Medical Genetics Quiz 2

Front 1

Describe the action of restriction endonucleases

Back 1

Cleave double stranded DNA at specific bases sequences. They generate dsDNA with one of three kinds of ends: blunt, sticky 5' extension, sticky 3' extension

Front 2

Describe the DNA sequences where restriction endonucleases usually cleave

Back 2

typically palindromic
2 fold rotational symmetry

Front 3

Describe how to construct rebombinant DNA using restriction enzymes

Back 3

1. Digest the DNA of interest and the vector with the same restriction enzyme that produces sticky ends
2. Allow the two strands to reanneal
3. Seal with ligase

Front 4

List 3 requirements of a plasmid to be used in transformation

Back 4

1. Origin of replication
2. Resistance gene/ selection method
3. Restriction site where foregin DNA can be inserted

Front 5

WHat is cDNA?

Back 5

cDNA is a double stranded copy of mRNA made by reverse transcriptase (RNA dependent DNA polymerase)

Front 6

Describe how sanger sequencing works

Back 6

Based on random termination of the DNA chain during replication. A small amount of labled ddNTPs (only a H not 3' OH) are added to a replication reaction. When these bases are added the chain terminates and the identity of the base at this position can be determined. This is done many times and the fragments are run out on a gel to separate by size. The sequence can then be "read" down the gel.

Front 7

Describe how a southern blot is preformed to detect a DNA fragment with a specific sequence

Back 7

1.The total genomic DNA is digested by a restriction endonuclease
2. The fragments are run out on a gel and the double strand is denatured.
3. The fragments are transfered to a membrane
4. A radiolabeled probe is added, it anneals to the target sequence

Front 8

What is the purpose of a northern blot

Back 8

Analogous to the southern blot it allows one to determine the expression levels of a sepcific gene
hint:SNOW
DROP
Southern-DNA, Northern RNA, Western-Protein

Front 9

Explain the advantage of microarrays over northern blots. How do microarrays work?

Back 9

Southern blots look at one gene at a time. Microarrays allow integration of thousands of genes. cDNA is generated from total mRNA and then labled with a dye. The cDNA is then hybridized to DNA probes depositied on a chip

Front 10

What are the three discreet steps of PCR

Back 10

1. denature DNA
2. Anneal primers
3. primer extension

Front 11

What are the 4 necessary components in a PCR reaction

Back 11

1. template
2. primers
3. thermostable polymerase
4. dNTPs

Front 12

How many PCR cycles must you go through to isolate just target DNA

Back 12

3

Front 13

Describe a typical PCR cycle

Back 13

1. Heat to separate the DNA strands
2.Cool to allow the primers to anneal
3. Heat to initiate elongation

Front 14

What is the purpose of RT PCR

Back 14

RT PCR converts mRNA into cDNA and then PCR is preformed on the cDNA. It allows you to quantitativley compare the levels of gene expression

Front 15

What are the "obligatory elements" of a eukaryotic chromosome

Back 15

-replication origin
-centromere
-telomere

Front 16

Describe the purpose and mechanism of telomerase

Back 16

Adds 6 bp sequence "TTAGGG" repetitivley to ends of chromosomes, prevents chromosome shortening after each replication cycle

Front 17

Describe the clinical manifestations of trisomy 21

Back 17

Down syndrome

Front 18

Describe the role of mosaism in down syndrome

Back 18

Trisomy 21 resulting from a mitotic (not meiotic) non-disjunction, results in milder disease phenotype

Front 19

Describe the clinical manifestations of trisomy 13

Back 19

Patau syndrome, heart defects, facial midline defects, polydactyly, prodound developmental delay, most lost before term

Front 20

Describe the clinical manifestations of trisomy 18

Back 20

Ewards syndrome. Heart defects, profound developmental delay

Front 21

Why are sex chromosome aneuploidies generally less severe than autosomal aneuploidies

Back 21

X chromosome dosage compensation. The other chromosome is able to make up for the missing one

Front 22

Describe the clinical manifestations of XXX

Back 22

no observable phenotype, occasional psychiatric disturbances, fertile

Front 23

Describe the clinical manifestations of Turner's syndrome (XO)

Back 23

Short stature, sterile, unique cognitive faculties, poor spatial orientation

Front 24

Describe the clinical manifestations of Klinefelter syndrome XXY

Back 24

feminization, infertility due to mostly immature sperm (ICSI can assist), dificulty w/ psychosocial relationships but can benefit from androgen therapy

Front 25

Describe the role of X inactivation in aneuploidic diseases

Back 25

Only 1 X chromosome is active in mammals but note that there are some areas on the inactivated chromosome that are still active. Extra X's have less of an effect than an extra autosome would but each additional X can begin to affect phenotype. For example, XXXXY males have much lower IQs than XXY males

Front 26

Describe the clinical manifestations of XYY males

Back 26

Tall , impulsive, complex effects on social/ psychological profile

Front 27

Aproximately what % of the human nuclear genome is nongenic?

Back 27

75%

Front 28

The majority of the human genome is
repetitive
unique./ low copy

Back 28

unique/ low copy (60% of extragenic DNA, all of geneic)

Front 29

Euchromatin consists of

Back 29

Nonoding, Gene related DNA
-pseudogenes
-gene fragments
-introns, untranslated sequences,etc
Coding DNA

Front 30

Heterochromatin consists of

Back 30

Moderate to highly repetitive DNA both tandemly repeated or clustered repeates and interspersed repeates

Front 31

List 4 types of tandemly repeated DNA. What distinguishes them?

Back 31

Distingished by Length and location
1. megasatellie= serveral Kb in length, varous locations on selected chromosomes
2. Satellite DNA= 5-171 bp, centromeres (mnemoinic= satellites revolve around the center)
3. minisatellite DNA= 6-64 bp, telomeres
4. Microsatellite DNA=1-4 bp, dispersed throughout genome

Front 32

What type of repetitive DNA would be found at the telomere of a chromosome

Back 32

minisatellite

Front 33

What type of repetitive DNA would be found at the centromere

Back 33

Satellitel DNA
hint "satellites revolve around the center"

Front 34

What is a line 1 element

Back 34

most abundant repreated mega satellite, resemebles virus or transposable element, located in heterochromatin regions

Front 35

Define genetic marker

Back 35

an identifiable physical location on a chromosome whose inheritance can be monitored, they distinguish the two copies of a chromosome and allow the observation of which allele of a chromosome is inherited from a parent to a child

Front 36

List four types of genetic markers

Back 36

1. Genes (blood groups)
2. RFLPs
3. Simple Sequence Length Polymorphism (SSLP) (microsatelite, CA repreat, STRP, SSR)
4. SNPs

Front 37

Describe how RFLPs are generated

Back 37

CHromosomal DNA is cleaved with a restriction endonuclease and the DNA fragments are separated on a gel

Front 38

Describe Short Sequence Length Polymorphisms (SSLP) aka microsatelite DNA

Back 38

-Short repeats of 2-4 nucelotides
-Randomly distributed throughout the genome
-Different numbers of repeates exists and they can be separated by size
-Heterozygous induviduals have two products
-RFLPs can be used for genotyping, paternity tests etc

Front 39

Describe how RFLP genotyping would be preformed

Back 39

-Add a PCR primer for the sequence flanking the repeate section (the flanking sequence is identical across induviduals even though the # of repeates varies)
-Run the products on a gel and determine which alleles each person has, can be done fluorescently

Front 40

T/F SSLPs are biallelic

Back 40

False. Unlike SNPs, SSLPs (RFLPs) come in many flavors, the number of repeates that occur varies extensivley
note: RFLPs refer specifically to SSLPs that appear when the genome is clevaed by an enzyme. Not all SSLPs are RFLPs but all RFLPs are SSLPs (rectangle square thing)

Front 41

T/F SNPs are biallelic

Back 41

True, this is in contrast to SSLPs which are not

Front 42

The most common variations in the human genome are

Back 42

SNPs

Front 43

Describe interspersed repeitive non coding DNA

Back 43

repeats are not clustered but rather distributed across the entire genome, may contain transposable elements or undergo retrotransposition. Accout for over 1/3 of human genome

Front 44

T/F polymorpisms of microsatelites often result in diseases/ significant clinical outcomes

Back 44

False. WIth a few exceptions, microsatellites do not have functional consequences on clinical outcomes. They are most commonly found in intergenic or intronic portions of the genome. (exception includes huntingtons)

Front 45

A pedigree analysis revealing a history of multiple miscarriages might suggest which type of genetic disorder

Back 45

Chromosomal disorders (aneuploidy, etc.)

Front 46

What would be the predicted gender distribution for an autosomal disorder

Back 46

equal probability for males and females

Front 47

What is the probability that an offspring of a heterozygote will inherit a mutant allele for an autosomal disorder

Back 47

1/2. Since alleles segregate independently at meiosis, there is a 1 in 2 change that the offspring of a heterozygote will inherit the mutant allele

Front 48

A pedigree displaying absence of male to male transmission of a genetic disorder would suggest what type of disease

Back 48

X linked. Males always contribute a Y chromosome to their sons so an X linked disorder cannot be transmitted from a father to a son. The mother must be a carrier or affected

Front 49

What percentage of daughters of a male who is affected with an X linked trait will inherit the mutant allele from their father?

Back 49

100%. If a male is affected with an X linked disorder, his only X chromosome is mutant. A father must contribute his X chromosome to form a daughter so all daughters will have at least 1 mutant copy. Whether or not they are affected depends upon which allele is inherited from the mother

Front 50

Describe the features of a pedigree for an autosomal dominant inheritance pattern

Back 50

-Trait is usually found in every generation, each affected induvidual has at least one affectd parent (except in the case of de novo mutations)
-normal children who mate with a normal will only have normal offspring (they must be homozygous normal)
-male to male transmission occurs
-equal gender distribution

Front 51

Describe the features of an autosomal recessive pedigree

Back 51

-Normal parents of an affected induvidual are heterozygotes
-Consanguineous matings more often produce affected offspring

Front 52

A pedigree displaying:
-an affected induvidual in every generaton
-equally affected males and females
-normal partners producing only normal children
is most likely

Back 52

autosomal dominant

Front 53

A pedigree displaying:
-normal parents with affected children
-high number of affected children in consaguineoous marriages
is most likely

Back 53

autosomal recessive

Front 54

Describe the features of an X linked domiant inheritance pedigree

Back 54

-all unaffected females must be homozygous normal
-males phenotype= genotype
-never passed from father to son

Front 55

A pedigree demonstrating:
-a trait never passed from father to son
-all daughters of an affected male and normal female are affected
-all sons of an affected male and normal female are affected
is most likely

Back 55

X linked dominant

Front 56

In an x linked recessive disorder, what must the genotype of all affected females be

Back 56

homozygous for the mutant allele

Front 57

A pedigree that demonstrates:
-a disease never passed from father to son
-a disease passed from an affected grandfather through his normal daughter to 1/2 of his grandsons

Back 57

X linked recessive

Front 58

How would you calculate the probability of the realization of one or the other of two mutually exclusive events.
Example: Calcuate the expected proportion of affected offspring produced by AAxAa mating in an autosomla dominant disease

Back 58

The probability is calculated by adding the separate probabilities.
In the example, AA and Aa are two mutally exclusive events, you can be one or the other but not both.
The probability of having an affected child depends on the probability of being AA or Aa. The probability of AA is 1/2 and the probability of Aa is 1/2 (from punnett square) so the probability of being affected is 1/2 + 1/2 or 1. All children will be affected

Front 59

How do you calculate the probability of simultaneous realization of two independent possibilites?
Example. Two offspring are born from the same parents Aa X aa. What is the probability that both ofspring have the dominant phenotype A-

Back 59

The probability is calculated by multiplying the product of the separate probabilities.
The probability of having the dominant phenotype is 1/2(from punnet square).The probability that both children will is 1/2 *1/2= 1/4. The possibilites are independent because the genotype of one child does not influence the genotype of another.

Front 60

Explain the concept of variable expressivity

Back 60

-affected induviduals may express a wide range of symptoms
Do not confuse this with incomplete penetrance which is an absolute situation.

Front 61

Explain the concept of incomplete penetrance

Back 61

-in auosomal dominant disease with incomplete penetrance, the person with an affected dominant allele may not express the disease phenotype, usuall expressed as a % (100%= all people with alllele express sxs, 50%= only 1/2 of people with affected allele actually show sxs)
In contrast to variable expressivity, these pts display no symptoms

Front 62

What is the difference between variable expressivity and incomplete penetrance

Back 62

Variable expressivity describes the wide range of symptoms that may be dispalyed by affected induviduals. In complete penetrance means that a certain percentage of induviduals with a disease genotype do not express the disease phenotype at all.

Front 63

Describe the concept of genetic anticipation

Back 63

-progressivley earlier age of onset and increased severity of disorder in each successive generation
-basis- expansion of trinucleotide repeates (myotonic dystrophy size of repeated region increases in sucssive generations)
-may be due to simply Dx'ing earlier because of family Hx

Front 64

Describe the concept of genomic imprinting

Back 64

-In most genes expression occurs from both alleles
-In imprinted genes, expression occurs in only 1 allele depending on parental origin
-the imprint is establishe during parental gametogenesis and is maintained in the somatic cells of the offspring. The offspring then erases the impriniting and reestablished gender specific imprints upon gametogenesis

Front 65

Describe the concept of mosaicism

Back 65

-mutation during embryogenesis resulting in cells with two different genotypes within the same person
-May be somatic or germline
-if in the germline the children and resulting pedigree will have features of both recessive and dominant pedigrees

Front 66

Describe the concept of genetic (locus) heterogeneity

Back 66

Existence of mutiple genes which, when mutated, could cause the same pheontype

Front 67

describe the concept of phenocopy

Back 67

occurenece within a family of a phenotype that is similar to the disorder under study but not caused by an inherited genotype, ie they have something that looks like the diease but it's not caused by the same mutation. Common for adult onset conditions

Front 68

Describe a situation in which a pedigree for a recessive disorder may resemble an autosomal dominant disorder

Back 68

-Situations in which population characteristics influence the frequency of a mutant allele including founder affect, isolation, etc

Front 69

Describe a pedigree for a mitochondrial inheritance

Back 69

-maternal transmission
-affected fathers produce no affected offspring
-affected mothers produce only affected offspring

Front 70

define heritability

Back 70

a measure of the genetic contribution in multifactorial inheritance, in comparison to environmental liability

Front 71

Describe the Lod score method

Back 71

-the logarithm of the odds of linakge between two loci
-calculated from pedigree data as the log of the ratio of the probability of the observed pedigree assuming linkage to the probability of the observed pedigree assuming no linkage
-no linkage has a recombinatino fraction of 0.5
-score of +3 means linkage, -2 means no linkage
simple: p(linkage)/p(no linkage)

Front 72

What is the difference between forward and reverse genetic analysis

Back 72

foward-create a mutation that produces a specific trait
reverse-find the gene that causes the an existing phenotype

Front 73

In order to perform linkage anaylsis you need

Back 73

-pedigree, a large family
-accurate phenotype (phenocopy etc)

Front 74

Describe the processes used to ID the CF mutation

Back 74

-A region was identified using linkage anaylysis
-region was sequenced using positional cloning, 4 cadidate genes were discovered
-Northern blot from different tissues showed CTFR to be the only gene that was expressed in all affected tissues

Front 75

Describe the role of imprinting in Prader-Willi and Angelman syndrome

Back 75

The root of both syndromes is the deletion of a region in chromosome 15. The "flavor" of the disease depends on which intact copy is inherited. If the maternally imprinted copy is inherited the result is PWS, if the paternally imprinted copy is inherited, the result is Angelman

Front 76

Huntington's disease is caused by

Back 76

a microsatellite repeating too many times

Front 77

What type of inheritance is hutningtons disease

Back 77

autosomal dominant
note "revised" characterization with modifier genes that affect severity, genomic imprinting, and anticipation

Front 78

what type of inheritance is DMD

Back 78

x linked recessive
(note weird features such as sxs in heterozygotes, different pheontypes in monozygotic twin girls, had prescence of dystrophin)

Front 79

How does a mutation become a SNP

Back 79

-most increased in allele frequency by random chance (genetic drift)
-only a few are under selection as most have no discernable function
-note the majority of newly occuring mutations disappear quickly from the genome/gene pool

Front 80

What is the Hardy-Weinbery Law

Back 80

Mendelian segregation of two alleles in a randomly mating poplation leads to an equilibrium distribution of genotypes after one generation.
For anyone p + q, genotype frequences after one generation of random mating will equilibrate according to p2+2pq +q2

Front 81

Describe the primer extension method used to genotype SNPs

Back 81

Primer for region just before SNP, PCR with labled nucleotides determins base ID at SNP site

Front 82

What is a haplotype

Back 82

The physical arrangement of the individual SNP alleles along a chromosome

Front 83

Describe linkage disequilibrium

Back 83

The non-random association of SNP allels at closely linked loci, it measures the predictive power of one SNP over another.

Front 84

T/F linkage disequilibrium continously declines with distance

Back 84

false, LD blocks are scattered throughout the genome

Front 85

How do you calculate the number of possible haplotypes

Back 85

2^n where n is the number of SNPs

Front 86

How could you use the 2^n haplotype calcuation to find a region of high linkage disequalibrium

Back 86

The number of haplotypes will be much less than the 2^n predicted amount.

Front 87

How are genetic markers used in linakge analysis

Back 87

The different alleles of a marker are used only to distinguish the four parental chromosomes. If a marker is linked to the disorder, then ONE of the marker alleles from the affected parent is ALWYAS present in affected offspring. The linked markers define the REGION that contains the disease causing mutation

Front 88

Linkage analyses are most powerful for disorders that are (3)

Back 88

-single gene
-strong effect
-rare

Front 89

T/F linkage analysis is an effective tool for studying polygenic (quantitative) disorders

Back 89

false, LA is best for single gene, strong effect, or rare disorders

Front 90

What type of genetic study is best for polygenic disorders

Back 90

association

Front 91

Describe a case-control association study

Back 91

-Select induviduals from both diseased and non-diseased categories
-Identify freuency differences betweetn two groups (chi ^2 test)

Front 92

Describe a population based association study

Back 92

-select induviduals randomly from population
-identify phenotypic differences between genotype groups
-analysis by t test

Front 93

What is the difference between direct and indirect SNP association studies

Back 93

direct-catalog and test all functional SNPs
indirect-use dense map of tagSNPs and test for linkage disequilibrium

Front 94

Compare linkage and assocation studies in terms of:
what samples are used

Back 94

LA=family based
Asc.=family based or unrealated

Front 95

Compare linkage and assocation studies in terms of:
how many markers are used

Back 95

LA= ~300 STR markers genome wide
Asc= Hundreds of thousands of SNPs genome wide or candidate genes, direct or indirect association

Front 96

Compare linkage and assocation studies in terms of:
what they are best suited to study

Back 96

LA= single gene disorders with large gene effect
Asc= complex disorders (polygenic), moderate individual gene effects, common disorders

Front 97

Compare linkage and assocation studies in terms of:
the results obtained

Back 97

LA= identification of linked region on chromosome
Asc= Identification of asociated alleles of SNPs
hint: Linkage=Locus, Association=Allele

Front 98

About how many SNPs must be selected to do a genome wide association study

Back 98

500,000

Front 99

What statistical technique must be employed when preforming genome wide assocation studies

Back 99

bonferroni correction, divide the significant p of <0.05 by the number of SNPs tested

Front 100

What assumptions are made when using animal models for genomic studies

Back 100

-the same genes are causing the disease (not necesarily the same mutation)
-same clinical manifestation

Front 101

While linkage studies identify a disease causing ____, association stuides identify disease causing___.

Back 101

While linkage studies identify a disease causing LOCUS, association studies identify disease causing ALLELES