Difference between revisions of "Libre Pathology talk:Study Group"

From Libre Pathology
Jump to navigation Jump to search
 
(13 intermediate revisions by 2 users not shown)
Line 48: Line 48:
[[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|List three differences between DNA and RNA.|[[DNA (double stranded, thymine, deoxyribose, more stable; RNA single stranded, ribose, uracil]]}}
 
{{hidden|What are the three stop codons?|[UAA, UGA, UAG]]}}
 
{{hidden|Where does transcription begin?|[[promoters at the 5' end  before the coding region]]}}
 
{{hidden|List 2 enzymes necessary for transcription and their function. |[[helicase, polymerase]]}}
 
{{hidden|List and describe three post transcription modifications of RNA.|[[Splicing, cappping, 3'polyadenylation, ]]}}
 
{{hidden| Why is alternative splicing important?|[[Using the basic construction blocks of coding sequences allows a large variety of recombinations, more efficient coding (e.g. creating functions to call))]]}}
 
{{hidden|List three differences between somatic and germline mutations. |<center>[[Somatic: not passed on to progeny, only tumour or particular tissue cells with mutation, Germline: passed onto progeny, all cells have mutation * unless mosaicism or chimerism]]</center>}}
 
{{hidden|What is the difference between a missense and a non-sense mutation?|<center>[[Missense the new base pair does not change the amino acid found in the protein at that location, non-sense changes the amino acid in the protein at that location]]</center>}}
{{hidden|Define a frameshift mutation. |<center>[[deletion of a non-multiple of 3 which causes all further trinucleotide combinations to no longer code for the correct amino acid, often results in a premature stop codon]]</center>}}
{{hidden|Why are inversion mutations difficult to detect?|<center>[[When the are smal, e.g. only a few base pairs]]</center>}}
{{hidden|Describe the potential sequelae of a translocation mutation. |<center>[[when a segment on one chromosome is transferred to another, make a gene non-functional or can result in a fusion gene]]</center>}}
 
===UNIT 2===
{{hidden|Translate the following: c.1524_1527delCGTA.|<center>[[a small deletion  of CGTA between the 1524 and 1527 base pairs]]</center>}}
{{hidden|List 5 features of SNPs.|<center>[[most common DNA sequence variation in humans, must occur in >=1% of a particular population, frequency of SNPs varies by groups, but responsible for >90% of human genetic variation, an can be found in any region of genome]]</center>}}
{{hidden|Define a regulatory SNP and a synonymous SNP?|<center>[[Regulatory SNP: occur in non-coding regions e.g. promoters where they affect mRNA expression and stability, as occur in the splice site where can result in abnormal protein production]</center>}}
{{hidden|What is the difference between a microstalellite and a minisattelite?|<center>[[Microsatellite = stretches of DNA with sequences of 2-4 base pairs repeated a few dozen times (STRP), minisatellite = variable number of tandem repeats 10-100bp in lenght]]</center>}}
{{hidden|Describe Hardy-Weinberg Equilibrium?|<center>[[Mathematical probability function to describe allelic and genotype frequency in a random mating scenario]]</center>}}
{{hidden|What factors can disrupt the H-W equilibrium?|<center>[[non random mating, migration, genetic drift, founder effects, mutation, natural selection]]</center>}}
{{hidden|What is linkage disequilibrium?|<center>[[The closer two genes are together on the chromosome the more likely they are to be found toghether in a population, during meiosis some exchange of material happens between the two chromosomes]]</center>}}
 
===UNIT 3===
{{hidden|What are the three major steps of PCR?|<center>[[denaturing, primer annealing, strand extending]]</center>}}
{{hidden|What is the hallmark of PCR?|<center>[[The cycling at different temperatures, in the presence of key reaction components to traget and exponentially amplify a specific DNA target sequence]]</center>}}
{{hidden|What factors affect the method of genotyping chosen?|<center>[[throughput, type of variants that can be genotyped, equipment and costs, TAT, technical expertise, and multiplex ability]]</center>}}
{{hidden|Define sensitivity, specificity, positive predictive value and negative predictive value. |<center>[[Sensitivity = probability of a positive test in a disease, specificity = probability of a negative dest in a non-diseased patient ]]</center>}}
{{hidden|Define reproducibility and accuracy of an analytical test. |<center>[[Reproducability = probability of the test repeatedly producing the same reults in the same person, Accuracy = the degree to which the observed genotype matches the true genotype]]</center>}}
{{hidden|Describe briefly Sanger sequencing.|<center>[[DIdeoxynucleotides are used in a mix with deoxynucleotides, the Di*** terminate the chain, and so you get all possible lengths of chains so then you put them all in order and you can read (based on weight) which one is at each position]]</center>}}
{{hidden|Describe briefly how Taqman automated genotyping is used for allele detection. |<center>[[Microsatellite instability]]</center>}}
{{hidden|How are DNA microarrays used to identify drug disposition or responses?|<center>[[Microsatellite instability]]</center>}}
 
===UNIT 4===
{{hidden|Describe the procedure for submitting FFPE slides for KRAS for colorectal cancer.|<center>[[Microsatellite instability]]</center>}}
{{hidden|Compare and contrast uniplex versus multiplex genotyping. |<center>[[Microsatellite instability]]</center>}}
{{hidden|Compare and contrast conventional vs massively parallel sequencing. |<center>[[Microsatellite instability]]</center>}}
{{hidden|What is multiplex ligation-dependent ligation (MLPA)?|<center>[[Microsatellite instability]]</center>}}
{{hidden|What is fragment analysis?|<center>[[Microsatellite instability]]</center>}}
{{hidden|Compare and contrast RT-PCR vs qRTPCR.|<center>[[Microsatellite instability]]</center>}}
{{hidden|What is MSI?|<center>[[Microsatellite instability]]</center>}}
{{hidden|What is methylation analysis?|<center>[[Microsatellite instability]]</center>}}
 
===UNIT 5===
{{hidden|What are the four test features required to be documented by the CLIA?|<center>[[Microsatellite instability]]</center>}}
{{hidden|What are "in vitro diagnostics" vs "laboratory developed tests"?|<center>[[Microsatellite instability]]</center>}}
{{hidden|What does validation mean? |<center>[[Microsatellite instability]]</center>}}
{{hidden|What are the four performance characteristics that need to be verified for FDA cleared/approved tests?|<center>[[Microsatellite instability]]</center>}}
{{hidden|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|List the components of a molecular pathology report.|<center>[[Microsatellite instability]]</center>}}
{{hidden|Define analytical sensitivity and clinical sensitivity. |<center>[[Microsatellite instability]]</center>}}
{{hidden|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|Define ammended report versus addendum report.|<center>[[Microsatellite instability]]</center>}}
{{hidden|Whose responsibility is it to sythesize the test results with other clinico-pathological information?|<center>[[Microsatellite instability]]</center>}}
{{hidden|How long are cytogenetic reports required to be kept by CAP?|<center>[[Microsatellite instability]]</center>}}
{{hidden|What is the recommended process to use test results if an assay is not yet validated for clinical use?|<center>[[Microsatellite instability]]</center>}}
{{hidden|Give three examples of "grey areas" which warrant discretion of professionals involved to use a non-validated test?|<center>[[Microsatellite instability]]</center>}}
{{hidden|What reference standard is available for gene nomenclature?|<center>[[Microsatellite instability]]</center>}}
{{hidden|Create a table of the most common gene rearrangements associated with heme and soft tissue diseases. |<center>[[Microsatellite instability]]</center>}}
{{hidden|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 mutations.
 
===Discussion===
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. This is just like LaTEX!!! 
 
:I hope to get a few other ppl involved.  I am just thinking about how to organize the pages. [[User:Michael|Michael]] ([[User talk:Michael|talk]]) 04:52, 14 May 2015 (EDT)

Latest revision as of 13:29, 12 August 2015

Michael's thoughts on the exam

  • I wrote it and passed it in 2012. I also did the American exam the same year and passed that.
  • The pass rate for the FRCPC exam is pretty high.
    • 2009-2011 it was 96+/-3.9% for Canadian medical school grads on their first attempt.

Written

  • I though it was picking at details. Some things are very relevant to practise... other less so.
    • The pocketbook version of Robbins covers most of it.

Practical (slide) exam

  • You should know the answer almost immediately.
    • If you don't know, write something down and move on.
  • It is set to broadly cover everything.
  • If it isn't a spot diagnosis... it should not be on.
  • Somethings are PGY2/PGY3 stuff. One should not overthink things.
  • Anecdotally, the first impression is usually the right one.
    • I think one should stick with the first impression.

Gross exam

  • Go with the most probable if you're uncertain.
  • I worked through the Atlas of Gross Pathology with Histologic Correlation (see Pathology books for the reference).
    • I am not sure this is necessary... but I thought it was useful.
  • Flickr.com/Google images has a lot to offer in this respect.
  • Gross spot diagnosis.

Forensic exam

  • I thought this was tricky... and I liked forensics.
  • Residents that took the exam prior to me said the same.

Cytology exam

  • Some of the cases have several images.
  • I remember being confused... the first three images were from one case. I remember thinking... I have the same diagnosis three times.
  • Like the forensics and gross sections - this section isn't too long. From an exam strategy point-of-view, this makes it less likely that a diagnosis is repeated.

Oral exam

  • I think this is to test if you are safe and useful.
    • By "safe" I mean: knowing your limits and consulting with a colleague when appropriate.
    • By "useful" I mean: you don't need to consult on everything.
  • The examiners ask a pre-determined list of questions.
    • Questions may depend on one another and, in fairness, they are told to redirect you.
      • Example: You see a lung biopsy with hyaline material... and you go down the fibrosis route-- but it is really amyloidosis.
        • The examiners will say something like "how would one work-up suspected amyloid?" or "lets assume this is amyloid..."
  • If you're a Canadian resident, you cannot be examined by someone within your residency program.
  • As far as I know, examiners are told to be stone-faced, i.e. show no emotion.
  • Some of the cases were very straight forward.
  • I didn't think anything was really exotic.

Michael (talk) 23:43, 25 October 2014 (EDT)

Short answer questions submitted by Tate

Retrieved from "https://librepathology.org/w/index.php?title=Libre_Pathology_talk:Study_Group&oldid=39161"