Exome and genome sequencing in a heterogeneous population of patients with rare disease: Identifying predictors of a diagnosis

PURPOSE

Exome (ES) and genome sequencing (GS) are increasingly being utilized for individuals with rare and undiagnosed diseases; however, guidelines on their use remain limited. This study aimed to identify factors associated with diagnosis by ES and/or GS in a heterogeneous population of patients with rare and undiagnosed diseases.

METHODS

In this case control study, we reviewed data from 400 diagnosed and 400 undiagnosed randomly selected participants in the Undiagnosed Diseases Network, all of whom had undergone ES and/or GS. We analyzed factors associated with receiving a diagnosis by ES and/or GS.

RESULTS

Factors associated with a decreased odds of being diagnosed included adult symptom onset, singleton sequencing, and having undergone ES and/or GS before acceptance to the Undiagnosed Diseases Network (48%, 51%, and 32% lower odds, respectively). Factors that increased the odds of being diagnosed by ES and/or GS included having primarily neurological symptoms and having undergone prior chromosomal microarray testing (44% and 59% higher odds, respectively).

CONCLUSION

We identified several factors that were associated with receiving a diagnosis by ES and/or GS. This will ideally inform the utilization of ES and/or GS and help manage expectations of individuals and families undergoing these tests.

Seeking a better balance between efficiency and interpretability: Comparing the likert response format with the Guttman response format

The Likert item response format for items is almost ubiquitous in the social sciences and has particular virtues regarding the relative simplicity of item-generation and the efficiency for coding responses. However, in this article, we critique this very common item format, focusing on its affordance for interpretation in terms of internal structure validity evidence. We suggest an alternative, the Guttman response format, which we see as providing a better approach for gathering and interpreting internal structure validity evidence. Using a specific survey-based example, we illustrate how items in this alternative format can be developed, exemplify how such items operate, and explore some comparisons between the results from using the two formats. In conclusion, we recommend usage of the Guttman response format for improving the interpretability of the resulting outcomes. Finally, we also note how this approach may be used in tandem with items that use the Likert response format to help balance efficiency with interpretability. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

Genetic counseling for fetal sex prediction by NIPT: Challenges and opportunities

Non-invasive prenatal testing (NIPT) has grown in ubiquity in the last decade and is now endorsed by Society for Maternal Fetal Medicine and American College of Obstetricians and Gynecologists as a screening tool for aneuploidy in all patients. Past studies have demonstrated a tendency among obstetrics patients to focus on the ability of NIPT to predict fetal sex chromosomes; however, data on the experiences of genetic counselors (GCs) counseling on NIPT and fetal sex prediction are limited. This mixed-methods study aimed to explore how GCs counsel about NIPT and fetal sex prediction, as well as the use of gender-inclusive language in this setting. A 36-item survey with multiple choice, Likert scale, and open-ended questions was distributed to GCs who currently offer NIPT to patients. Quantitative data were analyzed using R and qualitative data were manually analyzed and coded via inductive content analysis. A total of 147 individuals completed at least some portion of the survey. A majority of participants (68.5%) reported frequent interchangeable use of the terms 'sex' and 'gender' by patients. A majority (72.9%) of participants reported that they rarely or never discuss the difference between these terms in sessions (Spearman's rho = 0.17, p = 0.052). Seventy-five respondents (59.5%) indicated that they had taken continuing education courses on inclusive clinical practices for trans and gender-diverse (TGD) patients. Several themes arose from free responses; the most frequently identified themes were the need for thorough pretest counseling that properly describes the scope of NIPT and the challenge of discrepant pretest counseling by other healthcare providers. Results from our research identified challenges and misconceptions GCs face when offering NIPT and various tactics implemented to mitigate these. Our study highlighted the need for the standardization of pretest counseling regarding NIPT, additional guidance from professional organizations, and continuing education focused on gender-inclusive language and clinical practices.

Does the Dizziness Handicap Inventory-Children and Adolescents (DHI-CA) Demonstrate Properties to Support Clinical Application in the Post-Concussion Population: A Rasch Analysis

The purpose of this cross-sectional validation study was to evaluate the clinical utility of the DHI-CA by (1) examining its dimensionality using exploratory factor analysis (EFA) and (2) calibrating DHI-CA items (using the multidimensional Rasch model) to obtain item difficulty levels. A retrospective chart review was conducted for 132 patients between the ages of 8 and 18 years (mean age = 15.3 ± 2.1 years) from a multidisciplinary post-concussion management tertiary center. Data were extracted on age, sex, and DHI-CA. EFA revealed that 12 out of 25 items did not fit in the subscale that they were originally described under, indicating poor dimensionality. Calibration of items on the Wright Maps revealed that 50% of the items pooled in the lower difficulty level, indicating a potential ceiling effect. Corrected item-rest correlations for the physical, emotional, walking/mobility, and community participation ranged from 0.44-0.66, 0.27-0.61, 0.54-0.57, and 0.32-0.69 (p < 0.001), respectively. The clinical utility of the DHI-CA was found to be questionable due to the presence of double-barreled items and the ceiling effect. Clinicians must supplement data from the DHI-CA with other measures and patient interviews to make informed clinical decisions specific to the post-concussion population until new, robust, and valid measures are developed.

Sensitivity to Change and Responsiveness of the Upper Extremity Fugl-Meyer Assessment in Individuals With Moderate to Severe Acute Stroke

BACKGROUND

The Fugl-Meyer Assessment-Upper Extremity (FMA-UE) is a widely used outcome measure for quantifying motor impairment in stroke recovery. Meaningful change (responsiveness) in the acute to subacute phase of stroke recovery has not been determined.

OBJECTIVE

Determine responsiveness and sensitivity to change of the FMA-UE from 1-week to 6-weeks (subacute) after stroke in individuals with moderate to severe arm impairment who received standard clinical care.

METHODS

A total of 51 participants with resulting moderate and severe UE hemiparesis after stroke had FMA-UE assessment at baseline (within 2 weeks of stroke) and 6-weeks later. Sensitivity to change was assessed using Glass's delta, standardized response means (SRM), standard error of measure (SEM), and minimal detectable change (MDC). Responsiveness was assessed with the minimal clinically important difference (MCID), estimated using receiver operating characteristic curve analysis with patient-reported global rating of change scales (GROC) and a provider-reported modified Rankin Scale (mRS) as anchors.

RESULTS

The MCID estimates were 13, 12, and 9 anchored to the GROC Arm Weakness, GROC Recovery, and mRS. Glass's delta and the SRM revealed large effect sizes, indicating high sensitivity to change, (∆ = 1.24, 95% CI [0.64, 1.82], SRM = 1.10). Results for the SEM and MDC were 2.46 and 6.82, respectively.

CONCLUSION

The estimated MCID for the FMA-UE for individuals with moderate to severe motor impairment from 1 to 6-weeks after stroke is 13. These estimates will provide clinical context for FMA-UE change scores by helping to identify the change in upper-extremity motor impairment that is both beyond measurement error and clinically meaningful.

Measuring social norms of intimate partner violence to exert control over wife agency, sexuality, and reproductive autonomy: an item response modelling of the IPV-ASRA scale

BACKGROUND

The field of violence prevention research is unequivocal that interventions must target contextual factors, like social norms, to reduce gender-based violence. Limited research, however, on the social norms contributing to intimate partner violence or reproductive coercion exists. One of the driving factors is lack of measurement tools to accurately assess social norms.

METHODS

Using an item response modelling approach, this study psychometrically assesses the reliability and validity of a social norms measure of the acceptability of intimate partner violence to exert control over wife agency, sexuality, and reproductive autonomy with data from a population-based sample of married adolescent girls (ages 13-18) and their husbands in rural Niger (n = 559 husband-wife dyads) collected in 2019.

RESULTS

A two-dimensional Partial Credit Model for polytomous items was fit, showing evidence of reliability and validity. Higher scores on the "challenging husband authority" dimension were statistically associated with husband perpetration of intimate partner violence.

CONCLUSIONS

This brief scale is a short (5 items), practical measure with strong reliability and validity evidence. This scale can help identify populations with high-need for social norms-focused IPV prevention and to help measure the impact of such efforts.

Item Analysis of Functional Measure Indicators in the National Health and Nutrition Examination Survey: A Cross-sectional Study

OBJECTIVE

This study aimed to develop a function, activities, and participation measurement scale using the questions on the National Health and Nutrition Examination Survey (NHANES) by applying item response theory approaches.

DESIGN

This was a cross-sectional study.

PARTICIPANTS

Survey data were collected from 2512 participants within the NHANES.

METHODS

Twenty questions from the NHANES physical functioning section were included. Exploratory and confirmatory factor analyses were conducted to evaluate the factorial structure and model fit of the NHANES instrument. A multidimensional Rasch modeling was used to model the response data after confirming its model fit. To assess validity across subgroups, differential item functioning test was conducted with respect to sex and race using the three-dimensional partial credit model.

RESULTS

Item fit indices indicated a good fit (root-mean-square error of approximation = 0.049, standardized root-mean-square residual = 0.052, Tucker-Lewis index = 0.975). Rasch analysis indicated that "stoop/crouch/kneel," "stand for long periods," and "push/pull large objects" were the three most difficult items, whereas "walk between rooms," "use fork/knife," and "leisure at home" were the easiest. The measure demonstrated good internal consistency overall (Cronbach α = 0.90).

CONCLUSION

The NHANES function, activities, and participation measure demonstrates sufficient evidence of reliability, internal consistency, and validity in noninstitutionalized community-dwelling population.

TO CLAIM CME CREDITS

Complete the self-assessment activity and evaluation online at http://www.physiatry.org/JournalCME.

CME OBJECTIVES

Upon completion of this article, the reader should be able to (1) Recognize the potential benefits of using validated patient-reported functional outcome measures within the publically available National Health and Nutrition Examination Survey (NHANES) data for rehabilitation research; (2) Describe the process of scale development and validation; (3) Identify item difficulty based on the item difficulty distribution; and (4) Identify the applicability of the measure to different population groups based on differential item functioning.

LEVEL

Advanced.

ACCREDITATION

The Association of Academic Physiatrists is accredited by the Accreditation Council for Continuing Medical Education to provide continuing medical education for physicians.The Association of Academic Physiatrists designates this Journal-based CME activity for a maximum of 1.0 AMA PRA Category 1 Credit(s) ™. Physicians should only claim credit commensurate with the extent of their participation in the activity.

Initial treatment approaches and healthcare utilization among veterans with low back pain: a propensity score analysis

BACKGROUND

Opioid prescriptions for Veterans with low back pain (LBP) persist despite the availability of PT, a lower medical risk treatment option. Patterns of treatment and subsequent healthcare utilization for Veterans with LBP are unknown. The purpose of this study was to evaluate the association of physical therapy (PT) and opioids and outcomes of spinal surgery and chronic opioid use for Veterans with incident LBP.

METHODS

We conducted a retrospective cohort study identifying Veterans with a new diagnosis of LBP using ICD codes from the Veterans Administration national database from 2012 to 2017. Veterans were classified into three treatment groups based on the first treatment received within 30 days of incident LBP: receipt of PT, opioids, or neither PT nor opioids. Outcomes, events of spinal surgery and chronic opioid use, were identified beginning on day 31 up to one year following initial treatment. We used propensity score matching to account for the potential selection bias in evaluating the associations between initial treatment and outcomes.

RESULTS

There were 373,717 incident cases of LBP between 2012 and 2017. Of those 28,850 (7.7%) received PT, 48,978 (13.1%) received opioids, and 295,889 (79.2%) received neither PT or opioids. Pain, marital status and the presence of cardiovascular, pulmonary, or metabolic chronic conditions had the strongest statistically significant differences between treatment groups. Veterans receiving opioids compared to no treatment had higher odds of having a spinal surgery (2.04, 99% CI: 1.67, 2.49) and progressing to chronic opioid use (11.8, 99% CI: 11.3, 12.3). Compared to Veterans receiving PT those receiving opioids had higher odds (1.69, 99% CI: 1.21, 2.37) of having spinal surgery and progressing to chronic opioid use (17.8, 99% CI: 16.0, 19.9).

CONCLUSION

Initiating treatment with opioids compared to PT was associated with higher odds of spinal surgery and chronic opioid use for Veterans with incident LBP. More Veterans received opioids compared to PT as an initial treatment for incident LBP. Our findings can inform rehabilitation care practices for Veterans with incident LBP.

SMS-text messaging for collecting outcome measures after acute stroke

Introduction

Traditional methods for obtaining outcomes for patients after acute stroke are resource-intensive. This study aimed to examine the feasibility, reliability, cost, and acceptability of collecting outcomes after acute stroke with a short message service (SMS)-text messaging program.

Methods

Patients were enrolled in an SMS-text messaging program at acute stroke hospitalization discharge. Participants were prompted to complete assessments including the modified Rankin scale (mRS) and Patient-Reported Outcomes Measurement (PROM) Information System Global-10 at 30, 60, and 90 days postdischarge via SMS-text. Agreement and cost of SMS-text data collection were compared to those obtained from traditional follow-up methods (via phone or in the clinic). Participant satisfaction was surveyed upon program conclusion.

Results

Of the 350 patients who agreed to receive SMS texts, 40.5% responded to one or more assessments. Assessment responders were more likely to have English listed as their preferred language (p = 0.009), have a shorter length of hospital stay (p = 0.01), lower NIH stroke scale upon admission (p < 0.001), and be discharged home (p < 0.001) as compared to nonresponders. Weighted Cohen's kappa revealed that the agreement between SMS texting and traditional methods was almost perfect for dichotomized (good vs. poor) (κ = 0.8) and ordinal levels of the mRS score (κ = 0.8). Polychoric correlations revealed a significant association for PROM scores ( ρ  = 0.4, p < 0.01 and ρ  = 0.4, p < 0.01). A cost equation showed that gathering outcomes via SMS texting would be less costly than phone follow-up for cohorts with more than 181 patients. Nearly all participants (91%) found the program acceptable and not burdensome (94%), and most (53%) felt it was helpful. Poststroke outcome data collection via SMS texting is feasible, reliable, low-cost, and acceptable. Reliability was higher for functional outcomes as compared to PROMs.

Conclusions

While further validation is required, our findings suggest that SMS texting is a feasible method for gathering outcomes after stroke at scale to evaluate the efficacy of acute stroke treatments.

Novel Platform for Quantitative Assessment of Functional Object Interactions After Stroke

Many persons with stroke exhibit upper extremity motor impairments. These impairments often lead to dysfunction and affect performance in activities of daily living, where successful manipulation of objects is essential. Hence, understanding how upper extremity motor deficits manifest in functional interactions with objects is critical for rehabilitation. However, quantifying skill in these tasks has been a challenge. Traditional rehabilitation assessments require highly trained clinicians, are time-consuming, and yield subjective scores. This paper introduces a custom-designed device, the "MAGIC Table", that can record real-time kinematics of persons with stroke during interaction with objects, specifically a 'cup of coffee'. The task and its quantitative assessments were derived from previous basic-science studies. Six participants after stroke and six able-bodied participants moved a 3D-printed cup with a rolling ball inside, representing sloshing coffee, with 3 levels of difficulty. Movements were captured via a high-resolution camera above the table. Conventional kinematic metrics (movement time and smoothness) and novel kinematic metrics accounting for object interaction (risk and predictability) evaluated performance. Expectedly, persons with stroke moved more slowly and less smoothly than able-bodied participants, in both simple reaches and during transport of the cup-and-ball system. However, the more sensitive metric was mutual information, which captured the predictability of interactions, essential in cup transport as shown in previous theoretical research. Predictability sensitively measured differences in performance with increasing levels of difficulty. It also showed the best intraclass consistency, promising sensitive differentiation between different levels of impairment. This first study highlights the feasibility of this new device and indicates that examining dynamic object interaction may provide valuable insights into upper extremity function after stroke useful for assessment and rehabilitation.

The efficacy of acoustic-based articulatory phenotyping for characterizing and classifying four divergent neurodegenerative diseases using sequential motion rates

Despite the impacts of neurodegeneration on speech function, little is known about how to comprehensively characterize the resulting speech abnormalities using a set of objective measures. Quantitative phenotyping of speech motor impairments may have important implications for identifying clinical syndromes and their underlying etiologies, monitoring disease progression over time, and improving treatment efficacy. The goal of this research was to investigate the validity and classification accuracy of comprehensive acoustic-based articulatory phenotypes in speakers with distinct neurodegenerative diseases. Articulatory phenotypes were characterized based on acoustic features that were selected to represent five components of motor performance: Coordination, Consistency, Speed, Precision, and Rate. The phenotypes were first used to characterize the articulatory abnormalities across four progressive neurologic diseases known to have divergent speech motor deficits: amyotrophic lateral sclerosis (ALS), progressive ataxia (PA), Parkinson's disease (PD), and the nonfluent variant of primary progressive aphasia and progressive apraxia of speech (nfPPA + PAOS). We then examined the efficacy of articulatory phenotyping for disease classification. Acoustic analyses were conducted on audio recordings of 217 participants (i.e., 46 ALS, 52 PA, 60 PD, 20 nfPPA + PAOS, and 39 controls) during a sequential speech task. Results revealed evidence of distinct articulatory phenotypes for the four clinical groups and that the phenotypes demonstrated strong classification accuracy for all groups except ALS. Our results highlight the phenotypic variability present across neurodegenerative diseases, which, in turn, may inform (1) the differential diagnosis of neurological diseases and (2) the development of sensitive outcome measures for monitoring disease progression or assessing treatment efficacy.

Introduction of the genetic counseling profession by teachers in BIPOC ‐majority high schools

The field of genetic counseling is racially and ethnically (RE) homogenous, with 90% of genetic counselors identifying as white. As awareness of genetic counseling increases interest in the career, one proposed method to increase the profession's RE diversity is to introduce genetic counseling as a career option to Black, Indigenous, and people of color (BIPOC) students during high school. This study explores the knowledge, presentation, and perceptions of the genetic counseling profession by high school teachers at BIPOC-majority high schools in the United States (US). Science teachers working at public high schools in Massachusetts and New York where greater than 75% of the student body identifies as BIPOC were invited to participate in a survey and focus groups for this study. A total of 456 teachers participated in the survey and a total of seven teachers participated in two focus groups. The survey data revealed that most (91.8%) participating teachers presented genetic counseling, though BIPOC-identifying teachers were more likely to report never presenting genetic counseling than white-identifying teachers. In addition, teachers' knowledge of the genetic counseling career and frequency of presenting it were strongly associated, suggesting that increasing knowledge of genetic counseling among teachers, particularly those who are BIPOC-identifying, could lead to increased presentation to BIPOC students. Major themes that emerged through the focus groups included (1) teachers perceiving genetic counseling as novel and complex in comparison to other healthcare professions, (2) teachers sharing that multiple methods can and should be used when introducing genetic counseling to students, and (3) the notion that teachers could have an important role in introducing genetic counseling to their students. Considering findings from the survey and focus groups, recommendations from this study include increasing awareness of genetic counseling among BIPOC-identifying science teachers at BIPOC-majority high schools, gradually introducing genetic counseling topics to students beginning at a young age, and utilizing student-led teaching activities.

Association of Modified Rankin Scale With Recovery Phenotypes in Patients With Upper Extremity Weakness After Stroke

BACKGROUND

Precise measurement of outcomes is essential for stroke trials and clinical care. Prior research has highlighted conceptual differences between global outcome measures such as the Modified Rankin Scale (mRS) and domain-specific measures (e.g. motor, sensory, language or cognitive function). This study related motor phenotypes to the mRS, specifically aiming to (1) determine whether mRS levels distinguish motor impairment and function phenotypes, and (2) compare mRS outcomes to meaningful changes in impairment and function from acute to subacute recovery after stroke.

METHODS

Patients with upper extremity weakness after ischemic stroke were assessed with a battery of impairment and functional measures within the first week and at 90-days post-stroke. Impairment and functional outcomes were examined in relation to 90-day mRS scores. Clinically meaningful changes in motor impairment, activities of daily living, and mobility were examined in relation to 90-day mRS.

RESULTS

In this cohort of n = 73 stroke patients, impairment and functional outcomes were associated with 90-day mRS scores but showed substantial variability within individual mRS levels: within mRS level 2, upper extremity impairment ranged from near hemiplegia (with an upper extremity Fugl-Meyer 8) to no deficits (upper extremity Fugl-Meyer 66). Overall, there were few differences in impairment and functional outcomes between adjacent mRS levels. While some outcome measures were significantly different between mRS levels 3 and 4 (Nine-Hole Peg, Leg Motor, Gait Velocity, Timed Up and Go, National Institutes of Health Stroke Scale, and Barthel Index), none of the outcome measures differed between mRS levels 1 and 2. Fugl-Meyer and Grip Strength were not different between any adjacent mRS levels. A substantial number of patients experienced clinically meaningful changes in impairment and function in the first 90 days post-stroke but did not achieve good mRS outcome (mRS ≤ 2).

CONCLUSIONS

The mRS broadly relates to domain-specific outcomes after stroke confirming its established value in stroke trials, but it does not precisely distinguish differences in impairment and function nor does it sufficiently capture meaningful clinical changes across impairment, ADL status, and mobility. These findings underscore the potential utility of incorporating detailed phenotypic measures alongside the mRS in future stroke trials.

Efficiently assessing firm, fair, and caring relationships: Short form of the Dual Role Relationship Inventory

Many people involved in the justice system and people with serious mental illness are required to participate in psychosocial treatment, whether they want it or not. With these clients, case managers, probation officers, and other providers are tasked with both promoting client recovery (a helping, therapeutic role) and protecting community safety (a controlling, surveillance role). The 30-item revised Dual-Role Relationship Inventory (DRI-R) assesses the quality of provider-client relationships in mandated treatment-and DRI-R based research indicates that firm, fair, and caring relationships (authoritative, not authoritarian) predict better client outcomes. In this study, we developed and validated a short form of the DRI-R-the 9-item DRI-SF-by applying multidimensional item response theory methods to four data sets (N = 815). We simultaneously refined the measure by selecting items that cleanly assessed relationship features (i.e., minimized construct-irrelevant variance from provider traits) and performed similarly across client groups (juveniles and adults; with-and-without mental illness). DRI-SF total scores strongly predict DRI-R total scores (r = .97). The DRI-SF fully represented the DRI-R's range of item difficulties, produced the same three-factor structure, predicted theoretically relevant external covariates as strongly (i.e., groups known to differ in relationship quality, relationship satisfaction ratings, future arrests)-without item bias by sex or race. Moreover, the favorable psychometric properties of the DRI-SF were replicated in a new sample and shown to generalize across provider groups (from probation officers to treatment providers). This newly developed DRI-SF applies to a range of provider-client relationships in mandated treatment-and will benefit practitioners and researchers with ease of administration. (PsycINFO Database Record (c) 2019 APA, all rights reserved).

Hierarchical and Higher-Order Factor Structures in the Rasch Tradition: A Didactic

In this paper, we consider hierarchical and higher-order factor models and the relationship between them, and, in particular, we use Rasch models to focus on the exploration of these models. We present these models, their similarities and/or differences from within the Rasch modeling perspective and discuss their use in various settings. One motivation for this work is that certain well-known similarities and differences between the equivalent models in the two-parameter logistic model (2PL) approach do not apply in the Rasch modeling tradition. Another motivation is that there is some ambiguity as to the potential uses of these models, and we seek to clarify those uses. In recent work in the Item Response Theory (IRT) literature, the estimation of these models has been mostly presented using the Bayesian framework: here we show the use of these models using traditional maximum likelihood methods. We also show how to re-parameterize these models, which in some cases can improve estimation and convergence. These alternative parameterizations are also useful in "translating" suggestions for the 2PL models to the Rasch tradition (since these suggestions involve the interpretation of item discriminations, which are required to be unity in the Rasch tradition). Alternative parameterizations can also be used to clarify the relationship among these models. We discuss the use of these models for modeling multidimensionality and testlet effects and compare the interpretation of the obtained solutions to the interpretation for the multidimenisional Rasch model - a more common approach for accounting multidimensionality in the Rasch tradition. We demonstrate the use of these models using the partial credit model.