COSMIC: High-Resolution Cancer Genetics Using the Catalogue of Somatic Mutations in Cancer.

COSMIC (http://cancer.sanger.ac.uk) is an expert-curated database of somatic mutations in human cancer. Broad and comprehensive in scope, recent releases in 2016 describe over 4 million coding mutations across all human cancer disease types. Mutations are annotated across the entire genome, but expert curation is focused on over 400 key cancer genes. Now encompassing the majority of molecular mutation mechanisms in oncogenetics, COSMIC additionally describes 10 million non-coding mutations, 1 million copy-number aberrations, 9 million gene-expression variants, and almost 8 million differentially methylated CpGs. This information combines a consistent interpretation of the data from the major cancer genome consortia and cancer genome literature with exhaustive hand curation of over 22,000 gene-specific literature publications. This unit describes the graphical Web site in detail; alternative protocols overview other ways the entire database can be accessed, analyzed, and downloaded. © 2016 by John Wiley & Sons, Inc.

The Catalogue of Somatic Mutations in Cancer (COSMIC).

COSMIC is currently the most comprehensive global resource for information on somatic mutations in human cancer, combining curation of the scientific literature with tumor resequencing data from the Cancer Genome Project at the Sanger Institute, U.K. Almost 4800 genes and 250000 tumors have been examined, resulting in over 50000 mutations available for investigation. This information can be accessed in a number of ways, the most convenient being the Web-based system which allows detailed data mining, presenting the results in easily interpretable formats. This unit describes the graphical system in detail, elaborating an example walkthrough and the many ways that the resulting information can be thoroughly investigated by combining data, respecializing the query, or viewing the results in different ways. Alternate protocols overview the available precompiled data files available for download.

Multiple endocrine neoplasia type 1 (MEN1) germline mutations in familial isolated primary hyperparathyroidism.

BACKGROUND: Familial isolated hyperparathyroidism (FIHP) is an autosomal dominant disorder characterized by uniglandular or multiglandular parathyroid tumours that occur in the absence of other endocrine tumours. The disorder may represent either an early stage of multiple endocrine neoplasia type 1 (MEN1), or an allelic variant of MEN1, or a distinct entity involving another locus. We have explored these possibilities in seven families in whom primary hyperparathyroidism occurred as the sole endocrinopathy. METHODS: Seven FIHP families were ascertained and venous blood samples obtained from 35 members (17 affected and 18 unaffected) for DNA sequence analysis of the MEN1 gene. The mean (+/- SD) follow-up period in the 17 affected members was 15.06 (+/- 8.83) years. RESULTS: Four heterozygous germline mutations of the MEN1 gene were identified. These consisted of two 4-bp intragenic deletions that would result in prematurely truncated proteins, and two missense (Asp153Val and Ala411Pro) mutations. Furthermore, analysis of parathyroid tumour DNA from one individual revealed a loss of the wild-type allele and retention of the mutant allele, consistent with Knudson's 'two-hit' model of hereditary cancer and a tumour suppressor role for MEN1 in FIHP. CONCLUSIONS: Our results provide further support for FIHP being a distinct allelic variant of MEN1, and an analysis of the 16 mutations reported to date indicate that FIHP is associated with a higher frequency of missense MEN1 mutations.

MHC-linked olfactory receptor loci exhibit polymorphism and contribute to extended HLA/OR-haplotypes.

Clusters of olfactory receptor (OR) genes are found on most human chromosomes. They are one of the largest mammalian multigene families. Here, we report a systematic study of polymorphism of OR genes belonging to the largest fully sequenced OR cluster. The cluster contains 36 OR genes, of which two belong to the vomeronasal 1 (V1-OR) family. The cluster is divided into a major and a minor region at the telomeric end of the HLA complex on chromosome 6. These OR genes could be involved in MHC-related mate preferences. The polymorphism screen was carried out with 13 genes from the HLA-linked OR cluster and three genes from chromosomes 7, 17, and 19 as controls. Ten human cell lines, representing 18 different chromosome 6s, were analyzed. They were from various ethnic origins and exhibited different HLA haplotypes. All OR genes tested, including those not linked to the HLA complex, were polymorphic. These polymorphisms were dispersed along the coding region and resulted in up to seven alleles for a given OR gene. Three polymorphisms resulted either in stop codons (genes hs6M1-4P, hs6M1-17) or in a 16-bp deletion (gene hs6M1-19P), possibly leading to lack of ligand recognition by the respective receptors in the cell line donors. In total, 13 HLA-linked OR haplotypes could be defined. Therefore, allelic variation appears to be a general feature of human OR genes.

Studies of the murine homolog of the multiple endocrine neoplasia type 1 (MEN1) gene, men1.

The murine homolog of the multiple endocrine neoplasia type 1 (MEN1) gene (men1), which in humans is associated with tumors of the parathyroids, pancreas, and pituitary, has been characterized by isolating 27 clones from a mouse embryonic stem cell cDNA library. The insert sizes ranged from 600-2500 bp, and sequence analysis identified a 1833 bp open reading frame encoding a 611 amino acid protein. In addition, two clones contained an unspliced intron 1, and another two clones contained 20-29 bp of an upstream sequence, which suggested the presence of an alternate exon 1. This was supported by an analysis of the homologous human sequence. The mouse and human coding regions had 89% and 96% identity of the nucleotide and amino acid sequences, respectively. Investigation of clones isolated from a 129ola mouse genomic library, revealed the men1 gene to consist of 10 exons that spanned approximately 6 kb. Northern blot analysis demonstrated the ubiquitous expression of 2.9 kb and 3. 4 kb transcripts in mouse adult tissues and embryos from 7 days. DNA sequence analysis of the larger 3.4 kb transcript revealed it to result from a retention of intron 1. In situ hybridization confirmed an early ubiquitous expression in whole mount mouse embryos and adult tissues, but in the latter, different levels of cellular expression were observed, e.g., men1 expression was higher in testicular Sertoli cells than in germ cells. Thus, the mouse men1 gene and the basis of alternative transcripts have been defined, and these will help to facilitate studies of a mouse model.

A putative human zinc-finger gene (ZFPL1) on 11q13, highly conserved in the mouse and expressed in exocrine pancreas. The European Consortium on MEN 1.

In the process of identification of the multiple endocrine neoplasia type 1 gene, which was recently published, we isolated a novel gene in the 11q13 region. This gene (named ZFPL1, for zinc-finger protein-like 1) is expressed strongly in the exocrine pancreas as a 1.4-kb polyadenylated RNA encoding a putative protein of 310 amino acids. A mouse EST contig predicts an equally sized murine protein with 91% amino acid sequence identity to the human protein. No significant homology with known proteins could be found through database screening. However, zinc-finger-like domains and leucine-zipper-like motifs in the predicted ZFPL1 protein were identified, suggesting the presence of DNA-binding and dimerization domains possibly involved in transcription regulation. This notion is supported by the presence of a putative bipartite nuclear localization signal. This paper presents the full-length cDNA sequence for this gene, its genomic structure and chromosomal orientation, and expression studies by Northern blot hybridization and RNA in situ hybridization.

Characterization of mutations in patients with multiple endocrine neoplasia type 1.

Multiple endocrine neoplasia type 1 (MEN1) is an autosomal dominant disorder characterized by tumors of the parathyroids, pancreatic islets, and anterior pituitary. The MEN1 gene, on chromosome 11q13, has recently been cloned, and mutations have been identified. We have characterized such MEN1 mutations, assessed the reliability of SSCP analysis for the detection of these mutations, and estimated the age-related penetrance for MEN1. Sixty-three unrelated MEN1 kindreds (195 affected and 396 unaffected members) were investigated for mutations in the 2,790-bp coding region and splice sites, by SSCP and DNA sequence analysis. We identified 47 mutations (12 nonsense mutations, 21 deletions, 7 insertions, 1 donor splice-site mutation, and 6 missense mutations), that were scattered throughout the coding region, together with six polymorphisms that had heterozygosity frequencies of 2%-44%. More than 10% of the mutations arose de novo, and four mutation hot spots accounted for >25% of the mutations. SSCP was found to be a sensitive and specific mutational screening method that detected >85% of the mutations. Two hundred and one MEN1 mutant-gene carriers (155 affected and 46 unaffected) were identified, and these helped to define the age-related penetrance of MEN1 as 7%, 52%, 87%, 98%, 99%, and 100% at 10, 20, 30, 40, 50, and 60 years of age, respectively. These results provide the basis for a molecular-genetic screening approach that will supplement the clinical evaluation and genetic counseling of members of MEN1 families.

Review criteria for stroke rehabilitation outcomes.

OBJECTIVES: To develop review criteria from the Agency for Health Care Policy and Research Stroke Rehabilitation Guidelines, to review chart records from three sites of care, and to evaluate the interrater and intrarater reliability for the chart review. DESIGN: A descriptive cross-sectional study using a convenience sample. SETTING: Charts for abstraction were obtained from three sites of care home health care, nursing facilities, and inpatient rehabilitation centers. PARTICIPANTS: Charts were included in the study from the three sites of care if the following conditions were met: (1) the client's first admission to a rehabilitation setting; (2) the client's care was Medicare reimbursed; (3) the client lived in the community prior to the stroke; and (4) the client was receiving skilled rehabilitation services. MEASURES: Review criteria, developed directly from the AHCPR Stroke Rehabilitation guidelines, consisted of 11 global quality criteria representative of comprehensive multidisciplinary rehabilitative care. There were approximately 150 variables, comprised of specific criteria to measure each of the 11 global quality criteria plus comprehensive demographic and client-specific information. RESULTS: Results of this study suggest that differences exist in documentation of care across the three sites of care. There was difficulty in obtaining adequate numbers of home health charts. Intrarater reliability, using Cohen's Kappa, was .78 and interrater reliability was .64. CONCLUSIONS: Based on chart documentation, there is variability in the process of stroke rehabilitation care across nursing facilities, inpatient rehabilitation facilities, and home health. This variability can be reliably assessed by chart review. This study provides the impetus for future research specifically evaluating the associations between documentation of the processes of care and patient outcomes.

Estimation of the age of the ancestral arginine3500-->glutamine mutation in human apoB-100.

Familial defective apoB-100 (R3500Q) [FDB (R3500Q)] is caused by a mutation in the apoB gene (2p23.24). Almost all individuals with this disorder are of European descent, and in almost all cases the mutation is on a chromosome with a rare haplotype (194) at the apoB locus, suggesting that all FDB (R3500Q) probands are descended from a common ancestor in whom the original mutation occurred. The distribution of the mutation is consistent with an origin in Europe 6000-7000 years ago. We have estimated the amount of recombination between the apoB gene and markers on chromosome 2 in 34 FDB (R3500Q) probands in whom the mutation is on a 194 haplotype. Significant linkage disequilibrium was found between the apoB gene and marker D2S220. We have identified three YACs that contain the apoB gene and D2S220. The shortest restriction fragment common to the three YACs that contained both loci was 240 kb long. No shorter fragments with both loci were identified. On the assumption that 1000 kb corresponds to 1 cM, we deduce that the recombination distance between D2S220 and the apoB gene is about 0.24 cM. Combining this value with the linkage disequilibrium observed between the two loci in the probands, we estimate that the ancestral mutation occurred about 270 generations ago. We postulate that the original mutation occurred in the common ancestor of living FDB (R3500Q) probands, who lived in Europe about 6750 years ago. The errors in this estimate are discussed.

Mapping of the gene encoding the B56 beta subunit of protein phosphatase 2A (PPP2R5B) to a 0.5-Mb region of chromosome 11q13 and its exclusion as a candidate gene for multiple endocrine neoplasia type 1 (MEN1).

The multiple endocrine neoplasia type 1 (MEN1) locus has been previously localised to 11q13 by combined tumour deletion mapping and recombination studies, and a 0.5-Mb region, flanked by PYGM and D11S449, has been defined. In the course of constructing a conting, we have identified the location of the gene encoding the B56 beta subunit of protein phosphatase 2A (PP2A), which is involved in cell signal transduction pathways and thus represents a candidate gene for MEN1. We have searched for mutations in the PP2A-B56 beta coding region, together with the 5' and 3' untranslated regions in six MEN1 patients. DNA sequence abnormalities were not identified and thus the PP2A-B56 beta gene is excluded as the candidate gene for MEN1. However, our precise localisation of PP2A-B56 beta to this region of 11q13 may help in elucidating the basis for other disease genes mapping to this generich region.

Decision making by high functional status elders regarding nursing home placement.

An analysis of the Minimum Data Set Plus (MDS+) from one midwestern state revealed a group of "high functional elders" entering nursing homes, who potentially could be served in the community at a lower cost. The purpose of this qualitative study was to identify and better understand the reasons why these apparently high functioning elder adults entered nursing homes. Data from the 1995 MDS+ were used to identify "high functional" elders recently admitted to the nursing home from two urban and seven rural counties. Data were collected through in-depth, face-to-face, semi-structured interviews and analyzed using qualitative content analysis. Of the 33 persons judged to be high functional, only 36% remained in the nursing home 3 to 6 months later. Most elders were using a wide array of community-based services and extensive informal support networks prior to entering the nursing home. Most described specific events that forced them into the nursing home environment. Health needs, specifically the need for 24-hour care or supervision, emerged as the dominant factor for remaining in the nursing home. Of the 12 elders interviewed, all demonstrated some evidence of cognitive impairment. This study suggests that there are persons in nursing facilities today for whom community-based services, such as affordable assisted-living, would be reasonable and appropriate. Case managers may be the most qualified not only to assess for and coordinate services, but also to advocate for affordable services that preserve elders' functional status.

Control over nursing practice: a construct coming of age.

The purpose of this study was to assess the psychometric properties of the Control Over Nursing Practice Scales using data from registered nurses (N = 1117) employed in four acute care hospitals in the Midwest. Psychometric evaluation included dimensional analysis, reliability estimation, and validity assessment of six dimensions of a 33-item instrument: responsibility and influence of head nurses, staff nurses, and committees; access to ideas; use of personal resources; and research utilization. Factor analysis reproduced six dimensions that explained 61% of the variance. Coefficient alphas ranged from .75-.89. Correlations between Control Over Nursing Practice with autonomy, group cohesion, job stress, and job satisfaction supported construct validity. Empirical testing of known group differences to obtain new information about the construct revealed that critical care nurses scored higher on research utilization than medical-surgical or obstetrical nurses; baccalaureate-prepared nurses scored higher than associate or diploma nurses on responsibility and influence: committees. Contrary to our hypothesis, there were no differences between part-time and full-time nurses on any of the six dimensions.

Definition of the minimal MEN1 candidate area based on a 5-Mb integrated map of proximal 11q13. The European Consortium on Men1, (GENEM 1; Groupe d'Etude des Néoplasies Endocriniennes Multiples de type 1).

Multiple endocrine neoplasia type 1 (MEN1) is an autosomal dominant disorder with a high penetrance characterized by tumors of the parathyroid glands, the endocrine pancreas, and the anterior pituitary. The MEN1 gene, a putative tumor suppressor gene, has been mapped to a 3- to 8-cM region in chromosome 11q13 but it remains elusive as yet. We have combined the efforts and resources from four laboratories to form the European Consortium on MEN1 with the aims of establishing the genetic and the physical maps of 11q13 and of further narrowing the MEN1 region. A 5-Mb integrated map of the region was established by fluorescence in situ hybridization on both metaphase chromosomes and DNA fibers, by hybridization to DNA from somatic cell hybrids containing various parts of human chromosome 11, by long-range restriction mapping, and by characterization of YACs and cosmids. Polymorphic markers were positioned and ordered by physical mapping and genetic linkage in 86 MEN1 families with 452 affected individuals. Two critical recombinants identified in two affected cases placed the MEN1 gene in an approximately 2-Mb region around PYGM, flanked by D11S1883 and D11S449.

Refined mapping and YAC contig construction of the X-linked cleft palate and ankyloglossia locus (CPX) including the proximal X-Y homology breakpoint within Xq21.3.

The gene for X-linked cleft palate (CPX) has previously been mapped in an Icelandic kindred between the unordered proximal markers DXS1002/DXS349/DXS95 and the distal marker DXYS1X, which maps to the proximal end of the X-Y homology region in Xq21.3. Using six sequence-tagged sites (STSs) within the region, a total of 91 yeast artificial chromosome (YAC) clones were isolated and overlapped in a single contig that spans approximately 3.1 Mb between DXS1002 and DXYS1X. The order of microsatellite and STS markers in this was established as DXS1002-DXS1168-DSX349-DXS95-DXS364-DXS 1196-DXS262-DXS110-DXS1066-(DXS1169, DXS1222)-DXS472-DXS1217-DXYS1X. A long-range restriction map of this region was created using eight nonchimeric, overlapping YAC clones. Analysis of newly positioned polymorphic markers in recombinant individuals from the Icelandic family has enabled us to identify DXS1196 and DXS1217 as the flanking markers for CPX. The maximum physical distance containing the CPX gene has been estimated to be 2.0 Mb, which is spanned by a minimum set of five nonchimeric YAC clones. In addition, YAC end clone and STS analyses have pinpointed the location of the proximal boundary of the X-Y homology region within the map.

Refinement of the X-linked cleft palate and ankyloglossia (CPX) localisation by genetic mapping in an Icelandic kindred.

The gene responsible for X-linked cleft palate and ankyloglossia (CPX) has previously been localized to the proximal region of the q arm of the X chromosome in both Icelandic and North American Indian kindreds. In this study, further linkage analysis has been performed on the Icelandic family and has resulted in a significant reduction in the size of the interval containing the mutated gene. A new polymorphism at DXS95, together with DXS1002 and DXS349, defines the proximal boundary of the CPX interval, whereas DXYS1X defines the distal boundary. Multipoint analysis supports this localisation with a peak lod score of 12.7, more than 2 lod score units higher than the next most likely position. In order to assess the physical size of the CPX interval prior to initiating yeast artificial chromosome cloning, metaphase fluorescence in situ hybridisation analysis was performed with the closest flanking markers. The size of the interval between DXS95 and DXYS1X was estimated to be approximately 2-3 Mb.

Linkage analysis of 62 X-chromosomal loci excludes the X chromosome in an Icelandic family showing apparent X-linked recessive inheritance of neural tube defects.

We report here the findings of a linkage analysis, involving numerous markers from the human X chromosome, in an attempt to localise a putative gene causing apparent X-linked spina bifida and anencephaly (SBA) in a large Icelandic pedigree. Two-point linkage analysis was performed using markers from 62 informative loci in this family. Although small positive lod scores were found at a number of these loci, none reached the significance level for linkage. Haplotypes were extensively analysed and found to exclude linkage to the X chromosome.

The localization of a gene causing X-linked cleft palate and ankyloglossia (CPX) in an Icelandic kindred is between DXS326 and DXYS1X.

The locus responsible for X-linked, nonsyndromic cleft palate and/or ankyloglossia (CPX) has previously been mapped to the proximal long arm of the human X chromosome between Xq21.31 and q21.33 in an Icelandic kindred. We have extended these studies by analyzing an additional 14 informative markers in the family as well as including several newly investigated family members. Recombination analysis indicates that the CPX locus is more proximal than previously thought, within the interval Xq21.1-q21.31. Two recombinants place DXYS1X as the distal flanking marker, while one recombinant defines DXS326 as the proximal flanking marker, an interval of less than 5 cM. Each of the flanking markers recombines with the CPX locus, giving 2-point lod scores of Zmax = 4.16 at theta = 0.08 (DXS326) and Zmax = 5.80 at theta = 0.06 (DXYS1X).