Mtc: Block 3 - Genetics

Front 1

How many bp of DNA are there in each human cell?

Back 1

3.3 billion

Front 2

How many genes are there in the human genome?

Back 2

25,000 - 30,000 genes

Front 3

What is a mutation?

Back 3

- Any change in DNA sequence away from normal
- Often disease-causing
- Rare frequency

Front 4

What is a Single Nucleotide Polymorphism (SNP)?

Back 4

- DNA sequence variation that is common in the population (>1%)
- Affects only one single nucleotide base
- Usually non-disease causing

Front 5

How frequent are SNPs?

Back 5

~1 SNP for every 1000 base pairs (> 4 million total); although frequency varies by race

Front 6

What is a haplotype?

Back 6

Set or group of SNPs (single nucleotide polymorphisms)

Front 7

What are copy number variations (CNVs)?

Back 7

Abnormal number of copies of DNA (gene deletions/duplication)

Front 8

How many CNV (copy number variations) have been identified?

Back 8

>1400 CNV regions (covering ~12% of genome)

Front 9

How long are CNVs (Copy number variations)?

Back 9

1 kilobase to several megabases

Front 10

What are Low Copy Repeats (LCRs)?

Back 10

Region-specific repeat sequences, susceptible to genomic rearrangements, which can result in CNVs (Copy Number Variations)

Front 11

What are some methods for SNP genotyping and mutation detection?

Back 11

- Restriction fragment length polymorphism (RFLP) - used when a SNP creates or abolishes a restriction site
- High Resolution Melting Analysis
- Real-Time PCR
- SNP Microarrays - analyze gene expression
- First Generation Sequencing (Sanger Method)
- Next-Generation Sequencing (NGS)

Front 12

What is necessary for Restriction Fragment Length Polymorphism (RFLP) to be a technique usable for SNP Genotyping and Mutation Detection? How is it performed?

Back 12

- Requires SNP to create or abolish a restriction site
- Amplify region of interest with flanking primers
- Digestion of PCR product with enzymes
- Resolve products by gel electrophoresis

Front 13

What is an example of a SNP that was located via restriction fragment length polymorphism (RFLP)?

Back 13

- Cystic Fibrosis mutation 2789 + 5G>A
- Creates an Ssp1 cut site
- Generates 3 fragments compared to 2 fragments in WT

Front 14

Where on a melting curve is the melting temperature?

Back 14

The midpoint of the transition is the Tm

Front 15

What factors can influence the melting temperature?

Back 15

pH, Ionic Strength, and Size/Base composition of DNA

Front 16

How is the High Resolution Melting Analysis performed for SNP Genotyping and Mutation Detection?

Back 16

- PCR performed using primers flanking targeted region of interest and double-stranded nucleic acid dye
- Melting temp of entire amplicon determined
- When double-stranded DNA melts into single strands, dye is released, causing change in fluorescence
- Melting temp difference between samples due to sequence variation

Front 17

How is Real-Time PCR (qPCR) used for SNP genotyping and mutation detection?

Back 17

- Amplify and quantify targeted DNA molecule with qPCR in real-time
- Allele-specific probes designed for both alleles of a SNP w/ nucleotide of interest in middle
- 5' end of oligo labeled with fluorophore, 3' end contains quencher
- Fluorescence of 5' is quenched as long as fluorophore is in close proximity to quencher
- During PCR, 5' nuclease enzyme only cleaves hybridized probe, freeing the fluorescent label from quencher
- Allele-specific increase in fluorescence w/ each cycle of PCR
- If probe doesn't match and hybridize to allele than the fluorophore will not be detected

Front 18

How are Microarrays conducted?

Back 18

- mRNA samples are collected from cells at two different stages in development of a frog
- mRNA samples converted to cDNAs by reverse transcriptase using fluorescently labeled DNA nucleotides
- Add cDNAs to a microarray; fluorescent cDNAs anneal to complementary sequences on microarray
- Each spot represents a gene expressed in the cells
- Green spots represent mRNAs more abundant at single-cell stage; red for later in development; and yellow for equal abundance at both stages

Front 19

How are Microarrays used to detect SNPs?

Back 19

- High-density oligonucleotide SNP arrays, hundreds of thousands of probes with DNA variants are arrayed on a small chip
- Many SNPs are interrogated simultaneously
- Once DNA is attached to solid surface, microarray can be probed with DNA from an individual that has been fluorescently labeled
- Fluorescent nucleic acids anneal to complimentary sequences on microarray

Front 20

What is the procedure for the First Generation Sequencing (Automated Sanger) Method?

Back 20

- PCR amplification of target of interest
- PCR product is denatured and a sequencing primer is annealed to region of interest
- Extension reaction performed using dNTPs and dideoxynuclotides (ddNTPs) labeled w/ different colored fluorescent tags
- Incorporation of a ddNTP will terminate extension, resulting in various dye-labeled segments of DNA
- Colored fragments are separated by size when analyzed by gel-electrophoresis
- DNA sequence is ready as colors pass through detector

Front 21

What is the principle behind the Next-Generation Sequencing Method?

Back 21

- Sequencing DNA molecules in a massively parallel fashion in a flow cell
- Each clonal template or single molecular is "individually" sequenced and can be counted among the total sequences generated

Front 22

What is a potential problem with second-generation NGS (next-generation sequencing) methods?

Back 22

- PCR amplification may introduce base sequence errors or favor certain sequences over others
- This would change the relative frequency and abundance of various DNA fragments that existed before amplification

Front 23

How do third-generation NGS (next-generation sequencing) methods overcome the issue of spontaneous sequencing errors that have been demonstrated in second-generation methods?

Back 23

Third-generation method baesd on sequencing from a single DNA molecule without prior amplification

Front 24

How does the Sanger method (first generation sequencing) compare to Next-Generation Sequencing (NGS) methods?

Back 24

- NGS platforms generate shorter reads with lower quality (but bioinformatics tools assist in mapping shorter reads to reference sequences
- NGS has higher throughput and faster turnaround time
- NGS has a small amount of starting material needed
- NGS is lower in cost - $1000 for entire genome

Front 25

What is the purpose of molecular diagnostic testing?

Back 25

- Detects variations associated with a disease or disorder
- Also predicts a patient's response to medications (or explain drug-related toxicity)

Front 26

What is pharmacogenetics (PGx)? What is its goal?

Back 26

- Study of individual genetic variations in DNA sequence related to drug response
- Goal is to select the right drug, at the right dose in order to avoid adverse drug reactions (ADRs) and ineffective treatment
- Used to personalize patient's medical treatment

Front 27

What are the benefits of pharmacogenetic (PGx) testing?

Back 27

- Optimize drug therapy (dose and medication choice) based on individual's DNA
- Limit drug toxicity/decrease number of adverse reactions
- Decrease number of treatment failures
- Increase clinical effectiveness of drug treatment
- Decrease overall health care costs
- Increase patient quality of care

Front 28

Which enzymes are important for metabolism and bioactivation of ~75% of total drugs and xenobiotics?

Back 28

Cytochrome P450 (CYP450)

Front 29

How are Cytochrome P450s (CYP450) SNP alleles denoted?

Back 29

- CYP450 SNP alleles are given a star nomenclature that corresponds to a specific genomic location
- e.g., CYP2C19*2 = CYP2C19:g, 19154G>A (reference nucleotide G at genomic "g" position is changed to A)
- Reference gene sequence (functional allele) is indicated as CYP2C19*1

Front 30

How are SNPs categorized?

Back 30

Based on overall function of the protein: functional, decreased-function, nonfunctional, increased function

Front 31

What is an example of a drug that depends upon a CYP450 enzyme to activate it?

Back 31

- Clopidogrel (Plavix) - given to prevent heart attack and stroke by limiting platelet aggregation
- CYP2C19 metabolizes the drug to its active form

Front 32

What are the implications of having a variant of CYP450 (*2 or *3)?

Back 32

- Results in decreased or poor metabolism of of Clopidogrel (Plavix)
- Poor metabolizers have a higher rate of cardiovascular events because Clopidogrel is ineffective at reducing platelet aggregation

Front 33

What is the most common fatal autosomal recessive disorder in Caucasian populations? How common is it?

Back 33

Cystic Fibrosis (CF): ~1:2000-3000 live births

Front 34

What causes Cystic Fibrosis (CF)?

Back 34

Mutation in CFTR gene, which encodes a Cl- channel; >1500 mutations in CFTR gene have been identified

Front 35

What is the most common mutation that causes Cystic Fibrosis (CF)?

Back 35

ΔF508 (frequency = 0.68)

Front 36

If a rare mutation is suspected to be causing Cystic Fibrosis (CF) what is done?

Back 36

Full gene sequencing of CFTR gene

Front 37

How are newborns in WI screened for Cystic Fibrosis (CF)?

Back 37

23 ACMG-recommended mutations are screened for (although larger mutation panels are available to increase detection rate)

Front 38

What is the most prevalent inheritable genetic deletion syndrome (1:3000-4000 live births)?

Back 38

- 22q11.2 deletion syndrome (22qDS) - 1.5 to 3.0 Mb hemizygous deletion of chromosome 22q between low copy repeat regions (LCRs) (>35 genes)
- Found in most patients with DiGeorge Syndrome and Velocardiofacial Syndrome

Front 39

How is 22q11.2 Deletion Syndrome (22q DS) obtained?

Back 39

- Most cases are sporadic
- 10% of cases are inherited
- Autosomal dominant

Front 40

Why is early detection of 22q11.2 Deletion Syndrome (22q DS) so important?

Back 40

75% of FISH-positive 22q11.2 deletion subjects have congenital heart disease (major cause of mortality)

Front 41

How can the 22q11.2 Deletion Syndrome (22q DS) be detected?

Back 41

- Standard FISH probe (HIRA)
- Although it can miss 22q DS in subjects who carry smaller microdeletions within the typical deleted region
- PCR-based assays, such as multiplex quantitative rtPCR to detect TBX1 gene deletion (major genetic determinant of chromosome 22q DS) which is more sensitive than Standard FISH Probe

Front 42

What is the "karyotype" of a cell?

Back 42

Morphological characteristics of a cell's chromosomes (showing all 46+/- chromosomes)

Front 43

Each haploid (2N) genome has how many genes?

Back 43

~25,000 genes so ~1000 genes/chromosome

Front 44

Each gene copy in a diploid genome is called what?

Back 44

Allele

Front 45

What are some examples of hyomozygous recessive conditions?

Back 45

- Albinism
- Cystic Fibrosis
- Galactosemia
- Phenylketonuria
- Tay-Sachs Disease

Front 46

How do you know that the mother is a carrier?

Back 46

A recessive allele on the X chromosome (e.g., red-green color blindness and Duchenne Muscular Dystrophy)

Front 47

What happens to the DNA during S phase?

Back 47

2N DNA becomes 4N

Front 48

What is the "phenotype"?

Back 48

- Biochemical, anatomical, physiological, or behavioral trait
- Mediated by genotype and environment

Front 49

What is the "genotype"?

Back 49

One's genetic makeup, governed by allelic differences

Front 50

What stimulates mitosis?

Back 50

Phosphorylation, mediated by Mitotic CDK (CDK-1 + Cyclin B), which is activated by de-phosphorylation of CDK-1 (via cdc25 phosphatase)

Front 51

What is the goal of mitosis?

Back 51

To restore the 2N condition by preciselyy splitting into two cells

Front 52

What happens at the end of G2 phase?

Back 52

Mitotic CDK (CDK-1) induces separation of the centrosomes, which had duplicated in S-phase, initiating formation of the mitotic spindle

Front 53

What are the stages of mitosis?

Back 53

1. Prophase
2. Metaphase
3. Anaphase
4. Telophase
5. Cytokinesis

Front 54

What happens during early prophase?

Back 54

- Mitotic CDK induces "condensin" which stimulates chromatin condensation
- Sister chromatids pair-up and are held together at the centromere
- Centrosomes arrive at spindle poles

Front 55

What happens during late prophase?

Back 55

- Mitotic CDK causes nuclear envelope breakdown
- Protein complexes called kinetochores envelop each centromere (center of chromatid) and kinetochore tubules connect the chromatids to the centrosomes (at poles)
- Astral microtubules decorate each centrosome
- Polar microtubules do not attach to chromatids but extend from centrosomes and overlap at equator

Front 56

What happens during metaphase?

Back 56

- Kinetochores microtubules align the chromosomes at the metaphase plate, which is halfway between the poles (centrosomes)
- Continued microtubule assembly via incorporation of tubulin subunits must happen for mitosis to continue

Front 57

What kind of drugs block microtubule assembly and prolong metaphase, essentially blocking mitosis?

Back 57

- Colchicine blocks microtubule assembly
- Chemotherapy: taxol and vinblastine
- Vinblastine also inhibits microtubule assembly by binding tubulin
- Taxol inhibits microtubule disassembly

Front 58

What happens during anaphase?

Back 58

- Anaphase-promoting complex (APC), which contains ubiquitin, initiates anaphase
- In the kinetochore, APC degrades securin, threby release separase which in turn degrades cohesin, permitting the release of the sister chromatids
- Chromatids move to opposite poles via a "push-pull" mechanism involving microtubules and microtubule motor proteins

Front 59

What is the "push-pull" mechanism that occurs during anaphase?

Back 59

- "Push" - via elongation of polar microtubules
- "Pull" - via shortening of kinetochore microtubules

Front 60

What happens during telophase?

Back 60

- Kinetochore tubules become extinct
- Polar tubules still elongating ("push")
- New nuclear envelope forms (lamin B)
- Nuclear division = karyokinesis

Front 61

What is karyokinesis?

Back 61

Nuclear division (Prophase - Telophase)

Front 62

What happens during cytokinesis?

Back 62

- Cytoplasm divides at the cleavage furrow
- Cleavage furrow is created by a ring of contractile proteins (including actin and myosin)
- Completes cytoplasmic division

Front 63

How does mitosis and meiosis differ in the number of cell divisions and cells created?

Back 63

- Mitosis: 1 cell division --> 2 cells
- Meiosis: 2 cell divisions --> 4 cells

Front 64

How does the number of chromosomes throughout mitosis and meiosis differ?

Back 64

- Mitosis: chromosome number stays the same (diploid, start with 2N --> 4N --> 2N)
- Meiosis: chromosome number is reduced (diploid --> haploid, start with 2N --> 4N --> 2N --> N)

Front 65

How many S-phases are there per division in mitosis vs meiosis?

Back 65

- Mitosis: 1 S-phase per division
- Meiosis: 1 S-phase per 2 divisions (no S-phase in meiosis-2)

Front 66

How does chromosome pairing differ during prophase for mitosis and meiosis?

Back 66

- Mitosis: Normally, no pairing of homologous chromosomes (each daughter cell receives maternal and paternal chromosomes)
- Meiosis: Homologous chromosomes do 'pair' during prophase I

Front 67

How does the number of cross-overs during mitosis and meiosis differ?

Back 67

- Mitosis: no crossovers
- Meiosis: at least 1 crossover per homologous pair

Front 68

When do the centromeres that bind chromatids separate in mitosis vs. meiosis?

Back 68

- Mitosis: Anaphase
- Meiosis: Anaphase II (not anaphase I)

Front 69

How is the genotype of the daughter cells compare to the parental cells in mitosis and meiosis?

Back 69

- Mitosis: daughter cell genotype is identical (conservative)
- Meiosis: daugther cell (gamete) genotype is variable

Front 70

What happens during anaphase I in meiosis? in anaphase II?

Back 70

- Anaphase I - Homologous chromosomes separate
- Anaphase II - chromatids separate

Front 71

How many chromosomes are there in mitosis at S/G2? How many chromatids?

Back 71

4N = 46 chromosomes = 92 chromatids

Front 72

How many chromosomes are there in mitosis at metaphase? How many chromatids?

Back 72

4N = 46 chromosomes = 92 chromatids

Front 73

How many chromosomes are there in mitosis at anaphase? How many chromatids?

Back 73

4N = 92 chromosomes (cells have not yet divided but the sister chromatids have separated) = 92 chromatids

Front 74

How many chromosomes are there in meiosis-1 at S/G2? How many chromatids?

Back 74

4N = 46 chromosomes = 92 chromatids

Front 75

How many chromosomes are there in meiosis-1 at metaphase? How many chromatids?

Back 75

4N = 46 chromosomes = 92 chromatids (chromosomes are lined up in pairs)

Front 76

How many chromosomes are there in meiosis-1 at anaphase? How many chromatids?

Back 76

4N = 46 chromosomes = 92 chromatids (homologous pairs have separated but cell is not divided)

Front 77

How many chromosomes are there in daughter cells of meiosis-1? How many chromatids?

Back 77

2N = 23 chromosomes = 46 chromatids

Front 78

How many chromosomes are there in daughter cells of mitosis? How many chromatids?

Back 78

2N = 46 chromosomes = 46 chromatids

Front 79

How many chromosomes are there in meiosis-2 at anaphase? How many chromatids?

Back 79

2N = 46 chromosomes (because 23 chromosomes have separated into two and the cell has not divided yet) = 46 chromatids

Front 80

How many chromosomes are there in daughter cells of meiosis-2? How many chromatids?

Back 80

N = 23 chromosomes = 23 chromatid

Front 81

In mitosis, how do the daughter cells compare to each other?

Back 81

They are genetically identical (2N)

Front 82

In meiosis, how do the daughter cells compare to each other?

Back 82

Produce gametes with different genotypes (by exploiting heterozygosity)

Front 83

What is Mendel's 1st Law?

Back 83

- Equal segregation of alleles
- When gametes are made, the two allelic copies of each gene, i.e., the maternal and paternal alleles respectively residing on the two homologous chromosomes, separate in a fashion wherein each gamete receives only one allele
- A gamete can receive only one allele or the other, never both, i.e. "equal segregation"

Front 84

What is Mendel's 2nd Law?

Back 84

- Independent Assortment of Alleles
- During gamete formation, alleles of different genes assort independently of each other
- Independent traits are sorted independently of each other

Front 85

When does independent assortment of alleles occur?

Back 85

During meiosis-1 (consequent to metaphase-1)

Front 86

Why is it important to have independent assortment of alleles?

Back 86

To generate genetic diversity

Front 87

What kind of division is meiosis-1?

Back 87

A Reductive Division - chromosome number in 2 daughter cells is reduced by half because the paired homologous chromosomes (each still with 2 chromatids) are apportioned to 2 daughter cells

Front 88

What kind of division is meiosis-2?

Back 88

A Mitotic Division - although there is no S-phase, the centromeres divide at anaphase II and the chromatids are apportioned to the daughter cells (gametes) which then have haploid (N) DNA content

Front 89

What happens during genetic recombination?

Back 89

- Randomly, segments of matching regions of homologous chromosomes break and re-connect
- Mediated by double-stranded DNA breaks
- Then independent assortment occurs at anaphase-1 as crossed-over chromatids independently assort to opposite poles

Front 90

What are recombinant gametes?

Back 90

Products of meiosis with allelic combinations differing from the original haploid cells

Front 91

What are parental gametes?

Back 91

Products of meiosis that have the same allelic combinations as the original haploid cells

Front 92

When does crossing-over occur between chromatids of homologous choromsomes in meiosis?

Back 92

During Zygotene/Pachytene stage of Meisois-1

Front 93

When does independent assortment occur?

Back 93

Following metaphase of meiosis-1 (when paired homologous chromosomes have crossed-over and separate/migrate to opposite poles)

Front 94

What are the benefits of crossing-over besides generating genetic diversity?

Back 94

- Promote proper chromosome segregation by establishing chiasmata
- Chiasmata represent the positions of crossovers

Front 95

What are chiasmata and where do they occur?

Back 95

- Positions of crossovers
- Occur anywhere along the length of a homologous pair
- Occur randomly

Front 96

What is a possible detrimental effect of crossing-over?

Back 96

- Crossing over requires double-stranded breaks (DSBs)
- Chromosome segregation in presence of persistent DSBs results in loss or mis-segregation of entire chromosome arms and can form aneuploid gametes
- Aneuploidy - abnormal number of chromosomes

Front 97

Why is it important for cells to limit crossing-over during vegetative growth and to promote it during meiosis?

Back 97

- Crossing over causes Double-Stranded Breaks (DSBs) which can lead to loss or mis-segregation of chromosome arms or formation of aneuploid gametes
- Associated with birth defects, stillbirths, and cancer susceptibility

Front 98

How does the probability of breaking and crossing-over change as the distance changes between two genes?

Back 98

- As distance between two genes increases, probability of crossing-over increases
- Contrarily, decreased distance leads to decreased probability of crossing-over

Front 99

What are genes called that have a high frequency of crossing over?

Back 99

"Loosely linked"

Front 100

What are genes called that have a low frequency of crossing over?

Back 100

"Tightly linked"

Front 101

Are tightly linked genes close together or far apart?

Back 101

Close together - less likely to crossover

Front 102

Are loosely linked genes close together or far apart?

Back 102

Far apart - more likely to crossover

Front 103

What measurement is used to describe the distance between two genes?

Back 103

1 chromosome map unit = 1 centiMorgan (cM) = 1% frequency of cross-over
1 cM in humans = 1 million bp DNA

Front 104

What structures on a chromosome are the minimal requirements?

Back 104

- Centromere - middle (with accompanying heterochromatin)
- Replication origins
- Telomere - ends

Front 105

What are the ways to stain chromosomes?

Back 105

- Unbanded - only stained, not organized
- G-banded - showing up to 850 discreet chr regions (organized by chr #)
- C-banding - reveals sites of repeats of 174-base pair subunits of alphoid DNA sequences at centromeres - "heterochromatin"

Front 106

What is the role of DNA Polymerase I?

Back 106

Extends DNA 5'-->3'
Can't prime at extreme end so shortening occurs at each replication

Front 107

What is the role of Telomerase?

Back 107

Protects germ cells by adding "TTAGGG" repeats at extreme end

Front 108

What is progeria?

Back 108

- Premature aging
- Associated with shortened telomeres (not causative though)

Front 109

What are aneuploidies?

Back 109

Chromosomal disorderes (aneuploidies) - too much or too little, but nearly always deleterious consequences

Front 110

What chromosome abnormality is associated with Down Syndrome?

Back 110

Trisomy of chromosome 21 (some partial trisomy 21 causes a mosaic)

Front 111

What are the clinical and cognitive characteristics of someone with a trisomy 21?

Back 111

- Down Syndrome
- Severe mental retardation
- Hypotonia (decreased muscle tone)
- Epicanthic folds (skin fold of upper eyelid)
- Flat occiput (back of head)
- Short, broad hands with simian crease
- Large, furrowed tongue
- AV canal defects (septum between atria and ventricle), ASD, VSD
- Duodenal atresia (incomplete closing of duodenum)

Front 112

What is the incidence rate of Down Syndrome (trisomy 21)?

Back 112

1/700, but 1% recurrence risk for moms following a +21 birth

Front 113

What percent of Down Syndrome (trisomy 21) cases are due to maternal non-disjunction?

Back 113

95%

Front 114

What are the risks a person with Down Syndrome (trisomy 21) has for other diseases?

Back 114

- 15x higher risk for leukemia
- Higher risk for Alzheimers

Front 115

What percent of patients with Down Syndrome (trisomy 21) have a mixture of normal and +21 cells (mosaicism)? What are the implications of this?

Back 115

1%
- Phenotype may be less severe, depends on proportion and lineage of cells affected
- Results from mitotic non-disjunction
- May involve fetus, chorion or both

Front 116

What are the special educational/medical needs of someone with Down Syndrome (trisomy 21)?

Back 116

- Patients may do well in structured environment
- Others may be institutionalized

Front 117

What is the chromosome abnormality associated with Patau Syndrome? What is the incidence rate?

Back 117

Trisomy 13 - 1/15,000

Front 118

What are the clinical and cognitive characteristics of someone with a trisomy 13?

Back 118

- Heart defects
- Cleft lip/palate
- Holoprosencephaly (malformed forebrain)
- Other midline defects
- Profound developmental delay
- Prominent heel
- Polydactyly (extra fingers)
- Long-term survival rare

Front 119

What is the chromosome abnormality associated with Edwards Syndrome? What is the incidence rate?

Back 119

Trisomy 18 - 1/8000

Front 120

What are the clinical and cognitive characteristics of someone with a trisomy 18?

Back 120

- Severe heart defects
- Profound developmental delay
- Micrognathia
- Overlapping digits
- Long-term survival rare

Front 121

How do sex chromosome aneuploidies compare to autosomal aneuploidies?

Back 121

Sex chromosome aneuploidies are much less severe due to X chromosome dosage compensation, but infertility and cognitive changes may result

Front 122

What are the implications of a 47-XXX aneuploidy?

Back 122

- No observable phenotype
- Occasional psychiatric disturbances
- Fertile

Front 123

What chromosomal abnormality is associated with Turner Syndrome? What is the incidence rate?

Back 123

45-X
1/2000 live born
99% lost before term

Front 124

Is Turner Syndrome (45-X) associated with the loss of the maternal or paternal sex chromosome?

Back 124

75% due to loss of paternal sex chromosome

Front 125

What are the clinical and cognitive characteristics of someone with Turner Syndrome (45-X)?

Back 125

- Short stature: 4'10" average
- Broad webbed neck from in utero edema
- Absence of menarche
- Oocytes involute prior to birth --> infertile
- Heart defects common
- Intellectual status in normal range, but unique deficit in spatial perception; may be high achieving
- "Hard wiring" of CNS altered

Front 126

What are some treatments for Turner Syndrome (45-X)?

Back 126

- Estrogen, growth hormone treatment may lead to greater stature, secondary sexual characteristics, sexual drive
- Does not restore fertility
- May carry pregnancy following oocyte donation and IVF

Front 127

What chromosomal abnormality is associated with Klinefelter Syndrome? What is the incidence rate?

Back 127

47-XXY (extra X chromosome) - 1/700

Front 128

What are the clinical and cognitive characteristics of someone with Klinefelter Syndrome (47-XXY)?

Back 128

- Tall, feminized features: low androgen, small testes, feminine fat distribution, gynecomastia (breasts)
- Normal IQ, but often difficulty in psycho/social, sexual, work relationships
- Infertile (androgen treatment doesn't help)
- Sterile secondary to immature sperm

Front 129

What kind of treatments can be offered to a patient with Klinefelter Syndrome (47-XXY)?

Back 129

- Androgen treatment (but still infertile)
- Sterile secondary to immature sperm, but can father children by intracytoplasmic sperm injection (ICSI) following testicular biopsy to find islands of XY spermatocytes (i.e. mosaic cells that don't have aneuploidy)

Front 130

What can sex chromosome aneuploidies be tolerated?

Back 130

- For all but one X, most but not the entirety of genes on those X's are inactivated by XIST transcript
- XIST = X-inactivation center
- Small number of genes escape inactivation so that is why there are some abnormal features still

Front 131

How does the increased number of Xs for an aneuploidy effect the patient?

Back 131

- Increasing developmental delay
- Due to extra "dose" of active genes

Front 132

What are the clinical and cognitive characteristics of someone with 47-XYY?

Back 132

- Tall, large canines, fertile
- Impulsive, poor self concept, difficulty controlling anxiety
- More prone to break the law, overrepresented in penal institutions
- Sub-average IQ --> poor peer group choices
- EEG changes (changes in hard wiring of brain)

Front 133

What kind of symptoms are exaggerated regarding patients with 47-XYY?

Back 133

- Unduly sensationalized in press as violent, mostly petty, non-personal crimes
- Not necessarily a "double dose of aggressiveness"

Front 134

How common is the 47-XYY aneuploidy?

Back 134

1/700

Front 135

How does maternal and paternal age affect the occurrence of trisomies?

Back 135

- Female oogenesis initiated before birth - chromosomes remain paired up for decades in dictyotene (prolonged resting phase in oogenesis)
- Predisposes maternal chromosomes to non-disjunction which results in trisomy or monosomy
- Paternal age is not correlated with aneuploidy

Front 136

What is the timeline of meiosis for oogenesis?

Back 136

- Following DNA replication, meiosis I separates maternal from paternal homologues, resulting in 23 chromosomes, each with 2 chromatids
- Meiosis II is arrested in dictyotene
- Meiosis II is completed at fertilization (10-50 years later!)

Front 137

What kind of tests can be done on a fetus to test for aneuploidies?

Back 137

- Amniocentesis at >/= 16 weeks
- Chorionic Villus Samplint at > 9 weeks

Front 138

What are some possible structural rearrangements following two breaks and re-ligation?

Back 138

- Deletions (same chromosome)
- Ring (same chromosome)
- Pericentric inversion (same chromosome)
- Paracentric inversion (same chromosome)
- Reciprocal translocation (on different chromosomes)

Front 139

What is the mechanism of a deletion rearrangement?

Back 139

- Simple two break (ex: Cri-du-chat)
- OR Unequal, staggered crossover between identical repeats --> duplicated and deleted strand

Front 140

What is the chromosomal abnormality in Cri-du-Chat Syndrome?

Back 140

Missing portion of chromosome 5 (5p15.3) due to a simple two break deletion

Front 141

What are the genotypic consequences of deletions (due to spontaneous chromosome breaks)?

Back 141

- Missing genes ("haplo-insufficiency")
- Expression of recessive genes

Front 142

What is a pericentric inversion?

Back 142

- Pericentric inversions include the centromere and there is a break point in each arm
- Leads to duplication of one end, deficiency of other end of chromosome (reversed on other chromatid)
- May be viable

Front 143

What is a paracentric inversion?

Back 143

Paracentric inversions do not include the centromere and both breaks occur in one arm of the chromosome.

Front 144

What is reciprocal translocation?

Back 144

- Two chromosomes swap segments
- Duplication / deficiency gametes possible (as in inversion)
- 1st generation fine phenotypically
- 2nd generation more likely to have a problem

Front 145

What are the two outcomes of reciprocal translocation?

Back 145

- Balanced gametes - may disrupt genes, abnormal phenotype risk about 5-10%
- Unbalanced gametes

Front 146

How can chromosomal abnormalities be diagnosed?

Back 146

Using Fluorescence in situ hybridization (FISH)

Front 147

In prenatal diagnosis, which chromosome specific centromeres are most important to label with contrasting flurochromes?

Back 147

X, Y, 13, 18, and 21

Front 148

How does a graph of maternal age vs frequency of aneuploidy / 1000 births look?

Back 148

- Low occurrence of aneuploidy through age 30
- Starts increasing around 30
- Gets very steep around late 30s

Front 149

What is done in a genomic microarray analysis?

Back 149

- Fluorochrome-labelled human DNA is hybridized to 1000s or millions of individual DNA sequences anchored onto a slide
- Strength of fluorescence at each spot reflects the dosage for that region in the human DNA sample
- Can therefore detect copy number (deletion, duplication/deficiency from unbalanced translocation) of many genomic regions simultaneously

Front 150

How can a microarray be designed to uniformly sample the human chromosomes?

Back 150

- Microarray with 1000 sequences will sample the genome at approx. every 3 million bp
- More than that will exceed the resolution attainable by microscopic cytogenetic analysis (so extremely powerful)

Front 151

Was the public human genome sequenced from one individual or many?

Back 151

Many different individuals = consensus sequence

Front 152

How similar are humans genetically?

Back 152

- 99.9% identical (for humans of the same gender)
- Differences occur through variation in repeat sequences, chromosomal rearrangements, or single base pair sequences changes (mutations, single nucleotide polymorphisms SNPs)

Front 153

How many Single Nucleotide Polymorphisms (SNPs) have been identified?

Back 153

Over 10 million

Front 154

How similar are male and female humans genetically?

Back 154

- 98.5% identical (~1.5% is the approximate size of the Y chromosome)
- However the autosomes and the X chromosomes are still 99.9% identical on average

Front 155

How similar are humans and chimps genetically?

Back 155

- 98.5% identical
- Differences are not uniformly distributed throughout genome, rather, specific small regions in genome can be identified that are more conserved between species while others show greater differences

Front 156

How big is the nuclear genome? the mitochondrial genome?

Back 156

- Nuclear genome = 3.3 billion bp (25,000 genes)
- Mitochondrial genome = 16,600 bp (37 genes)

Front 157

What percentage of the nuclear genome is coding DNA?

Back 157

2.5%

Front 158

What percentage of the nuclear genome is for genes and gene-related sequences? for extragenic DNA?

Back 158

~25% genes and gene-related sequences (although of that only 10% (so 2.5% of total) is coding DNA, the rest is non-coding)
~75% extragenic DNA

Front 159

The rest of the genome that is not "coding DNA" can be separated into what?

Back 159

- Unique or moderately repetitive euchromatin (~70%)
- Highly repetitive regions of heterochromatin (~30%)

Front 160

How is mitochondrial DNA inherited?

Back 160

From maternal side only (no meiosis)

Front 161

How can euchromatin and heterochromatin be distinguished when stained?

Back 161

- Euchromatin - functional, stains lightly
- Heterochromatin - inactive, stains darkly

Front 162

What are the types of tandemly repeated DNA in the human genome?

Back 162

- Megasatellite DNA (hundreds of kb)
- Satellite DNA (100 kb to several Mb)
- Minisatellite DNA (0.1 - 20 kb)
- Microsatellite DNA (< 150 bp)

Front 163

What percent of the nuclear genome is transcribed into a large variety of different RNA molecules?

Back 163

62% - 31% are transcribed from intergenic regions

Front 164

What percent of the nuclear genome contains binding sites for known or currently unknown DNA-binding proteins?

Back 164

19.4%

Front 165

What percent of the nuclear genome is estimated to have a functional role?

Back 165

- 80.4% functional role
- 95% is within 8 kb of a site of protein-DNA interaction that may influence and regulate genome function
- Although this was based on a limited number of cell types so it may be probably that very little if any of genome has no function

Front 166

Does the human genome contain a lot or a little amount of highly repeated DNA sequences? What happens to it?

Back 166

A lot - majority of these are not transcribed

Front 167

Non-coding repetitive DNA is organized into what two major categories?

Back 167

- Tandemly repeated non-coding DNA
- Interspersed repetitive non-coding DNA

Front 168

What kind of repetitive DNA is found at the telomere?

Back 168

Tandem repeats of TTAGGG minisatellite (length = several kb)

Front 169

How are non-coding DNA that is tandemly repeated characterized?

Back 169

- Blocks of repeated sequences
- Can occur at a few or many different locations across all chromosomes
- Grouped into three subclasses based on the avg size of repeat units (satellite, minisatellite, and microsatellite DNA)

Front 170

Where are Satellite tandemly repeated non-coding DNA regions found? How long are the repeats and the blocks?

Back 170

- Primarily in and around the centromeric heterochromatin
- Consists of repeat units containing 5-171 bp
- Repeated extensively forming blocks of 100 kb to several Mb in length

Front 171

Where are minisatellite tandemly repeated non-coding DNA regions found? How long are the repeats and the blocks?

Back 171

- At or near telomeric ends of chromosomes
- Repeat units 6-64 bp in length
- Form blocks up to 20 kb in size

Front 172

Where are microsatellite tandemly repeated non-coding DNA regions found? How long are the repeats and the blocks?

Back 172

- Throughout entire genome, with no usual preference or bias in distribution
- Repeat units 1-4 bp
- Form blocks of less than 160 bp (usually 5-40 repeats)

Front 173

Where are interspersed repetitive non-coding DNA elements found?

Back 173

- Repeat units are not clustered
- Distributed throughout entire genome
- Sequences contain transposable elements and others are capable of undergoing retrotransposition

Front 174

How prevalent are interspersed repetitive non-coding DNA elements?

Back 174

Account for over 1/3 of the entire human genome

Front 175

The majority of the differences in the genome between two humans are from what?

Back 175

Single base changes

Front 176

What is a genetic marker?

Back 176

- An identifiable physical location on a chromosome whose inheritance can be monitored
- Distinguishes two copies (alleles) of a chromosome
- Allows for observation of which allele of a chromosome is inherited from a parent to a child

Front 177

In what kind of analysis are genetic markers used?

Back 177

Linkage analysis - allows the identification of chromosomal regions that are inherited in affected children from each parent

Front 178

What are some types of genetic markers?

Back 178

- RFLPs (Restriction Fragment Length Polymorphisms)
- SSLPs (Simple Sequence Length Polymorphisms)
- SNPs (Single Nucleotide Polymorphisms)
- CNVs (Copy Number Variations)

Front 179

How can restriction fragment length polymorphisms (RFLPs) be used as a genetic marker?

Back 179

- Restriction enzymes cut DNA at specific recognition sequences (usually 4-8bp palindormic sequences)
- Can be in coding or non-coding DNA
- If DNA is digested with enzyme it will generate DNA fragments of various sizes
- If any recognition sequences is mutated, resulting product is of different size since enzyme won't cut there
- Southern blot hybridization with specific probes can detect size difference and use this as a genetic marker

Front 180

How can Short Sequence Length Polymorphisms (SSLPs) (Microsatellite DNA) be used as a genetic marker?

Back 180

- Short repeats of 2, 3, or 4 nucleotides (STR - short tandem repeat)
- Randomly distributed throughout genome
- Different forms (alleles) of marker (microsatellite) can easily be differentiated by size
- Heterozygous individuals have two different products

Front 181

What is the most abundant class of microsatellite repeats? How often do they appear?

Back 181

Dinucleotide repeat of cytosine and adenine (aka "CA repeats"); occur every 30-60 kb corresponding to ~50,000-100,000 microsatellites in 3 billion bp genome

Front 182

What is the variation in length of the microsatellite repeat thought to be caused by?

Back 182

Errors in DNA replication - polymerase machinery may "slip" either eliminating or adding a few repeat units

Front 183

What are the functional consequences of microsatellites?

Back 183

They don't have any for the most part

Front 184

Where are microsatellites most commonly found?

Back 184

In intergenic or intronic portions of a eukaryotic genome

Front 185

How can microsatellites be compared with an assay?

Back 185

- Use PCR followed by gel electrophoresis
- Different numbers of repeats will result in a size difference in PCR products
- Size differences can be identified and distinguished by gel electrophoresis

Front 186

How could assaying of microsatellites be useful as a genetic marker?

Back 186

- For example, mom has two shorter differing lengths of CA repeats and dad has two longer differing lengths of CA repeats
- Look at children's DNA and look at length of CA repeats
- Match up to determine which chromosome it came from (which of moms and which of dads)
- Then you which chromosomes the child inherited from mom and dad

Front 187

How frequent are SNPs in the genome?

Back 187

1/1000bp so over 3 million SNPs when any two genomes are compared

Front 188

How can single nucleotide polymorphisms (SNPs) be used as a genetic marker?

Back 188

- Since they are biallelic (only one of two nucleotides is present in sequence at a particular position) genotyping is significantly easier than microsatellite analyses
- Test for presence or absence of both SNP alleles
- If only one is present then individual is homozygous, if both are present they are heterozygous
- PCR-based (fast)

Front 189

Which is easier, microsatellite or SNP analysis of genetic markers?

Back 189

SNP analysis since they are biallelic (one or the other nucleotides)

Front 190

What is a drawback about SNP genotyping?

Back 190

Only provides information on presence or absence of one particular nucleotide at one particular position in genome

Front 191

What are copy number variants (CNVs)?

Back 191

- Imbalances that alter the diploid status of a locus
- Leads to increases (duplications) or decreases (deletions) in copy number

Front 192

How long are copy number variations (CNVs) usually?

Back 192

- Between 50 bp and >1 Mbp

Front 193

What percentage of the human genome is affected by copy number variations (CNVs)? How many CNVs are found in the average person compared to the reference genome?

Back 193

15% - 12 CNVs exist per individual when compared to reference

Front 194

Do Copy Number Variations (CNVs) have functional consequences?

Back 194

Yes - such as changing expression levels of genes in or near the affected regions, due to positional effects, gene dosage alteration, and disruption or fusion of genes

Front 195

What diseases have been associated with Copy Number Variations (CNVs)?

Back 195

- Alzheimer's disease
- Autism
- Schizophrenia
- Breast cancer
- Obesity
- Developmental delays

Front 196

What are the primary mechanisms that generate Copy Number Variations (CNVs)?

Back 196

- Non-homologous end joining (NHEJ)
- Non-allelic homologous recombination (NAHR)
- Transposition of transposable elements or pseudogenes
- Variable numbers of tandem repeats
- Replication errors bought about by fork stalling or template switching during replication of DNA

Front 197

What kind of genes have are enriched with copy number variants (CNVs)?

Back 197

- Genes involved in immunity and cell-cell signaling
- Genes encoding proteins involved in interaction with the environent (e.g., immune response, perception of smell)
- Retrovirus- and transposition-related protein coding genes

Front 198

What kind of genes have a reduced number of copy number variations (CNVs)?

Back 198

- Genes that encode proteins that mediate their effect via protein-protein interactions
- Dosage-sensitive genes

Front 199

What kind of technologies are used to analyze Copy Number Variations (CNVs)?

Back 199

- Comparative genomic hybridization (CGH)
- Array-based methodologies
- Targeted quantitative PCR (qPCR)

Front 200

Where are a large number of repetitive sequences found?

Back 200

Heterochromatin

Front 201

What are three types of genetic disorders?

Back 201

- Chromosomal
- Monogenic (single-gene)
- Complex (polygenic / multifactorial) disorders

Front 202

How can the characteristic inheritance patterns of genetic disorders be established?

Back 202

Using pedigree analysis

Front 203

Chromosomal disorders are associated with what kind of issues?

Back 203

- Aneuploidy (addition or loss of chromosome(s))
- Deletions or duplications of chromosomal material
- Translocations (balanced and unbalanced) of chromosomal material

Front 204

How do chromosomal disorders appear in the genome

Back 204

- Sporadically during gamete formation
- Inherited

Front 205

How are chromosomal disorders detected?

Back 205

Easily by modern cytogenetic techniques but are often difficult to dissect to individual genes

Front 206

What are chromosomal disorders associated with?

Back 206

History of multiple miscarriages on a pedigree

Front 207

What kind of inheritance patterns do monogenic disorders follow?

Back 207

- Autosomal dominant and recessive
- X-linked dominant and recessive
- Y-linked
- Mitochondrial (maternal)

Front 208

How common are monogenic disorders?

Back 208

Relatively rare: 6-8% of diseases among hospitalized children

Front 209

How can monogenic disorders be identified?

Back 209

Genetic techniques/tests:
- Gene-specific PCR/DNA sequencing or conformational analyses
- Copy Number Variation Analysis
- Whole exome/genome sequencing

Front 210

What kind of mutations cause complex disorders?

Back 210

- Mutations at more than one gene locus (polygenic inheritance)
- A combination of genetic and environmental factors (multifactorial inheritance)

Front 211

What kind of patterns in pedigrees do complex disorders show?

Back 211

- No specific pattern of inheritance
- Shows familial clustering or aggregating (genetic predisposition)

Front 212

What is the recurrence risk for a complex disorder as compared to a monogenic disorder?

Back 212

Much lower for a complex disorder than would be expected for a monogenic disorder based on direct observations from a pedigree

Front 213

Can complex disorders be dissected down to their individual genetic and environmental contributions?

Back 213

Very challenging

Front 214

What is another term for "monogenic" disorders?

Back 214

Mendialian disorders - monogenic disorders follow Mendel's postulates

Front 215

What are Mendel's postulates for inheritance of traits?

Back 215

- Genetic traits are controlled by alleles that exist in pairs in individual organisms
- When two unlike alleles responsible for a single trait are present in a single individual, one is dominant and the other is recessive
- Paired alleles separate in such a way that each gamete is equally likely to contain either member of the pair (principle of segregation)
- Segregating pairs of alleles assort independently of each other (principle of independent assortment)

Front 216

Monogenic disorders exhibit characteristic patterns of inheritance based on what?

Back 216

- Location of gene (chromosomal vs mitochondrial)
- Dominance/recessivity of mutant allele associated with disease

Front 217

What is a medical pedigree?

Back 217

- Graphic representation of family's genetic interrelationships and health problems
- Focuses on a specific diagnosis observed in multiple family members

Front 218

How is a medical pedigree drawn?

Back 218

- Start with proband (affected individual) and immediate relatives expanding downward (offspring), outward (siblings), and upward (parents and past generations)
- Contains information about ethnicity, religious heritage, and country of origin
- Utilizes standard pedigree nomenclature

Front 219

What does the analysis of a medical pedigree do?

Back 219

- Helps obtain additional information about a disease such as mode of inheritance (dominant, recessive, etc) and disease features (age of onset, phenotypic spectrum, etc)
- Information is used to quantify the risk for developing the disease for family members and to guide potential diagnostic procedures

Front 220

What is the common pedigree symbol for a male and a female?

Back 220

- Male - square
- Female - circle

Front 221

How are affected individuals symbolized on a pedigree?

Back 221

- Affected - shaded
- Not affected - white

Front 222

How is a deceased individual symbolized on a pedigree?

Back 222

With a slash through it indicating age and cause of death if known

Front 223

How is the proband identified on a pedigree?

Back 223

An arrow is pointing at their symbol

Front 224

Do the parents of an individual with an autosomal-dominant disorder (monogenic) have the disorder?

Back 224

Must have an affected parent (exception: new mutation arises in parental sperm or ovum)

Front 225

Do the normal children of an individual with an autosomal-dominant disorder (monogenic) have children with the disorder?

Back 225

No, they will have normal offspring (unless partner has disorder)

Front 226

How are males and females affected by an individual with an autosomal-dominant disorder (monogenic)?

Back 226

Equal proportions of males and females get disorder

Front 227

Does the gender of an individual with an autosomal-dominant disorder (monogenic) affect transmission to offspring?

Back 227

No - each sex is equally likely to transmit the condition to male and female offspring

Front 228

Is it likely for every generation to have an affected individual when an autsomal-dominant (monogenic) disorder is in the family?

Back 228

Yes - every generation tends to have an affected individual

Front 229

An affected parent is usually heterozygous or homozygous for an autosomal-dominant disorder? How does this affect their children's probability of getting the disorder?

Back 229

Usually heterozygous:
- Probability for affected child (Heterozygous for mutant allele) is 0.50
- Probability for an unaffected child (homozygous for normal allele) is 0.50

Front 230

The less frequent a mutant allele is in the population, the stronger the likelihood that the affected individuals with an autosomal-recessive disorder are from what kind of parents?

Back 230

Parents from an isolated population ("consanguineous marriage" - same ancestor)

Front 231

What is the genotype of unaffected parents of an affected child with an autosomal-recessive disorder?

Back 231

Both heterozygous for the autosomal recessive allele

Front 232

When two parents are heterozygous for an autosomal recessive disorder, what are the probabilities for the different outcomes of children they could have?

Back 232

- Affected child: 0.25
- Heterozygote (carrier) = 0.50
- Non-carrier = 0.25

Front 233

What is the term to describe males for all X-linked traits?

Back 233

Hemizygous

Front 234

How many versions of an allele do you need for an X-linked dominant disorder?

Back 234

Only one version of a mutant allele is necessary

Front 235

A male with an X-linked dominant disorder can pass it to which of his children?

Back 235

Only daughters, not sons (because he only gives them a Y)

Front 236

Which type of inheritance pattern is never passed from father to son?

Back 236

X-linked disorders (dominant or recessive)

Front 237

If a father has an X-linked dominant disorder and the mother is normal, which of their children will have the disorder?

Back 237

100% of daughters
0% of sons

Front 238

If a mother has an X-linked dominant disorder and the father is normal, which of their children will have the disorder?

Back 238

50% of daughters
50% of sons

Front 239

Which gender is more likely to be affected by an X-linked dominant disorder?

Back 239

Females

Front 240

What is necessary for a female to have an X-linked recessive disorder?

Back 240

Both alleles must be mutant

Front 241

What is necessary for a male to have an X-linked recessive disorder?

Back 241

His only X allele is mutant

Front 242

How can a grandfather affected by an X-linked recessive disorder pass on the disorder?

Back 242

- Daughters are carriers
- Daughters pass to 1/2 of their sons
- So 1/2 of grandsons from daughters are affected

Front 243

Which gender is more likely to be affected by an X-linked recessive disorder?

Back 243

Males

Front 244

How do affected males get X-linked disorders?

Back 244

From mothers

Front 245

If a male has a Y-linked disorder, which of his family member will also be affected?

Back 245

- His father, and grandfather, and so on
- His sons, and their sons, and so on

Front 246

Can a father with a mitochondrial inherited disorder have children with the disorder?

Back 246

No (unless his wife has it too)

Front 247

Can a mother with a mitochondrial inherited disorder have children with the disorder?

Back 247

Yes, all of her children will have it

Front 248

The probability of the realization of one or the other of two mutually exclusive possibilities is calculated how?

Back 248

Sum of their separate possibilities

Front 249

The probability of the realization of two simultaneous things with independent possibilities is calculated how?

Back 249

Product of their separate probabilities

Front 250

In a Punnett square, the vertical columns represent which parent and the horizontal columns represent which parent?

Back 250

- Vertical - mom
- Horizontal - dad

Front 251

What is meant by variable expressivity?

Back 251

- Affected individuals may express all of the symptoms or only a few
- Severity of features may vary

Front 252

What is meant by incomplete penetrance?

Back 252

- Person with an affected dominant allele may not express the disease phenotype (penetrance is usually expressed as a %)
- If they express some of the symptoms it is not incomplete penetrance rather it is variable expressivity

Front 253

What is meant by genetic anticipation?

Back 253

- Members of a pedigree exhibit a progressively earlier age of onset and an increased severity of the disorder in each successive generation
- Basis: expansion of trinucleotide repeats (unstable mutations)

Front 254

When does mosaicism of a disorder come about?

Back 254

- Mutation originated as a somatic mutation during embryogenesis of one of the parents of the affected child
- Two cell types are present, one normal and one containing the mutant allele

Front 255

What determines the severity of a disorder that is a mosaic?

Back 255

- Proportion of cells affected
- Type of cells affected

Front 256

What is a de novo mutation?

Back 256

Mutation originated spontaneously in parental gamete

Front 257

What is Achondroplasia? How common is it?

Back 257

- One of major causes of dwarfism
- 1/10,000 live births
- Close to 85% of all cases are results of new mutations, with both parents having a normal phenotype/genotype

Front 258

Why is the mutant gene for dwarfism so common in the population?

Back 258

High recurrent mutation rate

Front 259

What is meant by a "genetic (locus) heterogeneity"?

Back 259

- Multiple genes when mutated can cause the same phenotype
- Ex: retinitis pigmentosa - at least 45 causative genes known

Front 260

What is meant by lethality?

Back 260

Mutation results in a phenotype associated with premature death

Front 261

What can affect the frequency of a mutant allele?

Back 261

Population characteristics: Founder effect, cultural/geographic isolation
- Increased risk for recessive disorders
- Pedigree may resemble dominant

Front 262

What does the term "syntenic" genes describe?

Back 262

Two genes on the same chromosome

Front 263

What does the term "linked" genes describe?

Back 263

Genes on the same chromosome that are so close that they don't segregate independently

Front 264

What is a polymorphic marker?

Back 264

Contains variation within sequence resulting in several alleles

Front 265

What is the "Lod Score Method" for linkage analysis?

Back 265

- Logarithm of the odds of linkage between two loci is calculated
- Calculated from pedigree data as the log of the ratio of the prob. of observed pedigree assuming linkage w/ a specified recombination fraction q/ to the prob. of observed pedigree assuming no linkage

Front 266

What does a "Lod Score" mean?

Back 266

Logarithm of Odds - measure of the probability that a particular region of the chromosome contains the mutation
+3 or greater = odds of 1000:1 is regarded as evidence of linkage
-2 or less = odds of 1:100 indicates no linkage

Front 267

What are some benefits of genetic testing?

Back 267

- Determine a specific genetic diagnosis
- Give explanation for an otherwise "unexpected problem"
- Guide clinical management/monitoring recommendations
- Opportunity for family planning by defining recurrence risk

Front 268

What factors can improve the success of a linkage study?

Back 268

- Number of family members included in pedigree
- LOD score increases with more people included and with number of affected individuals
- Accuracy of phenotypes for family members in pedigree

Front 269

What is "reverse genetics"?

Back 269

- Start with a phenotype that is in multiple family members
- Linkage analysis to identify a narrow region of an individual chromosome containing the disease-causing mutation
- Mutation identified by positional cloning
- Overall: start with a phenotype and trace it back to the genetic information coding it

Front 270

What is the most frequent lethal genetic disease of childhood? How common is it?

Back 270

Cystic Fibrosis (CF) - 1/3,900 live births in U.S.
(30,000 individuals have CF in U.S.)

Front 271

People of what descent are at higher risk for Cystic Fibrosis (CF)? What are the rates of carriers for various ethnicities?

Back 271

European or Middle-Easter descent at highest risk
- 1 in 25 people of European descent
- 1 in 29 people of Ashkenazi Jewish descent
- 1 in 46 Hispanics
- 1 in 65 Africans
- 1 in 90 Asians

Front 272

What are the symptoms of Cystic Fibrosis?

Back 272

- Respiratory problems
- Problems clearing mucus from airways
- Abnormalities in pancreas, liver, and sweat glands

Front 273

What type of disorder is Cystic Fibrosis (CF)? How is it inherited?

Back 273

- Single gene disorder
- Inherited in an autosomal recessive mode

Front 274

Where is the disease causing mutation that is responsible for Cystic Fibrosis (CF)?

Back 274

- Chromosome 7 in small region on 7q22
- CFTR gene (Cystic Fibrosis Transmembrane Conductance Regulator)

Front 275

What is the CFTR gene for? What is wrong if its mutated?

Back 275

- Cystic Fibrosis Transmembrane Conductance Regulator gene
- Membrane chloride channel responsible for salt balance
- Mutations either impair function of channel or lead to clearance of the channel protein from membrane

Front 276

What is the most common mutation that causes Cystic Fibrosis (CF)?

Back 276

- ΔF508 (deletion of Phe at position 508), but over 120 mutations have been described in CFTR gene
- ΔF508 is most common in individuals of N. European descent (88% of cases in Denmark) but less common in those with Mediterranean ancestry (30% of cases in Turkey)

Front 277

Hungtington's disease is what kind of a disorder? How is it inherited?

Back 277

- Single gene disorder
- Degenerative
- Autsomal dominant

Front 278

What is the rate of people affected by Huntington's Disease?

Back 278

30-70 per 1,000,000 on average, but the following groups have even lower rates:
- South African blacks: 0.6 per 1,000,000
- Japanese and Chines: 3.8 per 1,000,000
- Finland: 5.0 per 1,000,000
- North-American blacks: 15 per 1,000,000

Front 279

What are the symptoms of Huntington's Disease?

Back 279

- Degenerative disorder of brain
- Progressive dementia
- Uncontrolled movement

Front 280

What is the age of onset of Huntington's Disease?

Back 280

Variable: 17-60 years

Front 281

How soon after the age of onset do most people die from Huntington's Disease?

Back 281

On average about 17 years from occurrence of first symptoms

Front 282

Patients with late-onset HD were more likely to inherit HD from which parent?

Back 282

Affected mother

Front 283

Patients who inherit Huntington's disease from their late-onset fathers are more likely to have onset when?

Back 283

Earlier-onset HD

Front 284

Do people in the same family have the same symptoms for Huntington's disease?

Back 284

They could, but there is a variability of symptoms

Front 285

How do scientists explain the variability of symptoms within families?

Back 285

Modifier gene(s) that affect disease severity

Front 286

Why does the manifestation of Huntington's disease differ when the disease allele is inherited from the mother as compared to the father?

Back 286

Differential methylation (inactivation) of individual genes and gene regions in the paternal and maternal germline cells

Front 287

What is an example of two different diseases caused by the same deletion but only differing in whether the deletion was on the maternal or paternal chromosome?

Back 287

- Prader-Willi Syndrome - heterozygous deletion of 15q11 in sperm - maternal imprinting of normal chromosome copy
- Angelman Syndrome - heterozygous deletion of 15q11 in egg - paternal imprinting of normal chromosome copy

Front 288

What may be responsible for the "anticipation" effect noticed in children with Huntington's disease (earlier disease onset than in parents)?

Back 288

Perhaps there is more alert and intense observation of the children for disease symptoms once a parent has been diagnosed (if you're looking for symptoms you'll find them sooner)

Front 289

What mutation is responsible for Huntington's disease?

Back 289

On tip of chromosome 4 (4p16.3)
- Gene - "huntingtin"

Front 290

What is the gene "huntingtin" required for? What happens if it is mutated?

Back 290

- Widely expressed in multiple tissues and required for normal development
- Mutation = Huntington's disease

Front 291

What is the mutation in the gene "huntingtin" like?

Back 291

- Repeat of a (CAG) trinucleotide in the coding region
- Normal individuals: repeated 9-36 times
- HD patients: repeated 37-100 times, expanding polyglutamine tract in protein

Front 292

What are some examples of "triplet expansion" disorders?

Back 292

- Huntington's Disease - repeat of CAG trinucleotide 37+ times causes disease (9-36 times is normal)
- Fragile X syndrome
- Kennedy syndrome
- Myotonic dystrophy
- All are dominant, affect the brain, and a specific threshold can be defined for number of triplet repeats that causes deleterious effects

Front 293

What kind of disorder is Duchenne Muscular Dystrophy? How is it inherited?

Back 293

- Single-gene disorder
- X-linked inheritance

Front 294

What is the timeline for Duchenne Muscular Dystrophy?

Back 294

- Diagnosed before age 3
- Require wheelchair by age 12
- Die before age 20

Front 295

What is Duchenne Muscular Dystrophy? What is usually the cause of death?

Back 295

- Progressive muscular dystrophy
- Death from heart failure and/or smooth muscle failure in digestive and urinary tract

Front 296

What is the disease causing gene for Duchenne Muscular Dystrophy?

Back 296

"Dystrophin" - located on Xp21.2
3rd largest protein (3685 AA)

Front 297

What causes Duchenne Muscular Dystrophy?

Back 297

Deletion or duplication of individual exons (55-65%) but also by spontaneous mutations (22%); Dystrophin protein is completely absent in those with DMD

Front 298

Is there a correlation between the extent of the deletion and the severity of Duchenne Muscular Dystrophy?

Back 298

No correlation

Front 299

What is the protein Dystrophin needed for?

Back 299

- Muscle function
- Possibly Ca2+ release for muscle contraction

Front 300

What are some inconsistencies regarding Duchenne Muscular Dystrophy (DMD) that are not completely explained yet?

Back 300

- 2.5% of heterozygous individuals have symptoms
- Monozygotic twin girls have different phenotypes
- Many DMD patients have muscle fibers that can be strained for the presence of Dystrophin protein
- Germline mosaicism

Front 301

In general, what tissues are affected by Cystic Fibrosis (CF)?

Back 301

Exocrine tissues - tissues that make secretions

Front 302

What are the most frequent organs affected by Cystic Fibrosis (CF)?

Back 302

- Upper and lower respiratory tract
- Pancreas
- Sweat glands
- Reproductive tract
- Hepatobiliary tree

Front 303

What is the classic triad of Cystic Fibrosis (CF)?

Back 303

- Recurrent sinopulmonary disease
- Elevated sweat chloride
- Pancreatic insufficiency

Front 304

When was Cystic Fibrosis (CF) first described? How old was the patient when they died?

Back 304

- 1938 frist described
- Death from malnutrition in infancy

Front 305

What was the first treatment for Cystic Fibrosis (CF)? When did it begin? What else was noted at that time?

Back 305

-1940s
- Pancreatic enzyme replacement
- Recessive inheritance pattern noted

Front 306

What was discovered in the 1950s about Cystic Fibrosis (CF)? What was the median survival at that time?

Back 306

- Sweat salt defect
- Median survival: 12 months

Front 307

When was the "sweat test" for Cystic Fibrosis (CF) developed?

Back 307

1959

Front 308

When was the chloride ion transport defect discovered for Cystic Fibrosis (CF)? At this point, what is the median survival time?

Back 308

- 1981 defect discovered
- Median survival 18 years

Front 309

What happens in 1989 related to Cystic Fibrosis (CF)? At this point, what is the median survival time?

Back 309

- CF gene cloned
- Median survival 25 years

Front 310

By 2005, what is the median survival for Cystic Fibrosis (CF)?

Back 310

~34 years

Front 311

How many new cases of Cystic Fibrosis (CF) are diagnosed each year?

Back 311

1000

Front 312

What is the carrier rate for Cystic Fibrosis (CF)?

Back 312

3-5%

Front 313

90% of people with Cystic Fibrosis (CF) are under what age?

Back 313

35-40 yo (as of 2003)

Front 314

As of 2007, what percent of patients with Cystic Fibrosis (CF) are under 18 years old?

Back 314

~50% less than 18, ~50% greater or equal to 18

Front 315

Which chromosome is the CF gene on?

Back 315

Chromosome 7

Front 316

How is the CFTR (Cystic Fibrosis Transmembrane Receptor) channel for Cl- activated?

Back 316

ATP hydrolysis - moves R subunit out of the way so Cl- can pass through

Front 317

How is CFTR Cl- channel oriented in the membrane?

Back 317

- Must be in outer layer of apical cell pointed in correct direction
- Helps Cl- get out of cell into lumen

Front 318

What is the CFTR Cl- channel important for regulating?

Back 318

Controls reabsorption of Na+ through epithelial channel ; if not regulated excessive reabsorption of Na+ causes excessive reabsorption of H2O

Front 319

What kind of mucus do patients with Cystic Fibrosis (CF) have?

Back 319

Abnormally thick mucus --> complications

Front 320

What are the 6 classes of CFTR mutations?

Back 320

- I - no synthesis (premature stop codon)
- II - defective processing (ΔF508)
- III - disordered regulation
- IV - abnormal conduction
- V - reduced synthesis
- VI - accelerated turnover
- Variable disease severity

Front 321

To change lifespan, what amount of functionality of the Cl- channel do you need?

Back 321

15-20%

Front 322

Heterozygotes for Cystic Fibrosis (CF) mutation have what functionality of the Cl- channel?

Back 322

50% and they are normal

Front 323

What is the pathogenesis of Cystic Fibrosis (CF)?

Back 323

- Defective CF gene
- Leads to defective/deficient CFTR
- Leads to decreased Cl- secretion and increased Na+ absorption
- Leads to bronchial obstruction
- Leads to infection
- Leads to inflammation
- Leads to bronchiectasis (increased widening of bronchioles)

Front 324

What are some respiratory infections that are very common in patients with Cystic Fibrosis (CF)?

Back 324

- Any Staph (65.3%)
- P. aeruginosa (52.5%)
- S. aureus (50.9%)
- MRSA (22.6%)
- H. influenza (16.3%)
- S. maltophilia (12.5%)
- B. cepacia complex (2.8%)

Front 325

If Cystic Fibrosis (CF) patients never are infected by P. aeruginosa or B. cepacia how is their median survival compare to those who have been infected and just the overall median survival?

Back 325

Data from 1991-1995 (but relative trends still important)
- Overall median survival ~30 yo
- Colonized P. aeruginosa ~29 yo
- Colonized B. cepacia ~21 yo
- Never colonized b P.A. or B.C. ~51 yo

Front 326

Cystic Fibrosis (CF) patients with infections have what complications?

Back 326

- Trapping of bacteria in mucus layer
- Biofilm formation
- Excess inflammation
- Poor oxygenation of tissues
- Neutrophil damage

Front 327

In lungs of patients with Cystic Fibrosis (CF) how do they differ?

Back 327

- Shouldn't be able to see bronchi at edges of lungs
- in CF patients can see dilated bronchi much bigger than it should be

Front 328

When lungs are examined of patients with Cystic Fibrosis (CF) how do they look?

Back 328

Covered in pus and mucus from infections

Front 329

What information is used to diagnose someone with Cystic Fibrosis (CF)?

Back 329

- Appropriate clinical symptoms
- Family history
- Sweat chloride / pilocarpine iontophoresis
- CF genotype / gene sequencing
- Nasal potential difference
- Newborn screening

Front 330

How common are the "common" clinical symptoms of Cystic Fibrosis (CF)?

Back 330

- Meconium ileus (blockage of baby's first poop in ileum) - 13%
- Respiratory symptoms - 45%
- Failure to thrive - 27%
- Steatorrhea (fat in poop) - 20%
- Neonatal screening - 11%
- Family history - 15%

Front 331

How is sweating induced for a sweat test (to test for Cystic Fibrosis (CF))?

Back 331

Pilocarpine iontophoresis

Front 332

What is an adequate collection of sweat for a sweat test?

Back 332

>75 mg

Front 333

What do the concentrations of sweat chloride tell you from a sweat test?

Back 333

> 60 mEq/L --> most frequently CF
40-55 mEq/L --> indeterminate
>35 mEq/L in infants --> most likely CF
~1% CF patients have normal Cl- levels

Front 334

How does sweat chloride change with age?

Back 334

Tends to increase with age

Front 335

What can cause a false positive sweat test for Cystic Fibrosis (CF)?

Back 335

- Hypothyroidism
- Hypoadrenalism
- Nephrogenic Diabetes Insipidus
- Severe malnutrition
- Hypoparathyroidism
- Pseudohypoparathyroidism
- Ectodermal dysplasia
- Glycogen Storage Disease
- Severe edema
- Poor collection

Front 336

What is the purpose of the nasal potential difference (NPD) measurement?

Back 336

- Diagnosis of CF usually based on high sweat chloride concentrations, characteristic clinical findings, and/or family history
- Small portion of CF patients, especially those with "mild" mutations of CFTR, have near-normal sweat tests
- In these cases, a useful diagnostic involves measuring the nasal transepithelial potential difference (ie, the charge on the respiratory eithelial surface as compared to interstitial fluid)
- Individuals with CF have a significantly more negative nasoepithelial surface than normal, due to increased luminal Na+ absorption

Front 337

When are most patients diagnosed with Cystic Fibrosis (CF)?

Back 337

< 3 yo, but some are still not diagnosed until 40s!

Front 338

What are the respiratory manifestations seen in patients with Cystic Fibrosis (CF)?

Back 338

- Air trapping and mucus plugging
- Ongoing chronic airway inflammation and bronchitis
- CF exacerbation (cough, sputum, malaise, weight loss)
- 100% of CF patients have chronic or recurrent sinus disease (headache, anosmia, deformity of bony structures, halitosis, etc)
- Nasal polyps in 25% of patients

Front 339

Nasal polyps should prompt suspicion of what?

Back 339

Cystic Fibrosis (CF)

Front 340

What kind of therapy is used for Cystic Fibrosis (CF) patients with sinus disease?

Back 340

Topical coupled with antibiotics

Front 341

Nasal polyps for Cystic Fibrosis (CF) are treated with what?

Back 341

Nasal steroids and anti-inflammatory drugs

Front 342

What kind of implications are there for the liver in patients with Cystic Fibrosis (CF)?

Back 342

- CFTR channels localized to epithelial cells lining biliary ductules
- Extensive, diffuse plugging leads to obstruction and cirrhosis (>25% of patients)
- Elevated liver function tests (5%)
- Portal hypertension leads to hypersplenism and esophageal varices (2%)
- Abnormal mucus in gallbladder leads to cholelithiasis (gallstones) (15%)

Front 343

What kind of implications are there for the pancreas in patients with Cystic Fibrosis (CF)?

Back 343

- Plugging of pancreatic ducts leads to loss of exocrine function (85%)
- Autodigestion of pancreas causes recurrent pancreatitis (2-4%)
- CF related diabetes (12-20%)

Front 344

What happens to the fingers of patients with Cystic Fibrosis (CF)?

Back 344

- Clubbing - changes in distal aspect of digits
- Distal phalangeal depth greater than interphalangeal
- Changes in nailbed angle
- Hypertrophic osteoarthropathy

Front 345

What are the treatments for Cystic Fibrosis (CF)?

Back 345

- Antibiotics
- Airway clearance (help them cough up gunk)
- Nutrition (need to eat 20-50% more calories)
- Anti-inflammatories
- Mucolytics
- Airway surface fluid restoration

Front 346

What is the goal with using antibiotics to treat Cystic Fibrosis (CF)?

Back 346

- Airway sterilization infrequent if not impossible with Pseudomonas
- Goals: reduce bacterial burden to preserve lung function and improve nutrition as well as to delay onset of Pseudomonas

Front 347

What kinds of antibiotics are used for Cystic Fibrosis (CF)?

Back 347

- Oral: anti-staphylococcal or fluoroquinolones
- Intravenous: aminoglycoside + broad spectrum antibiotic for 10-21 days
- Inhaled tobramycin into nebulizer

Front 348

How can nutrition be improved in patients with Cystic Fibrosis (CF)?

Back 348

- Pancreatic enzyme replacement ~85%
- Dosed per units of lipase
- High calorie requirements (~20-50% greater than non-CF)
- Supplements vital especially during growth periods
- Fat soluble vitamin replacement

Front 349

What is the current survival rate for Cystic Fibrosis (CF)?

Back 349

37 years

Front 350

What are the primary causes of death in patients with Cystic Fibrosis (CF)?

Back 350

- Cardiorespiratory (70%)
- Liver disease/failure (2-3%)
- Transplant complication (10%)

Front 351

When is it indicated for a lung transplant for someone with Cystic Fibrosis (CF)?

Back 351

- FEV < 30% predicted (forced expiratory volume)
- Need for supplemental O2
- Increasing need for IV antibiotics
- Poor quality of life
- Do not wait for increased pCO2

Front 352

What are the two types of SNPs?

Back 352

SNPs found in coding sequence and SNPs in introns or intergenic (noncoding) regions; both are equally common

Front 353

What impact do SNPs have?

Back 353

- Majority of SNPs have no discernible function
- Some cause premature stop codons
- Some cause changes in amino acid sequence
- Some cause changes in gene expression (promoter SNPs or SNPs altering regulatory elements)
- Some cause changes in mRNA processing (SNPs that alter sequence of splice sites)

Front 354

For SNPs with no discernible function, how do you know which is the wild-type (original) and which is the "mutant"?

Back 354

It is not easy to tell which is which

Front 355

What is a "transition" mutation?

Back 355

When a purine is substituted for another purine (G, A), or a pyrimidine switched for another pyrimidine (C, T)

Front 356

What is a "transversion" mutation?

Back 356

When a purine is substituted to a pyrimidine or vice versa
(purine - G, A; pyrimidine - C, T)

Front 357

Which are more common, transition or transversion mutations?

Back 357

Transitions (one purine for another, or one pyrimidine for another) are twice as common as transversions

Front 358

How are mutations that cause a loss of function usually inherited?

Back 358

Usually recessive

Front 359

How are mutations that cause a gain of function usually inherited?

Back 359

Usually dominant or co-dominant

Front 360

What is the mutation rate of the human genome?

Back 360

- 2.5 x 10^-8 per bp per generation
- Each new gamete contains ~75 new DNA sequence variants
- In the average lifetime of a human, each base in the genome will have been mutated more than a billion times
- But for any one DNA sequence, only an extremely small fraction of all cells will carry that mutation

Front 361

Which mutations are passed on to offspring?

Back 361

Only mutations in the germline (and even then only a 50% chance of transmission)

Front 362

What influences the "fate" (frequency) of a mutation?

Back 362

- Selection (positive or negative - only acts on mutations that have an effect on reproductive fitness, which is not many)
- Genetic drift
- Migration
- Inbreeding

Front 363

What is genetic drift?

Back 363

- Purely random rise and fall in frequency of a mutation in the population
- Some mutations will be transmitted and others will disappear

Front 364

What frequency is necessary for a mutation to become "permanent" by genetic drift?

Back 364

~10%

Front 365

What does "reproductive fitness" mean?

Back 365

An individual's ability to have children

Front 366

What is "selection"?

Back 366

- When a mutation increases an individual's reproductive fitness = positive selection
- When a mutation decreases an individual's reproductive fitness = negative selection

Front 367

Mutations that have a negative selection, undergo what?

Back 367

- Negative or purifying selection
- Reduces allele frequency in population
- Allele will not be transmitted since individuals have reduced reproductive success

Front 368

Mutations that have a positive selection, undergo what?

Back 368

- Increase in allele frequency
- Allele will be transmitted since individuals have increased reproductive success

Front 369

Are many mutations under selection?

Back 369

No, because they do not affect reproductive fitness negatively or positively (e.g. Alzheimer's disease occurs later in life beyond reproductive years)

Front 370

Why does selection rarely completely eliminate a deleterious allele?

Back 370

- Lower the frequency of a deleterious allele in the population, the more frequently it occurs in heterozygotes, compared to homozygotes
- This makes selection against it increasingly inefficient because the less frequent it becomes, the greater percent of what is left is "protected" in the heterozygous state

Front 371

What happens to the majority of newly occurring mutations?

Back 371

Disappear quickly from the genome / gene pool (because hard to meet 10% frequency threshold by genetic drift)

Front 372

How does migration affect the fate of a mutation?

Back 372

- Migrating and mating between two sub-populations with a different frequency of the allele will result in altered allele frequency for offspring population
- This may potentially add additional sequence variants to gene pool (increase in variation)

Front 373

How does inbreeding affect the fate of a mutation?

Back 373

- The mating of close relatives, eventually leads to complete homozygosity
- This reduces the overall variation in the population
- Leads to an increased chance of recessive disorders

Front 374

What is the Hardy-Weinbert Law?

Back 374

Mendelian segregation of two alleles in a randomly mating population leads to an equilibration distribution of genotypes after one generation

Front 375

How can p, the frequency of the dominant allele (A), be calculated?

Back 375

p = f (A/A) + 1/2 f (A/a)

f (A/A) = frequency of homozygous dominant alleles
f (A/a) = frequency of heterozygosity

Front 376

How can q, the frequency of the recessive allele (a), be calculated?

Back 376

q = f (a/a) + 1/2 f (A/a)

f (a/a) = frequency of homozygous recessive alleles
f (A/a) = frequency of heterozygosity

Front 377

For any "p" and "q" (frequencies of dominant allele, A, and recessive allele, a) how do you determine the genotype frequencies (A/A), (A/a), and (a/a) after one generation?

Back 377

p^2 + 2pq + q^2

p^2 = f (A/A)
2pq = f (A/a)
q^2 = f (a/a)

Front 378

What are haplotypes?

Back 378

Patterns of SNP alleles on a single chromosome (haploid)

Front 379

What is linkage disequilibrium?

Back 379

- The non-random association of SNP alleles at closely linked loci
- Recombination breaks up association

Front 380

In an individual that is heterozygous for two neighboring biallelic SNPs, how many combinations of alleles are present on each of the two chromosome copies if the individual is in linkage equilibrium?

Back 380

- Four combinations are possible (and present in population at significant frequencies)
- Allele 1 of SNP1 with allele 1 of SNP2
- Allele 1 of SNP1 with allele 2 of SNP2
- Allele 2 of SNP1 with allele 1 of SNP2
- Allele 2 of SNP1 with allele 2 of SNP2

Front 381

In an individual that is heterozygous for two neighboring biallelic SNPs, how many combinations of alleles are present on each of the two chromosome copies if the individual is in linkage disequilibrium?

Back 381

- Not all combinations are found in population, rather certain allelic combinations are more likely
- Ex: Allele 1 of SNP1 with allele 1 of SNP2
- & Allele 2 of SNP1 with allele 2 of SNP2

Front 382

How is the extent of linkage disequilibrium between two SNPs determined?

Back 382

By extent of recombination (i.e., the number of recombination events) over successive generations

Front 383

How can all four allelic combinations of two SNPs occur if the mutation resulted from a single mutation event?

Back 383

Recombination

Front 384

What happens to linkage disequilibrium as the SNPs are further apart?

Back 384

Decreasing likelihood of linkage disequilibrium (however there are "LD blocks" scattered throughout genome so LD does not continuously decline with distance)

Front 385

What is the average length of linkage disequilibrium blocks in individuals of North European descent? vs African descent?

Back 385

- N. European - ~60 kb
- African - ~6 kb

Front 386

What is the maximum number of haplotypes (patterns of SNP alleles on a single chromosome)?

Back 386

2^n
n = number of SNPs

Front 387

In regions of high Linkage Disequilibrium, what is the number of haplotypes possible?

Back 387

<< 2^n (which is the max number of haplotypes possible)
n = number of SNPs

Front 388

What are tagSNPs?

Back 388

- Subset of SNPs in a region of high linkage disequilibrium that can be used to predict the haplotype of the rest of the SNPs that were not genotyped
- Hypothetically, you could only genotype 2 TagSNPs to determine all 16 SNPs allele in a LD block!

Front 389

In what regions of the genome can tagSNPs be used to determine haplotypes?

Back 389

In Linkage Disequilibrium blocks, because these regions have far fewer haplotypes observed than theoretically possible (2^n)

Front 390

What can a linkage analysis identify?

Back 390

A region of the genome that contains the mutation responsible for the disease

Front 391

What are linkage analyses most powerful for?

Back 391

Identifying mutations that have a large effect (e.g. single gene disorders or rare disorders that occur only in specific families)

Front 392

If two pieces of DNA are very far apart, what are the chances for recombination between them?

Back 392

50% (independent assortment

Front 393

If two pieces of DNA are very close together, what are the chances for recombination between them?

Back 393

<50%

Front 394

What do the four allele markers represent (A, B, C, and D) for a linkage analysis?

Back 394

- Used 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 always present in affected offspring
- Linkage markers define the region that contains the disease causing mutation

Front 395

What are polygenic disorders?

Back 395

- Disorders influenced by more than one gene
- Environmental factors (nutrition, lifestyle) also influence the phenotype
- Often called "complex traits"

Front 396

What is the purpose of an "association study"?

Back 396

- Determines whether an allele of a SNP is correlated with a disease
- Whether the allele occurs more frequently in individuals who are affected by the disease

Front 397

How do linkage studies and association studies differ in who they sample?

Back 397

- Linkage = family-based
- Association = family-based or unrelated individuals in a population

Front 398

How do linkage studies and association studies differ in how they sample?

Back 398

- Linkage = ~300 STR (short-tandem repeats) markers (genome-wide)
- Association = hundreds of thousands of SNPs (genome-wide) or candidate genes; direct or indirect association

Front 399

How do linkage studies and association studies differ in what kind of disorders they are best suited for?

Back 399

- Linkage = single gene disorders, disorders with large gene effect
- Association = complex disorders (polygenic), moderate individual gene effects, common disorders

Front 400

How do linkage studies and association studies differ in results?

Back 400

- Linkage = identification of linkage region on chromosome
- Association = identification of associated alleles of SNPs

Front 401

How do linkage studies and association studies differ in the frequency of the disorders being studied in the population?

Back 401

- Linkage = rare (except within families)
- Association = common

Front 402

How do linkage studies and association studies differ in inheritance patterns?

Back 402

- Linkage = Mendelian inheritance
- Association = Complex inheritance (disease susceptibility with environmental factors influencing phenotype too)

Front 403

What are the two types of association studies based on participants used?

Back 403

- Case-Control Study
- Population-Based Study

Front 404

What analysis is used for a case-control study?

Back 404

- Select individuals from both categories (disease and control)
- Identify frequency differences between two groups (how many from each category have each allele)
- Use a Chi-square test

Front 405

What analysis is used for a population-based study?

Back 405

- Select individuals randomly from population
- Identify phenotypic differences between genotype groups
- Analyze using a t-test

Front 406

What are the benefits of a population-based study over a case-control study?

Back 406

Population-based study avoids any potential bias or stratification easily possible in a case-control study

Front 407

What are the two types of association studies based on SNPs used?

Back 407

- Direct Association Study - catalog and test all functional SNPs (assume that they would directly cause disease when associated)
- Indirect Association Study - use dense map of tagSNPs and test for linkage disequilibrium (site association) (assume that in region of high LD, all other SNPs would be tested indirectly)

Front 408

What is a major limitation of direct association studies?

Back 408

Limited knowledge and public availability of information on functional SNPs

Front 409

How do you select SNPs to study with association studies?

Back 409

- Candidate Gene Studies
- Genome-Wide Association Studies (GWAS)

Front 410

What is wrong with association studies that focus on SNPs in individual candidate genes?

Back 410

- Your study can only be as good as the initial guess about the appropriate candidate gene
- Only studying genes we already know are involved in pathways that are abnormally regulated in a disease
- No discovery of novel candidate genes

Front 411

What is an example of a candidate gene study?

Back 411

- Peroxisome Proliferator-Activated Receptor Gamma (PPARγ) gene
- Candidate gene for diabetes (on chromosome 3)
- Codes for a nuclear hormone receptor
- Over-expression of this gene inhibits insulin release (in mice)

Front 412

What mutation on the Peroxisome Proliferator-Activated Receptor Gamma (PPARγ) gene has been associated with diabetes?

Back 412

- Pro12Ala mutation associated with lower diabetes risk
- 16% frequency
- However, subsequent studies trying to confirm results failed

Front 413

How does the Peroxisome Proliferator-Activated Receptor Gamma (PPARγ) gene work?

Back 413

- Thiazolidinediones (TZDs) act through binding to PPARγ
- This normalizes elevated plasma glucose levels
- Overexpression of this gene in mice inhibits insulin release

Front 414

What are some common problems with candidate gene studies?

Back 414

- Hard to replicate results
- Selection of candidate genes
- Selection of SNPs (comprehensive analysis better than analysis of individual SNPs; use of linkage disequilibrium and haplotypes)

Front 415

What is done in a genome-wide association study (GWAS)?

Back 415

- Selection of a representative set of SNPs to cover the entire genome
- Select informative tagSNPs
- 500,000 - 1,000,000 SNPs are needed for a genome-wide analysis
- Statistical analysis: must correct for number of SNPs tested, so a significant p value is < 5 x 10^-8

Front 416

How do you calculate the actual p value you need for statistical significance?

Back 416

p < 0.05 / (# of SNPs tested)

Front 417

What is an example of a Genome Wide Association Study (GWAS)?

Back 417

- Age-Related Macular Degeneration
- Leading cause of vision loss and blindness among older individuals
- 10% of AMD patients have wet form (new blood vessels form and break beneath retina)
- One SNP showed up as significantly statistic (transcription factor binding site for Heat Shock Serine Protease HTRA1)

Front 418

What are some common problems with Genome Wide Association Studies (GWAS)?

Back 418

- Not always successful in finding a statistically significant SNP with small sample sizes
- Primarily due to statistical problems (such small p value required)
- Even with large sample sizes, results are rarely obtained

Front 419

What are common problems in genetics studies of complex diseases?

Back 419

- Genome-wide analyses are difficult and elaborate
- Phenotype/diseases are often heterogenous (individuals with same symptoms may have different causes of disease and not all individuals have same severity)
- When tagSNPs are used, the ID of "true" causal functional mutations is difficult
- Connection between SNPs/mutations and physiological mechanisms leading to disease is unclear

Front 420

What are two studies that re-sequenced the exons of entire genomes to identify disease-causing mutations for two distinct diseases?

Back 420

- At Univ. of Washington - Miller Syndrome in 4 individuals
- At CHW - Inflammatory Bowel Disease in 15 mo. child

Front 421

What is Miller Syndrome?

Back 421

- Rare autosomal recessive disorder
- Limb malformations, missing toes, cleft palate

Front 422

What was the outcome of the study at the Univ. of Washington that studied the genomes of 4 individuals with Miller Syndrome?

Back 422

- 4 individuals from 3 unrelated families
- Identification of a single gene, DHODH, which encodes a key enzyme in pyrimidine biosynthesis pathway
- Mutation identified was subsequently confirmed in three additional cases

Front 423

What was the outcome of the study at CHW that studied a 15 mo child with a rapidly progressing form of inflammatory bowel disease?

Back 423

- Re-sequenced all exons of his genome
- Identified 27,982 sequence changes
- Ultimately revealed single point mutation in XIAP, gene mutated in a distinct unrelated immune disorder
- Now successfully treated with immune reconsititution