Genetics Terms Flashcards

DNA
Terms Definitions
SNP
Single Nucleotide Polymorphism. Disease allele in individuals from same ethnic group associated with characteristic SNPs.
Frequency of Cytogenetic Disorders
50% spontaneous abortions and .5% congenital malformations due to abnormal chromosomes. Most babies not even born though
Cytogenetic Analysis Requirements
Need cells in mitosis which are growing and dividing. Treat cells with spindle inhibitor colchicine to prevent separation of chromatids then hypotonic solution to cause cell swelling. Finally stain cells
Where can you do cytogenetic analysis?
peripheral blood is easiest, skin biopsy, bone marrow, amniotic fluid, placenta, tumor cells
Ways to have genetic disorders
Single gene, chromosomal (extra, missing, rearrangement), or multifactorial (environment and genes, inherit susceptibility)
Why use skin culture for cytogenetic testing?
Use it for autopsy since skin can be cultured longer post death than blood or in rare cases where blood cant be cultured or if abnormality is online in the skin (mosaicism)
Chromosome Banding
light and dark regions on chromosome after staining with a dye
G-Banding
Treatment with proteolytic enzyme like trypsin followed by staining with Giemsa which will bind the DNA
Important Features of Chromosomes
1. Centromere: constriction region where spindle fibers attach and heterochromatin that is on either side of which stains darker 2. Telomere: at the end of each chromosome arm, repeated sequence but not distinguishable at microscopic lvl
Centromere types
Metacentric = middle; Submetacentric = closer to one end; acrocentric = at one end. All divide chromosome to short arm (p) and long arm (q). Numbering begins at center of centromere
Acrocentric Chromosomes
Short arm contain genes for 18S and 28S rRNA, many copies of them, no clinical consequences is missing (chromosomes 13, 14, 15, 21, 22, Y)
What do del, i, inv, t, ins, dup, der mean ?
deletion, isochromosome, inversion, translocation, insertion, duplication, derivative
FISH
Flourescence in situ hybridization- permits determination of number and location of specific DNA sequences in human cells, requires molecular probe and denatured chromosomes (high temp treatment)
Issues with standard cytogenetic analysis
only permits diagnosis of numerical and structural analysis, small deletions not seen, novel banding patterns hard to interpret, need dividing cells (which may not be representative of whole population)
Issues with FISH
Have to know what you are looking for and choose correct probes
Array Cytogenetic analysis
increased resolution, look at much of genome in one experiment. Types: comparative genomic hybridization and SNP array analysis
Issues with Array based analysis
there are copy number polymorphisms (deletions and duplications) in healthy people and need to know which are clinically significant
How to analyze Log2 R ratio for SNP Array Analysis
It is comparison of intensity of each SNP to reference sample. SHould have 2 copies= 0. If deletion= -1 and if dulpication =.58. R is sample copy number/copy number in controls
How to analyze B allele frequency on Array
plots genotypes of each SNP and each SNP is biallelic and should have 3 bands (0, .5, 1). If duplication see four bands and if homozygous (UPD) see 2 bands
How to decide if copy number alterations are pathogenic
1. See what's in the region (genes, RNA) and use database 2. Are there deletions/duplications in controls or normal ppl in this region? Use database of genomic variants (DGV) 3. Does it contain known disease genes like tumor suppresor? 4. Is it inherited from unaffected parent?
What is most severe type of Chromosomal abnormality?
Deletions- they are worse than duplications
when are deletions or duplications pathogenic?
when they contain dosage sensitive genes
FOP
Fibrodysplasia Ossificans Progressiva- very rare. Responsible gene is component of cell signaling pathway that regulates cell fate decision - normal bone tissue forms in non-skeletal tissue due to abnormal induction of osteogenesis. Disease of heterotopic (extra-skeletal0 ossification. Most cases are new and single nucleotide substitution
what is first sign of FOP?
congenital great toe malformations
Aneuploidy
Abnormal number of chromosome. Missing = monosomy. Extra = trisomy
Clinically Significant Monosomy
45X. only 95% make it to term but have mild phenotype if they do
Trisomy
4% all conceptions. 21, 13, 18 trisomies found in live births for autosomes b/c these chromosomes have less genes and for sex chromosomes
Trisomy 21Features
AKA Downs. hypotonia (decreased muscle), short head (brachycephaly), flat nasal bridge, palmar crease, low set ears, short neck with skin flap, intellectual disabilities
Trisomy 13
Very severe, severe CNS defects, deformities, cleft lip/palate. rarely survive past 6 months
Nondisjunction (NDJ)
can happen in meiosis I (homologs dont separate) or meiosis II (sister chromatids dont separate) or mitosis (depending on when it occurs, may not be in every cell in body)
What Causes NDJ
Maternal meiosis I appears to be most common source of trisomy and maternal age is most important factor
Mosaicism
Not all cells have mutation. For instance chromosome abnormalities can occur in mitosis. Can happen anywhere- only blood, skin. Types: somatic only (wont pass on), somatic and gonads, gonads only
Germ line mosaicism
revealed when phenotypicaly normal individual has more than one kid with same abnormality
Structural Rearrangements
Result of chromosome breakage during meiosis or mitosis. Balanced if all genetic info appears present. Example is translocation
Transolocation
Exchange of segments b/w non homologous chromosomes. No material lost than reciprocal or balanced but often there is submicroscopic deletion or duplication
Quadrivalent chromosome configuration
When four chromosomes with segments in common (due to translocation) come together in cross shaped configuration during meiosis 1. The translocated gene made of two different chromosomes is called a derivative
Segregation of Quadrivalent configuration
1. Alternate segregation- normal karyotype. 2. Adjacent 1 segregation- non homologous centromere travel to same daughter cell, variable unbalanced 3. Adjacent 2- uncommon, homologous centromeres go to same daughter cell, many trisomic and monosomic kids
incomplete penetrance
unaffected individual may possess gene normally associated with a disease
Loss of Heterozygosity
A heterogenous person loses normal allele and now only have mutant allele. May appear hetero in other cells but looks homozygous in tumor
Hardy Weinberg Requirements
large population, no selection against genotype, no mutation, no migration
Why is family history important?
Tells you more information than just a physical exam, no ones disease exists in vacuum, problem may have begun right at conception, draw pedigreee and determine mode of inheritance
Pleitoropy
One gene causes multiple phenotypic effects, individuals may show different genetic problems in pedigree and unrelated symptoms may be important
HW equation
p+q=1 and q is frequency of allele, q^2 is frequency of disease, and 2pq is carrier frequency
Genetic Heterogeneity
same condition caused by different genes, phenotype may appear same but different basis
Allelic Heterogeneity
Different Alleles at same loci
Locus Heterogeneity
mutations at different loci- affected parents may have heterozygous unaffected kids like with deafness or blindness
Autosomal Recessive
Usually caused by mutant alleles failing to encode gene product- lose of function. large number of inborn errors of metabolism follow this pattern
Phases of Mitosis
G1- quiescent, S- synthesis (sister chromatids), G2- checkpoint, prophase, metaphase, anaphase, telophase
Kinetochore
During metaphase where spindle attaches, it is a protein on the chromosome
Chiasma
Cytologically visible structure that corresponds to crossover events (want at least 1 per chromosome)
Meiosis events
Prophase- maternal and paternal homologs synapse to form tetrad. centromeres dont divide until MII
Haplotype
block of closely linked genes which goes through meiosis without crossing over is known as haplotype- these can be used as markers when mapping out genes
Female Meisosis for Germ Cells
Blocked at MI prophase and completed at ovulation, MII only upon fertilization, cell division is asymmetrical (form Barr Bodies)
DNA Sequencing
next generation sequencing done on chip and no need for gel electrophoresis, very fast. old was used tagged dideocynucleotides
Linkage disequalibrium
Result of haplotypes and closely located genes, we all have millions of short haplotypes that can be identifies in other ppl with similar ethnic backgrounds
Alternative Splicing function
enhance functional versatility of single gene
Crossing over
It is proportional to the physical distance between genes, if they are close together they will not recombine as frequently and law of independent assortment is not valid (nonrecombinant if two genes from same parent)
mRNA processing
mRNA also called Pol II transcript and it must have 5' cap, splicing, 3' polyadenylation tail generate functional and translatable mRNA
what determines gene expression?
chromatin structure and packaging determines how accessible the gene promoter is to Pol II
Histone Modifications
directly alter packaging of DNA or indirectly create recognition sites for recruitment of co activator or repressors, N terminus tails are targets of modifications. Acetylation (HATS) form euchromatin by neutralizing + lysine
DNA methylation
Epigenetic modification to inhibit transcription by: 1. blocking Pol II binding or 2. recruit repressive proteins (HDAC) to deacetyl and make tigher. AKA cytosine methylation
Epigenetic Modifications
control chromatin structure at each gene locus to activate or repress transcription
cDNA
complimentary DNA made from RNA which allows you to focus on expressed sequences and exclude introns
5' Cap
protects mRNA and helps recognize for translation
3' Poly A tail
protects the end and is biological clock- gets shorter until degraded
Splicing of mRNA
Forms open and uninterrupted reading frame
DNA and Histone interaction
DNA is acidic and negative, Histones are basic and positive so tight interaction
General Transcription Factors
Protein complexes which recognize the promoter region and facilitate Pol II engagement with DNA in order to initiate txn. Help assemble initiation complex. Needed for basal transcription
Regulatory Factors
Decide whether or not to initiate tx, decide when and where. Bind to regulatory determinants (enhancers and repressor) which are cis to the gene
How Regulatory Factors work
modulate levels of txn by modifying chromatin structure (epigenetic modifications) at target gene. can act over extensive distances (looping, or phospohorylate Pol II to enhance initiation)
Enhancers and Promoters
Enhancers indiscriminately work on promoters and position does not need to be specific. so if enhancer next to oncogene can lead to overexpression and malignancy
Transcription Factor Structure
Modular Structure with TAD (transactivation domain) and DBD (DNA binding domain) which establish specificity. TAD directly modify chrom structures, dimerization and recruit protein complexes. Modular in structure
Recombinations of Genes (repercussion)
can result in loss of normal txn control by juxtaposing coding region of one gene with the regulatory determinants of another- can lead to ectopic expression (wrong lvls) with cell overgrowth if next to strong regulatory elements
Myc-Max-Mad equilibrium
Myc is txn factor the promotes cell growth (tightly controlled b/c could cause cancer). Max binds Myc and recruits HAT (histone acetyl transferase) and promotes growth. Max binds Mad prevents growth. Dynamic equilibrium
Where do miRNA bind?
Bind 3' untranslated region of mRNA. Cant bind coding region b/c ribosome could remove it easily
miRNA
play major role in post transcriptional control by base pairing with mRNA. Tight match will degrade it, loose match will silen with RISC (RNA induced silencing complex) and prevent translation
miRNA and lncRNA levels in body
highly abundant and expressed in all tissues
Nuclear Hormone receptors
family of txn control proteins and have corresponding hormone ligands. link hormonal actions with txn controls. Design: N terminal TAD, DBD, C terminal for ligand binding
Long Noncoding RNA
serve as platform that can bind to target gene and protein complexes, target modifying complexes to specific loci. Can interact with DNA, RNA, proteins
What is unit of inheritance?
itt is a mutation in a gene and pattern is determined by the functional consequences of the mutation- dominant if trait is manifested in heterozygotes, recessive if homo
How do mutations arise?
Endogenous- byproducts of normal cellular function. Exogenous- UV, radiation. DNA replication errors
Missense mutation
change in amino acid
Nonsense mutation
Premature stop codon
Consanguinity
Related individuals breeding which increase chances carrying same alleles and having affected child (inbreeding is small population)
Autosomal Dominant Inheritance Characteristics
Every affected individual has at least one affected parent- vertical inheritance pattern in pedigree, males and females equally affected (HOWEVER there is also variable expression...) EX. Neurofibromatosis (growth of tumors, highly penetrant). often gain of function
Variable Expression
Autosomal dominant traits complicated by this b/c quantitative and qualitative differences between ppl with same genotype
Autosomal Recessive Inheritance Patterns
Carriers usually unaffected, two unaffected parents can have affected kid, if trait is rare then unaffected parents may be related
hemogloniopathies
autosomal recessive cause. sickle cell with aa change but heterozygote advantage to malaria. thalassemia in alpha and beta chains of hemoglobin synthesis
PKU
autosomal recessive inborn. cant degrade phenylalanine and damages CNS, avoid with dietary modifications. loss of function. over 100 different mutations (allelic hertogeneity)
Loss of function mutation
can be recessive or dominant (when 50% of normal is not enough for normal function)
hemoglobin
Have 4 copies of alpha chain and 2 of beta, need tight control to equal amounts made. mutations in alpha more serious because in all types of hemoglobin (fetal gamma if beta is mutated at least)
Founder Effect
Small population breaks off with different gene frequencies from parent group, genetic drift
osteogenesis imperfecta
collagen band of three bands, two of proa1 and one of proa2. more serious if mutation in proa1. better to produce none than defective ones.
Mosaicism
Presence in individual or tissue of at least two cell lines that differ genetically but are derived from single zygote
X linked dominant
lack male to male transition and often female can inactive mutant gene more if hetero. Males transmit to ALL daughters (good way to differeniate from autosomal dominant). Ex Rett's Syndrome (males with 2 X may survive)
Trinucleotide Diseases
Hungtinton's is example of autosomal dominant but it shows anticipation 9age onset decreases each generation) and Fragile X syndrome where unstable repeat expansion can happen
x linked recessive
males more likely to have it, ex is hemophilia where blot wont clot
Dominant Negative mutation
example is osteogenesis imperfecta- mutation in one chain impairs contribution of normal chains. better t have mutation that generates no gens than one that produces abnormal gene products
Selection Balance in x linked recessive
if incidence of disease is not changing the mutation rate must equal rate of mutant alleles not passed on in men (1/3). So 1/3 of all ppl who carry it is new mutation
Parental Transmission Bias and Triplet Expansion
triplet repeat areas can expand during meiosis and normal parents can have affected kids. Huntingtons shows parental bias and occurs more frequently during male gametogensis (can also have expansion during mitosis and pass on to some somatic cells(
Gene Therapy
Method of treatment whereby a genetic defect caused by mutation in single can be revered by introduction of normal function copy of the gene. Can use retroviruses to integrate genome into host cells. Non viral approaches- direct introduction (only some tissues), liposome artifical lipid, linking DNA to molecule that bind cell receptors
T cell based immunotherapy
Persons own T cells reprogramed to target and kill own malignant cells . genetically modified and grown in lab and then reimplanted into person
Risk of de novo translocation being abnormal
10% chance. if de novo translocaiton is observed on prenatal study, couple would be counseled that there is 10% risk for some sort of abnormality
Robertsonian Translation
when two acrocentric chromosomes fuse their centric ends. chromosomes counted by # of centromeres so if balanced then person has 45 chromosomes but doesnt affect phenotype of carrier. risk of offspring being unbalanced
Counseling for Robertsonian translocation
increased risk for spontaneous abortions . homologous chromosome translocation pose unique problems since carriers cannot product any normal gametes
Chromosome Deletions
terminal- at end of chromosome or interstitial- within. clincal consequenes depend on size of deleted segment and fucntion of genes it contains
Low Copy Repeats and Deletions
flanking repeated regions surrounding the deleted region and these repeats cause misalignment during meiosis with the deletion of the region between the repeats
Inversion on Chromosome
Single chromosome has two breaks and segment between the breaks is inverted. Can be paracentric (same side of centromere) or pericentric (both arms). Usually normal but if interrupt a gene can be abnormal
Uniparental Disomy
two copies of chromosome from one parent and none from other- usually because of non disjunction and monosomy rescue or trisomy rescure. Can be issues if gene is imprinted (differential methylation). cause disorder from loss of imprinted gene or 2 copies of recessive
Epigenetic factors
Those that can affect the phenotype with change in the genotype (DNA methylation , histone acetylation, phosphorylation)
Prader-Wili and Angelman
imprinting defects of genes on chromosome 15. prader lacks father, angelman misses mom. can be diagnosed by array analysis (copy number is normal, b allele frequency shows NO heterozygotes). Causes- deletion, UPD, mutation in genes, failure to imprint
Dosage Compensation
in females only one chromosome is transcriptionally active, second x condensed and is Barr Body, inactivation occurs early in embryo development, inactive x can be maternal or patneral- thus each female is mosaic of cells each cell functionally hemizygous
X inactivation
gives females more phenotypic variabliity for x linked traits. MOST but not all txn genes silenced, 75% permanent, 15% escape inactivation, 10% variable
XiST
x inactive specific transcript. location of inactivation inactivation center and expressed only from inactive X chromosome. product of XIST is noncoding RNA that stays in nucleus in close assocation with inactive x
Sex determination for males
Presence of Y chromosome with intact SRY gene
Disorder of Sex chromosomes
comparing to autosomal aneuploidies, sex chromosome ones are less severe (x are inactivated, duplication of y has little phenotypic effect because so gene poor)
Turner Syndrome
45x, females. usually die within first trimester but those that make it may be unrecognized mosaics
Klinefelter Syndrome
XXY- the more xs they have the more serious it is. 47XYY is another disorder but less serious, phenotypically normalish
DAX1 gene
antagonizes the SRY gene so if duplication it may override SRY and have 46XY female. It is located on the X chromosome
Unanticipated findings
nonpaternity, incest, deletions or duplications that confer risk for future disorders
How do you know that a trait has genetic basis?
heritability and we perform genetic studies to discover unknown disease etiology. a genetic trait is complex if non mendelian inheritance
how do you indentify disease alleles that segregate in families?
linkage analysis
heritability
variation or the occurrence of a trait among individuals in a population or family can be explained (in part) by genetics. aggregates within families and segregates proportionally to genetic similarity - concordance of traits in twins is good test
Why do mapping studies?
We need gene targets and casual mutations but we can only get these by looking at relationship between genotype and phenotype through mapping studies
Complex genetic trait
genetic heterogeneity, allele heterogeneity, clinical geterogeneity, incomplete penetrance, variable expressivity, environment, behavior, interactions between genes
Polygenic inheritance
the collection of multiple alleles at many sites which creates a distribution of variation in population - quantitative trait
Log of Odds Score (LOD score)
1. calculated form information in pedigree transmissions. 2. localize where mutations must exist (by recombo disitance) 3. direction is interpretable (positive = linkage, neg= no linkage) 4. quantifies evidence and uncertinty (>3 denote significant genome wide linkage). If you do not see LOD greater than 3, get more families to build evidence or find markers more cloesly linked to disease allele
Family based linkage analysis
works well to identify determinants for mendelian conditions, harder for non medeliam (not resonable to use that many families) make catalog instead of general population
linkage vs linkage disequilibrium
linkage is transmission of haplotypes to offspring with family. LD is co segregation of alleles within a population (not through a pedigree)
Genotype wide study (GWAS) steps
design study, genotype samples, control for quality, test for assocaiation, replicate. chi sqaured test returns the change the oberved freuquency of snp is same as controls. OVERALL- the idea is common factros are associated with common disease
Population structure and studies
need to be careful about confounders . inference of assocation can be confounded without proper control
Explaining varaince equation
=2pq + b^2. this factors in how rare or common it is and how much the allele variance affects it. tells you how much of the variance is explained in the population
odds ratio
1.35 = 35% increased chance that affected status will occur with carriage of the allele. Measure of allelic effect
chi squared
tests deviation from expectations. summation of (observed- expected)^2/expected. gives you a p value (.05 is significant or below and shows that is is not random). it shows if two different variables are dependent or not
DNA Polymerase Types
B family- nuclear DNA and A family (gamma)- mitochondrial. common domains- polymerase domain (carboxylates bind metal ions) and different functional domains which have exonuclease activity for proofreading
How do DNA polymerases ensure replication fidelity?
selectivity, proofreading, and repair mechanisms
General DNA damage response
1. sense damage 2. recruitment of signaling protein to determine cell fate 3a. cell cycle arrest and repair or 3b. cell death
Things which cause DNA damage
Ionizing radiation, chemical exposure, replication errors, UV light exposure, cellular metabolism (reactive oxygen species)
DNA mismatch repair
when DNA pol add nucleotide that does not BP with template strand. Repaired with Muts, MutL, and MutH
MutS and MutL and mismatch repair
Muts is heterodimer and slides along DNA and when senses mismatch- ATP converted to ADP and signals MutL. Binding of MutL displaces DNA pol and recruits MutH
MutH and mismatch
It is an exonuclease I and recognizes "old" strand by methylation and removes base from new strand
Lynch Syndrome
Underlie colorectal cancer. mutation in MutS and MutL which compromises fidelity of DNA replication- microsatellite instability will be seen. autosomal dominant disorder
Microsatellite Instability (MSI)
Microsatellites are repetitive DNA stretches of 2 to 4 nucleotides, might cause DNA machinery to slip and get different number of repeats between the two strands- if repair mechs working, this should be corrected. Easy way to diagnose mismatch repair disorders like lynch syndrome
Double Strand Break
most hazardous form of DNA damage (no complementary strand). Happens during meiosis (homologous chrom. recombining), ionizing radiation, and during v(d)J and immunoglobulin class switch
DSB repair
Recognie break by nuclear protein complexes (MRN complex) which polishes ends or holds ends in place. chromatin modication occurs which signals protein kinases (PIKK- ATM, ATR) and stop DNA synthesis so repair can occur
Ataxia telangiectasia mutated (ATM)
activated by phosphorylation when cell senses DSB. ATM phosphorylates downstream targets which induce cell cycle arrest and facilitate DNA repair. Can also induce cell death if extensive damage
Repair pathways for DSB
1. homologous recombination (sister homolog as template- BRCA 1 and 2 play role in migrating template), favored in S and G2 phase 2. non homologous- simple but error prone. use DNA ligase to join ends of break, good for G1
V(D)J recombination
uses non homologous end joining to make immune cells to make unique T cells and immunoglobin
Ataxia Telangiectasia
autosomal recessive with ATM gene mutation - immune disorder and predisposition to cancer. increased sensitivity to RADIATION and cycle cycle continues even though damage
Most Common DNA base change
cytosine to uracil- deamination by water, very common. this is why no uracil in DNA
Tests for Lynch Syndrome
Do microsatellite instability assay (MHI) if immunohistochemical study (IHC) is negative- use antibodies to stain for proteins.
Mitochondria Roles
Energy production, calcium homeostasis, initiation of apoptosis, metabolic pathways (steroid synthesis, fat metabolism, aa metabolism)
Mitochondria Structure
double membrane- outer is highly permeable and inner is relatively impermeable. ETC in on inner membrane. over 1500 proteins in mitochondria and most encoded by nuclear genes and imported in
ETC
NADH puts electrons to complex 1 and FADH2 puts electrons to complex 2. both go to coenzyme q10, then complex 3, cytochrome C, and finally complex 4. complex 5 is ATP synthase- need 85 different proteins for all complexes, only 13 from mito DNA
Mitochondrial DNA
no noncoding DNA, single precise copies of tRNA, circular DNA, flexible number of copies of DNA per cell (not just 2 copies like nDNA), replication is not synchronized process with phases (no meiosis equivalent), specific RNAs that dont have UGA as stop codon, matrilineal inheritance, homoplasmic and heteroplasmic (vs homozygous and heterzygous)
Maternal Inheritance of mtDNA
mtDNA transmitted almost exclusively from oocyte to fertilized embryo- sperm mito are destroyed. disease transmission only through females but both males and females affected
Heteroplasmy
presence of two different populations of mtDNA in given cell or tissue. It is inherently unstable and changes during the course of people's lives even varying from tissue to tissue. example is MELAS
Threshold Effect
Heteroplasmy lvls of given mutation may be different between person's own tissues and change over time. So severity of disease depends on percentage of mutation to wild type sequence
Mitochondrial Mutations
Happen more often because PolG is not as good at proofreading. Free radical rich environment predisposes them to new mutations
Mutations and the Oocyte
mtDNA is protected in the female primary oocyte lineage- woman who is pregnant with fetus already carries mtDNA that will be used to generate grandkids (mtDNA are arrested in oocyte lineage)- this puts strict limitation on mtDNA replication b/w generations
Bottleneck and heteroplasmy in offspring
potential for mtDNA to radically shift heteroplasmy b/w generations (pulling colored balls from hat)
Mitochondrial Disease Inheritance Pattern
nDNA defect- diagnosed in infancy. mtDNA- later onset b/c caused by mutation in the mt genome. recurrence risk for full siblings with recessive is 25%, lower for mt.
Homoplasy
when copies of mtDNA are all identical. Homoplasmic mtDNA copies may be normal or mutated
How to rule out point mtDNA mutation
symptomatic tissue must be tested by mtDNA whole genome sequence analysis such as muscle, b/c heteroplasmy lvl in blood may be too low to detect by common methods
OsPhos dysfunction symptoms
progressive, multisystemic involvement of high energy demand tissues. if you see three or more systems affected you should consider mitochondrial disease- huge extensive variability in manifestations, prognosis, and inheritance of "mt disease." also no biomarkers known with sufficient sensitivity to diagnose mt dysfunction
Treatment for Mt disease
one of biggest challenges in medicine, mt are absolutely critical to cell survival. therapies consist of symptomatic support and counseling to prevent recurrence of diease. new ideas: destroy mutant mt DNA with restriction enzyme that leaves wild type DNA alone, injure mature tissues so replaced by stem cells (hopefully have better mt DNA), "force" improvement of mt genotypes by stressing cells nutritionally and train mt to work bette. Give "mito cocktail" of vitamins and antioxidants
Why diagnose mt disease if cant fix?
Diagnosis ends search of cause of disease for pt and family, untreatable disease today may be treatable in the future, care of whole family at risk through genetic counseling is critical (interpret diagnostic tests, review recurrence risk for future kids, discuss prognosis)
Why does mt genome persist?
inability to transport hydrophobic proteins from cytoplasm- some evolutionary limit
Mitochondrial bottleneck
mutation present in mother may not be present in her eggs if mutation developed later in embryogenesis or after birth
mt DNA most common mutation
missence is most common and nonsense mutations are rare
Complications with mt disease
degree of heteroplasmy, genetic modifiers that affect disease expression- family members could have two different diseases from these two factors listed
Hap Map Project
project was organized to identify millions of SNPs across human genome and determine the correlations among these SNPs in order to build haplotype maps of the human genome- identify disease susceptibility
Pharmacogenomics
individuals differ in response and sensitivity to drugs. drug is administered- absorbed and distributed to different sites in body to be metabolized and excreted. many steps can be affected by genetic variation (isoniazid, TPMT, Warfarin sensitivity )
N acetylation of isoniazid
drug for treatment of tuberculosis, metabolized in liver and some people clear faster than others due to genetic variants in NAT2 gene. Poor acetylators accumulate more isoniazid in their plasma and need less of drug
S methylation of thiopurines by TPMT
TPMT is thiopurine s methyltransferase. thiopurine is a purine analog used for immunosuppression. people have different activity lvls of TPMT in RBC and need to check to determine appropriate dosage
Warfarin
prescribed anticoagulant for thrombosis prevention and they do this by blocking vit K pathway. small window and dont want to cause excessive bleeding- two genes which can be sequenced which are responsible for 40% variability
Gene Expression Studies
useful for understanding gene pathways and regulation in different normal and disease processes. examples: quantitative reverse transcription PCR, microarray, RNA sequencing
Quantitative Reverse Txn PCR
RNA samples are extracted and converted to cDNA which is then used as template fo rPCR
Microarrays
like mini southern or northern blots of small pieces of glass. have transcripts on slide in excess and hybridization intensity is proportional to transcript abundance. read by laser scanners to get numerical values
RNA sequencing
RNA extracted from cDNA libraries, sequences mapped to genome and idenfity region they represent - data analysis more complex than microarray but you can use counts of sequences and get basepair resolution
How will new sequencing technology change practice of medicine?
1. to identify bacteria by sequence: microbio labs in future will be using NDA sequencing rather than staining to identify infectious agents 2. complete genome sequence of individuals (identify mutations. Overall play a role in prevention (know if susceptible to heart diease and eat healthy), diagnosis, and treatment of disease (dont give certain drugs)
OMIM
online mendelian inheritance in man. compilation of phenotypic and genotypic info on every known human hereditary condition and every gene for which function has been determined
HHT take home lessons
Uncommon hereditary disorders often present with common symptoms (fatigue, breathlessness, nosebleeds). family history is simplest and least expensive genetic test
Benefits of studying common complex diseases (like LDL)
new insights into human biology and pathophysiology of disease, assessing potential causality of epidemiologic associations with disease, improving ability to predict future risk of disease, identifying novel targets for therapeutic intervention
LDL levels in blood are determined by...
production by liver via precursor VLDL and removal by liver by LDL receptor
Variants in LDL and genetic diseases
Inverse relationship between allele frequency and effect size (rare variants/mendelian to low frequency to common variants)
Rare LDL ppl (extremely high levels)findings
found familial hypercholesterolemia- loss of function mutation in LDL receptor in liver. one of most common single gene disorders. lead to statin development (inhibit synthesis of vldl and upregulate receptors)
Extremely low LDL findings
nonesense mutaiton in apoB cause low levels because cant make VLDL or mutant in MTP and cant make it - 2 NEW therapies to treat high lvels (however both would increase triglyceride in liver)
PCSK9 and LDL receptors
Found in ppl with high LDL have gain of function in PCSK and low LDL have mutation in it. PCSK negetively regulates LDL receptors. NEW therapy
Common varaints and LDL
requires tons of people to have power to find small change that has effect- with GWAS found 1p13 associated with low LDL levels - found if you increase Sort1 you have gain of function and lower LDL. Sort targets proteins from golgi to lysosome (NEW BIOLOGY)
Primers for PCR if given one piece of sequence
If sequence written 5 to 3. copy the first 5 to 3 and this will be primer for other strand- forward primer. go to end of sequence at 3 end and do base pairs (primer for this strand) - reverse primer
How many BP in genome?
3 million or 3 x 10^9
Why do we have combination of regulatory factors for txn?
allows for proteins to generate specificity of gene control and economizes on the number of tx factors necessary to control multitude of txn responses in the hundreds of different cell types
TATA vs GC rich promoter region'
exact positioning of start site of TATA linked promoter is consequence of sequence specific binding of a general txn factor to the TATA box. GC rich promoter lacks well defined binding site for the pre initiation complex so it generally has a cluster of multiple tx start sites for Pol 2
Ret 1 mRNA in wild type and mutant explanations
1. could but microRNA (something which responds to it but not miRNA itself since disease is linked to REt1) which works via translation inhibition (NOT destruction since still see mRNA in wild type). mutant could be by mutation in miRNA recognition element, mutation in alternative splicing so loose miRNA response element, or alternative polyA site utilization. 2. Ret 1 protein is post txn modified and targeted for rapid clearance
X linked lethal disorders...
if a male has it there is a 2/3 chance from mom and a 1/3 chance it is a new mutation
risk that de novo balance translocation associated with disorder
10%
chromosomal microarray disadvantage
dont get positional info (dont see where translocation occured) and benefit is better resolution, break point precision, and dont need dividing cells
Why test kids with Downs
Need to know if "free" trisomy of 47 chromosomes or from parents translocation. test with cytogenetics and not array-b/c cant see transolcation
Variable expressivity in cytogenomic diseaes
1. epigenetic effects 2. environmental which affect expressed phenotype 3. deletion may be bigger or smaller b/w pt and involve different genes 4. if deletion chormosome- maybe other one is over expressed or maybe there is mutation in normal one
Why is X linked trait found mainly in girls?
if guy gets it, it may be fatal. also if dad has mutation then he will only pass on to daughters also males have higher chance of germline mosaicism b/c life history of sperms
lyonization
x inactivation
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