MixupMapper: correcting sample mix-ups in genome-wide datasets increases power to detect small genetic effects

MOTIVATION: Sample mix-ups can arise during sample collection, handling, genotyping or data management. It is unclear how often sample mix-ups occur in genome-wide studies, as there currently are no post hoc methods that can identify these mix-ups in unrelated samples. We have therefore developed an algorithm (MixupMapper) that can both detect and correct sample mix-ups in genome-wide studies that study gene expression levels. RESULTS: We applied MixupMapper to five publicly available human genetical genomics datasets. On average, 3% of all analyzed samples had been assigned incorrect expression phenotypes: in one of the datasets 23% of the samples had incorrect expression phenotypes. The consequences of sample mix-ups are substantial: when we corrected these sample mix-ups, we identified on average 15% more significant cis-expression quantitative trait loci (cis-eQTLs). In one dataset, we identified three times as many significant cis-eQTLs after correction. Furthermore, we show through simulations that sample mix-ups can lead to an underestimation of the explained heritability of complex traits in genome-wide association datasets. Availability and implementation: MixupMapper is freely available at http://www.genenetwork.nl/mixupmapper/     

Prevalence of primary and secondary hypertension: studies in a random population sample.

The prevalence of primary and secondary hypertension was determined in a random sample of 7455 Swedish men aged 47 to 54 years. Three hundred and sizty-one men were undergoing treatment for hypertension. Seven hundred and ninety-eight men who had blood pressures above 175/115 mm Hg at preliminary screening were recalled for further blood pressure measurements. Those on treatment and all the untreated men whose blood pressures were still over 175/115 mm Hg then underwent extensive investigation for secondary hypertension. Renal parenchymal hypertension was found in 25 (3-6%) patients, renovascular hypertension in four (0-6%), and other forms of secondary hypertension in 11 (1-6%). The investigation led to surgical treatment in only two cases (0-3%). The low prevalence of secondary hypertension, especially surgically curable forms of hypertension, makes routine screening for these cases unnecessary, at least when patients with hypertension have been found at screening. These data must be taken into account in planning community control programmes in hypertension.     

Chromosome mosaicism in a population sample.

An analysis has been made of mosaicism found in the different types of chromosome abnormalities among the 19000 persons examined at the Cytogenetic Laboratory, Risskov. The percentage with mosaicism was 36 in both triple-X and Turner's syndrome, it was 7 and 11% in XYY and Klinefelter's syndrome, respectively, and 2 in autosomal abnormalities. We found a mosaicism frequency of 11% in population studies with 5 cells analyzed primarily compared with 7% in other studies, in which 10-50 cells were analyzed primarily. (The difference is not significant.) The total frequency of mosaicism was 8%. The first cell with the chromosome aberration establishing the mosaicism was found among the first 5 cells in 40 of the 44 cases with mosaicism, and all but one of the 44 cases would have been established as mosaics, if the guidlines indicated by Bochkov et al. (1974) had been followed; that is 11 cells analyzed primarily, and if one of these cells has a chromosome aberration, the number of cells analyzed is increased to 17; if 2 cells have the same chromosome aberration, the number of cells analyzed is extended to 23, and if 3 cells with the same chromosome aberration is found among these 23 cells, the mosaicism is established. Aneuploid or structural chromosome abnormalities present in all cells may be detected by analysis of 2-3 cells of good quality. Mosaicism with 2 or more cell clones with different chromosome patterns are extremely difficult to detect, if the percentage of cell clones with chromosome aberration is low. The incidence of chromosome abnormalities found in all cells in newborn children in the different studies is very similar as shown in a recent survey of 6 different studies by Jacobs et al. (1974). The incidence of mosaicism varies according to the frequency of artefactual aneuploidy, the variety of tissue studied, number of cells analyzed from each tissue as well as the acuity of the observer and the checking procedures.     

Haptoglobin subtypes in a Bengalee population sample.

HP1 subtyping has been performed on a Bengalee population sample of heterogeneous caste composition. The total sample size comes to n = 140 nonrelated adult individuals (68 males, 72 females). The following allele frequencies were observed: HP*1F = 0.0714, HP*1S = 0.1178, and HP*2 = 0.8107. It can be pointed out that the HP subtype distribution pattern found in the Bengalee sample follows in general the Oriental distribution pattern, though some differences are seen, especially concerning the HP*1F frequency.     

Aneuploidy and ageing: chromosome studies on a random sample of the population using G-banding.

Chromosome analysis using G-banding was carried out on cells from 65 males and 102 females of all ages from a random sample of the population. The frequency of aneuploid cells showed a significant increase with age in both sexes, and in females the increase in hypodiploidy and hyperdiploidy was more marked than in males, and involved a high proportion of cells that had lost or gained an X chromosome, 45,X cells being much more common than 47,XXX cells. In females, the occurrence of a "fragment" of an X chromosome also correlated with increasing age, and this "fragment" appears to be an X chromosome that has simply divided prematurely at the centromere. The effects of time in culture and of repeating cultures of blood samples from the same individual on proportions of abnormal cells of various types were also investigated, and the results are discussed in the light of findings from several other "ageing surveys".     

Detecting sample misidentifications in genetic association studies

Genetic association studies require that the genotype data from a given person can be correctly linked to the phenotype data from the same person. However, sample misidentification errors sometimes happen, whereby the link becomes invalid for some of the subjects in a study. This can have substantial consequences in terms of power to detect truly associated variants. In family-based studies, Mendelian inconsistencies can be used to detect sample misidentification. Genome-wide association studies (GWAS), however, typically use unrelated individuals, making error detection more problematic. Here we present a method for identifying potential sample misidentifications in GWAS and other genetic association studies building on ideas from forensic sciences. A widely used ad-hoc method for error detection is to check if the sex of an individual matches its X-linked genotype. We generalize this idea to less stringent associations between known genotypes and phenotypes, and show that if several known associations are combined, the power to detect misidentifications increases substantially. Individuals with an unlikely set of phenotypes given their genotypes are flagged as potential errors. We provide analytical and simulation results comparing the odds that the genotype and phenotype are both from the same individual for different numbers of available genotype-p henotype associations and for different information content of the associations. Our method has good sensitivity and specificity with as few as ten moderately informative genotype-phenotype associations. We apply the method to GWAS data from the Danish National Birth Cohort.     

Micronuclei and ageing in a sample of Yugoslavian population

OBJECTIVE: Instability in the organization and expression of the genetic material has been hypothesized as the basic mechanism of ageing. Aim of this study was to quantify the effect of ageing on spontaneous micronuclei (MN) frequency in peripheral blood lymphocytes. METHOD: Analysis of Yugoslavian population sample (164 tested individuals, age 0-62 years) has performed by application of cytokinesis-block technique (CB). RESULTS: There was an increase of MN frequency with age, from newborns to 40-year-old persons. The total average of MN frequency per 1000 analyzed binuclear cells amounts to 8.03 +/- 0.42, with variation from 0 to 26 MNs. In a sample of 29 newborns the recorded average MN frequency was 6.91 +/- 0.81, while among 69 persons 25-39 years old, the MN frequency was 9.16 +/- 1.00. The lowest average MN frequency, however, was noted in the sample of 34 tested individuals 40 to 62 years of age. CONCLUSION: An increase with age in MN frequency has been observed in samples of studied individuals from newborns to 40-year-old persons. A decrease of MN frequency in older groups could be explained by a gradual decrease of proliferative cell capacities.     

Distribution of anti-HAV in a population sample from Puglia

To investigate the prevalence and distribution of antibody to hepatitis A virus (anti-HAV), we tested by solid phase radioimmunoassay method 461 sera of selected people of Bari, according to age. In addiction, sera from cord blood of 11 newborns and their mothers at delivery were also investigated for anti-HAV. Taken together 64.4 per cent of subjects tested were found to be anti-HAV positive. The rate of antibody detection was strongly correlated with age. The prevalence were 4.5 per cent from 6 months to 3 years but gradually increased throughout childhood (from 35.6 to 80 per cent). Anti-HAV was detected in all cord blood samples from newborns whose mothers carried anti-HAV. These data suggest that circulation of hepatitis A virus in our area is very high, so that serological evidence of infection become evident in the majority of individuals during infancy.     

Middle phalangeal hair distribution in a Sardinian population sample

Data relating to middle phalangeal hair (MPH) among unrelated individuals of both sexes born and living in Sardinia are presented. The occurrence of MPH is generally manifested on the 3-4-5 digits of both hands in the two sexes. The observed sex differences are statistically non-significant. The Sardinian sample seems to have a marked decrease in the frequency of individuals with MPH with regard to Mediterranean and other European populations.     

Power and sample size estimation in microarray studies

Background  

Before conducting a microarray experiment, one important issue that needs to be determined is the number of arrays required in order to have adequate power to identify differentially expressed genes. This paper discusses some crucial issues in the problem formulation, parameter specifications, and approaches that are commonly proposed for sample size estimation in microarray experiments. Common methods for sample size estimation are formulated as the minimum sample size necessary to achieve a specified sensitivity (proportion of detected truly differentially expressed genes) on average at a specified false discovery rate (FDR) level and specified expected proportion (π ₁) of the true differentially expression genes in the array. Unfortunately, the probability of detecting the specified sensitivity in such a formulation can be low. We formulate the sample size problem as the number of arrays needed to achieve a specified sensitivity with 95% probability at the specified significance level. A permutation method using a small pilot dataset to estimate sample size is proposed. This method accounts for correlation and effect size heterogeneity among genes.     

Characterization of gout in a skeletal population sample: Presumptive diagnosis in a micronesian population

Characterization of the nature and skeletal distribution of gout was accomplished in a Chamoru (Chamorros) population with predilection to the disease. Uniform excavation by the gouty diathesis produces a punched-out appearance to these predominantly monarticular lesions. The lesion is distinct from that seen in rheumatoid arthritis, spondyloarthropathy, or infection. Reactive new bone formation in some gouty lesions also has an apparently unique, ivory-like discoloration (contrasted with the adjacent bone), which facilitates diagnosis. © 1995 Wiley-Liss, Inc.     

Chromosome studies in a neonatal population

The results of chromosome studies on 6809 consecutive newborn infants are presented. One hundred and one (1.48%) were heterozygous for a marker chromosome, the significance of which is not at present clear. Twenty-two infants (0.32%) had a major chromosome abnormality. Only six of these infants (0.09%) had a clinically recognizable abnormal phenotype (Down''s syndrome). The occult chromosome abnormalities included five sex chromosome abnormalities (one 47,XYY; two 47,XXY; two 47,XXX) and 11 balanced translocations. Seven of these were t(DqDq) and four were reciprocal translocations. The results of the present survey are combined with four other similar neonatal surveys in which a total of 23,328 newborns have been screened. Of these, 117 (0.5%; range 0.65-0.32%) had major chromosome abnormalities. The majority of these (72.7%) would not have been detected at birth without chromosome studies, an important fact in the context of prenatal diagnosis of chromosome disease and the early ascertainment of high-risk families.     

Mutagen sensitivity assays in population studies

Human population monitoring studies are frequently conducted to determine if exposure to environmental mutagenic agents can cause health problems or not. In these studies, a variety of biomarkers are used to identify biological events that are predictive of health consequences. An emphasis in this report is on the use of mutagen sensitivity assays to understand health risk. The assay is based on the assumption that exposure to mutagenic chemicals or mixtures of chemicals for a long time can cause cellular changes that are expressed as mutagen sensitivity. From experience in using these assays in cancer patients and in mutagen-exposed populations, it is clear that the expression of mutagen sensitivity is based on the interactions between mutagen exposure and individual susceptibility. When studies are conducted under appropriate conditions, expression of mutagen sensitivity is suggestive of increased risk for environmental disease such as cancer.