Gene Information and Courses from MediaLab, Inc.

Thalassemia is best thought of as a group of disorders rather than a single disease. They demonstrate a hemoglobin synthesis disorder in which there exists a defect in the rate of production of one or more of the globin chains. This defect results from either a heterozygous or homozygous deletion or inactivation of a globin chain gene.

Chromosome 16 contains the genetic codes for the zeta and alpha hemoglobin chains.Each chromosome has two loci alpha chains 1 and 2. This equals a total of four loci of material coding for the alpha hemoglobin chain. See the image for a visual representation of these loci.In the genotypic notation of alpha thalassemia an "" represents the presence of an alpha locus. A "-" represents a deletion of a locus.The notation for the normal number of alpha loci is /. The amount of Hb A produced by this normal gene is 97-98 %.(drawing modified from Harmening, 1999)

Thalassemias are part of a group of hemoglobin synthesis disorders in which a defect exists in the rate of production of one or more of the globin chains. This defect results from either a heterozygous or homozygous deletion or inactivation of a globin chain gene.Thalassemias are named according to the affected gene or the globin chain that is showing reduced or absent synthesis.Globin chain loci are found on: chromosome 11 (beta, delta, epsilon, and gamma) chromosome 16 (alpha, and zeta)

Beta thalassemia minor (one gene mutation or deletion). This condition results in a range in beta chain synthesis from 10 - 50%. Beta thalassemia minor exists in several states that are identified with plus or zero. These notations correlate with the degree of gene deletion or inactivation.Because the delta gene is in close proximity to the beta gene, it is included in the beta thalassemia classification.The following pages include illustrations of beta thalassemia states.

Beta thalassemia major, B0/B0 (two gene mutations, deletions or combination) results in very few to no beta chains being produced.Hemoglobin A levels are at or near 0%.(drawing modified from Harmening, 1999)

In Beta thalassemia minor B+/B, one beta gene locus is partially deleted or inactive. With this deletion, only 85% to 95% of the normal level of Hb A is made.(drawing modified from Harmening, 1999)

Occasionally, the beta chain gene deletion extends to include the locus for the delta chain gene. If this deletion occurs on only one chromosome of the pair, it creates delta-beta thalassemia minor. Delta-Beta 0/ BetaHb A and A2 will both be decreased and Hb F will be increased.(drawing modified from Harmening, 1999)

In Beta thalassemia intermedia B0/B+s, there is one completely deleted or inactive beta chain gene, while the other is partially deleted or inactive.This state also results in Hb A production of 55%-75% of normal.(drawing modified from Harmening, 1999)

Delta-beta thalassemia major, Delta-beta 0/ Delta-beta0, exists when both gene loci for beta and delta chains are completely deleted or inactive on both chromosomes. In this state, only Hb F can be made.(drawing modified from Harmening, 1999)

As a high percentage of Enterococcus faecium strains carry the Van A gene and are highly resistant to vancomycin. Species identifications are performed in some laboratories where MIC susceptibility testing may not be available.Methods for the phenotypic separation of E. faecium from E. faecalis are limited.Illustrated in this photograph are positive reactions for acid production from arabinose and melibiose (yellow color), characteristic of E. faecium. E. faecalis are negative for these reactions.A few preformed substrates such as beta galactosidase (E. faecium positive, E. faecalis negative) also serve to separate these two species, accomplished by certain commercial systems that include these substrates.E. faecium is not motile, an additional characteristic helpful to separate vancomycin-resistant Enterococcus species from E. cassiloflavus and E. gallinarum, both of which are motile, and carry the low level resistant gene VAN-c.

Because of the two separation processes, more information and separated solutes can be gained from a sample. The use of two-dimensional electrophoresis is specialized and most applications are in research fields. It is used to study families of proteins in the field of proteomics and protein content in different types of cells. It is also used extensively in genetics to study differences in diseases, gene mutations, and bacterial DNA. In an effort to find ways to detect malignancies earlier, two-dimensional electrophoresis is used to study tumor cells.

A gene is a hereditary unit or sequence of the nucleotide bases ACGT, occupying a fixed location or locus on the chromosome. It is these genes that carry all the information for life processes.DNA is rewritten into 3 types of RNA, each with a specific task: Messenger RNA (mRNA)carries the protein message to the cytoplasm. Ribosomal RNA (rRNA) is the location of protein synthesis. Transfer RNA (tRNA) is responsible for amino acid transport.Each 3-base nucleotide sequence (codon) codes for a specific amino acid. Some amino acids have more than one codon to direct their placement; this is termed degeneracy.

A hemochromatosis gene, HFE, was identified in 1996. Mutations in the HFE gene are found in the majority of patients diagnosed with hereditary hemochromatosis (HH). The locus for the gene is on the long arm of chromosome 6 where it codes for a membrane protein, HFE. The exact mechanism of the role of HFE protein in iron metabolism is incompletely understood. It is thought that HFE, along with a second protein, beta-2 microglobin, interacts with transferrin receptors (TfR) on cell membranes. This interaction supresses the affinity of transferrin for TfR, thus lowering the uptake of transferrin--and its attached iron--into the cell. Transferrin receptors have been found on the surface of a variety of cells, with the greatest concentration on cell membranes of intestinal cells, hepatocytes, and RBC precursors. In addition to HFE, HH is also associated with mutations in other genes involved in iron homeostasis, including hemojuvelin (HJV), TfR, hepcidin, and ferroportin. Hepcidin production is reduced in HH due to all of these genetic causes, with a resulting increase in iron absorption. Mutations in HFE are the most common cause of HH.

Several mutations of the HFE gene have been described. In the C282Y mutation, a base substitution leads to a change in the amino acid in position 282 from cysteine (C) to tyrosine (Y). The loss of the sulfhydryl-containing amino acid disrupts the tertiary structure of HFE so that it no longer binds to beta-2 microglobulin. Beta-2 microglobulin appears to act along with other proteins to chaperone the newly synthesized HFE out of the Golgi apparatus and to the cell surface where it can then bind to TfR. In the C282Y mutation, HFE remains in the Golgi, never making it to the cell surface. The result is that transferrin binding to TfR is enhanced and excessive amounts of iron enter the cells of the small intestine, liver, and other tissues. A second mutation, H63D, causes a histidine (H) residue in position 63 to be replaced by aspartic acid (D). The mechanism by which this mutation leads to increased iron uptake is less well understood when compared to the C282Y mutation. Unlike the C282Y mutation, the H63D mutation does not seem to affect the binding of beta-2 microglobulin and intracellular movement, since detectable concentrations of the mutated protein are found on cell membranes. Some researchers speculate that the H63D mutation affects the binding of proteins involved in iron regulation and uptake at the cell surface.A third mutation, S65C, leads to a serine-to-cysteine substitution in its associated protein. This mutation has been been found in some compound heterozygotes for C282Y or H63D, but is rarely associated with iron overload in HH.Additional mutations of HFE have been identified, but their clinical significance is unclear. Most laboratories performing molecular assays test for only the C282Y, H63D, and S65C mutations.

The diagnosis of hereditary hemochromatosis (HH) is made through a combination of laboratory tests and medical evaluation of a patient's signs and symptoms. Iron overload is identified by tests that evaluate iron metabolism, while molecular assays are needed to document mutations in the HFE gene or others such as hepcidin, hemojuvelin, or transferrin receptor. Individuals with documented iron overload who exhibit signs and symptoms consistent with HH and who possess HFE or other mutations are considered to have HH. Other causes of secondary iron overload may need to be ruled out.An example of a testing algorithm is shown.

HIV consists of nine genes. Three of the genes provide genetic information for the capsid proteins, envelope proteins, and viral enzymes. The other six genes are regulatory genes, controlling functions such as uncoating of the HIV genome and the penetration of host cells. Gene Number Abbreviation Gene Function 1 gag capsid proteins 2 pol viral enzymes 3 env envelope proteins 4 vif regulatory gene 5 tat regulatory gene 6 vpu regulatory gene 7 nef regulatory gene 8 vpr regulatory gene 9 rev regulatory gene

HIV consists of nine genes. Three of the genes provide genetic information for the capsid proteins, envelope proteins, and viral enzymes. The other six genes are regulatory genes, controlling functions such as uncoating of the HIV genome and the penetration of host cells. Gene NumberAbbreviationGene Function1gagcapsid proteins2polviral enzymes3envenvelope proteins4vifregulatory gene5tatregulatory gene6vpuregulatory gene7nefregulatory gene8vprregulatory gene9revregulatory gene

Three separate loci (ABO, Hh, and Se) contain the genes that control the location and occurrence of the A and B antigens. Hh and Se genes are closely linked on chromosome 19. The precursor substance is acted upon by the H gene and is converted to H substance. The product of the H gene is an enzyme fucosyltransferase, responsible for attaching fucose to the terminal galactose of the precursor substance on the RBC membrane and thus forming H substance. There are only two recognized alleles at this locus: the active form, H, and an amorph, h. The H gene is a high-incidence gene. People who inherit hh are extremely rare. Since the h gene is amorphic, it does not act on the precursor substance.

As mentioned previously, the A and B genes cannot act directly on the precursor substance. Thus, since individuals with the Bombay phenotype have only the precursor substance and no H antigen, they cannot have A or B antigens, even if they have the A and/or B gene.

The presence of A and/or B antigen on the red cells can be recognized by serological tests with the appropriate antisera so that the presence of the gene that controls its production can be deduced in the absence of both A and B genes (when no A or B antigen is present on the red cells).

To discuss PGx, we must first define two terms - polymorphism and cytochrome P450 (CYP450).A polymorphism is a variation in a gene (allele) that affects at least 1% of the population. CYP450 refers to a family of enzymes found predominantly in the liver. CYP450 enzymes work on a variety of substrates (drugs), altering their chemical structures to facilitate excretion in the urine and feces. There are many known polymorphisms in CYP450 enzymes.

CYP2D6 has received the most attention: It is estimated that about 25% of common drugs are metabolized by CYP2D6. CYP2D6 accounts for only about 1% of all CYP450 enzymes, but it is important in the metabolism of about 100 drugs. There are more than 80 genetic variants that have been described in the CYP2D6 gene. The normal, wild-type allele displays normal metabolic activity whereas some of the variant forms have enhanced or diminished activity. The variants can be grouped generally according to the resulting alterations in protein function. The groupings correlate with four major enzyme metabolic capacities (phenotypes): poor, intermediate, extensive (normal), or ultra-rapid metabolizers.

The patient's pretransfusion red cells and all donor red cells involved in the case (two group O Rh-negative RBC and four group O Rh-positive red cells initially crossmatched) were phenotyped for Jka.As expected, the patient typed as Jk(a-). The six donor RBC that were incompatible in the initial crossmatch were Jk(a+).The frequency of the Jka gene in Caucasians is ~77%, with most Caucasian red cells (50%) typing as Jk(a+b+).

Chediak-Higashi syndrome is a rare autosomal recessive disorder. It results from a mutation of the gene LYST which encodes a protein with multiple phosphorylation sites. This defect causes a cellular abnormality involving the fusion of cytoplasmic granules. Early in neutrophil maturation normal azurophilic granules form, but they fuse together to form megagranules. Later during the myelocyte stage, normal specific granules form. The mature neutrophils contain both normal specific granules and abnormal azurophilic granules. These large abnormal granules can be seen in the cytoplasm of neutrophils, eosinophils, basophils, monocytes and lymphocytes. These abnormal granules are able to kill bacteria in neutrophils and monocytes; however, the process is much less effective than in normal cells in part, because these neutrophils have impaired locomotion. For these reasons, individuals with Chediak-Higashi have recurrent infections. An accelerated lymphoma-like phase occurs, with lymphadenopathy, hepatosplenomegaly, and pancytopenia. Death often occurs at an early age.