An efficient method for selecting unique-sequence clones from DNA libraries and its application to fluorescent staining of human chromosome 21 using in situ hybridization

Construction of repeat-free fluorescence in situ hybridization probes

FISH probes are generally made out of BAC clones with genomic DNA containing a variable amount of repetitive DNA that will need to be removed or blocked for FISH analysis. To generate repeat free (RF) Probes without loss in genomic coverage, a random library is made from BAC clones by whole-genome amplification (WGA). Libraries are denatured in the presence of excess C₀t-1 DNA and allowed to re-anneal followed by digestion of all double-stranded elements by duplex-specific nuclease (DSN). Selective amplification of all elements not containing repetitive sequences is realized by a sequential amplification. The final RF products can be re-amplified and used as a stock for future probe production. The RF probes have a lower background, the signal intensity build up is faster and there is no need for blocking DNA. The signal to background ratio of the RF was higher as compared to repeat containing probes.

Sequence-based, in situ detection of chromosomal abnormalities at high resolution

We developed single copy probes from the draft genome sequence for fluorescence in situ hybridization (scFISH) which precisely delineate chromosome abnormalities at a resolution equivalent to genomic Southern analysis. This study illustrates how scFISH probes detect cryptic and subtle abnormalities and localize the sites of chromosome rearrangements. scFISH probes are substantially shorter than conventional recombinant DNA-derived probes, and C(o)t1 DNA is not required to suppress repetitive sequence hybridization. In this study, 74 single copy sequence probes (>1,500 bp) have been developed from >/=100 kb genomic intervals associated with either constitutional or acquired disorders. Applications of these probes include detection of congenital microdeletion syndromes on chromosomes 1, 4, 7, 15, 17, 22 and submicroscopic deletions involving the imprinting center on chromosome 15q11.2q13. We demonstrate how hybridization with multiple combinations of probes derived from the Smith-Magenis syndrome interval on chromosome 17 identified a patient with an atypical, proximal deletion breakpoint. A similar multi-probe hybridization strategy has also been used to delineate the translocation breakpoint region on chromosome 9 in chronic myelogenous leukemia. Probes have also been designed to hybridize to multiple cis paralogs, both enhancing the chromosomal target size and detecting chromosome rearrangements, for example, by splitting and separating a family of related sequences flanking an inversion breakpoint on chromosome 16 in acute myelogenous leukemia. These novel strategies for rapid and precise characterization of cytogenetic abnormalities are feasible because of the sequence-defined properties and dense euchromatic organization of single copy probes.

Use of fluorescent sequence-specific polyamides to discriminate human chromosomes by microscopy and flow cytometry

In this paper, we demonstrate the use of synthetic polyamide probes to fluorescently label heterochromatic regions on human chromosomes for discrimination in cytogenetic preparations and by flow cytometry. Polyamides bind to the minor groove of DNA in a sequence-specific manner. Unlike conventional sequence-specific DNA or RNA probes, polyamides can recognize their target sequence without the need to subject chromosomes to harsh denaturing conditions. For this study, we designed and synthesized a polyamide to target the TTCCA-motif repeated in the heterochromatic regions of chromosome 9, Y and 1. We demonstrate that the fluorescently labeled polyamide binds to its target sequence in both conventional cytogenetic preparations of metaphase chromosomes and suspended chromosomes without denaturation. Chromosomes 9 and Y can be discriminated and purified by flow sorting on the basis of polyamide binding and Hoechst 33258 staining. We generate chromosome 9- and Y-specific 'paints' from the sorted fractions. We demonstrate the utility of this technology by characterizing the sequence of an olfactory receptor gene that is duplicated on multiple chromosomes. By separating chromosome 9 from chromosomes 10-12 on the basis of polyamide fluorescence, we determine and differentiate the haplotypes of the highly similar copies of this gene on chromosomes 9 and 11.

Sequence-based design of single-copy genomic DNA probes for fluorescence in situ hybridization

Chromosomal rearrangements are frequently monitored by fluorescence in situ hybridization (FISH) using large, recombinant DNA probes consisting of contiguous genomic intervals that are often distant from disease loci. We developed smaller, targeted, single-copy probes directly from the human genome sequence. These single-copy FISH (scFISH) probes were designed by computational sequence analysis of approximately 100-kb genomic sequences. ScFISH probes are produced by long PCR, then purified, labeled, and hybridized individually or in combination to human chromosomes. Preannealing or blocking with unlabeled, repetitive DNA is unnecessary, as scFISH probes lack repetitive DNA sequences. The hybridization results are analogous to conventional FISH, except that shorter probes can be readily visualized. Combinations of probes from the same region gave single hybridization signals on metaphase chromosomes. ScFISH probes are produced directly from genomic DNA, and thus more quickly than by recombinant DNA techniques. We developed single-copy probes for three chromosomal regions-the CDC2L1 (chromosome 1p36), MAGEL2 (chromosome 15q11.2), and HIRA (chromosome 22q11.2) genes-and show their utility for FISH. The smallest probe tested was 2290 bp in length. To assess the potential utility of scFISH for high-resolution analysis, we determined chromosomal distributions of such probes. Single-copy intervals of this length or greater are separated by an average of 29.2 and 22.3 kb on chromosomes 21 and 22, respectively. This indicates that abnormalities seen on metaphase chromosomes could be characterized with scFISH probes at a resolution greater than previously possible.

Chromosome missegregation and trisomy 21 mosaicism in Alzheimer's disease

A connection between Alzheimer's disease (AD) and Down syndrome (trisomy 21) is indicated by the fact that all Down syndrome individuals develop Alzheimer's disease neuropathology by the 4th decade of life. Previous studies have examined the frequency of aneuploidy and other chromosomal defects in cells from familial Alzheimer's disease (FAD) patients, with varying results. To investigate the possibility that a specific type of aneuploidy--trisomy 21 mosaicism--may contribute to Alzheimer's disease, we used quantitative fluorescence in situ hybridization to measure the number of trisomy 21 cells in primary fibroblast cultures from AD and unaffected subjects. The 27 AD cultures, including 15 that were derived from individuals carrying FAD mutations in presenilin 1 or 2, exhibited a significant approximately twofold increase in the number of trisomy 21 cells compared to 13 control cultures. A small double-hybridization experiment suggested that the aneuploidy in AD cells was not limited to chromosome 21 but extended at least to chromosome 18 as well. In a parallel study, the endogenous presenilin proteins in fibroblasts were localized to the centrosomes, the nuclear envelope, and its associated interphase kinetochores. Together these results indicate that the presenilin proteins may be involved in mitosis and that FAD mutations in the presenilin genes may predispose to chromosome missegregation (nondisjunction). The data reported here also suggest that trisomy 21 mosaicism may contribute to other forms of AD that are not caused by a presenilin mutation.

Multicolor FISHing: what's the catch?

Recent advances in protocols for multicolor fluorescence in situ hybridization (FISH) mark a major milestone in the field of molecular cytogenetics. Brilliant chromosome images have been presented, where each chromosome homolog is depicted in a different color. The easy recognition of chromosomes seems to simplify karyotype analysis considerably and the procedure is meant to open new avenues for scanning human and other genomes for chromosomal rearrangements. How will this development change the field of cytogenetics? In this review the current applications that benefit from the new protocols are summarized and future perspectives are discussed.

Rapid in situ detection of chromosome 21 by PRINS technique

The "PRimed IN Situ labeling" (PRINS) method is an interesting alternative to in situ hybridization for chromosomal detection. In this procedure, chromosome labeling is performed by in situ annealing of specific oligonucleotide primers, followed by primer elongation by a Taq polymerase in the presence of labeled nucleotides. Using this process, we have developed a simple and semi-automatic method for rapid in situ detection of human chromosome 21. The reaction was performed on a programmable temperature cycler, with a chromosome 21 specific oligonucleotide primer. Different samples of normal and trisomic lymphocytes and amniotic fluid cells were used for testing the method. Specific labeling of chromosome 21 was obtained in both metaphases and interphase nuclei in a 1 hour reaction. The use of oligonucleotide primer for in situ labeling overcomes the need for complex preparations of specific DNA probes. The present results demonstrate that PRINS may be a simple and reliable technique for rapidly detecting aneuploidies.

Mapping and chromosome analysis: the potential of fluorescence in situ hybridization

Fluorescence in situ hybridization (FISH) is a method widely used for the delineation of chromosomal DNA. FISH is applied in many areas of basic research as well as in clinical cytogenetics. In this review important technical improvements as well as the various applications of this method are summarized. In the first part different labeling and detection procedures are described and the potential of various kinds of probes are discussed. Recent developments in optical instrumentation and digital imaging procedures are outlined in the second part. The following important applications of FISH are discussed: (a) new strategies for high resolution mapping of DNA sequences; (b) detection of chromosomal aberrations in clinical material; (c) techniques allowing the simultaneous detection of numerous probes by multiple color FISH; and (d) the new approach of comparative genomic hybridization, allowing a rapid and comprehensive analysis of chromosomal imbalances in cell populations, which is particularly useful for the cytogenetic analysis of tumor samples.

Homologous loci DXYS156X and DXYS156Y contain a polymorphic pentanucleotide repeat (TAAAA)n and map to human X and Y chromosomes

We report the isolation and characterization of a polymorphic pentanucleotide repeat (TAAAA)n, which was mapped to human chromosomes X and Y (loci DXYS156X and DXYS156Y) by PCR amplification of DNA from a monochromosomal somatic cell hybrid panel (NIGMS panel 2). The (TAAAA)n repeat of loci DXYS156 occurs within a human LINE element at a position where the consensus sequence contains a single TAAAA motif. In 72 unrelated CEPH individuals seven alleles were detected which ranged in size from 125 to 165 bp in 5 bp intervals. The two largest alleles (160 and 165 bp) were observed only in males, which suggests that they were amplified from the Y chromosome DXYS156Y locus. The other 5 alleles were present in two copies in females and in a single copy in males, which suggests that they were amplified from the X chromosome DXYS156X locus. Locus DXYS156X was polymorphic in CEPH families with an observed heterozygosity in females of 46% (27 of 59). Linkage analysis with DNA markers on the X chromosome revealed significant lod scores for a location of DXYS156X close to markers DXS1002 (theta = 0.000; zeta = 8.43), DXYS1X (theta = 0.015; zeta = 17.3), DXS3, and PGK1 in the region of chromosome Xq13. The sequence of DXYS156Y derived from the 165 bp allele has been deposited in Genbank with accession number X71600.

Cloning and linkage mapping of three polymorphic tetranucleotide (TAAA)n repeats on human chromosome 21

We report the cloning, sequencing, and mapping of three short sequence repeat polymorphisms due to tetranucleotide (TAAA)n repeats from human chromosome 21. These DNA markers (D21S221, D21S225, D21S226) have been cloned from the chromosome 21-specific plasmid library of J. C. Fuscoe, C. C. Collins, D. Pinkel, and J. W. Gray (1989, Genomics 5: 100-109) and were shown to be polymorphic by polymerase chain reaction amplification and polyacrylamide gel electrophoresis. Genotypes were determined in informative CEPH pedigrees and used in linkage analysis relative to other mapped markers on human chromosome 21. One of these markers, D21S221, is closely linked to the amyloid precursor protein gene (APP), which has been implicated in the etiology of familial Alzheimer disease in some families.

Dinucleotide repeat (GT)n markers on chromosome 21

To further develop the linkage map of human chromosome 21 (HC21), we have concentrated on identifying highly polymorphic markers based on dinucleotide repeat sequences such as (GT)n, as these are often highly polymorphic, are widespread throughout the human genome, and can be rapidly analyzed by the polymerase chain reaction. We report here nine (GT)n polymorphic markers from HC21.

Reassessment of a chromosome 12q+ marker by fluorescent in situ hybridization (FISH)

We present a case previously described by Jenkins et al. (1983) as atypical Down syndrome (DS). The initial diagnosis was first made on the basis of phenotypic and cytogenetic data. This analysis was supported by studies of superoxide dismutase (SOD1) activity that maps to band 21q22.1. Results from phenotypic, chromosome banding and SOD1 studies suggested a karyotype of 46,XX,-12,+t(12pter to 12qter::21q21 to 21q22.?2). Using fluorescent in situ hybridization (FISH) for chromosome painting with DNA libraries derived from sorted human chromosomes to stain selectively the chromosomes No. 21 and No. 12, we demonstrate that the marker chromosome 12q+ has no chromosome 21 content but it is derived from chromosome 12.

D21S215 is a (GT)n polymorphic marker close to centromeric alphoid sequences on chromosome 21

A plasmid, AWZ1, that contained a dinucleotide (GT)n repeat was identified from a chromosome 21-specific genomic library. When amplified by PCR from human genomic DNA, the repeat length was highly polymorphic between individuals; its location, D21S215, was mapped in the CEPH pedigrees by linkage analysis to the pericentromeric region of chromosome 21. It is the closest polymorphic marker to alphoid sequences on this chromosome.

Molecular cytogenetics in human cancer diagnosis

This report summarizes the application of fluorescence in situ hybridization for detection and diagnosis of human cancers and for detection of residual cancer cells. This approach allows individual interphase cancer cells to be stained so that aberrations such as aneusomies, translocations, deletions, and gene amplification can be seen in the light microscope. This is accomplished using probes for repeated sequences found at the chromosome centromeres, whole chromosome probes, and/or probes for specific aberrant sequences.

PCR amplification of chromosome-specific DNA isolated from flow cytometry-sorted chromosomes

We have established a method for amplifying and obtaining large quantities of chromosome-specific DNA by linker/adaptor ligation and polymerase chain reaction (PCR). Small quantities of DNA isolated from flow cytometry-sorted chromosomes 17 and 21 were digested with MboI, ligated to a linker/adaptor, and then subjected to 35 cycles of PCR. Using this procedure, 20 micrograms of chromosome-specific DNA can be obtained. Southern blot analysis using several DNA probes previously localized to chromosomes 17 and 21 indicated that these gene sequences were present in the amplified chromosome-specific DNA. A small quantity of the chromosome-specific DNA obtained from the first round of PCR amplification was used to amplify DNA for a second, third, and fourth round of PCR (30 cycles), and specific DNA sequences were still detectable. Fluorescence in situ hybridization using these chromosome-specific DNA probes clearly indicated the hybridization signals to the designated chromosomes. We showed that PCR-amplified chromosome 17-specific DNA can be used to detect nonrandom chromosomal translocation of t(15;17) in acute promyelocytic leukemia by fluorescence in situ hybridization.

Construction and characterization of plasmid libraries enriched in sequences from single human chromosomes

Plasmid libraries enriched in sequences from single chromosome types have been constructed for all human chromosomes. This was accomplished by transferring inserts from the Charon 21A phage libraries constructed by the National Laboratory Gene Library Project into Bluescribe plasmids. Insert material freed by complete digestion of the phage libraries with HindIII or EcoRI was cloned into the corresponding sites in Bluescribe plasmids. The sizes of the Bluescribe library inserts determined by gel electrophoresis range from near 0 to approximately 6 kb. Fluorescence in situ hybridization (FISH) with the plasmid libraries showed that all hybridize along both arms of the expected (target) chromosome type with varying intensity. However, the plasmid libraries for chromosomes 1, 4, 9, 11, 16, 18, and 20 hybridize weakly or not at all near the centromeres of the target chromosome types. The libraries for chromosomes 13, 14, 15, 21, and 22 cross-hybridize near the centromeres of all members of this group and hybridize weakly to the short arms of the target chromosomes. FISH with each library allows specific staining of the target chromosome type in metaphase spreads. The signals resulting from FISH with libraries for chromosomes 1, 4, 8, 9, 13, 14, 17, 18, 21, and Y are sufficiently intense to permit analysis in interphase nuclei. Examples of the use of these libraries for translocation detection, marker chromosome characterization, and interphase aneuploidy analysis are presented.

Translocation (8;21) in acute nonlymphocytic leukemia delineated by chromosomal in situ suppression hybridization

In situ suppression hybridization with recombinant bacteriophage DNA libraries for chromosomes 8 and 21 was performed in two cases of acute nonlymphocytic leukemia, type FAB M2. In both cases, cytogenetic analysis by conventional G-banding revealed t(8;21)(q22;q22). In situ suppression hybridization was able to prove the reciprocal nature of the translocation in both cases by identifying the terminal end of chromosome 21 translocated to the derivative chromosome 8q-.

Characterization and mapping of human genes encoding zinc finger proteins

The zinc finger motif, exemplified by a segment of the Drosophila gap gene Krüppel, is a nucleic acid-binding domain present in many transcription factors. To investigate the gene family encoding this motif in the human genome, a placental genomic library was screened at moderate stringency with a degenerate oligodeoxynucleotide probe designed to hybridize to the His/Cys (H/C) link region between adjoining zinc fingers. Over 200 phage clones were obtained and are being sorted into groups by partial sequencing, cross-hybridization with oligodeoxynucleotide probes, and PCR amplification. Further, the genomic clones were cross-hybridized with a set of 30 zinc finger-encoding cDNAs (Kox1-Kox30) isolated from a human T-cell cDNA library. Four cDNAs (Kox4, Kox7, Kox12, and Kox15) were identified that match one or more genomic clones; these matches were confirmed by nucleotide sequence analysis. One or more clones from each locus were mapped onto human metaphase chromosomes by chromosomal in situ suppression hybridization with fluorescent probe detection. We mapped ZNF7/Kox4 to chromosome 8qter, ZNF19/Kox12 to 16q22, ZNF22/Kox15 to 10q11, and ZNF44/Kox7 to 16p11. The results of these analyses support the conclusion that the human genome contains many, probably several hundred, zinc finger genes with consensus H/C link regions.

Application of fluorescence in situ hybridization techniques in clinical genetics: use of two alphoid repeat probes detecting the centromeres of chromosomes 13 and 21 or chromosomes 14 and 22, respectively

Two cloned DNA fragments, one derived from an alpha satellite subfamily common to chromosomes 13 and 21, and the other derived from a similar subfamily common to chromosomes 14 and 22, have been used as biotinylated probes in in situ hybridization studies. Under high stringency conditions, chromosome specific centromeric labelling can be obtained. The applications of this technique in clinical situations are illustrated on metaphases from a fetus with trisomy 21, a fetus with trisomy 13, and a child with clinical features of cat-eye syndrome.

Clinical applications of fluorescence in situ hybridization

We review here the application of fluorescence in situ hybridization with chromosome-specific probes to chromosome classification and to detection of changes in chromosome number or structure associated with genetic disease. Information is presented on probe types that are available for disease detection. We discuss the application of these probes to detection of numerical aberrations important for prenatal diagnosis and to detection and characterization of numerical and structural aberrations in metaphase spreads and in interphase nuclei to facilitate tumor diagnosis.

Genes occupy a fixed and symmetrical position on sister chromatids

A high-resolution fluorescence methodology for nonisotopic in situ hybridization was applied to determine the positions occupied by several single-copy genes, DNA sequences, and integrated viral genomes on sister chromatids. The lateral and longitudinal mapping of the probes was performed on prometaphase and metaphase chromosomes. A fixed lateral position, exterior or median in relation to the longitudinal axis of the chromatids, was observed for a given probe, with a symmetrical position of the double fluorescent spots. This position appears to be independent of chromosome condensation stage from prometaphase to metaphase. These observations suggest an opposite helical-handedness conformation of DNA on both chromatids with a mirror symmetry. They support the model of chromosome packaging recently proposed by Boy de la Tour and Laemmli. Moreover, our results indicate that the last stages of chromosome condensation occur by packing down the coils without further coiling.

Analysis of genes and chromosomes by nonisotopic in situ hybridization

Nonisotopic in situ hybridization is a powerful tool to analyze the organization of complex genomes. Current approaches utilizing this technique for the analysis of linear and spatial genome organizations are presented. Clinical applications of these approaches, which open new avenues for diagnosis of disease-related chromosomal changes, are also discussed.

The Chinese hamster HPRT gene: restriction map, sequence analysis, and multiplex PCR deletion screen

The fine structure of the Chinese hamster hypoxanthine guanine phosphoribosyltransferase (HPRT) gene has been determined; the gene has nine exons and is dispersed over 36 kb DNA. Exons 2-9 are contained within overlapping lambda bacteriophage clones and exon 1 was obtained by an inverse polymerase chain reaction (PCR). All the exons have been sequenced, together with their immediate flanking regions, and these sequences compared to those of the mouse and human HPRT genes. Sequences immediately flanking all exons but the first show considerable homology between the different species but the region around exon 1 is less conserved, apart from the preserved location of putative functional elements. Oligonucleotide primers derived from sequences flanking the HPRT gene exons were used to amplify simultaneously seven exon-containing fragments in a multiplex PCR. This simple procedure was used to identify total and partial gene deletions among Chinese hamster HPRT-deficient mutants. The multiplex PCR is quicker to perform than Southern analysis, traditionally used to study such mutants, and also provides specific exon-containing fragments for further analysis. The Chinese hamster HPRT gene is often used as a target for mutation studies in vitro because of the ease of selection of forward and reverse mutants; the information presented here will enhance the means of investigating molecular defects within this gene.

The molecular biology of radiation carcinogenesis

Major new insights into carcinogenesis have come from recent advances in cellular and molecular biology. The concept of oncogenes provides a simple explanation for how agents as diverse as radiation, chemicals or retroviruses can induce tumors that are indistinguishable one from another. Oncogenes may be activated by a point mutation, by a chromosome translocation, or by amplification. Ionizing radiations are efficient at the first two mechanisms. While oncogenes are frequently associated with leukemias and lymphomas, they are associated with only 10 to 15% of human solid cancers. The importance of the loss of suppressor genes was suggested first from studies with human-hamster hybrid cells, but has since been shown to be of importance in an increasing number of human solid tumors, from rare tumors such as retinoblastoma to more common tumors such as small cell lung cancer and colorectal cancer. The mechanism of somatic homozygosity clearly involves several steps, some of which, such as a deletion, could be readily produced by ionizing radiation. The multi-step nature of carcinogenesis can be demonstrated in the petri dish, where the transfection of multiple oncogenes is required to transform normal cells from short-term explants. It can be shown, too, in colorectal cancer in the human, where the activation of an oncogene and the loss of more than one suppressor gene may be involved in the progression from normal epithelium to a frank malignancy.

Physical mapping of chromosome 21 DNA markers in Alzheimer's disease region using somatic cell hybrids

From a chromosome 21 phage library, we selected 10 clones located proximal of the senile plaque amyloid precursor protein gene. Since a locus for Alzheimer's disease (AD) has been localized in the pericentromeric region of chromosome 21, the selected phage clones are potential candidate probes for genetic analysis of AD. In this study, we subcloned single-copy fragments of the selected phage clones, refined their physical localization, and examined their chromosomal distribution in relation to their position on chromosome 21. The results indicated that the phage clones are identifying nine chromosome 21 loci, which, if polymorphic, may be helpful in localizing the AD locus more precisely. Moreover, since all phage clones are located close to the centromere of chromosome 21, they can be used to determine the parental origin of nondisjunction in trisomy 21 with high reliability.