1.1 Genetics Flashcards
human genes
25,000 - less than twice as many as a worm –> alternative splicing?
percentage of shared genome btw 2 people
99.50%
the 0.5% of difference in humans indicates
polymorphisms, muations - 15million base pairs
most common polymorphism
SNP - single nucleotide polymorphism –> 6 x 10^6 are known
SNPs are usually biallelic meaning
only 2 choices at a given site withing the population
Are SNPs mutations?
NO - they do not totally remove activity
less than 1% of SNPs occur in
coding regions meaning that most will have to undergo linkage analysis that may prove to be significant
linkage disequilibirum
bc less than 1% of SNPs occur in coding cregions, SNPs are most often co-inherited as a marker linked to a gene causing disease
CNPs
copy number variations - can be bi-allelic or multipel - 50% involve gene coding sequences, genes involved in immune system and CNS over represented in containing CNPs, much less is known about CNPs and disease susceptibility than SNPs
when you see an SNP in 90% of a disease population
that is significant information bc you can look to see if that SNP is linked with a gene that causes the disease
genetics
study of single genes
genomics
study of entire genome and interactions
how do you use DNA chips
can use them to study tumor vs normal tissue or stimualted cells vs control cell
Proteonomics
study of all of the proteins in a tissue/cell 2d electrophoresis/mass spec. or isotope coding affinity tags (heavy and light isotopes and mass spec) –>not every thing that transcribed is translated into protein so studying proteins is very important
laser capture microdissection
if you have a tumor, remember it is normal to have vessles and stromal tissue so you used this micordisection to just cut out the tumor cells
microarrays
you can do a blind scree just by hybridizing dna testing for thousands of genes, looking at diseased vs no disease – then you can go and look at the genes and make a hypothesis
with microarrayes the colors mean something
red - tumor dna, green- normal dna, yellow -mixed dna
functional cloning - classical approach
gene product and defect are known - you clone the normal gene, make probes, clone and sequence the gene from affected individuals (many metabolic disorders)–find a way to fix it
positional cloning - candidate gene approach
gene is not known - uses cytogenetic or SNP marker to localize candidate genes to a narrow area of a chromosome, clone DNA from that area express normal and disease products – find out what’s wrong
cloning and the production of ultra pure proteins examples
insuline, factor 8, soluble TNF receptor, humanized antibodies
gene therapy is complex because
cannot anticipate for all factor – SCIDS (gamma cahin of cytokine receptor) gene inserted next to host gene regulating cell growth _. Gave the patient T-cell leukemia
how insuline was adjusted
first we made insuline from pigs, but we were making reactive Ab against the pig inuline so we made human insuline, but if it wasn_t refridgerated it would not be effective and pts were not getting their full dose, so now things are added to it to make it heat stable
With rhematoid arthritis why is giving the Abs to TNF bad
the Abs will clear the TNF so that is good to reduce inflammation, but if you have TB and you need to wall it off you need TNF to maintain the granuloma and if you don’t then you can’t maintain it — so you need to make sure that the person doesn’t have TB or that they are vaccinated to make sure anti-TNF treatment is appropriate (also given in Psoriasis)
sickle cell treatment
could be treated by giving normal Hg cells but its not a thrapy
Anti amyilid Ab in alzhimers
if animal is immunized with Ab towards tau that causes plaques alzheimers can be reversed, but in humans if immunized with the Ab they got inflammatory encephalitis and some people die
RNA analysis
many alteration in DNA are single gene effects so copy number is low. mRNA has higher copy number if gene is transcribed. Many genes are rearranged (BCR-ABL) over larger areas than PCR can replicate, but looking for the mRNA that is formed after splicing and cutting is easier.
Epigenetic effects include
DNA methylation, histone acetylation, miRNAs –> we know genetic alterations in DNA seq cannot explain the diversity of human phenotypes such as phenotypic difference in monzygotic twins – so we look at epigenetc changes
too much miRNA and cancer
too much scilencing of tumor suppressor genes can lead to cancer
too little miRNA and cancer
too little scilencing of oncogenes can lead to cancer
Congenital
means present at birth. If you are starved for air during birth and you have massive CNS problems it is congenital NOT genetic. Congenital diseases may or may not be genetic.
Familial
multifactorial diseases that run in families but show no inheritance patterns
Hereditary
gene passed down
Genetic
involves genes
Prevalence of chromosomal abnormalities
50% of spontaneous abortions contain a chromosomal abnormaility–the earlier the abortion, the more likely a chromosomal abnormality. 1% of live births have an identifiable chromosomal abnormalitiy. Chromosomal abnormalities visible, other mutations are not. 5% of individuals less than 25 develop a disease with a significant genetic component –but these are not chormosomal
interplay of genetics and environment
the most common diseases afflicting man have goth genetic and environmentla components (diabetes, atherosclerotic heart disease, cancer, obesity)
which diabetes has a stronger genetic component
type 2 but also has a strong environmental compoent like obesity
genes and environment leading to disease
lots of genetic w/ few environmental factors, lots of environmental with few genetic factors, or lots of genetic and environmental factors will lead to diseas — usually one genetic and one environmental factor is not going to lead to disease
point mutations
occur bc the DNA code is degenerate – missence, nonsense, promoter activation/inactivation
missense
AA substitution, full lenth protein made, variable preservation of structure and function
Nonsense mutation
AA change introducing a stop codon
Point mutations in Sicle cell
DNA: CTC to CAC , RNA: GAG to GUG, AA: Glutamic acid to Valine
deletions or additions result in
fame shifts
examples of triple expansion repeats
Huntington, Fragile X, —- mostly repeating CG sequences
What kind of mutations are more common?
loss of function bc it is easier to destroy something than give it an alternative fn. altered gene product that affects other proteins (dominant negative), gain ro altered function (rarer, Huntington disease)
Mendelian Disorders
single gene alterations, predictable inheritance pattern, Pleiotrophism (single gene with multiple effects - Marfans), Heterogenetity (multiple genes same effect: profound deafness)
Patterns of inheritance
autosomal dominant, autosomal recessive, x-linked, multifactorial
What form do you see disease in AD cases
Heterozygotes – homozygotes are usually fatal
Children of one affected AD parent
have 50% cance of developing the disease
Autosomal Dominant and new mutations
some patients do not have an affected parent –new mutations account for variable percentages of cases. Usually older males increase the incicence of mutations in sperm – 30% of marfan’s is denovo
Penetrance
percentage of individuals with the gene that have the disease – we only consider penetrance with autosomal dominant cases
Variable expression
all individuals have the disease but different severity or character
