Three-color Fluorescence In Situ Hybridization Research Articles

Predicting Normal Tissue Radiotoxicity in Radiotherapy Patients Based on the Individual Radiosensitivity Using Three-Color Fluorescence In Situ Hybridization: A Literature Review

Background: The variability of clinical response in radiotherapy (RT) patients revealed that individual radiosensitivity exists in humans. Although several techniques for radiosensitivity assessment are available, fluorescence in situ hybridization (FISH) has proven to be the most reliable cytogenetic technique. This study will review the use of three-color FISH to evaluate the individual radiosensitivity in cancer patients, particularly breast and prostate cancer patients. Also, it will explain factors that should be considered when using this assay in RT patients.Methods: We used the “radiosensitivity”, “fluorescence in situ hybridization”, “FISH”, and “cancer” as medical subject headings. Non-English articles were excluded. Only articles written in English with a full-text PDF format could be found and using three-color FISH for individual radiosensitivity prediction in radiotherapy patients as subjects were included in this review.Results: : In total, 1,905 articles were retrieved from PubMed and PubMed Central databases from 1990 to 2020. The articles were screened, and those that met the inclusion criteria and did not meet the exclusion criteria were reviewed. Finally, we evaluated eight articles in this reviewConclusions: Appropriate assays such as three-color FISH for individual radiosensitivity assessment could optimize the effectiveness of RT treatment and predict the severity of normal tissue toxicity reactions in RT patients.

Kinase inhibitors increase individual radiation sensitivity in normal cells of cancer patients

PurposeKinase inhibitors (KI) are known to increase radiosensitivity, which can lead to increased risk of side effects. Data about interactions of commonly used KI with ionizing radiation on healthy tissue are rare.Patients and methodsFreshly drawn blood samples were analyzed using three-color FISH (fluorescence in situ hybridization) to measure individual radiosensitivity via chromosomal aberrations after irradiation (2 Gy). Thresholds of 0.5 and 0.6 breaks/metaphase (B/M) indicate moderate or clearly increased radiosensitivity.ResultsThe cohorts consisted of healthy individuals (NEG, n = 219), radiosensitive patients (POS, n = 24), cancer patients (n = 452) and cancer patients during KI therapy (n = 49). In healthy individuals radiosensitivity (≥ 0.6 B/M) was clearly increased in 5% of all cases, while in the radiosensitive cohort 79% were elevated. KI therapy increased the rate of sensitive patients (≥ 0.6 B/M) to 35% significantly compared to 19% in cancer patients without KI (p = 0.014). Increased radiosensitivity of peripheral blood mononuclear cells (PBMCs) among patients occurred in six of seven KI subgroups. The mean B/M values significantly increased during KI therapy (0.47 ± 0.20 B/M without compared to 0.50 ± 0.19 B/M with KI, p = 0.047).ConclusionsKinase inhibitors can intensify individual radiosensitivity of PBMCs distinctly in 85% of tested drugs.

Abstract P2-10-17: Tissue prevalence and cellular heterogeneity of 9p24.1 amplification in TNBC in African American women

Abstract Introduction: Amplification of chromosome 9p24.1 encoding PDL1, PDL2, and JAK2 (the PDJ amplicon) has been detected in 5-25% of triplenegative breast cancers (TNBC), and is associated with poor outcome and activation of the JAK/STAT pathway. Here, we have developed a robust multiplexed fluorescence in situ hybridization (FISH) assay for detection of 9p24.1 amplification, and assessed the frequency and cellular distribution of the PDJ amplicon in a cohort of African American (AA) women with TNBC. Methods: The FISH assay combines three chromosome 9 probes to simultaneously target JAK2 and PD-L1 (9p24.1, PDJ), chromosome 9q22, and the 9q34.1 regions. This enables discrimination of PDJ amplicons from whole chromosome 9p arm gains and from chromosome 9 ploidies that occur in the background of genomic instability in aneuploid cancer genomes. Fifty cells were scored for each probe and the average copy number was obtained. We defined PDJ amplification as PDJ>4, PDJ/9q22 ratio≥2, and/or PDJ/9q34.1 ratio≥2. The assay was benchmarked to array CGH of flow sorted TNBC tissue from Mayo Clinic Arizona (n=14). Tissue microarrays from TNBC PDX tumors (n=20) and from African American women with TNBC (n=87) were assessed. Results: Using selected TNBC tissue with known CGH data, the FISH assay tightly correlated with PDJ copy number in 13/14 cases. The discordant case was negative by CGH on a biopsy with low tumor content, but FISH positive on tissue section (PDJ >7.5 and a PDJ/9q22 ratio=4). Of 20 TNBC PDX tumors, 5 were amplified by FISH. Twelve of 87 (14%) of tumors had PDJ amplification by FISH, of which ten were from breast tissue and two were from lymph node. Of these 12, PDJ>4 (n=0), PDJ/9q22 ratio≥2 (n=6), and PDJ/9q34.1 ratio≥2 (n=10). Significant intratumoral variation was observed with the presence of single cells with >10 PDJ copies in 8/17 (47%) amplified and 0/90 non-amplified total cases. Conclusion: 9p24.1 (PDJ) amplification encoding JAK2, PD-L1, and PD-L2 is detected by three-color FISH in 14% of TNBC from African American women. Individual cells with ≥10 copies of PDJ was seen exclusively in 8/17 amplified cases. We identified 5 PDX tumors which may provide valuable preclinical models for the amplicon. The association of this biomarker with clinical outcome will be presented. Citation Format: Karen S. Anderson, Tammey Naab, Lori K Koslosky, Megan Anderson, Michael Lewis, Yasmine Kanaan, Ali Afsari, Luisel Ricks-Santi, Barbara A. Pockaj, Michael T Barrett. Tissue prevalence and cellular heterogeneity of 9p24.1 amplification in TNBC in African American women [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P2-10-17.

Construction of a cytogenetic dose–response curve for low-dose range gamma-irradiation in human peripheral blood lymphocytes using three-color FISH

In order to estimate biological doses after low-dose ionizing radiation exposure, fluorescence in situ hybridization (FISH) using three differentially colored chromosome painting probes was employed to detect exchange-type chromosome aberrations. A reference dose response curve was constructed using blood samples from a female donor whose lymphocytes consistently exhibited a low frequency of cells at the second mitosis under routine culture conditions. Aberration yields were studied for a total of about 155 thousand metaphases obtained from seven dose-points of gamma irradiations (0, 50, 100, 150, 200, 250 and 300mGy). In situ hybridization was performed using commercially available painting probes for chromosomes 1, 2 and 4. With the aid of an automated image-capturing method, exchange-type aberrations involving painted chromosomes were detected with considerable accuracy and speed. The results on the exchange-type aberrations (dicentrics plus translocations) at the seven dose-points showed a good fit to the linear-quadratic model (y=0.0023+0.0015x+0.0819x2, P=0.83). A blind test proved the reproducibility of the reference dose–response relationship. In the control experiments using blood samples from another donor, the estimated doses calculated on the basis of the present reference curve were proved to be in good agreement with the actual physical doses applied. The present dose–response curve may serve as a means to assess the individual differences in cytogenetical radio-sensitivities.

Sperm chromosome analysis and preimplantation genetic diagnos is in an infertile male with mosaic trisomy 18

To analyze the numerical aberration rate of X, Y and chromosome 18 in sperms from an oligozoospermic male with mosaic trisomy 18 and to perform preimplantation genetic diagnosis (PGD) for the couple. G-banding and fluorescence in situ hybridization (FISH) were performed on metaphase chromosome. Sperm was analyzed in three-color FISH with a probe mixture containing CEP18, CEPY and Tel Xq/Yq. A healthy man with normal semen parameters was used as control. Significant difference in the rates of disomy for chromosome 18 (0.63% vs. 0.16%) and the gonosomes (0.945% vs. 0.35%) and diploidy (0.87% vs. 0.31%) was found in the spermatozoa between the patient and the control. After four embryos were biopsied in one PGD cycle, two embryos with XY1818 and XX1818 were selected for implanting and clinical pregnancy was ongoing. Sperm-FISH allows further understanding of aneuploidy rate and accurate genetic counseling. FISHPGD was effective for patient with mosaic trisomy 18.

Lower sperm aneuploidy rate is associated with a higher pregnancy rate in unselected patients undergoing intracytoplasmic sperm injection

Objective: Infertile patients with oligo-astheno-teratozoospermia (OAT) and normal karyotype have a higher rate of sperm aneuploidy which is correlates with the severity of OAT. These patients frequently undergo intracytoplasmic sperm injection (ICSI) to father a child, raising concerns about the possible increased risk of chromosomal aneuploidies for the concepti, since a natural selection does not occur with this technique. Accordingly, few reports have shown that a high proportion of patients undergoing ICSI program have an increased sperm aneuploidy rate. Another important issue, addressed in this study, is to evaluate the impact of the abnormal sperm chromosome asset on ICSI outcome.Design: Forty-eight consecutive and unselected male partners of couples undergoing ICSI had sperm aneuploidy rate evaluated in the same sperm preparation used for ICSI and obtained by swim-up. They were divided into two groups whether their sperm aneuploidy rate was below (group A) or above (group B) the upper range (1.55%) found in 14 healthy normozoospermic men (control group). Their main ICSI outcome measures were compared.Materials/Methods: Sperm chromosome analysis was conducted by fluorescence in-situ hybridization (FISH), using alpha-centromeric DNA probes for chromosomes 8, 18 (two-color) and 12, X and Y (three-color FISH).Results: Twelve out of 48 patients (25%) had a total sperm aneuploidy rate below the cut-off value of the control group (median: 1.25%; range: 0.85–1.52%), whereas the remaining 36 (75%) patients had an elevated sperm aneuploidy rate (median: 3.25%; range: 1.64–23.60%). Group A patients’ age (median: 33 years; range: 23–40) was similar to that of group B patients’ (median 35 years; range: 25–52). Fertilization (93% vs. 85%) and cleavage (100% vs. 98%) rates resulted similar in both groups of patients. Patients of group A had a significantly higher clinical pregnancy (75% vs. 34%) and implantation (34% vs. 13%) rates compared to the patients of group B. Thirty-two percent of implanted embryos miscarried (preclinical and clinical abortion) in group B compared to the 11% of group A, but the difference did not reach the statistical significance. Other factors which may account for this difference, such as the age of the female partner, theirs infertility factor and the main sperm parameters, resulted to be similar in both groups of patients.Conclusions: This study confirmed that an elevated proportion of patients undergoing ICSI have an increased sperm aneuploidy rate and that cytogenetically abnormal spermatozoa have a negative impact on ICSI outcome.Supported by: A grant from MURST, Rome, Italy, 1999. Objective: Infertile patients with oligo-astheno-teratozoospermia (OAT) and normal karyotype have a higher rate of sperm aneuploidy which is correlates with the severity of OAT. These patients frequently undergo intracytoplasmic sperm injection (ICSI) to father a child, raising concerns about the possible increased risk of chromosomal aneuploidies for the concepti, since a natural selection does not occur with this technique. Accordingly, few reports have shown that a high proportion of patients undergoing ICSI program have an increased sperm aneuploidy rate. Another important issue, addressed in this study, is to evaluate the impact of the abnormal sperm chromosome asset on ICSI outcome. Design: Forty-eight consecutive and unselected male partners of couples undergoing ICSI had sperm aneuploidy rate evaluated in the same sperm preparation used for ICSI and obtained by swim-up. They were divided into two groups whether their sperm aneuploidy rate was below (group A) or above (group B) the upper range (1.55%) found in 14 healthy normozoospermic men (control group). Their main ICSI outcome measures were compared. Materials/Methods: Sperm chromosome analysis was conducted by fluorescence in-situ hybridization (FISH), using alpha-centromeric DNA probes for chromosomes 8, 18 (two-color) and 12, X and Y (three-color FISH). Results: Twelve out of 48 patients (25%) had a total sperm aneuploidy rate below the cut-off value of the control group (median: 1.25%; range: 0.85–1.52%), whereas the remaining 36 (75%) patients had an elevated sperm aneuploidy rate (median: 3.25%; range: 1.64–23.60%). Group A patients’ age (median: 33 years; range: 23–40) was similar to that of group B patients’ (median 35 years; range: 25–52). Fertilization (93% vs. 85%) and cleavage (100% vs. 98%) rates resulted similar in both groups of patients. Patients of group A had a significantly higher clinical pregnancy (75% vs. 34%) and implantation (34% vs. 13%) rates compared to the patients of group B. Thirty-two percent of implanted embryos miscarried (preclinical and clinical abortion) in group B compared to the 11% of group A, but the difference did not reach the statistical significance. Other factors which may account for this difference, such as the age of the female partner, theirs infertility factor and the main sperm parameters, resulted to be similar in both groups of patients. Conclusions: This study confirmed that an elevated proportion of patients undergoing ICSI have an increased sperm aneuploidy rate and that cytogenetically abnormal spermatozoa have a negative impact on ICSI outcome. Supported by: A grant from MURST, Rome, Italy, 1999.

Multicolor fluorescence in situ hybridization analysis of meiotic chromosome segregation in a 47,XYY male and a review of the literature

The frequencies of aneuploid and diploid sperm were determined in a 47,XYY male using multi-color fluorescence in situ hybridization (FISH) analysis, and compared with those from 10 control donors. A total of 30,078 sperm from the patient was scored, 15,044 by two-color FISH for chromosomes 13 and 21, and 15,034 by three-color FISH for the sex chromosomes using chromosome 1 as an internal autosomal control for diploidy and lack of hybridization. The frequencies of X-bearing (49.73%) and Y-bearing sperm (49.46%) in control males were not significantly different from the expected 50% (chi(2)-test for goodness of fit). The ratio of 24,X (50.60%) to 24, Y sperm (48.35%) in the patient, however, was significantly different from the controls (P = 0.0144, chi(2)-test for independence) and from the expected 1:1 ratio (P = 0.0055, chi(2)-test for goodness of fit). There was no significant increase in the frequency of diploid sperm when compared with the controls (chi(2)-test for independence). Significantly increased frequencies were found for 24,YY (0.07% vs. 0.02%, P = 0.0009) and 24,XY (0.44% vs. 0.29%, P = 0.0025), but not for 24,XX (0.05% vs. 0.05%, P > 0. 05), 24,+13 (0.07% vs. 0.07%, P > 0.05) or 24,+21 sperm (0.21% vs. 0. 18%, P > 0.05) in the 47,XYY male when compared with control donors (chi(2)-test for independence). Our results support the theory that loss of the extra Y chromosome occurs during spermatogenesis in most cells. In this XYY patient there was a significant increase in the frequency of sperm with sex chromosomal abnormalities but no suggestion of an inter-chromosomal effect on autosomes. All 3-color FISH studies in the literature demonstrate a significantly increased risk of gonosomal aneuploidy in XYY males, with the risk being on the order of 1%.

Analysis of NotI linking clones isolated from human chromosome 3 specific libraries.

We have partially sequenced more than 1000 NotI linking clones isolated from human chromosome 3-specific libraries. Of these clones, 152 were unique chromosome 3-specific clones. The clones were precisely mapped using a combination of fluorescence in situ hybridization (FISH) and hybridization to somatic cell or radiation hybrids. Two- and three-color FISH was used to order the clones that mapped to the same chromosomal region, and in some cases, chromosome jumping was used to resolve ambiguous mapping. When this NotI restriction map was compared with the yeast artificial chromosome (YAC) based chromosome 3 map, significant differences in several chromosome 3 regions were observed. A search of the EMBL nucleotide database with these sequences revealed homologies (90-100%) to more than 100 different genes or expressed sequence tags (ESTs). Many of these homologies were used to map new genes to chromosome 3. These results suggest that sequencing NotI linking clones, and sequencing CpG islands in general, may complement the EST project and aid in the discovery of all human genes by sequencing random cDNAs. This method may also yield information that cannot be obtained by the EST project alone; namely, the identification of the 5' ends of genes, including potential promoter/enhancer regions and other regulatory sequences

Griseofulvin-induced aneuploidy and meiotic delay in male mouse germ cells: detected by using conventional cytogenetics and three-color FISH

Griseofulvin (GF) was tested in male mouse germ cells for the induction of meiotic delay and aneuploidy. Starved mice were orally treated with 500, 1000 and 2000 mg/kg of GF in corn oil and testes were sampled 22 h later for meiotic delay analysis and chromosome counting in spermatocytes at the second meiotic metaphase (MMII). A dose-related increase in meiotic delay by dose-dependently arresting spermatocytes in first meiotic metaphase (MMI) or/and prolonging interkinesis was observed. Hyperhaploid MMII cells were not significantly increased. Sperm were sampled from the Caudae epididymes 22 days after GF-treatment of the males for three-color fluorescence in situ hybridization (FISH). The frequencies of diploidies were 0.01–0.02% in sperm of the solvent control animals and increased dose-dependently to 0.03%, 0.068% and 0.091%, respectively, for 500, 1000 and 2000 mg/kg of GF. The frequencies of disomic sperm were increased significantly above the controls in all GF-treated groups but showed no dose response. The data for individual classes of disomic sperm indicated that MII was more sensitive than MI to GF-induced non-disjunction in male mice. A comparison of the present data from male mice and literature data from female mice suggests that mouse oocytes are more sensitive than mouse spermatocytes to GF-induced meiotic delay and aneuploidy.

Characterization of Multiple 12p Rearrangements in Testicular Germ Cell Tumor Cell Line 833K and Its Subclone 64CP by Chromosome Microdissection

Rearrangements of chromosome arm 12p are known to be common in germ cell tumors (GCT). Previous studies, using fluorescence in situ hybridization (FISH) with a whole chromosome 12 painting probe, showed unusual distributions of chromosome 12-derived chromatin in GCT cell line 833K and its cisplatin-resistant subclone, 64CP, located next to AgNOR (silver staining nucleolus organizer regions), some of which were ectopic. In this study, the ectopic stalk regions were shown by FISH to be composed of 18s and 28s rDNA, but were flanked by β-satellite DNA, which may form a barrier around the rDNA. In order to determine the specific origins of the rearranged chromosome 12 segments, three different derived chromosome 12 regions were isolated from 64CP, using chromosomal microdissection. The microdissected fragments were labeled and hybridized by FISH to normal human chromosomes. All three segments localized to distal 12p; 12p12 →12pter, but with apparently different breakpoints for each segment. Furthermore, three-color FISH experiments with 12p band-specific probes demonstrated that the derivative chromosome 12 regions in 833K also originate from distal 12p (12p12 →p13). These sequences now can be evaluated for degree of overlap or common breakpoints which may be of significance in the development or progression of GCT.

Detection of chromosomal aneuploidy in endometriosis by multi-color fluorescence in situ hybridization (FISH)

Endometriosis affects 10-15% of women of reproductive age and is a common cause of infertility and pelvic pain. Although endometriosis is characterized by abnormal growth or turn-over of cells, the genetic changes involved remain unclear. We employed a multi-color fluorescence in situ hybridization (FISH) strategy to determine the incidence of somatic chromosomal numeric alterations in severe/late stage endometriosis. Using alpha-satellite sequence-specific DNA probes for chromosomes 7, 8, 11, 12, 16, 17, and 18, simultaneous two- and three-color FISH were performed to evaluate the frequency of monosomic, disomic, and trisomic cells in normal control and endometriotic tissue specimens. In one of four endometriosis samples studied, a significantly higher frequency of monosomy for chromosome 17 (14.8%, chi 2(4) = 53.3, P < 0.0001) and 16 (8.8%, chi 2(4) = 11.4, P < 0.05) was observed. An increased number of cells with chromosome 11 trisomy (14.8%, chi 2(4) = 96.2, P < 0.0001) were detected in a second case. In a third case, a distinct colony of nuclei with chromosome 16 monosomy (14.1%, chi 2(4) = 21.39, P < 0.005) was detected. Acquired chromosome-specific aneuploidy may be involved in endometriosis, reflecting clonal expansion of chromosomally abnormal cells. That candidate tumor suppressor genes and oncogenes have been mapped to chromosomes 11, 16, and 17 suggests that chromosomal loss or gain plays a role in the development and/or progression of endometriosis.

Statistical methods for gene map construction by fluorescence in situ hybridization.

Fluorescence in situ hybridization (FISH) provides an efficient and powerful technique for ordering loci both on metaphase chromosomes and in less condensed interphase chromatin. Two-color metaphase FISH can be used to order pairs of loci relative to the centromere; two- and three-color interphase FISH can be used to accurately order trios of loci spaced within 1 Mb relative to one another. Loci separated by a distance > 1-2 Mb exhibit chromatin loops that often give rise to a statistically significant but incorrect order. We derive Bayesian methods for selecting the best locus order based on microscopic evaluation for each of these types of FISH mapping data. We then describe how the results from several two- and three-locus analyses can be combined to evaluate the approximate posterior probability of a given multilocus order within the limits of the technology utilized. These methods directly address the question of interest: What is the probability that the inferred two-, three-, or multilocus order actually is correct? We illustrate our analysis methods by applying them to previously described FISH mapping data of 14 markers in the BRCA1 region on chromosome 17q12-q21. We also propose design strategies to order a group of closely spaced (< 1 Mb) loci, two and three loci at a time, using a bisection strategy for two-color FISH data and a trisection strategy for three-color FISH data. These strategies have the best worst-case performance for ordering a new locus relative to a group of ordered loci and are nearly optimal for ordering a group of loci of unknown order. These, in conjunction with physical mapping strategies, provide efficient and reliable methods for gene map construction by FISH.

Meiotic segregation of the X and Y chromosomes and chromosome 1 analyzed by three-color FISH in human interphase spermatozoa.

Meiotic segregation of the X and Y chromosomes and chromosome 1 was analyzed by three-color fluorescence in situ hybridization (FISH) in 94,575 human interphase spermatozoa from four control subjects. More than 99% of the sperm cells were labeled. The proportions of X- and Y-bearing sperm were estimated to be 49.83% and 48.30%, respectively. The disomy rates were 0.04%, 0.009%, and 0.20% for the X and Y chromosomes and chromosome 1, respectively. Hyperhaploidy with an extra gonosome was found in 0.34% of spermatozoa, due to nondisjunction during meiosis I. The frequency of diploidy was 0.11% at meiosis I and 0.036% at meiosis II. Cohybridization of one autosomal and two gonosomal probes, in three-color FISH in interphase spermatozoa, seems to accurately discriminate diploidies from disomies, as well as the meiotic origin of gonosomal aneuploidies in sperm cells.

Aneuploidy in human sperm: results of two- and three-color fluorescence in situ hybridization using centromeric probes for chromosomes 1, 12, 15, 18, X, and Y

To understand the mechanisms that affect aneuploidy, fluorescence in situ hybridization (FISH), using chromosome-specific centromeric probes, was employed to screen a large population of human sperm for numerical errors. To determine the true rate of disomy for chromosomes 1, 12, 15, and 18, two-color FISH was performed, and for the gonosomes, three-color FISH. The use of multiple, differently colored probes allows one to distinguish a true disomic sperm from a diploid cell. A minimum of 10,000 sperm nuclei from each of five donors was scored per set of centromeric probes, giving a total of 165,330 sperm nuclei. The disomy frequencies for autosomes 1, 12, 15, and 18 were found to be similar, with a mean of 0.10% (range, 0.05%-0.16%) for chromosome 1, 0.16% (0.10%-0.25%) for chromosome 12, 0.11% (0.07%-0.20%) for chromosome 15, and 0.11% (0.08%-0.17%) for chromosome 18. For the sex chromosomes, the mean frequency of disomy was found to be 0.43% (range, 0.23%-0.71%), with XX disomy accounting for 0.07% (0.03%-0.10%), YY disomy 0.21% (0.10%-0.43%), and XY disomy 0.15% (0.08%-0.24%). The incidence of disomic sperm for the sex chromosomes was significantly increased, compared to the frequency of disomy for the autosomes (chi 2 = 218.61, P < 0.0001). Diploidy was observed in 0.05%-0.47% of the sperm nuclei counted. Interdonor heterogeneity for disomy frequencies was found to exist for the sex chromosomes and for chromosomes 1 and 15, suggesting significant variation among normal men.

A strategy for the characterization of minute chromosome rearrangements using multiple color fluorescence in situ hybridization with chromosome-specific DNA libraries and YAC clones.

The identification of marker chromosomes in clinical and tumor cytogenetics by chromosome banding analysis can create problems. In this study, we present a strategy to define minute chromosomal rearrangements by multicolor fluorescence in situ hybridization (FISH) with "whole chromosome painting" probes derived from chromosome-specific DNA libraries and Alu-polymerase chain reaction (PCR) products of various region-specific yeast artificial chromosome (YAC) clones. To demonstrate the usefulness of this strategy for the characterization of chromosome rearrangements unidentifiable by banding techniques, an 8p+ marker chromosome with two extra bands present in the karyotype of a child with multiple anomalies, malformations, and severe mental retardation was investigated. A series of seven-color FISH experiments with sets of fluorochrome-labeled DNA library probes from flow-sorted chromosomes demonstrated that the additional segment on 8p+ was derived from chromosome 6. For a more detailed characterization of the marker chromosome, three-color FISH experiments with library probes specific to chromosomes 6 and 8 were performed in combination with newly established telomeric and subtelomeric YAC clones from 6q25, 6p23, and 8p23. These experiments demonstrated a trisomy 6pter-->6p22 and a monosomy 8pter-->8p23 in the patient. The present limitations for a broad application of this strategy and its possible improvements are discussed.

Fine mapping of the human MHC class II region within chromosome band 6p21 and evaluation of probe ordering using interphase fluorescence in situ hybridization.

Eight previously well-characterized and mapped probes derived from the human major histocompatibility complex (MHC) class II region were used to investigate the advantages and limitations of fluorescence in situ hybridization (FISH) techniques for fine mapping. The class II region of the MHC was localized within subband 6p21.31 by in situ hybridization on metaphase chromosomes that were banded by immunofluorescence staining with an antibody against 5-bromodeoxyuridine (BrdU). Ordering of probes that were separated by up to 900 kb was achieved by simultaneous hybridization of two or three probes on interphase nuclei. Three-color FISH proved to be an excellent method for ordering of probes within distances of 200-1,000 kb. Under certain conditions, closer probes could be ordered by comparing measured distances between their hybridization signals in interphase nuclei. A linear correlation between measured interphase distances and kilobase distances was observed up to 500 kb. With increasing distances, the measurements become more inaccurate due to chromatin folding.