Identification of distant family relationships

MOTIVATION

Family relationships can be estimated from DNA marker data. Applications arise in a large number of areas including evolution and conservation research, genealogical research in human, plant and animal populations, forensic problems and genetic mapping via linkage and association analyses. Traditionally, likelihood-based approaches to relationship estimation have used unlinked genetic markers. Due to the fact that some relationships cannot be distinguished from data at unlinked markers, and given the limited number of such markers available, there are considerable constraints on the type of identification problem that can be satisfactorily addressed with such approaches. The aim of this article is to explore the potential of linked autosomal single nucleotide polymorphism markers in this context. Throughout, we will view the problem of relationship estimation as one of pedigree identification rather than identity-by-descent, and thus focus on applications where determination of the exact relationship is important.

RESULTS

We show that the increase in information obtained by exploiting large sets of linked markers substantially increases the number of problems that can be solved. Results are presented based on simulations as well as on real data.

AVAILABILITY

The R library FEST is freely available from http://folk.uio.no/thoree/FEST.

A TLR2 polymorphism is associated with type 1 diabetes and allergic asthma

Type 1 diabetes (T1D) and allergic asthma are immune-mediated diseases. Pattern recognition receptors are proteins expressed by cells in the immune system to identify microbial pathogens and endogenous ligands. Toll-like receptors (TLRs) and CD14 are members of this family and could represent a molecular link between microbial infections and immune-mediated diseases. Diverging hypotheses regarding whether there exists a common or inverse genetic etiology behind these immune-mediated diseases have been presented. We aimed to test whether there exist common or inverse associations between polymorphisms in the pattern recognition receptors TLR2, TLR4 and CD14 and T1D and allergic asthma. Eighteen single nucleotide polymorphisms (SNPs) were genotyped in TLR2 (2), TLR4 (12) and CD14 (4) in 700 T1D children, 357 nuclear families with T1D children and 796 children from the 'Environment and Childhood Asthma' study. Allele and haplotype frequencies were analyzed in relation to diseases and in addition transmission disequilibrium test analyses were performed in the family material. Both T1D and allergic asthma were significantly associated with the TLR2 rs3804100 T allele and further associated with the haplotype including this SNP, possibly representing a susceptibility locus common for the two diseases. Neither TLR4 nor CD14 were associated with T1D or allergic asthma.

Estimating haplotype frequency and coverage of databases

A variety of forensic, population, and disease studies are based on haploid DNA (e.g. mitochondrial DNA or Y-chromosome data). For any set of genetic markers databases of conventional size will normally contain only a fraction of all haplotypes. For several applications, reliable estimates of haplotype frequencies, the total number of haplotypes and coverage of the database (the probability that the next random haplotype is contained in the database) will be useful. We propose different approaches to the problem based on classical methods as well as new applications of Principal Component Analysis (PCA). We also discuss previous proposals based on saturation curves. Several conclusions can be inferred from simulated and real data. First, classical estimates of the fraction of unseen haplotypes can be seriously biased. Second, there is no obvious way to decide on required sample size based on traditional approaches. Methods based on testing of hypotheses or length of confidence intervals may appear artificial since no single test or parameter stands out as particularly relevant. Rather the coverage may be more relevant since it indicates the percentage of different haplotypes that are contained in a database; if the coverage is low, there is a considerable chance that the next haplotype to be observed does not appear in the database and this indicates that the database needs to be expanded. Finally, freeware and example data sets accompany the methods discussed in this paper: http://folk.uio.no/thoree/nhap/.

Genome-wide Linkage Analysis with Clustered SNP Markers

Single nucleotide polymorphisms (SNPs) have recently replaced microsatellites as the genetic markers of choice in linkage analysis, primarily because they are more abundant and the genotypes more amenable for automatic calling. One of the most recently launched linkage mapping sets (LMS) is the Applied Biosystems Human LMS 4K, which is a genome-wide linkage set based on the SNPlex™ technology and the use of clustered SNPs. In this article the authors report on their experience with this set and the associated genotyping software GeneMapper® version 4.0, which they have used for linkage analyses in 17 moderate to large families with assumed monogenic disease. For comparison of methods, they also performed a genome-wide linkage analysis in 1 of the 17 families using the Affymetrix GeneChip® Human Mapping 10K 2.0 array. The conclusion is that both methods performed technically well, with high call rates and comparable and low rates of Mendelian inconsistencies. However, genotyping is less automated in GeneMapper® version 4.0 than in the Affymetrix software and thus more time consuming. ( Journal of Biomolecular Screening 2009:92-96)

Polymorphisms in CLEC16A and CIITA at 16p13 are associated with primary adrenal insufficiency

CONTEXT/OBJECTIVES

It is known that different autoimmune diseases often share the same susceptibility genes. In this study we aimed to investigate if loci found associated with common autoimmune diseases in recent genome-wide association studies also could be susceptibility loci for autoimmune Addison's disease (primary adrenal insufficiency).

DESIGN/PATIENTS

A total of 139 tagging single nucleotide polymorphisms (SNPs) in 11 candidate genes (IL2, IL21, IL2RA, CLEC2D, CD69, ERBB3, PTPN11, SH2B3, CLEC16A, CIITA, and PTPN2) were genotyped in a case/control study design consisting of Norwegian Addison's disease patients (n = 332) and Norwegian healthy control individuals (n = 1029). Five SNPs were subsequently selected for analysis in a United Kingdom sample set consisting of Addison's disease patients (n = 210) and controls (n = 191).

RESULTS

Polymorphisms in CLEC16A and CIITA remained significantly associated with Addison's disease in the Norwegian sample set at the 0.05 level, even after correction for multiple testing. CLEC16A and CIITA are both located at 16p13, but linkage disequilibrium patterns and logistical regression analyses suggest that SNPs in these two genes are independently associated with Addison's disease. We were not able to confirm these associations in the United Kingdom material, however, this may well be due to the limited sample size and lack of statistical power.

CONCLUSION

Two alleles at 16p13 are independently associated with the risk of Addison's disease in the Norwegian population, suggesting this chromosomal region to harbor common autoimmunity gene(s), CLEC16A and CIITA being possible independent candidates.

Genetic screening of Scandinavian families with febrile seizures and epilepsy or GEFS+

BACKGROUND

Mutations in the three genes SCN1A, SCN1B and GABRG2, all encoding subunits of ion channels, have been known to cause generalized epilepsy with febrile seizures plus (GEFS+) in families of different origin.

OBJECTIVE

To study the occurrence of mutations in these genes in families with GEFS+ or a GEFS+ resembling phenotype of Scandinavian origin.

MATERIAL AND METHODS

We performed linkage analysis in 19 Scandinavian families with a history of febrile seizures (FS) and epilepsy or GEFS+. Where linkage could not be excluded, the genes of interest were sequenced.

RESULTS

We identified only one mutation in SCN1A, which seems to be a rare variant with no functional consequence.

CONCLUSION

This suggests that mutations in these three genes are not a prevalent cause of familial cases of FS and epilepsy or GEFS+ in Scandinavia.

Mutation screening of PTPN22: association of the 1858T-allele with Addison's disease

The tyrosine-protein phosphatase non-receptor type 22 (PTPN22) gene was recently identified as an important genetic susceptibility factor in several autoimmune diseases. The increased risk has been broadly explained by the 1858T-allele (rs2476601). As two smaller studies on Addison's disease (AD) have shown diverging results, we aimed to elucidate the predisposing effect of the single-nucleotide polymorphism (SNP) 1858CT in a larger population of AD patients, especially focusing on the AD patients with known autoimmune etiology. We also screened for unknown rare or common variants in the PTPN22 gene that could predispose for AD. The case-control study of Norwegian AD patients (n=332) and controls (n=990) showed a significant association between autoimmune AD (n=302) and the PTPN22 1858T risk allele (P=0.016). The association of AD with 1858T was supported by a meta-analysis combining our genotype data with that of others published previously (P=0.003). The mutation screening of PTPN22 in AD patients (n=332) and controls (n=112) revealed eight missense variants, five of which have not been reported previously. In conclusion, the 1858T-allele is a PTPN22 genetic susceptibility factor for autoimmune AD. Other rare variants in PTPN22 do occur, and may also be involved in the pathogenesis.

Adjusting for founder relatedness in a linkage analysis using prior information

In genetic linkage studies, while the pedigrees are generally known, background relatedness between the founding individuals, assumed by definition to be unrelated, can seriously affect the results of the analysis. Likelihood approaches to relationship estimation from genetic marker data can all be expressed in terms of finding the most likely pedigree connecting the individuals of interest. When the true relationship is the main focus, the set of all possible alternative pedigrees can be too large to consider. However, prior information is often available which, when incorporated in a formal and structured way, can restrict this set to a manageable size thus enabling the calculation of a posterior distribution from which inferences can be drawn. Here, the unknown relationships are more of a nuisance factor than of interest in their own right, so the focus is on adjusting the results of the analysis rather than on direct estimation. In this paper, we show how prior information on founder relationships can be exploited in some applications to generate a set of candidate extended pedigrees. We then weight the relevant pedigree-specific likelihoods by their posterior probabilities to adjust the lod score statistics.

T cell-specific T-box transcription factor haplotype is associated with allergic asthma in children

BACKGROUND

T cell-specific T-box transcription factor (T-bet) is a member of the T-box family of transcription factors regulating lineage commitment of T(H) lymphocytes toward a predominant T(H)1 phenotype. Asthma and allergy are common complex diseases characterized by T(H)2-mediated inflammation.

OBJECTIVE

We aimed to assess possible relationships between the T-bet gene (TBX21) and asthma and allergy in children.

METHOD

Twelve single nucleotide polymorphisms (SNPs) in the TBX21 region were genotyped in 948 children from the Environment and Childhood Asthma study. Allele and haplotype frequencies were compared in children with and without asthma (by 10 years) and allergy (> or =1 positive skin prick test response), as well as for the quantitative traits bronchial hyperresponsiveness determined by means of methacholine bronchial challenge testing, lung function determined by means of forced flow volume loops, fractional exhaled nitric oxide measurement, eosinophil count, and serum total IgE level.

RESULTS

Allergic asthma was significantly associated with 2 of the tested SNPs (rs11650354 and rs16947078) and further associated with the particular haplotype including these SNPs, with homozygote status resulting in an odds ratio of 8.3 (95% CI, 2.5-26.9) for allergic asthma. Neither nonallergic asthma or "allergy alone" nor the remaining quantitative variables were associated with TBX21 SNPs or haplotypes.

CONCLUSION

An association between a specific TBX21 haplotype and allergic asthma in children is demonstrated for the first time and might explain previously detected associations between SNPs within TBX21 and asthma and bronchial hyperresponsiveness.

Cross-sex pattern of bone mineral density in early onset gender identity disorder

Hormonally controlled differences in bone mineral density (BMD) between males and females are well studied. The effects of cross-sex hormones on bone metabolism in patients with early onset gender identity disorder (EO-GID), however, are unclear. We examined BMD, total body fat (TBF) and total lean body mass (TLBM) in patients prior to initiation of sex hormone treatment and during treatment at months 3 and 12. The study included 33 EO-GID patients who were approved for sex reassignment and a control group of 122 healthy Norwegians (males, n=77; females, n=45). Male patients (n=12) received an oral dose of 50 mug ethinylestradiol daily for the first 3 months and 100 mug daily thereafter. Female patients (n=21) received 250 mg testosterone enantate intramuscularly every third week. BMD, TBF and TLBM were estimated using dual energy X-ray absorptiometry (DXA). In male patients, the DXA measurements except TBF were significantly lower compared to their same-sex control group at baseline and did not change during treatment. In female patients, the DXA measurements were slightly higher than in same-sex controls at baseline and also remained unchanged during treatment. In conclusion, this study reports that body composition and bone density of EO-GID patients show less pronounced sex differences compared to controls and that bone density was unaffected by cross-sex hormone treatment.

HLA Dr-Dq haplotypes and the TNFA-308 polymorphism: associations with asthma and allergy

BACKGROUND

The HLA (human leukocyte antigen) class II genes DQB1 and DRB1 and the Tumor Necrosis Factor alpha gene (TNFA) within the HLA complex (chromosome 6p21) have been associated with asthma and allergy. Due to the strong linkage disequilibrium characterizing this complex and the multiple asthma/allergy expressions, we aimed to determine which of these genes were primarily involved in specific asthma/allergy traits.

METHODS

The DRB1-DQB1 alleles and TNFA-308 polymorphism were genotyped in 959 children from the Environment and Childhood Asthma study and analyzed for possible associations with allergic and non-allergic asthma (with/without at least one positive skin prick test for allergens) and specific allergic sensitization, as well as bronchial hyperresponsiveness and total IgE, using both allele and extended haplotype analyses.

RESULTS

Different genes within the HLA complex were associated with separate asthma and allergy traits. Nonallergic asthma was associated with both the TNFA-308A allele [Odds ratio (OR) 1.7 (1.3-2.3)] and DRB1 03 allele [OR 1.6(1-2.6)], but extended DRB1 03-TNFA-308 haplotype analysis suggested that the DRB1-DQB1 association was secondary to linkage disequilibrium with the TNFA-308 polymorphism. Allergies were associated with HLA class II alleles only; birch sensitization with DQB1 0603-DRB1 13 [OR 2.3 (1.4-4.0)] and mugwort sensitization with DQB1 0609-DRB1 13 [OR 7.1 (1.9-27.0)] and DQB1 0501-DRB1 01 [OR 2.0 (1.0-4.0)].

CONCLUSIONS

Our data suggests that asthma is not associated with DRB1 or DQB1 but rather TNFA or a gene(s) in linkage disequilibrium, while sensitization to specific allergens is associated with particular alleles at the DQ and/or DR loci. A novel association between DQB1 0603-DRB1 13 and birch allergy is identified.

Eosinophil cationic protein (ECP) polymorphisms and association with asthma, s-ECP levels and related phenotypes

BACKGROUND

Eosinophil cationic protein (ECP) is a potent cytotoxic secretory protein with bactericidal and antiviral properties. ECP is released by activated eosinophils and regarded as a marker of eosinophilic inflammation. High levels of ECP have been reported in cases of active asthma and other allergic diseases. This study aimed to assess whether three single-nucleotide polymorphisms (SNPs) in the ECP gene (RNASE3) on chromosome 14 q24-q31 or their haplotypes are associated with asthma, allergy, or related phenotypes.

METHODS

The three SNPs -38CA, +371CG and +499CG in RNASE3 and their haplotypes were analyzed for associations with asthma, serum-ECP (s-ECP) levels, allergic sensitization (positive skin-prick test to common allergens), bronchial hyperresponsiveness (BHR) assessed by methacholine inhalation, and serum-IgE (s-IgE) levels in 177 families from Norway and the Netherlands identified through siblings with asthma.

RESULTS

Transmission disequilibrium test (TDT) demonstrated significant associations between the A-G-G haplotype and asthma as well as the specific phenotypes allergic asthma (but not non-allergic asthma), high s-ECP, high s-IgE and BHR, while the C-G-G haplotype was associated with reduced occurrence of these traits. In addition, the -38A allele was associated with high s-ECP levels and allergic asthma.

CONCLUSION

The present study suggests that the A-G-G haplotype in the RNASE3 gene influences the development of asthma, in particular, an allergic form of asthma. Furthermore, as the -38CA SNP lies in close vicinity of known intron-regulatory sites, results of SNP analysis suggest that the detected association is possibly linked to a genetic transcriptional control of s-ECP levels.

[Nuts and bolts of percentiles]

BACKGROUND

Decisions regarding diagnosis and treatment of medical conditions are often based on reference values, and these are frequently based on percentiles. We have studied the impact of statistical methods and software on estimates of percentiles.

MATERIAL AND METHODS

Reference values for semen parameters have been based on measured values in fertile men. We have reanalysed our previously published data with different statistical methods for estimation of percentiles. These methods are available in the programme R through the quantile function and include those used in standard programmes such as Minitab, SAS and SPSS.

RESULTS AND INTERPRETATION

Analyses of semen parameters by different non-parametric methods have revealed considerable differences in 5 and 10 percentiles for semen concentration. The differences were substantially smaller for semen motility. Our results imply that reference values should be accompanied by a detailed explanation of the statistical methods used for the estimation of percentiles. In a clinical setting, the choice of method may determine if a test result close to the reference values is considered pathological or not. It is therefore vital to realise that different methods may produce different results. Moreover, it may be difficult to compare reference values reported by different laboratories if the statistical methods differ.

The DNA Database Search Controversy Revisited: Bridging the Bayesian-Frequentist Gap

Two different quantities have been suggested for quantification of evidence in cases where a suspect is found by a search through a database of DNA profiles. The likelihood ratio, typically motivated from a Bayesian setting, is preferred by most experts in the field. The so-called np rule has been suggested through frequentist arguments and has been suggested by the American National Research Council and Stockmarr (1999, Biometrics55, 671-677). The two quantities differ substantially and have given rise to the DNA database search controversy. Although several authors have criticized the different approaches, a full explanation of why these differences appear is still lacking. In this article we show that a P-value in a frequentist hypothesis setting is approximately equal to the result of the np rule. We argue, however, that a more reasonable procedure in this case is to use conditional testing, in which case a P-value directly related to posterior probabilities and the likelihood ratio is obtained. This way of viewing the problem bridges the gap between the Bayesian and frequentist approaches. At the same time it indicates that the np rule should not be used to quantify evidence.

Structured Incorporation of Prior Information in Relationship Identification Problems

The objective of this paper is to show how various sources of information can be modelled and integrated to address relationship identification problems. Applications come from areas as diverse as evolution and conservation research, genealogical research in human, plant and animal populations, and forensic problems including paternity cases, identification following disasters, family reunions and immigration issues. We propose assigning a prior probability distribution to the sample space of pedigrees, calculating the likelihood based on DNA data using available software and posterior probabilities using Bayes' Theorem. Our emphasis here is on the modelling of this prior information in a formal and consistent manner. We introduce the distinction between local and global prior information, whereby local information usually applies to particular components of the pedigree and global prior information refers to more general features. When it is difficult to decide on a prior distribution, robustness to various choices should be studied. When suitable prior information is not available, a flat prior can be used which will then correspond to a strict likelihood approach. In practice, prior information is often considered for these problems, but in a generally ad hoc manner. This paper offers a consistent alternative. We emphasise that many practical problems can be addressed using freely available software.

Prenatal diagnosis of congenital malformations and parental psychological distress-a prospective longitudinal cohort study

OBJECTIVE

To test whether postnatal psychological distress in parents of babies with congenital malformations is reduced by prenatal diagnosis.

METHODS

A prospective observational longitudinal cohort study was conducted at two Norwegian hospitals. We included 293 parents of babies with congenital malformations (prenatal detection rate: 36.5%) referred for neonatal surgery and 249 parents of healthy babies (comparison group). Parental psychological responses were assessed on three postnatal occasions by psychometric instruments (GHQ-28, STAI-X1, and IES).

RESULTS

Significantly increased psychological distress (GHQ-28) was reported by parents who received prenatal diagnosis as compared to postnatal diagnosis; acutely 28.9 versus 24.4, P = 0.006 (comparison group: 19.6); at 6 weeks 26.8 versus 21.5, P < 0.001 (comparison group: 17.7); and at 6 months 22.6 versus 18.7, P = 0.015 (comparison group: 16.6). Mothers consistently reported higher levels of distress than fathers. Multiple linear regression analysis showed that prenatal diagnosis and being a mother significantly predicted severity of acute psychological distress. At 6 weeks and 6 months, mortality and associated anomalies were significant independent predictors of psychological distress.

CONCLUSION

Controlling for other covariates, we found that prenatal diagnosis of congenital malformations was a significant independent predictor of acute parental psychological distress after birth.

Semen parameters in Norwegian fertile men

The World Health Organization (WHO) provides guidelines for assessing the various semen variables. A set of reference ranges is given in the WHO Laboratory Manual for the Examination of Human Semen and Sperm-Cervical Mucus Interaction, but several studies indicate that the values should be revised. Furthermore, semen parameters obtained at different laboratories are not directly comparable even if the same methods are used. Thus, it is recommended that each laboratory establish its own reference ranges. In this study, semen from 99 men who had recently achieved a pregnancy were analyzed to establish reference ranges for semen variables. The reference values were based on the group with time to pregnancy (TTP) 12 cycles or less (92%) and abstinence time from 2 to 7 days. The 5th and 10th percentiles for sperm concentration were 10.6 and 16.9 x 10(6)/mL, respectively, and 33% (5th percentile) and 43% (10th percentile) for spermatozoa with progressive motility. These values were below the WHO lower limit. The percentages of ideal spermatozoa (percentage with normal morphology according to WHO strict criteria) were 3 (5th percentile) and 4 (10th percentile). Thirty-nine percent reported that their partners became pregnant during the first cycle after they had stopped using contraception. The semen parameters in this group were compared with the others. Overall, the semen parameters were more favorable in the group with TTP = 1 cycle than in the group with TTP > 1. Sperm concentration, progressive motility, and percentage of ideal spermatozoa according to WHO strict criteria were significantly different in the 2 groups. However, when analyzed by multiple logistic regression, only "total numbers of sperm with progressive motility" remained in the model (P = .002). This is in accordance with previous studies indicating that a combination of semen characteristics provides a better predictor of male fertility potential than the single parameters. In conclusion, new reference ranges for semen variables deviating from the WHO values are established for our laboratory.

Cross-sex hormone treatment does not change sex-sensitive cognitive performance in gender identity disorder patients

Cognitive performance in untreated early onset gender identity disorder (GID) patients might correspond to their born sex and not to their perceived gender. As a current mode of intervention, cross-sex hormone treatment causes considerable physical changes in GID patients. We asked, as has been suggested, whether this treatment skews cognitive performance towards that of the acquired sex. Somatically healthy male and female early onset GID patients were neuropsychologically tested before, 3 and 12 months after initiating cross-sex hormone treatment, whereas untreated healthy subjects without GID served as controls (C). Performance was assessed by testing six cognitive abilities (perception, arithmetic, rotation, visualization, logic, and verbalization), and controlled for age, education, born sex, endocrine differences and treatment by means of repeated measures analysis of variance. GID patients and controls showed an identical time-dependent improvement in cognitive performance. The slopes were essentially parallel for males and females. There was no significant three-way interaction of born sex by group by time for the six investigated cognitive abilities. Only education and age significantly influenced this improvement. Despite the substantial somatic cross-sex changes in GID patients, no differential effect on cognition over time was found between C and GID participants. The cognitive performance of cross-sex hormone-treated GID patients was virtually identical to that of the control group. The documented test-retest effect should be taken into consideration when evaluating treatment effects generally in psychiatry.

[External cephalic version of breech presentation at term]

BACKGROUND

External cephalic version could be an alternative to either vaginal delivery or caesarean section in breech presentation at term.

MATERIAL AND METHODS

A systematic literature review about external cephalic version in breech presentation.

RESULTS

The numbers of breech presentation delivered by caesarean section could probably be reduced in Norway by offering version, but this would not affect perinatal mortality.