positron emission tomography regional cerebral blood flow (rCBF) measurements using O15-labeled water were performed in six healthy right-handed male subjects (mean age 32 +/- 2 years). Each subject underwent 12 sequential rCBF measurements. In all subjects a standardized skin prick test was performed on the right forearm 2 min before each rCBF measurement. For activation, histamine was applied in nine tests in logarithmically increasing concentrations from 0.03 to 8%. Three tests were performed with isotonic saline solution serving as a control condition. Itch intensity and unpleasantness were registered with a visual analogue scale during each test. Subtraction analysis between activation and control conditions as well as correlation analysis with covariates were performed. Itch induced a significant activation in the predominantly contralateral somatosensory cortex and in the ipsilateral and contralateral motor areas (supplementary motor area (SMA), premotor cortex, primary motor cortex). Additional significant activations were found in the prefrontal cortex and the cingulate gyrus, but not in subcortical structures nor in the secondary somatosensory cortex. In correlation analyses, several cortical areas showed a graded increase in rCBF with the logarithm of the histamine concentration (bilateral sensorimotor areas and cingulate cortex; contralateral insula, superior temporal cortex and prefrontal cortex) and with itch unpleasantness (contralateral sensorimotor cortex, prefrontal cortex and posterior insula; ipsilateral SMA). Induction of itch results in the activation of a distributed cerebral network. Itch and pain seem to share common pathways (a medial and a lateral processing pathway and a strong projection to the motor system). In contrast to pain activation studies, no subcortical (i.e. thalamic) activations were detected and correlation analyses suggest differences in subjective processing of the two sensations.

Appendectomy and subsequent risk of inflammatory bowel diseases

BACKGROUND

Case-control studies have reported an inverse relationship between appendectomy and the risk of ulcerative colitis, but the association has not been confirmed in prospective studies.

METHODS

Using national hospital discharge registry data in Denmark, the authors followed up 154,434 patients who underwent appendectomy during the period 1977 to 1989 to investigate whether they had subsequent hospitalizations for ulcerative colitis and Crohn's disease. Ratios of observed-to-expected first hospitalizations for inflammatory bowel diseases served as measures of the relative risk (RR).

RESULTS

Hospitalization for ulcerative colitis occurred in 84 patients who had appendectomies versus 97.0 expected (RR = 0.87; 95% CI, 0.69-1.07). RRs were not significantly reduced in subgroups defined by sex, age, time since appendectomy, calendar period, or cause of appendectomy. Hospitalization for Crohn's disease occurred in excess (RR = 2.88; 95% CI, 2.45-3.39; n = 150), notably in the first year after appendectomy (RR = 10.83; 95% CI, 8.49-13.62; n = 73); but after 5 years, the RR was not significantly elevated.

CONCLUSIONS

This large population-based cohort study failed to support a significant inverse association between appendectomy and ulcerative colitis risk in the first decade after the operation. The excess of Crohn's disease shortly after appendectomy most likely reflects differential diagnostic problems in patients newly presenting with abdominal pain.