Final Study Guide Flashcards
1
Q
what are the 5 points of control?
A
chromatin stage
transcriptional stage
translational stage
post-transitional control into cytoplasm (regulation of RNA transport)
2
Q
what does the chromatin stage involve?
A
regulation at the chromatin stage can occur through a variety of mechanisms
including CpG islands and histone modification
3
Q
what are CpG islands? what does methylation of cytidine cause?
A
target sites of methylation are cytidine residues
areas rich w/CpG are known as CpG islands
methylation of cytidine down-regulates transcription
4
Q
what is histone modification? what does methylation vs acetylation do?
A
methylation or demethylation of lysine and arginine
methylation = down-regulation of transcription
acetylation = up-regulation of transcription
5
Q
how can histone be modified?
A
ubiquination
sumoylation
phosphorylation
6
Q
why is the chromatin stage important in relation to CA?
A
b/c potential therapeutic for CA are often designed to demethylate or deacetylate depending on the needed end result
7
Q
what is involved in the transcriptional stage?
A
copies genes, splits strands, mRNA shuttled out to nucleus to cytoplasm
promoters cause conformation changes and are seen in all coding genes
8
Q
what do promoters start? examples? located where?
A
signal for DNA production
ex: TATA, CCATT boxes
located upstream of transcription site
9
Q
what is involved in the translational stage?
A
RNA processing - addition of 5’ cap and 3’ poly (A) tail; removal of introns; splicing of exons
cap/tail communication - communication btw 5’ and 3’ ends of mRNA leading to enhanced translation
10
Q
what is in the post-translational control into the cytoplasm?
A
only some RNA fxns w/in nucleus so rest needs to get out so proteins can be made
leaves nucleus via nuclear pores
able to leave through pore by caps being added to the ends of the mRNA which causes a shape change
11
Q
what are the proteins involved in moving mRNA to the cytoplasm? what is required for entry vs exit?
A
NPCs (nuclear pore complexes)
karyopherins
Ran (Ra-s related nuclear protein)
small molecules can enter nucleus w/o regulation but macros like RNA and proteins require associated with karyopherins called importins to enter the nucleus and exportins to exit
12
Q
what is in post-translational modification? how can proteins be modified?
A
protein biosynthesis
ribosomes translate mRNA
ribosomes translate mRNA into polypeptide chains
protein modified by folding, cutting or other processes like adding functional groups or phosphorylation
13
Q
what are the 5 genetic dzs to know for boards?
A
klinefelter syndrome (47XXY) turner syndrome (45X, 46XX, 47XXX) alien 3 syndrome - 47XYY fragile X huntington dz
14
Q
what is klinefelter’s syndrome? genetic makeup? also known as? error where? what is likely to occur to sex organs?
A
47XXY
aka hermaphrodite d/o
sex chromosome aneuploidy
error in meiosis 1 - non-disjunction of X chromosomes
presence of both sex organs VERY rare
hypogonadism more likely dt dec T and incr LH, FSH
15
Q
ssxs of klinefelters? associated RFs and diseases?
A
appears over time, not at birth
physical traits become more evident during puberty dt lower T levels - less muscular body, less facial and body hair, broader hips, larger breasts, weaker bones, lower E, decr muscle mass, strength, may be taller than average
associated RFs/dz: breast CA, thromboembolic dz, osteoporosis
16
Q
what is turner syndrome? what is special about turner syndrome? presentation?
A
45X, 46XX, 47XXX sex chromosome aneuploidy only monosomy consistent with life! 50% are 45X presentation: short stature, infertility (ovarian dysgenesis, primary gonadal failure), osteoporosis, cubitus valgus, low posterior hairline, carb intolerance, HTN, short metacarpals, high arched palate, structural abn in KDs, Hashimoto's, neurocognitive problems
17
Q
what is “alien 3 syndrome?” common misconception? presentation? error where?
A
47XYY
not overtly violent
tall stature otherwise normal clinical phenotype
nondisjuction occurs during meiosis II - sperm gets extra Y chromosome
18
Q
what is Fragile X syndrome? why is it called this? what is it due to? severity of dz dt what?
A
called fragile b/c portion of X chromosome is “dangling by a thread”
due to unstable CGG repeat at Xq27 - expansion of CGG affects fragile X mental retardation gene on X chromosome which results in failure to express a protein required for normal neural development
expansion from pre to full mutation occurs through female meiosis
severity of dz correlates w/# of CGG repeats
19
Q
how common is fragile X? characteristics?
A
MC form of mental retardation
most widespread single gene cause of autism
characteristics = broad forehead, elongated face, large prominent ears, strabismus, highly arched palate, hyper extensible joints, hand calluses, pectus excavatum, MVP, enlarged testicles, hypotonia, soft/fleshy skin, flat feet, seizures, hyper extensible finger joints, double jointed thumbs, postpubescent macroorchidism
20
Q
what is huntington dz dt? chance of having the dz if a parent is affected? ssxs usu appear when? presentation?
A
neurodegenerative AD dz caused by expansion of CAG triplet repeat stretch w/in huntington gene (37-80 repeats in HD vs 10-26 in healthy genes) - results in mutation protein that damages the brain
any child of an affected parent has 50% chance of getting the dz
usu ssxs begin at 35-44 yo
presentation: chorea, mood and cognitive changes (dementia), gait abn
21
Q
what are proto-oncogenes? 5 types? functions?
A
highly regulated proteins involved in control of cell growth
- EC GFs
- GF receptors
- IC signal transducers
- nuclear transcription factors
- tumor suppressor genes
functions: synthesis of receptors, synthesis of messenger system, involved in a nuclear transcription
22
Q
3 places in the cell that proto-oncogenes become oncogenes?
A
receptors
messenger systems
nuclear transcription
23
Q
what can go wrong with receptor synthesis?
A
amplification: HER2/neu (aka ERB2) leading to BrCA
point mutation: RET –> MEN IIa, IIb
24
Q
what can go wrong with cells messenger system and what can it result in?
A
point mutation: RAS –> colon and pancreatic CA, leukemia (GTP signal transduction, receptor function)
translocation: ABL –> 9,22 CML (tyrosine kinase activity, non-receptor fxn)
25
what do oncogenes provide? need one hit or two hit process?
gain of function --> stimulate cell cycle, creates more active protein
need mutation in 1 copy of the allele = 1 hit process
26
what do tumor suppressor genes provide? need one hit or two hit process?
loss of fxn
inhibit cell cycle, no active protein
need mutation in BOTH copies of allele (2 hit process)
27
are tumor markers used to dx CA? what are they used for?
markers of serum enzymes released from target organ when damaged
not used to dx CA - gold standard is BX
tumor markers are useful: prognosis, determining the type of tx, evaluating the effects of tx/monitoring regression or progression, monitoring for recurrence after remission
28
markers for the following CAs: colon, hepatic, pancreatic, ovarian, testicular, breast
colon: CEA
hepatic: APF
pancreatic: CA 19-9
ovarian: CA125
testicular: beta-HCG
breast: BRCA1/2
29
what do traditional gene maps show?
physical locations based upon the sequence of nucleotide BPs
30
what do epigenomic maps show?
physical locations but "annotated" or marked as locations where modifications are made above BP sequences altering, activating, repressing, winding/unwinding and opening/closing sequences
31
what do CA genomic maps show?
location where gain-of-fxn and loss-of-fxn genes or epigenetic elements reside causing oncogenesis
32
what do physical maps show?
measured in BPs, genome sequence is the ultimate physical map; distribution of genes based on sequence data
33
what do cytogenetic maps show?
karyotype
34
what do linkage maps show? importance of frequency and spacing?
also known as genetic maps
show distance measured in the frequency of recombination coupling arrangements of alleles on linked genes, most important maps developed!
appear closer together when low recombination frequency
appear farther apart when there is high recombination frequency
35
what is an epigenomic map and what is a cancer map?
epigenomic map: physical locations that are annotated or marked as locations where modifications are made above BP sequences - can be altered, activated, repressed, wound/unwound, open/closed sequences
cancer genomic map: locations where "gain or loss of function" genes or epigenetic elements reside causing oncogenesis
36
what is linkage?
genes that occur close in proximity to one another or on the same chromosome
37
what is crossover?
homologous chromosomes lineup during prophase I of meiosis and exchange portions of DNA; tightly linked genes are very close to e/o on the chromosome and therefore are unlikely to crossover
38
what is recombination?
new combos of chromosome pieces, occurs multiple times at random places
39
what is gene linkage? how does location of two genes in relation to each other affect linkage? how is it used for mapping?
gene linkage: genes are said to be linked when they occur in close proximity to one another on the same chromosome
if two genes are close (tightly linked), they are unlikely to crossover during prophase I of meiosis dt mechanical reasons
used for mapping b/c recombination frequency provides a means of assessing distance btw loci on chromosomes
40
what is the linkage 50% rule?
if gene and marker are close together on the same chromosome, crossover is unlikely, showing <50% recombination = those genes are linked
if gene and marker are on different chromosomes or on the same chromosome but far apart, the alleles will remain together in an egg or sperm 50% of the time = those genes are unlinked
41
what is a prerequisite for a successful linkage analysis? what is the first step? what does this allow for?
polymorphic markers are a prereq for successful linkage analysis b/c these markers have been identified at a specific location on the gene
first step is to establish a linkage w/a known polymorphic marker
markers provide a marker "map" of each chromosome that serves as a guide to the position of a diseased gene - gene's position can be located relative to one or more markers by recombination mapping
allows genome wide screening for mapping genes
used to determine where a gene is located and the distance btw genes
42
how do transposons make gene mapping difficult?
```
transposon elements (TEs) are mutagens that can damage the genome of their host cell
TEs insert into a functional gene and disable that gene
after TE leaves the gene, the gap will probably not be repaired correctly
multiple copies of the same sequence can hinder precise chromosomal pairing during mitosis and meiosis = unequal crossover
```
43
what dzs are caused by transposon elements?
hemophilia A/B, SCID, porphyria, predisposition to CA, Duchenne MD
44
what is the chromosome theory and who proposed it along with genes as the basic unit of inheritance and when?
sutton and boveri in 1902 - chromosome is a linkage group of Mendelian factors (genes)
45
describe Morgan's contribution to genetics and how his linkage studies worked
genes are in a linear sequence on the chromosome that can be mapped
bred white mutate male fly w/red eyed normal female fly and noticed in their offspring that the white-eyed mutant flies were all males so must be related to males having only 1 X chromosome
46
what do restriction enzymes or restriction endonucleases recognize? many REs are what? what do they serve as? what is an allele specific oligonucleotide?
restriction enzymes or restriction endonucleases recognize a specific sequence of nucleotides and produce double-stranded cute in the DNA
many REs are pallindromic
they can serve as two-allele markers, where a specific site may be present in some individuals and absent in others
allele-specific oligonucleotide = short piece of synthetic DNA complimentary to the sequence of a variable target DNA, short nucleotide sequences that bind specifically to a single allele of a gene - used in Southern blot and Dot blot
47
what is a palindrome in genetics? what is it used for? often created by what process?
sequence of nucleotides along a DNA or RNA strand that contains the same series of nitrogenous bases regardless from which direction the strand is analyzed
often site of binding for specific enzymes designed to cut the DNA strands at specific locations
may arise from breakage and chromosomal inversions that form inverted repeats that compliment each other
48
when does a restriction fragment length polymorphism occur?
occurs when length of a detected fragment varies btw individuals
DNA sample is broken into pieces by restriction enzymes and the resulting restriction fragments are separated according to their lengths on gel electrophoresis
basic technique for detecting RFLPs involves fragmenting a sample of DNA by restriction enzyme which can recognize and cut DNA wherever a specific short sequence occurs, resulting DNA fragments are then separated by length via gel electrophoresis and transferred to a membrane via the Southern blot, Hybridization of the membrane to a labeled DNA probe then determines the length of the fragments which are complimentary to the probe
49
what are the types of DNA polymorphisms? which type is used for paternity testing and forensics?
VNTRs (variable number of tandem repeats)
STRPs (short tandem repeat polymorphism)
SNPs (single nucleotide polymorphisms)
STRPs used for paternity testing, forensics, gene mapping
VNTRs used for paternity testing and DNA fingerprinting
50
what are VNTRs?
variable number of tandem repeats
variation in fragment lengths is produced by differences in the numbers of tandem repeats located btw 2 restriction sites
repeated until generally 20-70 bases long, repeat flanked on both sides by restriction site
used infrequently in current genetic mapping as they tend to cluster near the ends of chromosomes so not very useful
when they are used, they're used for parental testing or DNA fingerprinting
51
what are STRPs?
short tandem repeat polymorphism
variation in fragment lengths is produced by differences in the number of microsatellite repeats found btw 2 PCR primer sites
repetitive sequence where repeated unit generally 2-5 bases long
can be amplified with PCR and visualized w/gel electrophoresis
STRPs distributed throughout the chromosomes, making them very useful in mapping genes
52
what are SNPs?
single differences in nucleotide sequences
represent nucleotide positions where only 2 nucleotides are found
occur about once every 1000 BPs
extremely useful, can be typed by PCR or probes on DNA chips
2000 of our 20-25k genes have SNPs - 200 deleteriously affect the gene, 5 are recessive lethals if homozygous
53
which polymorphism occurs in Huntington Dz and Fragile X ?
Fragile X: CGG repeat
| Huntington: CAG repeat
54
what is hybridization?
probe attached to 3 fragments that have been cleaved by restriction enzymes
probe determines which DNA fragments are seen
FMR1 gene is present in the liver but expressed in the brain
55
what are ASOs?
allele-specific oligonucleotide = DNA probe, short piece of synthetic DNA complimentary to the sequence of a variable target DNA that bind specifically to a single allele of a gene
used in Souther or Dot blot assays
used on DNA chips for dz testing
56
what is direct DNA sequencing?
rarely used
| Dot blot is used most frequently to determine genetic problems
57
process of direct genetic diagnosis?
use agarose gel electrophoresis of PCR products (if known mutation changes the length of the gene)
58
what is indirect genetic dx?
used if the mutation causing a dz in a family is not known, can be used to infer if a parent has transmitted the mutation to their offspring, uses genetic markers that are closely linked to the diseased locus
STRPs often used though all direct testing markers can be used
59
what is the difference btw Northern, Southern, Western and Dot blots?
```
Southern = DNA
Northern = RNA
Western = proteins using enzyme-linked antibody
Dot = RNA, DNA, proteins, does not use gel electrophoresis
```
60
what is the difference in fetal loss rates btw amniocentesis and CVS? how soon in PG can each be done?
amniocentesis: fetal loss rate 0.5%, can be done at 16 wks
CVS (chorionic villous sampling): associated w/small diagnostic error b/c of placental mosaicism; fetal loss rate 1%, can be done btw 10-12 wks
61
when can cfDNA be taken from mother's blood and how does cfDNA work?
can be done at 9 wks and is for numerical abn
draw blood from mom b/c fetal DNA fragments enter her blood stream via the placenta
DNA is amplified, SNPs can be analzyed
more accurate than other non-invasive tests that rely on "counting"
cfDNA = cell free fetal DNA testing - very short 1/2 life, not detected 48 hrs postpartum, looking for Duchenne MD, Rh compatibility
technique awaiting testing in large, blinded, prospective study
62
what has one unintended consequence of cfDNA testing in mothers?
test has picked up malignancies in mothers but that is not what the test was designed for so problem with reporting
63
what is Beckwith-Wiedemann syndrome? what is its significance? what procedure is BW associated with?
overgrowth d/o usu present at birth characterized by an incr risk of childhood CA and certain congenital features
also may have severe incr in sz of adrenals
five common features: macroglossia, macrosomnia, midline abd defect, ear creases or pits, neonatal hypoglycemia
EMG = exomphalos-macroglossia-gigantism = hernia, large tongues, large bodies and/or long limbs
associated with amniocentesis/IVF
64
what is the fxn of BRCA 1 and 2? what happens if each becomes mutated?
BRCA1 on chromosome 17, produces BrCA type 1 susceptibility protein --> responsible for repairing double strand breaks in DNA or destroying cells that cannot be repaired
if BRCA1 is damaged, damaged DNA is not repaired = incr risk for CA
BRCA2 on chromosome 13, binds single strand DNA, interacts with RAD51 to stimulate strand invasion and recombination
both are tumor suppressor genes and interact with RAD51
proteins made by both genes are essential for repairing damaged DNA
altered or mutated copies of either leads to BrCA, ovarian CA, prostate CA, male BrCA
65
women with hereditary breast ovarian cancer syndrome with abn BRCA1 or 2 are what risk for BrCA by 90 yo? if abn BRCA1? if abn BRCA2?
60% if BRCA1/2
55% risk for ovarian CA, also incr risk for fallopian tube CA if BRCA1 abn
25% risk for ovarian CA if BRCA2 abn
66
if pathogenic mutation of BRCA1 or 2 present?
incr risk of ovarian CA, fallopian tube CA, peritoneal CA, leukemia, lymphoma, melanoma, pancreatic CA, GB CA, bile duct CA, stomach CA, prostate CA
67
what is the fxn of RAD51?
BRCA1 and BRCA2 interacts w/RAD51 during repair of DNA double-strand breaks
these 3 proteins play a role in maintaining the stability of the human genome
68
what is the founder effect? in what country is virtually all breast ovarian cancer a result of just 1 person?
founder effect: all germ line BRCA1/2 mutations identified as being inherited --> suggests possibility of a founder effect where a certain mutation is common to a well defined population and can then be traced to a common ancestor
leads to clusters of dzs
founder effect seen among Ashkenazi Jews
in Iceland, a single BRCA2 mutation (deletion) accounts for virtually all breast/ovarian CA
69
what happens in the very rare case where you get a person where both BRCA2 alleles are mutated? what is the dz named? do we know what happens if a person is homozygous for BRCA1 mutations?
Fanconi anemia
majority develop CA - AML
90% develop bone marrow failure by age 40
may have congenital defects - short stature, developmental disabilities, abn of skin, arms, head, eyes
75% have endocrine abn
megaloblastic anemia by 1st detected abn (usu w/in 1st decade)
thrombocytopenia MC precedes neutropenia; usu develops into pancytopenia
70
if a non-jewish person wishes genetic testing for BrCA or if a jewish person known to have an atypical BRCA1/2 mutation, what test do you order?
comprehensive BRCA analysis
| also ordered if no one in the family has been tested yet
71
what test is ordered if a person is of Ashkenazi jewish descent?
multisite 3 point BRCA analysis
| checks for 2 deletions and 1 insertion (MC mutations)
72
if a person has a relative where the gene mutation is already known, what test is ordered?
single site BRCA test
73
what is the BRCAPlus panel? who do you use to test for BrCA?
targets detection of mutations in six high-risk BrCA susceptibility genes
consider for individuals w/personal or FHx of early onset BrCA or B/L BrCA, 2 primary breast CA or clustering of breast and ovarian CA, presence of male BrCA, ovarian CA at any age, at-risk population (Ashkenazi jews)
74
what is CDH1?
hereditary diffuse gastric CA and lobular BrCA in females
75
what is PTEN?
associated with Cowden syndrome, PTEN hamartoma tumor syndrome, autism spectrum d/o
Cowden syndrome is characterized by multiple hamartomas and high risk of thyroid, breast and endometrial tumors, also mucocutaneous lesions, thyroid abn, fibrocystic dz, multiple uterine leiomyomas and macroencephaly
76
what is STK11?
Peutz-Jegher syndrome
AD d/o characterized by development of GI hamartomatous polyps and melanin hyperpigmentation of the skin and mucous membranes
77
what is TP53?
Li-Fraumeni and Li-Fraumeni-like syndrome
increased risk for sarcomas, BrCA, brain tumors, adrenocortical carcinoma
small %age of women who are BRCA1/2 (=) have the TP53 mutation
78
know the NCCN guidelines for ppl who are at increased risk for breast or ovarian CA, but do not have the well known BRCA1/2 mutations
BrCA for women >/= 20-25% lifetime risk
breast self-exam training/education starts at 18 yo
clinical breast exam q 6-12 mos starting at 25 yo or 5-10 yrs before earliest BrCA dx in family
annual mammography and breast MRI screening to start at 30-35yo or 5-10 yrs before earliest BrCA dx in family
ovarian CA
consider risk-reducing oophorectomy after childbearing yrs
consider TVUS and CA-125 analysis q 6 mos starting at 35 yo or 5-10 yrs before earliest ovarian CA dx in family
79
what is materniT21 plus?
1st noninvasive prenatal test
80
what is DNA sequencing?
reads BP sequence, does not detect deletions or duplications, may miss changes in areas such as promoter regions or introns that affect gene fxn
81
pros and cons of direct to consumer genetic testing?
reliability: not very good as not regulated, no independent checks on quality or accuracy, results are inconsistent, some tests are not scientifically validated
interpreting results: not always easy to determine what the results mean, info may be incomplete
cost: can be very pricy and not covered by insurance
confidentiality: not protected under HIPPA
82
common indications for genetic testing?
expected phenotype expression (CF for ex.)
FHx
prenatal dx for an at-risk fetus
carrier testing
presymptomatic testing
confirm/deny DTC testing
at-risk family members with a known familial mutation
83
who do you complete genetic testing on?
fetus w/1+ anomalies
| FHx of childhood onset d/os (pediatric tumors, etc)
84
what types of genetic tests are commonly used?
karyotype: looks for deletions, rearrangements, translocations, duplications
used when looking for trisomy, monosomy, multiple miscarriages
FISH: detects microdeletions, counts chromosomes in a lg # of cells, used when a mosaicism is suspected (Turner's), microdeletions (PW, AS)
85
what are inborn errors of metabolism?
diverse collection of d/os of intermediate metabolism (carb, AA, lipid), that are caused by dysfxn of an enzyme encoded by a single gene
mb greater suspicion for IEMs in children whose parents are either consanguineous or have had kids w/similar problems or unexplained death or fetal demise
important to consider IEMs b/c for some, neuro sxs can be improved w/specific dietary or metabolic tx
86
when testing for IEMs when is the preferred time to collect the sample?
when child is sickest
| don't rely on newborn screen as it is just a moment in time, if you suspect an IEM then test for it
87
why might you, when trying to identify the cause of developmental d/os, repeat the rest a couple years later if the original results weren't helpful?
CGH microarray: if negative see them back in 1-2 yrs b/c the CGH microarray will be better and new things will have been added
88
how has CMA testing increased the yield in genetic testing?
CMA = microarray-based CGH test to detect changes in genomic copy # - more detailed than karotype, systematically moves down the chromosome and measures how much DNA is there, looking for very small deletions
CMA has incr rate of dx among individuals w/unexplained developmental delay and mental retardation
89
even if you have already established a diagnosis of CF, why might you re-sequence them?
to check the expected phenotypic expression
90
what type of abn is the CMA test looking for in terms of mutations?
looks for very small deletions
| <1 MB
91
how is GDD distinguished from other d/os causing intellectual delay?
many kids don't present w/syndromic feature or a (+) FHx
usu GDD doesn't worsen with time
delayed in 2+ areas: motor skills, speech and language, ability to learn, social and personal skills, daily activities
etiological dx for GDD or ID only occasionally leads ot a specific therapy that improves the child's outcome
dx helps get government funds for medical care rather than actionable material to be able to tx
92
testing recommendations for GDD?
G-banded karyotype, Fragile X molecular genetic testing and aCGH
93
what is CGH?
broad genomic coverage (chromosomal microarray/CMA testing) = higher diagnostic yield than G-banded karyotype and FISH for dx of developmental delay and mental retardation, detects abn in up to 8% of pts w/previously normal karyotypes, no other test has as good clinical sensitivity for these d/os
94
what is Rett syndrome?
leading dx etiology of GDD in girls
| these girls appear to develop normally until 6-18 mos then lose developmental abilities
95
what is XLID? significance?
XLID= x-linked intellectual disability
estimated to account for 10% of intellectual disability
>70 genes responsible for XLID in which mutations have been identified have been cloned
there are >100 genes that have been identified but not cloned
testing for XLID genes has a yield of up to 42% in males w/appropriate FHx
96
what are 4 diff evolutionary processes that give rise to changes in allele frequency distribution?
natural selection
genetic drift
mutation
gene flow
97
what is natural selection? AD vs RD and NS impact?
increases the frequency of alleles that promote survival or fertility and reduce alleles that cause dzs
explains why genetic dzs are rare
in dominant dzs, the disease causing allele is more readily exposed to the effects of natural selection and have lower allele frequencies
recessive dzs have higher allele frequencies as their alleles are typically hidden in heterozygotes
98
what is genetic drift?
change in allele frequencies caused by random sampling (alleles in offspring are random sample of parents)
may reduce genetic variability by causing variants to disappear
not driven by environmental or adaptive pressures, mb beneficial, neutral or detrimental to reproductive success
effect is larger for alleles present in a smaller # of copies and smaller when an allele is present in many copies
99
what is mutation?
ultimate source of genetic variation in form of new alleles (changes in DNA)
100
what is gene flow?
exchange of genes btw a population (usu of same species)
works by gain/loss of genes into a population through immigration or emigration of individual organisms btw established populations
101
what does the Hardy-Weinberg principle contend?
provides a solution to how variation is maintained w/in a Mendelian population
frequency of alleles will remain constant in the absence of selection, mutation, migration, genetic drift
refers to this stability of allele frequencies over time
102
what is the practical clinical use of the Hardy-Weinberg principle?
principle says that there is a constant and predictable relationship btw genotype and allele frequency
if allele frequency is known, the number of affected individuals can be determined helpful in determining carrier frequency
103
describe the hx of MTHFR gene and homocysteine
first published by Mudd et al who identified a pt w/homocysteinuria dt severe enzyme deficiency
MTHFR deficiency is MC inborn error of folate metabolism but it is relatively rare
in 1988 thermolabile variant of MTHFR was identified in pts w/CVD - this milder deficiency which is more common, resulted in a mild to moderate evaluation of plasma total homocysteine (emerging factor for CVD)
cDNA isolation in 1994 opened up avenues for molecular genetic approaches to study MTHFR deficiencies
cDNA isolation quickly followed by identification of a common sequence variatn at BP 677 (C-->T) which encoded the thermolabile enzyme
this variant has become recognized as the MC genetic cause of hyperhomocysteinemia and has been extensively investigated as RF for several multifactorial d/os associated with disturbances in homocysteine metabolism
104
describe the normal role and fxn of MTHFR
MTHFR gene provides instructions for making an enzyme called metylenetetrahydrofolate reductase
plays a role in processing a.a.s
important for chemical reaction involving forms of B vitamin folate
converts 5,10-MTHF to 5-MTHF
this reaction is required for the conversion of homocysteine to methionine
methionine used to make proteins and other important compounds
105
what is the mode of inheritance of MTHFR mutations?
AR
106
list the location of the gene and SNPs on the 677 and 1298 alleles
C replaced with T at 677 (677 C>T) = most well studied polymorphism related to risk of neural tube defects; MC genetic cause of hyperhomocysteinemia
A replaced with C at position 1298 (1298A>C)
107
know the %age of enzyme activity reduced w/each SNP and combination of SNPs
C677T (cardio): 1 copy = 40% loss, 2 copies = 70% loss
A1298 (NT): 1 copy = 20% loss, 2 copies = 40% loss
C677T +/- and A1298C +/- = 50% loss
C677T +/+ and A1298C +/- = 70% loss
C677T +/+ and A1298C +/+ = 80-100% loss (RARE)
108
know the consequence of one or more alleles on the MTHFR gene being mutated
mutations in MTHFR gene change single a.a. in MTHFR --> impair enzyme fxn
some changes cause the enzyme to be inactivated
some mutations lead to production of an abnormally small, nonfunctional version of the enzyme
w/o MTHFR, homocysteine cannot be converted to methionine which leads to increased homocysteine
related to neural tube defects
109
what is a single gene d/o?
dz caused by alteration in single gene or in a specific chromosome
can be dx via lab test - person either has dz or doesn't
MOA understood
recurrence risk can be derived based on known principles of inheritance
110
what are common diseases?
common dzs tend to cluster in families but do not conform to Mendelian pedigree pattern
many variants of small effect contribute to ddz risk, along w/many environmental factors
cannot be dx via lab test, have to use diagnostic criteria
underlying multifactorial traits have not been identified specifically
empirical recurrence risks must be derived based on direct observation of data
111
how is recurrence rate calculated differently from AR and AD dzs than in common dzs?
recurrence risk increases when # of affected relatives increases, severity of dz expression increases, # of affected children in a family increases, affected individual is a member of the less commonly affected sex, prevalence of the dz increases in a population, parent more severely affected, there is consanguinity
112
development of monozygotic vs dizygotic twins?
mono: 1 egg, 1 sperm, embryo splits
di: 2 eggs, 2 sperm
113
what is concordance?
share same trait
114
what is discordance?
don't share same trait
115
how do adoption studies of twins help tease out genetic contribution vs epigenetic contribution in common dzs?
adoption: measures prevalence of trait in ppl who had one biologic parent w/ the trait but who are adopted by parents who do not have the trait, supports gene involvement in schizophrenia for ex for if a trait that is determined strictly by gene then one would expect 100% concordance in MZ twins and 50% concordance in MZ twins and if a trait that is strictly determined by environment then we would expect equal concordance in MZ and DZ twins
116
what does p53 do and what happens if it is mutated?
p53 is a tumor suppressor gene that stops a cell w/damaged DNA from entering S phase
if it is mutated then increased risk/liability for CA (90% chance)
double hit - if they incur a loss-of-fxn somatic mutation in a cell, it will lead to CA
Li-Fraumeni syndrome is an example
117
what is genetic liability? how does it relate to common diseases?
summation of genetic and environmental RFs
distribution in a population represented as a Gaussian curve
relative risk: incidence on exposure/incidence of non-exposure
although the recurrence risk for a single-gene d/o remains the same regardless of the prevalence of the disease in a population, the empirical risk for multifactorial dzs increases as the population prevalence increases - this is b/c w/higher prevalence rates have higher preponderance of genetic and environmental factors
118
what is Edward's syndrome?
trisomy 18
very poor prognosis
AVSD, PDA
hand, foot malformations, low set ears, micrognathia
119
what is Patau syndrome?
trisomy 13
polydactyly, cleft palate, microphthalmia (small eyes), microcephaly, cardiac and renal defects
very poor prognosis
120
what can go wrong with cell messenger system? which gene is affected by each process and what disease does that cause?
translocation of chromosome 9,22 on tumor suppressor gene causes Philadelphia chromosome --> CML
translocation of 15,17 --> AML
translocation of 8,14 --> Burkitt's
translocation of 11,14 --> mantel cell lymphoma
121
what is PW a result of?
microdeletion on paternal chromosome 15
| floppy baby, hungry
122
what is AS a result of?
microdeletion on maternal chromosome 15
| happy baby
123
what is Marfan's a result of?
AD deletion of fibrillin
124
what is Cri-du-chat a result of?
deletion on p arm of chromosome 5, larynx normal after 2 yo
125
what is Li-Fraumeni?
missing tumor suppressor p53, AD, 25x higher risk of CA by 50 yo
126
what can go wrong with nuclear transcription?
translocation: c-MYC --> 8,14 Burkitt's lymphoma
amplification: n-MYC --> neuroblastoma
