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PubMed1985

The effect of Mendelian disease on human health: a measurement.

We describe an attempt to measure effects of Mendelian phenotypes on human health (homeostasis) in man. We used the McKusick Catalogs as the source for descriptions of autosomal dominant, recessive, and X-linked phenotypes. Three hundred and fifty one entries (76% of the initial sample) were disadaptive causing an impairment, disability, or handicap. (Terms used are in accordance with World Health Organization (WHO) definitions.) Phenotypic effects were scored to measure impact on life-span, reproductive capability, and psychosocial characteristics. We found 1) 25% of the disadaptive Mendelian phenotypes were apparent at birth and over 90% by the end of puberty; age at onset is unimodal in distribution for autosomal recessive and X-linked diseases, and trimodal for autosomal dominant (with modes during morphogenesis, infancy, and early adult life); 2) 58% of phenotypes involved more than one anatomical or functional system; autosomal dominants were more likely to involve only a single system; 3) life-span was reduced in 57%, particularly in those with onset in pre- or intra-reproductive life, and more often in recessive and X-linked diseases (data corrected for genetic lethals); prognosis varied with system involvement; 4) reproductive capability was impaired in 69% of phenotypes; and 5) most phenotypes compatible with life beyond infancy caused psychosocial handicap and limited the access to schooling and work. These findings have implications for medical care.

Adaptation, Psychological↗
PubMed1985

The effect of Mendelian disease on human health. II: Response to treatment.

We describe an attempt to measure efficacy of treatment in the Mendelian diseases of man. We used the McKusick Catalogs to identify 351 single gene diseases. We scored the impact of each disease in seven phenotypic categories: lifespan, reproductive capability, somatic growth, intellectual development, learning ability, capacity to work, and cosmetic effect. We then scored the success of treatment in ameliorating each of these component manifestations separately and together. The response to treatment was slight in the whole sample (n = 351): lifespan was increased in 15%, reproductive capability in 11%, and social adaptation in 6%. We observed that the mutant gene product was known in only 15% of the conditions comprising our sample. Since the mutant polypeptide is known in most inborn errors of metabolism, the diseases of this type (n = 65) in our sample of Mendelian traits were studied separately. In each of the seven categories of phenotypic impact, only a few of the hereditary metabolic diseases responded in any degree to specific treatment: the treatment gave complete relief in 12%, there was a partial response in 40%, and none in the remaining 48%. These findings have implications for prognosis, genetic counseling, and medical care of patients with Mendelian disease.

Adaptation, Psychological↗
PubMed1990

Hereditary cranium bifidum and symmetric parietal foramina are the same entity.

Cranium bifidum is literally "cleft skull." Numerous reports describe the anatomy of this defect, and crude estimates of the population prevalence suggest it is a relatively infrequent occurrence. McKusick's catalog contains only one family with cranium bifidum but several familial reports of symmetrical parietal foramina. Available information indicates that cranium bifidum and symmetrical parietal foramina are inherited in an autosomal dominant fashion and occur in orientals, blacks, whites, and native Americans. Here we report on a family with serial radiographs that document ontogenic development of parietal foramina in late childhood and adulthood from apparent cranium bifidum and parietal foramina during infancy and early childhood. We conclude that these are the same entity, differentiated only by the time during life in which the defect is demonstrated.

Cranial Sutures↗
PubMed1991

New clinical aspects of hereditary mucoepithelial dysplasia.

Hereditary mucoepithelial dysplasia (HMD) is a multiepithelial disorder. It is transmitted as an autosomal dominant trait (McKusick: Mendelian Inheritance in Man-Catalogs of Autosomal Dominant, Autosomal Recessive, and X-Linked Phenotypes, 8th edition. Baltimore: The Johns Hopkins University Press, pp 499, 1988). HMD is characterized by variable combinations of lesions of skin, hair, orificial mucosa, gingiva, eyes, and lungs. In some previously described patients, the corneal and pulmonary lesions were progressive and led to blindness, recurrent pneumonia, and/or premature death. On light microscopy, the lesion is characterized by dyskeratosis, and, on electron microscopy, by a paucity of gap junctions and desmosomes. Here, we describe a new 5-generation kindred in which affected individuals had the same histologic characteristics but a somewhat different clinical spectrum and a more benign course. HMD should be considered in the differential diagnosis of childhood alopecia, follicular hyperkeratosis, keratoconjunctivitis, juvenile cataracts, gingival hyperemia, restrictive lung disease, and esophageal stenosis or webs.

Alopecia↗
PubMed1995

Femoral-facial syndrome--prenatal diagnosis--autosomal dominant inheritance.

Fetal micrognathia and short, bowed femora were found on a routine prenatal ultrasonogram. At birth, a cleft palate and the characteristic facial appearance confirmed the diagnosis of the femoral-facial syndrome. (The femoral-facial syndrome [McKusick 137840] was first delineated by Daentl et al. [1975: J Pediatr 86:197-211] and called the "femoral hypoplasia-unusual facies syndrome." We prefer the "femoral-facial syndrome" because it is shorter, more easily translated, and because the McKusick catalog is the most widely recognized standard of nomenclature.) A paternal great uncle, deceased at age 4 years, seems to have had the same condition.

Female↗
PubMed2005

Glial fibrillary acidic protein mutations in infantile, juvenile, and adult forms of Alexander disease.

Alexander disease is a progressive, usually fatal neurological disorder defined by the widespread and abundant presence in astrocytes of protein aggregates called Rosenthal fibers. The disease most often occurs in infants younger than 2 years and has been labeled a leukodystrophy because of an accompanying severe myelin deficit in the frontal lobes. Later onset forms have also been recognized based on the presence of abundant Rosenthal fibers. In these cases, clinical signs and pathology can be quite different from the infantile form, raising the question whether they share the same underlying cause. Recently, we and others have found pathogenic, de novo missense mutations in the glial fibrillary acidic protein gene in most infantile patients examined and in a few later onset patients. To obtain further information about the role of glial fibrillary acidic protein mutations in Alexander disease, we analyzed 41 new patients and another 3 previously described clinically, including 18 later onset patients. Our results show that dominant missense glial fibrillary acidic protein mutations account for nearly all forms of this disorder. They also significantly expand the catalog of responsible mutations, verify the value of magnetic resonance imaging diagnosis, indicate an unexpected male predominance for the juvenile form, and provide insights into phenotype-genotype relations.

Adolescent↗
PubMed2004

Functional porous coordination polymers.

The chemistry of the coordination polymers has in recent years advanced extensively, affording various architectures, which are constructed from a variety of molecular building blocks with different interactions between them. The next challenge is the chemical and physical functionalization of these architectures, through the porous properties of the frameworks. This review concentrates on three aspects of coordination polymers: 1). the use of crystal engineering to construct porous frameworks from connectors and linkers ("nanospace engineering"), 2). characterizing and cataloging the porous properties by functions for storage, exchange, separation, etc., and 3). the next generation of porous functions based on dynamic crystal transformations caused by guest molecules or physical stimuli. Our aim is to present the state of the art chemistry and physics of and in the micropores of porous coordination polymers.

Journal Article↗
PubMed2002

Laboratory testing in rheumatoid arthritis patients taking disease-modifying antirheumatic drugs: clinical evaluation and cost analysis.

OBJECTIVE: To develop and validate evidence-based recommendations for routine laboratory tests in patients with rheumatoid arthritis (RA) receiving traditional disease-modifying antirheumatic drugs (DMARDs), and to calculate the monitoring costs. METHODS: Outpatient charts of 362 RA patients taking DMARDs were reviewed, and all laboratory abnormalities recorded. Recommendations on monitoring DMARD therapy were derived and then tested in an independent validation cohort of 231 patients. Cost analysis was performed using a cost catalog. RESULTS: Laboratory abnormalities were seen in 10% of treatment courses; relevant abnormalities were seen only during the first 4 months of therapy. Laboratory tests should be performed in week 2 and 4, then monthly for the first 4 months of therapy, then 2 to 4 times per year. These were capable of detecting 98.3% of laboratory abnormalities in a timely manner in another RA cohort. Up to 78% of costs can be saved when the presented recommendations are compared with those of international rheumatology societies. CONCLUSION: Laboratory tests can be reduced substantially in patients receiving DMARD therapy. In consequence, costs can decrease significantly without oversight of adverse events.

Antirheumatic Agents↗
PubMed2004

Genetic approaches to identify disease genes for birth defects with cleft lip/palate as a model.

BACKGROUND: Understanding the etiology of birth defects is an important step toward developing improved treatment and preventive strategies. Most birth defects have an underlying genetic basis, ranging from single genes playing dominant or recessive roles in Mendelian disorders to a mixture of contributions from multiple genes and environmental triggers in complex traits. The purpose of this article is to provide an overview of genetic approaches to identifying disease genes for genetically complex birth defects. METHODS: A review of the literature describing successes and limitations for identifying disease genes for complex traits was conducted. RESULTS: Cleft lip and cleft palate are common congenital anomalies with significant medical, psychological, social, and economic ramifications. The Online Mendelian Inheritance in Man catalog (OMIM; http://www3.ncbi.nlm.nih.gov/Omim) lists more than 400 single-gene causes of clefts of the lip and/or palate. Genetic causes of clefting also include chromosomal rearrangements, genetic susceptibility to teratogenic exposures, and complex genetic contributions of multiple genes. CONCLUSIONS: Genetic causes of birth defects can be identified using an increasingly powerful combination of careful sample collection, molecular analytic methods, and statistical evaluations. We will describe a range of approaches to search for genetic factors of birth defects and use our own work with cleft lip and palate as a model.

Chromosome Aberrations↗
PubMed2005

Identification of early-responsive genes correlated to valproic acid-induced neural tube defects in mice.

BACKGROUND: Valproic acid (VPA) causes the failure of neural tube closure in newborn mice. However, the molecular mechanism of its teratogenesis is unknown. This study was conducted to investigate the genomewide effects of VPA disruption of normal neural tube development in mice. METHODS: Microarray analysis was performed on the head part of NMRI mouse embryos treated for 1 hr with VPA on gestational day (GD) 8. Subsequently, we attempted to isolate genes that changed in correlation with the teratogenic action of VPA by employing reduced teratogenic VPA analogs, valpromide (VPD) and valnoctamide (VCD), in a real-time PCR study. RESULTS: Microarray results demonstrated that during neurulation, many genes, some of whose functions are known and some unknown, were either increased or decreased after VPA injection. Some genes were affected by VPD or VCD in the same way as VPA, but others were not changed by the analogs. In this way, our system identified 11 increased and 20 decreased genes. Annotation analysis revealed that the increased genes included gadd45b, ier5, per1, phfl3, pou3f1, and sox4, and the decreased genes included ccne2, ccnl, gas5, egr2, sirt1, and zfp105. CONCLUSIONS: These findings demonstrate that expression changes in genes having roles in the cell cycle and apoptosis pathways of neural tube cells were strongly expected to relate to the teratogenic, but not antiepileptic, activity of VPA. Our approach has allowed the expansion of the catalog of molecules immediately affected by VPA in the developing neural tube.

Abnormalities, Drug-Induced↗
PubMed2007

A model of fluid-biofilm interaction using a Burger material law.

A two-dimensional finite element model of the biofilm response to flow was developed. The numerical code sequentially coupled the fluid dynamics of turbulent, incompressible flow with the mechanical response of a single hemispherical biofilm cluster (approximately 100 microm) attached to the flow boundary. A non-linear Burger material law was used to represent the viscoelastic response of a representative microbial biofilm. This constitutive law was incorporated into the numerical model as a Prony series representation of the biofilm's relaxation modulus. Model simulations illuminated interesting details of this fluid-structure interaction. Simulations revealed that softer biofilms (characterized by lower elastic moduli) were highly susceptible to lift forces and consequently were subject to even greater drag forces found higher in the velocity field. A bimodal deformation path due to the two Burger relaxation times was also observed in several simulations. This suggested that interfacial biofilm may be most susceptible to hydrodynamically induced detachment during the initial relaxation time. This result may prove useful in developing removal strategies. Additionally, plots of lift versus drag suggested that the deformation paths taken by viscoelastic biofilms are largely insensitive to specific material coefficients. Softer biofilms merely seem to follow the same path (as a stiffer biofilm) at a faster rate. These relationships may be useful in estimating the hydrodynamic forces acting on an attached biofilm based on changes in scale and cataloged material properties.

Biofilms↗
PubMed1990

MacProMass: a computer program to correlate mass spectral data to peptide and protein structures.

A program known as MacProMass has been written for Macintosh computers to assist in the analysis of mass spectral data of peptides and proteins. The program employs a user friendly, graphical interface and accommodates a variety of protein structures including cyclic peptides and multiple chain proteins. In addition to molecular mass calculations for positive and negative molecular ions, MacProMass also calculates elemental composition, amino acid composition, isoelectric point, surface free energy, and high-performance liquid chromatography index values for whole structures and peptide fragments resulting from enzymatic or chemical degradation. Users can program their own amino acid residues and terminal groups. In addition to search routines for both mass and sequence, theoretical fragment ions for peptide mass spectra can be calculated. Analysis of variant proteins is facilitated with a subroutine that systematically catalogs single amino acid substitutions that correspond to mass differences between observed and expected molecular ions. Interchain and intrachain disulfide bonds and other types of linkages are maintained throughout the chemical and enzymatic degradation operations.

Amino Acid Sequence↗
PubMed2026

Clinical Function Assignment of NAT2 Alleles by the Clinical Pharmacogenetics Implementation Consortium Pharmacogene Curation Expert Panel.

NAT2 encodes arylamine N-acetyltransferase 2, a key enzyme in the phase II metabolism of arylamines and arylhydrazines. NAT2 is highly polymorphic, resulting in variable distributions of rapid and poor metabolizers across global populations. Here, we detail the process undertaken by the Clinical Pharmacogenetics Implementation Consortium (CPIC) NAT2 Pharmacogene Curation Expert Panel (PCEP) to assign clinical function to NAT2 star (*) alleles using CPIC's standard terminology. Given the observed impact of NAT2 genetic variability on drug response, CPIC convened the NAT2-PCEP to standardize clinical allele function assignments. The NAT2-PCEP is comprised of multidisciplinary and international members, including researchers, clinicians, and implementers with expertise in pharmacogenomics and NAT2 molecular biology. Extensive in vitro and clinical literature was curated from PubMed and other sources to assess NAT2 genotype-to-phenotype concordance as well as the biochemical function of NAT2 star alleles. The NAT2-PCEP assigned allele clinical function using CPIC's standard terminology (increased, decreased, uncertain, and unknown function) to 59 star alleles cataloged by the Pharmacogene Variation Consortium (PharmVar). Two alleles, NAT2*1 and NAT2*4, were assigned increased function (historically known as rapid), 40 alleles were assigned decreased function (historically known as slow), 10 alleles were assigned uncertain function, and seven alleles were assigned unknown function. Rigorous evidence review and in-depth PCEP discussion were crucial in determining these function assignments. The findings reported here underscore the importance of standardized allele functional terms and diplotype-to-phenotype assignments to further the clinical implementation of NAT2 pharmacogenetic test results.

Arylamine N-Acetyltransferase↗
PubMedDate not supplied

Genes expressed in the developing endocrine pancreas and their importance for stem cell and diabetes research.

The genes that regulate endocrine pancreas development, maintain adult endocrine cells, and stimulate progenitor/stem cells during regeneration remain largely unstudied. There is ample evidence that many of the genes involved in endocrine pancreas development also function in the homeostasis of the adult islet. In light of the potential benefits to diabetic research, it is surprising that there is little information about the genes expressed throughout the ontogeny of the endocrine pancreas. In the past few years, efforts have been made to establish the Endocrine Pancreas Consortium database (EPConDB), in which many of the genes expressed in the developing endocrine pancreas are in a database with a corresponding publicly available clone bank. In addition, advances in microarray technology now allow for a quantitative expression analysis of thousands of genes simultaneously, which makes it possible to generate a quantitative catalog of the genes expressed at each step of endocrine differentiation, from embryonic endoderm to mature beta cells. In this review, I will discuss how genes discovered by virtue of their role in endocrine pancreas development may function in the maintenance of pancreatic stem cells and the regeneration of islets. I will further summarize the recent advances in genomics-based studies of the developing endocrine pancreas and will discuss how they might impact on the discovery of diagnostics and research into stem cell-based approaches for the treatment of diabetes.

Animals↗
PubMed2006

Toward a global picture of development: lessons from genome-scale analysis in Caenorhabditis elegans embryonic development.

Development is the result of complex events, including cascades of transcriptional programs and numerous molecular interactions. Traditionally, research focus has been given to the characterization of individual mutants, regulators, or interactions. With the availability of complete genome sequences and high-throughput (HT) experimental techniques, probing development on a system level has become feasible. Pioneering work initiated in invertebrate model systems such as Caenorhabditis elegans has provided first drafts of catalogs of essential components, transcriptional regulatory diagrams and molecular interaction networks underlying developmental processes. Integrating these drafts approximates a system-level picture of development and provides local models for protein/gene functions. Here we summarize the progress toward elucidating developmental processes on a system level, including the applications of genomic technologies and computational analyses. We discuss C. elegans embryonic development in case studies to illustrate how various HT approaches can be integrated and how biological insights can be gained from these approaches.

Animals↗
PubMed1992

The gene-protein database of Escherichia coli: edition 5.

The gene-protein database of Escherichia coli is both an index relating a gene to its protein product on two-dimensional gels, and a catalog of information about the function, regulation, and genetics of individual proteins obtained from two-dimensional gel analysis or collated from the literature. Edition 5 has 102 new entries--a 15% increase in the number of annotated two-dimensional gel spots. The large increase in this edition was accomplished in part by the use of a new method for expression analysis of ordered segments of the E. coli genome, which has resulted in linking 50 gel spots to their genes (or open reading frames) and another 45 to specific regions of the chromosome awaiting the availability of DNA sequence information. Communication of information from the scientific community resulted in additional identifications and regulatory information. To increase accessibility of the database it has been placed in the repository at the National Center for Biotechnology Information (NCBI) at the National Library of Medicine under the name ECO2DBASE. It will be updated twice yearly. This edition of the gene-protein database is estimated to contain entries for one-sixth of the protein-encoding genes of E. coli.

Bacterial Proteins↗
PubMed2005

The interactive online SKY/M-FISH & CGH database and the Entrez cancer chromosomes search database: linkage of chromosomal aberrations with the genome sequence.

To catalog data on chromosomal aberrations in cancer derived from emerging molecular cytogenetic techniques and to integrate these data with genome maps, we have established two resources, the NCI and NCBI SKY/M-FISH & CGH Database and the Cancer Chromosomes database. The goal of the former is to allow investigators to submit and analyze clinical and research cytogenetic data. It contains a karyotype parser tool, which automatically converts the ISCN short-form karyotype into an internal representation displayed in detailed form and as a colored ideogram with band overlay, and also has a tool to compare CGH profiles from multiple cases. The Cancer Chromosomes database integrates the SKY/M-FISH & CGH Database with the Mitelman Database of Chromosome Aberrations in Cancer and the Recurrent Chromosome Aberrations in Cancer database. These three datasets can now be searched seamlessly by use of the Entrez search and retrieval system for chromosome aberrations, clinical data, and reference citations. Common diagnoses, anatomic sites, chromosome breakpoints, junctions, numerical and structural abnormalities, and bands gained and lost among selected cases can be compared by use of the "similarity" report. Because the model used for CGH data is a subset of the karyotype data, it is now possible to examine the similarities between CGH results and karyotypes directly. All chromosomal bands are directly linked to the Entrez Map Viewer database, providing integration of cytogenetic data with the sequence assembly. These resources, developed as a part of the Cancer Chromosome Aberration Project (CCAP) initiative, aid the search for new cancer-associated genes and foster insights into the causes and consequences of genetic alterations in cancer.

Base Sequence↗
PubMed2006

Comprehensive assessment of DNA copy number alterations in human prostate cancers using Affymetrix 100K SNP mapping array.

Although multiple recurrent chromosomal alterations have been identified in prostate cancer cells, the specific genes driving the apparent selection of these changes remain largely unknown. In part, this uncertainty is due to the limited resolution of the techniques used to detect these alterations. In this study, we applied a high-resolution genome-wide method, Affymetrix 100K SNP mapping array, to screen for somatic DNA copy number (CN) alterations among 22 pairs of samples from primary prostate cancers and matched nonmalignant tissues. We detected 355 recurrent deletions and 223 recurrent gains, many of which were novel. As expected, the sizes of novel alterations tend to be smaller. Importantly, among tumors with increasing grade, Gleason sum 6, 7, and 8, we found a significant trend of larger number of alterations in the tumors with higher grade. Overall, gains are significantly more likely to occur within genes (74%) than are deletions (49%). However, when we looked at the most frequent CN alterations, defined as those in > or =4 subjects, we observed that both gains (85%) and deletions (57%) occur preferentially within genes. An example of a novel, recurrent alteration observed in this study was a deletion between the ERG and TMPRSS2 genes on chromosome 21, presumably related to the recently identified fusion transcripts from these two genes. Results from this study provide a basis for a systematic and comprehensive cataloging of CN alterations associated with grades of prostate cancer, and the subsequent identification of specific genes that associated with initiation and progression of the disease. This article contains supplementary material available via the Internet at http://www.interscience.wiley.com/jpages/1045-2257/suppmat

Aged↗