Principles Genetics Flashcards
What is the difference between DNA and RNA?
Sugar: 2-deoxyribose vs 2-ribose (OH)
Base: Thymine vs Uracil
Strand: Double vs Single
Stability: Stable vs Unstable
What is the difference between mitosis and meiosis?
Mitosis: 1 diploid parent cell gives rise to 2 identical diploid daughter cell
Meiosis: 1 diploid parent cell gives rise to 4 Haploid daughter cells + crossing over, independent segregation of genes, occurs in gamete formation
What is the central dogma?
DNA -> pre mRNA -> processed mRNA -> protein -> modified and transported
*Amt of proteins produced depends on rate of transcription to mRNA, rate of splicing of pre mRNA, half-life of mRNA, rate of polypeptide processing
What are polymorphisms?
Any variation in human genome that has a population frequency of >1%
OR
Variation in human genome that does not cause disease in its own right but may predispose to common disease
What are mutations?
Gene change/variation causing a genetic disorder OR any heritable change in human genome
Which phase does DNA replication occur at?
S phase. Children can have new variants which parents don’t thus mutations can be acquired from mitosis in somatic cells.
*Variants segregate independently unless they are very close together
How many % of the genomes are genes?
2%.
Nomenclature of chromosome
Female: 46, XX
Male: 46, XY
Recognition of chromosome
Banding patterns with specific stains, length and position of chromosome.
Normal chromosome: Telomeres, Short arm (p), Centromere, Long arm (q), Telomeres
What is an acrocentric chromosome?
Short arm is not significant.
What kind of chromosomal changes are there?
Balanced rearrangement: All c/s material present but in different arrangement
Unbalanced rearrangement: extra/missing c/s material; usually 1 (lack) or 3 (extra) copies of part of genome
What is aneuploidy?
Whole extra/missing c/s
What is translocation?
Rearrangement of c/s
What is insertion/ deletion?
Duplicated/ missing material
What are microdeletions?
1 -3 Mb long involving several contiguous genes, CANNOT be detected by conventional cytogenetic methods
What is down syndrome?
Trisomy 21, 47XY + 21
Extra 21 or translocated c/s14 p arm
What is Edwards Syndrome?
Trisomy 18, 47XY + 18
What is Patau Syndrome?
Trisomy 13, 47XY + 13
What is Klinefelter syndrome?
47, XXY
What is turner syndrome?
45, X
Is X chromosome aneuploidy better tolerated?
Yes, due to X inactivation. Thus 1 X is enough.
What is a Robertsonian Translocation and its consequence?
Most common form of translocation; 2 acrocentric c/s stuck end to end (E.g. R(14;21))
- Increased risk of trisomy in pregnancy
- If 1 parent is a carrier –> 25% normal, 25% balanced translocation, 25% trisomy 14 (miscarriage), 25% trisomy 21
Reproductive risk of translocation
~50% will have normal c/s or balanced translocation
Unbalanced c/s will lead to miscarriage (large translocation) or dysmorphic delayed child (small segments; more viable)
What is karyotyping?
It is a conventional clinical analysis looking at >5 million bases under light microscope.
(FOR BALANCED REARRANGEMENTS ONLY)
What is FISH?
Probe DNA labelled with fluorescence dye is denatured and hybridized to target sequence.
HAVE TO KNOW TARGET SEQUENCE FIRST
What is molecular cytogenetics?
Only detects UNBALANCE C/S, small changes which can be polymorphisms
Modern, quick, cheap, sensitive
What is aCGH?
Uses reference DNA and patient’s DNA in metaphase.
First-line c/s test, genome wide, detects for any size of IMBALANCE and a lot of polymorphisms. DNA-based reflecting underlying c/s.
Mainly for deletions and duplications.
Cannot detect balanced rearrangements.
What is Digeorge Syndrome?
Deletion of small segment of c/s22
What can PCR and Sanger sequence do?
They can select 1 small piece of human genome (range 100 - 10,000 bases) and amplify it.
Allele with mutation is not amplified.
What is next-generation sequencing?
Genomic DNA is extracted and fragmented into library of small segments. Each are sequenced in parallel and individual sequence are re-assembled by aligning to reference genome.
Different bases in alignment of short reads might be from variant allele with either polymorphism or disease causing mutation.
Variant sequences are cataloged.
What could genetic change identified from NGS be?
3,00,000 polymorphisms identified ->could be disease causing mutation, polymorphism or variant of unknown significance
How is filtering done for NGS?
It is to find the mutation that matters.
3,000,000 genetic variants -> exclude known polymorphisms -> keep if variant affects gene function (e.g. stop/ splice) -> see if gene can explain the phenotype -> single down to 1 or some variants that may be causative
What is the Philadelphia chromosome and its treatment?
t(9;22) where 22q has bcr-abl gene fusion producing p210 protein that increases proliferation, decrease apoptosis, and disturb interaction with extracellular matrix.
Tx
- HER2 amplification (malignant): Trastuzumab
- Ph C/s: Imatinib (Tyrosine kinase inhibitor)
Where can mutations act?
- Promoter mutation (reduce/stop transcription)
- Splice consensus altered (mutation occur where intron splicing occur, directly next to exon -> abnormal splicing/ absent protein)
- Early stop (short/ absent protein)
- aa seq changed (different/ non-functioning protein)
Types of mutation in DNA seq
Nonsense (premature stop), Missense (aa change), Insertion (in/out of frame), Deletion (in/out of frame), Triplet expansion
What is penetrance?
Extent at which a certain gene is expressed in phenotype
Measured by proportion of carriers showing the phenotype (E.g. 3 out of 10 people with the gene) or likelihood of having disease if gene is present
What disease has 100% penetrance?
Huntington’s Disease
What are Mendelian disorders?
Disease predominantly caused by change in single gene (high penetrance, small environmental influence, low mutation/polymorphism frequency)
What is Autosomal Dominant?
Seen in every generation, 1 copy of defective gene needed
- 50% risk if 1 parent affect and 75% if both
- Disease severity can vary (Penetrance)
- Male and female equally likely to be affected
E.g. Achondroplasia, Huntington’s Disease
What is Autosomal Recessive?
Usually skips generation, 2 copies of defective gene needed
- 25% risk if both parents are carriers
- Increased likelihood in consanguineous families
E.g. Cystic Fibrosis
What is X-linked recessive?
Passed from mother to son, daughters usually carriers.
- Females carry mutation but will not show MAJOR features of disease -> 50% of son will be affected and 50% daughters will be carriers
- Affected father -> ALL sons will be normal (inherits Y c/s) and ALL daughters are carriers
- Female carriers can show mild features due to random X inactivation thus 50% of cells have the working gene of average
Relevance of Y chromosome in disease causing genes
Almost irrelevant (very little gene contact)
When does X inactivation occur?
Early embryo stage to prevent double dose of X-linked genes but inactivation is not absolute; can still be leaky
What are some non-mendelian inheritance?
- Methylation/ Imprinting
- Mitochondrial Inheritance
- Mosaicism
- Multifactorial inheritance
What is multifactorial inheritance?
High mutation/polymorphism frequency ( a lot of SNPs involved)
Individual genetic factors are treated the same way as environmental factors.
Genetic change is just another risk factor.
Low penetrance for any one mutation.
What is mosaicism and somatic mosaicism?
Mosaicism: Different cells have different genetic constitution -> could arise from mosaic c/s abnormality or from point mutation
Somatic mosaicism: All cells can acquire mutation from mitosis/ meiosis
What are SNPs?
Not likely to exert effects of causing disease by themselves but effects can still show through gene function -> can increase predisposition.
Some SNPs can completely destroy gene without causing disease.
Question: Where, What, Effect of SNP and population frequency
What is Copy number variation?
Extra/missing stretches of DNA (size range widely varied)
Highly prevalent in genome and at least 12% of human genome can be variable.
How can low penetrance risk polymorphism be investigated?
Via case-control study to see if variant is found more in affected people.
Within normal distribution: Proportion of population vs risk of disease is classified by sum of different risk factors involved which can be genetic or environmental.
What is Spinomuscular atrophy type 1?
Babies with SMN1 gene deletion (loss of function) can undergo RNA targeted therapy (Spinraza tx via alternate splicing of SMN2 to SMN1)
Route of Administration: Intrathecal
*targeting mRNA is currently the most effective method to control the central dogma
