Publications by authors named "Christian P Schaaf"

110 Publications

Genetic Variation in Associates with Stanford Type B Aortic Dissection Risk and Clinical Outcome.

J Cardiovasc Dev Dis 2022 Jan 5;9(1). Epub 2022 Jan 5.

Department of Vascular and Endovascular Surgery, Heidelberg University Hospital, 69120 Heidelberg, Germany.

Genetic variation in (low-density lipoprotein receptor-related protein 1) was reported to be associated with thoracic aortic dissections and aneurysms. The aims of this study were to confirm this association in a prospective single-center patient cohort of patients with acute Stanford type B aortic dissections (STBAD) and to assess the impact of variation on clinical outcome. The single nucleotide variation (SNV) rs11172113 within the gene was genotyped in 113 STBAD patients and 768 healthy control subjects from the same population. The T-allele of rs11172113 was more common in STBAD patients as compared to the reference group (72.6% vs. 59.6%) and confirmed to be an independent risk factor for STBAD ( = 0.002) after sex and age adjustment in a logistic regression model analyzing diabetes, smoking and hypertension as additional risk factors. Analysis of clinical follow-up (median follow-up 2.0 years) revealed that patients with the T-allele were more likely to suffer aorta-related complications (T-allele 75.6% vs. 63.8%; = 0.022). In this study sample of STBAD patients, variation in was an independent risk factor for STBAD and affected clinical outcome.
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http://dx.doi.org/10.3390/jcdd9010014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8780592PMC
January 2022

Facebook Support Groups for Pediatric Rare Diseases: Cross-Sectional Study to Investigate Opportunities, Limitations, and Privacy Concerns.

JMIR Pediatr Parent 2022 Jan 6;5(1):e31411. Epub 2022 Jan 6.

Institute of Human Genetics, Heidelberg University, Heidelberg, Germany.

Background: Because of the nature of rare diseases with affected individuals being widely geographically dispersed, finding an in-person/offline support group itself can be a challenge. Affected individuals therefore turn to social networking platforms such as Facebook for online support groups.

Objective: We aim to put into perspective the opportunities Facebook offers as a tool for pediatric rare disease support groups by investigating its use, advantages, and limitations including privacy concerns. We analyze group accessibility and usage, advantages specific to rare diseases, perceived privacy, and views on using Facebook for communication between health professionals and parents, pharmaceutical companies, and study recruitment.

Methods: We contacted 12 Facebook support groups for 12 respective rare diseases with pediatric onset and invited group members to participate in a cross-sectional online survey.

Results: Of 231 respondents, 87.0% (n=201) of respondents were female, 12.6% (n=29) were male, and 0.4% reported another sex (n=1). Respondents' mean age was 41.56 years (SD 9.375); 91.3% (n=211) of respondents were parents (183 mothers, 27 fathers, 1 other sex); 59.7% (n=138) reported a self-initiated search for the Facebook group, 24.2% (n=56) received recommendations from their health professionals, and 12.6% (n=29) recommendations from someone else affected by the disease. On average, support group members visited Facebook at least once a day, visited and passively participated (read/liked posts) several times a week, and participated actively (commented/posted) once a month. As much as 79.2% (183/231) agreed that they would like to have health professionals as members of the respective Facebook group. Group members expressed more concern about privacy issues on Facebook in general than in their respective Facebook support groups, with concerns mostly related to Facebook itself and nongroup members.

Conclusions: Our study confirmed that Facebook enhances support group accessibility for parents of children with rare diseases. Group participants perceive a reduction and elimination of distance, a common challenge in rare disease, and Facebook support groups create an environment of perceived privacy. The group's privacy setting can be a critical factor for active support group participation. Sharing personal information and pictures on Facebook is very common among group participants, which shows the importance of discussing and protecting children's privacy rights in this context.

Trial Registration: German Clinical Trials Register DRKS00016067; https://www.drks.de/drks_web/navigate.do?navigationId=trial.HTML&TRIAL_ID=DRKS00016067.
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http://dx.doi.org/10.2196/31411DOI Listing
January 2022

Translational pediatrics: clinical perspective for Phelan-McDermid syndrome and autism research.

Pediatr Res 2021 Oct 26. Epub 2021 Oct 26.

Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan.

Phelan-McDermid syndrome (PMS) is a rare genetic disorder presenting with developmental delay, epilepsy, and autism spectrum disorder (ASD). The segmental deletion of chromosome 22q13.3 affects the copy number of SHANK3, the gene encoding a scaffolding protein at the postsynaptic density. Biological studies indicate that SHANK3 plays crucial roles in the development of synaptic functions in the postnatal brain. Notably, induced pluripotent stem (iPS) cells have enabled researchers to develop brain organoids and microglia from patients and to explore the pathophysiology of neurodevelopmental disorders in human cells. Single-cell RNA sequencing of these cells revealed that human-specific genes are uniquely expressed during cortical development. Thus, patient-derived disease models are expected to identify as-yet-unidentified functions of SHANK3 in the development of human brain. These efforts may help establish a new style of translational research in pediatrics, which is expected to provide therapeutic insight for children with PMS and broader categories of disease. IMPACT: Phelan-McDermid syndrome is a prototypic model for molecular studies of autism spectrum disorder. Brain organoids are expected to provide therapeutic insight. Single-cell RNA sequencing of microglia may uncover the functional roles of human-specific genes.
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http://dx.doi.org/10.1038/s41390-021-01806-xDOI Listing
October 2021

Parental perceptions of genetic testing for children with autism spectrum disorders.

Am J Med Genet A 2022 01 25;188(1):178-186. Epub 2021 Sep 25.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.

Children with autism spectrum disorder (ASD) routinely undergo genetic testing (GT) to identify the causative genetic etiology of their ASD. As there are questions about the impact of GT beyond clinical diagnosis, we conducted a mixed methods study to assess the perceived benefits of GT by exploring factors that lead parents to pursue these tests and the benefits experienced. Respondents were part of a pretest or posttest group. The pretest group (N = 22) expressed intent to pursue GT and the posttest group (N = 32) had undergone GT and received results at least 3 months prior to completing the survey. Responses were compared between and within groups. Free text responses were coded for themes and selection questions were analyzed using Fisher's exact tests. Our results demonstrate significant differences between the groups with participants in the pretest group more likely to choose "increased access to therapies" (p = 0.026) and "improved healthcare" (p < 0.000) as reasons to pursue testing. Benefits were also significantly different with "improved healthcare" (p = 0.009), "improved access to services" (p = 0.012), and "improved access to therapies" (p = 0.003) more frequently anticipated by the pretest group than reported by the posttest group. A relationship between GT and clinical management changes was reported by 34.4-50.0% of the posttest group. Among that group, genetic result type (positive, negative, or variant of uncertain significance) was associated with differing perceived benefits of testing. Thematic analysis revealed increased knowledge and coping as reported benefits in both groups. Our findings indicate a discrepancy between parental expectations and experiences of GT. Comprehensive pretest and posttest genetic counseling are necessary to improve information retention, address potential outcomes, and set expectations of GT for parents of children with ASD.
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http://dx.doi.org/10.1002/ajmg.a.62517DOI Listing
January 2022

Assigning evidence to actionability: An introduction to variant interpretation in precision cancer medicine.

Genes Chromosomes Cancer 2021 Jul 30. Epub 2021 Jul 30.

German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany.

Modern concepts in precision cancer medicine are based on increasingly complex genomic analyses and require standardized criteria for the functional evaluation and reporting of detected genomic alterations in order to assess their clinical relevance. In this article, we propose and address the necessary steps in systematic variant evaluation consisting of bioinformatic analysis, functional annotation and clinical interpretation, focusing on the latter two aspects. We discuss the role and clinical application of current variant classification systems and point out their scope and limitations. Finally, we highlight the significance of the molecular tumor board as a platform for clinical decision-making based on genomic analyses.
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http://dx.doi.org/10.1002/gcc.22987DOI Listing
July 2021

O'Donnell-Luria-Rodan syndrome: description of a second multinational cohort and refinement of the phenotypic spectrum.

J Med Genet 2021 Jul 28. Epub 2021 Jul 28.

Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA.

Background: O'Donnell-Luria-Rodan syndrome (ODLURO) is an autosomal-dominant neurodevelopmental disorder caused by pathogenic, mostly truncating variants in . It was first described by O'Donnell-Luria in 2019 in a cohort of 38 patients. Clinical features encompass macrocephaly, mild intellectual disability (ID), autism spectrum disorder (ASD) susceptibility and seizure susceptibility.

Methods: Affected individuals were ascertained at paediatric and genetic centres in various countries by diagnostic chromosome microarray or exome/genome sequencing. Patients were collected into a case cohort and were systematically phenotyped where possible.

Results: We report 18 additional patients from 17 families with genetically confirmed ODLURO. We identified 15 different heterozygous likely pathogenic or pathogenic sequence variants (14 novel) and two partial microdeletions of . We confirm and refine the phenotypic spectrum of the -related neurodevelopmental disorder, especially concerning cognitive development, with rather mild ID and macrocephaly with subtle facial features in most patients. We observe a high prevalence of ASD in our cohort (41%), while seizures are present in only two patients. We extend the phenotypic spectrum by sleep disturbances.

Conclusion: Our study, bringing the total of known patients with ODLURO to more than 60 within 2 years of the first publication, suggests an unexpectedly high relative frequency of this syndrome worldwide. It seems likely that ODLURO, although just recently described, is among the more common single-gene aetiologies of neurodevelopmental delay and ASD. We present the second systematic case series of patients with ODLURO, further refining the mutational and phenotypic spectrum of this not-so-rare syndrome.
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http://dx.doi.org/10.1136/jmedgenet-2020-107470DOI Listing
July 2021

Birth defect co-occurrence patterns in the Texas Birth Defects Registry.

Pediatr Res 2021 Jun 30. Epub 2021 Jun 30.

Department of Epidemiology, Human Genetics and Environmental Sciences, UTHealth School of Public Health, Houston, TX, USA.

Background: The population-level landscape of co-occurring birth defects among infants without a syndromic diagnosis is not well understood.

Methods: We analyzed data from 40,771 infants with two or more major birth defects in the Texas Birth Defects Registry (TBDR; 1999-2014). We calculated adjusted observed-to-expected (O/E) ratios for all two, three, four, and five-way combinations of 138 major defects.

Results: Among 530 patterns with the highest adjusted O/E ratios (top 5% of 10,595 patterns), 66% included only defects co-occurring within one organ system and 28% were suggestive of known patterns (e.g., midline developmental defects). Of the remaining patterns, the combination of defects with the highest O/E ratio (193.8) encompassed the diaphragm, spine, spleen, and heart defects. Fourteen patterns involved heart and spine defects with or without rib defects. Ten additional patterns primarily involved two hallmark components of VACTERL association (specifically, vertebral defects, anal atresia, cardiac defects, renal, or limb defects, but not tracheoesophageal fistula).

Conclusions: Our analyses provide a description of the birth defect co-occurrence patterns in a multi-ethnic, population-based sample, and revealed several patterns of interest. This work complements prior work that has suggested etiologic connections between select defects (e.g., diaphragmatic hernia and heart and spleen anomalies; heart and spine defects).

Impact: In this large-scale, population-based study of birth defect co-occurrence patterns, we found several birth defect combinations of potential interest that warrant further investigation: congenital diaphragmatic hernia, heart, spine, and spleen defects and scimitar syndrome with vertebral defects. The majority of patterns of co-occurring defects observed more frequently than expected involved multiple defects within the same system and combinations suggestive of known associations. Nearly all of the top patterns (beyond the same system and those suggestive of known associations) involved organ systems that are components of the VACTERL association, with heart, spine, and rib defect patterns being the most common.
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http://dx.doi.org/10.1038/s41390-021-01629-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8716666PMC
June 2021

Further evidence for de novo variants in SYNCRIP as the cause of a neurodevelopmental disorder.

Hum Mutat 2021 09 5;42(9):1094-1100. Epub 2021 Jul 5.

Division of Pediatric Epileptology, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany.

SYNCRIP encodes for the Synaptotagmin-binding cytoplasmic RNA-interacting protein, involved in RNA-binding and regulation of multiple cellular pathways. It has been proposed as a candidate gene for neurodevelopmental disorders (NDDs) with autism spectrum disorder (ASD), intellectual disability (ID), and epilepsy. We ascertained genetic, clinical, and neuroradiological data of three additional individuals with novel de novo SYNCRIP variants. All individuals had ID. Autistic features were observed in two. One individual showed myoclonic-atonic epilepsy. Neuroradiological features comprised periventricular nodular heterotopia and widening of subarachnoid spaces. Two frameshift variants in the more severely affected individuals, likely result in haploinsufficiency. The third missense variant lies in the conserved RNA recognition motif (RRM) 2 domain likely affecting RNA-binding. Our findings support the importance of RRM domains for SYNCRIP functionality and suggest genotype-phenotype correlations. Our study provides further evidence for a SYNCRIP-associated NDD characterized by ID and ASD sporadically accompanied by malformations of cortical development and myoclonic-atonic epilepsy.
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http://dx.doi.org/10.1002/humu.24245DOI Listing
September 2021

Birth Defect Co-Occurrence Patterns Among Infants With Cleft Lip and/or Palate.

Cleft Palate Craniofac J 2021 Apr 28:10556656211010060. Epub 2021 Apr 28.

Department of Epidemiology, Human Genetics and Environmental Sciences, UTHealth School of Public Health, Houston, TX, USA.

Objective: To investigate 2- to 5-way patterns of defects co-occurring with orofacial clefts using data from a population-based registry.

Design: We used data from the Texas Birth Defects Registry for deliveries between 1999 and 2014 to Texas residents, including 1884 cases with cleft palate (CP) and 5289 cases with cleft lip with or without cleft palate (CL±P) without a known syndrome. We identified patterns of defects co-occurring with CP and with CL±P observed more frequently than would be expected if these defects occurred independently. We calculated adjusted observed-to-expected (/) ratios to account for the known tendency of birth defects to cluster nonspecifically.

Results: Among infants without a syndrome, 23% with CP and 21% with CL±P had at least 1 additional congenital anomaly. Several combinations of defects were observed much more often than expected. For example, the combination of CL±P, congenital hydrocephaly, anophthalmia, and other nose anomalies had an / ratio of 605. For both CP and CL±P, co-occurrence patterns with the highest / ratios involved craniofacial and brain abnormalities, and many included the skeletal, cardiovascular, and renal systems.

Conclusions: The patterns of defects we observed co-occurring with clefts more often than expected may help improve our understanding of the relationships between multiple defects. Further work to better understand some of the top defect combinations could reveal new phenotypic subgroups and increase our knowledge of the developmental mechanisms that underlie the respective defects.
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http://dx.doi.org/10.1177/10556656211010060DOI Listing
April 2021

Variants in PRKAR1B cause a neurodevelopmental disorder with autism spectrum disorder, apraxia, and insensitivity to pain.

Genet Med 2021 08 8;23(8):1465-1473. Epub 2021 Apr 8.

Institute of Human Genetics, Heidelberg University, Heidelberg, Germany.

Purpose: We characterize the clinical and molecular phenotypes of six unrelated individuals with intellectual disability and autism spectrum disorder who carry heterozygous missense variants of the PRKAR1B gene, which encodes the R1β subunit of the cyclic AMP-dependent protein kinase A (PKA).

Methods: Variants of PRKAR1B were identified by single- or trio-exome analysis. We contacted the families and physicians of the six individuals to collect phenotypic information, performed in vitro analyses of the identified PRKAR1B-variants, and investigated PRKAR1B expression during embryonic development.

Results: Recent studies of large patient cohorts with neurodevelopmental disorders found significant enrichment of de novo missense variants in PRKAR1B. In our cohort, de novo origin of the PRKAR1B variants could be confirmed in five of six individuals, and four carried the same heterozygous de novo variant c.1003C>T (p.Arg335Trp; NM_001164760). Global developmental delay, autism spectrum disorder, and apraxia/dyspraxia have been reported in all six, and reduced pain sensitivity was found in three individuals carrying the c.1003C>T variant. PRKAR1B expression in the brain was demonstrated during human embryonal development. Additionally, in vitro analyses revealed altered basal PKA activity in cells transfected with variant-harboring PRKAR1B expression constructs.

Conclusion: Our study provides strong evidence for a PRKAR1B-related neurodevelopmental disorder.
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http://dx.doi.org/10.1038/s41436-021-01152-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8354857PMC
August 2021

Patterns of congenital anomalies among individuals with trisomy 13 in Texas.

Am J Med Genet A 2021 06 22;185(6):1787-1793. Epub 2021 Mar 22.

Department of Epidemiology, Human Genetics and Environmental Sciences, UTHealth School of Public Health, Houston, Texas, USA.

Few population-based studies have analyzed patterns of co-occurring birth defects among those with trisomy 13. We evaluated the frequency of all possible combinations of any one, two, three, or four additional co-occurring birth defects among 736 individuals with trisomy 13 using data from the Texas Birth Defects Registry for deliveries during 1999-2014. We calculated the observed-to-expected ratio for each combination, adjusting for the known tendency for birth defects to cluster non-specifically. To address potential ascertainment differences among live births and non-live births, we repeated analyses specifically among live births. The combination of defects with the largest observed-to-expected ratio was microcephalus, reduction deformities of brain (e.g., holoprosencephaly), anomalies of nose, and polydactyly. As expected, most of the highest 30 observed-to-expected ratios involved combinations with documented features of trisomy 13, including defects of the scalp (e.g., aplasia cutis) and heart. Results were similar among sensitivity analyses restricted to live births. Our findings may help further delineate the phenotypic spectrum for trisomy 13 and may inform future research related to improving screening and counseling for the condition.
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http://dx.doi.org/10.1002/ajmg.a.62175DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8193718PMC
June 2021

Genomic newborn screening: Proposal of a two-stage approach.

J Inherit Metab Dis 2021 05 29;44(3):518-520. Epub 2021 Mar 29.

University Hospital Heidelberg, Center for Pediatric and Adolescent Medicine, Clinic I, Heidelberg, Germany.

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http://dx.doi.org/10.1002/jimd.12381DOI Listing
May 2021

Brain Network Analysis of EEG Recordings Can Be Used to Assess Cognitive Function in Teenagers With 15q13.3 Microdeletion Syndrome.

Front Neurosci 2021 28;15:622329. Epub 2021 Jan 28.

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States.

15q13.3 microdeletion syndrome causes a spectrum of cognitive disorders, including intellectual disability and autism. We assessed the ability of the EEG analysis algorithm Brain Network Analysis (BNA) to measure cognitive function in 15q13.3 deletion patients, and to differentiate between patient and control groups. EEG data was collected from 10 individuals with 15q13.3 microdeletion syndrome (14-18 years of age), as well as 30 age-matched healthy controls, as the subjects responded to Auditory Oddball (AOB) and Go/NoGo cognitive tasks. It was determined that BNA can be used to evaluate cognitive function in 15q13.3 microdeletion patients. This analysis also significantly differentiates between patient and control groups using 5 scores, all of which are produced from ERP peaks related to late cortical components that represent higher cognitive functions of attention allocation and response inhibition ( < 0.05).
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http://dx.doi.org/10.3389/fnins.2021.622329DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7876406PMC
January 2021

A Comprehensive Assessment of Co-occurring Birth Defects among Infants with Non-Syndromic Anophthalmia or Microphthalmia.

Ophthalmic Epidemiol 2021 10 20;28(5):428-435. Epub 2020 Dec 20.

Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Texas.

Purpose: Infants with anophthalmia or microphthalmia frequently have co-occurring birth defects. Nonetheless, there have been few investigations of birth defect patterns among these children. Such studies may identify novel multiple malformation syndromes, which could inform future research into the developmental processes that lead to anophthalmia/microphthalmia and assist physicians in determining whether further testing is appropriate.

Methods: This study includes cases with anophthalmia/microphthalmia identified by the Texas Birth Defects Registry from 1999 to 2014 without clinical or chromosomal diagnoses of recognized syndromes. We calculated adjusted observed-to-expected ratios for two - through five-way birth defect combinations involving anophthalmia/microphthalmia to estimate whether these combinations co-occur more often than would be expected if they were independent. We report combinations observed in ≥5 cases.

Results: We identified 653 eligible cases with anophthalmia/microphthalmia (514 [79%] with co-occurring birth defects), and 111 birth defect combinations, of which 44 were two-way combinations, 61 were three-way combinations, six were four-way combinations and none were five-way combinations. Combinations with the largest observed-to-expected ratios were those involving central nervous system (CNS) defects, head/neck defects, and orofacial clefts. We also observed multiple combinations involving cardiovascular and musculoskeletal defects.

Conclusion: Consistent with previous reports, we observed that a large proportion of children diagnosed with anophthalmia/microphthalmia have co-occurring birth defects. While some of these defects may be part of a sequence involving anophthalmia/microphthalmia (e.g., CNS defects), other combinations could point to as yet undescribed susceptibility patterns (e.g., musculoskeletal defects). Data from population-based birth defect registries may be useful for accelerating the discovery of previously uncharacterized malformation syndromes.
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http://dx.doi.org/10.1080/09286586.2020.1862244DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8214631PMC
October 2021

Patterns of co-occurring birth defects among infants with hypospadias.

J Pediatr Urol 2021 02 12;17(1):64.e1-64.e8. Epub 2020 Nov 12.

Department of Epidemiology, Human Genetics and Environmental Sciences, UTHealth School of Public Health, Houston, TX, USA. Electronic address:

Introduction: Hypospadias, one of the most common male genital birth defects, occurs in 1 out of every 200 male births in the United States and is increasing in prevalence globally.

Objective: This study aimed to characterize the combinations of birth defects that co-occur with hypospadias more often than expected by chance, while accounting for the complex clustering patterns of congenital defects.

Study Design: We analyzed cases with hypospadias and at least one additional co-occurring defect from the Texas Birth Defect Registry born between 1999 and 2014. For each combination, we calculated adjusted observed-to-expected (O/E) ratios, using Co-Occurring Defect Analysis (CODA).

Results: Among 16,442 cases with hypospadias and without known syndromes, 2,084 (12.7%) had at least one additional defect. Many of the birth defect combinations within the highest adjusted O/E ratios included cardiac, musculoskeletal, and additional urogenital defects. For example, a top combination with an adjusted O/E of 139.0 included renal agenesis and dysgenesis, reduction defects of the upper limb, and other anomalies of upper limb (including shoulder girdle). High adjusted O/E ratios were also observed in combinations that included defects outside of the urogenital developmental field. For instance, the combination with the highest O/E ratio included buphthalmos, and congenital cataract and lens anomalies (adjusted O/E ratio: 192.9). Similar results were obtained when we restricted our analyses to cases with second- or third-degree hypospadias.

Discussion: Many combinations in the top results were expected (e.g., multiple urogenital defects); however, some combinations with seemingly unrelated patterns of defects may suggest the presence of some etiologic mechanisms yet to be identified.

Conclusion: In summary, this study described patterns of co-occurring defect combinations with hypospadias that can inform further study and may provide insights for screening and diagnostic practices.
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http://dx.doi.org/10.1016/j.jpurol.2020.11.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7935759PMC
February 2021

A complementary study approach unravels novel players in the pathoetiology of Hirschsprung disease.

PLoS Genet 2020 11 5;16(11):e1009106. Epub 2020 Nov 5.

Center of Medical Research, Medical Faculty Mannheim, Mannheim, Germany.

Hirschsprung disease (HSCR, OMIM 142623) involves congenital intestinal obstruction caused by dysfunction of neural crest cells and their progeny during enteric nervous system (ENS) development. HSCR is a multifactorial disorder; pathogenetic variants accounting for disease phenotype are identified only in a minority of cases, and the identification of novel disease-relevant genes remains challenging. In order to identify and to validate a potential disease-causing relevance of novel HSCR candidate genes, we established a complementary study approach, combining whole exome sequencing (WES) with transcriptome analysis of murine embryonic ENS-related tissues, literature and database searches, in silico network analyses, and functional readouts using candidate gene-specific genome-edited cell clones. WES datasets of two patients with HSCR and their non-affected parents were analysed, and four novel HSCR candidate genes could be identified: ATP7A, SREBF1, ABCD1 and PIAS2. Further rare variants in these genes were identified in additional HSCR patients, suggesting disease relevance. Transcriptomics revealed that these genes are expressed in embryonic and fetal gastrointestinal tissues. Knockout of these genes in neuronal cells demonstrated impaired cell differentiation, proliferation and/or survival. Our approach identified and validated candidate HSCR genes and provided further insight into the underlying pathomechanisms of HSCR.
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http://dx.doi.org/10.1371/journal.pgen.1009106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7643938PMC
November 2020

Germline testing for homologous recombination repair genes-opportunities and challenges.

Genes Chromosomes Cancer 2021 05 29;60(5):332-343. Epub 2020 Oct 29.

Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany.

Pathogenic variants in the BRCA1 and BRCA2 genes are well known causes of hereditary breast and ovarian cancer. Other genes involved in the homologous recombination pathway can also be associated with increased probability of cancer development, for example, breast and ovarian cancer, prostate and pancreatic cancer, colorectal cancer, and even childhood tumors like medulloblastoma. Traditionally, patients and families likely to harbor a genetic predisposition have been identified using personal and family history. Several checklists and risk prediction tools have proven to be useful in the clinic. Through the widespread application of next generation sequencing of tumor tissue, a growing number of individuals with genetic cancer predisposition is now identified molecularly, even in the absence of a suggestive family history. Any constitutional variant identified during molecular genetic testing has to be assessed for its relevance, both functionally and in the context of patient phenotype. Variant curation is time consuming, but has been increasingly standardized by introduction of several guidelines to allow reliable and reproducible classification of constitutional variants. Variant classification by expert panels using data mining tools, evidence-based decision trees and gene specific criteria represents the gold standard. Participation of geneticists in molecular tumor boards facilitates the curation of potential constitutional variants, germline validation and thus directing the patient to appropriate counselling and care pathways. Due to the high relevance of germline variants for treatment and surveillance of the index patient and predictive testing and surveillance of relatives, only pathogenic or likely pathogenic variants must be used for clinical decision-making.
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http://dx.doi.org/10.1002/gcc.22900DOI Listing
May 2021

The adult phenotype of Schaaf-Yang syndrome.

Orphanet J Rare Dis 2020 10 19;15(1):294. Epub 2020 Oct 19.

Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany.

Background: MAGEL2-associated Schaaf-Yang syndrome (SHFYNG, OMIM #615547, ORPHA: 398069), which was identified in 2013, is a rare disorder caused by truncating variants of the paternal copy of MAGEL2, which is localized in the imprinted region on 15q11.2q13. The phenotype of SHFYNG in childhood partially overlaps with that of the well-established Prader-Willi syndrome (PWS, OMIM #176270). While larger numbers of younger individuals with SHFYNG have been recently published, the phenotype in adulthood is not well established. We recruited 7 adult individuals (aged 18 to 36) with molecularly confirmed SHFYNG and collected data regarding the clinical profile including eating habits, sleep, behavior, personal autonomy, psychiatric abnormalities and other medical conditions, as well as information about the respective phenotypes in childhood.

Results: Within our small cohort, we identified a range of common features, such as disturbed sleep, hypoactivity, social withdrawal and anxiety, but also noted considerable differences at the level of personal autonomy and skills. Behavioral problems were frequent, and a majority of individuals displayed weight gain and food-seeking behavior, along with mild intellectual disability or borderline intellectual function. Classical symptoms of SHFYNG in childhood were reported for most individuals.

Conclusion: Our findings indicate a high variability of the functional abilities and social participation of adults with SHFYNG. A high prevalence of obesity within our cohort was notable, and uncontrollable food intake was a major concern for some caregivers. The phenotypes of PWS and SHFYNG in adulthood might be more difficult to discern than the phenotypes in childhood. Molecular genetic testing for SHFYNG should therefore be considered in adults with the suspected diagnosis of PWS, if testing for PWS has been negative.
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http://dx.doi.org/10.1186/s13023-020-01557-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7574436PMC
October 2020

Response to Briuglia et al.

Genet Med 2021 02 5;23(2):423-424. Epub 2020 Oct 5.

Institute of Human Genetics, Heidelberg University, Heidelberg, Germany.

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http://dx.doi.org/10.1038/s41436-020-00977-yDOI Listing
February 2021

Polysomnographic characteristics and sleep-disordered breathing in Schaaf-Yang syndrome.

Pediatr Pulmonol 2020 11 12;55(11):3162-3167. Epub 2020 Sep 12.

Division of Pulmonary and Sleep Medicine, Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington, USA.

Introduction: Schaaf-Yang syndrome (SYS) is a genetic disorder caused by truncating variants in the MAGEL2 gene located in the maternally imprinted Prader-Willi syndrome (PWS) region at 15q11-13. The SYS phenotype shares features with PWS, a syndrome with known high incidence of sleep disorders. However, the spectrum of sleep-disorders in SYS has not been described.

Methods: We performed a retrospective analysis of polysomnograms from 22 patients in an international SYS cohort. Sleep characteristics for individuals with the common c.1996dupC variant (n = 10) were compared to other truncating variants (n = 11).

Results: We collected 33 sleep study reports from 22 patients, ages 2 months - 18.5 years (mean 6.5 years). Mean sleep efficiency was 70.5% (range 45%-93%) with arousal index 14.1/h (1.2-45/h). The mean apnea-hypopnea index (AHI) was 19.1/h (0.9-49/h) with mean obstructive AHI (oAHI) of 16.3/h (0.6-49/h). Mean central apnea index was 2.8/h (0-14/h). Mean oxygen desaturation index was 20.8/h (range 0-85/hr). Obstructive sleep apnea (OSA) was diagnosed in 81%, and 62% had moderate or severe OSA. Elevated central apnea index occurred in 9.5%. Comparison by genotype groups and age did not reveal any difference in OSA findings. Periodic limb movement index (PLMI) was elevated in 4/15 (26%).

Conclusion: OSA is frequently identified on polysomnography in patients with SYS. The mean PLMI is elevated compared to normative data. Patients with SYS should have routine polysomnography screening due to high risk of sleep disorders.
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http://dx.doi.org/10.1002/ppul.25056DOI Listing
November 2020

Birth defects that co-occur with non-syndromic gastroschisis and omphalocele.

Am J Med Genet A 2020 11 4;182(11):2581-2593. Epub 2020 Sep 4.

Department of Epidemiology, Human Genetics and Environmental Sciences, UTHealth School of Public Health, Houston, Texas, USA.

Gastroschisis and omphalocele are the two most common abdominal wall birth defects, and epidemiologic characteristics and frequency of occurrence as part of a syndromic condition suggest distinct etiologies between the two defects. We assessed complex patterns of defect co-occurrence with these defects separately using the Texas Birth Defects Registry. We used co-occurring defect analysis (CODA) to compute adjusted observed-to-expected (O/E) ratios for all observed birth defect patterns. There were 2,998 non-syndromic (i.e., no documented syndrome diagnosis identified) cases with gastroschisis and 789 (26%) of these had additional co-occurring defects. There were 720 non-syndromic cases with omphalocele, and 404 (56%) had additional co-occurring defects. Among the top 30 adjusted O/E ratios for gastroschisis, most of the co-occurring defects were related to the gastrointestinal system, though cardiovascular and kidney anomalies were also present. Several of the top 30 combinations co-occurring with omphalocele appeared suggestive of OEIS (omphalocele, exstrophy of cloaca, imperforate anus, spinal defects) complex. After the exclusion of additional cases with features suggestive of OEIS in a post-hoc sensitivity analysis, the top combinations involving defects associated with OEIS (e.g., spina bifida) were no longer present. The remaining top combinations involving omphalocele included cardiovascular, gastrointestinal, and urogenital defects. In summary, we identified complex patterns of defects that co-occurred more frequently than expected with gastroschisis and omphalocele using a novel software platform. Better understanding differences in the patterns between gastroschisis and omphalocele could lead to additional etiologic insights.
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http://dx.doi.org/10.1002/ajmg.a.61830DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8259712PMC
November 2020

Next Generation Sequencing of 134 Children with Autism Spectrum Disorder and Regression.

Genes (Basel) 2020 07 25;11(8). Epub 2020 Jul 25.

Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX 77030, USA.

Approximately 30% of individuals with autism spectrum disorder (ASD) experience developmental regression, the etiology of which remains largely unknown. We performed a complete literature search and identified 47 genes that had been implicated in such cases. We sequenced these genes in a preselected cohort of 134 individuals with regressive autism. In total, 16 variants in 12 genes with evidence supportive of pathogenicity were identified. They were classified as variants of uncertain significance based on ACMG standards and guidelines. Among these were recurring variants in and , variants in genes that were linked to syndromic forms of ASD (, , , , , and ), and variants in the form of oligogenic heterozygosity (, , and ).
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http://dx.doi.org/10.3390/genes11080853DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7463850PMC
July 2020

The expanding clinical phenotype of germline ABL1-associated congenital heart defects and skeletal malformations syndrome.

Hum Mutat 2020 10 19;41(10):1738-1744. Epub 2020 Jul 19.

Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas.

Congenital heart defects and skeletal malformations syndrome (CHDSKM) is a rare autosomal dominant disorder characterized by congenital heart disease, skeletal abnormalities, and failure to thrive. CHDSKM is caused by germline mutations in ABL1. To date, three variants have been in association with CHDSKM. In this study, we describe three de novo missense variants, c.407C>T (p.Thr136Met), c.746C>T (p.Pro249Leu), and c.1573G>A (p.Val525Met), and one recurrent variant, c.1066G>A (p.Ala356Thr), in six patients, thereby expanding the phenotypic spectrum of CHDSKM to include hearing impairment, lipodystrophy-like features, renal hypoplasia, and distinct ocular abnormalities. Functional investigation of the three novel variants showed an increased ABL1 kinase activity. The cardiac findings in additional patients with p.Ala356Thr contribute to the accumulating evidence that patients carrying either one of the recurrent variants, p.Tyr245Cys and p.Ala356Thr, have a high incidence of cardiac abnormalities. The phenotypic expansion has implications for the clinical diagnosis of CHDSKM in patients with germline ABL1 variants.
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http://dx.doi.org/10.1002/humu.24075DOI Listing
October 2020

Phenotypic and Imaging Spectrum Associated With WDR45.

Pediatr Neurol 2020 08 11;109:56-62. Epub 2020 Mar 11.

Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.

Background: Mutations in the X-linked gene WDR45 cause neurodegeneration with brain iron accumulation type 5. Global developmental delay occurs at an early age with slow progression to dystonia, parkinsonism, and dementia due to progressive iron accumulation in the brain.

Methods: We present 17 new cases and reviewed 106 reported cases of neurodegeneration with brain iron accumulation type 5. Detailed information related to developmental history and key time to event measures was collected.

Results: Within this cohort, there were 19 males. Most individuals were molecularly diagnosed by whole-exome testing. Overall 10 novel variants were identified across 11 subjects. All individuals were affected by developmental delay, most prominently in verbal skills. Most individuals experienced a decline in motor and cognitive skills. Although most individuals were affected by seizures, the spectrum ranged from provoked seizures to intractable epilepsy. The imaging findings varied as well, often evolving over time. The classic iron accumulation in the globus pallidus and substantia nigra was noted in half of our cohort and was associated with older age of image acquisition, whereas myelination abnormalities were associated with younger age.

Conclusions: WDR45 mutations lead to a progressive and evolving disorder whose diagnosis is often delayed. Developmental delay and seizures predominate in early childhood, followed by a progressive decline of neurological function. There is variable expressivity in the clinical phenotypes of individuals with WDR45 mutations, suggesting that this gene should be considered in the diagnostic evaluation of children with myelination abnormalities, iron deposition, developmental delay, and epilepsy depending on the age at evaluation.
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http://dx.doi.org/10.1016/j.pediatrneurol.2020.03.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7387198PMC
August 2020

A framework for an evidence-based gene list relevant to autism spectrum disorder.

Nat Rev Genet 2020 06 21;21(6):367-376. Epub 2020 Apr 21.

The Centre for Applied Genomics, Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.

Autism spectrum disorder (ASD) is often grouped with other brain-related phenotypes into a broader category of neurodevelopmental disorders (NDDs). In clinical practice, providers need to decide which genes to test in individuals with ASD phenotypes, which requires an understanding of the level of evidence for individual NDD genes that supports an association with ASD. Consensus is currently lacking about which NDD genes have sufficient evidence to support a relationship to ASD. Estimates of the number of genes relevant to ASD differ greatly among research groups and clinical sequencing panels, varying from a few to several hundred. This Roadmap discusses important considerations necessary to provide an evidence-based framework for the curation of NDD genes based on the level of information supporting a clinically relevant relationship between a given gene and ASD.
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http://dx.doi.org/10.1038/s41576-020-0231-2DOI Listing
June 2020

Phenotypic expansion of Bosch-Boonstra-Schaaf optic atrophy syndrome and further evidence for genotype-phenotype correlations.

Am J Med Genet A 2020 06 10;182(6):1426-1437. Epub 2020 Apr 10.

Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, Texas, USA.

Bosch-Boonstra-Schaaf Optic Atrophy Syndrome (BBSOAS) is an autosomal dominant neurodevelopmental disorder caused by loss-of-function variants in NR2F1 and characterized by visual impairment, developmental delay, and intellectual disability. Here we report 18 new cases, provide additional clinical information for 9 previously reported individuals, and review an additional 27 published cases to present a total of 54 patients. Among these are 22 individuals with point mutations or in-frame deletions in the DNA-binding domain (DBD), and 32 individuals with other types of variants including whole-gene deletions, nonsense and frameshift variants, and point mutations outside the DBD. We corroborate previously described clinical characteristics including developmental delay, intellectual disability, autism spectrum disorder diagnoses/features thereof, cognitive/behavioral anomalies, hypotonia, feeding difficulties, abnormal brain MRI findings, and seizures. We also confirm a vision phenotype that includes optic nerve hypoplasia, optic atrophy, and cortical visual impairment. Additionally, we expand the vision phenotype to include alacrima and manifest latent nystagmus (fusional maldevelopment), and we broaden the behavioral phenotypic spectrum to include a love of music, an unusually good long-term memory, sleep difficulties, a high pain tolerance, and touch sensitivity. Furthermore, we provide additional evidence for genotype-phenotype correlations, specifically supporting a more severe phenotype associated with DBD variants.
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http://dx.doi.org/10.1002/ajmg.a.61580DOI Listing
June 2020

Combination of whole exome sequencing and animal modeling identifies TMPRSS9 as a candidate gene for autism spectrum disorder.

Hum Mol Genet 2020 02;29(3):459-470

Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX, USA.

Autism spectrum disorders are associated with some degree of developmental regression in up to 30% of all cases. Rarely, however, is the regression so extreme that a developmentally advanced young child would lose almost all ability to communicate and interact with her surroundings. We applied trio whole exome sequencing to a young woman who experienced extreme developmental regression starting at 2.5 years of age and identified compound heterozygous nonsense mutations in TMPRSS9, which encodes for polyserase-1, a transmembrane serine protease of poorly understood physiological function. Using semiquantitative polymerase chain reaction, we showed that Tmprss9 is expressed in various mouse tissues, including the brain. To study the consequences of TMPRSS9 loss of function on the mammalian brain, we generated a knockout mouse model. Through a battery of behavioral assays, we found that Tmprss9-/- mice showed decreased social interest and social recognition. We observed a borderline recognition memory deficit by novel object recognition in aged Tmprss9-/- female mice, but not in aged Tmprss9-/- male mice or younger adult Tmprss9-/- mice in both sexes. This study provides evidence to suggest that loss of function variants in TMPRSS9 are related to an autism spectrum disorder. However, the identification of more individuals with similar phenotypes and TMPRSS9 loss of function variants is required to establish a robust gene-disease relationship.
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http://dx.doi.org/10.1093/hmg/ddz305DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7015847PMC
February 2020
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