A questionnaire-based study evaluating differences between dental students in Paris (F) and Malmö (SE) regarding diagnosis and treatment decisions of patients with different severity levels of periodontal diseases

AIM

To evaluate differences between last-year dental students in Paris (F) and Malmö (SE) Dental Schools, in regard to their judgement and decision-making within periodontology.

MATERIALS AND METHODS

Ninety-six last-year dental students from Paris and 45 from Malmö participated in a questionnaire study based on four patient cases: (i) Patient case with generalised alveolar bone loss but no signs of inflammation (Well-maintained), (ii) Patient case with generalised alveolar bone loss and signs of inflammation (Periodontitis), (iii) Patient case with no alveolar bone loss and no signs of inflammation (Healthy) and (iv) Patient case with no alveolar bone loss but with signs of inflammation (Gingivitis). Through multiple-choice questions, the students judged each case as healthy or diseased proposed a diagnosis and treatment measures and estimated the treatment time for each patient. Furthermore, they assessed the prognosis of each patient in case of no treatment.

RESULTS

Based on a response rate of 83%, the majority in both groups judged all the patients as diseased. More Paris students diagnosed the healthy and the gingivitis case as having periodontitis (P < .05). Furthermore, a larger number of students from Paris recommended several treatment measures and estimated longer treatment times for all the cases (P < .05) and estimated a higher risk for disease progression for the healthy and the gingivitis case (P < .05).

CONCLUSIONS

Significant variation between students from Paris and Malmö Dental Schools in regard to judgement and decision-making was observed; this may in turn imply that there is still need of improving consistency amongst undergraduate educations in periodontology in Europe.

Providing Access to Genomic Variant Knowledge in a Healthcare Setting: A Vision for the ClinGen Electronic Health Records Workgroup

The Clinical Genome Resource (ClinGen) is a National Institutes of Health (NIH)-funded collaborative program that brings together a variety of projects designed to provide high-quality, curated information on clinically relevant genes and variants. ClinGen's EHR (Electronic Health Record) Workgroup aims to ensure that ClinGen is accessible to providers and patients through EHR and related systems. This article describes the current scope of these efforts and progress to date. The ClinGen public portal can be accessed at www.clinicalgenome.org.

Abstract P6-05-12: Lack of Frequent Estrogen Receptor Mutation in Primary Breast Tumors

The estrogen receptor alpha (ESR1) is a critical driver of breast tumorigenesis, and as such has been a target for therapy for many years. Early reports using Sanger sequencing and conformational assays reported that there were little if any mutations in ER-positive tumors, although a few somatic mutations have recently been described in tumors and cell lines. We set out to validate the authenticity of these reported somatic mutations by performing analysis of ER DNA sequence variants (DSVs) in 66 ER+ breast tumors, and 39 breast cancer cell lines. We utilized a combined approach of target capture sequencing of ESR1, and subsequent testing for novel and previously identified DSVs using an orthogonal mass spectrometry based sequencing approach. A DNA capture approach was designed to capture all exons, flanking splice sites, and the 3′ UTR of ESR1. DNA was captured and sequenced using SOLiD.

Using stringency with a cut-off with at least 2 variant reads, variants in at least 20% of the reads, and requiring evidence for the variants in both strands, we identified 4 previously reported SNPs (rs2077647; rs46432; rs1801132; rs2228480), and two previously reported somatic mutations H6Y and N532Y. We developed mass-spectrometry assays, including controls, for these DSVs, and in addition, we included 10 DSVs which had previously been reported as somatic mutations in breast (and other) cancer. Applying mass-spec based analysis to breast tumors and cell lines, we were able to confirm previously reported SNPs, and one previously reported mutations (H6Y). This mutation was found in one breast tumor and one cell line. None of the other reported somatic mutations could be confirmed in tumors or cell lines. Functional assays on the ESR1H6Y DSV failed to identify differences to wildtype receptor. The lack of a phenotype, and the infrequent occurrence of this DSV do not support a major driver role for ESR1H6Y.

This analysis suggests that ESR1 mutations are a rare event in ER+ primary breast cancer.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P6-05-12.

Evolution of Genomic Diversity in the Breast Cancer Cell Line MCF-7

Background: Tumors arise from an accumulation of genetic changes via a multi-step process. Genetic rearrangements can potentially lead to fusions with consequent deregulation of a gene, or the generation of new genes (through the fusion of two genes) that maybe functionally important in tumor development and progression. Our knowledge of rearrangements in solid tumors is limited and it is likely that solid tumors are defined by fusion genes that are not yet discovered. We recently reported 157 genomic breakpoints that were identified in a BAC library generated from MCF-7 cells (termed MCF-7/BAC), and could be confirmed by PCR across breakpoint joins as likely somatic mutations. To gain insight into the heterogeneity of genomic breakpoints in breast cancer cell lines, we studied these 157 validated breakpoints in a two common MCF-7 sublines.Methods: DNA was isolated from MCF-7/ATCC and MCF-7/B and genomic breakpoints were amplified by PCR and visualized by gel electrophoresis. Breakpoints were called present or absent based upon amplification of a product at the predicted size. By mapping the breakpoints to specific stages in the evolution of MCF-7 we reconstructed the sequence of chromosomal rearrangement events in the cancer genomesResults: MCF-7/B harbored only 91 of the breakpoints from the original 157 identified from MCF-7/BAC, and MCF-7/ATCC only shared 40. MCF-7 had 3 breakpoints that were found in MCF-7/BAC but not in MCF-7/B. Thus, of the original 157 breakpoints, 37 (23.6%) were shared all three sublines. MCF-7/ATCC contained the least breakpoints, which might indicate that MCF-7/ATCC is ancestral to MCF-7/B and MCF-7/BAC. Consistent with this, of the 157 genomic breakpoints in MCF-7/BAC, 50.3% contained genes, while this was enriched in the MCF-7/ATCC to 72.5%. Interestingly, two breakpoints involving genes in double strand break repair are retained in all three sublines, indicating that these breakpoints might originate from an ancestral cell line, and that deficient double strand break repair might be the underlying cause of genomic instability in these cell lines.Discussion: These preliminary results imply that MCF-7/ATCC maybe ancestral to other MCF-7 sublines. We are now expanding our data set with six other MCF-7 sublines to reconstruct the phylogeny of this breast cancer cell lines. With this information we may get a better understanding of the evolution and heterogeneity of genomic instability and rearrangements in breast cancer.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 3171.

Polymorphic microsatellite loci for the common marmoset (Callithrix jacchus) designed using a cost- and time-efficient method

We describe a cost- and time-efficient method for designing new microsatellite markers in any species with substantial genomic DNA sequence data available. Using this technique, we report 14 new polymorphic dinucleotide microsatellite loci isolated from the common marmoset. The relative yield of new polymorphisms was higher with less labor than described in previous marmoset studies. Of 20 loci initially evaluated, 14 were polymorphic and amplified reliably (70% success rate). The number of alleles ranged from 3 to 9 with heterozygosity varying from 0.48 to 0.83.

Human-specific changes of genome structure detected by genomic triangulation

Knowledge of the rhesus macaque genome sequence enables reconstruction of the ancestral state of the human genome before the divergence of chimpanzees. However, the draft quality of nonhuman primate genome assemblies challenges the ability of current methods to detect insertions, deletions, and copy-number variations between humans, chimpanzees, and rhesus macaques and hinders the identification of evolutionary changes between these species. Because of the abundance of segmental duplications, genome comparisons require the integration of genomic assemblies and data from large-insert clones, linkage maps, and radiation hybrid maps. With genomic triangulation, an integrative method that reconstructs ancestral states and the structural evolution of genomes, we identified 130 human-specific breakpoints in genome structure due to rearrangements at an intermediate scale (10 kilobases to 4 megabases), including 64 insertions affecting 58 genes. Comparison with a human structural polymorphism database indicates that many of the rearrangements are polymorphic.

Identification of genes regulated by UV/salicylic acid

PURPOSE

Previous work from the authors' group and others has demonstrated that some of the effects of UV irradiation on gene expression are modulated in response to the addition of salicylic acid to irradiated cells. The presumed effector molecule responsible for this modulation is NF-kappaB. In the experiments described here, differential-display RT-PCR was used to identify those cDNAs that are differentially modulated by UV radiation with and without the addition of salicylic acid.

MATERIALS AND METHODS

Differential-display RT-PCR was used to identify differentially expressed genes.

RESULTS

Eight such cDNAs are presented: lactate dehydrogenase (LDH-beta), nuclear encoded mitochondrial NADH ubiquinone reductase 24 kDa (NDUFV2), elongation initiation factor 4B (eIF4B), nuclear dots protein SP100, nuclear encoded mitochondrial ATPase inhibitor (IF1), a cDNA similar to a subunit of yeast CCAAT transcription factor HAP5, and two expressed sequence tags (AA187906 and AA513156).

CONCLUSIONS

Sequences of four of these genes contained NF-kappaB DNA binding sites of the type that may attract transrepressor p55/p55 NF-kappaB homodimers. Down-regulation of these genes upon UV irradiation may contribute to increased cell survival via suppression of p53 independent apoptosis.

Discovering distinct genes represented in 29,570 clones from infant brain cDNA libraries by applying sequencing by hybridization methodology

To discover all distinct human genes and to determine their patterns of expression across different cell types, developmental stages, and physiological conditions, a procedure is needed for fast, mutual comparison of hundreds of thousands (and perhaps millions) of clones from cDNA libraries, as well as their comparison against data bases of sequenced DNA. In a pilot study, 29,570 clones in duplicate from both original and normalized, directional, infant brain cDNA libraries were hybridized with 107-215 heptamer oligonucleotide probes to obtain oligonucleotide sequence signatures (OSSs). The OSSs were compared and clustered based on mutual similarity into 16,741 clusters, each corresponding to a distinct cDNA. A number of distinct cDNAs were successfully recognized by matching their 107-probe OSSs against GenBank entries, indicating the possibility of sequence recognition with only a few hundred randomly chosen oligomers.

Identification and characterization of new human medium reiteration frequency repeats

We report nine new families of human medium reiteration frequency interspersed repetitive elements (MER elements). They were identified by computer-assisted analyses. Six of them were independently confirmed as repetitive families by DNA-DNA hybridization, and the number of elements for each of these families was estimated by plaque hybridization assay. The involvement of some of the reported MER elements in genetic rearrangements is demonstrated.

Prototypic sequences for human repetitive DNA

We report a collection of 53 prototypic sequences representing known families of repetitive elements from the human genome. The prototypic sequences are either consensus sequences or selected examples of repetitive sequences. The collection includes: prototypes for high and medium reiteration frequency interspersed repeats, long terminal repeats of endogenous retroviruses, alphoid repeats, telomere-associated repeats, and some miscellaneous repeats. The collection is annotated and available electronically.

Enhanced malignant transformation induced by expression of a distinct protein domain of ribonucleotide reductase large subunit from herpes simplex virus type 2

The 1.3-kilobase (kb) Pst I DNA fragment C (Pst I-C) of herpes simplex virus type 2 (HSV-2) morphological transforming region III (mtrIII; map unit 0.562-0.570) encodes part of the N-terminal half of the large subunit of ribonucleotide reductase (RR1; amino acid residues 71-502) and induces the neoplastic transformation of immortalized cell lines. To assess directly the role of these RR1 protein sequences in cell transformation, the Pst I-C fragment was cloned in an expression vector (p91023) containing an adenovirus-simian virus 40 promoter-enhancer to generate recombinant plasmid p9-C. Expression of a protein domain (approximately 65 kDa) was observed in p9-C-transfected COS-7 and Rat2 cells but not in those transfected with plasmid pHC-14 (Pst I-C in a promoterless vector). In Rat2 cells, p9-C induced highly transformed foci at an elevated frequency compared with that of pHC-14. Introduction of translation termination (TAG) condons within the RR1 coding sequence and within all three reading frames inactivated RR1 protein expression from p9-C and reduced its transforming activity to the level seen with the standard pHC-14 construct. Wild-type p9-C specified a protein kinase capable of autophosphorylation. Computer-assisted analysis further revealed significant similarity between regions of mtrIII-specific RR1 and amino acid patterns conserved within the proinsulin precursor family and DNA transposition proteins. These results identify a distinct domain of the HSV-2 RR1 protein involved in the induction of enhanced malignant transformation. In addition, the data indicate that the mtrIII DNA itself can induce basal-level transformation in the absence of protein expression.

Reconstruction and analysis of human Alu genes

The existing classification of human Alu sequences is revised and expanded using a novel methodology and a larger set of sequence data. Our study confirms that there are two major Alu subfamilies, Alu-J and Alu-S. The Alu-S subfamily consists of at least five distinct subfamilies referred to as Alu-Sx, Alu-Sq, Alu-Sp, Alu-Sc, and Alu-Sb. The Alu-Sp and Alu-Sq subfamilies have been revealed by this study. Alu subfamilies differ from one another in a number of positions called diagnostic. In this paper the diagnostic positions are defined in quantitative terms and are used to evaluate statistical significance of the observed subfamilies. Each Alu subfamily most likely represents pseudogenes retroposed from evolving functional source Alu genes. Evidence presented in this paper indicates that Alu-Sp and Alu-Sc pseudogenes were retroposed from different source genes, during overlapping periods of time, and at different rates. Our analysis also indicates that the previously identified Alu-type transcript BC200 comes from an active Alu gene that might have existed even before the origin of dimeric Alu sequences. The source genes for Alu pseudogene families are reconstructed. It is assumed that diagnostic differences between reconstructed source genes reflect mutations that have occurred in true source Alu genes under natural selection. Some of these mutations are compensatory and are used to reconstruct a common secondary structure of Alu RNAs transcribed from the source genes. The biological function of Alu RNA is discussed in the context of its homology to the elongation-arresting domain of 7SL RNA.(ABSTRACT TRUNCATED AT 250 WORDS)