A holistic approach to maximise diagnostic output in trio exome sequencing

Introduction

Rare genetic diseases are a major cause for severe illness in children. Whole exome sequencing (WES) is a powerful tool for identifying genetic causes of rare diseases. For a better and faster assessment of the vast number of variants that are identified in the index patient in WES, parental sequencing can be applied ("trio WES").

Methods

We assessed the diagnostic rate of routine trio WES including analysis of copy number variants in 224 pediatric patients during an evaluation period of three years.

Results

Trio WES provided a diagnosis in 67 (30%) of all 224 analysed children. The turnaround time of trio WES analysis has been reduced significantly from 41 days in 2019 to 23 days in 2021. Copy number variants could be identified to be causative in 10 cases (4.5%), underlying the importance of copy number variant analysis. Variants in three genes which were previously not associated with a clinical condition (GAD1, TMEM222 and ZNFX1) were identified using the matching tool GeneMatcher and were part of the first description of a new syndrome.

Discussion

Trio WES has proven to have a high diagnostic yield and to shorten the process of identifying the correct diagnosis in paediatric patients. Re-evaluation of all 224 trio WES 1-3 years after initial analysis did not establish new diagnoses. Initiating (trio) WES as a first-tier diagnostics including copy number variant detection should be considered as early as possible, especially for children treated in ICU, if a monogenetic disease is suspected.

[Challenges and Influencial Factors in Autism-Specific Diagnostics in Toddlers]

Challenges and Influencial Factors in Autism-Specific Diagnostics in Toddlers Abstract. Objective: What are the particular challenges that make early diagnosis of young children difficult in the clinical routine? What recommendations can be derived from this in practice? Methods: Our interdisciplinary social pediatric team examined 31 toddlers aged 2 to 3 years twice in intervals of 6-9 months in the for outpatient diagnostics regarding suspected autism spectrum disorder (ASD). In addition, we conducted an online survey with further experts. Results: After the first anamnestic interview, 8 of the 31 (26 %) children were diagnosed with a differential diagnosis of ASD. Comorbid disorders, familial peculiarities, and challenges posed by the examination setting and anamnesis made a reliable clinical classification difficult. Conclusion: In our experience, many toddlers can only receive a valid diagnosis after a follow-up examination after starting one or more therapies and regularly carrying out these therapies over a period of 6-9 months and possibly also after structural changes have taken place (care in nursery, implementation of youth welfare measures, or similar).

Incidence tendency, etiological classification and outcome of congenital hypothyroidism in Guangzhou, China: an 11-year retrospective population-based study

OBJECTIVES

An increased incidence of congenital hypothyroidism (CH) has been described worldwide over the years. In this study, we aimed to investigate the epidemiologic characteristics of CH, the iodine status in Guangzhou, China and to investigate which factors might influence the CH incidence during the period 2010-2020.

METHODS

We retrospectively reviewed all cases of CH detected by newborn screening during the period 2010-2020. CH was classified as either suspected thyroid dyshormonogenesis (SDH) or thyroid dysgenesis (TD) based on thyroid ultrasound at first diagnosis. Patients were re-evaluated after 4 weeks of L-thyroxine withdrawal at age of 2-3 years to confirm the diagnosis of permanent CH (PCH) or transient CH (TCH).

RESULTS

From 2010 to 2020, 1,655 patients with CH were confirmed from 2,400,383 newborns (1:1,450). The CH incidence increased from 1:2,584 in period [2010-2014] to 1:1,086 in period [2015-2020]. Among the 1,337 patients with thyroid ultrasound, 84.29% were SDH whereas 15.71% had TD. Further analysis revealed that more SDH (78.32%) were TCH whereas more TD (87.12%) turned to be PCH. The proportion of blood spot thyrotropin values >5 mIU/L ranged from 8.03 to 20.46%, indicating iodine deficiency. The prevalence of preterm infants increased from 5.50% in period [2010-2014] to 7.06% in period [2015-2020] (p<0.001).

CONCLUSIONS

In the past decade, the CH incidence has increased progressively. SDH was the majority of CH, most of which were TCH, while most patients with TD were PCH. The increased incidence might be mainly due to iodine deficiency and increased rates of preterm infants in our study.

SOD-1 Variants in Amyotrophic Lateral Sclerosis: Systematic Re-Evaluation According to ACMG-AMP Guidelines

Amyotrophic lateral sclerosis (ALS) is the most common type of motor neuron disease whose causes are unclear. The first ALS gene associated with the autosomal dominant form of the disease was SOD1. This gene has a high rate of rare variants, and an appropriate classification is essential for a correct ALS diagnosis. In this study, we re-evaluated the classification of all previously reported SOD1 variants (n = 202) from ALSoD, project MinE, and in-house databases by applying the ACMG-AMP criteria to ALS. New bioinformatics analysis, frequency rating, and a thorough search for functional studies were performed. We also proposed adjusting criteria strength describing how to apply them to SOD1 variants. Most of the previously reported variants have been reclassified as likely pathogenic and pathogenic based on the modified weight of the PS3 criterion, highlighting how in vivo or in vitro functional studies are determining their interpretation and classification. Furthermore, this study reveals the concordance and discordance of annotations between open databases, indicating the need for expert review to adapt the study of variants to a specific disease. Indeed, in complex diseases, such as ALS, the oligogenic inheritance, the presence of genes that act as risk factors and the reduced penetration must be considered. Overall, the diagnosis of ALS remains clinical, and improving variant classification could support genetic data as diagnostic criteria.

Long-Term Course of Hypothyroidism Detected through Neonatal TSH Screening in a Population-Based Cohort of Very Preterm Infants Born at Less than 32 Weeks of Gestation

After several decades of successful newborn screening (NBS) for congenital hypothyroidism, the optimal hypothyroidism NBS algorithm for very preterm infants is still controversial. Due to concerns about an elevated risk of a false-negative initial thyroid-stimulation hormone (TSH) screening, repeat NBS has been implemented for this group. While transient hypothyroidism is known to be more frequent among very preterm infants, the prevalence of permanent hypothyroidism is generally assumed to be the same as in more mature newborns. This study analyses screening and long-term follow-up data from the population-based cohort of 51 infants born from 1999-2017 at less than 32 weeks of gestation and diagnosed with hypothyroidism after NBS in the German Federal State of Bavaria (total number of infants screened 2,107,864). Severe permanent hypothyroidism was always detected at initial TSH screening unless there was a known confounding factor. Cases detected by repeat screening after a negative initial screen most frequently proved to be transient, less frequently mild permanent, or a definitive diagnosis was not possible because of inadequate re-evaluation of the thyroid axis. The prevalence of both permanent and transient hypothyroidism was elevated compared to a cohort of children from the same region born at a higher gestational age. The results seem to support the need for the repeated NBS of very preterm infants. However, as the recommendation to treat mild hypothyroidism is not based on high quality evidence, important issues for future research include treatment outcome studies or even a general review of whether this diagnosis meets the screening criteria. Meanwhile, involving a paediatric endocrinologist in treatment decisions is crucial for optimising the benefit of hypothyroidism screening for this particularly vulnerable group.

APP, PSEN1, and PSEN2 Variants in Alzheimer's Disease: Systematic Re-evaluation According to ACMG Guidelines

The strategies of classifying APP, PSEN1, and PSEN2 variants varied substantially in the previous studies. We aimed to re-evaluate these variants systematically according to the American college of medical genetics and genomics and the association for molecular pathology (ACMG-AMP) guidelines. In our study, APP, PSEN1, and PSEN2 variants were collected by searching Alzforum and PubMed database with keywords “PSEN1,” “PSEN2,” and “APP.” These variants were re-evaluated based on the ACMG-AMP guidelines. We compared the number of pathogenic/likely pathogenic variants of APP, PSEN1, and PSEN2. In total, 66 APP variants, 323 PSEN1 variants, and 63 PSEN2 variants were re-evaluated in our study. 94.91% of previously reported pathogenic variants were re-classified as pathogenic/likely pathogenic variants, while 5.09% of them were variants of uncertain significance (VUS). PSEN1 carried the most prevalent pathogenic/likely pathogenic variants, followed by APP and PSEN2. Significant statistically difference was identified among these three genes when comparing the number of pathogenic/likely pathogenic variants (P < 2.2 × 10^–16). Most of the previously reported pathogenic variants were re-classified as pathogenic/likely pathogenic variants while the others were re-evaluated as VUS, highlighting the importance of interpreting APP, PSEN1, and PSEN2 variants with caution according to ACMG-AMP guidelines.

Critical reagent characterization and re-evaluation to ensure long-term stability: two case studies

Characterization of critical reagents can mitigate adverse impact to ligand-binding assay performance. We investigated the conjugation conditions of a bispecific protein to SULFO-TAG NHS-Ester™ ruthenium to resolve a steady increase in ligand-binding assay background signal. Functional and biophysical attributes in stability samples revealed low pH (4.0) conjugation and formulation buffers were key to decrease aggregate formation. We also identified pH-specific (3.0) purification conditions to reduce aggregate levels from 37% to <5% of a mouse IgG3 reagent antibody. These case studies support the utility of biophysical and functional characterization of critical reagents as a proactive approach to maintain long-term stability and provide the basis for our recommendations a risk-based approach to establish re-evaluation intervals for traditional and novel reagents.

Re-evaluation of neurobehavioural toxicity of clothianidin using statistical methods for ordered alternatives assuming dose-response effect

Neurobehavioural toxicity of clothianidin in previous studies was re-evaluated using statistical methods for ordered alternatives assuming a dose-response effect. In a maternal exposure study, clothianidin was added into the diet to provide levels of 0% (control), 0.002%, 0.006% and 0.018% during the gestation and lactation periods in mice. In exploratory behaviour of male offspring in the F₁ generation, average speed increased significantly in a dose-related manner in the Jonckheere test. Total distance lengthened in the high-dose group and average speed increased in the high-dose group in the Shirley-Williams test. In a two-generation toxicity study, clothianidin was added in the diet to provide levels of 0% (control), 0.003%, 0.006% and 0.012% from 5 weeks of age of the F₀ generation to 11 weeks of age of the F₁ generation in mice. The exploratory behaviour of adult males in the F₀ generation, the average time of movement, and the number of rearing and rearing time increased significantly in a dose-related manner in the Jonckheere test. The average speed increased in the middle- and high-dose groups, number of rearing increased in the high-dose group and rearing time lengthened in middle- and high-dose groups in the Shirley-Williams test. These results suggest that the use of the appropriate statistical methods adjusted to the objectives of the study and the characteristics of the data could provide more definite conclusions.

Evolution of congenital hypothyroidism in a cohort of preterm born children

BACKGROUND

Congenital hypothyroidism (CH) is reported to be more common in preterm infants than in term infants, especially in sick preterm infants. Though a frequent possibility of transitory thyroidal alterations in this category of neonates, the evolution of CH to transient or permanent forms is unpredictable.

METHODS

We retrospectively analyzed medical records of 28 preterm infants (<37 weeks gestation) who had exhibited a positive screening for CH at birth during the period 2000-2015 followed in our Center. Children were divided into three groups: permanent CH (PCH) with thyroid dysgenesis, PCH with eutopic normal-sized thyroid gland, and transient CH (TCH) with eutopic normal-sized thyroid gland. In all groups we described clinical and biochemical characteristics. Secondly, we analyzed the differences between patients with thyroid dysgenesis and patients with eutopic normal-sized gland and we compared PCH and TCH groups with normal-sized thyroid gland in order to identify clinical or biochemical data for early detection of transient forms.

RESULTS

Of all patients, 21.4% showed thyroid dysgenesis while 78.6% presented eutopic normal-sized gland. Infants with thyroid dysgenesis had higher median (IQR) baseline s-TSH and levothyroxine (L-T4) dose per weight at 12 months (12 m-dose) than patients with eutopic normal-sized gland. At re-evaluation of the patients with eutopic normal-sized gland, 36% showed PCH and 64% had TCH. The age of the patients at the beginning of L-T4 treatment, gestational age (GA), birth weight, blood thyroid stimulating hormone levels (b-TSH) at first newborn screening (NBS), baseline serum thyroid stimulating hormone (s-TSH), and L-T4 12 m-dose were statistically different between the two groups.

CONCLUSIONS

Our results demonstrate that factors as GA, birth weight, b-TSH levels at first NBS, baseline s-TSH, L-T4 12 m-dose and age at the start of the treatment may be considered useful predictive elements for the evolution of CH.

Re-Evaluation of Prognostic Factors for Survival After Radiotherapy of Cerebral Gliomas: A Supplementary Analysis to a Previous Study

BACKGROUND/AIM

Previously, we identified predictors of survival after irradiation of grade II-IV cerebral gliomas. In this supplementary analysis, survival was calculated in a more appropriate way than the original study.

PATIENTS AND METHODS

Ten factors were re-evaluated for survival in patients of the original study including pre-radiotherapy seizures. In the original study, survival was calculated from the end of the last radiotherapy course (primary or re-irradiation). After re-review, this approach was considered inappropriate. Survival should have always been calculated from the first radiotherapy course, as done in this supplementary analysis.

RESULTS

On multivariate analysis, WHO-grade II (p=0.006) and upfront resection (p=0.001) were associated with better survival. Unifocal glioma was significant on univariate analysis (p=0.001), where a trend could be identified for age ≤59 years (p=0.057) and seizures (p=0.060).

CONCLUSION

The findings of this supplementary analysis regarding the identification of prognostic factors for survival agree with the results of the original study.

Postmortem examination protocol and systematic re-evaluation reduce the proportion of unexplained stillbirths

Background Stillbirth often remains unexplained, mostly due to a lack of any postmortem examination or one that is incomplete and misinterpreted. Methods This retrospective cohort study was conducted at the Department of Obstetrics and Gynecology, Helsinki University Hospital, Finland, and comprised 214 antepartum singleton stillbirths from 2003 to 2015. Maternal and fetal characteristics and the results of the systematic postmortem examination protocol were collected from medical records. Causes of death were divided into 10 specific categories. Re-evaluation of the postmortem examination results followed. Results Based on our systematic protocol, the cause of death was originally defined and reported as such to parents in 133 (62.1%) cases. Re-evaluation of the postmortem examination results revealed the cause of death in an additional 43 (20.1%) cases, with only 23 (10.7%) cases remaining truly unexplained. The most common cause of stillbirth was placental insufficiency in 56 (26.2%) cases. A higher proportion of stillbirths that occurred at ≥39 gestational weeks remained unexplained compared to those that occurred earlier (24.1% vs. 8.6%) (P = 0.02). Conclusion A standardized postmortem examination and a re-evaluation of the results reduced the rate of unexplained stillbirth. Better knowledge of causes of death may have a major impact on the follow-up and outcome of subsequent pregnancies. Also, closer examination and better interpretation of postmortem findings is time-consuming but well worth the effort in order to provide better counseling for the grieving parents.

Re-evaluation of challenging telepathological diagnoses in support of a hospital in Tanzania

Since 2007, a hospital in Tanzania has been supported with histopathological reports via telepathology (TP) by German pathologists. For this, the Internet-based platform iPath is used. The aim of this study was to analyse the rate of discrepancies in defined diagnostic groups. After shipment of paraffin-embedded tissue to Germany, specimens were processed according to recent diagnostic standards. All diagnoses were grouped into eight benign and 11 malignant main categories. The comparison comprised the following categories: 1, identical diagnosis; 2, mild discordance; 3, correct distinction between benign and malignant process, 4, false malignant; 5, false benign; and 6, no primary diagnosis possible. The cohort comprised 396 benign and 336 malignant diseases. Of the benign diseases, 62% were category 1, 23% category 2, 2% category 3, 6% category 4 and 7% category 6. Of the malignant diseases, 42% were category 1, 16% category 2, 12% category 3, 14% category 5 and 15% category 6. Exclusive support with static TP cannot meet all requirements of modern medical diagnostics. However, the project shows a approach for how pathologists in industrial countries can help low-income countries. In difficult cases, the opportunity for a final work-up using additional methods must be given for useful diagnostic purposes.

[Restraint in geriatric care, an overview]

Restraint is a deprivation of liberty which in certain, clearly codified situations is a necessary part of the care process. The multidisciplinary objective evaluation of the risk/benefit ratio must take into consideration the person's dignity. The situation is often encountered in geriatric care where the fundamental principles are the maintaining of autonomy or the functional improvement of the patient or resident.

[Technical specification for re-evaluation of post-marketing clinical effectiveness of traditional Chinese medicine (first draft)]

The post-marketing re-evaluation of traditional Chinese medicine (TCM) is a crucial stage for drug evaluation. Due to the particularity of TCM, it is necessary to re-evaluate the effectiveness of certain Chinese medicines by studying and collecting the studies on safety of long-term/extensive populations under actual clinical application, in order to verify the effectiveness of post-marketing TCM. However, there is an absence in technical specifications for relevant clinical trials on re-evaluation of effectiveness at present. As a consequence, the preliminary technical specifications were drafted in this article, focusing on several perspectives related to the re-evaluation of post-marketing clinical effectiveness of TCM, including ethical protection, research plan formulation, real-world research methods, randomized controlled trial methods, research methods of clinical pharmacological mechanism, sublimation method of TCM theory and so on. The objective of writing this article is to provide general methodological guidance for the re-evaluation of TCM post-marketing effectiveness, so that the process and results of post-marketing re-evaluation of TCM can be more scientific and reasonable.

Marked yield of re-evaluating phenotype and exome/target sequencing data in 33 individuals with intellectual disabilities

The diagnosis of intellectual disability/developmental delay (ID/DD) benefits from the clinical application of target/exome sequencing. The yield in Mendelian diseases varies from 25% to 68%. The aim of the present study was to identify the genetic causes of 33 ID/DD patients using target/exome sequencing. Recent studies have demonstrated that reanalyzing undiagnosed exomes could yield additional diagnosis. Therefore, in addition to the normal data analysis, in this study, re-evaluation was performed prior to manuscript preparation after updating OMIM annotations, calling copy number variations (CNVs) and reviewing the current literature. Molecular diagnosis was obtained for 19/33 patients in the first round of analysis. Notably, five patients were diagnosed during the re-evaluation of the geno/phenotypic data. This study confirmed the utility of exome sequencing in the diagnosis of ID/DD. Furthermore, re-evaluation leads to a 15% improvement in diagnostic yield. Thus, to maximize the diagnostic yield of next-generation sequencing (NGS), periodical re-evaluation of the geno/phenotypic data of undiagnosed individuals is recommended by updating the OMIM annotation, applying new algorithms, reviewing the literature, sharing pheno/genotypic data, and re-contacting patients.

Emotional Dissonance and Burnout: The Moderating Role of Team Reflexivity and Re-Evaluation

The aim of the present study was to better understand the relationship between emotional dissonance and burnout by exploring the buffering effects of re-evaluation and team reflexivity. The study was conducted with a sample of 445 nurses and healthcare assistants from a general hospital. Team reflexivity was evaluated with the validation of the French version of the team reflexivity scale (Facchin, Tschan, Gurtner, Cohen, & Dupuis, 2006). Burnout was measured with the MBI General Survey (Schaufeli, Leiter, Maslach, & Jackson, 1996). Emotional dissonance and re-evaluation were measured with the scale developed by Andela, Truchot, & Borteyrou (2015). With reference to Rimé's theoretical model (2009), we suggested that both dimensions of team reflexivity (task and social reflexivity) respond to both psychological necessities induced by dissonance (cognitive clarification and socio-affective necessities). Firstly, results indicated that emotional dissonance was related to burnout. Secondly, regression analysis confirmed the buffering role of re-evaluation and social reflexivity on the emotional exhaustion of emotional dissonance. Overall, results contribute to the literature by highlighting the moderating effect of re-evaluation and team reflexivity in analysing the relationship between emotional dissonance and burnout. Copyright © 2016 John Wiley & Sons, Ltd.

Feasibility re-evaluation of 75 mg/m² docetaxel in Japanese patients with previously treated non-small cell lung cancer

OBJECTIVE

The primary objective of this study was to re-evaluate the feasibility of docetaxel at doses of up to 75 mg/m² in Japanese patients with previously treated non-small cell lung cancer.

METHODS

Patients received escalated doses of docetaxel at 70 mg/m² (level 1) or 75 mg/m² (level 2) every 3 weeks until disease progression or unacceptable toxicities. Dose escalation was decided on the basis of dose-limiting toxicity in the first cycle of chemotherapy.

RESULTS

At dose level 1, dose-limiting toxicity--Grade 3 febrile neutropenia--was observed in one of the six patients and at dose level 2, it was seen in one of the first six patients. Therefore, an additional 14 patients were enrolled at dose level 2, as originally planned. Among the total of 20 patients at dose level 2, 6 (<33%) developed dose-limiting toxicity in the first cycle: febrile neutropenia in 5 and pneumonia in 1. Finally, 10 (50%) of the 20 patients experienced toxicities that met the dose-limiting toxicity criteria, including 8 with febrile neutropenia throughout the treatment period, but this was manageable with dose reduction or appropriate supportive care. Other observed toxicities were predictable from the safety profile of decetaxel and were also well managed. Four partial responses were observed, giving an overall response rate of 15.4%. The median progression-free survival period of the patients overall was 4.0 months (95% confidence interval 1.4-6.6 months).

CONCLUSIONS

Although docetaxel administration at an initial dose of 75 mg/m² requires careful attention because of the high incidence of febrile neutropenia, this dose is considered feasible according to the protocol definition in Japanese patients with previously treated non-small cell lung cancer.