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Logo of nihpaAbout Author manuscriptsSubmit a manuscriptHHS Public Access; Author Manuscript; Accepted for publication in peer reviewed journal;
J Autism Dev Disord. Author manuscript; available in PMC 2017 March 23.
Published in final edited form as:
PMCID: PMC5362964

Assessment of cognitive outcome measures in teenagers with 15q13.3 microdeletion syndrome

Emeline Crutcher, B.S.,1,2,3 May Ali, M.D.,2,3 John Harrison, PhD,4 Judit Sovago, M.D., PhD,5 Baltazar Gomez-Mancilla, M.D., PhD,5 and Christian P. Schaaf, M.D., PhD1,2,3,


15q13.3 microdeletion syndrome causes a spectrum of cognitive disorders, including intellectual disability and autism. We aimed to determine if any or all of three cognitive tests (the KiTAP, CogState, and Stanford-Binet) are suitable for assessment of cognitive function in affected individuals. These three tests were administered to ten individuals with 15q13.3 microdeletion syndrome (14–18 years of age), and the results were analyzed to determine feasibility of use, potential for improvement, and internal consistency. It was determined that the KiTAP, CogState, and Stanford-Binet are valid tests of cognitive function in 15q13.3 microdeletion patients. Therefore, these tests may be considered for use as objective outcome measures in future clinical trials, assessing change in cognitive function over a period of pharmacological treatment.

Keywords: neuropsychiatric disease, autism, intellectual disability, cognitive tests, cognitive function


15q13.3 microdeletion syndrome (OMIM #612001) is caused by small deletions in the extremely unstable q13.2–q13.3 region of chromosome 15, and is implicated in multiple neurodevelopmental disorders (Tropeano et al., 2014), (Lowther et al., 2014). This chromosomal region contains seven genes and is flanked by a breakpoint (BP) on each side. The breakpoints are marked by clusters of low copy repeat (LCR) elements, which are vulnerable to inversion and subsequent non-allelic homologous recombination (NAHR), resulting in deletion of the involved region (Gillentine & Schaaf, 2015). Most clinical cases of this syndrome present with microdeletions occurring between BP4 and BP5 (Tropeano et al., 2014). About 80% of patients with this syndrome have one or more neuropsychiatric diagnoses, with 57.5% diagnosed with developmental disability/intellectual disability, 10.9% diagnosed with autism spectrum disorder, 15.9% diagnosed with speech problems, and 6.5% diagnosed with attention deficit hyperactivity disorder (ADHD) (Lowther et al., 2014). The neuropsychiatric phenotypes of 15q13.3 microdeletion syndrome have been proposed to be caused by haploinsufficiency of CHRNA7, which is one of the seven genes in the region affected by the microdeletions (Gillentine & Schaaf, 2015).

CHRNA7 codes for the α7 subunits composing the α7 homopentameric nicotinic acetylcholine receptor (α7nAChR), which is expressed throughout the brain (Schaaf, 2014). Here, the receptors are involved in neuronal calcium signaling, which helps to mediate synaptic plasticity, learning, and memory (Gillentine & Schaaf, 2015). The heterozygous deletion of this gene, as present in 15q13.3 microdeletion cases, has been proposed to lead to a decreased number of functional receptors, causing altered calcium signaling and, consequently, deficits in cognitive function. Agonists of α7nAChR have been shown to improve cognitive function in patients with schizophrenia during phase 1 clinical trials (Freedman, 2014). However, the therapeutic potential of such treatments in individuals with 15q13.3 microdeletion syndrome has not been assessed to date.

As is true for other groups of individuals with intellectual disability (ID), there is a lack of well-established, objective tests validated for assessment of cognitive function in 15q13.3 microdeletion patients. This makes it difficult to accurately track changes in cognitive function of these patients throughout life. In addition, the efficacy of potential treatments in respective clinical trials is assessed primarily through subjective questionnaires. This results in a large placebo effect, and likely contributes to the low number of approved treatments for individuals with ID (Sandler, 2005).

Here, we assess performance of three test systems for cognitive function in a cohort of 15q13 del patients, aiming to identify potential outcome measures for clinical trials to be considered in this patient population.



Ten study participants were recruited for this study. Individuals were recruited from our own patient registry, based on a known diagnosis of 15q13.3 microdeletion syndrome. That diagnosis had been made by clinical chromosome microarray analysis prior to this study. A total of 18 families were contacted, with affected individuals between 12 and 21 years of age. The first 10 individuals to respond were consented for enrollment under a research protocol approved by the Institutional Review Board. Clinical details for these individuals are listed in Table 1 [Table 1].

Table 1
Clinical Information of 15q13.3 Deletion Subjects


Components of three test systems were administered to each subject: KiTAP (test of attentional performance in younger children), CogState, and Stanford-Binet (5th edition). Both the KiTAP and CogState were administered by the principal investigator (C.S.). These tests contain multiple components the user can choose to administer based upon the cognitive function they wish to assess. Components administered to these subjects, and cognitive functions assessed by each, are detailed in Table 2 [Table 2] for the KiTAP and Table 3 [Table 3] for the CogState. Outcome measures assessed for each component are those listed as primary outcome measures by each test’s instruction booklet and are noted in Table 2 for the KiTAP and Table 3 for the CogState. Data generated from each component of the KiTAP and the CogState tests were analyzed using Microsoft Excel. The Stanford-Binet test (5th edition) was administered by certified, research-reliable psychologists. The test administrator, following the instructions given in the test’s instruction booklet, calculated scores for the Stanford-Binet.

Table 2
Primary Outcome Measures and Cognitive Domains Assessed by Test Components of the KiTAP
Table 3
Primary Outcome Measures and Cognitive Domains Assessed by Test Components of the CogState

For the KiTAP and Cogstate components (except as noted below), regarding the “Feasibility” assessment (Table 4), individuals “Able to Perform Test” were determined to be those who were able to respond to the test stimuli adequately enough to generate a score for the test component indicated [Table 4]. The subjects determined to be unable to perform the test component got zero answers correct for that component. “Basal Effect” represents subjects that responded incorrectly to greater than 50% of the test component stimuli. This was set under the assumption that individuals with <50% accuracy are essentially guessing. Percent incorrect was calculated using the equation:


“Ceiling Effect” indicates the subjects that made no errors in response to stimuli on that test component. For the International Shopping List Task (ISLT) and ISLT delayed (same day and 24hrs) components of the CogState, and all Stanford-Binet components, “Able to Perform Test” were determined to be those who attempted to respond to the questions presented, and “Basal Effect” represents subjects who generated the lowest possible score for that component.

Table 4
Feasibility of Test Components in 15q13.3 Deletion Subjects

For the “Proof of Potential for Improvement” assessment (Table 5), mean percentile rankings for the KiTAP outcome measures were obtained through converting the T-scores calculated by the testing software to percentile rankings using Appendix B in the KiTAP users manual. The normed values for this calculation were from test scores generated by healthy 8–10 year olds [Table 5]. Mean percentile rankings for the CogState components were obtained by calculating Z-scores for each individual and outcome, using normed data obtained from a true age-matched cohort. These Z-scores were then converted to percentile rankings using the table found on MedFriendly.(“MedFriendly: Standard Score to Percentile Conversion,” n.d.) Z scores were calculated using the formula below.


For both the KiTAP and the CogState tests, mean percentile rankings were calculated for all outcome measures with normed data available for each component. For the CogState, mean percentile rankings were calculated only for components and outcome measures with true age-matched norms available. Mean percentile rankings for the Stanford-Binet were calculated by the test administrator, and are based on standard scores obtained by comparison to normed data from a true age matched cohort.

Table 5
Potential for Improvement in 15q13.3 Deletion Subjects

To assess the internal consistency of each test’s components, Cronbach’s alpha or Kuder Richardson 20 was calculated (Table 6) [Table 6]. The test used to calculate this value was dependent upon the outcome variable assessed for each test component. Cronbach’s alpha calculation was used to determine internal consistency in outcome variables with response measured on a scale i.e. reaction time (RT). Kuder Richardson 20 calculation was used to determine internal consistency in outcome variables with dichotomous responses i.e. correct or incorrect response. Test components with a value at or above 0.70 are considered to have an acceptable level of internal consistency. All internal consistency calculations were performed by assessing response via the primary outcome variable for each component, as determined by the testing instructions for each test. If more than one primary outcome variable was listed for a component, the first variable listed was used for the calculation.

Table 6
Internal Consistency in the KiTAP and CogState for 15q13.3 Deletion Subjects


Based on the results in Table 4, individuals with 15q13.3 deletions are capable of performing all administered components of both the KiTAP and CogState test, with minimal basal and ceiling effects. All individuals were able to perform all test components of both the KiTAP and the CogState, except for the psychomotor speed component of the CogState. For this component, only 8 of the 10 individuals were able to generate a score (Table 4). Components for both tests exhibited minimal basal effects in our cohort, with only two components displaying basal effects above 20%. Ceiling effects were also minimal for components of both tests, with all components displaying ceiling effects over 10% having a primary outcome measure of mean reaction time rather than number of correct or incorrect answers. Table 5 shows definite potential for score improvement on components of all three tests in our 15q13.3 deletion cohort. As expected, the mean percentile ranking of our cohort compared to age-matched norms for both the CogState and the Stanford-Binet test components were very low, with all but one falling below the 20th percentile (Table 5). For the KiTAP test components, the percentile rankings were mostly below the 50th percentile. Based on the standard cut-off value of 0.70 for acceptable internal consistency, all evaluated test components in both the KiTAP and the CogState have an acceptable level of internal consistency in our cohort (Table 6).


This is the first description of validation of these three test systems, assessing various elements of cognition, including memory, and attention, in a cohort of individuals with 15q13.3 microdeletion syndrome. Both the KiTAP and CogState have been used to assess cognitive function in ADHD populations, but use of the CogState has never been verified for use in subjects with ASD or ID (Jucaite et al., 2014), (Mollica et al., 2004), (Yamashita et al., 2011), (Rothmann et al., 2014), (Hellwig-Brida et al., 2011), (Kaufmann et al., 2010). Assessment of feasibility for use of the KiTAP in a Fragile X Syndrome (FXS) cohort has been previously investigated, and it was found that this test is a valid assessment of cognitive function in FXS patients (Knox et al., 2012). Although the 5th edition of the Stanford-Binet included some subjects diagnosed with ASD in its normative population, its ability to accurately assess cognitive function in these individuals has not been validated (Grondhuis & Mulick, 2013), (Ozonoff et al., 2005), (Silverman et al., 2010).

Impact of similarities and differences between the KiTAP, CogState, and Stanford-Binet cognitive batteries

Although these three test systems all assess cognitive function, the KiTAP and CogState assess more ‘plastic’ cognitive functions, while the Stanford-Binet is the gold standard for IQ testing and assesses cognitive functions that are more resistant to change. While the functions assessed by the KiTAP and the CogState are nearly identical, there is little overlap between these functions and those assessed by the Stanford-Binet. All three test systems are composed of multiple components, each meant to assess a different cognitive domain. However, unlike the KiTAP and CogState, the Stanford-Binet has a single outcome reading for each component. The Stanford-Binet is hand-scored by the test administrator, and is given a numerical score between 0 and 2, based upon the subject’s response. Importantly, the difficulty level at which you start each component of the Stanford-Binet depends on performance in a placement section at the beginning of the test, which dictates the starting position of each component for that individual. The testing for each individual will continue until that subject scores all zeros on a sub-section of a component. Because of this, different subjects may be responding to different questions on each component, based upon where their starting level was determined to be, and how far past the starting point they make it. The Stanford-Binet, like other IQ tests, is considered a poor choice for measuring clinical outcomes over the period of a standard trial treatment (Aman et al., 2004). This is partially due to the 0–2 type scoring method of these tests, which creates low sensitivity, and makes it almost impossible to detect small changes in cognitive function (Aman et al., 2004). The KiTAP and CogState are more sensitive to change due to the broad range of outcome measures collected for each component. Additionally, each component of these tests administers the same type of stimulus repeatedly over the period of the test component, and collects response data for each outcome measure upon each stimulus. This allows a more accurate assessment of how a subject is responding to a particular stimulus, as opposed to each stimulus being different from the next, and scored separately, which is the case for the Stanford-Binet. Since both the KiTAP and CogState are computerized, the possibility of human bias or error affecting the results is greatly reduced compared to a test that is hand-scored, such as the Stanford-Binet. Although standardized IQ tests such as the Stanford-Binet may not be the best measure of change in cognitive function over the period of a clinical trial, they are still useful for long term assessments, as well as for baseline comparisons to performance on less characterized cognitive tests, such as the KiTAP and CogState.

Although the KiTAP and CogState test components measure very similar cognitive functions, the method by which each test’s stimuli evoke a response is quite different. The KiTAP was specifically designed to engage children, and each test component has a theme based around the main premise of being in a haunted castle. Each component contains colorful animations serving as the response stimulus. Additionally, each component’s theme is different from the others, with themes including colorful caricatures of ghosts, witches, and dragons. Conversely, the CogState was not designed to engage children specifically, and each test component’s response stimulus is similar. While each component of the Cogstate asks a different question (i.e. is the card black vs. have you seen this card before), the stimulus presented remains the face of a random playing card. This type of repetitive stimulus across multiple test components presents the challenge of not being able to hold the attention of test takers as well as the more engaging KiTAP. This is especially true for adolescent populations, or any populations having attention deficits. Considering that our population is composed mostly of teenagers (average age = 15.6 years), and attention deficit hyperactivity disorder (ADHD) is one of the known clinical manifestations of 15q13.3 deletion, we conclude that the CogState may not be as good an assessment of cognitive function as the KiTAP in that particular population. This is supported by the fact that the two components displaying a basal effect over 20% both come from the CogState test. Additionally, the percentile rankings of the CogState components are much lower than either the KiTAP or the Stanford-Binet. Although some of the difference between the CogState and KiTAP mean percentile rankings can be explained by age differences in the sources of normed values (age matched vs. 8–10 year olds), it is unlikely that the 4 to 8 year difference between normed values and actual age of test subjects in the KiTAP has such a profound effect on difference in percentile ranking. If this were the case, we would expect to see much more similar percentile rankings between components of the CogState and Stanford-Binet, since percentile rankings for both were calculated from age-matched norms. The lack of variance in mean percentile ranking between components of the CogState when compared to variances between components of the other two tests reinforces the concept that monotony in the CogState stimuli may result in less efficient distinction of different cognitive domains when compared to the KiTAP and Stanford-Binet. A larger cohort of 15q13.3 deletion individuals, as well as a healthy, age-matched control cohort for all components of the CogState, and KiTAP tests would help determine if indeed one of these tests is superior to the other for measuring cognitive function in 15q13.3 deletion patients.

Individuals with 15q13.3 deletion are capable of obtaining valid scores on components of the KiTAP, CogState, and Stanford-Binet cognitive batteries

When validating cognitive tests in a population with cognitive abnormalities, it is important to ensure that the subjects have the ability to respond to the test stimulus adequately enough to generate a valid score. Inability to generate a score on a test component could be a result of unwillingness to participate, or physical or mental disabilities resulting in a lack of ability to respond to the test stimulus appropriately. Based on the observation that all subjects were able to perform all but one test component, we conclude that our cohort is capable of responding to the stimuli presented by each test. For the one CogState test component that only 8 of 10 subjects were able to perform, it is likely that the two non-responding subjects were simply not engaged with this particular test component as they were both able to respond to all other test components with similar stimuli. It is also essential to verify that there is not a large basal or ‘floor’ effect, as is often the case when such populations take tests created to assess cognitive function in the normal population. The presence of a basal effect indicates that some individuals in the cohort being studied are generating a score at or below the guessing rate. This could indicate that the individual did not understand the test component instructions, or that they were not fully engaged in taking the test during that component. Ultimately, a large basal effect for a test component indicates that component is not a good measure of cognitive function in that group of individuals, likely because the task requires a higher level of function than the average individual in the group is capable of. The overall percentage of basal effect across test components of all three tests is low, and indicates that most of these test components are at an appropriate level of difficulty for our cohort. The presence of some basal effect in our subject population is expected due to the wide range and severity of phenotypes in 15q13.3 deletion patients. There were two components of the CogState presenting with a basal effect higher than 20%. It is possible that these components are testing cognitive function at a level unsuitable for many of these subjects. However, it would be ideal to test these components on a larger cohort to determine if these results hold true over a more inclusive population of 15q13.3 deletion patients. Verifying a low ceiling effect is important in order to ensure that the cohort being studied does not perform so well on the test components that there is no room to improve scores. It is important to note that ceiling effect is based off of correct answers, as mentioned in the methods and results section. Therefore, for those test components whose primary outcome measure does not depend on correct response (i.e. mean RT), a large ceiling effect holds no meaning. This is the case in our cohort for all test components with a ceiling effect over 10% (Table 2). Based on this, we can conclude that the test components assessed in this study are testing cognitive function at a level that challenges our cohort, and that improvement upon initial test scores is possible.

Ample potential for improvement in 15q13.3 deletion cohort

To assess potential for improvement of test scores upon increased cognitive function in our 15q13.3 deletion cohort, we calculated the average baseline percentile rankings for our cohort across test components for all outcome measures having available normed values. The Stanford-Binet has been thoroughly standardized, with norms available for age matched standardization of each subject’s scores. This has been done to a lesser extent for the KiTAP and CogState. For the KiTAP, a complete set of norms is available for age groups 6–7 and 8–10. However, no norms for age groups older than that are available. In the case of the CogState, a complete set of norms for primary outcome measures is available for age groups 18 and older, but only incomplete norms exist for ages younger than 18. While other assessments of test validity can be performed, this makes it difficult to accurately determine the average percentile ranking of our 15q13.3 deletion cohort. Some argue that these percentile rankings are not valid in ID populations (Knox et al., 2012). While this may be accurate in some cases, the main point of assessing these rankings in our case is to show that there is definite room for improvement in the scores generated on the respective test components in individuals with 15q13.3 microdeletion syndrome. Comparing the scores generated by our cohort to those generated by healthy controls, we show that this is indeed the case. Both for the CogState and the Stanford-Binet tests, all of the mean percentile rankings obtained by the 15q13.3 deletion cohort are below the 50th %ile. The CogState mean percentile rankings are especially low (~3rd percentile), while the Stanford-Binet rankings are more variable depending on the skill being measured (6th–38th percentile). This is to be expected since the Stanford-Binet was developed primarily to assess IQ and reasoning ability, while the CogState was developed to assess more interactive cognitive functions such as psychomotor speed and attention. For the KiTAP, most of the mean percentile rankings are still below average (<50th percentile). However, it is important to remember that these percentile rankings compare our cohort to a normal cohort aged 8–10. Since our subjects were 14–18 years old (true ages) at the time of testing, it is reasonable to expect that they will score higher when compared to 8–10 year olds than when compared to an age-matched cohort. The fact that the large majority of primary outcomes show percentile scores below average leaves room for improvement, in particular when considering clinical trials of pharmacologic intervention. Although a change in IQ scores (as measured by the Stanford-Binet) may not be seen over the course of a treatment trial period, it is likely that an effective treatment could be identified by monitoring changes in cognitive functions with the more sensitive CogState and KiTAP tests.

Acceptable levels of internal consistency across components of the KiTAP and CogState cognitive batteries

Internal consistency is a measure of intra-individual agreement between different items/questions testing the same general function. A value of 1 represents perfect internal consistency, and any value above 0.70 indicates that the test component has an acceptable level of internal consistency.

Cronbach’s alpha is the statistical test most often used to determine internal consistency across a group of questions meant to measure the same function. However, this test was created to measure how consistently individuals answered questions with the response being measured on a scale. For several test components we wished to assess, the primary outcome measure is not measured on a scale, but rather dichotomous (number of correct responses or number of errors). For these cases, Kuder-Richardson Formula 20 was used.

Since each component of these tests is essentially asking the same question over and over again, we would expect to see an alpha value close to 1 for components which the subjects understood instructions well, and were able to respond similarly to each question/stimulus.

Internal consistency statistics were not performed on Stanford-Binet components due to the nature of scoring (not every child starts at the same place, therefore questions will be different between children).

Based on the internal consistency statistics presented in Table 6, it appears that each evaluated test component in both the KiTAP and the CogState has acceptable internal consistency in our cohort, with all but two components achieving a score above 0.80. There is only one test component, “sustained attention” from the KiTAP, which is on the border of the acceptable range. This value rounds up to 0.7 from 0.69, and would potentially be higher upon evaluation of a larger group of subjects.


Based on the data presented, we conclude that the KiTAP, CogState, and the Stanford-Binet are valid measures of cognitive function in individuals with 15q13.3 microdeletion syndrome. Along with previous studies in individuals with Fragile X syndrome, the data presented herein provide encouragement that some cognitive tests established in healthy patients may be used to assess cognitive function in individuals with psycho-cognitive abnormalities stemming from a range of genetic or environmental causes. The 15q13.3 microdeletion syndrome has great potential for therapeutic intervention, with haploinsufficiency of CHRNA7 being considered a likely contributor to the overall phenotype, and promising alpha7 agonist drugs and positive allosteric modulators being developed (Schaaf, 2014). This pilot study provides important groundwork that will be useful for sample size calculations and consideration of quantifiable outcome measures to be considered in clinical trials for individuals with 15q13.3 microdeletion syndrome.


We are indebted to the patients and their families for their willingness to participate in our study.

This work was supported in part by the Doris Duke Charitable Foundation Grant # 2011034 and in part as an Investigator Initiated Research Protocol by Novartis Pharmaceuticals Corporation. The project was supported in part by IDDRC grant number 1U54 HD083092 from the Eunice Kennedy Shriver National Institute of Child Health & Human Development.  Cores: Tissue culture core, translational core. CS is generously supported by the Joan and Stanford Alexander Family.


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