Flashcards in Topics A34-38 Genetic Disorders/Developmental Abnormalities: Diagnosis, Autosominal Dominant, Recessive, Cytogenic, Single Gene - Atypical Inheritance Deck (54)
What "conventional" genetic disorder diagnostic method is older, but still used for copy number abnormalities (like Downs syndrome, trisomy 21)?
How does it work?
Cytogenic karyotype analysis with "G banding"
Giema stains chromosomes with bands during metaphase, then the chromosomes are organized based on alternating light/dark patterns to see if there are any chromosomal abnormalities like deletions.
[FISH and comparative genomic hybridization (CGH) have become popular for focused analysis of chromosomal regions]
What are 3 ways to categorize a chromosome, based on the position of the centromere in the middle or closer to one side, or just short chromosome with no clear centromere?
Metacentric: centromere is in the middle
Submetacentric: centromere closer to one side
Really short chromosome, no clear centromere: acrocentric
(helps identify which chromosome is which during G banding)
What letter is assigned for a short arm in a chromosome?
What about the long arm?
short arm is "p" for "petite"
long arm is "q" for "qlong"
(jk its just the next letter)
What are the possible numerical alterations in chromosomes?
1. Polypoidity: 3n, 4n, etc. Entire chromosome series (all 46 of them) have extra copies. A fetus with this will die before developing, but this can still occur in cancer cells.
2. Aneupoloidy: only certain chromosomes have less or extra copies. Monosomy, trisomy, etc. As in Down's syndrome, trisomy 21 - have extra copy of 21. Not immediately lethal but many health problems
How do numerical alterations like monosomy or trisomy develop? (2 ways)
1. Meiotic non-dysjunction at meiosis I: Failure of two members of a chromosome pair to separate from one another, causing both chromosomes to go to a single daughter cell.
2. Failure of sister chromatids to separate during meiosis II.
Results in some gametes with too many chromosomes, others with not enough.
Which two chromosomes tolerate aneuploidy (usually meaning monosomy or trisomy) better than others?
Sex chromosomes: don't need a Y chromosome to survive, and can also live with only one X (Turner syndrome). X is more commonly affected.
In general, loss of a chromosome produces more severe effects than gain
What are 3 major numerical chromosomal disorders involving autosomal chromosomes (not XY)?
All are trisomy:
1. Down syndrome: +21 (most common cause)
2. Patau syndrome +13
3. Edwards syndrome +18
(Edwards and Patau are very severe defects, usually die within one year. Not going to ask any more about them but Down Syndrome will come up later)
What are 3 major disorders involving numerical chromosomal differences in sex chromosomes?
1. Klinefelter's Syndrome (47, XXY)
2. Turner syndrome (45, X0)
3. Triple X syndrome (47, XXX) aka Vin Diesel Syndrome
What is a Barr body?
How does this relate to genetic abnormalities?
Inactivated X chromosome that is rendered inactive by "lyonization." Can be visualized (darker bc of heterochromatin) and used for diagnosis. Normal in females because they have two X chromosomes, and one must be inactivated. XY people have no Barr bodies.
Turner syndrome: no Barr bodies because only 1 X.
If they have 3 X's, then they will have 2 Barr bodies, 4 X's -> 3 Barr bodies, and so on.
What is the short way that you write the karyotype of translocations in chromosomal abnormalities, as in translocation from 2 to 5, and from the long 31 arm to short 14 arm?
For example for a woman it would be:
46, XX, t(2;5)(q31;p14)
What are the two types of translocations?
1. Balanced Reciprocal: exchange. No information is lost, it's just moved from one area to another
2. Central Fusion / Robertsonian: some genetic information is lost in translocation. May also be a cause of Down's syndrome, (t21;14) instead of trisomy 21
What are isochromosomes?
When sister chromatids (identical) separate horizontally rather than vertically, you get one chromosome of only short arms, and another of only long arms
[If this is your first time hearing about this and you're confused, just look up a picture because it's much simpler to visualize than explain]
What do frameshift mutations cause at a chromosomal level?
Deletion type of structural chromosomal abnormalities
What are inversions, regarding structural chromosomal abnormalities?
What are the 2 kinds?
Orientation of genes and genetic material changes.
1. Paracentric inversion: centromere not affected
2: Pericentric inversion: inversion occurs around the centromere
What are ring chromosomes?
Very rare structural chromosomal abnormality. After a deletion of terminal segments of the chromosome, the chromosome has "sticky ends" that end up looping around to connect to each other, forming a ring shape
What is the FISH method of diagnostics?
What are the advantages?
Fluorescent In Situ Hybridization: analyzes structural or numerical chromosomal alterations. Compared to conventional G banding, it's more expensive, higher resolution, don't need dividing cells for chromosome to be visible, software figures out problems automatically.
Major disadvantage: No "genome-wide picture" - need to have an idea what chromosomal regions to test for, and need specific probes for whatever you're looking for (i.e. 5p probe if you're looking for 5p deletion).
What is the array CGH method of molecular diagnostics of genetic diseases?
Array Comparative Genome Hybridization: most modern method, has both high resolution and genome-wide picture. Very expensive.
A sample of patient's DNA is dyed red and compared against reference "healthy' DNA that's dyed green. Combine the samples to get a "heat map." The two should combine to make a yellowish color, but if it's more red, then the patient's sample is amplified. If it's more green, then the patient's sample is under-represented.
What is the GWAS diagnostic method?
GWAS: Genome-Wide Association Studies.
This is used to analyze SNPs. Take a patient group (i.e. alcoholics), then compare their SNPs against a general population of non-alcoholics, making heat maps with CGH. From these, you see if there are any SNPs that are more common in the patient group vs the non-patient group.
Very popular research recently.
How does Sanger sequencing work to test for genetic mutations?
PCR sequencing of DNA. "Chain terminating method" - keep adding nucleotides that terminates a chain (e.g. ACGTCA-stop). Add 4 different fluorescent dyes (one for each stop nucleotide). Read the fluorescence as it goes through capillary electrophoresis (separates by size, short DNA strands go through first) and you can get the sequence.
Mutation may look like 2 peaks of different color in same region. Used for identification of point mutations, genetic diseases, oncology diagnosis, etc..
What are two invasive techniques to check for genetic fetal abnormalities?
1. Amniocentesis: amniotic fluid contains some fetal cells. Can also detect α-fetoprotein (AFP) levels that give a wide-array of diagnostic information, including things like neural tube defects
2. Chorionic villus sampling: Transcervically or transabdominally between 10th and 12th week. Results are available sooner than with amniocentesis.
What are two non-invasive tests to check for fetal genetic abnormalities?
1. Ultrasound. Can see some morphologies indicative of things like Down or Turner syndromes.
2. Maternal Triple Marker Screening. Can also see α-fetoprotein (AFP) levels in maternal serum, levels drop in Down syndrome. Low hCG levels and decrease in urine unconjugated estradiol are both indicators or Down syndrome.
What are two important non-coding RNAs? (only bringing it up because they spent a while on it in lecture)
1. MicroRNAs: short, regulate protein expression. Can be used in therapy: design small, interfering miRNA and target mRNA with it
2. Long non-coding RNAs (lncRNA): regulates transcription and translation. Can bind to DNA, RNA, etc... diverse functions. Has involvement in some disorders.
How are germline and somatic mutations different?
Germline: inherited, present in every cell (spread down through family line, may be nothing, may be pathological, or could be evolutionary advantage)
Somatic: acquired mutations, only present in somatic cells (like cancers)
What are the 4 main types of genetic mutation classifications that alter protein synthesis? (from lecture)
1. Missense: "point mutations" - change of just one nucleotide, can lead to change of just one amino acid that it codes for (example: Sickle Cell Anemia)
2. Nonsense: amino acid codon changes to a stop codon. Get truncated, shorter proteins that may decay faster.
3. Frameshift: Insertion or deletion of some nucleotides, but not of 3 of them and so the type of amino acid coded for is changed the entire way down the rest of the protein construction line
4. Trinucleotide Repeat: too many trinucleotide repeats makes the gene unstable. Seen in Fragile X Syndrome and Huntington's disease.
What is meant by Mendellian inheritance Disorders?
What are some modifying factors? (2 are listed)
Inheritance pattern involves classic dominant/ recessive alleles. "Autosomal" if not on an X or Y chromosome.
Mendellian genetics is true but too simple, so some modying factors:
1. Pleiotropy: one gene has many phenotypic effects (e.g. Cystic fibrosis is one mutation with many effects)
2. Genetic heterogeneity: different mutations lead to same trait (e.g. deafness can be caused by many different mutations)
What is characteristic in the family tree of people with autosomal dominant disorders?
There is an infected individual in every generation, and males and females are affected equally often.
It's enough to have 1 mutant allele (heterozygous) to have the disease.
With genetic disease inheritance, what do "penetrance" and "expressivity" mean?
Penetrance: not everyone with autosomal dominant gene is affected (they are phenotypically normal). for example if 10 patients have mutation but only 8 have the disease, the penetrance is 80%
Expressivity: Within patients that show the trait, this refers to the severity. Not everyone who inherits a disease has it equally severe ("variable expressivity").
What are two methods that epigenetic regulation occurs?
1. DNA methylation (cytosine residues methylated, made inaccessible to RNA polymerase, becomes silent)
2. Histone acetylation and methylation for either suppression or activation
What is a dominant negative allele?
A mutant allele that can impair the function of a normal allele