Michelle Fox

Clinical Exome Sequencing for Genetic Identification of Rare Mendelian Disorders

IMPORTANCE Clinical exome sequencing (CES) is rapidly becoming a common molecular diagnostic test for individuals with rare genetic disorders. OBJECTIVE To report on initial clinical indications for CES referrals and molecular diagnostic rates for different indications and for different test types. DESIGN, SETTING, AND PARTICIPANTS Clinical exome sequencing was performed on 814 consecutive patients with undiagnosed, suspected genetic conditions at the University of California, Los Angeles, Clinical Genomics Center between January 2012 and August 2014. Clinical exome sequencing was conducted as trio-CES (both parents and their affected child sequenced simultaneously) to effectively detect de novo and compound heterozygous variants or as proband-CES (only the affected individual sequenced) when parental samples were not available. MAIN OUTCOMES AND MEASURES Clinical indications for CES requests, molecular diagnostic rates of CES overall and for phenotypic subgroups, and differences in molecular diagnostic rates between trio-CES and proband-CES. RESULTS Of the 814 cases, the overall molecular diagnosis rate was 26% (213 of 814; 95% CI, 23%-29%). The molecular diagnosis rate for trio-CES was 31% (127 of 410 cases; 95% CI, 27%-36%) and 22% (74 of 338 cases; 95% CI, 18%-27%) for proband-CES. In cases of developmental delay in children (<5 years, n = 138), the molecular diagnosis rate was 41% (45 of 109; 95% CI, 32%-51%) for trio-CES cases and 9% (2 of 23, 95% CI, 1%-28%) for proband-CES cases. The significantly higher diagnostic yield (P value = .002; odds ratio, 7.4 [95% CI, 1.6-33.1]) of trio-CES was due to the identification of de novo and compound heterozygous variants. CONCLUSIONS AND RELEVANCE In this sample of patients with undiagnosed, suspected genetic conditions, trio-CES was associated with higher molecular diagnostic yield than proband-CES or traditional molecular diagnostic methods. Additional studies designed to validate these findings and to explore the effect of this approach on clinical and economic outcomes are warranted.

American College of Medical Genetics and Genomics guideline for the clinical evaluation and etiologic diagnosis of hearing loss

Hearing loss is a common and complex condition that can occur at any age, can be inherited or acquired, and is associated with a remarkably wide array of etiologies. The diverse causes of hearing loss, combined with the highly variable and often overlapping presentations of different forms of hearing loss, challenge the ability of traditional clinical evaluations to arrive at an etiologic diagnosis for many deaf and hard-of-hearing individuals. However, identifying the etiology of a hearing loss may affect clinical management, improve prognostic accuracy, and refine genetic counseling and assessment of the likelihood of recurrence for relatives of deaf and hard-of-hearing individuals. Linguistic and cultural identities associated with being deaf or hard of hearing can complicate access to and the effectiveness of clinical care. These concerns can be minimized when genetic and other health-care services are provided in a linguistically and culturally sensitive manner. This guideline offers information about the frequency, causes, and presentations of hearing loss and suggests approaches to the clinical evaluation of deaf and hard-of-hearing individuals aimed at identifying an etiologic diagnosis and providing informative and effective patient education and genetic counseling.Genet Med 2014:16(4):347–355.

Biochemical, neuropathological, and neuroimaging characteristics of early-onset Alzheimer’s disease due to a novel PSEN1 mutation

Familial Alzheimers disease (AD) due to PSEN1 mutations provides an opportunity to examine AD biomarkers in persons in whom the diagnosis is certain. We describe a 55 year-old woman with clinically probable AD and a novel PSEN1 mutation who underwent genetic, clinical, biochemical and magnetic resonance and nuclear imaging assessments. We also describe neuropathological findings in her similarly affected brother. Neuropsychological testing confirmed deficits in memory, visuospatial and language function. CSF t-tau and p-tau181 were markedly elevated and Aβ(42) levels reduced. FDG-PET revealed hypometabolism in the left parietotemporal cortex. FDDNP-PET showed increased binding of tracer in medial temporal and parietal lobes and in the head of the caudate and anterior putamen bilaterally. Neuropathological examination of her brother showed the typical findings of AD and the striatum demonstrated amyloid pathology and marked neurofibrillary pathology beyond that typically seen in late-onset AD. A novel S212Y substitution in PSEN1 was present in the index patient and her affected brother but not in an older unaffected sister. An in vitro assay in which the S212Y mutation was introduced in cell culture confirmed that it was associated with increased production of Aβ(42). We describe biochemical, imaging, and neuropathological changes in a pedigree with a novel PSEN1 mutation. This allows us to validate the pathogenicity of this mutation and the indices used to assess AD.

Infant hearing loss and connexin testing in a diverse population

Purpose: Previous studies of connexin-related hearing loss have typically reported on mixed age groups or adults. To further address epidemiology and natural history of connexin-related hearing loss, we conducted a longitudinal study in an ethnically diverse cohort of infants and toddlers under 3 years of age. Our study compares infants with and without connexin-related hearing loss to examine differences in the prevalence of connexin and non-connexin-related hearing loss by ethnic origin, detection by newborn hearing screening, phenotype, neonatal risk factors, and family history. This is the first study to differentiate infants with and without connexin-related hearing loss.Methods: We enrolled 95 infants with hearing loss from whom both exons of Cx26 were sequenced and the Cx30 deletion was assayed. Demographic, family history, newborn hearing screening data, perinatal, and audiologic records were analyzed.Results: Genetic testing identified biallelic Cx26/30 hearing loss-associated variants in 24.7% of infants with a significantly lower prevalence in Hispanic infants (9.1%). Eighty-two infants underwent newborn hearing screening; 12 infants passed, 3 had connexin-related hearing loss. No differences in newborn hearing screening pass rate, neonatal complications, or hearing loss severity were detected between infants with and without connexin-related hearing loss. Family history correlates with connexin-related hearing loss.Conclusions: Connexin-related hearing loss occurs in one quarter of infants in an ethnically diverse hearing loss population but with a lower prevalence in Hispanic infants. Not all infants with connexin-related hearing loss fail newborn hearing screening. Family history correlates significantly with connexin-related hearing loss. Genetic testing should not be deferred because of newborn complications. These results will have an impact on genetic testing for infant hearing loss.

A prospective, longitudinal study of the impact of GJB2/GJB6 genetic testing on the beliefs and attitudes of parents of deaf and hard-of-hearing infants.

There are limited data on the impact of incorporating genetic counseling and testing into the newborn hearing screening process. We report on results from a prospective, longitudinal study to determine the impact of genetic counseling and GJB2/GJB6 genetic testing on parental knowledge, attitudes, and beliefs about genetic testing. One hundred thirty culturally hearing parents of 93 deaf or hard‐of‐hearing children ages 0–3 years primarily identified through newborn hearing screening received pre‐ and post‐test genetic counseling for GJB2 and GJB6. Parents completed questionnaires following pre‐test counseling, and 1‐ and 6‐month post‐test result disclosure. Results indicate that following pre‐test counseling all parents perceived benefits to genetic testing. While parents who received positive results continued to perceive benefits from testing, perceived benefit declined among parents who received inconclusive or negative results. Parents did not perceive genetic testing as harmful following pre‐test counseling or receipt of test results. Parents who received positive test results performed better in understanding recurrence and causation of their childs deafness and indicated greater interest in prenatal genetic testing than those who received inconclusive or negative test results. Parents felt that pediatricians and audiologists should inform parents of genetic testing availability; however, there was no consensus on timing of this discussion. Thus culturally hearing parents do not perceive genetic testing of their deaf or hard‐of‐hearing infants/toddlers as harmful; they feel that primary care providers should discuss genetic testing with them; and positive genetic test results with genetic counseling give rise to better understanding and perceived benefit than negative or inconclusive results.

Multiple Sequence Variants in Hereditary Hemorrhagic Telangiectasia Cases: Illustration of Complexity in Molecular Diagnostic Interpretation

Hereditary hemorrhagic telangiectasia is an autosomal dominant disease caused by mutations in the ACVRL1 and ENG genes characterized by arterio-venous malformations and telangiectases. Over 700 mutations have been described in these two genes, and missense mutations are common. We describe 10 cases in which more than one potentially pathogenic mutation was identified. We report that 8 novel missense mutations, as well as previously reported pathogenic missense mutations, were seen in combination with a second mutation, which raises questions with regards to their respective pathogenicity. Our data and discussion indicate the challenges of classifying missense mutations as pathogenic or benign and the value of co-segregation studies, as well as suggest that there may be hereditary hemorrhagic telangiectasia gene mutations that have only mild phenotypic effects. We present evidence to suggest that four missense mutations (ENG p.G331S, ENG p.L8P, ENG p.P452L and ACVRL1 p.C344R) are pathogenic, two novel mutations (ACVRL1 p.A311T and ENG p.S576G) are neutral, and two previously reported disease-causing mutations are benign or have suspected benign variants (ACVRL1 p.A482V and ENG p.V504M). We conclude that for the purpose of establishing a causative hereditary hemorrhagic telangiectasia mutation in a family proband, all exons and intron/exon borders of both genes should be sequenced and deletion/duplication analysis should be performed unless a mutation that is well-proven to be pathogenic is identified.

Ethnic differences in parental perceptions of genetic testing for deaf infants.

As genetic testing becomes an integral part of the evaluation of deaf infants and children, it is important to understand parental views on genetic testing. The purpose of this study is to examine parental reasons for, and beliefs about, genetic testing for deafness in early-identified infants, and to determine if they differ as a function of ethnicity. We present baseline data collected from 56 Caucasian, 59 Hispanic, and 24 Asian parents of deaf children participating in a longitudinal, prospective study on genetic testing for connexin-related deafness. The overall finding is that reasons for, and beliefs about, genetic testing for deafness varied as a function of ethnicity. Virtually all parents sought genetic testing to understand why their child is deaf. However, Asian and/or Hispanic parents were more likely than Caucasian parents to view family planning, helping with their child’s medical care, and helping the family as other important reasons for testing, and were more likely than Caucasian parents to perceive genetic testing to be useful for these purposes. Asian and Hispanic parents were more likely than Caucasian parents to perceive genetic testing in harmful terms. Genetic testing fulfills a cognitive need for parents to understand why their child is deaf, yet differences in responses suggest that Asian and Hispanic parents may seek testing for other purposes. Understanding different perspectives on genetic testing for deafness will enhance genetic counselors’ cultural competence and facilitate the pre-test genetic counseling session.

Radiographic and morphologic findings in a previously undescribed type of mesomelic dysplasia resembling atelosteogenesis type II

The mesomelic chondrodysplasias are a heterogeneous group of dwarfing disorders characterized by shortness of the middle segments of limbs. We report on a 25-week fetus with disproportionate shortness of limbs with an apparently distinct form of mesomelic dysplasia. Radiographic findings at necropsy included ulnar deviation of hands, talipes equinovarus, distal tapering of the humeri, and hypoplastic fibulae, radii, and ulnae. Chondro-osseous morphology showed mild shortness of the physeal columns, overgrowth of perichondral bone, peripheral ingrowth of mesenchymal cells into the physis, and numerous areas of fibrillar degeneration with rings of collagen surrounding the chondrocytes. Ultrastructural findings included a degenerated territorial matrix, pericellular halos of collagen, and dilated loops of rough endoplasmic reticulum in chondrocytes. The radiographic appearance of the long bones is distinct from that of previously described mesomelic dysplasias. The chondro-osseous morphologic findings and the distal tapering of the humerus are somewhat reminiscent of atelosteogenesis type II, but the pattern of matrix degeneration and the presence of inclusion bodies in the chondrocytes distinguish it from disorders of sulfate transport.

A case of lethal hypophosphatasia providing new insights into the perinatal benign form of hypophosphatasia and expression of the ALPL gene

Hypophosphatasia is a rare inherited bone disease caused by mutations in the alkaline phosphatase liver‐type gene (ALPL) gene, with extensive allelic heterogeneity leading to a range of clinical phenotypes. We report here a patient who died from severe lethal hypophosphatasia, who was compound heterozygous for the mutation c.1133A>T (D361V) and the newly detected missense mutation c791A>G, and whose parents were both healthy. Because the c.1133A>T (D361V) mutation was previously reported to have a dominant‐negative effect and to be responsible for the uncommon perinatal benign form of the disease, we studied the expression of the ALPL gene in this family. Analysis at the messenger RNA (mRNA) level, both quantitative and qualitative, showed that the paternal c.1133A>T (D361V) mutation was associated with over‐expression of the ALPL gene and that the maternal c.791A>G mutation lead to complete skipping of exon 7. The results provide an explanation of the lethal phenotype in the patient where the two ALPL alleles are non‐functional and in the asymptomatic father where over‐expression of the normal allele could counteract the effect of the c.1133A>T (D361V) mutation by providing an increased level of normal mRNA. This may also explain the variable expression of hypophosphatasia observed in parents of patients with the perinatal benign form.

Prenatal diagnosis of glucose-6-phosphate-dehydrogenase deficiency.

Prior to the development of the DNA-based technology reliable prenatal diagnosis of G6PD deficiency was not possible. We show that, using PCR amplification and restriction endonuclease digestion, prenatal diagnosis is possible. We have now been able to determine that the male fetus of a mother heterozygous for G6PD Mediterranean had inherited the maternal X chromosome with the normal G6PD gene.