The first wave of information from the analysis of the human genome revealed SNPs to be the main source of genetic and phenotypic human variation. However, the advent of genome-scanning technologies has now uncovered an unexpectedly large extent of what we term 'structural variation' in the human genome. This comprises microscopic and, more commonly, submicroscopic variants, which include deletions, duplications and large-scale copy-number variants - collectively termed copy-number variants or copy-number polymorphisms - as well as insertions, inversions and translocations. Rapidly accumulating evidence indicates that structural variants can comprise millions of nucleotides of heterogeneity within every genome, and are likely to make an important contribution to human diversity and disease susceptibility.

Structural variation in the human genome

Pretreatment cytogenetic abnormalities are predictive of induction success, cumulative incidence of relapse, and overall survival in adult patients with de novo acute myeloid leukemia: results from Cancer and Leukemia Group B (CALGB 8461)

Holt-Oram syndrome is a developmental disorder affecting the heart and upper limb, the gene for which was mapped to chromosome 12 two years ago. We have now identified a gene for this disorder (HOS1). The gene (TBX5) is a member of the Brachyury (T) family corresponding to the mouse TbxS gene. We have identified six mutations, three in HOS families and three in sporadic HOS cases. Each of the mutations introduces a premature stop codon in the TBXS gene product. Tissue in situ hybridization studies on human embryos from days 26 to 52 of gestation reveal expression of TBXS in heart and limb, consistent with a role in human embryonic development.

Holt-Oram syndrome is caused by mutations in TBX5, a member of the Brachyury ( T ) gene family

The mitotic checkpoint protein hsMad2 is required to arrest cells in mitosis when chromosomes are unattached to the mitotic spindle. The presence of a single, lagging chromosome is sufficient to activate the checkpoint, producing a delay at the metaphase-anaphase transition until the last spindle attachment is made. Complete loss of the mitotic checkpoint results in embryonic lethality owing to chromosome mis-segregation in various organisms. Whether partial loss of checkpoint control leads to more subtle rates of chromosome instability compatible with cell viability remains unknown. Here we report that deletion of one MAD2 allele results in a defective mitotic checkpoint in both human cancer cells and murine primary embryonic fibroblasts. Checkpoint-defective cells show premature sister-chromatid separation in the presence of spindle inhibitors and an elevated rate of chromosome mis-segregation events in the absence of these agents. Furthermore, Mad2+/- mice develop lung tumours at high rates after long latencies, implicating defects in the mitotic checkpoint in tumorigenesis.

MAD2 haplo-insufficiency causes premature anaphase and chromosome instability in mammalian cells

DAPI (4',6-diamidino-2-phenylindole) is a DNA-specific probe which forms a fluorescent complex by attaching in the minor grove of A-T rich sequences of DNA. It also forms nonfluorescent intercalative complexes with double-stranded nucleic acids. The physicochemical properties of the dye and its complexes with nucleic acids and history of the development of this dye as a biological stain are described. The application of DAPI as a DNA-specific probe for flow cytometry, chromosome staining, DNA visualization and quantitation in histochemistry and biochemistry is reviewed. The mechanisms of DAPI-nucleic acid complex formation including minor groove binding, intercalation and condensation are discussed.

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DAPI: a DNA-Specific Fluorescent Probe

Tissue culture chromosome preparations diffential staining techniques selective staining techniques molecular cytogenetic techniques chromosome shorting nomenclature chromosome in clinical medicine.

Human chromosomes : principles and techniques

Human Chromosomes: Manual of Basic Techniques

Publisher Summary This chapter discusses the terms “euchromatin” and “heterochromatin” that have long been familiar for expressing primarily the state of chromatin condensation during the cell cycle. The term “heterochromatin,” in particular, has been used to describe such chromatin or chromosome segments that did not go through the uncoiling process toward the end of mitosis and so remained condensed throughout interphase. Usually this condensed state of chromatin results in a heteropyknotic property. On the other hand, the chromatin that uncoils in the subsequent interphase is considered euchromatin. The earlier studies on different chromatintypes were based on the staining variation in interphase nuclei. Similar studies using metaphase chromosomes were limited to those species where the heterochromatic segments were recognizable from the staining differences by conventional methods. However, recent advances in banding technology and in sequencing DNA replication using isotype-labeled nucleotides and BrdU have rendered the metaphase chromosomes amenable for such investigations. In metaphase chromosomes, the regions stained by the C-banding method and the latereplicating X chromosome (in females) are regarded as heterochromatic. The remaining regions are referred to as “euchromatic.”

Chromosome structure: euchromatin and heterochromatin.

Trisomy 13: A New Recurring Chromosome Abnormality in Acute Leukemia

Publisher Summary The heteromorphic chromosomes of the human genome can be classified by size, position, staining intensity, or any combination of these types using various banding techniques, such as QFQ (Q-bands by fluorescence using quinacrine), CBG (C-bands by barium hydroxide using Giemsa), and RFA (R-bands by fluorescence using acridine organe). The classification of different types of heteromorphisms is based on estimation rather than actual measurements. Moreover, variation is continuous rather than discrete. However, several attempts are made to classify them on the basis of arbitrary scales and different codes (levels) are assigned. Chromosomal heteromorphisms found in human chromosomes provide a useful tool for several studies because they are inherited in a Mendelian fashion, are stable, and are presumed to have a low mutation rate. By using heteromorphic markers of chromosome 21, the origin of the extra chromosome in Down syndrome can be determined. Applications of heteromorphisms as markers is in elucidating the chromosomal mechanisms involved in the production of mosaics, in studying chimeras, and in following the fate of transfused or transplanted cells.

Ram S. Verma

Papers

Human chromosomes : principles and techniques

Human Chromosomes: Manual of Basic Techniques

Chromosome structure: euchromatin and heterochromatin.

Trisomy 13: A New Recurring Chromosome Abnormality in Acute Leukemia

Human chromosomal heteromorphisms: nature and clinical significance.