Lecture 14 Flashcards by sita clark

Technologies facilitate genetic discovery and therapy

Can sequence genome easily
-ethical discussion
-cost has reduced so much that it could be used more clinically and easily
Cost per Raw Megabase of DNA : sudden drop in cost, as new technology has been introduced
-Technologies facilitating genetic discoveries

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What are the 4x major categories of Genetically determined Diseases?

Single gene disorders (variation/difference/mutation which leads to gene/phenotye)
Chromosomal disorders (contains over 100 genes. duplication more/loss of chromosome can lead to major change in cell and development. can lead to death before birth)- only small proportion make it alive
Multifactorial genetic disorders: Complex disroders, Multiple genes, interact with environment, pathogens etc
Somatic disorders (somatic cells arent in germline, not testes or ovaries, not involved with passing genetics to offspring) - include genetic changes in cancer

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Single Gene-Disorder

Beta-Thalassaemia
many organ systems effected
-mutation in single gene can have very broad reaching effects. different effects in different organs. can effect single organ (blood) leading to secondary effects in body
single gene =/= single tight phenotype
-can lead to both primary and secondary effects

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Chromosomal Disroders

100s of genes effected
Trisomy 21 (Downsyndrome)(3x copies)
large numbers of genes effective
more or less copies
-can often lead to embryionic nafality (not compatable with life)
-small number chromosomal disorders do allow human to survive
-also Trisomy 18, 13
Error in early cell division
Increased likelihood of down syndrome offspring with maternal age (rapid after mid 30s) (genetic disease that manifests itself late in maternal life)
Cause I: Non-disjunction, Metaphase I
during first stage of meiosis in ovaries there is a halt in metaphase 1, later reactivated. Longer gap, more likely for non-dysjunction (moving apart of chromosomes not occur evenly. one daughter cell gets 2x copies, other gets none)
Cause II: Translocations
-
1. Genetic disorder is discovered decades before understanding of how it arises
2. Genetic chromosomal disorders are often incompatable with life- only very small number are compatible (chromosome 13, 18, 21)
3. Mechanisms can range from very simple (Non-dysjunction in Meiosis, 2x copies to one daughter cell and none to the other) or much more complex (Robertsonian Translocation)

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Translocations results in Down syndrome

Chromosome 21 is very assymetrical (centromere in centre) - one arm contains nearly all genetic information, other arm contains hardly any
“Translocation”= cutting and rejoining
1. the short arm of acrocentric chromosome
Robertsonian Translocation:
2. is exchanged with long arm of another
3. creating a large metacentric chromosome (2x large arms= is essntially 2x copies of chromsomes)
4. and a fragment that often fails to segregate and is lost

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Multifactorial Genetic Disorders

Result from interaction of multiple genes(rather than just chromosme)
-each of the genes alone may have minor effect, but together they synergise (often also interaction with environment and infection); some may have a major effect but many have relatively minor effect
Most common and Least understood of genetic diseases
-Diabetes Mellitus
-Hypertension
common chronic diseases
-Coronary Artery Disease
-Schizophrenia
-Cleft lip, cleft palate, most congenital heart disease
All results from complex synergy of multiple genes + environment, nutrition, infection influences the likelihood of getting disease

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Somatic cell Genetic Disroder

-very different to germline disorders, where change in genome of germ cell can be passed on to offspring
Arise only in specific somatic cells (in contrast to other genetic disorders where the abnormality is found in the DNA of all cells of the body, including germ cells)
Are not transmitted to subsequent generations
Paradigm is CANCER; (not all tumours nescessarily involve somatic disorder) development of malignancy often a consequence of mutations in genes that control growth
Individual genes: APC. Grey lines= random fragments
Mutation in half of the bases = mutation of one copy
Whole genes: Chromosome 11 (1300 genes) - number of different alleles. chromosome 11 completely lost. remains of chromosome left over by normal cells of tumour. Germ cell can still survive and may make cancer tumour survive better

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Mutation

Any permenant heritable change in the sequence of genome DNA

Any alteration of DNA from its natural state: may be disease-causing or a benign normal variant

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Polymorphism

The occurance together in a population of two or more alternative genotypes, each at a frequency greater than that which could be maintained by recurrent mutation alone
-recurrent mutation alone is not maintaining multiple copies in the population. there has to be some other evolutionary reason for them to be maintained
Natural variations in genomic DNA sequence, that usually have no obvious adverse effects on the individual and occur with fairly high frequency in the general population
-Neutral, no particular advantage, just making us differnet. But may make some people better suited to certain environment (potential advantage)
Single nucleotide polymorphisms (SNPs) in human (‘1 per 100-300bp) being catealogued as extension of Human Genome Project (differences in population. almost always netural. doesnt give predisposition to disease. Good markers as linked to change in gene that may be associated with disease)
SNPS can be flags, if close enough to changed gene which leads to disease, can be used to identify/trace this disease causing gene sequencethrough population/family

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5x Types of Mutation

3x bases = code each aa.

Silent : single base change that does not result in aa amino acid change (triplet code degeneracy) - wobbly 3rd base, can be multiple bases in third position that can still code for the same protein/aa
Missense: Single bas change that does result in an aa amino acid change. May or may not cause abnormal phenotype (usually doesnt really change structural function of protein)- can result in change of phenotype - cnacer predisposition syndrome, inhereited neuroogical disease
Nonsense: single base change that changes an aa amino acid to a –> (premature) STOP codon (triplet of bases which codes for transcription to stop) (for transcription - is introduced preamturely/transcription therefore halted prematurely)
Frameshift: Insertion of deletion of bases in anything other than multiple of 3 (changes frame. changes protein encoded. often introduce stop codon by chace downstream)
Splice donor/Acceptor: Alteration of sequences for accurate splicing of introns ( RNA transcribed before translation, early RNA forms spliced. Sites introns removed and 2x extrons spliced together, having particular signals for splicing based on sequence of DNA. interrupted by mutation, cause skipping of exon or splice in another place = different protein made)

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Sickle Cell Anemia

Missense Mutation
Wild type DNA:CTC = RNA:GAG = instructs for Glutamic acid (aa in the protein)
Missense Mutation DNA:CAC= RNA=GUG = Valine aa in protein
A substituted for a T
= Sickle shaped erythrocyte

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Example of Frame shift Mutation

THE FAT CAT ATE HIS HAT
Insertion of A: THE FAA TCA TAT EHI SHA T
Deletion of A: THE FTC ATA TEH ISH AT
-still some sensible words. but not correct. alot are nonsense
“indel”= insertion or deletion, which can be more than a single base/nucleotides. Relavent to somatic mutations as well

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Classes of mutations

Pathogenic: Lead to another phenotype/disease

Non-Pathogenic: Neutral. Not lead to anything

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“indel”

insertion of deletion, which can be more than a single base/nucleotides
-relavent to somatic and frame shift mutations

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Deciding if a DNA change is Pathogenic

If a missense alteration (single bas change), is it at a functionally important site?
- structure-function studies
- in vitro mutagenesis (putting altered gene/proteins function in other cells) (Krisper Cass echnology revolutionalised)
- evolutionary conservation
Is predicted protein truncated? (nonsense mutation premature stop codon, protein shorter and not likely to function properly, may also gunk up system and prevent cell function(dominant negative effect))
Is RNA splicing affected? (deletion/insertion of multiple bases, esp if near splice sites (introns spliced out of RNA))
Does the change segregate with disease in the family?- raises suspicion is pathogenic/leading to the disease

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Somatic Mutation vs Germline Mutation

If a new mutation occurs in non-gamete-forming cells (Somatic cells), the consequence of the changes are limited to the person whom the changes occurred

If the new mutation occurs in cells that ultimately form the gametes (Germline cells- spermatocytes, spermatogonia, spermatids, oocytes), the change may be transmitted to subsequent generations

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Phenotypic Expression of Mutations

Several events had to happen between change in DNA sequence, change to protein/protein function/change to cell
Gain of function mutations
-Produce either an increased amount or increased activity of the product (melanoma in B-raf signalling molcule, increased development of melanoma stem cells to divide rapidly out of control = melanoma tumour develpment(Somatic gain of function mutation))
Loss of function mutations - more common
-Produce either a reduced amount or a reduced activity of the gene product (completely disabled - Premature stop codon of Nonsense mutation so that protein much shorter and not work at all)
-Usually have minimal effect on the phenotype unless both alleles affects (slows enzyme activity)
-If no product or function results from allele, known as NULL ALLELE
-Haplo-insufficiency sometimes occurs: 50% product levels results in an altered phenotype. Isnt sufficient-requires more than 50% of the amount of protein to perform the function. -Disrupt a single allele to see a disease/phenotype (not as simple as normally if loss/disruption of allele, complex mechanisms cause RNA/protein production from remaining allele to increase- compensation sometimes) (1/2 no functional protein/null allele, other 1/2 normal allele still producing protein, normally sufficient/no disease/phenotype as is producing enough protein)
-Some heterozygous loss-of-function mutations produce a DOMINANT NEGATIVE effect (abnormal product interferes with product of normal allele) (structural protein encoded genes. one allele from each parents, each encode protein, which will construct cell structure. Dads allele has/developed a mutation. Gene encodes protein is wrong shape. Half bricks in wall are now circle= weakens structure/prevents building)
-one gene carries a mutation that is sufficient to allow that protein it encodes to disrupt the function of the remaining normal protein from the remaining normal allele

Null allele

If no product or function results from allele, known as NULL ALLELE

Haplo-insufficiency

50% product levels results in an altered phenotype.
-Isnt sufficient-requires more than 50% of the amount of protein to perform the function.
-Disrupt a single allele to see a disease/phenotype (not as simple as normally if loss/disruption of allele, complex mechanisms cause RNA/protein production from remaining allele to increase- compensation sometimes)
(1/2 no functional protein/null allele, other 1/2 normal allele still producing protein, normally sufficient/no disease/phenotype as is producing enough protein)

Dominant Negative effect

Some heterozygous loss-of-function mutations produce a DOMINANT NEGATIVE effect (abnormal product interferes with product of normal allele) (structural protein encoded genes. one allele from each parents, each encode protein, which will construct cell structure. Dads allele has/developed a mutation. Gene encodes protein is wrong shape. Half bricks in wall are now circle= weakens structure/prevents building)
-one gene carries a mutation that is sufficient to allow that protein it encodes to disrupt the function of the remaining normal protein from the remaining normal allele

Single Gene Disorders

Result from mutations in one (dominant inheritance pattern) or both (recessive) of a pair of genes
May be autosomal, X chromosomal or Y chromosomal
To establish pattern of inheritance, construct family pedigree
Understanding of single gene disorders based on laws if heredity (Mendel)

Mendelian Patterns of Inheritance

autosomal dominant
autosomal recessive
X-linked recessive
x-linked dominant
Y-lined (holandric)
- a character is dominant if it is manifest in the heterozygote and recessive if it is not

Autosomal Inheritance

23 pair of chromosomes (22 autosomes, 1x pair of sex chromosomes)
Genes occupy specific loci (positions) on chromosomes (gene are paired (one paternal,on maternal))
Alleles are alternative forms of a gene (normal/unaffected = wild type. If maternal and parental alleles are identical = Homozygous. If maternal and paternal alleles differ= Heterozygous)

Autosomal dominant Inheritance

affected person usually has at least one affected parent
affects either sex
transmitted by either sex
child of affected x unaffected mating has 50% chance of being affected (assuming affected person is heterozygous)
in affected families the ratio of affected to unaffected is usually 1:1
if both parents are unaffected, all children are unaffected

Autosomal Recessive Inheritance

Unaffected people usually born to unaffected (carrier) parents
affects either sex
increased incidence of parental consanguinity
after birth of affected child, each subsequent child has 25% chance of being affected (assuming both parents phenotypically normal carriers)

Sex linked Inheritance

Female has 2x X chromosomes (one maternal, on paternal)
Male has one X chromosome (maternal) and one Y chromosome (paternal); Hemizygous for each X-linked gene
Lyonisation: Random inactivation of parts of one X chromosome in female somatic cells - basis of manifesting heterozygote

Lyonisation

Random inactivation of parts of one X chromosome in female somatic cells - basis of manifesting heterozygote

X-linked recessive inheritance

Affects mainly males
affected males usually born to unaffected parents (mother asymptomatic carrier and may have affected male relatives)
No male to male transmission
all daughters of affected males are obligate carriers

X-linked dominant inheritance

Affects either sex; but more female than males
Females often more mildly and variably affected than males (because of Lyonisation)
Child of an affected female, regardless of sex, has 50% chance of being affected
For an affected male, all his daughters but none of his sons are affected (distinguishes from autosomal dominant)

What is the distinguishing features between X-linked Dominant inheritance and Autosomal Dominant inheritance?

for X-linked dominant inheritance, for an affected male, all of his daughters, but none of his sons are affected

Y-linke Inheritance

affects only males
Affected males always have an affected father (unless is a new mutation)
All sons of an affected man are affected

What is the relationship between X-linked dominant inheritance and Females?

Females often more mildly and variably affected than males (because of Lyonisation)

Complications to basic Mendelian Pedigree Patterns

Common recessive conditions can give pseudo-dominant pattern (e.g. blood group O)
Variable penetrance: failure of dominant condition to manifest (due to many other factors being involved- other genes synergising etc)
Variable expression (including anticipation)
New Mutations/germline mosaicism (some parents sperm cells may have mutation and not others): "In Novo mutations": new mutation that arises in an individual that hasnt been inheritated by parent

Variable penetrance

failure of dominant condition to manifest (due to many other factors being involved- other genes synergising etc)

In Novo mutations

new mutation that arises in an individual that hasnt been inheritated by parent

Germline Mosaicism

some parents sperm cells may have mutation and not others

Autosomal Dominant with Variable Penetrance

Ectrodactyly

split hand-split foot deformity
e. g. duplication on 10q24
lesion of digits during development

Autosomal Dominant with Variable Expression

Waardenburg Syndrome
Shading of:
1st quadrent: hearing loss
2nd quadrent: different coloured eyes
3rd quadrent: white forelock
4th quadrent: premature grey hair

Autosomal Dominant Germline Mosaicism

Osteogenesis Imperfecta
(several)>1 offspring with disease (in contrast to new mutation); parent unaffected
May think new mutation if is a single offspring with disease with an unaffected parent
But several offspring with disease with unaffected parent= mutation that has arisen in parents germline

Genetic Heterogeneity

Allelic Heterogeneity = different mutations at the same locus(same gene)
-cystic fibrosis; >1000 mutations in the CFTR gene
-may be associated with different phenotypes
Locus heterogeneity= mutations at different loci (lead to similar disaese.)
-retinitis pigmentosa: 3XL, 12 AD, 5 AR forms (different ways to get the same disaese)

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Lecture 14 Flashcards

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