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PubMed2003

Zinc-based fixative improves preservation of genomic DNA and proteins in histoprocessing of human tissues.

Advantageous preservation of histology and detailed cellular morphology has rendered neutral buffered formalin (NBF) the most widely used fixative in clinical pathology. Despite excellent morphology for routine diagnostics, a major drawback of NBF fixation is its detrimental effect on DNA and RNA quality. In addition to complicating analysis of genes and transcripts in complex tissues, NBF denatures proteins and thereby hampers immunohistochemical visualization of certain antigens. In the present study, we evaluated a zinc-based fixative (ZBF) regarding its effects on tissue morphology, quality of genomic DNA, and preservation of protein immunoreactivity in a broad spectrum of tissues. Four different modes of fixation were analyzed: ZBF-paraffin embedding, NBF-paraffin embedding, ZBF-fixation prior to snap-freezing, and immediate snap-freezing. Laser-assisted microdissection, allowing retrieval of a defined number of cells for PCR, was used to study DNA quality. Genomic DNA was analyzed using primers for beta2-microglobulin and the transferrin receptor. Immunohistochemistry was performed using nine antibodies. Tissue microarray blocks were used for analysis of morphology and immunoreactivity. Only slight impairment of morphologic qualities was found after ZBF-paraffin embedding, whereas ZBF prior to freezing resulted in a more crisp morphology compared with routine cryosections. A significantly higher DNA yield was observed in samples isolated from ZBF-paraffin-embedded tissues compared with NBF-paraffin-embedded tissues. Both yield and quality of DNA was comparable in frozen tissues irrespective to prior ZBF fixation. Immunoreactivity in paraffin-embedded tissue was superior in ZBF-fixated tissue compared with NBF-fixated for a majority of tested antibodies. Furthermore, for seven out of nine antibodies, antigen retrieval pretreatment proved unnecessary in ZBF-fixated tissue. Thus, despite a slight impairment of morphology, ZBF preserves protein structures well. We conclude that ZBF is superior to NBF for analysis of DNA and protein expression. Fixation of tissues in ZBF may also be an alternative strategy to freeze storage of tissue specimens, eg, in future bio-banks.

Carcinoma, Transitional Cell↗
PubMed2003

Clonal tracking of autoaggressive T cells in polymyositis by combining laser microdissection, single-cell PCR, and CDR3-spectratype analysis.

Clonal expansions of CD8+ T cells have been identified in muscle and blood of polymyositis patients by PCR techniques, including T cell receptor (TCR) complementarity-determining region (CDR)3 length analysis (spectratyping). To examine a possible pathogenic role of these clonally expanded T cells, we combined CDR3 spectratyping with laser microdissection and single-cell PCR of individual myocytotoxic T cells that contact, invade, and destroy a skeletal muscle fiber. First, we screened cDNA from muscle biopsy specimens by CDR3 spectratyping for expanded TCR beta chain variable region (BV) sequences. To pinpoint the corresponding T cells in tissue, we stained cryostat sections with appropriate anti-TCR BV mAbs, isolated single BV+ T cells that directly contacted or invaded a muscle fiber by laser-assisted microdissection, and amplified their TCR BV chain sequences from rearranged genomic DNA. In this way, we could relate the oligoclonal peaks identified by CDR3-spectratype screening to morphologically characterized microdissected T cells. In one patient, a large fraction of the microdissected T cells carried a common TCR-BV amino acid CDR3 motif and conservative nucleotide exchanges in the CDR3 region, suggesting an antigen-driven response. In several cases, we tracked these T cell clones for several years in CD8+ (but not CD4+) blood lymphocytes and in two patients also in consecutive muscle biopsy specimens. During immunosuppressive therapy, oligoclonal CDR3-spectratype patterns tended to revert to more polyclonal Gaussian distribution-like patterns. Our findings demonstrate that CDR3 spectratyping and single-cell analysis can be combined to identify and track autoaggressive T cell clones in blood and target tissue. This approach should be applicable to other inflammatory and autoimmune disorders.

Adult↗
PubMed2002

Resolution of genotypic heterogeneity in prostate tumors using polymerase chain reaction and comparative genomic hybridization on microdissected carcinoma and prostatic intraepithelial neoplasia foci.

Prostate cancer (CaP) is a multifocal heterogenous disease. A major challenge in CaP research is to identify genetic biomarkers that herald aggressive transformation. To investigate the effect of tumor heterogeneity on the analysis of genomic aberration, we compared the results of comparative genomic hybridization (CGH) analysis of DNA extracted from tumor bulk against that of DNA amplified by degenerate oligonucleotide primed polymerase chain reaction (DOP-PCR) from homogeneous cell population obtained by laser capture microdissection of discrete tumor foci. Sampling by microdissection, aberrations were observed in three of three foci of carcinoma involved with prostatic capsule, and in two of three prostatic intraepithelial neoplasia (PIN) foci examined. Carcinoma foci consistently exhibited more extensive aberrations than the PIN samples obtained from the same tumor. Within these samples, the different tumor foci exhibited gain of 8q, whereas PIN showed no consistent aberration. Using bulk extracted DNA, CGH detected aberrations in only 3 of 21 samples investigated, despite the known trisomy 8 status, as revealed by fluorescence in situ hybridization. The results of this study demonstrate that CGH analysis using bulk dissected fresh tissue is insufficiently sensitive to fully detect the chromosomal numerical aberrations in CaP. Given the considerable intratumor genomic heterogeneity, CGH with microdissection and DOP-PCR amplification provides a more complete repertoire of aberrations as well as a better phenotype-genotype correlation in prostate tumors.

Carcinoma↗
PubMed1998

The microdissection cautery needle versus the cold scalpel in bicoronal incisions.

Craniofacial procedures commonly use scalp incisions to optimize surgical access and aesthetic results. Although the use of traditional electrocautery instruments on hair-bearing tissue has been limited secondary to the width of resulting alopecia, needle-tipped electrocautery devices with decreased energy transmission have been developed. This study investigates the cosmetic effect of such instruments on scalp incisions. Twelve children undergoing craniosynostotic correction via bicoronal incisions were included. One side of the incision was completed with the cold scalpel whereas the contralateral portion was effected using the Colorado MicroDissection Needle (Colorado Biomedical Inc., Evergreen, CO, U.S.A.) according to optimal usage instructions. At the conclusion of the study period, precise measurements of the resultant width of alopecia were obtained from the parietal and temporal regions bilaterally, and were analyzed statistically. Also, parents completed a questionnaire concerning subjective observations of the surgical incision and its healing. The portions of the incision completed with the Colorado MicroDissection Needle demonstrated a wider area of peri-incisional alopecia (5.8 +/- 1.8 mm) than that produced by the cold scalpel (3.5 +/- 0.87 mm). Not only was this increased width significant statistically (P < 0.05), in addition the disparity was noted by the majority of parents (10 of 12) either on the patient questionnaire or with nonsuggestive verbal questioning. The benefit of the hemostatic incisional technique of electrocautery with even needle-tipped instruments must be weighed carefully against its cosmetic consequences.

Alopecia↗
PubMed2000

[Microdissection--an important tool in molecular biology].

Our knowledge of cell biology is increasing rapidly through the introduction of new molecular biology techniques. Pathological processes always involve a number of cell types; obviously, there is a critical need to know exactly what is being examined. This can be achieved by applying in situ techniques (immunohistochemistry, in situ hybridization, and in situ PCR) on the light microscopical and electron microscopical levels. Microdissection of cells/tissues is an alternative approach. This can be done manually or with the help of a laser, which allows the dissection of single cells. The methods can be used on frozen tissues as well as on paraffin embedded material. Although the ensuing DNA material is not always optimal for further analysis, it is possible to apply special techniques to approve the situation, such as whole genome amplification PCR. Microdissection of cell clones allows us to analyse interactions between tumour cells and stromal cells. Microdissection is based on a simple principle and has proved to be very important in molecular biology analysis of histological material.

Clone Cells↗
PubMed2004

[Laser microdissection and molecular typing of dysplastic cells from Pap smears: a new approach to early detection of cervical cancer].

The Papanicolaou smear (Pap) is a worldwide screening tool for early detection of cervical cancer and its precursor lesions. The transition from dysplasia to cancer is a highly complex genetic process and cannot be predicted based solely on cell morphology. Molecular characterization of precursor lesions could yield a better definition of lesions at high risk for progression. We developed an analytical concept comprising not only morphological characterization but also molecular analysis with multiple parameters of dysplastic cells from cervical smears. We isolated dysplastic cells from 52 fixed Pap-stained smears of various grades by laser microdissection and analyzed them for genetic lesions typical for cervical carcinoma. The loss of heterozygosity (LOH) as published for cervical carcinoma tissue was detected. Markers for early stages showed a LOH in 43% and 22%, and those for late stages in 26% of the cases. Combining morphological characterization with molecular analysis by multiple molecular markers could open up new opportunities for early detection of cervical carcinoma.

Female↗
PubMed1997

The soft-tissue components of the vomeronasal organ in pigs, cows and horses.

The soft-tissue components of the vomeronasal organ of the pig, the cow and the horse were studied with the aid of dissection, microdissection, and light microscopy and immunohistochemistry of series of transverse sections. In horses, the rostral end of the incisive duct was blind: thus, unlike in pigs and cows, there was no communication between the vomeronasal organ and the oral cavity. In all three species, the central part of the vomeronasal duct bore the 'typical' respiratory/ receptor epithelium lining on its lateral and medical walls. The rostral part of the duct was characterized by stratified columnar epithelium, while more caudal parts bore simple columnar type. The patterns of distribution of glands, blood vessels and nerves were closely associated with the patterns of distribution of duct linings. The distribution of soft-tissue components in pigs was less clearly defined than in cows and horses. Of the three species, nerves were detected in the rostral half of the vomeronasal parenchyma only in the horse.

Animals↗
PubMed2006

A novel histology-directed strategy for MALDI-MS tissue profiling that improves throughput and cellular specificity in human breast cancer.

We describe a novel tissue profiling strategy that improves the cellular specificity and analysis throughput of protein profiles obtained by direct MALDI analysis. The new approach integrates the cellular specificity of histology, the accuracy and reproducibility of robotic liquid dispensing, and the speed and objectivity of automated spectra acquisition. Traditional methodologies for preparing and analyzing tissue samples rely heavily on manual procedures, which for various reasons discussed, restrict cellular specificity and sample throughput. Here, a robotic spotter deposits micron-sized droplets of matrix precisely onto foci of normal mammary epithelium, ductal carcinoma in situ, invasive mammary cancer, and peritumoral stroma selected by a pathologist from high resolution histological images of sectioned human breast cancer samples. The location of each matrix spot was then determined and uploaded into the instrument to facilitate automated profile acquisition by MALDI-TOF. In the example shown, the different lesions were clearly differentiated using mass profiling. Further, the workflow permits a visual projection of any information produced from the profile analyses directly on the histological image for a unique combination of proteomic and histological assessment of sample regions. The higher performance characteristics offered by the new workflow promises to be a significant advancement toward the next generation of tissue profiling studies.

Adult↗
PubMed1991

Morphometry and cell proliferation in endoscopic biopsies: evaluation of a technique.

A simple method for the quantification of intestinal epithelial cell proliferation in humans was evaluated. Endoscopic biopsy specimens were stained and microdissected, and the number of mitoses per gland or crypt was determined, as was the area of these units. The technique could readily be applied to tissue from the stomach, small intestine colon, and rectum. The number of mitoses and the size of the proliferative compartments increased caudally from the stomach to the cecum in humans. There was a good correlation between area and mitoses per gland or per crypt (r = 0.89; P less than 0.001), confirming the general equivalence between proliferative rate and compartment size. The method was validated by comparing microdissection-derived data with data previously obtained as part of an autoradiography-based study in the dog. This showed that similar differences in proliferation and crypt cell mass could be obtained but in less than one sixth of the time taken to score autoradiographs. It is concluded that this method for the estimation of gastrointestinal epithelial proliferation correlates well with other well-established techniques, confers speed as well as accuracy, has an all encompassing denominator, and can thus avoid many of the problems associated with the quantification of tissue sections.

Animals↗
PubMed1989

An improved method for Lowicryl K4M electron microscopic embedding of brain tissue.

The Lowicryl K4M low-temperature embedding technique was modified for brain tissue to facilitate antigen localization in neuronal structures by using postembedding immunoelectron microscopy. Rat brains fixed by perfusion with a mixture of 1% glutaraldehyde and 1% paraformaldehyde, were sectioned into 200-microns-thick coronal sections, and the appropriate area of the sections further microdissected into small samples (200 x 700 x 700 microns). These samples were processed for K4M embedding using prolonged incubation times at each step. This resulted in a homogeneously infiltrated tissue with good preservation of ultrastructure and antigen reactivity. Despite the lack of osmium fixation, the morphology of the synapses was clearly identifiable.

Acrylic Resins↗
PubMed2003

Distinct gene expression profiles characterize the histopathological stages of disease in Helicobacter-induced mucosa-associated lymphoid tissue lymphoma.

Long-term colonization of humans with Helicobacter pylori can cause the development of gastric B cell mucosa-associated lymphoid tissue lymphoma, yet little is known about the sequence of molecular steps that accompany disease progression. We used microarray analysis and laser microdissection to identify gene expression profiles characteristic and predictive of the various histopathological stages in a mouse model of the disease. The initial step in lymphoma development is marked by infiltration of reactive lymphocytes into the stomach and the launching of a mucosal immune response. Our analysis uncovered molecular markers of both of these processes, including genes coding for the immunoglobulins and the small proline-rich protein Sprr 2A. The subsequent step is characterized histologically by the antigen-driven proliferation and aggregation of B cells and the gradual appearance of lymphoepithelial lesions. In tissues of this stage, we observed increased expression of genes previously associated with malignancy, including the laminin receptor-1 and the multidrug-resistance channel MDR-1. Finally, we found that the transition to destructive lymphoepithelial lesions and malignant lymphoma is marked by an increase in transcription of a single gene encoding calgranulin AMrp-8.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed2003

Monoaminergic activity in subregions of raphé nuclei elicited by prior stress and the neuropeptide corticotropin-releasing factor.

Corticotropin-releasing factor (CRF) coordinates neuroendocrine responses to stressful stimuli; one mechanism through which CRF may modulate hypothalamic-pituitary-adrenal axis activity is via actions on neuromodulatory systems such as serotonergic systems. Recent electrophysiological studies and the distribution of CRF receptors within midbrain and pontine raphé nuclei suggest that stress and CRF may have actions on topographically organized subpopulations of serotonergic neurones. We compared the effects of vehicle or intracerebroventricular r/hCRF injections (0, 0.1, 1 or 10 micro g) in rats previously maintained in home cages or restrained for 1 h, 24 h before injection, on monoamine and monoamine metabolite tissue concentrations in the dorsal (lateral wings, rostral midline, caudal midline), median (rostral, caudal) and interfascicular raphé subdivisions of the midbrain and pontine raphé nuclei, using brain microdissection and high-performance liquid chromatography with electrochemical detection. At the lowest dose studied (0.1 micro g), CRF infusions in previously stressed rats decreased 5-hydroxytryptophan (5-HTP) and 5-hydroxyindoleacetic acid (5-HIAA) concentrations only within the rostral median raphé nucleus. At higher doses, CRF infusions in previously stressed rats increased tissue concentrations of 5-HTP, serotonin (5-HT), or the serotonin metabolite, 5-HIAA, within rostral (but not caudal) regions of the median and dorsal raphé nuclei. By contrast, restraint stress alone had no effect on tissue concentrations of 5-HTP, 5-HT or 5-HIAA measured 24 h later in any subdivision, while CRF injections in rats not previously exposed to restraint stress, with few exceptions, also had no effect. These results suggest that the effects of CRF on serotonergic function are context-dependent, dose-dependent, and regionally specific within subdivisions of the brainstem raphé nuclei.

5-Hydroxytryptophan↗
PubMed1999

Preliminary analysis of azoxymethane-induced colon tumorigenesis in mouse aggregation chimeras.

Inbred mice exhibit differential susceptibility to colon carcinogens. The following study addresses the possibility that differences are intrinsic to colonic mucosa (cell autonomous) or are mediated by extracolonic systemic factors (e.g. liver activation of carcinogens). Our approach was to construct mouse aggregation chimeras, mice whose tissues are a mosaic of cells derived from two parental genotypes, from a susceptible (SWR) and a resistant (DBA/2) strain. Forty-five embryo aggregations yielded 11 viable pups, four of which were chimeric by coat color. Six-week-old SWR<-->BA/2 chimeras were injected i.p. with azoxymethane (AOM) once a week for 8 weeks (5 and 7.5 mg/kg body wt for 2 weeks followed by 10 mg/kg for 6 weeks) and tumor incidence in distal colon was evaluated 15 weeks after the last injection. Additional groups of parental mice received the same treatment. In the parental SWR treatment group, 1.7 +/- 0.82 tumors/colon were found. No tumors were observed in AOM-treated DBA/2 mice. In SWR<-->DBA/2 chimeras exposed to AOM, 2.8 +/- 2.1 tumors/colon were found. Tumor lineage was examined in paraffin sections stained with Dolichos biflorus agglutinin-peroxidase, a cell surface specific marker that stains intestinal endothelial cells of SWR and epithelial cells of DBA/2. Cellular lineage of tumors was further evaluated by microsatellite analysis of DNA isolated by microdissection. There was no significant difference in tumor incidence between SWR parental and chimera treatment groups. Histochemical analysis of tumor tissue in chimeras suggested that most tumors were derived from SWR. However, subsequent genetic analysis of tumors indicated mixed parental composition. These preliminary studies suggest that DBA/2 resistance mechanisms are not sufficient to protect adjacent SWR-derived epithelium from the tumorigenic effects of AOM.

Animals↗
PubMed1996

Nuclear DNA content and pathology in radically treated pancreatic carcinoma. The prognostic significance of DNA ploidy, histology and nuclear grade.

BACKGROUND: Nuclear DNA content and pathology are considered to be prognostically relevant in several solid tumors, but controversial findings have emerged in pancreatic carcinoma (PC). Histopathology and DNA ploidy were each correlated with survival in radically treated PC to ascertain the hierarchy of their prognostic significance. METHODS: DNA ploidy was assessed by flow cytometry (FC) in neoplastic tissue samples from 60 patients with PC who were followed until death. Representative neoplastic areas were obtained by microdissection from archival paraffin embedded material (excluding any carcinoma with a coefficient of variation of the G0/G1 peak higher than 8%). Histologic data and FC patterns were related to prognostic behavior using univariate multivariate statistical analysis. RESULTS: Aneuploid cancers were detected in 39 of 60 patients. Univariate analysis showed that histologic grade, nuclear grade, and ploidy were significantly related to prognosis. On multivariate analysis, only histologic grade and DNA ploidy (diploid vs. aneuploid) were significant with significant interaction. CONCLUSIONS: The prognostic value of pathology and ploidy was demonstrated in patients treated radically for PC. As in other tumors characterized by a short survival, the clinical usefulness of any prognostic parameters is somewhat limited. However, the significant relationship between prognosis and DNA ploidy might be of interest in a cost-benefit analysis for selecting patients in whom an attempt at radical surgical treatment or adjunctive chemotherapy may be justified.

Adult↗
PubMed2001

Rapid changes in monoamine levels following administration of corticotropin-releasing factor or corticosterone are localized in the dorsomedial hypothalamus.

Monoaminergic systems are important modulators of the neuroendocrine, autonomic, and behavioral responses to stress-related stimuli. The male roughskin newt (Taricha granulosa) was used as a model system to investigate the effects of corticotropin-releasing factor (CRF) or corticosterone administration on tissue concentrations of norepinephrine, epinephrine, dopamine, 3,4-dihydroxyphenylacetic acid, serotonin, and 5-hydroxyindoleacetic acid (5-HIAA) in microdissected brain areas. Intracerebroventricular infusion of 25 or 50 ng of CRF increased locomotor activity and site-specifically increased dopamine concentrations within the dorsomedial hypothalamus 30 min after treatment when compared to vehicle-treated controls. In further studies, male newts were treated as follows: (1) no injection, no handling, (2) saline injection, or (3) 10 microg corticosterone and then placed in a novel environment. Monoamine and monoamine metabolite concentrations were similar in the unhandled and saline-injected controls 20 min after treatment. In contrast, corticosterone-injected newts had elevated concentrations of dopamine, serotonin, and 5-HIAA in the dorsomedial hypothalamus (a region that contains dopamine- and serotonin-accumulating neuronal cell bodies in representatives of all vertebrate classes) but not in several other regions studied. These site-specific neurochemical effects parallel neurochemical changes observed in the dorsomedial hypothalamic nucleus of mammals following exposure to a variety of physical and psychological stress-related stimuli. Therefore, these changes may reflect highly conserved, site-specific neurochemical responses to stress and stress-related neurochemicals in vertebrates. Given the important role of the dorsomedial hypothalamus in neuroendocrine, autonomic, and behavioral responses to stress, and a proposed role for this region in fast-feedback effects of glucocorticoids on the hypothalamo-pituitary-adrenal axis, these stress-related monoaminergic changes are likely to have important physiological or behavioral consequences.

Animals↗
PubMed2004

Prognostic significance of dysadherin expression in cervical squamous cell carcinoma.

The protein and mRNA expression of dysadherin was studied in a series of squamous cell cervical carcinomas, and their clinicopathological associations and prognostic value were explored. Immunohistochemistry was used to assess protein expression of dysadherin in 206 patients with squamous cell cervical carcinoma, FIGO stage Ia-IVb. Frozen tissues from 20 cases in which the tumors showed variable dysadherin protein expression were used for laser capture microdissection (LCM) and processed for RTPCR detection of dysadherin mRNA. Immunohistochemically, all the dysadherin-positive staining was membranous. Positive cell membranous dysadherinpositive staining was often observed at the edge of tumor nests, although strong immunoreactivity throughout whole tumor nests was also seen in some tumors. Basal cells of the normal cervical epithelia were positive for dysadherin while its expression in the squamous cell cervical carcinomas was variable. Among the 206 tumors, 23 (11.2%) were negative, 53 (25.7%) were scored 1+, 54 (26.2%) were scored 2+ and 76 (36.9%) were scored 3+. In the 20 tumors analyzed, mRNA expression of dysadherin basically corresponded to its protein expression. No significant correlation between expression of dysadherin and age, FIGO stage or lymph node status was observed. Higher level of dysadherin expression, however, was significantly associated with shorter overall survival (p=0.04). We conclude that there is dysadherin protein expression in basal and parabasal cells of normal cervical epithelia, and higher level of dysadherin protein expression in squamous cell cervical carcinoma is predictive of a shorter overall survival, indicating that dysadherin may be a valuable prognostic marker in cervical carcinoma.

Adult↗
PubMed1998

Qualitative and quantitative analysis of synapses in Hirschsprung's disease.

In Hirschsprung's disease (HD), certain intestinal nervous plexuses are absent. Sprouting nerve endings contain different amounts of synaptophysin (SY), a protein and main constituent of acetylcholinesterase (AChE) storage compartments. Due to the lack of specific markers for synapses, a qualitative analysis of nerve endings of intestinal segments affected by HD has not yet been undertaken. For this study, resected colorectal specimens from patients with HD (n = 8, mean age 2.1 years) were investigated in parallel for AChE, SY, and content of small synaptic vesicles by biochemical, immunohistochemical, and electronmicroscopic means. In the microdissected muscular layer, reduced SY (1.4 microgram/mg total protein, normal 24 +/- 0.3) was observed. Immunohistochemistry showed in affected tissues reduced numbers of SY-positive nerve fibers and nerve endings, which in turn were thickened and distorted, in both the muscle proper and the muscularis mucosae. Combining both morphologic and biochemical findings, in HD the number of cholinergic vesicles in the remaining nerve endings seems to be increased as measured by SY, a marker molecule specific for synaptic vesicles. Our data also suggest that nerve endings in HD may contain high concentrations of cholinergic vesicles, paralleling the known high amounts of acetylcholine and AChE found in intestinal segments of patients with HD.

Acetylcholinesterase↗
PubMed2006

Genome-wide detection of allelic imbalance in renal cell carcinoma using high-density single-nucleotide polymorphism microarrays.

OBJECTIVE: Renal cell carcinoma (RCC) appears in both a sporadic form and a hereditary form. Eighty-five percent of sporadic RCCs are of the clear-cell histologic type. The cytogenetic analysis of RCCs has revealed several recurring sites of chromosomal aberrations (non-disjunction, deletion or mitotic recombination) including segments of loss of heterozygosity (LOH) identifiable by polymorphic markers. In this pilot study, we performed a comprehensive genome-wide scan to identify LOH sites of RCCs in three Chinese patients using high-density single-nucleotide polymorphism microarrays (HuSNP arrays). DESIGN AND METHODS: Three sporadic clear-cell RCCs specimens were diagnosed histologically. Tumor genomic DNA was extracted from paraffin-embedded sections after microdissection to avoid gross contamination by non-tumor cells. Germline DNA was obtained from paired normal adjacent tissues. Affymetrix HuSNP mapping assay was performed according to the manufacturer's instructions. RESULTS: Using high-density single-nucleotide polymorphism microarrays, we were able to identify the previously described and new LOH sites in RCCs of the three Chinese patients. CONCLUSION: The high-density single-nucleotide polymorphism microarrays and assays offer significant operating cost benefits in sample preparation, processing, and data analysis for identification of LOH sites in cancer samples. In contrast to the typical microsatellite genotyping strategy, the entire genome scan is completed in one experiment taking less than 2 days.

Allelic Imbalance↗