Genetics Flashcards
locus
unique chromosomal location
allele
alternative forms of the same locus
genotype
allele combination at a locus
haplotype
a combination of alleles on the same chromosome
homozygosity
2 identical alleles at a locus
heterozygosity
2 different alleles at a locus
dominant allele
shows its effect on the phenotype in heterozygosity
recessive allele
does not show its effect on phenotype in heterozygosity
codominant alleles
when both alleles are dominant; alleles have additive effects
germ-line mutation
affects the gametes (sperm or egg); can be passed on to offspring
Somatic mutation
affects somatic (i.e. body) cells only; cannot be passed on (not heritable) Somatic mutations result in mosaicism: the presence of cells with different genotypes
minor allele frequency
the frequency of the least abundant allele in a population
polymorphism
a ‘common’ variant with MAF >1%, does not imply phenotype
mutation
a ‘rare’ variant with MAF <1%
major allele is often referred to as ‘wild-type’ or ‘normal’
does not imply phenotype
main forms of human genetic variation
- Single nucleotide variation- -DNA replication and repair, most abundant
- Structural variation- DNA recombination
- Chromosomal abnormalities- chromosome segregation in mitosis/meiosis
allele frequency equation
frequency of A= # of A alleles in population/ total # of alleles in the population
odds ratio
odds of disease in presence of allele/ odd of disease in absence of the allele
Silent variant
nucleotide substitution in a coding sequence that does not result in amino acid change.
misssense variant
nucleotide substitution that causes one amino acid change
nonsense variant
nucleotide substitution that replaces the codon for an amino acid with a premature termination codon (Ter, Stop, X or *).
frameshifting
a variant that alters the triplet reading frame of mRNA (by inserting or deleting a number of nucleotides that is not a multiple of 3). Usually results in premature termination codon.
regulatory variant
a variant that affects gene expression through effects on a transcriptional regulatory element (e.g. promoter, enhancer).
exon skipping
Altered splicing results in the exclusion of exon sequences from the mature mRNA
intron retention
inclusion of intronic sequences
renaming DNA strands
this3replaced with this
this3 replaced with this fs Ter%
loss of function variants
and example
reduced amount of activity more common,
typically recessive,
example: regulatory mutation reducing
b-globin expression (b-thalassemia)
variants responsible: missense, nonsense, frameshift, splicing, regulatory
2 dominant loss of function variants
Haploinsufficiency: when a single (haplo) functional allele is not sufficient for normal phenotype, nonsense mutations in GATA4 (a transcription factor) lead to congenital heart disease in heterozygous individuals
Dominant negative (DN) effect: when a mutant allele disrupts the function of the normal allele, missense mutations that inactivate the activity of STAT3 homodimers (a signaling molecule) lead to cancer
Haploinsufficiency:
when a single (haplo) functional allele is not sufficient for normal phenotype, nonsense mutations in GATA4 (a transcription factor) lead to congenital heart disease in heterozygous individuals
Dominant negative (DN) effect:
when a mutant allele disrupts the function of the normal allele, missense mutations that inactivate the activity of STAT3 homodimers (a signaling molecule) lead to cancer
gain of function variants
and example
increased amount of activity
regulatory or missense
dominant
example: Missense mutation in FGFR3 causing
receptor signaling without ligand
(Achondroplasia)
monogenetic
single variant, large effect, present in everyone with mutation, rare
polygentic
many variants with smaller allelic effects, more common
susceptibility threshold
Sum of all genetic and environmental factors, pass threshold= you have the disease
genome-wide association studies
why they are used?
Poly- you can’t use family tree because there are multiple factors, gene wide associate are used to determine tendency of allele and disease to occur together across populations
polygenic risk score (PRS)
The polygenic risk score (PRS) is a composite measure of genetic risk conferred by all disease-associated loci in an individual.
Step 1. Identify disease-associated variants in the population by GWAS.
Step 2. In each individual, add up the effects of all alleles (risk minus protective) to obtain the PRS.
Step 3. Correlate PRS with disease risk in the population.
Step 4. Estimate individual’s relative disease risk.
Autosomal dominance
Parent to child transmission (I 1&2)
- Every generation affected (vertical transmission) - Unaffected parents do not transmit to children (II 6&7) - Males & females equally affected - Male to male transmission (differentiates from XLD)
Autosomal Recessive
Unaffected parents can have affected children (III 3&4)
- 25% (1/4) of children affected
- Affected parents can have unaffected children (II 1 & 2)
- Males & females equally affected
X linked recessive
-Unaffected males do not transmit (I 1&2)
-Carrier women transmit to sons (50% of sons)(IV 3,5)
-All daughters of affected male are carriers
(obligate carriers)
X linked dominant
-Both males and females affected
-Mother transmits to daughters & sons
-Father transmits only to daughters
(distinguishes from autosomal dominant)
-Every generation affected
Consanguinty and results
Consanguinity- mating between relatives = higher chance of homozygosity at autosomal recessive loci, wide spread in population lads to increase in hemizygosities
incomplete penetrance
phenotype expressed in a fraction of individuals that all have the disease genotype
variable expressivity
phenotype is variable range
Delayed age of onset and examples
individual does not develop condition until later in life, (ex Huntington disease, hemochromatosis, hereditary cancers)
new mutation
no family history of disease occurs in offspring (ex common in achondroplasia)
uniparental disomy
offspring have both homologous chromones in a pair from a single parent (heterodisomy and isodisomy)
locus hetrogensity with examples
mutations in different loci (genes) produce same disorder, Retinitis pigmentosa, BRCA1 & BRCA 2
Mutational (allelic) heterogeneity
with examples
different mutations (alleles) in same locus (gene) produce the same disorder, ex. beta thalassemia, Cystic Fibrosis, PKU
Pleiotropy
with examples
a single genes affects multiple phenotypic traits, single gene involved in many pathways. Ex Marfan syndrome, phenylketonuria, CF
Hardy-Weinburg equations
p+q=1
AA=p^2
Aa-2pq
Aa=q^2
Hardy-Weinburg Assumptions
1) random mating (consanguinity is NOT random mating),
2) no selection for any genotype,
3) no population migration (i.e. no gene flow),
4) large population size
5) no new mutations
Describe how triplet repeat disorders are transmitted
Higher number of repeats for later generations
Occurs during gametogenesis & expanded # of repeats transmitted to offspring
(example Huntington disease)
define anticipation
progressively earlier age of onset and severity of symptoms, correlates with number of repeats
metacentric
p and q are about equal in length, central centromere
Submetacentric
centromere located in intermediate position
Acrocentric:
centromere located in terminal position
chromosome structure
Bands, arm, regions (regions get larger towards telomere)
abbreviation for:
deletion insertion duplication inversion translocation terminal (pter/qter) ring chromosome isochromosome
del: deletion
ins: insertion
dup: duplication
inv: inversion
t: translocation
ter: terminal (pter/qter)
r: ring chromosome
i: isochromosome
normal karyotype
46, XY or 46 XX
g-banding
low resolution (<4 Mb), longer, looks specifically at intact chromosomes, can detect trisomies, monosomies, and translocations if above resolution blood drawn and culture, cells stained on slide, develop karyotype
Fluorescent In Sito Hypbridization (FISH)-
high resolution, intact chromosomes, fluorescence under microscope, uses hybridization of complementary nucleic acid sequence, uses FISH probes (centromeric, telomeric, and chromosome-specific probes)
M-FISH or SKY- FISH
for all chromosomes at the same time, labeled with different colored dyes, you don’t have to know what you are looking for
Array Comparative Genomic Hybridization
can detect small abnormalities, high resolution, uses microarrays, CANNOT detect abnormalities NOT involving changes in amount of DNA (i.e. inversions & balanced translocations). CANNOT detect triploidy (presence of 23 extra chr) due to limitation of software. CANNOT detect mitochondrial DNA changes (mito DNA not on array).
Changes in chromosome structure
- Translocations
- Deletions
- Duplications
- Inversions
- Ring chromosomes
- Isochromosomes
Euploidsy
is the normal chromosome number
- 2n (46 chromosomes) for somatic cells - n (23 chromosomes) for gametes
Aneuploidy and causes
is a change in the number of one or more chromosomes (not in the entire set)
- can be gain or loss of one or more chromosomes (autosome or sex chromosome) loss of 1 ch=monosomy and gain of 1 chr=trisomy
- chromosome # is different than 2n (ex. 2n-1 for loss; 2n+1 for gain) - loss of autosome is not viable (spontaneous abortion) - gain of autosome can be compatible with life (ex trisomy 21 is viable) - loss or gain of sex chromosomes is viable (X0, XXY) - aneuploidies in gametes are classified as nullisomic (n-1: lack of a chromosome) or disomic (n+1: extra copy of a chromosome)
polyploidy
is the gain of an entire haploid set of chromosomes
- chromosome # is 3n (triploidy=69 chr), 4n (tetraploidy=92 chr) …
- not viable (spontaneous abortion)
Polyploidies can be detected by chromosome banding and FISH
Reciprocal translocations
involve breaking & exchange between 2 chromosomes and formation of 2 new derivative chromosomes (can be balanced or unbalanced)
- breaking & exchange between chromosomes
- formation of 2 new derivative chromosomes
- affects pairing & segregation during meiosis
- can be balanced or unbalanced
- incidence is 1:500 in general population
Robertsonian translocations
a type of translocation involving 2 acrocentric chromosomes
Translocations can be identified by karyotyping with banding or FISH (not aCGH)
- involves 2 acrocentric chromosomes (13, 14, 15, 21, 22)
- acrocentric chromosomes fuse at centromere
- formation of new derivative chromosome
- loss of satellite material from arms of acrocentric chromosomes
- affects pairing & segregation during meiosis
unbalanced translocation
loss or gain of chromosome material
balanced translocation
no loss or gain of chromosomal material
results of translocations
Translocations cause abnormal pairing & segregation of derivative chromosomes during meiosis & affect daughter cells
Carriers of translocations (parents) may be asymptomatic but may experience
reproductive problems (infertility, recurrent miscarriages & having a child with an unbalanced chromosome complement)
Methods used for identification of disease genes:
Linkage analysis
Whole exome sequencing
Whole-genome sequencing
Methods used for testing/screening:
PCR PCR-RFLP ARMS-PCR Allele-specific oligonucleotide hybridization Southern blotting Sanger Sequencing
other methods for genes
north blots
gene expression microarrays
linkage analysis
further away the loci are the more likely they will be separated by recombination (crossing over)
takes advantage of polymorphic markers (2+ forms/version of marker found in human population)
very time consuming, no longer used regularly
requires large family
ex: CF was identified this way
whole genome sequencing
DNA is fragmented, linkers or adapters are attached, fluoro-labeled, ACTG, multiple pics, assembles entire sequence
Very quick
Good for rarer disease, does not require large family only a few affected relatives or unrelated peoples
whole exon sequencing
Sequences all exons
Misses intronic, regulatory, and non-coding variants
Takes advantage of the fact that exons contains about 85% of disease causing mutations
Expensive
Can use 4 unrelated patients or parent trios
Ex: kabuki syndrome, achromatopsia, miller syndrome
PCR
more copies of a specific DNA regions, exponential amplification
primers flank region of interest
can detect insertions, deletions, point mutations, viral infections, bacterial infections
PCR-RFLP
For point mutations
Takes advantage that point mutation creates or removes restriction site
Restriction pattern is different in mutant vs normal
amplification-refractory mutation system PCR
Uses allele-specific primers for detection of point mutations
Mismatch at 3’ end
Detects point mutations
allele-specific oligonucleotide (ASO) hybridization
DNA is isolated to a region where disease gene is. If hybridization with specific oligo occurs, patient has that allele
Detects point mutations, small deletions (bps), small insertions
Can check for multiple mutations at the same time
Also used in CF
southern blotting
Fragments DNA, DNA separated by size with electrophoresis transferred to solid matrix, NO amplifications
Can detect insertions, deletions, point mutations
More time consuming than PCR, not used frequently
Ex sickle cell disease (every individual has the exact same point mutation), can also use PCR-RFLP
Most appropriate to detect triple repeats
sanger DNA sequencing (dideoxy)
Primer specific to gene or region of gene, will pick up all mutations within region sequenced
High fidelity, high quality, “gold standard”
More expensive and time consuming
Can detect deletions, insertions, duplications, point mutations
Only method that allows for identification of novel mutations
Ex: BRCA 1/2
Northern Blotting
RNA is isolated from tissue sample where gene of interest is expressed
DNA probe is complementary to mRNA sequence
Can detect changes in gene expression
gene expression microarrays
Detects change in gene expression
Yellow, green, red signals for RNA
gene therapy
Corrects mutations in genome, exogenously provide a copy of the functional gene, can only be done in somatic cells (legally)
Can be used to program cell death for cancer cells
Requires: vector to delivered to target cell where the functional gene product will be expressed
in vivo gene therapy
WT gene delivered to the patient (ex CF)
ex vivo gene therapy
target cells removed, cultured, gene introduced to cells, then put back into patient- much lower risks of immune rejection
delivering gene therapy with viral vectors vs non viral vectors
-viral methods, remove disease causing aspects of virus (infect but to lyse), just for delivery (vector and packaging)
Drawbacks- immune responses, can inactive essential gene causing malignancy
-non-viral methods- less efficient, lower risks, assemble lysosome for delivery
CRISPR
Edits DNA (cut and paste), for cell response memory, not clinical yet
