TAF1 Variants Are Associated with Dysmorphic Features, Intellectual Disability, and Neurological Manifestations.

We describe an X-linked genetic syndrome associated with mutations in TAF1 and manifesting with global developmental delay, intellectual disability (ID), characteristic facial dysmorphology, generalized hypotonia, and variable neurologic features, all in male individuals. Simultaneous studies using diverse strategies led to the identification of nine families with overlapping clinical presentations and affected by de novo or maternally inherited single-nucleotide changes. Two additional families harboring large duplications involving TAF1 were also found to share phenotypic overlap with the probands harboring single-nucleotide changes, but they also demonstrated a severe neurodegeneration phenotype. Functional analysis with RNA-seq for one of the families suggested that the phenotype is associated with downregulation of a set of genes notably enriched with genes regulated by E-box proteins. In addition, knockdown and mutant studies of this gene in zebrafish have shown a quantifiable, albeit small, effect on a neuronal phenotype. Our results suggest that mutations in TAF1 play a critical role in the development of this X-linked ID syndrome.

Yield of additional genetic testing after chromosomal microarray for diagnosis of neurodevelopmental disability and congenital anomalies: a clinical practice resource of the American College of Medical Genetics and Genomics (ACMG).

PURPOSE: Chromosomal microarray (CMA) is recommended as the first-tier test in evaluation of individuals with neurodevelopmental disability and congenital anomalies. CMA may not detect balanced cytogenomic abnormalities or uniparental disomy (UPD), and deletion/duplications and regions of homozygosity may require additional testing to clarify the mechanism and inform accurate counseling. We conducted an evidence review to synthesize data regarding the benefit of additional testing after CMA to inform a genetic diagnosis. METHODS: The review was guided by key questions related to the detection of genomic events that may require additional testing. A PubMed search for original research articles, systematic reviews, and meta-analyses was evaluated from articles published between 1 January 1983 and 31 March 2017. Based on the key questions, articles were retrieved and data extracted in parallel with comparison of results and discussion to resolve discrepancies. Variables assessed included study design and outcomes. RESULTS: A narrative synthesis was created for each question to describe the occurrence of, and clinical significance of, additional diagnostic findings from subsequent testing performed after CMA. CONCLUSION: These findings may be used to assist the laboratory and clinician when making recommendations about additional testing after CMA, as it impacts clinical care, counseling, and diagnosis.

Duplication 2p25 in a child with clinical features of CHARGE syndrome.

CHARGE syndrome is a dominant disorder characterized by ocular colobomata, heart defects, choanal atresia, retardation of growth and development, genital hypoplasia, and ear abnormalities including deafness and vestibular disorders. The majority of individuals with CHARGE have pathogenic variants in the gene encoding CHD7, a chromatin remodeling protein. Here, we present a 15-year-old girl with clinical features of CHARGE syndrome and a de novo 6.5 Mb gain of genomic material at 2p25.3-p25.2. The duplicated region contained 24 genes, including the early and broadly expressed transcription factor gene SOX11. Analysis of 28 other patients with CHARGE showed no SOX11 copy number changes or pathogenic sequence variants. To our knowledge, this child's chromosomal abnormality is unique and represents the first co-occurrence of duplication 2p25 and clinical features of CHARGE syndrome. We compare our patient's phenotype to ten previously published patients with isolated terminal duplication 2p, and elaborate on the clinical diagnosis of CHARGE in the context of atypical genetic findings.

Parents' Perspectives on Variants of Uncertain Significance from Chromosome Microarray Analysis.

Chromosomal microarray analysis (CMA) for unexplained anomalies and developmental delay has improved diagnosis rates, but results classified as variants of uncertain significance (VUS) may challenge both clinicians and families. We explored the impact of such results on families, including parental knowledge, understanding and interpretation. Semi-structured telephone interviews were conducted with parents (N = 14) who received genetic counseling for a VUS in their child. Transcripts were analyzed through an iterative coding process. Participants demonstrated a range of recall and personal interpretation regarding whether test results provided a causal explanation for their children's health issues. Participants maintained contradictory interpretations, describing results as answers while maintaining that little clarification of their child's condition had been provided. Reported benefits included obtaining medical services and personal validation. Parents described adaptation/coping processes similar to those occurring after positive test results. Recall of terminology, including "VUS" and precise CMA abnormalities, was poor. However, most demonstrated conceptual understanding of scientific uncertainty. All participants expressed intentions to return for recommended genetics follow-up but had misconceptions about how this would occur. These results provide insight into the patient-and-family experience when receiving uncertain genomic findings, emphasize the importance of exploring uncertainty during the communication process, and highlight areas for potential attention or improvement in the clinical encounter.

Haploinsufficiency of SF3B4, a component of the pre-mRNA spliceosomal complex, causes Nager syndrome.

Nager syndrome, first described more than 60 years ago, is the archetype of a class of disorders called the acrofacial dysostoses, which are characterized by craniofacial and limb malformations. Despite intensive efforts, no gene for Nager syndrome has yet been identified. In an international collaboration, FORGE Canada and the National Institutes of Health Centers for Mendelian Genomics used exome sequencing as a discovery tool and found that mutations in SF3B4, a component of the U2 pre-mRNA spliceosomal complex, cause Nager syndrome. After Sanger sequencing of SF3B4 in a validation cohort, 20 of 35 (57%) families affected by Nager syndrome had 1 of 18 different mutations, nearly all of which were frameshifts. These results suggest that most cases of Nager syndrome are caused by haploinsufficiency of SF3B4. Our findings add Nager syndrome to a growing list of disorders caused by mutations in genes that encode major components of the spliceosome and also highlight the synergistic potential of international collaboration when exome sequencing is applied in the search for genes responsible for rare Mendelian phenotypes.

Who counsels parents of newborns who are carriers of sickle cell anemia or cystic fibrosis?

Our objective was to describe: 1) physicians' knowledge of whether genetic counseling is provided to parents of newborns with sickle cell trait (SCT) or who are cystic fibrosis carriers (CFC), and 2) the prevalence of genetic counseling provided by primary care physicians. We conducted a cross-sectional descriptive survey of 600 randomly-sampled Michigan-based pediatricians and family physicians, assessing physician knowledge of where and whether genetic counseling is received by parents whose newborns are carriers. Chi-squared testing determined associations between genetic counseling location and physician demographic characteristics. Our response rate was 62 %: 298 (84 %) provided infant well care (183 pediatricians, 115 family physicians). Most respondents were non-Hispanic White (65 %). Virtually all physicians believed parents whose newborns are carriers of either SCT or CFC should receive some genetic counseling (from the physician and/or another source), yet 20 % reported that parents of newborns with SCT did not receive counseling. Parents of infants with CFC received more counseling overall (92 % vs. 80 %; p < 0.01) and were counseled more frequently by genetic counselors or specialty centers than parents of newborns with SCT (85 % vs. 60 %; p < 0.01). Although physicians agreed that parents whose newborns are carriers should receive genetic counseling, fewer parents of newborns with SCT than with CFC received counseling from any source. This finding strongly suggests the need for further education and investigation of this apparent health disparity.

Histone H3.3 beyond cancer: Germline mutations in Histone 3 Family 3A and 3B cause a previously unidentified neurodegenerative disorder in 46 patients.

Although somatic mutations in Histone 3.3 (H3.3) are well-studied drivers of oncogenesis, the role of germline mutations remains unreported. We analyze 46 patients bearing de novo germline mutations in histone 3 family 3A (H3F3A) or H3F3B with progressive neurologic dysfunction and congenital anomalies without malignancies. Molecular modeling of all 37 variants demonstrated clear disruptions in interactions with DNA, other histones, and histone chaperone proteins. Patient histone posttranslational modifications (PTMs) analysis revealed notably aberrant local PTM patterns distinct from the somatic lysine mutations that cause global PTM dysregulation. RNA sequencing on patient cells demonstrated up-regulated gene expression related to mitosis and cell division, and cellular assays confirmed an increased proliferative capacity. A zebrafish model showed craniofacial anomalies and a defect in Foxd3-derived glia. These data suggest that the mechanism of germline mutations are distinct from cancer-associated somatic histone mutations but may converge on control of cell proliferation.

Novel DICER1 mutation as cause of multinodular goiter in children.

BACKGROUND: The aim of this report was to present a rare case of an adolescent with multinodular goiter (MNG) found to have a DICER1 mutation. METHODS AND RESULTS: The methodology includes a presentation and discussion of a chart review including endocrine hormone tests, thyroid ultrasound, and genetic testing for DICER1. A 12-year-old girl presented with a diffusely enlarged thyroid gland. Family history revealed an older sister with a history of bilateral ovarian Sertoli-Leydig cell tumors and MNG. Thyroid function tests were normal. Serial thyroid ultrasounds showed enlarging multiple bilateral nodules. Fine-needle aspiration suggested MNG. Genetic testing revealed a novel heterozygous premature termination mutation (c.1525C>T p.R509X) in the DICER1 gene. CONCLUSIONS: Thyroid nodules are rare in children but carry a higher risk for malignancy. It is essential to inquire about family history and refer for genetic evaluation with a family history of MNG. In patients with DICER1 mutations, tumor surveillance is critical due to the increased risk of multiple tumors, including ovarian tumors and pleuropulmonary blastoma.

Guidelines for Writing Letters to Patients.

Patient letters provide a permanent record of the genetic counseling that was provided and are unique in medical care; rarely do other health care providers send summaries written specifically to their patients and families. We surveyed genetic counseling training program directors and found that while the acquisition of patient letter-writing skills was considered important, there were no specific guidelines made available to students. To develop letter-writing guidelines, we evaluated patient letters, reviewed references on professional correspondence, surveyed the medical literature, and worked with a writing consultant. The guidelines we subsequently developed and present here include a format for writing patient letters, suggestions on presenting medical information in understandable terms, and wording considerations. These patient letter-writing guidelines are intended to serve as a guide for teaching students this important skill and as a resource for practicing health care professionals.