As vertebrate genome sequences near completion and research refocuses to their analysis, the issue of effective genome annotation display becomes critical. A mature web tool for rapid and reliable display of any requested portion of the genome at any scale, together with several dozen aligned annotation tracks, is provided at http://genome.ucsc.edu. This browser displays assembly contigs and gaps, mRNA and expressed sequence tag alignments, multiple gene predictions, cross-species homologies, single nucleotide polymorphisms, sequence-tagged sites, radiation hybrid data, transposon repeats, and more as a stack of coregistered tracks. Text and sequence-based searches provide quick and precise access to any region of specific interest. Secondary links from individual features lead to sequence details and supplementary off-site databases. One-half of the annotation tracks are computed at the University of California, Santa Cruz from publicly available sequence data; collaborators worldwide provide the rest. Users can stably add their own custom tracks to the browser for educational or research purposes. The conceptual and technical framework of the browser, its underlying MYSQL database, and overall use are described. The web site currently serves over 50,000 pages per day to over 3000 different users.

/pdf/the-human-genome-browser-at-ucsc-4zclgthyly.pdf

The Human Genome Browser at UCSC

A rapid banding technique for human chromosomes

CELLS from nine consecutive patients with chronic myelogenous leukaemia (CML) have been analysed with quinacrine fluorescence and various Giemsa staining techniques. The Philadelphia (Ph1) chromosome in all nine patients represents a deletion of the long arm of chromosome 22 (22q−)1,2. An unsuspected abnormality in all cells from the nine patients has been detected with these new staining techniques. It consists of the addition of dully fluorescing material to the end of the long arm of one chromosome 9 (9q+). In Giemsa-stained preparations, this material appears as an additional faint terminal band in one chromosome 9. The amount of additional material is approximately equal to the amount missing from the Ph1 (22q−) chromosome, suggesting that there may be a hitherto undetected translocation between the long arm of 22 and the long arm of 9, producing the 9q+ chromosome.

Letter: A new consistent chromosomal abnormality in chronic myelogenous leukaemia identified by quinacrine fluorescence and Giemsa staining.

This report describes the use of fluorescence in situ hybridization for chromosome classification and detection of chromosome aberrations. Biotin-labeled DNA was hybridized to target chromosomes and subsequently rendered fluorescent by successive treatments with fluorescein-labeled avidin and biotinylated anti-avidin antibody. Human chromosomes in human-hamster hybrid cell lines were intensely and uniformly stained in metaphase spreads and interphase nuclei when human genomic DNA was used as a probe. Interspecies translocations were detected easily at metaphase. The human-specific fluorescence intensity from cell nuclei and chromosomes was proportional to the amount of target human DNA. Human Y chromosomes were fluorescently stained in metaphase and interphase nuclei by using a 0.8-kilobase DNA probe specific for the Y chromosome. Cells from males were 40 times brighter than those from females. Both Y chromosomal domains were visible in most interphase nuclei of XYY amniocytes. Human 28S ribosomal RNA genes on metaphase chromosomes were distinctly stained by using a 1.5-kilobase DNA probe.

https://www.pnas.org/content/pnas/83/9/2934.full.pdf

Cytogenetic analysis using quantitative, high-sensitivity, fluorescence hybridization.

Human chronic myelogenous leukemia cell-line with positive Philadelphia chromosome.

The distribution of DNA along metaphase chromosomes that are not excessively contracted can be visualized in the fluorescence microscope with the aid of fluorescent DNA-binding agents. Additional, characteristic details in the fluorescence patterns are obtained with fluorochromes that bind preferentially to certain chromosomal regions. The highly fluorescent alkylating agent quinacrine mustard (QM) effects discrete, fluorescent labeling of both plant and mammalian metaphase chromosomes, presumably by selective binding to guanine residues in DNA, and is also capable of intercalation in the DNA double helix. Chromosome regions fluorescing particularly strongly with QM have been demonstrated in human metaphase chromosomes 3, 13–15 and Y. A convenient measuring technique has been developed for the rapid and accurate recording of fluorescence patterns in human metaphase chromosomes. These photoelectric recordings of the fluorescence patterns contain far greater detail than can be seen by the human eye. The fluorescence patterns described are based on measurements of about 1,000 human metaphase chromosomes. This new technique of determining fluorescence patterns in human chromosomes should be particularly valuable for the identification of chromosomes 4–5 and the individual types in the 6–12 group. Individual, typical patterns also occur within the groups 13–15, 17–18, and 21–22.

Identification of human chromosomes by DNA-binding fluorescent agents

The karyotypes of cells from 10 Burkitt lymphoma (BL) biopsies, eight cell lines established from BL and nine cell lines from non-BL sources were studied by chromosome banding techniques. With the exception of the BL-derived cell lines BJAB, GC-BJAB, Maku and U-8691 all biopsies and lines of Burkitt origin contained an extra band at the distal region of the long arm of one chromosome 14. An extra band on chromosome 14 was also found in cells of one non-BL biopsy, in cells from a lymphosarcoma-derived cell line and in a long-established cell line derived from the pleural exudate of a patient with Hodgkin's disease. A distal region at the long arm of one chromosome 8 was missing in all metaphase figures of good technical quality in the same material. The size, morphology and stain-ability of the missing region corresponded fairly well to the extra region at chromosome 14. We therefore suggest that the chromosome 14 marker represents a translocation between chromosomes 8 and 14,t (8q-; 14q+). The translocation was present neither in lymphocytes of the peripheral blood of five Burkitt patients nor in five lymphoblastoid cell lines of non-BL origin. Trisomy 7 was found in two of the 10 BL biopsies, in two BL-derived cell lines, in one non-BL biopsy, in two lymphosarcoma-derived cell lines and in one cell line derived from a patient with Hodgkin's disease.

Characteristic chromosomal abnormalities in biopsies and lymphoid‐cell lines from patients with burkitt and non‐burkitt lymphomas

Differential binding of alkylating fluorochromes in human chromosomes.

Certain fluorescent DNA-binding compounds, among them quinacrine mustard and quinacrine, give characteristic banding patterns in human metaphase chromosomes; these patterns can be used to identify all the 24 chromosome types as well as chromosome aberrations. The patterns given by quinacrine mustard are especially clear and stable and are suitable for chromosome identification either visually—preferably after contrast enhancement by photography—or by photometric methods. The typical fluorescence pattern of each chromosome type is described.



The reproducibility and variability of the patterns have been analysed by photometric measurements of the patterns in a material of about 5000 chromosomes from 14 healthy subjects. Apart from certain minor but well defined chromosome regions with especially strong fluorescence, which are subject to certain individual variations, the fluorescence patterns were shown to be quite stable and reproducible.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1601-5223.1971.tb02363.x

Lore Zech

Papers

Identification of human chromosomes by DNA-binding fluorescent agents

Characteristic chromosomal abnormalities in biopsies and lymphoid‐cell lines from patients with burkitt and non‐burkitt lymphomas

Differential binding of alkylating fluorochromes in human chromosomes.

The 24 fluorescence patterns of the human metaphase chromosomes - distinguishing characters and variability.

Chemical differentiation along metaphase chromosomes.