Nonpaternity in Linkage Studies of Extremely Discordant Sib Pairs

An approach commonly used to increase statistical power in linkage studies is the study of extremely discordant sibling pairs. This design is powerful under both additive and dominant-gene models and across a wide range of allele frequencies. A practical problem with the design is that extremely discordant pairs that are ostensibly full sibs may be half sibs. Although estimates vary, the population rates of such nonpaternity may be as high as 5%-10%. The proportion in discordant pairs may be much higher. The present article explores this potential inflation as a function of the resemblance of sib pairs and the criteria for discordance used for selection.     

Intrauterine growth restriction in like-sex twins discordant for structural defects

BACKGROUND: An increased risk for intrauterine growth restriction in the affected member of like-sex twin pairs discordant for hypospadias has been reported. The purpose of this study was to document patterns of birth weight disparities in like-sex twins discordant for a variety of structural defects in order to determine if this is a general phenomenon seen in twins who are discordant for any malformation, is seen only in pairs discordant for certain specific malformations, or is unique to hypospadias. METHODS: Data were extracted from the Latin American Collaborative Study of Congenital Malformations (ECLAMC). Between 1967 and 1999, all like-sex twin pairs discordant for hypospadias or any other isolated defect that met the criteria of at least 5 discordant pairs for which birth weight was available on both twins were selected. All nonmalformed like-sex twin pairs in the ECLAMC data base collected over the same study years were selected as controls. RESULTS: A total of 216 discordant malformed like-sex twin pairs in 13 defect categories and 328 nonmalformed like-sex twin pairs met the criteria for inclusion. The proportion of affected infants who were > or =20% smaller than their co-twin was statistically significantly different from controls for hypospadias, heart defects, anencephaly, and esophageal atresia. CONCLUSIONS: Intrauterine growth restriction seen in the affected member of like-sex twin pairs discordant for hypospadias is not unique, but occurs as well in at least 3 additional structural malformations.     

Composite statistics for QTL mapping with moderately discordant sibling pairs

Extreme discordant sibling-pair (EDSP) designs have been shown in theory to be very powerful for mapping quantitative-trait loci (QTLs) in humans. However, their practical applicability has been somewhat limited by the need to phenotype very large populations to find enough pairs that are extremely discordant. In this paper, we demonstrate that there is also substantial power in pairs that are only moderately discordant, and that designs using moderately discordant pairs can yield a more practical balance between phenotyping and genotyping efforts. The power we demonstrate for moderately discordant pairs stems from a new statistical result. Statistical analysis in discordant-pair studies is generally done by testing for reduced identity by descent (IBD) sharing in the pairs. By contrast, the most commonly-used statistical methods for more standard QTL mapping are Haseman-Elston regression and variance-components analysis. Both of these use statistics that are functions of the trait values given IBD information for the pedigree. We show that IBD sharing statistics and "trait value given IBD" statistics contribute complementary rather than redundant information, and thus that statistics of the two types can be combined to form more powerful tests of linkage. We propose a simple composite statistic, and test it with simulation studies. The simulation results show that our composite statistic increases power only minimally for extremely discordant pairs. However, it boosts the power of moderately discordant pairs substantially and makes them a very practical alternative. Our composite statistic is straightforward to calculate with existing software; we give a practical example of its use by applying it to a Genetic Analysis Workshop (GAW) data set.     

Anxiety and depression in twin and sib pairs extremely discordant and concordant for neuroticism: prodromus to a linkage study.

Multivariate modelling of anxiety and depression data in twins has suggested that the two phenotypes are largely underpinned by one genetic factor, while other studies have indicated a relationship between these disorders and the neuroticism personality trait. As part of a study to identify quantitative trait loci for anxiety and depression, questionnaire responses and interviews of 15,027 Australian twins and 11,389 of their family members conducted during the past 20 years were reviewed to identify individuals with neuroticism, anxiety and depression scores in the upper or lower deciles of the population. This information was then used to identify extreme discordant and concordant (EDAC) sib pairs. 1373 high-scoring and 1571 low-scoring subjects (2357 sib pairs) were selected for participation, and extremely high participation rates were achieved, with over 90% of contactable prospective participants completing the interview phase, and over 90% of these providing blood or buccal samples. Participation bias arising from the nature of the selection variables was minimal, with only a small difference between rates of interview participation among prospective participants with high and low selection scores (89.4% vs 91.6%). The interview permitted the diagnosis of depression and several anxiety disorders (OCD, agoraphobia, panic disorder, generalised anxiety disorder) in this sample according to DSM-IV criteria. The methodology for selection of prospective subjects was demonstrated to be extremely successful, with highly significant differences in depression and anxiety disorder prevalence rates between individuals in the two selection groups. The success of this EDAC sampling scheme will enhance the power for QTL linkage and association analysis in this sample.     

Recent advances in human quantitative-trait-locus mapping: comparison of methods for discordant sibling pairs

Extreme discordant sibling pairs (EDSPs) are theoretically powerful for the mapping of quantitative-trait loci (QTLs) in humans. EDSPs have not been used much in practice, however, because of the need to screen very large populations to find enough pairs that are extreme and discordant. Given appropriate statistical methods, another alternative is to use moderately discordant sibling pairs (MDSPs)--pairs that are discordant but not at the far extremes of the distribution. Such pairs can be powerful yet far easier to collect than extreme discordant pairs. Recent work on statistical methods for QTL mapping in humans has included a number of methods that, though not developed specifically for discordant pairs, may well be powerful for MDSPs and possibly even EDSPs. In the present article, we survey the new statistics and discuss their applicability to discordant pairs. We then use simulation to study the type I error and the power of various statistics for EDSPs and for MDSPs. We conclude that the best statistic(s) for discordant pairs (moderate or extreme) is (are) to be found among the new statistics. We suggest that the new statistics are appropriate for many other designs as well-and that, in fact, they open the way for the exploration of entirely novel designs.     

Variations in genome-wide gene expression in identical twins – a study of primary osteoblast-like culture from female twins discordant for osteoporosis

Background  

Monozygotic twin pairs who are genetically identical would be potentially useful in gene expression study for specific traits as cases and controls, because there would be much less gene expression variation within pairs compared to two unrelated individuals. However the twin pair has to be discordant for the particular trait or phenotype excluding those resulting from known confounders. Such discordant monozygotic twin pairs are rare and very few studies have explored the potential usefulness of this approach.     

Birthweight discordance in multiple pregnancy.

This paper reviews several aspects of discordant growth in multiple pregnancies. Discordant growth is not a chance event and therefore several patterns can be discerned. About 75% of twins exhibit < 15% discordance (concordant), 20% are 15-25% (mildly) discordant, and about 5% are more than 25% (severely) discordant. Higher frequencies and increased severity are seen among triplets. Five observations regarding discordance became generally accepted: (a) not all discordant pairs are similar; (b) the larger the discordance level the greater is the risk for an adverse outcome; (c) discordant growth does not necessarily represent growth restriction; (d) a discordance level may have a different clinical implication in different gestational ages; and (e) the smaller fetuses in severely discordant pairs are at disproportionate risk for neonatal mortality. Mild discordance may represent a normal variation between sibs whereas severely discordant pairs often exhibit patterns of growth restriction. Not infrequently, discordance may represent an adaptation to the limited intrauterine space in order to increase gestational age.     

The Chronic Fatigue Twin Registry: method of construction, composition, and zygosity assignment.

Chronic fatigue syndrome (CFS) and the symptom of chronic fatigue are conditions of unknown etiology. The Centers for Disease Control and Prevention (CDC) define CFS as an illness characterized by > or = 6 months of disabling fatigue associated with muscle pain, pharyngitis, and alterations in mood, sleep and neurocognition. We constructed a registry of twins with chronic fatigue to facilitate research on the impact of illness, the associated medical and psychosocial factors, and the heterogeneous proposed mechanisms for these conditions. We have recruited 204 twin pairs in which one or both members reported persistent fatigue through patient support group newsletters (60%), clinicians/researchers familiar with CFS (12%), notices placed on electronic bulletin boards for CFS (11%), twin organizations and researchers (6%), relatives and friends (3%) and other sources (8%). Complete data are available for 177 pairs (87%). Twins completed an extensive questionnaire booklet that included measures of physical and mental health, functional status, and psychosocial factors; a structured psychiatric interview was also conducted by telephone. Twins were classified using three increasingly more stringent diagnostic criteria for chronic fatigue: 1) > or = 6 months of fatigue (115 discordant and 61 concordant pairs); 2) chronic fatigue with additional symptoms and application of the medial exclusions of the CDC CFS case definition as obtained by self-report (92 discordant and 41 concordant pairs) and; 3) chronic fatigue with additional symptoms unexplained by self-reported medical conditions and psychiatric diagnoses as determined by the structured interview (69 discordant pairs and 25 concordant pairs). Despite the limitations of a volunteer registry, the Chronic Fatigue Twin Registry promises to be an important resource for research on CFS and chronic fatigue.     

Height discordance in monozygotic females is not attributable to discordant inactivation of X-linked stature determining genes.

We tested the hypothesis that X-linked genes determining stature which are subject to skewed or non-random X-inactivation can account for discordance in height in monozygotic female twins. Height discordant female monozygotic adult twins (20 pairs) were identified from the Australian Twin Registry, employing the selection criteria of proven monozygosity and a measured height discordance of at least 5 cm. Differential X-inactivation was examined in genomic DNA extracted from peripheral lymphocytes by estimating differential methylation of alleles at the polymorphic CAG triplet repeat of the Androgen receptor gene (XAR). There were 17/20 MZ pairs heterozygous at this locus and informative for analysis. Of these, 10/17 both had random X-inactivation, 5/17 showed identical X-inactivation patterns of non random inactivation and 2/17 (12%) showed discordant X-inactivation. There was no relationship between inactivation patterns and self-report chorionicity. We conclude that non-random X-inactivation does not appear to be a major contributor to intra-pair height discordance in female MZ twins.     

Altered brain-derived neurotrophic factor blood levels and gene variability are associated with anorexia and bulimia

Murine models and association studies in eating disorder (ED) patients have shown a role for the brain-derived neurotrophic factor (BDNF) in eating behavior. Some studies have shown association of BDNF -270C/T single-nucleotide polymorphism (SNP) with bulimia nervosa (BN), while BDNF Val66Met variant has been shown to be associated with both BN and anorexia nervosa (AN). To further test the role of this neurotrophin in humans, we screened 36 SNPs in the BDNF gene and tested for their association with ED and plasma BDNF levels as a quantitative trait. We performed a family-based association study in 106 ED nuclear families and analyzed BDNF blood levels in 110 ED patients and in 50 sib pairs discordant for ED. The rs7124442T/rs11030102C/rs11030119G haplotype was found associated with high BDNF levels (mean BDNF TCG haplotype carriers = 43.6 ng/ml vs. mean others 23.0 ng/ml, P = 0.016) and BN (Z = 2.64; P recessive = 0.008), and the rs7934165A/270T haplotype was associated with AN (Z =-2.64; P additive = 0.008). The comparison of BDNF levels in 50 ED discordant sib pairs showed elevated plasma BDNF levels for the ED group (mean controls = 41.0 vs. mean ED = 52.7; P = 0.004). Our data strongly suggest that altered BDNF levels modulated by BDNF gene variability are associated with the susceptibility to ED, providing physiological evidence that BDNF plays a role in the development of AN and BN, and strongly arguing for its involvement in eating behavior and body weight regulation.     

The power to detect linkage disequilibrium with quantitative traits in selected samples

Results from power studies for linkage detection have led to many ongoing and planned collections of phenotypically extreme nuclear families. Given the great expense of collecting these families and the imminent availability of a dense diallelic marker map, the families are likely to be used in allelic-association as well as linkage studies. However, optimal selection strategies for linkage may not be equally powerful for association. We examine the power to detect linkage disequilibrium for quantitative traits after phenotypic selection. The results encompass six selection strategies that are in widespread use, including single selection (two designs), affected sib pairs, concordant and discordant pairs, and the extreme-concordant and -discordant design. Selection of sibships on the basis of one extreme proband with high or low trait scores provides as much power as discordant sib pairs but requires the screening and phenotyping of substantially fewer initial families from which to select. Analysis of the role of allele frequencies within each selection design indicates that common trait alleles generally offer the most power, but similarities between the marker- and trait-allele frequencies are much more important than the trait-locus frequency alone. Some of the most widespread selection designs, such as single selection, yield power gains only when both the marker and quantitative trait loci (QTL) are relatively rare in the population. In contrast, discordant pairs and the extreme-proband design provide power for the broadest range of QTL-marker-allele frequency differences. Overall, proband selection from either tail provides the best balance of power, robustness, and simplicity of ascertainment for family-based association analysis.     

Growth patterns in young adult monozygotic twin pairs discordant and concordant for obesity.

Weight discordance is very rare in monozygotic (MZ) twin pairs; when found, however, such pairs are advantageous in the search for either environmental or epigenetic causes and consequences of obesity. We analyzed the growth patterns of young adult MZ pairs discordant and concordant for obesity. Screening 5 consecutive birth cohorts (1975-1979) of 22- to 27-year-old Finnish twins (the FinnTwin16 study), we found 14 obesity discordant (Body Mass Index [BMI] difference > or = 4 kg/m2) MZ pairs out of 658. Ten pairs participated in clinical studies. Nine concordant pairs (BMI difference < or = 2 kg/m2) were examined as controls. Lifetime measured heights and weights recorded in hospitals and health centers were traced manually. Height development was similar in all the co-twins of both groups. The weight differences between the co-twins of the discordant pairs began to emerge at 18 years leading to an average discordance of 16.4 kg, 5.6 kg/m2 (p for both = .005) at 25.7 years. The heavier co-twin weighed 221 g (p = .066), 1.0 kg/m2 (p = .01) more already at birth than the leaner, but the differences waned by 6 months of age and reappeared only after adolescence. Both the leaner and the heavier co-twins of the discordant pairs weighed more than expected by the singleton reference values (Cole et al., 1998) after 8 years. The concordant co-twins, on the other hand, grew similarly and after 6 months, their mean growth was not distinguishable from the singleton patterns. Young adulthood represents a critical period of gaining weight irrespective of genetic background in this twin sample.     

Estimation of Odds Ratios from Matched Case-Control Studies with Incomplete Data

Matched case-control studies often include pairs with incomplete exposure information. This work presents and compares two estimators for the odds ratio that can be used when the exposures of some of the cases and controls are missing. A simulation study shows that the estimator that uses the marginal exposure frequencies is usually more efficient than the estimator based on discordant pairs.     

HLA-DR typing in identical twins with insulin-dependent diabetes: difference between concordant and discordant pairs.

A total of 106 pairs of identical twins, of whom 56 were concordant and 50 discordant for insulin-dependent diabetes, were typed for HLA-DR. In both the concordant and discordant groups there was a high prevalence of the antigens DR3 and DR4, a low prevalence of DR5 and DR7, and a virtual absence of DR2. The heterozygous phenotype DR3,DR4 was more prevalent in concordant than discordant pairs. This was therefore the first demonstration of a genetic difference between concordant and discordant identical twin pairs. These findings suggest that possession of both DR3 and DR4 antigens confers a greater genetic predisposition to insulin-dependent diabetes than does the possession of either antigen alone.     

Hypermethylation in the ZBTB20 gene is associated with major depressive disorder

Background

Although genetic variation is believed to contribute to an individual’s susceptibility to major depressive disorder, genome-wide association studies have not yet identified associations that could explain the full etiology of the disease. Epigenetics is increasingly believed to play a major role in the development of common clinical phenotypes, including major depressive disorder.

Results

Genome-wide MeDIP-Sequencing was carried out on a total of 50 monozygotic twin pairs from the UK and Australia that are discordant for depression. We show that major depressive disorder is associated with significant hypermethylation within the coding region of ZBTB20, and is replicated in an independent cohort of 356 unrelated case-control individuals. The twins with major depressive disorder also show increased global variation in methylation in comparison with their unaffected co-twins. ZBTB20 plays an essential role in the specification of the Cornu Ammonis-1 field identity in the developing hippocampus, a region previously implicated in the development of major depressive disorder.

Conclusions

Our results suggest that aberrant methylation profiles affecting the hippocampus are associated with major depressive disorder and show the potential of the epigenetic twin model in neuro-psychiatric disease.     

Asymmetries of the Arcuate Fasciculus in Monozygotic Twins: Genetic and Nongenetic Influences

We assessed cerebral asymmetry for language in 35 monozygotic twin pairs. Using DTI, we reconstructed the arcuate fasciculus in each twin. Among the male twins, right-handed pairs showed greater left-sided asymmetry of connectivity in the arcuate fasciculus than did those with discordant handedness, and within the discordant group the right-handers had greater left-sided volume asymmetry of the arcuate fasciculus than did their left-handed co-twins. There were no such effects in the female twins. Cerebral asymmetry for language showed more consistent results, with the more left-cerebrally dominant twins also showing more leftward asymmetry of high anisotropic fibers in the arcuate fasciculus, a result applying equally to female as to male twins. Reversals of arcuate fasciculus asymmetry were restricted to pairs discordant for language dominance, with the left-cerebrally dominant twins showing leftward and the right-cerebrally dominant twins rightward asymmetry of anisotropic diffusion in the arcuate fasciculus. Because monozygotic twin pairs share the same genotype, our results indicate a strong nongenetic component in arcuate fasciculus asymmetry, particularly in those discordant for cerebral asymmetry.     

Potential bias regarding birth weight in historical and contemporary twin data bases.

In this study we examine the hypothesis that monozygotic (MZ) twins in historical databases are less discordant for birth weight due to negative selection of severely discordant MZ twins. Furthermore, we test the hypothesis that MZ twins are less discordant for birth weight when comparing a volunteer based twin registry with a population based twin registry, due to selective registration. Data were available on 3927 twin pairs from the volunteer Australian Twin Registry born before 1964, 3059 volunteer twin pairs from the Netherlands Twin Register born 1987-1989 and 454 Belgian twin pairs from The East Flanders Prospective Twin Survey born 1987-1989. Intrapair relative birth weight differences (RBWD) were computed for MZ and dizygotic (DZ) twins from each twin registry. Comparing birth weight differences between MZ and DZ twins provides support for the hypothesis that MZ twins are subject to a negative selection in historical databases. Furthermore, Australian MZ twins have a lower RBWD compared to Dutch MZ twins when corrected for the RBWD of Australian and Dutch DZ twins, indicating circumstances which only affect MZ twins. Our hypothesis that MZ twins are less discordant for birth weight in a volunteer based twin registry compared to a population based twin registry had to be rejected. We suggest that investigators using historical databases to test the fetal origins hypothesis should be aware of this increased likelihood of selective exclusion of individuals with extreme morphometric parameters at time of birth.     

Cardiac structure and function in monozygotic twin pairs discordant for physical fitness.

Cross-sectional studies in athletes and untrained subjects suggest that exercise training induces adaptations in cardiac structure and function. However, the role of genetic variation on the results has largely been ignored in these studies. The purpose of this study was to investigate the effects of long-term volitionally increased physical activity on electrocardiographic and echocardiographic parameters in male monozygotic twin pairs discordant for physical activity and fitness. On the basis of the mailed questionnaires, a telephone interview, and the inclusion criteria, 12 pairs of young adult male monozygotic twins were recruited from a Finnish twin cohort. All subjects completed a maximal oxygen uptake (.VO2 (max)) test and electrocardiography and echocardiography studies. Nine pairs had at least 9% difference in .VO2(max) and were selected for further analysis and for a second echocardiography study. Twins were divided into the more (MAG) and less active group (LAG), according to their VO2(max). On average, MAG had 18% higher VO2(max) compared with LAG. In electrocardiography, MAG had 29% (P = 0.02) higher Cornell voltage and 37% (P = 0.01) higher right-side hypertrophy index. In echocardiography, no significant differences were observed between the groups, and left ventricular mass index was only 7% (P = 0.16) higher in MAG. These results show that the volitionally increased physical activity that has led to an 18% increase in cardiorespiratory fitness induces greater changes in electro- than echocardiographic parameters. Electrocardiographic changes were suggestive of left ventricular hypertrophy, and echocardiography showed a similar but statistically nonsignificant trend.     

Genome scan of human systemic lupus erythematosus by regression modeling: evidence of linkage and epistasis at 4p16-15.2

Systemic lupus erythematosus (SLE) is a complex autoimmune disorder involving at least hormonal, environmental, and genetic factors. Familial aggregation, a 2%-3% sibling recurrence rate, monozygotic twin concordance >20%, association with several candidate genes, as well as the results of five genome scans support a genetic component. We present here the results of a genome scan of 126 pedigrees multiplex for SLE, including 469 sibling pairs (affected and unaffected) and 175 affected relative pairs. Using the revised multipoint Haseman-Elston regression technique for concordant and discordant sibling pairs and a conditional logistic regression technique for affected relative pairs, we identify a novel linkage to chromosome 4p16-15.2 (P=.0003 and LOD=3.84) and present evidence of an epistatic interaction between chromosome 4p16-15.2 and chromosome 5p15 in our European American families. We confirm the evidence of linkage to chromosome 4p16-15.2 in European American families using data from an independent pedigree collection. In addition, our data support the published results of three independent studies for nine purportedly linked regions and agree with the previously published results from a subset of these data for three regions. In summary, results from two new analytical techniques establish and confirm linkage with SLE at 4p16-15.2, indicate epistasis between 4p16-15.2 and 5p15, and confirm other linkage effects with SLE that have been reported elsewhere.