Define allelic heterogeneity
Different mutations on same gene cause same disease (different mutations at same locus cause similar phenotype)
Which of these organ systems is not effected in CF? a) intestine b) male genital tract c) female genital tract d) hepatobiliary system e) exocrine sweat glands
In CF, what are the 5 molecular consequences that cause the disorder at the CFTR level? Which allele is most common?
- no synthesis, block in processing, block in regulation, altered conductance, reduced synthesis - delta F508 is in 70% of cases- block in processing
What is the difference between dominant and recessive forms of FIGHD (familial isolated growth hormone deficiency)? What happens in dominant negative form?
- dominant: mutations yield altered GH proteins - recessive: reduced GH expression - dominant negative - mutant binds to normal form and inactivates it
Type II Osteogenesis Imperfecta is a dominant negative, perinatal lethal disease that expresses locus heterogeneity. What two mutations at different loci/genes cause this disease?
- COL1A1 on chromosome 17 - COL1A2 on chromosome 7 Alpha 1/Alpha 2 proteins are mutant and lead to protein suicide
Type I Osteogenesis Imperfecta is a less severe, more common form that affects 1/5000 individuals. What mutation causes this disease?
COL1A1 on chromosome 17 that causes loss of expression or rapid degradation of mutant alpha-1; normal collagen formed but only 50% of normal level
Hemophilia A and Hemophilia B express locus heterogeneity. WHy is it important to know the type?
clinically indistinguishable, type affects treatment
In congenital deafness pedigree, why were all children of affected individuals not affected?
They were double heterozygotes - inherited two different mutations that cause same disease (locus heterogeneity)
What is the difference between achondroplasia and diastrophic dwarfism in regards to inheritance pattern?
Achondroplasia - auto dominant, 7/8 cases sporadic Diastrophic dwarfism - autosomal recessive
Charcot-Marie Tooth DZ: CMT1A is autosomal _________ while CMTX is X-linked.
Difference in modes of inheritance in male pattern baldness?
X-linked recessive OR Autosomal dominant (male sex influenced)
when a genetic trait present in a genotype does not manifest the phenotype
Retinoblastoma is an autosomal dominant disorder where 40% of cases are familial. Explain the "two hit" process in RB and why 10% of obligate heterozygotes are non-penetrant
Two hits - need two hits in same cell to cause disease In familial, inherit one of the hits, only need 2nd hit. 10% of carriers never get second hit.
Describe how to incorporate penetrance into probability calculations
Multiple proportion of penetrance (or non-penetrance) by probability of passing gene down in each applicable step
True or false: A disease cannot have both non-penetrance and variable expressivity
False, totally can
While penetrance is ___________, variable expressivity refers to __________
Neurofibromatosis type I (NF1) is autosomal dominant and an example of a disease that shows variable expressivity. Describe symptoms and occurrence/recurrence.
- 1/2 of NF1 are due to spontaneous new mutations - affects 1/3K - most (2/3) only have mild cutaneous involvement - sx include cafe-au-lait spots, lisch nodules, few neurofibromas - mildly affected parent can have a severely affected child - severe: 100s of fibromas, optic gliomas, learning disabilities, HTN, scoliosis, malignancies
Marfan Syndrome is an autosomal dominant connective tissue disease affecting 1/10K-1/20K that exhibits variable expressivity and pleiotropy. Explain.
- all affected individuals in one family have identical mutation in fibrillin gene, but will have different manifestations - Severe: aortic dilatation, pectus scoliosis, ectopia lentis - Mild - mitral valve prolapse, joint laxity, arachnodactyly, myopia - affects skeletal muscle, eye, heart
Diverse effects of a single gene on several organ systems and functions
In Osteogenesis Imperfecta II, all mutations are new mutations. What may be an exception in terms of inheritance?
If homozygous dominant, achondroplasia is _____________
In DMD, rate of loss of alleles in each generation is _____. In achondroplasia this number is ____
Why is the rate of loss for alleles low in Tay Sachs and Cystic fibrosis?
autosomal recessive, affected make up small portion of compared to carriers
In germline mosaicism, a new somatic mutation occurs during embryogenesis in germline progenitor cells of one of parents. The recurrence risk in a family is equal to what?
the proportion of germ cells in parent that carries the mutation
Germline mosaicism plays an important role in recurrence risk in DMD. Describe.
in de novo cases, RR is 1-5% due to possible germline mosaicism. in DMD and hemophilia, spontaneous new mutations cause 10-20% of disease
Huntington's disease is an autosomal dominant disease that is 100% penetrant and affects 1/20K people of European descent. Describe.
Loss of motor control, dementia between 30-50 Delayed age of onset
DNA cleavage by restriction enzymes facilitates isolation and manipulation of genes. The phosphodiester backbone is digested and produces palindromic type based on overhangs: ___, ___, ___
3', 5', blunt end
Nucleic acid hybridization identifies DNA/RNA on basis of binding to complimentary sequences. It is very sensitive, selective, and specific. Probes must be _________
Describe in-situ hybridization
Reveals position of or location of gene on a chromosome, reveals distribution, can be done with intact cell/chrom/tissue
Describe the differences between Southern Blot and Northern Blot
Both are hybridization techniques - Southern Blot - DNA, requires restriction enzyme digestion, can be used for DNA library screening, identification of methylation sites, RFLP genetic analysis, detecting SNPs - Northern Blot - RNA, NOT Quantitative, used to observe gene expression, determine transcript size, map intro/exon positions, identify isoforms
Describe microarray hybridization technique
Glass slides with probes that identify each gene, fluorescently labeled
DNA cloning uses cloning vectors and PCR. What two enzymes are required?
Restriction enzymes and DNA ligase
What are the features required for a vector in DNA cloning? (3)
origin of replication multiple cloning site (restriction sites) ABX resistance gene (selectable marker)
DNA cloning produces two types of DNA libraries. Describe differences.
gDNA - chromosomal DNA, digested then fragments can be cloned cDNA - DNA transcribed to RNA then reverse transcription then DNA cloned
Describe temperature steps for PCR
1) Denaturation (94C) 2) Annealing (depends on primer) 3) Extension (72C)
Real time PCR uses fluorescent probes/dyes to detect and quantify ____ in real time
DNA, if reverse transcriptase used, can quantify mRNA
Which of the following is not a use of PCR? a) genetic testing b) clone gDNA c) forensic/identity screens d) identify translocation
What is analyzed in Western blot and how?
proteins, travel based on molecular weight
Regulated gene expression uses a ______________ to turn genes on and off
miRNA and siRNA both cleaved to mature form by _______
miRNA is _______ expressed while siRNA is ________ expressed
Describe the mechanism of interference by siRNA
dsRNA processed by dicer --> siRNA comes with RISC --> RISC cleaves siRNA duplex --> RISC activated --> RISC guided to target DNA strand and cleaves
What are the four requirements for DNA sequencing?
free 3'OH group, DNA polymerase, primer, template
Describe Sanger sequencing
ddNTPs incorporated to initiation chain termination - no free 3' OH end
How would this gel (result of sequencing) be read?
From bottom up (ATGCT etc)
Describe an antisense molecule
Bind to specific complimentary sequences and inhibit gene expression
Automated sequencing accelerated the human genome project. What is the major limitation of this and how is it overcome?
LIMITATION = only short sequences can be obtained in a single rxn
Overcome by shotgun sequencing - gDNA broken into fragments then sequence rebuilt
Shotgun sequencing leads to creation of genome maps. Describe the difference between genetic and physical maps.
Genetic maps produced by genetic techniques
Physical maps produced by molecular bio techniques
- includes restriction mapping, FISH, and STS mapping (positions of unique sequences)
Genome mapping shows genes and DNA markers such as SNPs, ssLPs and RFLPS. Describe RFLPs.
Restriction Fragment Length Polymorphisms= result from polymorphic restriction sites. Important for genetic testing to indicate disease locus, can analyze via Southern Blot or PCR
Describe homologous recombination in producing transgenic animals
Plasmid vector construct identical except for TK and target gene which produces target locus after homologous recombination. Southern blot will show proteins.
Describe Cre/IoXP use in site specific recombination and conditional gene targeting
Targeted gene floxed in between two recombinase binding sites such as IoxP, Cre is recombinase that can eliminate gene under certain conditions (tissue, time)
Pronuclei injection can also be used to generate transgenic animals. Describe.
Desired gene injected into fertilized egg --> egg implanted
Describe the two components of CRISPR gene editing
Cas9 protein - molecular scissors
guide RNA - guides cas9
Double strand breaks caused by Cas9 can be repaired in two mechanisms. Describe.
Non-homologous end joining = disruption in reading frame of gene of interest
Homology directed repair = sequence of interest flanked by homology arms is knocked in
Describe CRISPR epigenetics
Broken Cas9 coupled to epigenetic modifiers can be used to study how specific modifications affect gene expression and DNA dynamics
Describe gene drive as a result of CRISPR gene editing
gene editing can be used to propagate genetic motif through generations
Cascade testing is a sequence of tests to diagnose a disease or process and starts by identifying what in the affected individual?
Describe three biochemical tests used in neonatal screening
Analytes, NZ assays, protein analysis
Describe 4 cytogenetic tests used in neonatal screening
karyotyping, FISH, CHIPS(microarray), CFF DNA (cell free fetal)
What is the limitation in sequence analysis testing?
Pt may have allelic variant of unknown significance --> until significance is determined, no meaningful risk info can be provided
Why wouldn't an alteration be detected via sequence analysis? (3)
- alteration in region not tested for - alteration due to large deletion - pt does not have mutation
Mutation scanning involves physically testing _____ to confirm presence of mutation before sequencing used to determine exact mutation
exons, reduces amount of DNA that needs to be sequenced
Targeting mutation analysis is used to test for three things. What are they
- presence of specific mutation - specific type of mutation (nucleotide expansion in HD) - set of mutations (panels for CF-microarray)
If targeting mutation analysis is negative, what does this mean?
Pt may still have mutation, should do sequence analysis or mutation scanning
CF exhibits allelic heterogeneity. What percentage of patients have mutation in delta F508?
70%, 28% have 96 common mutations 2% have rare mutations
Quantitative PCR must be used to detect what three things?
1) hetero deletion mutations 2) carriers of auto recessive disorder 3) carriers of X-linked disorder
3-5% of individuals with autism have other chromosomal abnormalities including ___________________, inversions, deletions and duplications
balanced and unbalanced translocations
Which of these would not be used for direct DNA testing? a) Protein electrophoresis b) Southern Blotting c) PCR d) Northern Blotting
a + d
Which of these would not be indicated for use in detecting hemaglobinopathies? a) Northern Blotting b) Southern Blotting c) Protein electrophoresis d) Biochemical assay
c - detects protein changes in charge or size
Which of these methods is not employed in protein detection (changes in protein and structure)? a) Western Blot b) ELISA c) Protein electrophoresis d) Immunohistochemistry
Which of these would not be used in assessing changes in chromosomal number and structure? a) karyotyping b) FISH c) biochemical assays
What would you use to detect promoter defects?
RNA and protein assays
What has northern analysis larger been replaced with?
RT-PCR and chip microarrays
Southern blots uses _________ digestion
True or false - Both Northern and Southern blots require specific labeled probes and can only distinguish LARGE differences
Alleles of VNTR polymorphisms are different sizes. How can these be detected?
What is the most common disease causing mutation in DMD?
2/3 of DMD patients have a deletion of one or more exons (X-chromosome, XLR)
How is disease detected in affected males?
Looking at mutant dystrophin protein via immunofluorescence
Can PCR be used to detect carrier females of DMD? What can be used?
No, can use FISH or Quant PCR. Point mutations can be detected via sequence analysis.
How is allele specific oligonucleotide (ASO) testing used to screen for sickle cell mutation?
ASO labeled (single BP difference causes SCA - Glu6Val) then normal /SCA DNA visualized If + for both normal and SCA gene then carrier
What is the single BP difference that causes sickle cell anemia? What percentage of AAs are carriers? Africans?
Glu6Val in B-globin 10%, 30%
Describe the amino acid changes in SCA and Sickle-C disease
Normal amino acid = Glutamine = negatively charge (travels furthest down gel) SCA = Valine = no charge Sickle-C = Lysine = + charge (travels least)
Thalessemias are caused by globin chain imbalances. Differentiate between the two types
ALpha - no alpha globin Beta- no beta globin
In alpha thalessemia trait, __ (number) copies are lost, and there is a reduced _____ but person is asymptomatic
2, RBC size
In Hemoglobin H disease there is moderate to marked _____ and loss of ___ copies
In alpha thalessemia there is a loss of ___ copies and _______ occurs
all 4, death/hydrops fetalis
In beta thalessemia minor, the heterozygote is asmpytomatic and has ___ mutant allele
In beta thalessemia trait, there are ____ mutant alleles and transfusion is/is not required
In beta thalessemia major, there are ___ mutant alleles and transfusion is/is not required
Hemoglobin lepore occurs when allele of B thalessemia is caused by _________ and is functionally active but expressed at low levels due to fetal promoter
Despite marked molecular heterogeneity, thalessemia molecular defects are limited in each at risk population, and 4-10 mutations account for ________ of dz alleles
What is the appropriate order for molecular genetic testing in thalessemias?
1) target mut analysis 2) mut scanning 3) seq analysis
What is the most common mutation that causes hemophilia?
Unequal crossover between intronic sequences Most likely need to use protein analysis - wont be detected via sequencing or northern blotting
How many skin cells do we lose an hour?
DNA extractions include solvent based, boiling and silica based. Identify key differences.
large dsDNA, high purity, RFLP and PCR used - Solvent based = time consuming, difficult to adapt to automation - SIlica Based = 1 hr per sample, amenable to automation small ssDNA, low purity, PCR used - Boiling - 30 min per sample
What are two characteristics in nuclear DNA used in forensic profiling?
short tandem repeats (STRs) single nucleotide polymorphisms (SNPs)
SNPs are less variable than STRs. Their low mutation rate makes them great for paternity testing. When are they used to analyze DNA?
When DNA is degraded since more abundant than STRs
mtDNA is more abundant than nucDNA but there is less variation. When is mtDNA used over nucDNA?
when nucDNA degraded found on hair shafts, bones and decomposed samples
Fingerprinting process employed by the FBI uses what as CODIS core loci?
13 STR loci and one amelogenin gene (sex-linked)
Variable number tandem repeats can be detected via PCR, sequencing and ________
STR genotyping occurs via
PCR (fluorescently labeled is great!) Allelic size and ID determined with gene mapper ID software. Data presented via allele size and intensity.
What is CODIS?
combined DNA index system, can be used nationally
What are the factors that influence DNA usefulness in profiling?
- rough/smooth surface - time of contact - regularity of contact by others - shedder/nonshedder status - time since last handwash
In which situations would Y-STR profiles be useful?
- vasectomized or azzospermic males in sexual assault - samples with a lot of female DNA - male-male mixtures such as gang rape - body fluid mixes (blood/saliva)
Which is the most polymorphic? a) VNTR b) SSLPs c) STRs d) SNPs
Describe the differences between spirituality and religion
Spirituality - internal to individual, based upon individual experience, quest for meaning or connectedness Religion - organized, based upon collective experiences, holy books, institution
What are FICA questions
- Faith and Belief - Importance - Community (part of religious community, anyone really important to you) - Address (how would you like me to address this in your care)
when is a discussion of spirituality NOT welcome? a) pt is seriously ill and may die b) pt is newly diagnosed with or suffering from serious illness c) pt is newly diagnosed with or suffering from mild illness d) patient is suffering grief over loss e) none of the above - always welcome
Describe the kinetic approach to diagnosing anemia
Mechanism responsible - Decreased production (iron deficiency, bone marrow problem, low erythropoietin) - Increased destruction (hemolysis due to bad transfusion) - Blood loss (trauma, GI bleeding)
DDX is developed based on RBC size then narrowed based on ___________
cell morphology, retic count
What are morphological differences between Reticulocytes and RBCs?
larger, blue tint, lack central pallor
What are morphologies seen in beta thalessemia trait?
target cells, hypochromic, microcytic
Which of these would NOT cause normocytic anemia? a) iron deficiency b) blood loss c) bone marrow suppression d) renal insufficiency e) hyperthyroid
Which of these would NOT cause macrocytic anemia? a) iron deficiency b) alcohol abuse c) folate deficiency d) vitamin b12 deficiency e) liver disease
a) iron deficiency - see in microcytic and normocytic
Hypersegmented neutrophils are seen in what?
What are common sx of anemia?
fatigue, DOE, dizziness, poor feeding in infants, bleeding (heavy menses, melena, hematochesis, hematuria)
What are common physical findings in anemia?
orthostatic HTN, tachycardia, pallor, jaundice, murmur, splenomegaly, liver changes
Which of these would NOT cause microcytic anemia? a) iron deficiency b) cu deficiency c) zn poisoning d) hypothyroid e) thalessemia
d) seen in macro and normo
How can you differentiate between males and females by looking at neutrophils?
Females - barr bodies (drumsticks) behind lobes Males - more lobes
From which blood vessel would you see bright red blood and increased pressure? a) artery b) vein
Monocytes differentiate to what in the following tissues? - brain - liver - lung - peripheral blood
- brain - microglia (CNS immune defense) - liver - Kupffer cells (break down RBC) - lung - alveolar macrophages (clear inhaled particles) - peripheral blood (macrophages)
How can you distinguish between band cells and monocytes
band cells have granules
Differentiate between acid and basic dye
Acidic - tissue is acidophilic, dye(-), binds to cationic groups, stains cytoplasm and connective tissue fibers, eosin Basic - tissue is basophilic, dye(+), binds to anionic groups, hematoxylin
The patient's current medical status, interventions that might improve prognosis, a pro opinion about alternatives, and a recommendation based on best clinical judgement are all needed in _______
Differentiate between intravascular and extravascular hemolysis
- intravascular - within blood vessels - extravascular - occurs within spleeen
What are treatments for beta thalessemia?
splenectomy, iron chelation, stem cell transplant, experimental DNA based therapy
barr bodies in neutrophil - female
plasma cells (tend to be bluer)