Detecting multi-way epistasis in family-based association studies

The era of genome-wide association studies (GWAS) has led to the discovery of numerous genetic variants associated with disease. Better understanding of whether these or other variants interact leading to differential risk compared with individual marker effects will increase our understanding of the genetic architecture of disease, which may be investigated using the family-based study design. We present M-TDT (the multi-locus transmission disequilibrium test), a tool for detecting family-based multi-locus multi-allelic effects for qualitative or quantitative traits, extended from the original transmission disequilibrium test (TDT). Tests to handle the comparison between additive and epistatic models, lack of independence between markers and multiple offspring are described. Performance of M-TDT is compared with a multifactor dimensionality reduction (MDR) approach designed for investigating families in the hypothesis-free genome-wide setting (the multifactor dimensionality reduction pedigree disequilibrium test, MDR-PDT). Other methods derived from the TDT or MDR to investigate genetic interaction in the family-based design are also discussed. The case of three independent biallelic loci is illustrated using simulations for one- to three-locus alternative hypotheses. M-TDT identified joint-locus effects and distinguished effectively between additive and epistatic models. We showed a practical example of M-TDT based on three genes already known to be implicated in malaria susceptibility. Our findings demonstrate the value of M-TDT in a hypothesis-driven context to test for multi-way epistasis underlying common disease etiology, whereas MDR-PDT-based methods are more appropriate in a hypothesis-free genome-wide setting.

Correlates of child-father and child-mother attachment in the preschool years

The increase in fathers' involvement in childrearing, particularly beyond infancy, warrants research exploring factors influencing the quality of child-father attachment relationships, and the impact of these relationships on children's social development. The current investigation explored various correlates of preschoolers' child-father attachment security to both parents, including contextual factors (i.e., socioeconomic status, child temperament, parenting stress), parental play sensitivity, and child social adaptation. Participants included 107 preschool-aged children (59 girls; M = 46.67 months, SD = 8.57) and their fathers and mothers. Results revealed that both mothers' and fathers' play sensitivity were associated with child attachment security after controlling for different contextual factors. Furthermore, the magnitude of the association between child conduct problems and child-father attachment insecurity was stronger than the corresponding association with child-mother attachment insecurity. Findings provide important information on caregiving factors associated with child-father attachment security in the preschool years and the importance of this bond to children's social adaptation.

The Mediating Effects of Emotion Regulation and Dyadic Coping on the Relationship Between Romantic Attachment and Non-suicidal Self-injury

Insecure attachment is believed to play a fundamental role in non-suicidal self-injury (NSSI). In fact, the quality of parent-child attachment relationships has become an emerging topic attracting a growing number of theoretical and research contributions in the field of NSSI. However, despite these considerable advances in the scientific study of NSSI, progress pertaining to investigating the quality of romantic attachment relationship is lacking. In an effort to expand current knowledge, the present study aims to not only explore the relationships between romantic attachment and NSSI, but also to explore the mechanisms by which these two variables relate by examining the mediating role that emotion regulation and dyadic coping might play in this relationship. Participants consisted of 797 (81.9 % female) university students, all of whom were involved in a romantic relationship for at least 6 months and between the ages of 17 and 25. Results revealed that although difficulties in emotion regulation mediated the relationships between romantic attachment insecurity (i.e., attachment anxiety and avoidance) and NSSI, dyadic coping was not found to be a significant mediator. These results highlight the importance of attachment security and internal processes to manage stress in the prevention of NSSI.

Is the maternal Q-Set a valid measure of preschool child attachment behavior?

The objective of this study is to examine preschool-age correlates of the maternal version of the Attachment Q-Set (AQS) (Waters & Deane, 1985) in order to provide validity data. Concurrent associations between the Attachment Q-Set and measures of separation-reunion attachment classifications (Cassidy & Marvin, 1992), quality of mother–child interaction, maternal stress, and child externalizing behavior problems were examined for a low-risk sample of 152 preschool children. Results showed that, even after controlling for maternal stress, ambivalent and disorganized children had lower scores on the AQS when compared with the secure group. However, avoidant and controlling children did not differ from secure children in maternal sorts. Significant associations between the maternal Q-Set and affective quality of mother–child interaction were also maintained, when controlling for maternal stress. The AQS was significantly associated with both mother and teacher reported externalizing behavior problem reports, but the association with teacher reports was not maintained when maternal stress was entered in the equation as a covariate. The discussion focuses on the validity of the maternal Q-Set as a measure of child attachment behavior in preschoolers.

Attachment Representations in a Sample of Neglected Preschool-Age Children

A number of studies (see Éthier, 1999) have shown that neglect has a deleterious impact on children's development. However, the effect of neglect on a child's internal representations of their family still needs to be investigated. The aim of this study was to examine the attachment patterns observed in a subsample of neglected children as compared with a control group, using a representational assessment method. The overall sample consisted of 74 preschool-age children, with a clinical group comprised of 39 children referred to social services because of neglect and a control group including 35 children recruited in ordinary kindergartens. Children's attachment representations were assessed with the Doll Play Narrative Classification System (George and Solomon, 1990, 1996, 2000) as well as the complementary Disorganization Scales (George and Solomon, 1998). Mothers' reports consisted of: (1) an in-house socio-demographical questionnaire and (2) the shorter French version of the Parental Stress Index (Bigras et al., 1996). Results showed: (1) a significant difference in attachment representation classifications between the neglected group and the control group even when socio-economic status and maternal stress were controlled for and (2) a significantly higher proportion of avoidant attachment classification in the neglected group. Moreover, neglected avoidant children displayed more overall disorganized markers, and specifically more frightening markers, than normative avoidant children; they also depicted their mother as being less available than normative children. These results are discussed in the light of other findings as well as on theoretical grounds.

Modulation of Malaria Phenotypes by Pyruvate Kinase (PKLR) Variants in a Thai Population

Pyruvate kinase (PKLR) is a critical erythrocyte enzyme that is required for glycolysis and production of ATP. We have shown that Pklr deficiency in mice reduces the severity (reduced parasitemia, increased survival) of blood stage malaria induced by infection with Plasmodium chabaudi AS. Likewise, studies in human erythrocytes infected ex vivo with P. falciparum show that presence of host PK-deficiency alleles reduces infection phenotypes. We have characterized the genetic diversity of the PKLR gene, including haplotype structure and presence of rare coding variants in two populations from malaria endemic areas of Thailand and Senegal. We investigated the effect of PKLR genotypes on rich longitudinal datasets including haematological and malaria-associated phenotypes. A coding and possibly damaging variant (R41Q) was identified in the Thai population with a minor allele frequency of ~4.7%. Arginine 41 (R41) is highly conserved in the pyruvate kinase family and its substitution to Glutamine (R41Q) affects protein stability. Heterozygosity for R41Q is shown to be associated with a significant reduction in the number of attacks with Plasmodium falciparum, while correlating with an increased number of Plasmodium vivax infections. These results strongly suggest that PKLR protein variants may affect the frequency, and the intensity of malaria episodes induced by different Plasmodium parasites in humans living in areas of endemic malaria.

Attachment and Temperament Revisited: Infant Distress, Attachment Disorganization, and the Serotonin Transporter Polymorphism

OBJECTIVE

This study's aim was to evaluate whether infant disorganized attachment and infant proneness to distress exhibited differential relations to infant genetic factors as indexed by the serotonin transporter polymorphism.

BACKGROUND

The role of the short allele of the serotonin transporter polymorphism (5-HTTLPR) in enhancing sensitivity to fearful and negative affect has been well-established (Canli & Lesch, 2007). In the current study, we used this known property of the short allele to provide a test of an important postulate of attachment theory, namely that infant attachment security or disorganization is not a function of the infant's proneness to distress.

METHODS

Participants were 39 parents and infants assessed between 12 and 18 months in the Strange Situation procedure. Genotype categories for the 5-HTTLPR (and rs25531) were created by both the original and the reclassified grouping system; infant proneness to distress was assessed directly in the Strange Situation Procedure. We also assessed maternal behavior at 18 months to evaluate whether any observed genetic effect indicated a passive effect through the mother.

RESULTS

Consistent with previous findings, the 5-HTTLPR short allele was significantly related to the infant's wariness and distress, but was not related to attachment security or attachment disorganization. In addition, maternal disrupted interaction with the infant was not related to infant genotype or infant distress.

CONCLUSION

Results support the concept that infant proneness to distress is associated with serotonergic factors while infant attachment security or disorganization is not a function of either 5-HTTLPR or behaviorally rated proneness to distress.

Emotion dysregulation mediates the influence of relationship difficulties on non-suicidal self-injury behavior in young adults

This study examined associations between relationship difficulties with parents and peers and non-suicidal self-injury (NSSI). Particular emphasis was placed on examining mediating pathways through emotion dysregulation, as per commonly accepted theory. Participants were 1153 university students (905 females; Mage=19.35 years, S.D.=1.49); 79 of these participants had engaged in NSSI during the previous 6 months (63 females, Mage=19.35 years, S.D.=1.51). Participants completed questionnaires assessing NSSI, quality of relationships with parents and peers, and emotion dysregulation. Hierarchical logistic regressions suggest that the quality of parent-child relationships has a greater impact on the prediction of NSSI engagement than the quality of peer relationships. Results of a structural equation model showed that feelings of alienation in both parent and peer relationships had indirect effects on NSSI through deficits in emotion regulation (ER). Results suggest the importance of examining emotion dysregulation in association with NSSI, and that both parent and peer relationships are implicated in NSSI engagement through emotion regulation deficits. Important clinical implications regarding the need to acknowledge both emotion dysregulation and interpersonal difficulties when treating NSSI in young adults are discussed.

Filter-free exhaustive odds ratio-based genome-wide interaction approach pinpoints evidence for interaction in the HLA region in psoriasis

Background

Deciphering the genetic architecture of complex traits is still a major challenge for human genetics. In most cases, genome-wide association studies have only partially explained the heritability of traits and diseases. Epistasis, one potentially important cause of this missing heritability, is difficult to explore at the genome-wide level. Here, we develop and assess a tool based on interactive odds ratios (I_OR), Fast Odds Ratio-based sCan for Epistasis (FORCE), as a novel approach for exhaustive genome-wide epistasis search. I_OR is the ratio between the multiplicative term of the odds ratio (OR) of having each variant over the OR of having both of them. By definition, an I_OR that significantly deviates from 1 suggests the occurrence of an interaction (epistasis). As the I_OR is fast to calculate, we used the I_OR to rank and select pairs of interacting polymorphisms for P value estimation, which is more time consuming.

Results

FORCE displayed power and accuracy similar to existing parametric and non-parametric methods, and is fast enough to complete a filter-free genome-wide epistasis search in a few days on a standard computer. Analysis of psoriasis data uncovered novel epistatic interactions in the HLA region, corroborating the known major and complex role of the HLA region in psoriasis susceptibility.

Conclusions

Our systematic study revealed the ability of FORCE to uncover novel interactions, highlighted the importance of exhaustiveness, as well as its specificity for certain types of interactions that were not detected by existing approaches. We therefore believe that FORCE is a valuable new tool for decoding the genetic basis of complex diseases.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-015-0174-3) contains supplementary material, which is available to authorized users.

Psychometric properties of the mother and father compulsive caregiving scales: a brief measure of current young adult caregiving behaviors toward parents

This study assessed the psychometric properties of the Mother and Father Compulsive Caregiving Scales (MFCC). Exploratory (N = 1283, 71.5% Caucasian) and confirmatory (N = 2203, 76.6% Caucasian) factor analyses revealed two-factor structures for each parent: burden and autonomy. Correlational analyses with retrospective self-reports of parent-child relationship quality, family risk indicators, and psychological symptoms demonstrated similar convergent validity for both mother and father burden factors while, interestingly, the findings for mother and father autonomous factors showed different patterns. Results support that the MFCC is a short and convenient measure that would be clinically useful for the assessment of controlling/caregiving behaviors in young adulthood.

Psychometric properties of the functions and addictive features scales of the Ottawa Self-Injury Inventory: a preliminary investigation using a university sample

Nonsuicidal self-injury (NSSI) is an issue primarily of concern in adolescents and young adults. Thus far, no single NSSI self-report measure offers a fully comprehensive assessment of NSSI, particularly including measurement of both its functions and potential addictive features. The Ottawa Self-Injury Inventory (OSI) permits simultaneous assessment of both these characteristics; the current study examined the psychometric properties of this measure in a sample of 149 young adults in a university student sample (82.6% girls, Mage = 19.43 years). Exploratory factor analyses revealed 4 functions factors (internal emotion regulation, social influence, external emotion regulation, and sensation seeking) and a single addictive features factor. Convergent evidence for the functions factor scores was demonstrated through significant correlations with an existing measure of NSSI functions and indicators of psychological well-being, risky behaviors, and context and frequency of NSSI behaviors. Convergent evidence was also shown for the addictive features scores, through associations with NSSI frequency, feeling relieved following NSSI, and inability to resist NSSI urges. Additional comment is made regarding the potential for addictive features of NSSI to be both negatively and positively reinforcing. Results show preliminary psychometric support for the OSI as a valid and reliable assessment tool to be used in both research and clinical contexts. The OSI can provide important information for case formulation and treatment planning, given the comprehensive and all-inclusive nature of its assessment capacities.

The NeST long ncRNA controls microbial susceptibility and epigenetic activation of the interferon-γ locus

Long noncoding RNAs (lncRNAs) are increasingly appreciated as regulators of cell-specific gene expression. Here, an enhancer-like lncRNA termed NeST (nettoie Salmonella pas Theiler's [cleanup Salmonella not Theiler's]) is shown to be causal for all phenotypes conferred by murine viral susceptibility locus Tmevp3. This locus was defined by crosses between SJL/J and B10.S mice and contains several candidate genes, including NeST. The SJL/J-derived locus confers higher lncRNA expression, increased interferon-γ (IFN-γ) abundance in activated CD8(+) T cells, increased Theiler's virus persistence, and decreased Salmonella enterica pathogenesis. Transgenic expression of NeST lncRNA alone was sufficient to confer all phenotypes of the SJL/J locus. NeST RNA was found to bind WDR5, a component of the histone H3 lysine 4 methyltransferase complex, and to alter histone 3 methylation at the IFN-γ locus. Thus, this lncRNA regulates epigenetic marking of IFN-γ-encoding chromatin, expression of IFN-γ, and susceptibility to a viral and a bacterial pathogen.

High number of previous Plasmodium falciparum clinical episodes increases risk of future episodes in a sub-group of individuals

There exists great disparity in the number of clinical P. falciparum episodes among children of the same age and living in similar conditions. The epidemiological determinants of such disparity are unclear. We used a data-mining approach to explore a nineteen-year longitudinal malaria cohort study dataset from Senegal and identify variables associated with increased risk of malaria episodes. These were then verified using classical statistics and replicated in a second cohort. In addition to age, we identified a novel high-risk group of children in whom the history of P. falciparum clinical episodes greatly increased risk of further episodes. Age and a high number of previous falciparum clinical episodes not only play major roles in explaining the risk of P. falciparum episodes but also are risk factors for different groups of people. Combined, they explain the majority of falciparum clinical attacks. Contrary to what is widely believed, clinical immunity to P. falciparum does not de facto occur following many P. falciparum clinical episodes. There exist a sub-group of children who suffer repeated clinical episodes. In addition to posing an important challenge for population stratification during clinical trials, this sub-group disproportionally contributes to the disease burden and may necessitate specific prevention and control measures.

A comparison of invalidating family environment characteristics between university students engaging in self-injurious thoughts & actions and non-self-injuring university students

Individuals experiencing non-suicidal self-injurious (NSSI) thoughts only are greatly overlooked by current research. This investigation aimed at determining how three groups of university students differed in their reported quality of childhood relationships with parents, and histories of physical and sexual abuses. These groups included students experiencing only NSSI thoughts (n = 126), students engaging in NSSI actions (n = 90), and students exhibiting neither (n = 1,080). Results showed that individuals experiencing NSSI thoughts only, and those engaging in NSSI actions reported poorer relationships with parents and more physical abuse than the No NSSI group; however, NSSI thoughts and NSSI action groups had similar outcomes to one another for most variables. These findings suggest that individuals experiencing only NSSI thoughts share similar negative childhood environments associated with engagement in NSSI action and that they should be included in future research, particularly investigations aimed at identifying protective factors that could prevent them from engaging in NSSI.

Behavioural precursors of attachment representations in middle childhood and links with child social adaptation

Concordance between age-6 attachment behaviour and age-8 doll play attachment representations during the school-age period, and associations between these measures and child social adaptation at school were examined. One hundred and twenty-nine 6-year-olds and their mothers participated in a separation/reunion protocol. Two years later, 104 children completed a doll play narrative task. Teachers evaluated child behaviour problems and prosocial behaviour at both ages. Results showed a significant four-way concordance between age-6 attachment behaviour and age-8 doll play classifications. Each of the four attachment classifications was concordant in the absence of major negative life-events, but only the disorganized classifications remained concordant when at least one negative life-event occurred between the two assessment times. Children with a disorganized attachment classification or representation had higher externalizing scores than secure and avoidant children at both timepoints. Finally, the avoidant and disorganized behavioural classifications predicted avoidant and disorganized representations, respectively, even when controlling for age-6 teacher reports of social adaptation.

Links between children's attachment behavior at early school-age, their attachment-related representations, and behavior problems in middle childhood

The objective of the present study was to examine associations between children's attachment behavior at early school-age, dimensions of narrative performance, and behavior problems as assessed in middle childhood. Children's attachment patterns with mother were assessed at age 6 ( N = 127) using the Main and Cassidy (1988) separation—reunion classification system. Two years later, these children ( N = 109) completed the Narrative Story Stem Battery (Bretherton, Oppenheim, Buchsbaum, Emde, & The MacArthur Narrative Group, 1990), and teachers rated their level of behavior problems using the Social Behavior Questionnaire (Tremblay, Vitaro, Gagnon, Piché, & Royer, 1992). Results indicated that secure children depicted fewer conflict themes in their narratives than did disorganized/controlling children, produced more discipline themes than avoidant children, and had higher coherence scores than ambivalent children. Avoidant children also depicted fewer conflict themes than disorganized/controlling children. Finally, children's narrative conflict themes significantly predicted both level of externalizing and total behavior problems, even after controlling for variance explained by gender and disorganized/controlling attachment behavior. Girls' narratives were more likely to evoke discipline and affection/affiliation themes, and to be more coherent than boys' narratives.

Maternal depressive symptoms in infancy: unique contribution to children's depressive symptoms in childhood and adolescence?

This prospective 20-year study assessed associations between maternal depressive symptoms in infancy, childhood, and adolescence, and child and adolescent depressive symptoms in a sample of families at high psychosocial risk. Maternal symptomatology was assessed with the Center for Epidemiological Studies Depression Scale (CES-D) when children were infants (12 months), school-aged (age 8), and adolescents (age 19). Children's depressive symptoms were measured at age 8 (Dimensions of Depression Profile for Children and Adolescents) and age 19 (CES-D). Maternal depressive symptoms during infancy contributed to the prediction of child depressive symptoms at age 8, after controlling for concurrent maternal depressive symptoms, clinical risk in infancy, and gender. Clinical risk in infancy marginally contributed to the prediction model. Disorganization of attachment in infancy and maternal hostility were independent predictors of depressive symptoms at age 8 and did not mediate the relation between maternal and child depressive symptoms. Depressive symptoms in adolescence were predicted by gender, children's depressive symptoms at age 8, maternal depressive symptoms in adolescence, and maternal depressive symptoms in infancy. There was no moderating effect of gender. Adding to previous evidence on the importance of early maternal depression, maternal depressive symptoms during infancy were related to the development of depressive symptoms in childhood and adolescence even when other variables of potential relevance were controlled.

Cortisol response to interpersonal stress in young adults with borderline personality disorder: a pilot study

Hypothalamic-pituitary-adrenal axis dysregulation after stress was found to be associated with borderline personality disorder (BPD). Nine female BPD young adults and 12 control subjects were investigated for stress reactivity and recovery after an interpersonal conflict discussion with their mothers. BPD subjects showed a delayed cortisol response after psychosocial stress.

Cortisol response to interpersonal stress in young adults with borderline personality disorder: a pilot study

Hypothalamic-pituitary-adrenal axis dysregulation after stress was found to be associated with borderline personality disorder (BPD). Nine female BPD young adults and 12 control subjects were investigated for stress reactivity and recovery after an interpersonal conflict discussion with their mothers. BPD subjects showed a delayed cortisol response after psychosocial stress.

Interleukin 22 is a candidate gene for Tmevp3, a locus controlling Theiler's virus-induced neurological diseases

After intracerebral inoculation, Theiler's virus induces in its natural host, the mouse, an acute encephalomyelitis followed, in susceptible animals, by chronic inflammation and primary demyelination. Susceptibility to demyelination among strains of laboratory mice is explained by the capacity of the immune system to control viral load during persistence. Also, differences of susceptibility to viral load between the susceptible SJL strain and the resistant B10.S strain are mainly due to two loci, Tmevp2 and Tmevp3, located close to the Ifng locus on chromosome 10. In this article, we show that the Tmevp3 locus controls both mortality during the acute encephalomyelitis and viral load during persistence. Most probably, two genes located in the Tmevp3 interval control these two different phenotypes with efficiencies that depend on the age of the mouse at inoculation. Il22, a member of the IL-10 cytokine family, is a candidate gene for the control of mortality during the acute encephalomyelitis.