The relationship between performance on the medical genetics and genomics in-training and certifying examinations.

PURPOSE: The American Board of Medical Genetics and Genomics (ABMGG) certifying examinations (CEs) are designed to assess relevant basic knowledge, clinical knowledge, and diagnostic skills of board-eligible candidates in primary specialty areas. The ABMGG in-training examinations (ITEs) provide formative feedback regarding knowledge and learning over time and assess readiness to attempt board certification. This study addresses the validity of the ABMGG ITE by evaluating its relationship with performance on CE utilizing established psychometric approaches. METHODS: Statistical analysis included bivariate Pearson correlation coefficients and linear regression to evaluate the strength of associations between ITE scores and CE scores. Logistic regression was used to assess the association between ITE scores and the probability of passing each CE. RESULTS: Logistic regression results indicated that ITE scores accounted for 22% to 44% of the variability in CE outcomes. Across 3 certification cycles, for every 1-point increase in ITE scores, the odds ratio for earning a passing score increased by a factor of 1.12 to 1.20 for the general CE, 1.14 to 1.25 for the clinical CE, and 1.12 to 1.20 for the laboratory CEs. CONCLUSION: The findings show a positive correlation between performance on the ITE examination and performance on and passing the ABMGG CE.

Training the next generation of genomic medicine providers: trends in medical education and national assessment.

PURPOSE: To assess the utilization of genetics on the United States Medical Licensing Examination (USMLE®). METHODS: A team of clinical genetics educators performed an analysis of the representation of genetics content on a robust sample of recent Step 1, Step 2 Clinical Knowledge (CK), and Step 3 examination forms. The content of each question was mapped to curriculum recommendations from the peer reviewed Association of Professors of Human and Medical Genetics white paper, Medical School Core Curriculum in Genetics, and the USMLE Content Outline. RESULTS: The committee identified 13.4%, 10.4%, and 4.4% of Steps 1, 2 and 3 respectively, as having genetics content. The genetics content of the exams became less pertinent to the questions from Step 1 to 3, with decreasing genetics content by exam and increasing percentages of questions identified as having genetics content in the distractors only. CONCLUSION: The current distribution of genetics in USMLE licensing examinations reflects traditional curricular approaches with genetics as a basic science course in the early years of medical school and de-emphasizes clinical relevance of the field. These observations support the notion that further integration is required to move genetics into the clinical curriculum of medical schools and the clinical content of USMLE Step exams.

Targeted exome analysis identifies the genetic basis of disease in over 50% of patients with a wide range of ataxia-related phenotypes.

PURPOSE: To examine the impact of a targeted exome approach for the molecular diagnosis of patients nationwide with a wide range of ataxia-related phenotypes. METHODS: One hundred and seventy patients with ataxia of unknown etiology referred from clinics throughout the United States and Canada were studied using a targeted exome approach. Patients ranged in age from 2 to 88 years. Analysis was focused on 441 curated genes associated with ataxia and ataxia-like conditions. RESULTS: Pathogenic and suspected diagnostic variants were identified in 88 of the 170 patients, providing a positive molecular diagnostic rate of 52%. Forty-six different genes were implicated, with the six most commonly mutated genes being SPG7, SYNE1, ADCK3, CACNA1A, ATP1A3, and SPTBN2, which accounted for >40% of the positive cases. In many cases a diagnosis was provided for conditions that were not suspected and resulted in the broadening of the clinical spectrum of several conditions. CONCLUSION: Exome sequencing with targeted analysis provides a high-yield approach for the genetic diagnosis of ataxia-related conditions. This is the largest targeted exome study performed to date in patients with ataxia and ataxia-like conditions and represents patients with a wide range of ataxia phenotypes typically encountered in neurology and genetics clinics.

The natural history of phytosterolemia: Observations on its homeostasis.

BACKGROUND AND AIMS: Phytosterolemia is a rare genetic disease caused by mutation of the ABCG5/8 gene. Our aim was to elucidate the natural history and homeostasis of phytosterolemia. METHODS: We analyzed a Hutterite kindred consisting of 21 homozygotes with phytosterolemia assembled over a period of two decades, all of whom carried the ABCG8 S107X mutation and were treated with ezetimibe. RESULTS: Most of these subjects were asymptomatic and devoid of clinical stigmata, and this, since they were ascertained primarily by a process of cascade testing, suggests that, relative to its true prevalence, phytosterolemia is a condition of low morbidity. All subjects have responded well to treatment with ezetimibe. Initial (pre-treatment) and post-ezetimibe levels of cholesterol and sitosterol were measured and percentage changes on ezetimibe were calculated. We found initial levels to be inversely related to subjects' ages as were percentage responses to ezetimibe therapy. There was also a direct correlation between initial levels and percentage responses to ezetimibe. Hence on-treatment levels were very uniform. CONCLUSIONS: This evidence of a link with age leads us to propose that an age-related change in cholesterol and sterol homeostasis occurs at puberty in phytosterolemia and that the change is due to high sterol and/or stanol levels causing feedback inhibition of sterol regulatory element-binding protein (SREBP-2) processing. This would explain the well-documented phenomenon of depressed cholesterol synthesis in phytosterolemia. It is also well-known that LDL-receptor activity is increased, and this feasibly explains reduced LDL levels and consequent reduction of plasma cholesterol and sitosterol levels. Downregulated SREBP-2 processing would be expected to also lower proprotein convertase subtilisin/kexin type 9 (PCSK9) levels and this would explain high LDL-receptor activity. The above state could be termed disrupted homeostasis and the alternative, seen mostly in children and characterized by hypercholesterolemia and hypersterolemia, simple homeostasis.

Recommendations for the integration of genomics into clinical practice.

The introduction of diagnostic clinical genome and exome sequencing (CGES) is changing the scope of practice for clinical geneticists. Many large institutions are making a significant investment in infrastructure and technology, allowing clinicians to access CGES, especially as health-care coverage begins to extend to clinically indicated genomic sequencing-based tests. Translating and realizing the comprehensive clinical benefits of genomic medicine remain a key challenge for the current and future care of patients. With the increasing application of CGES, it is necessary for geneticists and other health-care providers to understand its benefits and limitations in order to interpret the clinical relevance of genomic variants identified in the context of health and disease. New, collaborative working relationships with specialists across diverse disciplines (e.g., clinicians, laboratorians, bioinformaticians) will undoubtedly be key attributes of the future practice of clinical genetics and may serve as an example for other specialties in medicine. These new skills and relationships will also inform the development of the future model of clinical genetics training curricula. To address the evolving role of the clinical geneticist in the rapidly changing climate of genomic medicine, two Clinical Genetics Think Tank meetings were held that brought together physicians, laboratorians, scientists, genetic counselors, trainees, and patients with experience in clinical genetics, genetic diagnostics, and genetics education. This article provides recommendations that will guide the integration of genomics into clinical practice.Genet Med 18 11, 1075-1084.

BATTEN DISEASE CAUSED BY A NOVEL MUTATION IN THE PPT1 GENE.

PURPOSE: To report a case of Batten disease due to a previously unreported mutation in PPT1. METHODS: A 9-year-old girl presented with classic clinical findings of Batten Disease. RESULTS: Genetic testing for the mutations in the most common Batten disease gene, CLN3, was negative. Evaluation of a panel of genes known to be implicated in neuronal ceroid lipofuscinoses revealed disease causing mutations in PPT1, one of which was novel. CONCLUSION: Mutations in PPT1 typically cause the infantile form of neuronal ceroid lipofuscinosis. Clinical diagnosis of the juvenile form of neuronal ceroid lipofuscinosis, Batten disease, should still be considered in cases with negative CLN3 genetic testing. Batten disease can occur due to genetic heterogeneity. Testing of other members of the neuronal ceroid lipofuscinosis gene family can lead to confirmation of the correct diagnosis.

A Review of Fanconi Anemia for the Practicing Pediatrician.

Early recognition of a patient who might have Fancomi anemia by the general pediatrician and referral to a tertiary care center with a dedicated cancer risk program is critical for early diagnosis. Genetic testing and close multidisciplinary surveillance is required for patients with this syndrome and their families because of its multisystem involvement and propensity for early-onset bone marrow failure and leukemic transformation. This article reviews the clinical symptoms and signs, radiologic findings, and screening guidelines of FA for the general pediatrician.

Disclosure of genetic research results to members of a founder population.

There is currently extensive discussion and debate in the literature on how, when, and to whom genetic research results should be returned (see Genetics in Medicine, April 2012 issue). Here, we describe our experience in disclosing genetic information on Mendelian disorders discovered during the course of our research in the Hutterites. We first assessed attitudes toward the disclosure of carrier results, which revealed that many individuals wanted carrier information and that many intended to use the information in family planning. Based on this information, we developed a pilot study to test and disclose cystic fibrosis (CF) carrier status. Next, a larger scale project was developed in order to disclose genetic research results for 14 diseases to those interested in receiving the information. We developed brochures, offered a live interactive educational program, conducted a consent process, and disclosed results in letters mailed to the consented individuals. Overall, ~80% of individuals who participated in the educational program signed consent forms for the release of their results for 14 diseases. We describe our experience with returning individual genetic research results to participants in a population-based research study.

Professional medical education and genomics.

Genomic medicine is a relatively new concept that involves using individual patients' genomic results in their clinical care. Genetic technology has advanced swiftly over the past decade, and most providers have been left behind without an understanding of this complex field. To realize its full potential, genomic medicine must be both understood and accepted by the greater medical community. The current state of professional medical education in genomics and genomic medicine is reviewed, including ongoing plans to expand educational efforts for medical students, clinical geneticists, and nongeneticist physicians.

Internet resources in medical genetics.

This unit presents an overview of the most commonly used Web-based information resources for clinicians seeking to apply molecular or array-based genetic testing to patient care, learn more about newborn screening, or understand the molecular basis of inherited diseases. It is also for consumers seeking advocacy or scientific/management information, and for genetics professional societies.

Reciprocal deletion and duplication at 2q23.1 indicates a role for MBD5 in autism spectrum disorder.

Copy number variations associated with abnormal gene dosage have an important role in the genetic etiology of many neurodevelopmental disorders, including intellectual disability (ID) and autism. We hypothesize that the chromosome 2q23.1 region encompassing MBD5 is a dosage-dependent region, wherein deletion or duplication results in altered gene dosage. We previously established the 2q23.1 microdeletion syndrome and report herein 23 individuals with 2q23.1 duplications, thus establishing a complementary duplication syndrome. The observed phenotype includes ID, language impairments, infantile hypotonia and gross motor delay, behavioral problems, autistic features, dysmorphic facial features (pinnae anomalies, arched eyebrows, prominent nose, small chin, thin upper lip), and minor digital anomalies (fifth finger clinodactyly and large broad first toe). The microduplication size varies among all cases and ranges from 68 kb to 53.7 Mb, encompassing a region that includes MBD5, an important factor in methylation patterning and epigenetic regulation. We previously reported that haploinsufficiency of MBD5 is the primary causal factor in 2q23.1 microdeletion syndrome and that mutations in MBD5 are associated with autism. In this study, we demonstrate that MBD5 is the only gene in common among all duplication cases and that overexpression of MBD5 is likely responsible for the core clinical features present in 2q23.1 microduplication syndrome. Phenotypic analyses suggest that 2q23.1 duplication results in a slightly less severe phenotype than the reciprocal deletion. The features associated with a deletion, mutation or duplication of MBD5 and the gene expression changes observed support MBD5 as a dosage-sensitive gene critical for normal development.

RUNX2 quadruplication: additional evidence toward a new form of syndromic craniosynostosis.

The RUNX2 transcription factor regulates osteoblast differentiation. Its absence, as with cleidocranial dysplasia, results in deficient bone formation. However, its excess seems to follow a dose response of over ossification. RUNX2 duplications (3 copies) are exceedingly rare but have been reported to cause craniosynostosis. There are no existing reports of quadruplications (4 copies). We present a case study of a boy with an atypical skull deformity with pan-craniosynostosis whose microarray analysis revealed 4 copies of a 1.24-Mb region from 6p12.3 to 6p21.1 containing the RUNX2 gene. Further characterization of this osteogenic pathway may aid in our understanding of the pathogenesis and subsequent prevention and treatment of syndromic craniosynostosis.

A population-based study of autosomal-recessive disease-causing mutations in a founder population.

The decreasing cost of whole-genome and whole-exome sequencing has resulted in a renaissance for identifying Mendelian disease mutations, and for the first time it is possible to survey the distribution and characteristics of these mutations in large population samples. We conducted carrier screening for all autosomal-recessive (AR) mutations known to be present in members of a founder population and revealed surprisingly high carrier frequencies for many of these mutations. By utilizing the rich demographic, genetic, and phenotypic data available on these subjects and simulations in the exact pedigree that these individuals belong to, we show that the majority of mutations were most likely introduced into the population by a single founder and then drifted to the high carrier frequencies observed. We further show that although there is an increased incidence of AR diseases overall, the mean carrier burden is likely to be lower in the Hutterites than in the general population. Finally, on the basis of simulations, we predict the presence of 30 or more undiscovered recessive mutations among these subjects, and this would at least double the number of AR diseases that have been reported in this isolated population.

Evidence of a mechanism for isodicentric chromosome Y formation in a 45,X/46,X,idic(Y)(p11.31)/46,X,del(Y)(p11.31) mosaic karyotype.

Abnormalities involving sex chromosomes account for approximately 0.5% of live births. The phenotypes of individuals with mosaic cell lines having structural aberrations of the X and Y chromosomes are variable and hard to accurately predict. Phenotypes associated with sex chromosome mosaicism range from Turner syndrome to males with infertility, and often present with ambiguous genitalia. Previous studies of individuals with an 45,X/46,X,idic(Y)(p11) karyotype suggest that the presence of both cell lines should result from an intermediate, 46,XY cell line. Here we report a 2.5 year old female with phenotypic features of Turner syndrome with an isodicentric Y chromosome and a cell line with a deleted Y with a final karyotype of 45,X/46,X,idic(Y)(p11.31)/46,X,del(Y)(p11.31). Fluorescence in situ hybridization (FISH) mapping of the Y chromosome breakpoint revealed very low percentages of the deleted Y cells, but suggested a potential mechanism for the formation of the isodicentric Y chromosome. To our knowledge, the 46,X,del(Y) intermediate cell line in our patient has not been previously reported in individuals with mosaic sex chromosome structural abnormalities.

Expanding newborn screening for lysosomal disorders: opportunities and challenges.

Newborn screening (NBS), since its implementation in the 1960s, has traditionally been successful in reducing mortality and disability in children with a range of different conditions. Lysosomal storage disorders (LSD) are a heterogeneous group of inherited metabolic diseases that result from lysosomal dysfunction. Based on available treatment and suitable screening methods, the LSDs that are considered for NBS generally include Fabry, Gaucher, Krabbe, MPSI, MPSII, MPSV, Metachromatic leukodystrophy, Niemann-Pick, and Pompe. Utilizing traditional and expanded criteria for consideration of NBS leads to a set of fundamental questions that need to be explored when considering the opportunities and challenges of adding LSDs to NBS panels.

Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies.

Chromosomal microarray (CMA) is increasingly utilized for genetic testing of individuals with unexplained developmental delay/intellectual disability (DD/ID), autism spectrum disorders (ASD), or multiple congenital anomalies (MCA). Performing CMA and G-banded karyotyping on every patient substantially increases the total cost of genetic testing. The International Standard Cytogenomic Array (ISCA) Consortium held two international workshops and conducted a literature review of 33 studies, including 21,698 patients tested by CMA. We provide an evidence-based summary of clinical cytogenetic testing comparing CMA to G-banded karyotyping with respect to technical advantages and limitations, diagnostic yield for various types of chromosomal aberrations, and issues that affect test interpretation. CMA offers a much higher diagnostic yield (15%-20%) for genetic testing of individuals with unexplained DD/ID, ASD, or MCA than a G-banded karyotype ( approximately 3%, excluding Down syndrome and other recognizable chromosomal syndromes), primarily because of its higher sensitivity for submicroscopic deletions and duplications. Truly balanced rearrangements and low-level mosaicism are generally not detectable by arrays, but these are relatively infrequent causes of abnormal phenotypes in this population (<1%). Available evidence strongly supports the use of CMA in place of G-banded karyotyping as the first-tier cytogenetic diagnostic test for patients with DD/ID, ASD, or MCA. G-banded karyotype analysis should be reserved for patients with obvious chromosomal syndromes (e.g., Down syndrome), a family history of chromosomal rearrangement, or a history of multiple miscarriages.

SMC1A expression and mechanism of pathogenicity in probands with X-Linked Cornelia de Lange syndrome.

Cornelia de Lange Syndrome (CdLS) is a dominantly inherited heterogeneous genetic disorder with multisystem abnormalities. Sixty percent of probands with CdLS have heterozygous mutations in the Nipped-B-like (NIPBL) gene, 5% have mutations in the SMC1A gene, and one proband was found to have a mutation in the SMC3 gene. Cohesin is a multisubunit complex consisting of a SMC1A and SMC3 heterodimer and two non-SMC subunits. SMC1A is located on the human X chromosome and is reported to escape X inactivation. Twenty-nine unrelated CdLS probands with 21 unique SMC1A mutations have been identified including seven males. All mutations identified to date are either missense or small deletions, with all presumably preserving the protein open reading frame. Both wild-type and mutant alleles are expressed. Females quantitatively express twice the amount of SMC1A mRNA compared to males. The transcriptional profiling of 23 selected genes is different in SMC1A mutant probands, controls, and NIPBL mutant probands. These results suggest that mechanistically SMC1A-related CdLS is not due to altered levels of the SMC1A transcript, but rather that the mutant proteins maintain a residual function in males and enact a dominant negative effect in females.

Internet resources in medical genetics.

This unit presents an overview of the most commonly used Web-based information resources for clinicians seeking to apply molecular or array-based genetic testing to patient care, obtain information on metabolic disease testing, learn more about newborn screening, or understand the molecular basis of inherited diseases, as well as for consumers seeking advocacy or scientific/management information, and also for genetics professional societies.