Improvement in cystic fibrosis newborn screening program outcomes with genetic counseling via telemedicine

INTRODUCTION

The Cystic Fibrosis Foundation (CF Foundation) recommends the provision of genetic counseling (GC) to help educate families and decrease anxiety around the cystic fibrosis (CF) newborn screening process. Unfortunately, access to genetic counselors is limited, especially for CF trained genetic counselors. We hypothesized that the GC process for families could be improved by utilizing telemedicine to leverage the availability of two dedicated, CF trained genetic counselors to provide access to GC for several CF centers. In addition, we hoped to demonstrate that use of trained CF genetic counselors, delivering GC via telemedicine at the time of sweat testing, would provide families with understanding of CF genetics as well as result in high satisfaction with the newborn screening process.

METHODS

GC was provided by CF trained genetic counselors via telemedicine at the time of sweat testing. Following the counseling session, families were administered an anonymous written survey to evaluate their impression of the services provided. A subset of 50 families was recruited for an assessment of gained knowledge regarding CF genetics using the Ciske knowledge inventory. Using χ2  analysis, Ciske knowledge inventory data from our telemedicine GC families was compared to counseled and uncounseled Ciske historical controls. Lastly, in-depth interviews about the newborn screening process for CF were performed with 10 families and interviews were coded for emerging themes.

RESULTS

During the 4 years of the study, 250 patients received GC. Overall comfort with the counseling rated 4.77 out of 5 using a Likert scale. After counseling by telemedicine, parents demonstrated improved understanding of the genetic implications of an abnormal CF newborn screen for their family, with 100% of families understanding that their child was a carrier for CF as compared to 97.2% of counseled (p = .023) and 78.5% of uncounseled (p = .0007) from Ciske historical controls. The study group also showed improvement in understanding of both parents possibly being carriers, with an 87.7% correct response rate compared to a 37.0% correct response rate in the counseled group (p < .0001) and a 35.4% correct response rate in the non-counseled group (p < .0001) from Ciske historical controls. Subgroup analysis at one site showed a significant increase in the number of infants with completed sweat tests from previous years (49% in 2013 vs. 80% in 2017 during the study, p < .0001).

CONCLUSIONS

GC by telemedicine was well received by families and demonstrated improved family knowledge acquisition and understanding of CF as it related to risks for their child as well as identification of risks for other family members. Furthermore, in addition to an increase is those receiving GC, a subgroup analysis demonstrated a significant increase in the number of infants receiving sweat tests. This study demonstrates that GC via telemedicine for CF is feasible and demonstrates improvement in parent understanding of CF genetics. Furthermore, this method can be implemented effectively across a wide geographical area with a limited number of CF trained genetic counselors to improve access to care for patients and families.

Diagnostic capabilities of nanopore long-read sequencing in muscular dystrophy

Many individuals with muscular dystrophies remain genetically undiagnosed despite clinical diagnostic testing, including exome sequencing. Some may harbor previously undetected structural variants (SVs) or cryptic splice sites. We enrolled 10 unrelated families: nine had muscular dystrophy but lacked complete genetic diagnoses and one had an asymptomatic DMD duplication. Nanopore genomic long-read sequencing identified previously undetected pathogenic variants in four individuals: an SV in DMD, an SV in LAMA2, and two single nucleotide variants in DMD that alter splicing. The DMD duplication in the asymptomatic individual was in tandem. Nanopore sequencing may help streamline genetic diagnostic approaches for muscular dystrophy.

Telegenetic medicine: improved access to services in an underserved area

We used telemedicine to improve genetics services to patients in the rural northwestern region of Florida. Patients were first seen via videoconference by a genetic counsellor, who obtained family and medical history. A local paediatrician then performed the physical examination, and a plan for evaluation was established. The videoconferencing equipment was connected at a bandwidth of 384 kbit/s, using three ISDN lines. During the first three telemedicine clinics, seven patients were evaluated and then returned to the centre for a face-to-face consultation with the clinical geneticist. No new diagnoses were made face-to-face that had not been identified by telemedicine. No diagnoses made by telemedicine were judged to be wrong when the child was evaluated face-to-face. During a two-year study of patient satisfaction with 12 telegenetics clinics, the 50 families evaluated via videoconferencing were asked to complete surveys; 40 surveys were returned (a response rate of 80%). All individuals either strongly agreed or agreed that the evaluation of their child was appropriate, sufficient and sufficiently protective of their child's privacy. The waiting time for a new patient consultation with the clinical genetics team was 16.9 months (SD 1.9) at the start and 3.0 months (SD 1.0) at the end of the trial period. The difference was significant ( t-test, P<0.0001). Telegenetics allows more rapid assurance that a genetic syndrome has not been identified, or a quicker initial evaluation and diagnosis for children who do have an identifiable genetic syndrome.

Exome sequencing for the diagnosis of 46,XY disorders of sex development

CONTEXT

Disorders of sex development (DSD) are clinical conditions where there is a discrepancy between the chromosomal sex and the phenotypic (gonadal or genital) sex of an individual. Such conditions can be stressful for patients and their families and have historically been difficult to diagnose, especially at the genetic level. In particular, for cases of 46,XY gonadal dysgenesis, once variants in SRY and NR5A1 have been ruled out, there are few other single gene tests available.

OBJECTIVE

We used exome sequencing followed by analysis with a list of all known human DSD-associated genes to investigate the underlying genetic etiology of 46,XY DSD patients who had not previously received a genetic diagnosis.

DESIGN

Samples were either submitted to the research laboratory or submitted as clinical samples to the UCLA Clinical Genomic Center. Sequencing data were filtered using a list of genes known to be involved in DSD.

RESULTS

We were able to identify a likely genetic diagnosis in more than a third of cases, including 22.5% with a pathogenic finding, an additional 12.5% with likely pathogenic findings, and 15% with variants of unknown clinical significance.

CONCLUSIONS

Early identification of the genetic cause of a DSD will in many cases streamline and direct the clinical management of the patient, with more focused endocrine and imaging studies and better-informed surgical decisions. Exome sequencing proved an efficient method toward such a goal in 46,XY DSD patients.

Molecular analysis expands the spectrum of phenotypes associated with GLI3 mutations

A range of phenotypes including Greig cephalopolysyndactyly and Pallister-Hall syndromes (GCPS, PHS) are caused by pathogenic mutation of the GLI3 gene. To characterize the clinical variability of GLI3 mutations, we present a subset of a cohort of 174 probands referred for GLI3 analysis. Eighty-one probands with typical GCPS or PHS were previously reported, and we report the remaining 93 probands here. This includes 19 probands (12 mutations) who fulfilled clinical criteria for GCPS or PHS, 48 probands (16 mutations) with features of GCPS or PHS but who did not meet the clinical criteria (sub-GCPS and sub-PHS), 21 probands (6 mutations) with features of PHS or GCPS and oral-facial-digital syndrome, and 5 probands (1 mutation) with nonsyndromic polydactyly. These data support previously identified genotype-phenotype correlations and demonstrate a more variable degree of severity than previously recognized. The finding of GLI3 mutations in patients with features of oral-facial-digital syndrome supports the observation that GLI3 interacts with cilia. We conclude that the phenotypic spectrum of GLI3 mutations is broader than that encompassed by the clinical diagnostic criteria, but the genotype-phenotype correlation persists. Individuals with features of either GCPS or PHS should be screened for mutations in GLI3 even if they do not fulfill clinical criteria.

TFAP2A mutations result in branchio-oculo-facial syndrome

Branchio-oculo-facial syndrome (BOFS) is a rare autosomal-dominant cleft palate-craniofacial disorder with variable expressivity. The major features include cutaneous anomalies (cervical, infra- and/or supra-auricular defects, often with dermal thymus), ocular anomalies, characteristic facial appearance (malformed pinnae, oral clefts), and, less commonly, renal and ectodermal (dental and hair) anomalies. The molecular basis for this disorder is heretofore unknown. We detected a 3.2 Mb deletion by 500K SNP microarray in an affected mother and son with BOFS at chromosome 6p24.3. Candidate genes in this region were selected for sequencing on the basis of their expression patterns and involvement in developmental pathways associated with the clinical findings of BOFS. Four additional BOFS patients were found to have de novo missense mutations in the highly conserved exons 4 and 5 (basic region of the DNA binding domain) of the TFAP2A gene in the candidate deleted region. We conclude BOFS is caused by mutations involving TFAP2A. More patients need to be studied to determine possible genetic heterogeneity and to establish whether there are genotype-phenotype correlations.

A patient with the syndrome of megalencephaly, mega corpus callosum and complete lack of motor development

The syndrome of megalencephaly, mega corpus callosum and complete lack of motor development (MCC; OMIM 603387) is an apparently rare condition since only three sporadic cases have been reported [Gohlich-Ratmann et al. (1998); Am J Med Genet 79:161-167]. We describe an additional case that was not diagnosed until age 15 months. The MRI showed generalized, severe enlargement of the corpus callosum and thickening of the cortex. The cause for the MCC syndrome is unknown and both autosomal recessive and spontaneous dominant genetic mechanisms are possibilities.

High cognitive functioning and behavioral phenotype in Pallister-Killian syndrome

Pallister-Killian syndrome (PKS) is a rare syndrome of multiple congenital anomalies attributable to the presence of a mosaic supernumerary isochromosome 12p. The syndrome presents with a recognizable pattern of findings including: pigmentary skin changes, characteristic facial features (sparse anterior scalp hair, flattened midface, macrostomia, and coarsening of the facial features), and developmental delay. The developmental phenotype of PKS is quite variable, but most are considered to fall into the profound range of developmental retardation. We report on an individual with classical features of PKS with development significantly better than that reported in the literature. Developmental and behavioral testing in this individual alters the range of developmental expectation in PKS, and highlights the need for consideration of chromosomal analysis in individuals with normal or near-normal intelligence if other physical phenotypic features of PKS are present.

Fine mapping of chromosome 17 translocation breakpoints > or = 900 Kb upstream of SOX9 in acampomelic campomelic dysplasia and a mild, familial skeletal dysplasia

Previously, our group reported a five-generation family in which a balanced t(13;17) translocation is associated with a spectrum of skeletal abnormalities, including Robin sequence, hypoplastic scapulae, and a missing pair of ribs. Using polymerase chain reaction (PCR) with chromosome-specific markers to analyze DBA from somatic cell hybrids containing the derivative translocation chromosomes, we narrowed the breakpoint on each chromosome. Subsequent sequencing of PCR products spanning the breakpoints identified the breaks precisely. The chromosome 17 breakpoint maps approximately 932 kb upstream of the sex-determining region Y (SRY)-related high-mobility group box gene (SOX) within a noncoding transcript represented by two IMAGE cDNA clones. A growing number of reports have implicated chromosome 17 breakpoints at a distance of up to 1 Mb from SOX9 in some cases of campomelic dysplasia (CD). Although this multigeneration family has a disorder that shares some features with CD, their phenotype is significantly milder than any reported cases of (nonmosaic) CD. Therefore, this case may represent an etiologically distinct skeletal dysplasia or may be an extremely mild familial example of CD, caused by the most proximal translocation breakpoint from SOX9 reported to date. In addition, we have refined the breakpoint in a acampomelic CD case described elsewhere and have found that it lies approximately 900 kb upstream of SOX9.

Concurrence of fragile X syndrome and 47, XYY in an individual with a Prader-Willi-like phenotype

We report on a 34-year-old developmentally disabled man referred to our clinic for evaluation of possible Prader-Willi syndrome on the basis of obesity and voracious appetite. Cytogenetic and molecular analysis revealed a 47, XYY karyotype and the presence of a trinucleotide repeat expansion resulting in fragile X syndrome. To our knowledge, this is the first report of concurrence of XYY and fragile X syndrome in the medical literature. Review of sex chromosome abnormalities associated with fragile X syndrome and phenotypic considerations are presented.

A family with a grand-maternally derived interstitial duplication of proximal 15q

About 1% of individuals with autism or types of pervasive developmental disorder have a duplication of the 15q11-q13 region. These abnormalities can be detected by routine G-banded chromosome study, showing an extra marker chromosome, or demonstrated by fluorescence in situ hybridization (FISH) analysis, revealing an interstitial duplication. We report here the molecular, cytogenetic, clinical and neuropsychiatric evaluations of a family in whom 3 of 4 siblings inherited an interstitial duplication of 15q11-q13. This duplication was inherited from their mother who also had a maternally derived duplication. Affected family members had apraxia of speech, phonological awareness deficits, developmental language disorder, dyslexia, as well as limb apraxia but did not have any dysmorphic clinical features. The observations in this family suggest that the phenotypic manifestations of proximal 15q duplications may also involve language-based learning disabilities.

Clinical and molecular studies of a large family with desmin-associated restrictive cardiomyopathy

Patients with restrictive cardiomyopathy (RC) have impaired diastolic function, but intact systolic function until later stages of the disease, ultimately leading to heart failure. Primary RC is often sporadic, but also may be inherited in an autosomal dominant fashion, particularly the idiopathic forms. Recently there has been great interest in inherited cardiomyopathy associated with myocyte desmin deposition ('desminopathies'). In some such families, desmin or alpha-B crystallin gene mutation is the underlying cause, and the desmin accumulation affects skeletal muscle as well, usually causing skeletal myopathy. We describe a large family with apparent autosomal dominant inheritance of desmin-associated RC spanning four generations, with the age of onset and severity/rate of progression being highly variable. This family is relatively unique in that there is no symptom-based evidence of skeletal muscle involvement, and the known desminopathy and cardiomyopathy genes/loci have been ruled out. These data support literature suggesting that desmin deposition may be associated with different underlying gene defects, and that a novel desminopathy gene is responsible for the condition in this family.

NF1 mutation analysis using a combined heteroduplex/SSCP approach

Neurofibromatosis type 1 (NF1) is a common autosomal dominant disorder characterized predominantly by neurofibromas, café-au-lait spots, and Lisch nodules. The disease is caused by disruptive mutations of the large NF1 gene, with half of cases caused by new mutation. Less than 100 constitutional mutations have thus far been published, ranging from very large deletions to point mutations. We have pursued NF1 mutation analysis by heteroduplex analysis (HDA) and single-strand conformational polymorphism analysis (SSCP) of individual exons. We streamlined these techniques to eliminate the use of radioactivity, to apply both methods to the same PCR product, and to multiplex samples in gels. Applied simultaneously to a set of 67 unrelated NF1 patients, HDA and SSCP have thus far identified 26 mutations and/or variants in 45 of the 59 exons tested. Disease-causing mutations were found in 19% (13/67) of cases studied. Both techniques detected a variety of mutations including splice mutations, insertions, deletions, and point changes, with some overlap in the ability of each method to detect variants.

Analysis of CpG C-to-T mutations in neurofibromatosis type 1. Mutations in brief no. 129. Online

Neurofibromatosis type 1 (NF1) is a dominant disorder caused by mutations in the NF1 gene; approximately 100 NF1 gene mutations have been published. The CpG C-to-T transition is a frequent mutation mechanism in genetic disorders. To estimate its frequency in NF1, we employed a PCR-restriction digestion method to examine 17 CpGs in 65 patients, and also screened for a CpG nonsense transition (R1947X) that occurs in 1-2% of patients. The analysis revealed disease-related CpG C-to-T transitions (including a nonsense mutation that may be as frequent as R1947X) as well as a benign variant and another mutation at a CpG. Four patients showed CpG mutations in analysis of 18 sites (17 surveyed by restriction digest, plus the R1947X assay), including three C-to-T transitions and one C-to-G transversion. These 18 sites represent one-fifth of the 91 CpGs at which a C-to-T transition would result in a nonsense or nonconservative missense mutation. Thus, it is feasible that the CpG mutation rate at NF1 might be similar to that seen in other disorders with a high mutation rate, and that recurrent NF1 mutations may frequently reside at CpG sites.

Linkage analysis narrows the critical region for oculodentodigital dysplasia to chromosome 6q22-q23

Oculodentodigital dysplasia (ODDD) is an autosomal dominant condition with high penetrance and variable expressivity. The anomalies of the craniofacial region, eyes, teeth, and limbs indicate abnormal morphogenesis during early fetal development. Neurologic abnormalities occur later in life and appear to be secondary to white matter degeneration and basal ganglia changes. In familial cases, the dysmorphic and/or neurodegenerative components of the phenotype can be more severe and/or present at a younger age in subsequent generations, suggesting genetic anticipation. These clinical features suggest that the ODDD gene is pleiotropic with important functions throughout pre- and postnatal development. We have performed two-point linkage analysis with seven ODDD families and 19 microsatellite markers on chromosome 6q spanning a genetic distance of approximately 11 cM in males and 20 cM in females. We have refined the location of the ODDD gene between DNA markers D6S266/D6S261 (centromeric) and D6S1639 (telomeric), an interval of 1.01 (male) to 2.87 (female) cM. The strongest linkage was to DNA marker D6S433 (Zmax = 8.96, thetamax = 0.001). Families show significant linkage to chromosome 6q22-q23 and no evidence for genetic heterogeneity.

Genetic counseling in Angelman syndrome: the challenges of multiple causes

The causal heterogeneity of Angelman syndrome (AS) makes providing information regarding recurrence risk both important and challenging, and may have a dramatic impact on reproductive decision-making for the nuclear and extended family. Most cases of AS result from typical large de novo deletions of 15q11-q13, and are expected to have a low (<1%) risk of recurrence. AS due to paternal uniparental disomy (UPD), which occurs in the absence of a parental translocation, is likewise expected to have a <1% risk of recurrence. Parental transmission of a structurally or functionally unbalanced chromosome complement can lead to 15q11-q13 deletions or to UPD and will result in case-specific recurrence risks. In instances where there is no identifiable large deletion or UPD, the risk for recurrence may be as high as 50% as the result of either a maternally inherited imprinting center (IC) mutation or a ubiquitin-protein ligase (UBE3A) gene mutation. Individuals with AS who have none of the above abnormalities comprise a significant proportion of cases, and some may be at a 50% recurrence risk. Misdiagnoses, as well, can be represented in this group. In light of the many conditions which are clinically similar to AS, it is essential to address the possibility of diagnostic uncertainty and potential misdiagnosis prior to the provision of genetic counseling. Summaries of the different causal classes of AS as an algorithm for determination of recurrence risks are presented.

Prevalence of 22q11 region deletions in patients with velopharyngeal insufficiency

Velo-cardio-facial syndrome, DiGeorge syndrome, conotruncal anomaly face syndrome, tetralogy of Fallot, and pulmonary atresia with ventricular septal defect are all associated with hemizygosity of 22q11. While the prevalence of the deletions in these phenotypes has been studied, the frequency of deletions in patients presenting with velopharyngeal insufficiency (VPI) is unknown. We performed fluorescence in situ hybridization for locus D22S75 within the 22q11 region on 23 patients with VPI (age range 5-42 years) followed in the Craniofacial Clinic at the University of Florida. The VPI occurred either as a condition of unknown cause (n=16) or as a condition remaining following primary cleft palate surgery (n=7). Six of sixteen patients with VPI of unknown cause and one of seven with VPI following surgery had a deletion in the region. This study documents a high frequency of 22q11 deletions in those presenting with VPI unrelated to overt cleft palate surgery and suggests that deletion testing should be considered in patients with VPI.

Variable expression of rib, pectus, and scapular anomalies with Robin-type cleft palate in a 5-generation family: a new syndrome?

We report on a 5-generation family with multiple musculoskeletal anomalies, including: Robin-type cleft palate, rib "dysplasia," scapular hypoplasia, and pectus excavatum. Robin-type clefts are known to be associated with various skeletal malformations; however, most of these include limb anomalies which are not present in this family. To our knowledge, there are no reports of similar conditions in the literature. The transmission through 5 generations and the presence of male-to-male transmission are consistent with autosomal-dominant transmission of a trait with variable expressivity.

Juvenile rheumatoid arthritis in velo-cardio-facial syndrome: coincidence or unusual complication?

We report on two patients with velo-cardio-facial syndrome (VCFS) and juvenile rheumatoid arthritis (JRA). The first, a 9-year-old girl, presented with microcephaly, characteristic face, congenital heart disease, and velopharyngeal insufficiency. Fluorescence in situ hybridization (FISH) study showed deletion of D22S75 (N25), confirming the diagnosis of VCFS. At age 7, she developed joint pain, and polyarticular JRA was diagnosed. Awareness of this case led to the subsequent diagnosis of VCFS (also confirmed by FISH) in another, unrelated 12-year-old girl with characteristic face, hypernasal speech, and obesity. JRA was first diagnosed in this case at age 5 years, and she subsequently developed severe polyarticular disease. Neither patient had clinical or laboratory evidence of immunodeficiency. This observation represents the first report of the association of JRA with VCFS and raises the question of whether this is a coincidental association or a rare complication of this condition.

Concurrence of supravalvular aortic stenosis and peripheral pulmonary stenosis in three generations of a family: a form of arterial dysplasia

Isolated supravalvular aortic stenosis (SVAS) commonly is an autosomal dominant trait; it may also occur in the Williams syndrome (WS). While peripheral pulmonary stenosis (PPS) can occur in the same individual with familial isolated SVAS, concurrence of these lesions in different relatives of a family is uncommon. We describe five affected individuals in one family; three had isolated SVAS, one had isolated PPS, and one had SVAS and PPS. Based on this family and review of literature, we suggest that SVAS is a form of arterial dysplasia encompassing PPS in its spectrum. It is developmentally distinct from other left heart obstructive lesions that are hypothesized to be related to blood flow abnormalities in the developing embryo. We also conclude that the clinical disorder in this family represents one that is distinct from WS.

Duplication of 9q12-q33: a case report and implications for the dup(9q) syndrome

We report on a boy with a direct tandem duplication of 9(q12-q33) and dolichocephaly, beaked nose with prominent philtrum, deep-set eyes, receding small chin, failure to thrive, developmental delay, simian creases, long fingers, stiff joints, and hypoplastic scrotum. This patient is compared to the 5 other reported cases with pure partial dup(9q), and the "trisomy 9q syndrome" described by Turleau et al. [1975].

Phocomelia, oligodactyly, and acrania: the Schinzel-Phocomelia syndrome

We report on a girl born with phocomelia of both lower limbs, with 3-toed feet and partial sacral agenesis. She had normal growth of the upper limbs and trunk, and normal intelligence. Ultrasound study performed during the subsequent pregnancy documented a large skull defect with an intact brain. Fetal autopsy following the termination of that pregnancy was not done. We think this is a further report of the phocomelia syndrome with additional anomalies as reported by Schinzel [Hum Genet 84:539-541, 1990].

Hyperphalangism, facial anomalies, hallux valgus, and bronchomalacia: a new syndrome?

We report on a boy with hyperphalangism, partial syndactyly, facial anomalies, and diffuse bronchomalacia, born to a nonconsanguineous French-Canadian couple. To our knowledge, this is a hitherto undescribed syndrome.

Autosomal recessive oral-facial-digital syndrome with resemblance to OFD types II, III, IV and VI: a new OFD syndrome?

We report on a son and daughter of Ashkenazi-Jewish parents with postaxial polydactyly of the hands and feet associated with syndactyly and brachydactyly, mental retardation, cerebellar hypoplasia, pectus excavatum, mesomelic shortness of the upper and lower limbs, and pretibial dimples. Although this appears to be an example of one of the OFD syndromes and has many similarities to OFD type II, III, IV and VI, it does not fit satisfactorily into any of the types previously described. Thus this may be a new OFD syndrome, although we cannot exclude a possibility that most or all autosomal recessive OFD syndromes are the result of pleiotropy of a single mutation in a homozygous state.

Familial intestinal malrotation with midgut volvulus and facial anomalies: a disorder involving a gene controlling the normal gut rotation?

We report on 2 sisters with congenital midgut volvulus. Both had similar facial changes different from those of their parents and the other 2 unaffected sibs. Both parents had normal barium meal roentgenograms. The occurrence of these abnormalities in sibs born to parents with apparently normal gastrointestinal tract anatomy suggest autosomal recessive inheritance, although a coincidence, multifactorial or autosomal dominant inheritance with nonpenetrance in either of the parents cannot be excluded.