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[[User:Michael|Michael]] ([[User talk:Michael|talk]]) 23:43, 25 October 2014 (EDT)
[[User:Michael|Michael]] ([[User talk:Michael|talk]]) 23:43, 25 October 2014 (EDT)


== Short answer questions on genetics and molecular pathology.  ==
= [[Short answer questions submitted by Tate]]=
 
These are some questions I came up with that are plausible to me... let me know if they are out to lunch.
 
UNIT 1
{{hidden|1. List three differences between DNA and RNA.|<center>[[Microsatellite instability]]</center>}}
{{hidden|2. What are the three stop codons?|<center>[[Microsatellite instability]]</center>}}
{{hidden|3. Where does transcription begin?|<center>[[Microsatellite instability]]</center>}}
{{hidden|4. List three enzymes necessary for transcription and their function. |<center>[[Microsatellite instability]]</center>}}
{{hidden|5. List and describe four post transcription modifications of RNA.|<center>[[Microsatellite instability]]</center>}}
{{hidden|6. List three differences between somatic and germline mutations. |<center>[[Microsatellite instability]]</center>}}
{{hidden|7. What is the difference between a missense and a non-sense mutation?|<center>[[Microsatellite instability]]</center>}}
{{hidden|8. Define a frameshift mutation. |<center>[[Microsatellite instability]]</center>}}
{{hidden|9. Why are inversion mutations difficult to detect?|<center>[[Microsatellite instability]]</center>}}
{{hidden|10. Describe the potential sequelae of a translocation mutation. |<center>[[Microsatellite instability]]</center>}}
 
UNIT 2
{{hidden|1. Translate the following: c.1524_1527delCGTA.|<center>[[Microsatellite instability]]</center>}}
{{hidden|2. List 5 features of SNPs.|<center>[[Microsatellite instability]]</center>}}
{{hidden|3. Define a regulatory SNP and a synonymous SNP?|<center>[[Microsatellite instability]]</center>}}
{{hidden|4. What is the difference between a microstalellite and a minisattelite?|<center>[[Microsatellite instability]]</center>}}
{{hidden|5. Describe Hardy-Weinberg Equilibrium?|<center>[[Microsatellite instability]]</center>}}
{{hidden|6. What factors can disrupt the H-W equilibrium?|<center>[[Microsatellite instability]]</center>}}
{{hidden|7. What is linkage disequilibrium?|<center>[[Microsatellite instability]]</center>}}
 
UNIT 3
{{hidden|1. What are the three major steps of PCR?|<center>[[Microsatellite instability]]</center>}}
{{hidden|2. What is the hallmark of PCR?|<center>[[Microsatellite instability]]</center>}}
{{hidden|3.    What factors affect the method of genotyping chosen?|<center>[[Microsatellite instability]]</center>}}
{{hidden|4.    Define sensitivity, specificity, positive predictive value and negative predictive value. |<center>[[Microsatellite instability]]</center>}}
{{hidden|5.    Define reproducibility and accuracy of an analytical test. |<center>[[Microsatellite instability]]</center>}}
{{hidden|6.    Describe briefly Sanger sequencing.|<center>[[Microsatellite instability]]</center>}}
{{hidden|7.    Describe briefly how Taqman automated genotyping is used for allele detection. |<center>[[Microsatellite instability]]</center>}}
{{hidden|8.    How are DNA microarrays used to identify drug disposition or responses?|<center>[[Microsatellite instability]]</center>}}
 
UNIT 4
{{hidden|1.    Describe the procedure for submitting FFPE slides for KRAS for colorectal cancer.|<center>[[Microsatellite instability]]</center>}}
{{hidden|2.    Compare and contrast uniplex versus multiplex genotyping. |<center>[[Microsatellite instability]]</center>}}
{{hidden|3.    Compare and contrast conventional vs massively parallel sequencing. |<center>[[Microsatellite instability]]</center>}}
{{hidden|4.    What is multiplex ligation-dependent ligation (MLPA)?|<center>[[Microsatellite instability]]</center>}}
{{hidden|5.    What is fragment analysis?|<center>[[Microsatellite instability]]</center>}}
{{hidden|6.  Compare and contrast RT-PCR vs qRTPCR.|<center>[[Microsatellite instability]]</center>}}
{{hidden|7.  What is MSI?|<center>[[Microsatellite instability]]</center>}}
{{hidden|8.  What is methylation analysis?|<center>[[Microsatellite instability]]</center>}}
 
UNIT 5
{{hidden|1.  What are the four test features required to be documented by the CLIA?|<center>[[Microsatellite instability]]</center>}}
{{hidden|2.  What are "in vitro diagnostics" vs "laboratory developed tests"?|<center>[[Microsatellite instability]]</center>}}
{{hidden|3.  What does validation mean? |<center>[[Microsatellite instability]]</center>}}
{{hidden|4.  What are the four performance characteristics that need to be verified for FDA cleared/approved tests?|<center>[[Microsatellite instability]]</center>}}
{{hidden|5.  What are the six performance characteristics that need to be verified for FDA cleared LDTs or modified FDA cleared/approved tests?|<center>[[Microsatellite instability]]</center>}}
 
UNIT 6
{{hidden|1.  List the components of a molecular pathology report.|<center>[[Microsatellite instability]]</center>}}
{{hidden|2.  Define analytical sensitivity and clinical sensitivity. |<center>[[Microsatellite instability]]</center>}}
{{hidden|3.  What should be said in a report of a molecular test on a patient for residual disease if no previous positive assay was confirmed?|<center>[[Microsatellite instability]]</center>}}
{{hidden|4.  Define ammended report versus addendum report.|<center>[[Microsatellite instability]]</center>}}
{{hidden|5.  Whose responsibility is it to sythesize the test results with other clinico-pathological information?|<center>[[Microsatellite instability]]</center>}}
{{hidden|6.  How long are cytogenetic reports required to be kept by CAP?|<center>[[Microsatellite instability]]</center>}}
{{hidden|7,  What is the recommended process to use test results if an assay is not yet validated for clinical use?|<center>[[Microsatellite instability]]</center>}}
{{hidden|8.  Give three examples of "grey areas" which warrant discretion of professionals involved to use a non-validated test?|<center>[[Microsatellite instability]]</center>}}
{{hidden|9.  What reference standard is available for gene nomenclature?|<center>[[Microsatellite instability]]</center>}}
{{hidden|10. Create a table of the most common gene rearrangements associated with heme and soft tissue diseases. |<center>[[Microsatellite instability]]</center>}}
{{hidden|11. What is a "DNA fingerprint" and what can it be used for?|<center>[[A method that examines multiple areas of short tandem repeats to identify paternity, mosaicism, chimerism, and identity in forensics cases]]</center>}}
 
 
Robbins and Cotran Chapter 5 9th Edition:
 
{{hidden|MC cause of spontaneous abortion is ?|<center>[[ A demonstrable chromosomal abnormality.]]</center>}}
 
{{hidden|1% of all newborn infants possess a gross chromosomal abnormality and 5% of people <25y present with  |<center>[[a genetic disease. ]]</center>}}
 
{{hidden|Mutation|<center>[[permanent change in the DNA, if affect germ cells are transmitted to the progeny ]]</center>}}
 
{{hidden|List and describe 4 broad categories of human genetic disorders:|<center>[[Disorders related to mutation sin single genes with large effects i. Usually follow classic Mendelian pattern of inheritance
ii. Often highly penetrant (large proportion of pop with gene has disease)
b. Chromosomal disorders
i. Structural or numerical alterations in autosomes and sex chromosomes
ii. Uncommon, high penetrance
c. Complex multigenic disorders
i. Interactions between multiple variant forms of genes and environmental factors (polymorphisms), poly genic means disease when many polymorphism present
d. Single gene disorders with nonclassic patterns of inheritance (not mendelian)
i. Disorders resulting from triplet repeat mutations
ii. Mutations in mitochondrial DNA
iii. Those influenced by genomic imprinting
iv. Those influenced by gonadal mosaicism]]</center>}}
 
{{hidden|List and describe the possible outcomes of a point mutation in a coding region?|<center>[[a. Missense mutation – pt mutation changes amino acid code, conservative when the amino acid is preserved, non conservative when replaced with another amino acid
b. Nonsense mutation – makes a stop codon ]]</center>}}
 
{{hidden|List and describe the possible outcomes of point mutation or deletion in a non-coding region.|<center>[[a. Promoters/enhancers – interfere with binding of transcription factors, marker reduction or total lack of transcription, b. Introns – defective splicing > failure to make mature RNA > no translation]]</center>}}
{{hidden|List and describe the possible outcomes of deletions and insertions.|<center>[[a. Small coding: not multiple of three = frameshift, if multiple of 3 than add or del amino acids accordingly, often premature stop codon
i. Tay Sachs disease: 4 base pair insertion in Hexosaminidase A gene
{{hidden|List and describe the possible outcomes of trinucleotide repeat mutations.
a. Usually G&C, dynamic and increase during gametogenesis, “RNA stutters”
b. Fragile X – CGG 250-4000, Huntinton’s Disease * See Neuropath Notes
{{hidden|List and describe three examples of inheritance of single gene mutations
a. AD – manifested in the heterologous state, one parent of index case is usually affected, males and females affected and both can transmit condition
i. De novo cases may not have affected parent
ii. Penetrance = fraction of people with gene who have the trait
iii. Variable expressivity = those with mutant gene have variety of phenotypes
iv. Often age of onset is delayed so can reproduce before die from disease
v. Biochem mechanisms
1. Reduced production of a protein or dysfunctional/inactive protein
2. Involved in regulation of complex metabolic pathyway subject to feedback inhibition
3. Key structural proteins (collagen and cytoskeleton of RBC)
a. May be a dominant negative , e.g. osteogenesis imperfecta
4. Gain of function are rare, 2 forms
a. Increased in proteins normal function (excess enzyme activity)
b. Huntinton’s diseas (abn protein accumulates, toxic to neurons)
b. AR
i. Largest category – both alleles at a locus are mutated
1. Expression is uniform, complete penetrance common, early onset, unaffected carrier family members, mostly enzymes
c. X Linked
i. All sex linked, and almost all are recessive , if Y Chromosome affected usually infertile males > no progeny
ii. Male expression b/c hemizygous, daughter carriers with variable phenotype because of lionization of 2nd X e.g G6DP
iii. Dominant . vitamin D resistant rickets]]</center>}}
Stopped at P142
 
Molecular Genetic Diagnosis
1. List three basic molecular diagnostic techniques
a. Karyotyping
b. Southern blot
c. Sanger DNA sequencing
d. Polymerase chain reaction
2. Constitutional vs somatic mutaitons.
Hi Michael, I've started, but mostly just with the questions for now, as I study I will keep working on it. Can you help me, maybe we can make additional discussion pages for each of my "study" exams,e.g. molecular, robbins chapters, cap protocols etc.
Tate
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