Medical genetics and genomic medicine in the United States. Part 2: Reproductive genetics, newborn screening, genetic counseling, training, and registries.

Review of genetics in the United States with emphasis on the prenatal, metabolic, genetic counseling, and training aspects of the field.

Individualized iterative phenotyping for genome-wide analysis of loss-of-function mutations.

Next-generation sequencing provides the opportunity to practice predictive medicine based on identified variants. Putative loss-of-function (pLOF) variants are common in genomes and understanding their contribution to disease is critical for predictive medicine. To this end, we characterized the consequences of pLOF variants in an exome cohort by iterative phenotyping. Exome data were generated on 951 participants from the ClinSeq cohort and filtered for pLOF variants in genes likely to cause a phenotype in heterozygotes. 103 of 951 exomes had such a pLOF variant and 79 participants were evaluated. Of those 79, 34 had findings or family histories that could be attributed to the variant (28 variants in 18 genes), 2 had indeterminate findings (2 variants in 2 genes), and 43 had no findings or a negative family history for the trait (34 variants in 28 genes). The presence of a phenotype was correlated with two mutation attributes: prior report of pathogenicity for the variant (p = 0.0001) and prior report of other mutations in the same exon (p = 0.0001). We conclude that 1/30 unselected individuals harbor a pLOF mutation associated with a phenotype either in themselves or their family. This is more common than has been assumed and has implications for the setting of prior probabilities of affection status for predictive medicine.

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.

Human enamel phenotype associated with amelogenesis imperfecta and a kallikrein-4 (g.2142G>A) proteinase mutation.

Kallikrein-4 is known to be highly expressed during the maturation stage of enamel formation and is thought to be critical for the final phase of crystallite growth. The purpose of this study was to evaluate the enamel phenotype in humans with a known KLK-4 mutation (g.2142G>A). Primary teeth from two individuals with a known KLK-4 mutation were evaluated using amino acid analysis and light and electron microscopy. Light microscopy showed the enamel was of normal thickness but opaque throughout its width compared with normal enamel. Electron microscopy showed enamel affected by the KLK-4 mutation had a normal prismatic structure and generally had a well-organized and discernable crystallite composition. In some areas, globular structures were present where crystallites were not discernable or appeared to have an altered morphology. The KLK-4 mutant enamel had an increased protein content compared with normal enamel. Human enamel formed with a lack of functioning KLK-4 proteinase is altered primarily in the completeness of crystallite growth, while enamel thickness and prism structure remains essentially normal. Collectively, these studies suggest that the KLK-4 proteinase is essential for the final crystallite growth of enamel but is not critical for crystallite orientation, prism formation or enamel thickness.

Histone deacetylase activity is required for embryonic stem cell differentiation.

Mammalian development requires commitment of cells to restricted lineages, which requires epigenetic regulation of chromatin structure. Epigenetic modifications were examined during in vitro differentiation of murine embryonic stem (ES) cells. Global histone acetylation, a euchromatin marker, declines dramatically within 1 day of differentiation induction and partially rebounds by day 2. Histone H3-Lys9 methylation, a heterochromatin marker, increases during in vitro differentiation. Conversely, the euchromatin marker H3-Lys4 methylation transiently decreases, then increases to undifferentiated levels by day 4, and decreases by day 6. Global cytosine methylation, another heterochromatin marker, increases slightly during ES cell differentiation. Chromatin structure of the Oct4 and Brachyury gene promoters is modulated in concert with their pattern of expression during ES cell differentiation. Importantly, prevention of global histone deacetylation by treatment with trichostatin A prevents ES cell differentiation. Hence, ES cells undergo functionally important global and gene-specific remodeling of chromatin structure during in vitro differentiation. genesis 38:32-38, 2004.

Cloning and characterization of the gene encoding the mouse homologue of CpG binding protein.

Human CpG binding protein (CGBP) is a ubiquitously-expressed transcriptional activator that binds specifically to unmethylated CpG motifs. Several protein domains have been identified within CGBP including two plant homeodomains (PHD), acidic and basic regions, a coiled-coil domain, as well as a CXXC DNA-binding domain. The global function of CGBP remains unclear, although failure to express CGBP results in embryonic lethality in mice. This study reports the identification and characterization of the murine CGBP gene locus. A 2509 bp murine CGBP cDNA was cloned and nucleotide sequence determined. Comparison of the mouse and human CGBP sequences revealed 86% identity at the nucleotide level and 96% identity at the amino acid level. Examination of the deduced translation product revealed that the PHD, CXXC, coiled-coil, and basic domains are identical between mouse and human, while the acidic region exhibits approximately 90% identity with its human counterpart. A single murine CGBP transcript of approximately 2.6 kb was detected in a wide variety of adult tissues as well as embryonic stem cells. Analysis of the mouse gene locus revealed a relatively small gene spanning approximately 5 kb and comprised of 15 exons. Examination of the human CGBP gene showed a similar size and structure with identical intronic splice sites. In contrast to the human CGBP gene, which is located 800 bp upstream of the MBD1 gene, analysis of the murine CGBP gene locus failed to detect the murine MBD1 gene within several kilobases of the CGBP coding region.