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93 Cards in this Set
- Front
- Back
- 3rd side (hint)
What inheritance pattern does the pedigree demonstrate? |
AD |
Every generation affected M = F |
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What inheritance pattern does the pedigree demonstrate? |
AR |
Every OTHER generation affected M = F |
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What inheritance pattern does the pedigree demonstrate? |
XLD 50% risk to offspring of affected females 100% risk to female offspring of affected males No male-to-male (father-to-son) transmission Males = females Examples: one form of Vit. D resistant ricketts,incontinentia pigmenti (lethal in males) |
No dad to son Dad to daughter 100% |
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What inheritance pattern does the pedigree demonstrate? |
XLR Usually only males affected Females are carriers, extremely rarely affected 50% of carrier mom to son (affected) OR daughter (carrier) Examples: hemophilia A & B, Fabry’sdisease |
No dad to son All females carriers (rare disease, probally associated with consanguinity) Affected moms will transmit to son whereas 50% of carrier moms will |
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What inheritance pattern does the pedigree demonstrate? |
Mitochondrial inheritance Maternal transmission only with all offspring affected All offspring of affected females are affected Diseases affect oxidative phosphorylation Examples: Leber’s hereditary optic neuropathy,Kearns-Sayre syndrome, neurodegenerativediseases (related to ATP production) |
Mom to all. Dad to none. |
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The carrier rate of an unaffected child born to a pattern with an AR disease is what percent? |
66% or 2/3 Essentially, you know the kid is not AA. Therefore, he can be one of three possibilities: Aa, Aa, or aa |
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Which does not match? Wilsons & AR CF & AR Cowdens & AD Huntingtons & AR RB & AD |
Huntingtons is AD |
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Which does not match? Wilsons & chromosome 13 Wilsons & ATPase Cowdens & chromosome 10 CF & chromosome 7 Li Fraumeni & 17q13 |
Li Fraumeni is 17p13 (p53) |
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Incontinentia pigmenti pattern of inheritance |
XLD |
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Name the disease and pattern of inheritance |
Angiokeratoma; Fabry's disease: a sphingolipidosis Gene on Xq22, XLR Deficiency of alpha galactosidase A |
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Name the inheritance pattern where 100% of daughters are affected if dad is |
XLD |
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In XLD, dads cannot pass on disease to sons. True or false? |
True |
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Fabry's is an XLD disease associated with Xq22. True or false? |
False. Fabry's is linked to Xq22 but is XLR |
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Hemophilia is: AD AR XLD XLR |
XLR |
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What inheritance pattern shows disease in high energy requiring tissues, such as neural and muscular? |
Mitochondrial. Most of the genes are associated with oxidative phosphorylation. |
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Stop codons |
UAA, UAG, UGA |
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Beta 0 thalassemia is caused by a mutation where? |
Chromosome 11, codon 24 nonsense mutation (CAG to UAG) Note: the alpha chain is on chromosome 16 |
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Li Fraumeni gene |
p53 on 17p13 |
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All offspring of affected moms with mitochondrial mutations will be affected. True or false? |
True |
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Which is matched incorrectly? UAA & stop codon Normal DNA mutation rate & 10e5 CpG & mutation hotspot FAP & 5q21 FAP & cyclin D1 None of the above |
None. In FAP the APC gene of 5q21 shows a nonsense mutation. Without APC, the WNT pathway is activated, which results in increased beta-catenin, cyclin D1 and MYC. |
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Which is not true of FAP? It is the result of APC mutation The WNT pathway is decreased It is related to nonsense mutation on 5q21 It shows increased beta-catenin |
The WNT pathway is increased |
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Define polymorphism |
DNA sequence variation >1% of the population |
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Define mutation |
Any variation in DNA sequence |
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Most mutations are silent. True or false? |
True |
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Disruptions which lead to retained mRNA introns are called __ mutations? |
Splice mutations |
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Name a disease caused by a splice mutation |
HbE |
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A 4 bp deletion or insertion creates a __ mutation. |
Frameshift mutations are the result of insertion or deletion of a number of base pairs NOT a multiple of 3. |
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Blood group O is due to a single base deletion. True or false? |
True |
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Tay-Sachs is due to a 4 bp deletion. True or false? |
False. It is associated with a 4 bp insertion. |
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What disease is associated with insertion of L1 repeat in factor 8? |
Hemophilia A |
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Duchenne muscular dystrophy is associated with gene deletion. True or false? |
True |
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Cystic fibrosis affects 1 in __ Caucasians. The carrier rate is 1 in __. |
Affected: 1/3200 Carrier: 1/30 Gene 7q31.2 |
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Mutation involved in CF? |
Delta F508 of 7q31.2 (CFTR: CF transmembrane regulator) is most common, followed by G524X and G551D. This is involved in NaCl transport. |
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Which of the following unstable trinucleotide repeat diseases is incorrectly matched? Fragile-X syndrome (CGA, 5’UT) Myotonic dystrophy (CTG, 3’UT) Spinocerebellar ataxia, type 1 (CAG –polyglutamine) Friedreich ataxia (GAA, intron 1) |
Fragile X is associated with CGG, not CGA |
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Huntingtons is a progressive and lethal neurodegenerative disease affecting 1 in 10,000 people and usually starts in middle-age. True or false? |
True |
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Huntingtons is NOT: A. Is AD B. Is associated with CAA repeat on 4p16, IT15 C. Is associated with 10 to 26 CAG repeat |
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Why do neurons die in Huntingtons? |
Neuronal cell death may be related to toxic effects of polyglutamine |
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Individuals affected by Huntingtons typically show how many repeats? |
36 to 121 |
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4p16 (IT15) normally has how many CAG repeats? |
<27 |
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Intermediate Huntington alleles show how many CAG repeats? |
Between 27 and 35 36-39 is considered premutation status and 40 or more repeats means the individual WILL be affected |
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Define restriction length polymorphism (RFLP) |
A polymorphism at a restriction enzyme site, producing different allele lengths. In RFLP analysis, the DNA sample is broken into pieces and (digested) by restriction enzymes and the resulting restriction fragments are separated according to their lengths by gel electrophoresis |
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Restriction enzymes __. A. Cut DNA at specific sequences B. Usually recognize 4-8 bp sequence C. Restriction sites are frequently palindromes D. May cut in the recognition site E. All of the above |
E |
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This illustrates what disease by RFLP? |
Sickle cell disease |
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Nucleic acid hybridization is used in what molecular techniques? |
Southern and Northern blots. Both use probes of DNA complemetary to the DNA or RNA of interest. |
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Southern blots detect __ whereas Northern blots detect __. |
DNA: Southern blot RNA: Northern blot |
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Southern and Northern blots are used to screen for multiple diseases simultaneously. True or false? |
False. They use a specific known probe sequence to find a particular mutation of interest. |
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This step-by-step process describes what technique? Cut genomic DNA with restriction enzymes (RFLP). Then separate the DNA fragments by agarose gel electrophoresis . Next, transfer the separated DNA fragments onto a membrane by blotting . Hybridize with radioactively-labeled probes . Expose to XR film |
Southern blot |
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What is the clinical utility of Southern blot? |
Used for mutation detection: Some point mutations Gene deletions and amplifications (dosage) Large insertions in genes Gene rearrangements Sizing polymorphisms Determining methylation status of DNA However, due to disadvantages, PCR is often used instead. |
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What are disadvantagesof Southern blot? |
Requires large amount of high quality DNA Radiation exposure Labor intensive, time-consuming |
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What are disadvantages of Northern blot? |
RNase contamination Prevent by: Gloves, baked glassware Diethylpyrocarbonate (DEPC) RNase inhibitors |
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In Northern blotting, RNase contamination can be prevented by doing/using what? |
Wearing gloves Using baked glassware Diethylpyrocarbonate (DEPC) RNase inhibitors |
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Since the advent of PCR, Northern blots are now primarily used in research. True or false? |
True. It is used to: Detect RNA expression Determine RNA size Quantify RNA expression |
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What are variable number tandem repeats (VNTRs)? |
Repeats of 4-5 bp Highly polymorphic Used in BME profilers |
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How are VNTRs analyzed? |
PCR but Osler says RFLP (w/Southern blotting) too (only PCR is really used, at least at VUMC) |
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What are applications for VNTR? |
Forensics Paternity testing BME monitoring |
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Name the lab test shown |
PCR |
Each cycle doubles the sample |
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What is NOT true of PCR? A. It amplifies DNA up to 35 kb B. It involves multiple cycles of DNA denaturation, primer annealing, and polymerase extension |
C. The plateau effect limits PCR product yield to 1-2 ug/100 ul |
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Essential reagents for PCR does NOT include: A. Template DNA B. Primers (18 to 30 nucleotides long) C. dNTPs D. DNA polymerase (heat stable Taq) E. Mg2+ (1.5 to 3.0 mM) F. Suitable buffer G. Heme H. All are essential |
All are essential |
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PCR is very sensitive to [Mg]. True or false? |
True |
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What is the difference in expected PCR outcome if using 3.0 mM magnesium as opposed to 1.5? |
Greater binding activity at the sacrifice of amplification specificity |
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PCR primers allow for specificity of a particular reaction at allow at 180C temperature. True or false? |
False. PCR annealing temperatures vary based on primer used. |
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PCR annealing temperatures vary based on primer used. True or false? |
True. |
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PCR can be used to assess lymphocyte clonality. True or false? |
True. |
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What lab test converts mRNA into cDNA? |
rtPCR |
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The bright band shows what? |
A clone |
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DNA sequencing requires __. A. dNTPs B. ddNTPs C. PCR D. Electrophoresis E. All of the above |
E. All of the above Procedure: 1. DNA is first PCR amplified 2. Chain termination uses dNTPs (extension) and ddNTPs (lack 3’ hydroxyl, causing termination) 3. These fragments are separated by gelelectrophoresis or by an automated sequencer |
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In DNA sequencing ddNTPs are incorporated randomly, resulting in chains of variable length. True or false? |
True |
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In single strand conformation polymorphisms, __. A. single strand DNA curls up & adopts specific conformation B. DNA strands with a single nucleotide difference may adopt a different conformation C. different conformations will migrate to different positions on polyacrylamide gel D. single basepair mutations can be detected E. All of the above |
E. All of the above |
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What is heteroduplex formation? |
A process by which mutant DNA is amplified, mixed with WT-type DNA to form duplexes. The heteroduplexes (mutant plus WT) migrate slower. |
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Heteroduplexes migrate __ on the gel. A. slower B. faster |
A. slower |
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In __ comparison of patient chromosomes to those of a normal control occurs via fluor labeled DNA hybridization to normal 46 X,Y metaphase chromosomes. Gains (e.g., amplification) will show increase in fluorescence, losses (e.g., deletion) will show decrease in fluorescence. It can use microarrays to increase speed and ability to detect smaller chromosomal alterations. |
Comparative Genome Hybridization (CGH) |
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Comparative Genome Hybridization (CGH) can use microarrays to increase speed and ability to detect smaller chromosomal alterations. True or false? |
True |
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Microarray uses wells with probes. True or false? |
True |
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In microarray, the probes can be targeted to both gene or mRNA of interest. True or false? |
True. In microarray immobilization of probes, oligonucleotides ofknown genes (cDNA), or unknown expressed mRNAs (expressed sequence tags, ESTs) are used. |
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What is a common use for microarray? A. To detect gene expression in a particular tumoror other sample B. To detect presence of microorganism DNA C. Discovery of sequence variations D. All of the above. |
D. All of the above. |
A. e.g.: Determining if leukemic patient’s gene profile is that of AML vs. ALL C. e.g., can detect the presence or absence of particular allele |
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Hereditary hemochromatosis is NOT __. A- AD B- associated with C282Y on chromosome 7p C- associated with a protein related to HLA class I proteins and associates with ß2-microglobulin D- associated with a protein thought to regulate transferrin binding to its receptor E- associated with H36D in 5% of cases
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B. It is C282Y but on 6p |
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Hereditary hemochromatosis mutation & chromosome? |
C282Y on 6p |
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BRCA1 is associated with __. A- 17q13 B- Ovarian mucinous cancer C- Ovarian serous cancer D- ER+, PR+ breast cancers E- 80% lifetime risks of breast and ovarian cancer |
A. No. 17q21 B. No, only serous C. Yes. D. No. Breast cancers are typically higher grade, ER/PR negative, and p53 positive. E. No. 80% for breast but 40% for ovary. |
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BRCA2 is on what chromosome? |
13q12 |
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BRCA 1 vs 2 |
1 is on 17q21 and more common overall 2 is on 13q12 is more associated with multiple breast cancers and male breast cancer |
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What is this picture showing? |
Allele specific PCR See hint for more |
An allele specific primer binds mutation of interest Once it transcribes the DNA, the fluor is released |
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In allele specific PCR, both WT and mutant signals are produced. True or false? |
Not sure. The fluor is only released once the DNA is transcribed, which is blocked on the normal allele. So I guess it wouldn't? |
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What is the benefit of rtPCR? |
By analyzing cDNA, you remove introns (100s-1000s) of nucleotides. The smaller the PCR product, the better amplification. |
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The smaller the PCR primer, the less specific. True or false? |
True. For example, a 7 bp primer would bind to thousands of sites in the genome. |
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How can you bypass this disadvantage? |
By doing a 2 PCRs at once where the one amplifies the general region (eliminating the nuclear material for non-specific binding) and the other amplifies the mutation of interest. |
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What is the benefit of allele specific PCR? |
Allele specific PCR allows for a primer to be small and recognize single base pair changes. In conventional PCR, a single base pair difference is not enough. |
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What is DNA polymerase infidelity? |
In PCR, although highly specific primer are used, sometimes you get a small signal at mutation loci due to non-primed DNA polymerase binding. |
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Long face Big ears/jaw/testicles Hyperextensible joints/double jointed thumb MR Social anxiety/ADHD/autism spectrum Symptoms more common in males and tend to accentuate with age |
Fragile X Xq27.3, FMR1 CGG repeats >200 Note: >200 means males WILL be affected Note: normal is less than 44 repeats, grey zone between 45 and 54, and premutation status from 55-199 |
Females with >200 CGG repeats in one allele will be mosiacs, due to random X inactivation |
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Fragile X premutation tremor/ataxia syndrome (FXTAS) |
Neurodegenerative disease that occurs in patients >50 years old in 1/3 of patients with a premutation (55-199 CGG repeats). Symptoms include tremor and cerebellar ataxia & cognitive decline with global cerebral atrophy (Parkinson's-like). More common in males. |
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Fragile X-associated premature ovarian failure (FXPOF) |
More common in female carriers. |
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The premutation carrier frequency is 1 in __. The incidence of fragile X syndrome is 1 in __ males, 1 in __ females. |
250 4000 8000 Premutations predispose the patients to FXTAS and FXPOF |
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CGG expansions only occur from mom to son. Not daughter to son. Not dad to daughter or son. True or false? |
True. This is opposite of the pattern seen in Huntingtons disease. |
The risk of expansion is 5% if the mom has 55 to 59 repeats whereas this risk increases to 31% if it is 70 to 79 (premutation region). If >100, there is a near 100% chance for expansion. |
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CGG repeats in FMR1 cause FMR protein transcription/translation with resulting increased activity. True or false? |
False. This creates CpG islands, which are more prone to inactivation by methylation. The FMR1 protein functions to suppress mRNA translation and appears to bind ~4% of all mRNA. |
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