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Results for “reference mapping”

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PubMed2000

Systematic review processes and the management of opioid withdrawal.

OBJECTIVE: To assess the diversity of research on the management of opioid withdrawal, identify sources of heterogeneity and provide a context for subsequent systematic reviews to establish evidence-based best practice. METHODS: References were identified through searches of multiple electronic databases and handsearching the reference lists of retrieved articles. The principal criterion for inclusion in the literature mapping process was that it be a study of an intervention intended to manage the process of opioid withdrawal. RESULTS: Of 218 references assessed, all participants were dependent on heroin in 41% and on methadone or l-alpha acetyl methadol (LAAM) in 24%. More than 17 different types of treatment approach were identified. Only 42% of references used a rating instrument to assess withdrawal severity and reported sufficient results to indicate the timing and magnitude of the peak and/or duration of withdrawal. The type of rating instrument used and the way in which results were reported varied enormously. A clear parameter for completion of detoxification was used for 37% of references. CONCLUSIONS: The capacity for rigorous systematic reviews of the management of opioid withdrawal is currently limited. There are multiple sources of heterogeneity that will need to be taken into account. IMPLICATIONS: The use of narrative reviews and observational studies are important complements to formal systematic reviews in the establishment of evidence-based practice in any area that combines aspects of psychology, behaviour, social context and medical treatment.

Humans↗

PubMed2004

Pooled Genomic Indexing (PGI): analysis and design of experiments.

Pooled Genomic Indexing (PGI) is a novel method for physical mapping of clones onto known sequences. PGI is carried out by pooling arrayed clones and generating shotgun sequence reads from the pools. The shotgun sequences are compared to a reference sequence. In the simplest case, clones are placed on an array and are pooled by rows and columns. If a shotgun sequence from a row pool and another shotgun sequence from a column pool match the reference sequence at a close distance, they are both assigned to the clone at the intersection of the two pools. Accordingly, the clone is mapped onto the region of the reference sequence between the two matches. A probabilistic model for PGI is developed, and several pooling designs are described and analyzed, including transversal designs and designs from linear codes. The probabilistic model and the pooling schemes are validated in simulated experiments where 625 rat bacterial artificial chromosome (BAC) clones and 207 mouse BAC clones are mapped onto homologous human sequence.

Animals↗

PubMed2001

Epitope mapping of four novel CD44 monoclonal antibodies using surface plasmon resonance and soluble CD44.

CD44 is a ubiquitous multistructural and multifunctional cell surface adhesion molecule. The molecular diversity of this glycoprotein is generated by both post-translational modification and the differential use of alternatively spliced exons which play a critical role in determining the exact conformation of the molecule. CD44 isoforms are found in many tissues and in soluble form in plasma. Soluble CD44 was purified by a two-step purification combining ion exchange and immuno-affinity chromatography. Our aim was to check that all the known antigenic epitopes are present on sCD44, which could thus be used for the mapping of new anti-CD44 antibodies. Competitive binding assays using reference antibodies and novel anti-CD44 monoclonal antibodies were performed by real-time biospecific interaction analysis. Reference mAbs identified on soluble CD44 the three distinct epitopes previously defined using red blood cell membrane CD44. From the four novel CD44 mAbs, two mAbs (NaM198-6B5, NaM198-10B4) mapped to epitope group 1, whereas the others (NaM10-8F4, NaM77-9D6) mapped to epitope group 2. Immunopurified sCD44 obtained from the plasma of healthy donors appears to be a usable tool for the mapping of anti-CD44 mAbs.

Antibodies, Monoclonal↗

PubMedDate not supplied

Segmentation strategies for breast tumors from dynamic MR images.

This paper describes two semiautomated methods of segmentation of breast tumors from dynamic MR images obtained subsequent to administration of gadopentate dimeglumine. The first method, based on temporal correlation, generates a similarity map from the dynamic scans in which the value of each pixel is determined by its temporal similarity to a reference region of interest. The second method uses multispectral analysis and generates a feature map from a scatterplot of pixel intensities in the pre- and postcontrast images. The segmentation methods were tested on malignant and benign breast lesions in 11 patients with a range of tumor volumes and percentage contrast enhancement. The accuracy of both segmentation techniques and reproducibility of the multispectral method were investigated. A comparison of the two methods established that the temporal correlation method was superior based on accuracy, extent of user interaction, and speed of segmentation.

Breast Neoplasms↗

PubMed2005

Performance of the Roche AMPLICOR human papillomavirus (HPV) test in prediction of cervical intraepithelial neoplasia (CIN) in women with abnormal PAP smear.

OBJECTIVES: To assess the performance of a novel PCR-based assay (Roche AMPLICOR HPV test) in detection of cervical pathology as a part of management for abnormal PAP smear (MAPS) and in women participating in cervical cancer screening. STUDY DESIGN: Altogether, 504 women comprising 270 patients referred for colposcopy due to an abnormal Pap smear and another 234 women participating in cervical cancer screening (tested for comparison) were analyzed for oncogenic (HR) Human papillomavirus (HPV) types 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, and 68 using the Roche AMPLICOR HPV test in cervical samples collected in PreservCyt liquid media. Colposcopic biopsy and/or LEEP cone biopsy was used as the gold standard in the triage group, while liquid-based cytology (LBC) was the reference test in the screening group. RESULTS: The prevalence of HPV was significantly higher in the MAPS group (65.9%) than in the screening group (31.2%) (P = 0.0001). There was a poor concordance between the referral PAP and the current LBC, being only moderate in the screening series, ICC (weighted kappa) = 0.291 (95%CI 0.070-0.459) (P = 0.007), and almost poor in the MAPS Series, with ICC = 0.217 (95%CI 0.04-0.384) (P = 0.023). AMPLICOR HPV positivity increased linearly with the increasing grade of cervical lesions. In detecting high-grade (CIN2-3), colposcopy was the most sensitive test (96.5%), very similar to AMPLICOR (95.2%) (P = 0.731), while LBC with HSIL cutoff was by far the most specific test (99.5%) and showed the highest PPV (96.1%). NPV of colposcopy (97.2%) and AMPLICOR (96.7%) were similar (P = 0.839). Together with abnormal colposcopy and HSIL cytology, the AMPLICOR HPV test is a powerful independent predictor of high-grade CIN2-3, and as such suitable to replace cervical cytology in management of women with abnormal PAP test (MAPS). CONCLUSIONS: The Roche AMPLICOR HPV test is comparable to other HPV tests (HCII, PCR) in detecting CIN in MAPS. However, more data are clearly needed on the performance of AMPLICOR test in management of abnormal PAP and particularly as a screening tool.

Adolescent↗

PubMed2006

A genome-wide study of allelic imbalance in human testicular germ cell tumors using microsatellite markers.

Testicular germ cell tumors (TGCT) arise by multistep carcinogenesis pathways involving selective losses and gains of chromosome material. To locate cancer genes underlying this selection, we performed a genome-wide study of allelic imbalance (AI) in 32 tumors, using 710 microsatellite markers. The highest prevalence of AI was found at 12p, in line with previous studies finding consistent gain of the region in TGCTs. High frequency of AI was also observed at chromosome arms 4p, 9q, 10p, 11q, 11p, 13q, 16q, 18p, and 22q. Within 39 candidate regions identified by mapping of smallest regions of overlap (SROs), the highest frequency of AI was at 12p11.21 approximately p11.22 (62%), 12p12.1 approximately p13.1 (53%), 12p13.1 approximately p13.2 (53%), 11q14.1 approximately q14.2 (53%), 11p13 approximately p14.3 (47%), 9q21.13 approximately q21.32 (47%), and 4p15.1 approximately p15.2 (44%). Two genes known to be involved in cancer reside in these regions, ETV6 at 12p13.2 (TEL oncogene) and WT1 at 11p13. We also found a significant association (P = 0.02) between AI at 10q21.1 approximately q22.2 and higher clinical stage. This study contributes to the ongoing search for genes involved in transformation of germ cells and provides a useful reference point to previous studies using cytogenetic techniques to map chromosome changes in TGCTs.

Adolescent↗

PubMed2001

Human somatosensory area 2: observer-independent cytoarchitectonic mapping, interindividual variability, and population map.

We analyzed the topographical variability of human somatosensory area 2 in 10 postmortem brains. The brains were serially sectioned at 20 microm, and sections were stained for cell bodies. Area 2 was delineated with an observer-independent technique based on significant differences in the laminar densities of cell bodies. The sections were corrected with an MR scan of the same brain obtained before histological processing. Each brain's histological volume and representation of area 2 was subsequently reconstructed in 3-D. We found that the borders of area 2 are topographically variable. The rostral border lies between the convexity of the postcentral gyrus and some millimeters deep in the rostral wall of the postcentral sulcus. The caudal border lies between the fundus of the postcentral sulcus and some millimeters above it in the rostral wall. In contrast to Brodmann's map, area 2 does not extend onto the mesial cortical surface or into the intraparietal sulcus. When the postcentral sulcus is interrupted by a gyral bridge, area 2 crosses this bridge and is not separated into two segments. After cytoarchitectonic analysis, the histological volumes were warped to the reference brain of a computerized atlas and superimposed. A population map was generated in 3-D space, which describes how many brains have a representation of area 2 in a particular voxel. This microstructurally defined population map can be used to demonstrate activations of area 2 in functional imaging studies and therefore help to further understand the role of area 2 in somatosensory processing.

Adult↗

PubMed1991

A food polymer science approach to structure-property relationships in aqueous food systems: non-equilibrium behavior of carbohydrate-water systems.

Descriptions of the functional significance of carbohydrates based on the familiar equilibrium thermodynamics of very dilute solutions fail for pragmatical time scales and conditions, which are far from equilibrium. This is not too surprising, since limiting partial-molar properties reflect the independent behavior of solute in the limit of infinite dilution where free volume is maximum at a given temperature, while Tg'-Wg' properties reflect the cooperative behavior of solute-plasticizer blends at the limiting minimum value of free volume to observe relaxation within experimental time scales. Carbohydrate-water systems, with well-characterized structure and MW above and below the entanglement limit, provide a unique framework for the investigation of non-equilibrium behavior. Thermal analysis by DSC reveals the central role of water as a plasticizer for carbohydrates and of the glass transition as a physicochemical parameter that governs their properties, processing, and stability. A classical polymer science approach is used to study structure-property relationships of carbohydrates as water-compatible food polymers, which are treated as homologous systems of polymers, oligomers, and monomers with their plasticizers and solvents. Mechanical relaxation behavior is described by a "transformation map" of the critical variables of moisture content, temperature, and time. The glass curve is a reference contour, which represents the limiting isogram for free volume, local viscosity, relaxation rates, and rotational and translational mobility. Map domains are discussed as aspects of "water dynamics," to dispel the myth of "bound water," and "glass dynamics," to relate to macroscopic structure and collapse phenomena. A particular glass with invariant composition and Tg (prepared by freeze-concentration) is identified as a pivotal and practical reference state. The Tg observed during DSC analysis is often an effective Tg, resulting from instantaneous relative relaxation rates and non-uniform distribution of total sample moisture. Non-equilibrium melting, annealing, and gelation/recrystallization of kinetically metastable, partially crystalline carbohydrate systems exhibit non-Arrhenius kinetics which depend on the magnitude of delta T above the appropriate Tg, as defined by WLF relaxation transformations. Thermally reversible aqueous gels (crystallized from an under-cooled, rubbery melt) are described by a "fringed micelle" structural model for a three-dimensional polymer network, composed of microcrystalline junction zones crosslinking plasticized amorphous regions of flexible-coiled, entangled chain segments.

Carbohydrates↗

PubMed2026

Multimodal atlas of human atherosclerosis links granular vascular cell states to coronary artery disease risk.

Advances in single-cell and spatial assays have revolutionized the scale and resolution of molecular tissue profiling. Here we present MetaPlaq, a multimodal atlas of human atherosclerotic arterial beds comprising over a million cells across single-cell transcriptomics, epigenomics and high-resolution spatial expression assays. We map granular cell states and disease-relevant transcriptional programs within the native tissue context of coronary arteries. Furthermore, we map cardiovascular GWAS signals to smooth muscle cells (SMCs) and endothelial cells (ECs) and uncover the cis-regulatory architecture governing their phenotypic transitions. Our comprehensive epigenomic reference allowed us to build cell-specific enhancer-gene link maps and multimodal gene regulatory networks (GRNs) underlying disease-relevant states such as osteogenic SMCs and ECs undergoing mesenchymal transition. We also integrate SMC and EC disease-associated gene sets with GRNs to nominate key transcription factors such as PRRX1, BNC2 and ELK3 regulating atherosclerosis-relevant transcriptional programs. Finally, we layer single-cell and spatial modalities to fine-map GWAS variants with improved cell and anatomical context. We highlight candidate cell-specific regulatory mechanisms at less characterized CAD loci, including FGD5 and MCF2L in ECs. Together, this atlas represents an important step towards fully interpreting genetic risk loci and informing new therapeutic strategies for cardiovascular disease.

Journal Article↗

PubMed1999

Atrial flutter ablation using a technique for detection of conduction block within the posterior isthmus.

Catheter ablation orientated on the induction of a functional intraatrial block within the posterior isthmus of the tricuspid annulus has been shown to effectively abolish atrial flutter. In order to improve and simplify the current technique, a strategy based on an electrode catheter for combined right atrial and coronary sinus mapping and stimulation was explored prospectively. Twenty-four consecutive patients referred for catheter ablation of recurrent type I atrial flutter were included. A steerable 7 Fr catheter (Medtronic/Cardiorhythm) composed of two segments with 20 electrodes was used for right atrial and coronary sinus activation mapping and stimulation. Multiple steering mechanisms allowing intubation and positioning of the distal part within the coronary sinus were incorporated into the device. Adequate positioning of the mapping catheter was achieved solely via a transfemoral approach in all patients after 7.7 +/- 4.6 minutes, providing stable electrogram recordings during the entire ablation procedure. Radiofrequency current ablation (16.3 +/- 9.6 pulses) caused a significant bidirectional increase of the mean intraatrial conduction times via the posterior isthmus irrespective to the stimulation interval. Significant changes of intraatrial conduction properties were induced during ablation in 22 of 24 patients (bidirectional block: n = 18, unidirectional block: n = 3, conduction delay: n = 1, unchanged conduction: n = 2). Following ablation atrial flutter was noninducible in all patients. Twenty-two of 24 patients (92%) remained free of atrial flutter episodes during a follow-up of 12.5 +/- 5.7 months. Two of six patients without a bidirectional conduction block had a recurrence of atrial flutter. Atrial flutter ablation guided by the induction of an intraatrial conduction block can be effectively performed with this novel strategy for combined mapping of the posterior tricuspid isthmus, including coronary sinus and right atrial free wall. This transfemoral approach has a high accuracy with respect to the detection of radiofrequency current-induced changes of intraatrial conduction patterns.

Atrial Flutter↗

PubMed1993

Radiofrequency catheter ablation of sustained intra-atrial reentrant tachycardia in adult patients. Identification of electrophysiological characteristics and endocardial mapping techniques.

BACKGROUND: Information about electrophysiological characteristics and radiofrequency ablation of intra-atrial reentrant tachycardia has not been reported before. We proposed that induction and termination of intra-atrial reentrant tachycardia by atrial extrastimuli or rapid atrial pacing and resetting the response pattern by atrial extrastimuli during intra-atrial reentrant tachycardia could ensure the mechanism of reentry and that the earliest site of endocardial activation and concealed entrainment pace mapping with the shortest stimulus-P wave interval could localize a critical area responsible for intra-atrial reentrant tachycardia and radiofrequency ablation. METHODS AND RESULTS: Seven patients with refractory atrial tachycardia were referred for electrophysiological studies and radiofrequency ablation. Electrophysiological studies and endocardial mapping found (1) 10 atrial foci with atrial tachycardia cycle length of 406 +/- 41 ms; (2) atrial tachycardia had induction and termination by atrial extrastimuli (8 of 10) or rapid atrial pacing (10 of 10); (3) atrial tachycardia had increasing (6 of 10) or mixed (flat and increasing, 4 of 10) resetting response pattern, with resetting interval of 57 +/- 13 ms (14 +/- 4% of atrial tachycardia cycle length); (4) exit sites of atrial tachycardia in right atrial free wall (6 of 10), right atrial septum (3 of 10), and midposterior left atrium (1 of 10); and (5) earliest activation site had timing relative to P wave by -37 +/- 7 ms, and concealed entrainment pace mapping had shortest stimulus-P interval 23 +/- 3 ms. By the endocardial activation pace-mapping technique, radiofrequency energy (8 +/- 1 pulses, 31 +/- 3 W, 101 +/- 11 seconds) successfully eliminated the 10 atrial foci without recurrence (follow-up, 16 +/- 5 months). CONCLUSIONS: Mechanism of intra-atrial reentrant tachycardia could be confirmed by the electrophysiological characteristics, and radiofrequency ablation energy delivered to a critical area in the atrial reentrant circuit is safe and effective for the treatment of intra-atrial reentrant tachycardia.

Aged↗

PubMed2005

Mycoplasma gallisepticum hemagglutinin V1hA, pyruvate dehydrogenase PdhA, lactate dehydrogenase, and elongation factor Tu share epitopes with Mycoplasma imitans homologues.

Mycoplasma gallisepticum is a major pathogen of poultry. Mycoplasma imitans is genetically and antigenically closely related to M. gallisepticum, but so far, only a few proteins of M. imitans have been identified as sharing epitopes with M. gallisepticum. In this study, we identified three proteins of M. gallisepticum that share with M. imitans epitopes defined by monoclonal antibodies (MAbs). MAb 9D4 reacted with the 67-kD hemagglutinin V1hA (previously termed pMGA) of M. gallisepticum and with its continuously expressed 40-kD protein. This MAb also reacted with a 40-kD protein of M. imitans, but not with its putative V1hA. Two-dimensional (2D) immunoblots of M. gallisepticum strains showed that their 40-kD proteins reacting with MAb 9D4 are expressed as major forms with isoelectric points (pI) around 6, and also as less-abundant forms differing in pI. In M. imitans, major forms of 40-kD proteins recognized by MAb 9D4 had pI around 6, whereas minor forms had pI between 5.5 and 5.8. The N-terminal sequence of the M. gallisepticum 40-kD protein recognized by MAb 9D4 strongly indicates that this protein is pyruvate dehydrogenase E1, subunit alpha (PdhA protein, also termed AcoA). The position of elongation factor Tu (EF-Tu), detected by the reference MAb GB8, was very similar in the 2D proteome maps of M. gallisepticum and M. imitans (MW of about 45 kD; pI - 5.6). In both M. gallisepticum and M. imitans, MAb 7G1 reacted with proteins of about 36 kD with similar charges (major forms with pI of about 8). The position of this protein in the proteome map of M. gallisepticum and its N-terminal sequence strongly suggest that MAb 7G1 recognizes lactate (malate) dehydrogenase (Ldh or Mdh). Comparison of 2D proteomes of 10 M. gallisepticum strains indicated that positions of EF-Tu, PdhA, and Ldh proteins are rather consistent and can be used as reference points in further analyses of the M. gallisepticum proteome.

Amino Acid Sequence↗

PubMed2005

Feasibility study of new calibrators for thyroid-stimulating hormone (TSH) immunoprocedures based on remodeling of recombinant TSH to mimic glycoforms circulating in patients with thyroid disorders.

BACKGROUND: Differences between the glycosylation patterns of a pituitary thyroid-stimulating hormone calibrator (pitTSH) and serum samples have been shown to be responsible for nonidentical epitope expression and for introducing discrepancies in TSH measurements. We studied the feasibility of developing new candidate reference materials by remodeling recombinant TSH (recTSH) to generate potential mimics of serum TSH. METHODS: Terminal sialylation and/or inner fucosylation of recTSH were remodeled by a combination of enzyme treatments followed (or not) by lentil lectin-Sepharose affinity chromatography. The resulting TSH preparations were screened for epitope similarity in 23 immunoassays mapping 3 antigenic clusters common to the pitTSH 2nd International Reference Preparation (IRP) and the recTSH 1st IRP and then challenged against a pool of 63 patients with increased serum TSH (>60 mIU/L). RESULTS: pitTSH was poorly correlated with serum TSH, with a mean (SD) slope of 2.124 (0.001), in contrast to recTSH [slope, 1.178 (0.056)]. Comparison of variably sialylated preparations with recTSH gave slopes of 0.860 (0.057) for desialylated TSH, 1.064 (0.057) for alpha2,3/6-oversialylated recTSH, and 0.953 (0.033) for alpha2,6-resialylated recTSH, indicating that TSH forms enriched in sialic acid closely resemble serum TSH. Further testing against serum TSH showed satisfactory agreement with both TSH preparations containing alpha2,6-sialic acid [slopes, 1.064 (0.057) and 0.953 (0.033)], particularly in the absence of nonfucosylated forms [0.985 (0.044)]. CONCLUSIONS: Glyco-engineered recTSH preparations enriched in sialic acid and inner fucose are promising candidates for future reference materials. These preparations may have advantages over existing preparations used for standardizing TSH measurements.

Calibration↗

PubMed1994

Monoclonal antibodies against HIV type 1 integrase: clues to molecular structure.

Eleven murine hybridoma clones were selected for their ability to produce anti-HIV-1 integrase (IN) antibodies. Competition and epitope mapping studies allowed segregation of the monoclonal antibodies (MAbs) into four distinct classes. The five MAbs that comprise the first class showed high affinity for epitopes within an N-terminal domain of 58 amino acids that includes a conserved zinc finger motif. The second class, with two MAbs, showed high affinity for epitopes within 29 amino acids at the C terminus. Another two MAbs, which constitute the third class, displayed moderate affinities for epitopes that mapped to regions within the highly conserved catalytic core referred to as the D,D(35)E domain. One of these MAbs showed significant cross-reactivity with HIV-2 IN and weak, but detectable, cross-reactivity with RSV IN. The remaining two MAbs, which comprise the fourth class, exhibited fairly low binding affinities and appeared to recognize epitopes in the zinc finger motif domain as well as the C-terminal half of the IN protein. The MAbs can be used for immunoprecipitation and immunoblotting procedures as well as for purification of HIV-1 IN protein by affinity chromatography. We show that several can also be used to immunostain viral IN sequences in HIV-1-infected T cells, presumably as a component of Gag-Pol precursors. Finally, analysis of our mapping and competition data suggests a structure for mature IN in which the C terminus approaches the central core domain, and the N and C termini touch or are proximal to each other. These MAbs should prove useful for further analyses of the structure and function of IN both in vitro and in vivo.

Amino Acid Sequence↗

PubMed2006

Ultrastructure and gene mapping of the albino mutant al12 in rice (Oryza sativa L.).

Seedling albino mutation resistant to low temperature is an adaptability of rice (Oryza sativa L.) to cold. The mutant, a conditional expression controlled by development and temperature, differs from other albino mutants. The chlorophyll content of the mutant was measured using a portable chlorophyll meter, and the ultrastructure of the chloroplast was observed using a transmission electron microscope. Chlorophyll content was 1.2 SPAD, and the chloroplast did not develop, with only small vesicle-like structures. A segregation analysis of the reciprocal crosses between the albino mutation line with the rice line 9311 demonstrated that the albino trait was controlled by a single recessive gene, which was flanked by SSR markers RM5068 and RM3702 on the short arm of chromosome 8 with a distance of 0.5-1.1 cM and 4.9 cM, respectively. This gene was mapped within a 6 cM interval region and was tentatively referred to as al12.

Adaptation, Biological↗

PubMed1996

Acceleration of EEG theta wave precedes the phasic surge of arterial pressure during REM sleep in the rat.

We investigated temporal relationships among EEG theta frequency, eye movement (EM) burst and phasic surge of arterial pressure (AP) during rapid eye movement (REM) sleep in six rats. Changes in EEG theta frequency, EM number, mean AP (MAP) and heart rate (HR) during 1 s bins were obtained with reference to the onset of the EM bursts. The acceleration of EEG theta frequency preceded both the EM burst and the phasic increases of AP. The increase of MAP was closely correlated with the theta frequency but not the EM number during the period of EM burst. The possible involvement of the limbic system for the generation of phasic surge in AP during REM sleep is discussed.

Animals↗

PubMed2007

Evaluation of Phi29-based whole-genome amplification for microarray-based comparative genomic hybridisation.

For the optimal performance of high throughput genomic technologies sufficient yields of high-quality DNA are crucial. Following microdissection, most samples fail to produce sufficient quantities of DNA for genome-wide experiments. Various PCR-based amplification methods have been used, but these usually produce nonuniform representations of the genome. Bacteriophage Phi29 DNA polymerase random-primed DNA amplification is based on isothermal multiple displacement amplification. We sought to define the genome representation of this method in a bacterial artificial chromosome microarray comparative genomic hybridisation (aCGH) platform. Test genomic female DNA was amplified using Phi29 amplification at four different starting concentrations (0.5, 5, 10 and 50 ng). These products were combined with unamplified and amplified genomic female DNA as reference. In addition, 50 ng of DNA from five microdissected breast cancer frozen samples, were amplified using the same method. Three combinations were performed: unamplified test with unamplified reference, amplified test with unamplified reference and both amplified tumour and reference DNA. aCGH was performed with an in-house 16 K BAC platform (a resolution of approximately 100 Kb). Pearson's correlation tests and hierarchical clustering were performed to compare the profiles obtained. aCGH profiles obtained with amplified test and unamplified reference female genomic DNA showed copy number biases throughout the genome. These biases were more conspicuous with smaller amounts of starting material and mapped to regions of known copy number polymorphisms. When similar concentrations of test and reference DNA were amplified, the biases were significantly reduced, rendering accurate profiles. For the tumours, representative profiles were obtained when both test and reference DNA were amplified. Phi29 amplification induces copy number biases and unamplified material remains the gold standard for copy number analysis. For accurate results using Phi29 amplification, samples subjected to aCGH analysis should be combined with reference DNA amplified with the same method, using similar amounts of starting template.

Breast Neoplasms↗

PubMed1993

The retinoblastoma-related gene, RB2, maps to human chromosome 16q12 and rat chromosome 19.

A retinoblastoma-related human gene, referred to as RB2, has been cloned based on sequence homology of the E1A-binding domain of the retinoblastoma gene. Structural homology with the retinoblastoma gene suggests a possible function of RB2 as a tumor suppressor gene. In this study, we have mapped this gene to human chromosome 16q12.2 and rat chromosome 19, using fluorescence in situ hybridization and somatic hybrid cell analysis, respectively. Based on known syntenic relationships among human, rat and mouse, the data suggest that the mouse homolog resides on chromosome 8. Deletions of chromosome 16q have been found in several human neoplasias (including breast, ovarian, hepatic, and prostatic cancers) which is in support of an involvement of RB2 in human cancer as a tumor suppressor gene.

Animals↗