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9.4: Diagnosing Human Chromosome Abnormalities - Biology

9.4:  Diagnosing Human Chromosome Abnormalities - Biology


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Bright Field Microscopy

How can we confirm that a person has a specific chromosomal abnormality? The first method was simply to obtain a sample of their cells, stain the chromosomes with Giemsa dye, and examine the results with a light microscope (Figure (PageIndex{1})). Each chromosome can be recognized by its length, the location of its centromere, and the characteristic pattern of purple bands produced by the Giemsa. For example, if mitotic cells from a person consistently contained forty seven chromosomes in total with three chromosome 21s this would be indicative of Down syndrome. Bright field microscopy does has its limitations though - it only works with mitotic chromosomes and many chromosome rearrangements are either too subtle or too complex for even a skilled cytogeneticist to discern.

Fluorescence In Situ Hybridization

The solution to these problems was fluorescence in situ hybridization (FISH). The technique is similar to a Southern blot in that a single stranded DNA probe is allowed to hybridize to denatured target DNA (see Section 8.6). However, instead of the probe being radioactive it is fluorescent and instead of the target DNA being restriction fragments on a nylon membrane it is denatured chromosomes on a glass slide. Because there are several fluorescent colours available it is common to use more than one probe at the same time. Typically the chromosomes are also labeled with a fluorescent stain called DAPI which gives them a uniform blue colour. If the chromosomes have come from a mitotic cell it is possible to see all forty six of them spread out in a small area. Alternatively, if the chromosomes are within the nucleus of an interphase cell they appear together within a large blue circle.

Using FISH to Diagnose Down Syndrome

Most pregnancies result in healthy children. However in some cases there is an elevated chance that the fetus has trisomy-21. Older women are at a higher risk because the non-disjunction events that lead to trisomy become more frequent with age. The second consideration is what the fetus looks like during an ultrasound examination. Fetuses with trisomy-21 and some other chromosome abnormalities have a swelling in the back of the neck called a nuchal translucency. If either or both factors is present the woman may choose amniocentesis. In this test some amniotic fluid is withdrawn so that the fetal cells within it can be examined. Figure (PageIndex{2}) shows a positive result for trisomy-21. Based upon this image the fetus has two X chromosomes and three chromosome 21s and therefore has a karyotype of 47,XX,+21.

Using FISH to Diagnose Cri-du-Chat Syndrome

A physician may suspect that a patient has a specific genetic condition based upon the patient's physical appearance, mental abilities, health problems, and other factors. FISH can be used to confirm the diagnosis. For example, Figure (PageIndex{3}) shows a positive result for cri-du-chat syndrome. The probes are binding to two long arms of chromosome 5 but only one short arm. One of the chromosome 5s must therefore be missing part of its short arm.

Newer Techniques

FISH is an elegant technique that produces dramatic images of our chromosomes. Unfortunately, FISH is also expensive, time consuming, and requires a high degree of skill. For these reasons, FISH is slowly being replaced with PCR and DNA chip based methods. Versions of these techniques have been developed that can accurately quantify a person's DNA. For example a sample of DNA from a person with Down syndrome will contain 150% more DNA from chromosome 21 than the other chromosomes. Likewise DNA from a person with cri-du-chat syndrome will contain 50% less DNA from the end of chromosome 5. These techniques are very useful if the suspected abnormality is a deletion, a duplication, or a change in chromosome number. They are less useful for diagnosing chromosome inversions and translocations because these rearrangements often involve no net loss or gain of genes.

In the future all of these techniques will likely be replaced with DNA sequencing. Each new generation of genome sequencing machines can sequence more DNA in less time. Eventually it will be cheaper just to sequence a patient's entire genome than to use FISH or PCR to test for specific chromosome defects.


This adorable nursing infant (Figure 9.4.1) is part of a positive feedback loop . When he suckles on the nipple , it sends nerve impulses to his mother’s hypothalamus . Those nerve impulses “tell” her pituitary gland to release the hormone prolactin into her bloodstream. Prolactin travels to the mammary glands in the breasts and stimulates milk production, which motivates the infant to keep suckling.

The pituitary gland is the master gland of the endocrine system , which is the system of glands that secrete hormones into the bloodstream. Endocrine hormones control virtually all physiological processes. They control growth, sexual maturation, reproduction, body temperature, blood pressure, and metabolism. The pituitary gland is considered the master gland of the endocrine system, because it controls the rest of the endocrine system. Many pituitary hormones either promote or inhibit hormone secretion by other endocrine glands.


Figure 9.5.2 The thyroid gland is a two-lobed gland in the front of the neck.

The thyroid gland is one of the largest endocrine glands in the body. It is located in the front of the neck below the Adam’s apple (see Figure 9.5.2). The gland is butterfly shaped and composed of two lobes. The lobes are connected by a narrow band of thyroid tissue called an isthmus.

Internally, the thyroid gland is composed mainly of follicles. A follicle is a small cluster of cells surrounding a central cavity, which stores hormones and other molecules made by the follicular cells. Thyroid follicular cells are unique in being highly specialized to absorb and use iodine . They absorb iodine as iodide ions (I-) from the blood and use the iodide to produce thyroid hormones. The cells also use some of the iodide they absorb to form a protein called thyroglobulin , which serves to store iodide for later hormone synthesis. The outer layer of cells of each follicle secretes thyroid hormones as needed. Scattered among the follicles are another type of thyroid cells, called parafollicular cells (or C cells). These cells synthesize and secrete the hormone calcitonin .


9.4: Diagnosing Human Chromosome Abnormalities - Biology

One of the eggs from such a meiosis could receive both X chromosomes, and the other would receive no X chromosomes.

If these eggs are subsequently fertilized with normal sperm, various sex chromosome aneuploidies could occur:

XXY - sterile male who may have some female body characteristics, and in some cases increased learning hurdles.
(For more information visit the National Institute of Health's site on Understanding Klinefelter Syndrome, A Guide for XXY Males and their Families at http://www.nih.gov/health/chip/nichd/klinefelter/)

XXX - There are no real stigmata connected with this syndrome. Women with triple X usually are fertile.

XO - sterile female with short stature, with low mental ability, failure to undergo puberty (Turner's syndrome).

YO - Non-viable genes on X chromosome required for development and survival.

Nondisjunction during sperm production can also result in aneuploidy of sex chromosomes.


Mass of human chromosomes measured

Mass of human chromosomes have been measured for the first time.

The mass of human chromosomes, which contain the instructions for life in nearly every cell of our bodies, has been measured with X-rays for the first time in a new study led by UCL researchers.

For the study, published in Chromosome Research, researchers used a powerful X-ray beam at the UK's national synchrotron facility, Diamond Light Source, to determine the number of electrons in a spread of 46 chromosomes which they used to calculate mass.

They found that the chromosomes were about 20 times heavier than the DNA they contained -- a much larger mass than previously expected, suggesting there might be missing components yet to be discovered.

As well as DNA, chromosomes consist of proteins that serve a variety of functions, from reading the DNA to regulating processes of cell division to tightly packaging two-metre strands of DNA into our cells.

Senior author Professor Ian Robinson (London Centre for Nanotechnology at UCL) said: "Chromosomes have been investigated by scientists for 130 years but there are still parts of these complex structures that are poorly understood.

"The mass of DNA we know from the Human Genome Project, but this is the first time we have been able to precisely measure the masses of chromosomes that include this DNA.

"Our measurement suggests the 46 chromosomes in each of our cells weigh 242 picograms (trillionths of a gram). This is heavier than we would expect, and, if replicated, points to unexplained excess mass in chromosomes."

In the study, researchers used a method called X-ray ptychography, which involves stitching together the diffraction patterns that occur as the X-ray beam passes through the chromosomes, to create a highly sensitive 3D reconstruction. The fine resolution was possible as the beam deployed at Diamond Light Source was billions of times brighter than the Sun (ie, there was a very large number of photons passing through at a given time).

The chromosomes were imaged in metaphase, just before they were about to divide into two daughter cells. This is when packaging proteins wind up the DNA into very compact, precise structures.

Archana Bhartiya, a PhD student at the London Centre for Nanotechnology at UCL and lead author of the paper, said: "A better understanding of chromosomes may have important implications for human health.

"A vast amount of study of chromosomes is undertaken in medical labs to diagnose cancer from patient samples. Any improvements in our abilities to image chromosomes would therefore be highly valuable."

Each human cell, at metaphase, normally contains 23 pairs of chromosomes, or 46 in total. Within these are four copies of 3.5 billion base pairs of DNA.

The research was supported by Diamond Light Source, UKRI, the Biotechnology and Biological Sciences Research Council (BBSRC), the Engineering and Physical Sciences Research Council (EPSRC), the European Research Council, and the US Department of Energy.


Contents

An abnormal number of chromosomes is called aneuploidy, and occurs when an individual is either missing a chromosome from a pair (resulting in monosomy) or has more than two chromosomes of a pair (trisomy, tetrasomy, etc.). [3] [4] Aneuploidy can be full, involving a whole chromosome missing or added, or partial, where only part of a chromosome is missing or added. [3] Aneuploidy can occur with sex chromosomes or autosomes.

An example of trisomy in humans is Down syndrome, which is a developmental disorder caused by an extra copy of chromosome 21 the disorder is therefore also called trisomy 21. [5]

An example of monosomy in humans is Turner syndrome, where the individual is born with only one sex chromosome, an X. [6]

Sperm aneuploidy Edit

Exposure of males to certain lifestyle, environmental and/or occupational hazards may increase the risk of aneuploid spermatozoa. [7] In particular, risk of aneuploidy is increased by tobacco smoking, [8] [9] and occupational exposure to benzene, [10] insecticides, [11] [12] and perfluorinated compounds. [13] Increased aneuploidy is often associated with increased DNA damage in spermatozoa.

When the chromosome's structure is altered, this can take several forms: [14]

    : A portion of the chromosome is missing or has been deleted. Known disorders in humans include Wolf-Hirschhorn syndrome, which is caused by partial deletion of the short arm of chromosome 4 and Jacobsen syndrome, also called the terminal 11q deletion disorder. : A portion of the chromosome has been duplicated, resulting in extra genetic material. Known human disorders include Charcot-Marie-Tooth disease type 1A, which may be caused by duplication of the gene encoding peripheral myelin protein 22 (PMP22) on chromosome 17. : A portion of the chromosome has broken off, turned upside down, and reattached, therefore the genetic material is inverted. : A portion of one chromosome has been deleted from its normal place and inserted into another chromosome. : A portion of one chromosome has been transferred to another chromosome. There are two main types of translocations:
      : Segments from two different chromosomes have been exchanged. : An entire chromosome has attached to another at the centromere - in humans these only occur with chromosomes 13, 14, 15, 21, and 22.

    Chromosome instability syndromes are a group of disorders characterized by chromosomal instability and breakage. They often lead to an increased tendency to develop certain types of malignancies.

    Most chromosome abnormalities occur as an accident in the egg cell or sperm, and therefore the anomaly is present in every cell of the body. Some anomalies, however, can happen after conception, resulting in Mosaicism (where some cells have the anomaly and some do not). Chromosome anomalies can be inherited from a parent or be "de novo". This is why chromosome studies are often performed on parents when a child is found to have an anomaly. If the parents do not possess the abnormality it was not initially inherited however it may be transmitted to subsequent generations.

    Most cancers, if not all, could cause chromosome abnormalities, [15] with either the formation of hybrid genes and fusion proteins, deregulation of genes and overexpression of proteins, or loss of tumor suppressor genes (see the "Mitelman Database" [16] and the Atlas of Genetics and Cytogenetics in Oncology and Haematology, [17] ). Furthermore, certain consistent chromosomal abnormalities can turn normal cells into a leukemic cell such as the translocation of a gene, resulting in its inappropriate expression. [18]

    During the mitotic and meiotic cell divisions of mammalian gametogenesis, DNA repair is effective at removing DNA damages. [19] However, in spermatogenesis the ability to repair DNA damages decreases substantially in the latter part of the process as haploid spermatids undergo major nuclear chromatin remodeling into highly compacted sperm nuclei. As reviewed by Marchetti et al., [20] the last few weeks of sperm development before fertilization are highly susceptible to the accumulation of sperm DNA damage. Such sperm DNA damage can be transmitted unrepaired into the egg where it is subject to removal by the maternal repair machinery. However, errors in maternal DNA repair of sperm DNA damage can result in zygotes with chromosomal structural aberrations.

    Melphalan is a bifunctional alkylating agent frequently used in chemotherapy. Meiotic inter-strand DNA damages caused by melphalan can escape paternal repair and cause chromosomal aberrations in the zygote by maternal misrepair. [20] Thus both pre- and post-fertilization DNA repair appear to be important in avoiding chromosome abnormalities and assuring the genome integrity of the conceptus.

    Depending on the information one wants to obtain, different techniques and samples are needed.


    Genotype-first approach to diagnosis

    Many of the recently identified syndromes have been identified through a genotype-first approach, rather than a typical phenotype-first approach.6 In the phenotype-first approach, the astute clinician would gather patients based on clinical presentation. This approach took many years to observe several rare individuals and develop a syndrome. The resulting syndromes had very consistent phenotypes among patients. In contrast, the genotype-first approach identifies patients with the same or overlapping genomic alterations and then describes the phenotypes observed. In this latter approach, the patients often display varying features, and in hindsight would not have been grouped based on clinical presentation alone.

    Recently, microarrays designed to interrogate known segmental duplication “hotspots” of the genome have identified several previously unrecognized genomic disorders. Recurrent microdeletions of chromosome 10q22.3q23.3,90,91 15q24,13� 16p11.2p12.2,16 17q21.31,10� and 17q23.1q23.292 have been identified in such a manner. In all cases, the majority of patients identified met the classical definition of a recurrent genomic disorder. The deletions were flanked by segmental duplications, the deletions were always apparently de novo in origin, and the patients had similar clinical features.41 However, the clinical features of these syndromes do not usually evoke a diagnostic Gestalt, which demonstrates the utility of the genotype-first approach in the absence of striking clinical features.

    The genotype-first approach may also enable the identification of small deletions or duplications that reveal the causative genes for specific clinical features, which can aid diagnosis and prognosis. For example, researchers recently identified what is likely to be the causative gene for features of 2q32q33 microdeletion syndrome.92 Individuals with the syndrome have severe mental retardation, growth retardation, dysmorphic facial features, thin and sparse hair, feeding difficulties, and cleft or high palate. Although deletions of varying sizes have been reported, the smallest region deleted in all patients contains at least seven genes. One of these genes, SATB2, is a DNA-binding protein that regulates how genes are expressed. Deletion of SATB2 has been suggested to cause the cleft or high palate of individuals with 2q32q33 microdeletion syndrome. The recent study identified three individuals with small deletions of this region, all of which spanned part of SATB2. Common clinical features among these individuals included severe developmental delay, behavioral problems, and tooth abnormalities. Interestingly, only one of the individuals had a cleft palate. Because the individuals had a portion of only one gene missing and the presence of many of the features associated with the larger microdeletion syndrome, the study authors suggested deletion of SATB2 was sufficient to cause several of the clinical features associated with 2q32q33 microdeletion syndrome.92


    Chromosome Map

    Our genetic information is stored in 23 pairs of chromosomes that vary widely in size and shape. Chromosome 1 is the largest and is over three times bigger than chromosome 22. The 23rd pair of chromosomes are two special chromosomes, X and Y, that determine our sex. Females have a pair of X chromosomes (46, XX), whereas males have one X and one Y chromosomes (46, XY). Chromosomes are made of DNA, and genes are special units of chromosomal DNA. Each chromosome is a very long molecule, so it needs to be wrapped tightly around proteins for efficient packaging.

    Near the center of each chromosome is its centromere, a narrow region that divides the chromosome into a long arm (q) and a short arm (p). We can further divide the chromosomes using special stains that produce stripes known as a banding pattern. Each chromosome has a distinct banding pattern, and each band is numbered to help identify a particular region of a chromosome. This method of mapping a gene to a particular band of the chromosome is called cytogenetic mapping. For example, the hemoglobin beta gene (HBB) is found on chromosome 11p15.4. This means that the HBB gene lies on the short arm (p) of chromosome 11 and is found at the band labeled 15.4.

    With the advent of new techniques in DNA analysis, we are able to look at the chromosome in much greater detail. Whereas cytogenetic mapping gives a bird's eye view of the chromosome, more modern methods show DNA at a much higher resolution. The Human Genome Project aims to identify and sequence the


    Summary

    Chromosomal disorders are the most frequent cause of mental retardation and developmental disabilities in our population. The phenotypes are often complex, and the result of a gain or loss of multiple, dosage-sensitive genes in the altered segments. The characterization of these complex phenotypes with overlapping deletions has allowed for the identification of genes causing particular features of the syndrome. The use of high-resolution technologies, such as microarrays, has allowed for the identification of new syndromes through a genotype-first approach at an unprecedented frequency never before imagined through the light microscope. Cytogenetics is no longer in its infancy, and has emerged a “new” genome science that, with the use of new technologies, has established the causes of mental retardation, developmental disabilities, and birth defects in our population.


    Watch the video: Diagnostic Genetic Tests (February 2023).