Antigens assigned an ISBT number must be
detected by a specific antibody and must be shown to be inherited characters.
The mandate of the 1980 Working Party on Terminology for Red Cell Surface antigens was
to define a uniform nomenclature that would be both eye- and machine-readable.
Allele-specific oligonucleotide PCR (ASOPs), sequence-specific primer PCR:
Method by which allele specific primers (approx 20bp) are used for PCR amplification. Hybridization may be disrupted by a single nucleotide and therefore failure to amplify may signify a mutation or polymorphism in the gene.
Amplicon or replicon:
Specific points at which DNA replication is initiated. A molecule of DNA has multiple replicons.
Arbitrarily primed PCR (genomic fingerprinting technique):
use of an undefined primer to amplify unknown segments of the DNA.
A set of three nts that code for one amino acid of chain termination; three contiguous bases in a strand of DNA that provides the genetic code for a specific amino acid.
Double-stranded DNA that represents expressed sequences of the genome, obtained by the transcription of mRNA
Certain regions of DNA are highly conserved, within and across species. Such regions are most common in expressed sequences that tolerate little variability and in functional genes sequences, such that splice sites and initiation sequences.
Conserved 5' UTR (untranslated region)
Sequence downstream of transcription and upstream of translation start
Process by which the hydrogen bonds between bps are broken to create two single-stranded antiparallel and complementary strands of DNA
Incorporation of radio-labeled P (P^32) at the 5' end of an oligonucleotide via polynucleotide kinase and gamma-labeled ATP.
Polymerization of nts to create nucleic acid molecules. Elongation proceeds 5' to 3' via condensation reaction.
Segment of a gene that is expressed. It is present only in eukaryotes. It is the portion of a gene coding for part of the amino acids in the final protein gene product.
Forward or sense primer:
The forward or sense primer anneals to the 3' end of the anti-sense strand and primes the synthesis of the sense strand.
A unit of inheritance that is located in a specific region on a chromosome and that provides information for specific traits; A DNA segment that contributes to phenotype or function. In the absence of demonstrated function, a gene may be characterized by sequence, transcription, or homology.
(A directional transfer of nucleotides from one duplex to another during DNA repair of two homologous genes.) Nonreciprocal exchange of genetic information as a result of heteroduplex formation between non-sister chromatids. Mismatches in the region of the heteroduplex are corrected so that one strand acts as the acceptor, which is made to complement the second strand, the donor (i.e., base changes occur on one strand only, the accptor strand). Disruption of the duplex and subsequent of the donor strand. Heteroduplex formation between allele pairs results in allelic conversion, while heteroduplex formation between nonallelic pairs, due to a high degree of homology, results in interlocus conversion.
The entire genome of an organism that includes nuclear and extranuclear DNA (i.e., mitochondrial DNA)
A series of linked alleles within a defined region on a single maternal or paternal chromosome. At least two sets of closely linked alleles present on one chromosome that determine different antigen products; almost always inherited as a unit.
Segments of DNA from a variety of organisms may display sequence similarity, or homology. The amount of homology between species may be used to determine evolutionary relationships and degrees of divergence. Functional genes often display homology across species; for example, homeobox genes that control early development show high degrees of homology across species.
Method of PCR in which the enzyme used for the amplification reaction (i.e., Taq polymerase) is added to template DNA that has been heated to 95C.
Hypervariable region or hypervariable minisatellite DNA:
Highly polymorphic arrays of tandemly repeated DNA sequences (0.1-20kb). Most are found near the telomere and are not transcribed.
the intervening stretches of DNA between exons. They are spliced out of the gene at the RNA level and are not expressed as part of the gene product (protein).
An error or permanent alteration that has occurred in the coding sequence of a gene or genetic regulatory element. There are several classes of mutations (non-sense, frameshift, insertion, deletion, and point mutation)
Northern blot/Southern blot:
Hybridization techniques in which single-stranded target nucleic acids, separated by length by gel electrophoresis, are transferred and fixed to nitrocellulose or nylon membranes. Radiolabeled probes are used to demonstrate the presence or absence of the target nucleic acid sequences. In a Southern blot, the target is DNA. In a Northern blot, the target is RNA.
NCRs (noncoding regions) of the genome:
segments of the genome that are not expressed. Extensive regions of noncoding DNA are found at the teleomeres and around the centromere, often termed heterochromatic DNA. NCRs are also found within genes (e.g., introns and 5' and 3' UTRs).
Building blocks of DNA and RNA. Composed of phosphate groups, a 5-sided sugar molecule (ribose in RNA; deoxyribose in DNA), and nitrogen-containing bases.
Nucleotide substitutions are of two types: 1) transitions, purine to purine or pyrimidine to pyrimidine; and 2) transversions, purine to pyrimidine and pyrimidine to purine. Naturally occurring substitutions may occur via tautomerization of nucleotides. Nucleotide analogues may also cause substitutions.
Sort sequences of DNA that may be read the same in the forward and reverse direction: for example, ATATTAATAT on on DNA strand and TATAATTATA on the complementary strand. Palindoromes may assume a specific secondary structure that facilitates recognition.
In vitro method for the amplification of a specific sequence of DNA, using sequence-specific primer sets. The temperature of the reaction is controlled such that amplification occurs in cycles.
A virus of bacteria, phage such as lambda have been used to introduce foreign DNA into bacteria.
Nonessential, circular, supercoiled DNA that is found in bacteria. Copy number is high, and the plasmid replicates autonomously.
Short nucleic acid sequences, oligonucleotides, that bind specifically to single-stranded target DNA. The 3'end (hydroxy group) of the primer allows for elongation of the primer and therefore DNA synthesis. Primers are synthesized in vitro.
A labeled oligonucleotide that serves to detect specific sequences via heteroduplex formation.
proteins produced by the expression of a gene, modified or unmodified, that is engineered into an appropriate vector system (i.e., SV40 expression vector). For example, recombinant EPO may be produced by the insertion of the EPO gene into an expression vector, that may then be introduced into mammalian cells which serve to house the production of the recombinant proteins.
Restriction enzymes or endonucleases:
Enzymes that recognize and cleave specific sequences of double-stranded DNA. For cleavage to occur, sites may require methylation.
Reverse or anti-sense primer:
the reverse or anti-sense primer anneals to the 3' end of the sense strand and primes the synthesis of the anti-sense strand.
Method by which single-stranded RNA (i.e., cDNA) is converted to double-stranded DNA. Reverse transcriptase is required.
Restriction fragment length polymorphism (RFLP) fragments:
Obtained by the digestion of DNA with a particular restriction enzyme. Fragment lengths are dependent on the location and frequency of restriction sites, which may vary from one individual to the next because of natural variability or mutations in DNA sequence.
Ribosomal RNA is not translated, but collaborates with ribosomal proteins to make ribosomes. Three distinct species of rRNA exist in eukaryotes --28S, 18S and 5.8S rRNA-- where S is a measure of the sedimentation coefficient.
Ideal for the amplification of expressed sequences. The cDNA, isolated by reverse transcription of mRNA, acts as the template. Exon-specific primers are used to start the reaction.
Heteroduplex formation between probes and target DNA is accomplished by controlling the environment in which hybridization occurs. Mismatches may be tolerated in solutions of high salt concentration and low temperature or low stringency, because salts stabilize the association of DNA by minimizing electrostatic repulsion of the negatively charged DNA backbone. Low temperatures prevent "melting" of DNA or disruption of hydrogen bonding. Therefore, stringency is a measure of the specificity of heteroduplex formation. High stringency equates to increased specificity.
Transfer RNA (tRNA):
RNA that assumes a cloverleaf structure and facilitates protein synthesis. The tRNA binds specifically to mRNA codons via an anticodon and interacts with ribosomes and rRNA. Transfer of an amino acid to the 3' end of the tRNA is specified by the anticodon.
VNTR (variable number of tandem repeats)
Alleles may differ because of variability in the number of tandem repeats. VNTR polymorphism is observed by digesting DNA with restriction enzymes specific for sequences flanking a specific VNTR locus Fragment length corresponds to the number of repeats. A repeat unit is typically 5-64 bp in size.
An extrachromosomal genetic element that, when incorporated into a recombinant DNA molecule, can cause transfer of the DNA into a host cell.
All authenticated antigens fall into one of four classifications:
systems, collections, low incidence antigens (700 series) and high incidence antigens (901 series)
A blood group system consists of
one or more antigens controlled at a single gene locus, or by two or more very closely linked homologous genes with little or no observable recombination between them.
Blood group collections consist of
serologically, biochemically, or genetically related antigens, which do not fit the criteria required for system status.
Low-incidence antigens (700 series) consists of:
antigens with an incidence of less than 1% and which cannot be included in a system or collection.
1) Incidence of <1% in most populations tested.
2) Distinction from all other numbered low incidence antigens of the 700 series as well as those of the blood group systems and collections.
3) Demonstration of inheritance through at least 2 generations.
High-incidence antigens (901) series consists of:
antigens with an incidence of greater than 90% and which cannot be included in a system or collection.
1) Incidence of >90% in most populations tested.
2.) Distinction from all other numbered high incidence specificities.
3) Demonstration that the antigen is lacking from the red cells of at least 2 sibs, i.e., that the negative phenotype is genetically determined.
Criteria for the establishment of new blood group systems:
For an antigen to form a new blood group system it must be defined by a human alloantibody, be an inherited character, the gene encoding it must have been identified and sequenced, and its chromosomal location known. In addition the gene must be different from, and not a closely-linked homologue of, all other genes encoding antigens of existing blood group systems.
Criteria for the inclusion of a new specificity in an established system:
All antigens awarded an ISBT number must have been shown to be inherited and at least one of the following four criteria must be met.
1) An antithetical relationship between a new antigen and one already assigned to the system.
2) Demonstration that expression of the antigen is associated with a variation in the nucleotide sequence of the gene controlling the system.
3) Evidence, from a linkage analysis of family data, that the controlling allele is probably a newly recognized form of the pertinent gene, and supporting serological or biochemical information.
4) Demonstration that an antigen is located on a protein or glycoprotein that carries other antigens belonging to the system. It must be remembered, however, that this could result from post-translational modification of a gene product, such as glycosylation, which would not support inclusion within the system.
Criteria for establishment of a blood group collection:
A collection must contain two or more antigens that are related serologically, biochemically, or genetically, but which do not fit the criteria required for system status.
Structure on the red blood cell membrane that is capable of complexing with its specific antibody. It is also capable of stimulating an antibody when introduced in the circulation of individuals lacking the antigen.
exactly opposite to
Antigens (produced by alleles)are antithetical to each other...
Antigens CANNOT be allelic.
Alleles CANNOT be antithetical
List or description of which antigens are observed on red blood cells as demonstrated by antibodies used to type the cells
Any one of a series of two or more versions or alternative forms of the same genes that occupy the same position on a specific chromosome.
A gene loci having the same morphology and linear sequence loci as a gene on another chromosome;
two paired chromosomes.
Genes an individual possesses based on DNA sequencing or extensive family studies.
***Red cells can be phenotyped, not genotyped. Mature red cells do not carry genes.
An interpretation as to which genes an individual probably possesses in order to have red cells of an observed phenotype.
Concentration of an antibody in solution or the strength or the strength of the antibody determined by titration. A titer is expressed as the reciprocal of the serum dilution.
To determine the concentration of an antibody by titration or to perform the operation of titration.
***A medium containing antibody can be titrated, NOT titered.
Long thin strand of DNA and protein within a nucleus that carries the genes in a linear order. Each chromosome has a long arm (p) and a short arm (q). Short arm usually depicted at the top of the page.
Redistribution or exchange of genetic information between paired chromosomes; occurs during prophase of first division of meiosis.
Containing two copies of each chromosome: one inherited from the mother and one from the father (2N karyotype
Deoxyribonucleic acid is the chemical basis of heredity and the carrier of genetic information in the nucleus of every nucleated cell.
Mutual exchange of nucleotides and the production of two reciprocal recombinant genes.
Non-reciprocal interaction of non-allelic genes, e.g. when the expression of one gene masks the expression of another. Occurs when two different loci are required in the development of a biochemical end product, e.g., the failure to express A or B antigens in the absence of H.
Possessing identical alleles at a given locus, i.e., allele A from both mother and father
Possessing different alleles at a given locus, i.e., allele A from mother, allele B from father
Genes of closely linked loci which do not segregate independently and are transmitted to gametes together in a nonrandom fashion.
Alleles at two loci associate with frequencies that reflect their individual frequencies
Alleles of linked loci associate with one another either more or less frequently that would be predicted from allelic frequencies and recombination over many generations.
Log probabilities of linkage at various recombination values obtained for each family with double heterozygous propositus. They are derived from a formula to determine the total relative probability of linkage versus independent inheritance. Scores of +1 favor linkage, while values <1 are against linkage. A score of +3 or >, statistically indicates linkage, whereas as a score of -2 or less, indicates genes are not likely linked.
Occurs only once in primordial cells destined to be a reproductive cell of gamete and occurs only once for each cell.
Replaces dead or injured somatic cells. The division of a cell into two daughter cells maintaining the appropriate number of parental chromosomes (diploid or 2N karyotype).
Regulator genes or modifier genes
Genes that regulate the expression of one or more genes by controlling the production of a protein that determines the rate at which the products of other genes are synthesized.
Each individual has two alleles for each trait; these segregate at mete formation, only one of each pair going to a single gamete. The Law of Segregation postulates 1:2:1 segregation of crosses of heterozygotes and 1:1 in crosses of heterozygotes and homozygotes.
Syntenic or synteny
Presence together on same chromosome of two or more loci whether or not the loci exhibit linkage.
Law of Independent Segregation
Mendel's Law...postulates 1:2:1 segregation of crosses of heterozygotes and 1:1 in crosses of heterozygotes and homozygotes.
Law of Independent Assortment
Genes determining various traits are inherited independently from each other; random behavior of genes on separate chromosomes during meiosis that result in a mixture of genetic material in the offspring.
Inheritance of Genes
Genes on the same chromosome (syntenic genes) are generally inherited together because the genes do not segregate independently and are transmitted to gametes together in a nonrandom fashion. Individuals inherit one gene from each parent.
the genetic message is carried on chromosomes as a sequence of nucleotides in DNA. the DNA is transcribed into mRNA. The mRNA is processed by the ribosomes into a polypeptide chain that produces a protein.
Gene Action for blood groups
Blood group characteristics are inherited but they are not all protein structures. For example, the ABO blood group antigens are carbohydrates. The ABO genes code for an enzyme that transfers a specific carbohydrate to a lipid or protein chain.
A trait may be modified by the expression of other gens which may be called regulator, modifier , suppressor, or inhibitor genes. The products of regulator or modifier genes may control the rate at which the products of there genes are synthesized.
Suppressor gene example
e.g., the weakening of the D antigen when the C determining gene is in the trans position is an example of a suppressor.
Inhibitor gene example.
In(Lu) is an inhibitor gene which inhibits or weakens the expression of the Lu gene.
The Hardy Weinberg Equation
Hardy and Weinberg, developed an equation that provides the best estimates for population genetics.
p2 + 2pq + q2 = 1
p2 = genotype freq. for p homozygote
2pq = genotype freq. for pq heterozygote
q2 = genotype freq. for q homozygote
using this information the genotype frequency and phenotype incidence may be calculated.
Deviations from Hardy Weinberg estimates occur as
a result of: non-random mating, selection, mutation, migration, and genetic drift.
Formula to Calculate Number of Random Donors to Screen for Compatible Blood
# units needed/incidence of Ag neg units =
# units to screen
Hardy Weinberg equations for 2 and 3 alleles
p2 + 2pq + q2 = 1
(p + q + r)^2 = 1^2
p + q + r = 1
Patterns of Inheritance
A pedigree is a diagrammatic representation of the inheritance of traits within a family. there are four patterns of inheritance: autosomal dominant, autosomal recessive, X-linked dominant, and X-linked recessive
Autosomal Dominant Inheritance
Appears in every generation that inherits the dominant allele responsible for the trait. The trait occurs with near equal frequency in males and females. E.g., Inheritance of the autosomal dominant In(Lu) gene is an example of this type of inheritance in human blood groups.
Autosomal Recessive Inheritance
Occurs with near equal frequency in both genders. However, the recessive state requires the person expressing the trait to be homozygous for the recessive gene. Both parents are carriers, and may be consanguineous. If frequency of recessive allele is low, the trait will be rare and will generally be observed only in persons of one generation.
Sex-Linked dominant Inheritance (true of X chromosome)
The dominant trait appears in each generation, and there is absence of father to son transmission. Percent of children affected will vary with the hemizygosity of the male and with the heterozygosity or homozygosity of the female.
Sex-Linked Recessive Inheritance (true of X chromosome)
there is not father to son transmission of a recessive trait. Trait is usually seen in males who have inherited the gene from a carrier mother. Females must be homozygous for the gene in order to express the trait. Percent of children affected (males and females) will gary with the hemizygosity of the male and with the heterozygosity or homozygosity of the female. If the recessive allele is rare, the trait will be observed primarily in males.
Used in significance testing, implies no difference. Accept if a value or event is not significantly different from others or the expectation (probability of being different is greater than 5%, p=>0.05. Reject when an event occurs less often than 5% of the time or has a p value <0.05. Such an occurrence is regarded as significant.
Borderline: p = 0.05 or p>0.05 <0.1
Significant: p = <0.05
Highly significant: p = <0.01
Very highly significant: p = <0.001
Formula for calculation of probability
(Fisher's exact test)
p = [(A+B)! x (C+D)! x (A+C)! x (B+D)!]
N! x A! x B! xC! x D!
Chi-Square Analysis for "Good Fit" answers the question:
Is the variation from expectation due to chance alone or is it a significant divination for which some explanation should be sought?
Compares observed and expected frequencies to evaluate the probability that the differences are statistically significant. Ideally, each expected frequency should be greater than 5 for the formula to yield acceptable results. It is always a two-tailed test (e.g., is category I higher than category II) In a two-tailed test there is no hypothesis for which direction the difference may take. With the result and associated p value, one may determine whether to accept or reject the null hypothesis. The p value is always lower in a one-tailed test than a two-tailed test.
Formulas for Chi Square
x2 = sum of (observed-expected)^2/expected
x2 = sum of (o-e)^2/e or sum of d^2/e (where d = difference between observed and expected values)
x2 = (ad-bc)^2N/(a+b)(a+c)(b+d)(c+d)
df = 1
a= patients with antigen
b= patients without antigen
c= Healthy individuals (ctrl) with antigen
d= Healthy individuals (ctrl) without antigen
Significance of Chi Square Analysis
p = 0.50 (not significant)
If p value < 0.05, consider observed values differ significantly from expected values, more than could be attributed to chance alone. Possible explanations: additional unsuspected alleles (codominant or silent), heterogeneous population, typing errors, illegitimacy or polygenic inheritance. The latter being a characteristic or disease controlled by the interaction of genes at more than one locus.
Relative Risk formula
RR= ad/bc = (pt w/Ag) X (healthy individual w/o Ag)/ (pt w/out Ag) X (healthy individuals w/Ag)
How is the Relative Risk formula used
to determine how many times more often the disease will develop in an individual with the antigen as compared to persons lacking the antigen. A relative risk of 1 indicates no difference in susceptibility among persons with and without the antigen.
Chromosome Mapping involves
assignment of loci to specific chromosomes and position of loci on the chromosome as well as its relationship and distance from other loci on the chromosome.
Distance between loci is measured in
centiMorgans (cM), also known as map units or crossover units. The distance is defined by the percent of recombinants in the offspring.
Proof of linkage requires
many more than one family because there could be other contributing factors (Illegitimacy, identification errors, typing errors, etc.)
Formula for Recombination Frequency
RF= sum of recombinants in families studied
Total # of offspring in all families
Peripheral proteins (only on cytoplasmic surface) of RBC cytoskeleton:
Actin (band 5)
Ankyrin (band 2.1)
Band 4.1 and 4.2
the major portion of the RBC cytoskeleton, a protein of high molecular weight. Binds to specific lipids by covalent bonds and forms dimers, tetramers and oliogomers; binds to band 4.1
a subcomponent of spectrin, binds to the cytoplasmic membrane-bound proteins and to the internal protions of the transmembrane anion-exchange-channel glycoprotein (band3)
may play a role as a link between tetramers and to bind the cytoskeleton to membrane proteins.
Antigen Carrier Molecules consist of:
Single-pass proteins: type 1 (N-terminus outside the red cell membrane and the C-terminus within the cytoplasm); Type II (C-terminus outside, N-terminus inside)
Glycosylphosphatidylinositol (GPI)-linked proteins
Sodium dodecy sulphate, polyacrylamide gel electrophoresis (SDE-PAGE)
used to solubilize and separate the RBC membrane components. Electrophoresis allows the separation of individual polypeptide chains from the red cell membrane based on their molecular weight.
Proteins stained with Commassie Blue
Glycoproteins stained with Periodic-Acid Schiff (PAS)
Four major types of lipids that maintain the basic structure in the RBC membrane:
Phosphatidylcholine (PC), aka Lecithin