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.

Recommendations of the 2006 Human Variome Project meeting.

Lists of variations in genomic DNA and their effects have been kept for some time and have been used in diagnostics and research. Although these lists have been carefully gathered and curated, there has been little standardization and coordination, complicating their use. Given the myriad possible variations in the estimated 24,000 genes in the human genome, it would be useful to have standard criteria for databases of variation. Incomplete collection and ascertainment of variants demonstrates a need for a universally accessible system. These and other problems led to the World Heath Organization-cosponsored meeting on June 20-23, 2006 in Melbourne, Australia, which launched the Human Variome Project. This meeting addressed all areas of human genetics relevant to collection of information on variation and its effects. Members of each of eight sessions (the clinic and phenotype, the diagnostic laboratory, the research laboratory, curation and collection, informatics, relevance to the emerging world, integration and federation and funding and sustainability) developed a number of recommendations that were then organized into a total of 96 recommendations to act as a foundation for future work worldwide. Here we summarize the background of the project, the meeting and its recommendations.

Ambiguous genitalia: what prenatal genetic testing is practical?

Concern for ambiguous genitalia or chromosome-phenotype discordance detected in a prenatal setting has increased over the last two decades. Practitioners faced with this prenatal finding have a variety of genetic tests available to them; however, it is unclear to what extent prenatal testing for disorders of sex development (DSD) is useful or practical. We undertook a retrospective review of the medical records of 140 individuals evaluated through the DSD clinic at Seattle Children's Hospital with birthdates from 01/01/1994 through 08/16/2011 to determine the rate of prenatal detection of ambiguous genitalia in individuals with DSD, what prenatal diagnostic workup was undertaken, and the postnatal outcome, including whether a postnatal genetic diagnosis was confirmed. Of all 140 subjects, 34 (24%) were identified prenatally. The most common postnatal diagnoses were penoscrotal hypospadias with transposition of the scrotum with no known genetic cause (24/140; 17%) and 21-hydroxylase deficiency (20/140; 14%). Apart from these, no single diagnosis comprised more than a few cases. Prenatal diagnostic testing varied widely, from no tests to multiple molecular tests with amniotic fluid hormone concentrations. In the absence of other fetal anomalies or growth retardation on ultrasound, prenatal karyotype with fluorescence in situ hybridization for the SRY gene is the most useful test when ambiguous genitalia is suspected. Further prenatal testing for Smith-Lemli-Opitz syndrome in 46,XY individuals and congenital adrenal hyperplasia in 46,XX individuals may be considered. However, targeted molecular testing for rare DSD conditions in the absence of a family history of DSD has a low yield.

Implementation outcomes of a multiinstitutional web-based ethical, legal, and social implications genetics curriculum for primary care residents in three specialties.

PURPOSE: Medical genetics lends itself to disseminated teaching methods because of mismatches between numbers of physicians having patients with genetic disorders and availability of genetic specialists. METHOD: During 3 years, we implemented an interactive, web-based curriculum on ethical, legal, and social implications in medical genetics for primary care residents in three specialties at three institutions. Residents took five (of 10) cases and three (of five) tutorials that varied by specialty. We assessed changes in self-efficacy (primary outcome), knowledge, application, and viewpoints. RESULTS: Overall enrollment was 69% (279/403). One institution did not complete implementation and was dropped from pre-post comparisons. We developed a six-factor ethical, legal, and social implications self-efficacy scale (Cronbach α = 0.95). Baseline self-efficacy was moderate (71/115; range: 23-115) and increased 15% after participation. Pre-post knowledge scores were high and unchanged. Residents reported that this curriculum covered ethical, legal, and social implications/genetics better than their usual curricula. Most (68-91%) identified advantages, especially in providing flexibility and stimulating self-directed learning. After participation, residents reported creating learning goals (66%) and acting on those goals (62%). CONCLUSIONS: Ethical, legal, and social implications genetics curricular participation led to modest self-efficacy gains. Residents reported that the curriculum covered unique content areas, had advantages over traditional curriculum, and that they applied ethical, legal, and social implications content clinically. We share lessons from developing and implementing this complex web-based curriculum across multiple institutions.

Genome-wide association studies, field synopses, and the development of the knowledge base on genetic variation and human diseases.

Genome-wide association studies (GWAS) have led to a rapid increase in available data on common genetic variants and phenotypes and numerous discoveries of new loci associated with susceptibility to common complex diseases. Integrating the evidence from GWAS and candidate gene studies depends on concerted efforts in data production, online publication, database development, and continuously updated data synthesis. Here the authors summarize current experience and challenges on these fronts, which were discussed at a 2008 multidisciplinary workshop sponsored by the Human Genome Epidemiology Network. Comprehensive field synopses that integrate many reported gene-disease associations have been systematically developed for several fields, including Alzheimer's disease, schizophrenia, bladder cancer, coronary heart disease, preterm birth, and DNA repair genes in various cancers. The authors summarize insights from these field synopses and discuss remaining unresolved issues -- especially in the light of evidence from GWAS, for which they summarize empirical P-value and effect-size data on 223 discovered associations for binary outcomes (142 with P < 10(-7)). They also present a vision of collaboration that builds reliable cumulative evidence for genetic associations with common complex diseases and a transparent, distributed, authoritative knowledge base on genetic variation and human health. As a next step in the evolution of Human Genome Epidemiology reviews, the authors invite investigators to submit field synopses for possible publication in the American Journal of Epidemiology.

Clinician perspectives about molecular genetic testing for heritable conditions and development of a clinician-friendly laboratory report.

The use of molecular genetic tests for heritable conditions is expected to increase in medical settings, where genetic knowledge is often limited. As part of a project to improve the clarity of genetic test result reports to minimize misunderstandings that could compromise patient care, we sought input about format and content from practicing primary care clinicians. In facilitated workgroup discussions, clinicians from pediatric, obstetrics-gynecology, and family practice provided their perspectives about molecular genetic testing with a focus on the laboratory reporting of test results. Common principles for enhancing the readability and comprehension of test result reports were derived from these discussions. These principles address the presentation of patient- and test-specific information, the test result interpretation, and guidance for future steps. Model test result reports for DNA-based cystic fibrosis testing are presented that were developed based on workgroup discussions, previous studies, and professional guidelines. The format of these model test reports, which are applicable to a variety of molecular genetic tests, should be useful for communicating essential information from the laboratory to health care professionals.

Ordering molecular genetic tests and reporting results: practices in laboratory and clinical settings.

Previous studies have suggested that patient care may be compromised as a consequence of poor communication between clinicians and laboratory professionals in cases in which molecular genetic test results are reported. To understand better the contributing factors to such compromised care, we investigated both pre- and postanalytical processes using cystic fibrosis mutation analysis as our model. We found that although the majority of test requisition forms requested patient/family information that was necessary for the proper interpretation of test results, in many cases, these data were not provided by the individuals filling out the forms. We found instances in which result reports for simulated diagnostic testing described individuals as carriers where only a single mutation was found with no comment pertaining to a diagnosis of cystic fibrosis. Similarly, reports based on simulated scenarios for carrier testing were problematic when no mutations were identified, and the patient's race/ethnicity and family history were not discussed in reference to residual risk of disease. Remarkably, a pilot survey of obstetrician-gynecologists revealed that office staff, including secretaries, often helped order genetic tests and reported test results to patients, raising questions about what efforts are undertaken to ensure personnel competency. These findings are reviewed in light of what efforts should be taken to improve the quality of test-ordering and result-reporting practices.

A model program to increase translation of rare disease genetic tests: collaboration, education, and test translation program.

In 2006, The National Institutes of Health Office of Rare Diseases announced the Collaboration, Education, and Test Translation (CETT) Program, a pilot project to increase and improve the translation of genetic tests for rare diseases from research laboratories to clinical laboratories. The CETT Program created a new paradigm in which applicants must form a collaborative group consisting of a clinical laboratory, researcher, research laboratory, clinical expert, and disease-specific advocacy group. In addition, each collaborative group must assure that test results are written in a style and format appropriate for nonexpert clinicians; provide educational materials for clinicians and patients about the disease, as well as the use and limitations of the test in the care of persons with the disease; agree to collect clinical data necessary for test result interpretation; and store genotype information and clinical data in a publicly accessible deidentified database.

GeneTests: an online genetic information resource for health care providers.

OBJECTIVE: This paper describes the GeneTests genetic testing information resource with a focus on the GeneReviews component. METHODS AND FINDINGS: The need for authoritative genetic testing information and issues in the development and maintenance of GeneReviews are discussed: Hampered by lack of currency and content deficits, traditional medical information resources such as textbooks and the published literature are generally inadequate sources of genetic testing information. Problems encountered in developing GeneReviews include the evolution of new authorship models and academic and genetics professionals' skepticism about the quality of Web-based publications. CONCLUSIONS: GeneTests is an authoritative, highly used, and well-regarded resource in the international medical community that is intended for health care providers. Future development issues to address include ways to (1) manage the increasing editing and updating load as content grows and (2) address technical and content issues that need to be considered in displaying GeneReviews as a "just in time" resource in the electronic medical record to achieve the project goal of integrating appropriate use of genetic testing into patient care.

Genetic testing for disease susceptibilities: consequences for genetic counseling.

The role of genetic counseling in future testing for inherited susceptibilities for common diseases is debated. Currently, genetic testing, ideally supported by genetic counseling, is most often used to modify the assessment of genetic risk of Mendelian-inherited disease in high-risk individuals for the purpose of personal decision-making. By contrast, it is anticipated that genetic testing will be used to identify increased disease susceptibility in low-risk individuals for the purpose of instituting medical or lifestyle interventions to modify risk for future disease.

GeneTests-GeneClinics: genetic testing information for a growing audience.

The development and usage of two companion NIH-funded genetic testing information databases, GeneTests (www.genetests.org) and GeneClinics (www.geneclinics.org), now merged into one web site, reflect the steadily increasing use of genetic testing and the expanding audience for genetic testing information. Established in 1993 as Helix, a genetics laboratory directory of approximately 110 listings, GeneTests has grown into a database of over 900 tests for inherited diseases, a directory of over 500 international laboratories, a directory of over 1,000 U.S. and international genetics clinics, and a resource for educational/teaching materials and reports of summary genetic test data. GeneClinics, founded in 1997 as an expert-authored, peer-reviewed, disease-specific knowledge base relating genetic testing to patient care, has grown steadily, now containing over 130 expert-authored, peer-reviewed full-text entries relating genetic testing information to diagnosis, management, and genetic counseling of specific inherited diseases. In spring 2001 the two databases were merged and in October 2001 the two web sites were merged for the purpose of seamless navigation into the GeneTests-GeneClinics site (www.genetests.org or www.geneclinics.org); the GeneClinics knowledge base was renamed "GeneReviews" to avoid confusion with the U.S. and international clinic directories. As genetic testing has moved steadily out of research venues and into routine medical practice, the user audience for these databases has become international and expansive and includes healthcare providers, patients, educators, policy makers, and the media. The use of these combined resources has grown to approximately 3,200 visits/day.

Micropenis with testicular regression, low LH levels, and poor androgen and HCG responses: a distinct syndrome?

We report three boys, including two brothers, with micropenis and poor phallic growth in response to both exogenous human chorionic gonadotropin (HCG) and testosterone therapy in the newborn period. They exhibited low neonatal testosterone levels that failed to respond to HCG stimulation. These boys displayed a unique gonadotropin profile with reduced luteinizing hormone levels and elevated follicle-stimulating hormone levels. They had small, cryptorchid testes with subsequent testicular regression and atrophy. Moreover, all three boys have developed microcephaly and mild learning delays. We review the hormonal profiles and phenotypes of known causes of micropenis, and compare them to the features of our three patients. Although individuals with similar features may have been described in past series of males with micropenis, the data presented previously were insufficient for classification; thus, we propose that our patients may represent a distinct, not previously recognized, syndrome with either X-linked recessive inheritance or autosomal recessive inheritance with male sex limitation.

Molecular genetic testing for inherited disorders.

This review focuses on molecular genetic testing for heritable disorders. Molecular genetic testing has generated tremendous interest because of the scientific and social hype surrounding the Human Genome Project, the accelerating rate of gene discovery, the quick transition of scientific discoveries into clinically applicable genetic tests and the unique nonmedical applications of genetic testing. All of these developments have been superimposed upon increasing individual autonomy in medical care and the pervasive information-seeking behavior of the Information Age.

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.

A Gender Assessment Team: experience with 250 patients over a period of 25 years.

PURPOSE: To describe a Gender Assessment Team that has provided a multidisciplinary approach to the diagnosis, medical and surgical treatment, genetic counseling, and psychosocial support of patients with ambiguous genitalia, intersex disorders, and other genital anomalies, collectively termed disorders of sex development; and to determine the major diagnostic categories and approach. METHODS: A retrospective review of 250 patients evaluated by the Team at Children's Hospital and Regional Medical Center in Seattle, WA, from January 1981 through December 2005. The Team included the following specialties: medical genetics, cytogenetics, gynecology, pediatric urology, endocrinology, and psychiatry. RESULTS: Of the subjects, 177 were infants, 46 were children or adolescents, and 27 had a multisystem genetic condition. The most common diagnoses were congenital adrenal hyperplasia (14%), androgen insensitivity syndrome (10%), mixed gonadal dysgenesis (8%), clitoral/labial anomalies (7%), hypogonadotropic hypogonadism (6%), and 46,XY small-for-gestational-age males with hypospadias (6%). CONCLUSION: The six most common diagnoses comprised 50% of the cohort. The expertise of a multidisciplinary team allowed for integrated care for patients with disorders of sex development and identification of novel conditions. Geneticists play an important role in a team approach through knowledge of genetic testing options and diagnosis of patients with karyotypic abnormalities and syndromes with genital anomalies.

Internet resources in Medical Genetics.

This unit presents an overview of the most commonly used, Web-based information resources for (1) clinicians seeking to apply molecular genetic testing to patient care (see GeneTests) or to understand the molecular basis of inherited diseases (see OMIM), (2) consumers seeking advocacy information (see Genetic Alliance) or scientific and management information (see The Genetics Home Reference, The Genetics Education Center, The Family Village, NOAH, NORD, and Genes and Diseases), and (3) genetics professional societies.

Molecular and clinical analyses of Greig cephalopolysyndactyly and Pallister-Hall syndromes: robust phenotype prediction from the type and position of GLI3 mutations.

Mutations in the GLI3 zinc-finger transcription factor gene cause Greig cephalopolysyndactyly syndrome (GCPS) and Pallister-Hall syndrome (PHS), which are variable but distinct clinical entities. We hypothesized that GLI3 mutations that predict a truncated functional repressor protein cause PHS and that functional haploinsufficiency of GLI3 causes GCPS. To test these hypotheses, we screened patients with PHS and GCPS for GLI3 mutations. The patient group consisted of 135 individuals: 89 patients with GCPS and 46 patients with PHS. We detected 47 pathological mutations (among 60 probands); when these were combined with previously published mutations, two genotype-phenotype correlations were evident. First, GCPS was caused by many types of alterations, including translocations, large deletions, exonic deletions and duplications, small in-frame deletions, and missense, frameshift/nonsense, and splicing mutations. In contrast, PHS was caused only by frameshift/nonsense and splicing mutations. Second, among the frameshift/nonsense mutations, there was a clear genotype-phenotype correlation. Mutations in the first third of the gene (from open reading frame [ORF] nucleotides [nt] 1-1997) caused GCPS, and mutations in the second third of the gene (from ORF nt 1998-3481) caused primarily PHS. Surprisingly, there were 12 mutations in patients with GCPS in the 3' third of the gene (after ORF nt 3481), and no patients with PHS had mutations in this region. These results demonstrate a robust correlation of genotype and phenotype for GLI3 mutations and strongly support the hypothesis that these two allelic disorders have distinct modes of pathogenesis.

Loss of DNA-dependent dimerization of the transcription factor SOX9 as a cause for campomelic dysplasia.

Campomelic dysplasia (CD) is a semilethal osteochondrodysplasia, characterized by skeletal anomalies that include bending of the long bones, and by XY sex reversal. CD results from haploinsufficiency for the transcription factor SOX9, a key regulator at various steps of cartilage differentiation and of early testis development. Two functional domains are so far recognized for SOX9, a high-mobility group (HMG) DNA-binding domain and a C-terminal transactivation domain. We present two CD patients with de novo mutations in a conserved region preceding the HMG domain. A long-term survivor with the acampomelic form of CD has an A76E amino acid substitution, while a severely affected CD patient had an in-frame deletion of amino acid residues 66-75. The conserved domain has been shown to function in the related transcription factor SOX10 as a DNA-dependent dimerization domain. We show that, like SOX10, SOX9 also binds cooperatively as a dimer to response elements in regulatory regions of some target genes such as the cartilage genes Col11a2 and CD-Rap. Dimerization and the resulting capacity to activate promoters via dimeric binding sites is lost in both mutant SOX9 proteins while other features involved in SOX9 function remained unaltered. These findings establish the dimerization domain as the third domain essential for SOX9 function during chondrogenesis.