A dyadic approach to the delineation of diagnostic entities in clinical genomics.

The delineation of disease entities is complex, yet recent advances in the molecular characterization of diseases provide opportunities to designate diseases in a biologically valid manner. Here, we have formalized an approach to the delineation of Mendelian genetic disorders that encompasses two distinct but inter-related concepts: (1) the gene that is mutated and (2) the phenotypic descriptor, preferably a recognizably distinct phenotype. We assert that only by a combinatorial or dyadic approach taking both of these attributes into account can a unitary, distinct genetic disorder be designated. We propose that all Mendelian disorders should be designated as "GENE-related phenotype descriptor" (e.g., "CFTR-related cystic fibrosis"). This approach to delineating and naming disorders reconciles the complexity of gene-to-phenotype relationships in a simple and clear manner yet communicates the complexity and nuance of these relationships.

Fatal hyperkeratosis syndrome in four siblings due to dolichol kinase deficiency.

A diagnostic journey began in 1966 when a male was born with a lethal hyperkeratosis of undetermined etiology, only to be followed by three additional siblings with the same unknown disorder. All four siblings had unique circumferential skin constrictions on all of their digits. They died within 5 days after birth with no diagnosis or etiology established. The first author (BDH) maintained notes, partial medical records, photographs, and comments about one autopsy report. This information was regularly revisited in the hope of finding a literature match, but no etiological diagnosis was forthcoming. However, in 2017, Rush et al. reported two siblings with similar phenotype in whom they found dolichol kinase deficiency (DOLK). Ultimately, our family was relocated and DNA isolated from the pathology slides of the third affected infant showed compound heterozygous pathogenic variants in the DOLK gene. The variants were in trans, with different missense variants from the mother and father. This 52-year diagnostic pursuit, culminated in an answer that gave the family an explanation for their losses.

Epigenetic Determinants of Erythropoiesis: Role of the Histone Methyltransferase SetD8 in Promoting Erythroid Cell Maturation and Survival.

Erythropoiesis, in which committed progenitor cells generate millions of erythrocytes daily, involves dramatic changes in the chromatin structure and transcriptome of erythroblasts, prior to their enucleation. While the involvement of the master-regulatory transcription factors GATA binding protein 1 (GATA-1) and GATA-2 in this process is established, the mechanistic contributions of many chromatin-modifying/remodeling enzymes in red cell biology remain enigmatic. We demonstrated that SetD8, a histone methyltransferase that catalyzes monomethylation of histone H4 at lysine 20 (H4K20me1), is a context-dependent GATA-1 corepressor in erythroid cells. To determine whether SetD8 controls erythroid maturation and/or function, we used a small hairpin RNA (shRNA)-based loss-of-function strategy in a primary murine erythroblast culture system. In this system, SetD8 promoted erythroblast maturation and survival, and this did not involve upregulation of the established regulator of erythroblast survival Bcl-x(L). SetD8 catalyzed H4K20me1 at a critical Gata2 cis element and restricted occupancy by an enhancer of Gata2 transcription, Scl/TAL1, thereby repressing Gata2 transcription. Elevating GATA-2 levels in erythroid precursors yielded a maturation block comparable to that induced by SetD8 downregulation. As lowering GATA-2 expression in the context of SetD8 knockdown did not rescue erythroid maturation, we propose that SetD8 regulation of erythroid maturation involves multiple target genes. These results establish SetD8 as a determinant of erythroid cell maturation and provide a framework for understanding how a broadly expressed histone-modifying enzyme mediates cell-type-specific GATA factor function.

Loss-of-function HDAC8 mutations cause a phenotypic spectrum of Cornelia de Lange syndrome-like features, ocular hypertelorism, large fontanelle and X-linked inheritance.

Cornelia de Lange syndrome (CdLS) is a multisystem genetic disorder with distinct facies, growth failure, intellectual disability, distal limb anomalies, gastrointestinal and neurological disease. Mutations in NIPBL, encoding a cohesin regulatory protein, account for >80% of cases with typical facies. Mutations in the core cohesin complex proteins, encoded by the SMC1A, SMC3 and RAD21 genes, together account for ∼5% of subjects, often with atypical CdLS features. Recently, we identified mutations in the X-linked gene HDAC8 as the cause of a small number of CdLS cases. Here, we report a cohort of 38 individuals with an emerging spectrum of features caused by HDAC8 mutations. For several individuals, the diagnosis of CdLS was not considered prior to genomic testing. Most mutations identified are missense and de novo. Many cases are heterozygous females, each with marked skewing of X-inactivation in peripheral blood DNA. We also identified eight hemizygous males who are more severely affected. The craniofacial appearance caused by HDAC8 mutations overlaps that of typical CdLS but often displays delayed anterior fontanelle closure, ocular hypertelorism, hooding of the eyelids, a broader nose and dental anomalies, which may be useful discriminating features. HDAC8 encodes the lysine deacetylase for the cohesin subunit SMC3 and analysis of the functional consequences of the missense mutations indicates that all cause a loss of enzymatic function. These data demonstrate that loss-of-function mutations in HDAC8 cause a range of overlapping human developmental phenotypes, including a phenotypically distinct subgroup of CdLS.

A new case of a LUMBAR syndrome.

LUMBAR syndrome (lower body congenital infantile hemangiomas and other skin defects; urogenital anomalies and ulceration; myelopathy; bony deformities; anorectal malformations and arterial anomalies; and rectal anomalies) is a rare association between infantile hemangiomas of the lower half of the body and regional congenital anomalies. Since 1986, 53 cases have been reported and no etiology has been identified. We report on the 54th case in a male infant and review the literature concerning the manifestations of the LUMBAR syndrome.

Heterozygous missense mutations in SMARCA2 cause Nicolaides-Baraitser syndrome.

Nicolaides-Baraitser syndrome (NBS) is characterized by sparse hair, distinctive facial morphology, distal-limb anomalies and intellectual disability. We sequenced the exomes of ten individuals with NBS and identified heterozygous variants in SMARCA2 in eight of them. Extended molecular screening identified nonsynonymous SMARCA2 mutations in 36 of 44 individuals with NBS; these mutations were confirmed to be de novo when parental samples were available. SMARCA2 encodes the core catalytic unit of the SWI/SNF ATP-dependent chromatin remodeling complex that is involved in the regulation of gene transcription. The mutations cluster within sequences that encode ultra-conserved motifs in the catalytic ATPase region of the protein. These alterations likely do not impair SWI/SNF complex assembly but may be associated with disrupted ATPase activity. The identification of SMARCA2 mutations in humans provides insight into the function of the Snf2 helicase family.

Microdeletion 9q22.3 syndrome includes metopic craniosynostosis, hydrocephalus, macrosomia, and developmental delay.

Basal cell nevus syndrome (BCNS), also known as Gorlin syndrome (OMIM #109400) is a well-described rare autosomal dominant condition due to haploinsufficiency of PTCH1. With the availability of comparative genomic hybridization arrays, increasing numbers of individuals with microdeletions involving this locus are being identified. We present 10 previously unreported individuals with 9q22.3 deletions that include PTCH1. While 7 of the 10 patients (7 females, 3 males) did not meet strict clinical criteria for BCNS at the time of molecular diagnosis, almost all of the patients were too young to exhibit many of the diagnostic features. A number of the patients exhibited metopic craniosynostosis, severe obstructive hydrocephalus, and macrosomia, which are not typically observed in BCNS. All individuals older than a few months of age also had developmental delays and/or intellectual disability. Only facial features typical of BCNS, except in those with prominent midforeheads secondary to metopic craniosynostosis, were shared among the 10 patients. The deletions in these individuals ranged from 352 kb to 20.5 Mb in size, the largest spanning 9q21.33 through 9q31.2. There was significant overlap of the deleted segments among most of the patients. The smallest common regions shared among the deletions were identified in order to localize putative candidate genes that are potentially responsible for each of the non-BCNS features. These were a 929 kb region for metopic craniosynostosis, a 1.08 Mb region for obstructive hydrocephalus, and a 1.84 Mb region for macrosomia. Additional studies are needed to further characterize the candidate genes within these regions.

Grade 1 microtia, wide anterior fontanel and novel type tracheo-esophageal fistula in methimazole embryopathy.

Carbimazole (CMZ) and its active metabolite methimazole (MMI) are antithyroid medications, which can result in MMI/CMZ embryopathy in susceptible individuals. The incidence of birth defects related to MMI/CMZ embryopathy remains unclear as several epidemiologic studies failed to prove a correlation, despite positive case-control studies and numerous case reports. Malformations reported in exposed individuals and commonly recognized as MMI/CMZ embryopathy include cutis aplasia of the scalp, choanal atresia, esophageal atresia (EA), tracheo-esophageal fistula (TEF), persistent vitelline duct, athelia/hypothelia, and subtle facial dysmorphisms including sparse or arched eyebrows. Here, we report on individuals with early pregnancy exposure to MMI, with microtia and various other anomalies associated with MMI embryopathy, suggesting that microtia is also seen with increased frequency after prenatal MMI exposure. Additional unusual malformations among our patients include a previously unreported type of TEF with three separate esophageal pouches and a fistula connecting the middle pouch to the trachea in one child, and absence of the gall bladder in another. An enlarged anterior fontanel was seen in three patients, and clinodactyly of the fifth finger was noted in three. The similarities between our three patients with microtia after MMI exposure and the two previously reported with microtia after CMZ exposure support the concept of microtia being related to the MMI/CMZ exposure. Recognition of microtia as a manifestation of MMI/CMZ embryopathy will likely increase the number of diagnosed cases and thus affect ascertainment. We propose diagnostic criteria for MMI/CMZ embryopathy, including the presence of at least one major characteristic finding.

Petty syndrome and Fontaine-Farriaux syndrome: Delineation of a single syndrome.

In 1990, Petty et al. described two patients representing a novel syndrome with "congenital progeriod" features and neither had classical progeria nor Wiedemann-Rautenstrauch syndrome, though many findings were overlapping. One of the cases had previously been described by Dr. Wiedemann in 1948. The key features of Petty syndrome include pre and postnatal growth restriction, decreased subcutaneous fat with loose skin, enlarged fontanelle with underdeveloped calvarium, coronal synostosis, unruly hair pattern with non-uniform distribution, prominent eyebrows, umbilical hernia, distal digital hypoplasia, and normal or near normal development. Significant overlap to other syndromes, particularly the Fontaine-Farriaux syndrome, is apparent. In 2004, Ardinger postulated that Petty syndrome, like classical progeria, might be secondary to a defect in the lamin A/C (LMNA) gene. The purpose of this paper is to describe two new unrelated cases of this unique syndrome that further delineate the phenotype, compare to phenotypically similar syndromes, and postulate that Petty syndrome could represent a new laminopathy. In addition, evidence suggesting that the Petty syndrome and Fontaine-Farriaux syndromes are variable expressions of the same condition is discussed.

Elements of morphology: standard terminology for the periorbital region.

An international group of clinicians working in the field of dysmorphology has initiated the standardization of terms used to describe human morphology. The goals are to standardize these terms and reach consensus regarding their definitions. In this way, we will increase the utility of descriptions of the human phenotype and facilitate reliable comparisons of findings among patients. Discussions with other workers in dysmorphology and related fields, such as developmental biology and molecular genetics, will become more precise. Here we introduce the anatomy of the periorbital area and define and illustrate the terms that describe the major characteristics of the periorbital area.

Preaxial hallucal polydactyly as a marker for diabetic embryopathy.

BACKGROUND: Diabetes is the most common endocrinologic complication during pregnancy, and poor control can lead to a variety of congenital anomalies in the fetus. However, it is often difficult to differentiate between diabetes-related anomalies and an underlying genetic syndrome. In the 1990s it was proposed that preaxial hallucal polydactyly, particularly when proximally placed, was a distinguishing feature of diabetic embryopathy. METHODS: We summarize the clinical findings in 18 patients (five previously reported in abstract form) with diabetic embryopathy and preaxial hallucal polydactyly to determine which features are most suggestive of diabetic embryopathy. RESULTS: All 18 patients had preaxial hallucal polydactyly (seven bilateral, 11 unilateral), of which 15 patients had proximal implantation of the extra hallux. Further skeletal findings included the following: segmentation anomalies of the spine, equinovarus deformity of the feet, tibial hemimelia, hip dysplasia, and femoral hypoplasia. Upper limb malformations were rare. Eleven of the 18 mothers had prepregnancy insulin-dependent diabetes, while one mother had prepregnancy type 2 diabetes that required insulin therapy in the 3(rd) trimester. Five mothers had gestational diabetes that required insulin and one mother had gestational diabetes that was controlled by diet. The majority of mothers had poorly controlled diabetes during the pregnancy. CONCLUSIONS: Proximally placed preaxial hallucal polydactyly, particularly when coupled with segmentation anomalies of the spine and tibial hemimelia, is highly suggestive of diabetic embryopathy. Varying degrees of diabetes in the mothers point to a possible genetic predisposition interacting with the teratogenic effects of poor glycemic control leading to specific limb anomalies.

Further delineation of spondylometaphyseal dysplasia with cone-rod dystrophy.

There are several entities that combine a skeletal dysplasia with a retinal dystrophy. Recently, another possibly autosomal recessive entity was added to this group characterized by a specific spondylometaphyseal dysplasia and a cone-rod dystrophy, without other significant impairments. The entity was named SMD-CRD. We further delineate this disorder by reporting on a 16-year-old boy and a pair of twins with this entity. Possible etiologies are discussed. The boy showed low alpha-neuraminidase activity levels in fibroblasts, but normal levels in leucocytes. The meaning of this finding remains as yet unknown.

A cluster study of gastroschisis: single center experience.

BACKGROUND AND METHODS: A cluster of 10 neonates admitted with a diagnosis of gastroschisis at birth to the Neonatal Intensive Care Unit (NICU) at the University of Kentucky Medical Center in the year 1996, prompted us to perform a retrospective analysis to determine environmental or genetic causes. RESULTS: A total of 36 neonates with gastroschisis were admitted during the period 1/1992 to 12/1996, and the maternal and patient demographics were evaluated by chart review. The mean maternal age was 21.5 years (14-35 years) of which 42% were teenagers, 66% were primiparous, 42% were smokers, 6% had a history of illicit drug use, and 72% had a history of taking prenatal vitamins. Mean birth weight was 2438g (990-3700g) with 54% being preterm with a mean gestational age of 36 wks (29-40 wks). Family history was negative and chromosomes were normal in patients in whom a karyotype was performed (25%). There was no recurring environmental or drug exposure in the study group. The mothers were from 24 different counties of Kentucky. The 36 cases were not uniformly distributed over the five-year period (chi square statistic = 46.8, degrees of freedom = 4, p < 0.0001). However, there was no evidence that the cases clustered in any 1 year (p = 0.99 for Ederer-Myers-Mantel test). CONCLUSIONS: This is one of the few cluster studies of babies born with gastroschisis. Many of the mothers were teenagers, primiparous, and had an increased frequency of smoking. There was no evidence of temporal or spatial clustering in the gastroschisis cases. We conclude that the cluster of gastroschisis cases in our study occurred as a matter of chance.

DOOR syndrome: clinical report, literature review and discussion of natural history.

DOOR syndrome (deafness, onychodystrophy, osteodystrophy, and mental retardation) is a rarely described disorder with less than 35 reports in the literature. The hallmarks of the syndrome, represented in the DOOR acronym, include sensorineural hearing loss, hypoplastic or absent nails on the hands and feet, small or absent distal phalanges of the hands and feet, and mental retardation. The purpose of our communication is to report on an additional patient with DOOR syndrome, delineate common as well as less frequent manifestations of DOOR syndrome, bring attention to the under appreciated facial features in DOOR syndrome, document the natural history of this disorder, and propose a suggested workup of those suspected of DOOR syndrome. DOOR syndrome is associated with characteristic, coarse facial features with large nose with wide nasal bridge, bulbous tip and anteverted nares, a long prominent philtrum and downturned corners of the mouth. The natural history is one of a deteriorative course, with progressive neurological manifestations including sensorineural deafness, seizures from infancy, optic atrophy, and a peripheral polyneuropathy. The majority of patients with DOOR syndrome have elevated levels of 2-oxoglutarate in the urine and plasma. In this report, we present a newborn with manifestations consistent with DOOR syndrome and a progressive clinical course. A comprehensive literature review reveals 32 patients with DOOR syndrome. In conclusion, DOOR syndrome is a neurometabolic disorder with recognizable facial features and a progressive natural history.

Phakomatosis pigmentovascularis: Implications for severity with special reference to Mongolian spots associated with Sturge-Weber and Klippel-Trenaunay syndromes.

In 1947 the term phakomatosis pigmentovascularis (PPV) was coined to represent the association of widespread, aberrant, and persistent nevus flammeus and pigmentary abnormalities. Four types of PPV have been recognized with type II (nevus flammeus and Mongolian spots) being the most common. Most early cases were of Asian or African descent. Many cases were subsequently associated with Sturge-Weber (S-W) and Klippel-Trenaunay (K-T) syndromes. Almost no literature reports have appeared in the genetic or dysmorphology literature! We present six cases of PPV in which five were either African, Asian or Hispanic, and five of six had an admixture of K-T and S-W. Four had macrocephaly, and one had microcephaly. Four had CNS abnormalities (three with hydrocephalus, one with Arnold-Chiari and one with polymicrogyria), three had mental retardation, and one had seizures. One each had thumb hypoplasia, hydronephrosis, glaucoma, coronal synostosis, and 3-4 finger syndactyly. It is our suspicion and hypothesis that in the presence of persistent, extensive and aberrant Mongolian spots, vascular abnormalities as are seen in K-T and S-W carry a worse prognosis. This may be particularly true either of children of Asian, Hispanic or African heritage or any individuals from darker pigmented skin groups.

Further delineation of Kabuki syndrome in 48 well-defined new individuals.

Kabuki syndrome is a multiple congenital anomaly/mental retardation syndrome. This study of Kabuki syndrome had two objectives. The first was to further describe the syndrome features. In order to do so, clinical geneticists were asked to submit cases-providing clinical photographs and completing a phenotype questionnaire for individuals in whom they felt the diagnosis of Kabuki syndrome was secure. All submitted cases were reviewed by four diagnosticians familiar with Kabuki syndrome. The diagnosis was agreed upon in 48 previously unpublished individuals. Our data on these 48 individuals show that Kabuki syndrome variably affects the development and function of many organ systems. The second objective of the study was to explore possible etiological clues found in our data and from review of the literature. We discuss advanced paternal age, cytogenetic abnormalities, and familial cases, and explore syndromes with potentially informative overlapping features. We find support for a genetic etiology, with a probable autosomal dominant mode of inheritance, and speculate that there is involvement of the interferon regulatory factor 6 (IRF6) gene pathway. Very recently, a microduplication of 8p has been described in multiple affected individuals, the proportion of individuals with the duplication is yet to be determined.

Unexpected death and critical illness in Prader-Willi syndrome: report of ten individuals.

Individuals with Prader-Willi syndrome (PWS) generally survive into adulthood. Common causes of death are obesity related cor pulmonale and respiratory failure. We report on a case series of eight children and two adults with unexpected death or critical illness. Our data show age-specific characteristics of PWS patients with fatal or life-threatening illnesses. Under the age of 2 years, childhood illnesses in general were associated with high fever and rapid demise or near-demise. Hypothalamic dysfunction likely plays a role in exaggerated fever response, but also perhaps in central regulation of adrenal function. Below average sized adrenal glands were found in three children, which raises the possibility of unrecognized adrenal insufficiency in a subset of individuals with PWS and emphasizes the vital role of autopsy. The tub drowning death of an adult patient could be related to central hypersomnia, which has been reported in PWS. We suggest that increased risk for critical illness be considered in the discussion of anticipatory guidance for the care of infants with PWS. Since a number of children died while hospitalized, particularly close observation of PWS children who are ill enough to warrant hospital admission is recommended.

X-linked cubitus valgus with mental retardation and typical face.

In 1973, Jones and Smith described two maternal male first cousins with a similar pattern of malformation, including mental retardation, cubitus valgus, and unusual facies. The purpose of this report is to describe three additional cases, a 10-year-old male and his 30-year-old maternal uncle and an unrelated 15-year-old boy, bringing to five the total number of individuals with this disorder. The principal features include moderate mental retardation, mild microcephaly, a short philtrum, deep-set, downslanting palpebral fissures, multiple nevi, and striking cubitus valgus. Documentation of this disorder in two maternal male first cousins as well as in a male and his maternal uncle support an X-linked recessive mode of inheritance for this condition.