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.

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.

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.

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.

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.

Cognitive-behavioral features of children with Wolf-Hirschhorn syndrome: preliminary report of 12 cases.

As a subset of genetic abnormalities, subtelomeric deletions have been found in 7-10% of individuals with mental retardation (MR). One subtelomeric deletion, Wolf-Hirschhorn syndrome (WHS), causes mild to severe MR, but the cognitive-behavioral features of individuals with WHS have not been studied systematically. To that end, we administered a comprehensive cognitive-behavioral battery to 12 children with WHS, ages 4-17 years, who also had some expressive language. Using the Stanford-Binet (4th Edition), we found cognitive deficits ranged from mild to severe, with mean IQ = 44.1. Interviewing parents with the Vineland Adaptive Behavior Scales, we found mean adaptive behavior score (DQ) = 37.3, with females exhibiting slightly higher scores than males. Cognitive profiles indicated relative strengths in Verbal and Quantitative Reasoning. Adaptive behavior profiles noted significant relative strengths in the Socialization Domain. These cognitive-behavioral profiles differed from children with other subtelomeric deletion syndromes, 2q37 or 8p23. Attention deficits and hyperactivity (ADHD) were observed in 7/12 (58%) of the children we tested. One child attained a score on the Child Autism Rating Scale (CARS) suggestive of mild autism. We conclude that different genetic disorders, which cause MR, produce diverse cognitive-behavioral profiles. Consequently, cognitive-behavioral profiles of children with MR need to be assessed more comprehensively.

Task analysis of the preincision surgical period: an independent observer-based study of 1558 cases.

Intense production pressure has focused on the preincision period (from patient-on-table to incision) as an important component of overall operating room efficiency. We conducted a prospective study in which trained independent observers measured the performance of anesthesiologists, surgeons, and nursing staff to determine anesthesia release time (ART, patient-on-table until release for surgical preparation) and surgical preparation time (SPT, start surgical preparation to incision) and the factors, including delays, that affect their duration. We enrolled 1558 patients undergoing elective surgery in a tertiary medical center. The mean ART was 21 +/- 16 min. Mean SPT was 22 +/- 13 min, and mean case length was 207 +/- 123 min. Significant variation was seen in both ART (range, 1-115 min) and SPT (range, 1-130 min). Multivariate regression analysis revealed ASA physical status, age, level of resident training, invasive monitoring, case length, and case number in the room were all positive predictors of ART duration (P < 0.05). In contrast, gender, body mass index, number of anesthesia personnel concurrently in the room, and number of rooms covered per anesthesia attending were not predictors for ART (P > 0.05). Delays affected both ART and SPT and were encountered in 24.5% of all procedures (surgery 66.8%, anesthesiology 21.7%, and logistical 11.5%). For operating room scheduling purposes, we conclude that assigning a constant fixed duration for anesthetic induction is inappropriate and will result in creating erroneous administrative expectations.

Task analysis of the preincision period in a pediatric operating suite: an independent observer-based study of 656 cases.

We designed this cross-sectional investigation to assess anesthesia release time (ART = patient-on-table until release for surgical preparation) and surgical preparation time (start of surgical preparation to incision) of children undergoing anesthesia and surgery (n = 656). Data collected by trained independent observers included variables such as age, ASA physical status, anesthetic technique, and placement of invasive monitoring. We found that mean ART was 11.0 +/- 9.7 min and the mean surgical preparation time was 11.1 +/- 10.0 min. Also, ART ranged from 7 +/- 7 min (for mask anesthesia) to 52 +/- 18 min (general anesthesia/endotracheal tube and invasive hemodynamic monitoring). The percentage of ART of the total case length was 15% +/- 7%, with a wide variability depending on the total case length. We also found that there is a significant variability in ART as a function of the surgical service involved (analysis of variance; P = 0.0001), ASA physical status (P = 0.0001), and age. For example, younger children had a significantly longer ART as compared with older children (P = 0.001). Room coverage ratio by the attending anesthesiologist and training level of the anesthesia resident did not impact ART (P = not significant). We conclude that ART in children undergoing surgery is highly variable and is a function of factors such as the surgical service involved, age of the child, and ASA physical status of the child. These factors should be considered when scheduling a surgical case.

Resident teaching versus the operating room schedule: an independent observer-based study of 1558 cases.

Efforts to improve operating room efficiency may threaten clinician training. Therefore, we designed a prospective, observational study to determine the actual time spent teaching anesthesiology residents during the interval from patient-on-table to skin incision and to determine whether anesthesia teaching in the peri-induction period increases the time to surgical incision. This study was conducted in an inpatient operating room suite of a tertiary academic medical center. Of 1558 cases examined, 75% had an element of teaching (mean percent teaching per case = 46.4). A 33% decrease in teaching occurs when the attending anesthesiologist concurrently directed care in 2 rooms (P < 0.001). The percent teaching significantly increased as a function of ASA physical status classification and time of day of surgical case (P = 0.001). Teaching accounted for a mean increase of time to incision of 4.5 +/- 3.2 min, but represented only 3% of the mean surgical case length (207 +/- 132 min). We conclude that teaching occurs in the majority of cases in the operating room and although it contributes to increased time to incision, this increase is insignificant compared with the time required to complete the surgical procedure.

Can the attending anesthesiologist accurately predict the duration of anesthesia induction?

In a prospective, observational study, the attending anesthesiologists' prediction of anesthesia release time (ART) of the patient to the surgical team was highly correlated with actual ART (r = 0.77; P < or = 0.001). However, this was true only in the aggregate (n = 1265 patients). Indeed, offsetting degrees of under- and over-predicting (24% each) reduced accuracy to only 53% per individual case. For example, under-prediction was associated with ASA physical status IV, a regional anesthetic technique, age >65 yr, and the use of invasive hemodynamic monitoring (P = 0.006). In fact, as the degree of case difficulty increased, the correlation coefficient between predicted and actual ART decreased, indicating a poor predictive value with more difficult inductions (r = 0.82 to r = 0.44; P < or = 0.004). We conclude that knowledge of the presence of specific factors that lead to inaccurate predictions of time required for induction of anesthesia may enhance the accuracy of the operating room schedule.