Associating complex traits with genetic variants: polygenic risk scores, pleiotropy and endophenotypes.

Genotype-phenotype causal modeling has evolved significantly since Johannsen's and Wright's original designs were published. The development of genomewide assays to interrogate and detect possible causal variants associated with complex traits has expanded the scope of genotype-phenotype research considerably. Clusters of causal variants discovered by genomewide assays and associated with complex traits have been used to develop polygenic risk scores to predict clinical diagnoses of multidimensional human disorders. However, genomewide investigations have met with many challenges to their research designs and statistical complexities which have hindered the reliability and validity of their predictions. Findings linked to differences in heritability estimates between causal clusters and complex traits among unrelated individuals remain a research area of some controversy. Causal models developed from case-control studies as opposed to experiments, as well as other issues concerning the genotype-phenotype causal model and the extent to which various forms of pleiotropy and the concept of the endophenotype add to its complexity, will be reviewed.

Whither the genotype-phenotype relationship? An historical and methodological appraisal.

More than a century ago, Wilhelm Johannsen proposed the terms "genotype" and "phenotype" to study heredity. Much of what we know about genetics and behavior has evolved since then, especially how causality from genotypes can be inferred from observational studies of phenotypes. Unfortunately, there are genotypes that produce complex clinical-behavioral phenotypes-pleiotropy. In addition, there are often many genotypes that produce the same phenotype, adding a layer of complexity in establishing valid genotype-phenotype relationships. Unlike the relative simplicity of some phenotypes, behavioral phenotypes, especially those characteristics considered aberrant, are multidimensional and often not easily defined operationally. An alternate approach which attempts to identify less evident manifestations below the level of the phenotype but along the pathway to the prospective genotype-endophenotypes-could prove useful in detecting genes that generate these markers. However, operational definitions of intermediate phenotypes vary, less overt neurobiological expressions for some disorders-autism-have not been found, and studies of endophenotypes associated with schizophrenia have been not been very successful. Another approach, suggested by Sewall Wright, uses path analysis to identify causal variables that produce phenotypes. Innovative models of causality have been developed recently by genetic epidemiologists that incorporate Mendel's second law, and Mendelian randomization has been successful in identifying genotypes associated with some diseases, for example, diabetes and cancer. Regrettably, shortcomings regarding genetic markers associated with intermediate phenotypes have been found, although there are statistical procedures to remedy matters. As in any science, genetic researchers need to consider carefully the models of causality they choose.

Deletion 2q37 syndrome: Cognitive-behavioral trajectories and autistic features related to breakpoint and deletion size.

Subtelomeric deletions have been reported in ∼2.5% of individuals with developmental disabilities. Subtelomeric deletion 2q37 has been detected in many individuals diagnosed with intellectual disabilities (ID) and autism spectrum disorders (ASD). Previously, genotype-phenotype correspondences were examined for their relationship to breakpoints 37.1, 37.2, or 37.3. Our purpose was to ascertain whether there were phenotypic differences at these breakpoints, elucidate the cognitive-behavioral phenotype in del2q37, and examine the genotype-phenotype association in the deletion with respect to cognitive-behavioral profiles and ASD. We administered a comprehensive cognitive-behavioral battery to nine children diagnosed with del 2q37, ages 3.9-17.75 years. ID for five tested with the Stanford-Binet (4th Edition) (SBFE) ranged from severe to mild [IQ Range: 36-59]. Adaptive behavior scores from the Vineland Adaptive Behavior Scale (VABS) were much below adequate levels (DQ Range: floor value ["19"] to 55). Autism scores from the Child Autism Rating Scale (CARS) ranged from 22 [non-autistic] to 56 [extremely autistic]; 5/8 [63%] children received scores on the autism spectrum. Participants with the largest deletions, 10.1 and 9.5 Mb, attained the highest IQ and DQ scores while those with the smallest deletions, 7.9 and 6.6 Mb, made the lowest IQ and DQ scores. No association between deletion breakpoint and phenotype were found. Assessment of the various deleted regions suggested histone deacetylase 4 gene (HDAC4) was a likely candidate gene for ASD in our sample. However, two earlier reports found no association between HDAC4 haploinsufficiency and ASD. © 2016 Wiley Periodicals, Inc.

HIV-induced immunosuppression is associated with colonization of the proximal gut by environmental bacteria.

OBJECTIVES: To evaluate the impact of HIV infection on colonization resistance in the proximal gut. DESIGN: It was a case-control study. METHODS: We contrasted microbiota composition between eight HIV-1-infected patients and eight HIV-negative controls to characterize community alteration and detect exogenous bacteria in the esophagus, stomach, and duodenum, as well as the mouth using a universal 16s ribosomal RNA gene survey and correlated the findings with HIV serostatus and peripheral blood T-cell counts. RESULTS: HIV infection was associated with an enrichment of Proteobacteria (P=0.020) and depletion of Firmicutes (P = 0.005) in the proximal gut. In particular, environmental species Burkholderia fungorum and Bradyrhizobium pachyrhizi colonized the duodenum of HIV patients who had abnormal blood CD4 T-cell counts but were absent in HIV-negative controls or HIV patients whose CD4 cell counts were normal. The two species coexisted and exhibited a decreasing trend proximally toward the stomach and esophagus and were virtually absent in the mouth. B. fungorum always outnumbered B. pachyrhizi in a ratio of approximately 15 to 1 regardless of the body sites (P < 0.0001, r = 0.965). Their abundance was inversely correlated with CD4 cell counts (P = 0.004) but not viral load. Overgrowth of potential opportunistic pathogens for example, Prevotella, Fusobacterium, and Ralstonia and depletion of beneficial bacteria, for example, Lactobacillus was also observed in HIV patients. CONCLUSIONS: The colonization of the duodenum by environmental bacteria reflects loss of colonization resistance in HIV infection. Their correlation with CD4 cell counts suggests that compromised immunity could be responsible for the observed invasion by exogenous microbes.

Developmental trajectories in cognitive-behavioral phenotypes: Introduction.

Developmental trajectories in behavioral phenotypes are important areas for systematic research and have been for more than 30 years. They interweave several important strands related to human growth: that of individuals born with some form of intellectual impairment or disability (ID); second, the genetics associated with intellectual ability and disability; and third, at the behavioral level, the dynamic expression and variability of specific abnormalities as individuals age. ID, and the genetic disorders that produce ID, were often not well-received by earlier societies. While the inheritance of behavior and intellectual ability has probably been observed throughout human history, the systematic investigation of the inheritance of intellectual ability probably begins with Sir Francis Galton, in his treatise Hereditary Genius in 1869. The dynamic features of ID have its roots in late 19th century developmental psychology and early 20th century pediatrics. Alfred Binet, along with his colleague Theodore Simon, created the first methods of formal intelligence testing of children for the French school system. Scores based on the items administered would then be used to distinguish children who were prepared for enrollment in a standard educational program from those who were not. The confluence of these research topics brings us to the subject of our Special Issue.

Cognitive-behavioral characteristics and developmental trajectories in children with deletion 11qter (Jacobsen syndrome), and their relation to deletion size.

Subtelomeric deletions represent an important class of abnormalities to be considered when investigating genetic links to intellectual disability (ID). One subtelomeric deletion found on the long arm of chromosome 11q produces a characteristic phenotype that includes ID and is often referred to as Jacobsen syndrome (JBS). Previously, researchers found an inverse relationship between IQ and deletion size. While useful, IQ does not provide a comprehensive picture of the cognitive-behavioral strengths and weaknesses in JBS, nor does it reveal how the profiles evolve as these individuals age. One purpose of this study was to confirm the relationship between IQ or adaptive behavior (DQ) and deletion size. We also examined cognitive-behavioral profiles of children with JBS and the extent to which they changed over time. Initially, at T1, we examined 10 children, ages 5-20 years, diagnosed with JBS. Cognitive ability was assessed with the Stanford-Binet (4th Edition). Adaptive behavoir was evaluated with the Vineland Adaptive Behavior Scales (VABS). Eight children were reassessed 2 years later (T2). Results show a negative but non-significant correlation between IQ and deletion size. There was no statistically significant relationship between DQ and deletion size. As for our second aim, IQ and DQ scores were stable from T1 to T2. Cognitive profiles were not significantly different from T1 to T2. However, there were significant changes in adaptive behavior domain scores from T1 to T2. Lack of a significant relationship between cognitive-behavioral measures and deletion size, as well as changes in cognitive-behavioral profiles are discussed.

Design aspects of a case-control clinical investigation of the effect of HIV on oral and gastrointestinal soluble innate factors and microbes.

INTRODUCTION: The impaired host defense system in HIV infection impacts the oral and gastrointestinal microbiota and associated opportunistic infections. Antiretroviral treatment is predicted to partially restore host defenses and decrease the oral manifestation of HIV/AIDS. Well-designed longitudinal studies are needed to better understand the interactions of soluble host defense proteins with bacteria and virus in HIV/AIDS. "Crosstalk" was designed as a longitudinal study of host responses along the gastrointestinal (GI) tract and interactions between defense molecules and bacteria in HIV infection and subsequent therapy. PURPOSE: The clinical core formed the infrastructure for the study of the interactions between the proteome, microbiome and innate immune system. The core recruited and retained study subjects, scheduled visits, obtained demographic and medical data, assessed oral health status, collected samples, and guided analysis of the hypotheses. This manuscript presents a well-designed clinical core that may serve as a model for studies that combine clinical and laboratory data. METHODS: Crosstalk was a case-control longitudinal clinical study an initial planned enrollment of 170 subjects. HIV+ antiretroviral naïve subjects were followed for 9 visits over 96 weeks and HIV uninfected subjects for 3 visits over 24 weeks. Clinical prevalence of oral mucosal lesions, dental caries and periodontal disease were assessed. RESULTS: During the study, 116 subjects (47 HIV+, 69 HIV-) were enrolled. Cohorts of HIV+ and HIV- were demographically similar except for a larger proportion of women in the HIV- group. The most prevalent oral mucosal lesions were oral candidiasis and hairy leukoplakia in the HIV+ group. DISCUSSION: The clinical core was essential to enable the links between clinical and laboratory data. The study aims to determine specific differences between oral and GI tissues that account for unique patterns of opportunistic infections and to delineate the differences in their susceptibility to infection by HIV and their responses post-HAART.

HIV infection and microbial diversity in saliva.

Limited information is available about the effects of HIV and subsequent antiretroviral treatment on host-microbe interactions. This study aimed to determine the salivary microbial composition for 10 HIV-seropositive subjects, before and 6 months after highly active antiretroviral therapy (HAART), compared with that for 10 HIV-seronegative subjects. A conventional culture and two culture-independent analyses were used and consistently demonstrated differences in microbial composition among the three sets of samples. HIV-positive subjects had higher levels of total cultivable microbes, including oral streptococci, lactobacilli, Streptococcus mutans, and Candida, in saliva than did HIV-negative subjects. The total cultivable microbial levels were significantly correlated with CD4+ T cell counts. Denaturing gradient gel electrophoresis (DGGE), which compared the overall microbial profiles, showed distinct fingerprinting profiles for each group. The human oral microbe identification microarray (HOMIM) assay, which compared the 16S rRNA genes, showed clear separation among the three sample groups. Veillonella, Synergistetes, and Streptococcus were present in all 30 saliva samples. Only minor changes or no changes in the prevalence of Neisseria, Haemophilus, Gemella, Leptotrichia, Solobacterium, Parvimonas, and Rothia were observed. Seven genera, Capnocytophaga, Slackia, Porphyromonas, Kingella, Peptostreptococcaceae, Lactobacillus, and Atopobium, were detected only in HIV-negative samples. The prevalences of Fusobacterium, Campylobacter, Prevotella, Capnocytophaga, Selenomonas, Actinomyces, Granulicatella, and Atopobium were increased after HAART. In contrast, the prevalence of Aggregatibacter was significantly decreased after HAART. The findings of this study suggest that HIV infection and HAART can have significant effects on salivary microbial colonization and composition.

Autism and epistemology IV: Does autism need a theory of mind?

In their article, "Does the autistic child have a 'theory of mind'?," Baron-Cohen et al. [1985] proposed a novel paradigm to explain social impairment in children diagnosed as autistic (AD). Much research has been undertaken since their article went to print. The purpose of this commentary is to gauge whether Theory of Mind (ToM)-or lack thereof-is a valid model for explaining abnormal social behavior in children with AD. ToM is defined as "the ability to impute mental states to oneself and to others" and "the ability to make inferences about what other people believe to be the case." The source for their model was provided by an article published earlier by Premack and Woodruff, "Does the chimpanzee have a theory of mind?" Later research in chimpanzees did not support a ToM in primates. From the outset, ToM as a neurocognitive model of autism has had many shortcomings-methodological, logical, and empirical. Other ToM assumptions, for example, its universality in all children in all cultures and socioeconomic conditions, are not supported by data. The age at which a ToM emerges, or events that presage a ToM, are too often not corroborated. Recent studies of mirror neurons, their location and interconnections in brain, their relationship to social behavior and language, and the effect of lesions there on speech, language and social behavior, strongly suggests that a neurobiological as opposed to neurocognitive model of autism is a more parsimonious explanation for the social and behavioral phenotypes observed in autism.

Nosology and epidemiology in autism: classification counts.

Since its initial description by Kanner in 1943, the criteria by which a diagnosis of autism or autism-like disorders was made--and their alleged etiologies portrayed--have undergone manifold changes, from a psychiatric disorder engendered by "refridgerator" parents to a neurodevelopmental disability produced in the main by genetic abnormalities. In addition, the behavioral characterization of autism has also entered the public consciousness and professional domains increasingly in the past 30 years, the effects of which we are continually coming to terms. A diagnosis of autism that once seemed quite unusual is now considered almost epidemic. Increasing numbers of individuals diagnosed with autism and related pervasive developmental disabilities will, in turn, affect the calculated prevalence of the disorder. In this essay, I attempt to account for the increasing prevalence of autism and autism-related disorders by examining its changing criteria, the individuals and instruments used to make the diagnosis, the reliability and validity of same, and the sample sizes and other aspects of the methodology needed to make an accurate estimate of its prevalence.

Developmental trajectories in syndromes with intellectual disability, with a focus on Wolf-Hirschhorn and its cognitive-behavioral profile.

Few studies exist of developmental trajectories in children with intellectual disability, and none for those with subtelomeric deletions. We compared developmental trajectories of children with Wolf-Hirschhorn syndrome to other genetic disorders. We recruited 106 children diagnosed with fragile X, Williams-Beuren syndrome, or Wolf-Hirschhorn syndrome, assessing their intellectual and adaptive behavior abilities. We retested 61 children 2 years later. We compared Time 1 and Time 2 difference scores related to genetic disorder, age, initial IQ, or adaptive behavior composite. Results show genetic disorder and initial IQ score were significant factors for IQ differences, but only genetic disorder affected adaptive behavior differences. Results suggest different gene-brain-behavior pathways likely exist for these genetic disorders. Different developmental trajectories will influence the type and intensity of intervention implemented by caregivers.

Autism and epistemology III: Child development, behavioral stability, and reliability of measurement.

Early diagnosis and treatment of autism increases the likelihood that symptoms associated with the disorder can be alleviated. However, the behaviors of both typically and atypically developing young infants and toddlers are quite variable and often change as these children age. Studies have shown that this is the case for same-aged children who are diagnosed with autistic disorder (AD) or other Pervasive Developmental Disabilities (PDDs). Therefore, an early accurate assessment of AD or PDD may be problematic. Moreover, instruments used to make the diagnosis may not be as reliable as desired. Statistics employed to evaluate diagnostic accuracy and behavioral stability of instruments' or clinicians' assessments suggest that their diagnoses have been only moderately successful. In addition, the statistics themselves have limitations that would suggest that the measures of diagnostic accuracy and behavioral stability implemented may not be as effective as they would seem. A resolution to these problems is proposed.

Genotype-phenotype association studies of chromosome 8p inverted duplication deletion syndrome.

Individuals diagnosed with chromosome 8p inverted duplication deletion (invdupdel(8p)) manifest a wide range of clinical features and cognitive impairment. The purpose of this study is to employ array CGH technology to define more precisely the cytogenetic breakpoints and regions of copy number variation found in several individuals with invdupdel(8p), and compare these results with their neuropsychological characteristics. We examined the cognitive-behavioral features of two male and two female children, ages 3-15 years, with invdupdel(8p). We noted cognitive deficits that ranged from mild to severe, and adaptive behavior composites that ranged from significantly to substantially lower than adequate levels. CARS scores, a measure of autistic behavior, identified three children with autism or autistic-like features. Three of the four children exhibited attention deficits and hyperactivity consistent with a DSM-IV-TR diagnosis of ADHD. One child showed extreme emotional lability. Interestingly, intellectual disability was not correlated with deletion size, nor was the deletion location associated with the autistic phenotype. On the other hand, the duplication length in 8p21.1/8p22 was associated with cognitive deficit. In addition, a small locus of over-expression in 8p21.3 was common for all three participants diagnosed as autistic. A limitation of the study is its small sample size. Further analyses of the deleted and over-expressed regions are needed to ascertain the genes involved in cognitive function and, possibly, autism.

Cognitive-behavioral features of Wolf-Hirschhorn syndrome and other subtelomeric microdeletions.

Wolf-Hirschhorn syndrome (WHS) is a complex congenital malformation produced by a loss of genomic material at the locus 4p16.3. In addition to its dysmorphic features, the deletion produces a range of intellectual disability (ID). Many clinical aspects of WHS are well-characterized; however, the cognitive-behavioral characteristics have been rarely examined in a systematic fashion. The purpose of our study was to examine the cognitive-behavioral features of WHS and to compare them to children with other subtelomeric deletions that also produce ID. We recruited 45 children with subtelomeric deletions and examined their cognitive-behavioral abilities using a neuropsychological assessment battery composed of standardized instruments. Nineteen children were diagnosed with WHS and 26 children with one of three other subtelomeric deletions-11q25 (Jacobsen syndrome), deletion 2q37, and inversion duplication deletion 8p21-23. We found children with WHS to be more severely impacted cognitively than children from any of the other groups. Their overall adaptive behavior was lower as well. However, children with WHS exhibit strengths in socialization skills comparable to the levels attained by the other groups we assessed. Importantly, the proportion of children with WHS with autism or autistic-like features is significantly lower than the rates of autism found in the other subtelomeric disorders we examined.

Use of a mucoadhesive disk for relief of dry mouth: a randomized, double-masked, controlled crossover study.

BACKGROUND: Dry mouth is a frequent complaint of adults worldwide. In those who experience dry mouth, therapeutic options include the use of salivary substitutes and sialogogues. METHODS: The authors compared the efficacy and safety of mucoadhesive disks (OraMoist, Axiomedic, Zurich; distributed by Quantum Health, Eugene, Ore.) applied three times daily with those of placebo mucoadhesive disks in a double-masked, randomized, controlled crossover study. The primary end point of interest was within-participant differences in subjective (visual analog scale) ratings of dry mouth according to the New York University Bluestone Mouthfeel Questionnaire. The secondary end point was within-participant differences in salivary flow rates. RESULTS: Twenty-seven participants completed the single-site study. The results showed no significant difference between the two types of mucoadhesive disks, both of which were associated with a statistically significant improvement in the subjective experience of moistness across the 60-minute period after application and compared with baseline measures after two weeks of use. Furthermore, both disks were associated with a statistically significant improvement in salivary flow rates across the 60-minute period after application and compared with baseline measures after one and two weeks of use. The disks were well tolerated, and participants did not report any adverse events. CONCLUSIONS: The mucoadhesive disks used in this study were safe and provided symptomatic relief from dry mouth. Practice Implications. Patients with dry mouth may benefit from this novel delivery system.

The course of cognitive-behavioral development in children with the FMR1 mutation, Williams-Beuren syndrome, and neurofibromatosis type 1: The effect of gender.

The course of cognitive-behavioral development in children with intellectual disabilities produced by genetic disorders has only recently begun to be examined systematically. Unfortunately, these studies are few in number. Previously, we examined cognitive-behavioral development in children with the fragile X (FMR1) mutation and found longitudinal decreases in both IQ and adaptive behavior (DQ) scores in most males and females with the full mutation. In this study, we examine longitudinal changes in IQ and DQ in children with neurofibromatosis type 1 (NF1) and Williams-Beuren Syndrome (WBS) by examining differences in composite IQ and DQ scores between the first test (T1) and retest (T2), and compare their developmental trajectory to children with the FMR1 mutation. Sixty-five children with the FMR1 mutation, or NF1, or WBS, ages 4-16 years, were retested two years after initial testing with the Stanford-Binet 4th Edition (SBFE) and the Vineland Adaptive Behavior Scale (VABS). In addition to significant longitudinal declines in IQ and DQ noted previously in children with the FMR1 mutation, we found significant decreases in IQ in males compared to females in the remainder of our sample. We also observed statistically significant decreases in DQ scores among children the FMR1 mutation, as noted previously, but not among children with NF1 or WBS. Moreover, significant declines were found only among males with the FMR1 mutation. Unlike declines in IQ scores, decreases in DQ were not significantly different between males and females.

Pathogenic significance of deletions distal to the currently described Wolf-Hirschhorn syndrome critical regions on 4p16.3.

Within recent years, numerous individuals have been identified with terminal 4p microdeletions distal to the currently described critical regions for the Wolf-Hirschhorn syndrome (WHS). Some of these individuals do not display features consistent with WHS whereas others have a clinical phenotype with some overlap to the WHS phenotype. In this review we discuss the genetic and clinical presentation of these cases in an attempt to understand the consequence of monosomy of the genes distal to the proposed critical regions and identify the distal boundary for pathogenic genes involved in components of the WHS phenotype.