Hereditary Disorders + Molecular Diagnosis of Genetic Disorders (P) Flashcards
During cell division, what is the form of chromosome?
The chromosome during cell division is in its condensed form
What is DNA?
It is a NA in the form of a double-stranded helix
Each strand of DNA is composed of 4 types of what?
Nitrogen bases
What are the nitrogen bases that composes each strand of DNA?
1) Adenine
2) Guanine
3) Cytosine
4) Thymine
What is the most energetically favorable state of DNA?
The double stranded helix
The double stranded helix of DNA is so stable, what are the factors that can lose its conformation?
1) Extreme heat
2) Extreme pH
3) By use of destabilizing agents
What is RNA?
It is a NA that has 3 types
What are the 3 types of RNA?
1) Messenger RNA (mRNA)
2) Ribosomal RNA (rRNA)
3) Transfer RNA (tRNA)
What is mRNA?
It is the transcribed copy of DNA
Where is rRNA found?
It is found in the ribosomes
What is the function of rRNA?
It is involved in the translation of mRNA to protein
What is the function of tRNA?
It carries AAs to ribosome for translation of mRNA to protein
In terms of characteristic, what is the comparison bet DNA and RNA?
RNA is less stable than DNA
What are the reasons why RNA is less stable than DNA?
1) Because it is single stranded
2) The hydroxyl grp (-OH) predisposes susceptibility from alkaline hydrolysis
What does DNA contain?
It contains our genetic info
What is the process (or steps) from DNA to proteins?
1) DNA is transcribed to RNA
2) Then translated to proteins
What is the purpose of reverse transcriptase?
It allows reverse transcription of DNA from RNA
True or False
Some viruses have reverse transcriptase
True
What is the percentage of the human genome that encodes proteins?
< 2%
What is the amt of genes that code for proteins?
20,000 - 25,000 genes
In connection to DNA discovery (or developments w/ regards to DNA), what happened during the ff timelines:
1) 1953
2) 1975
3) 1985
4) 1987
1) Double-stranded DNA
- > beginning of molecular medicine
2) DNA can be sequenced
- > “Book of Life” (human genome) can be read base by base
3) DNA can be amplified w/ PCR
- > DNA diagnostics - unlimited potential
4) Automated DNA sequencing becomes available
- > Critical development for Human Genome Project
In connection w/ Human Genome Project, what happened during the ff timelines:
1) 1990
2) 1991
3) 1995
4) 1996
1) Human Genome Project starts, and first successful gene therapy
- > Modern molecular medicine era
2) Controversy - NIH pts anonymous DNA sequences
- > Commercialization increasingly prominent
3) DNA sequence for 1st model organism (H. influenzae) published
- > Success w/ model organisms fuels enthusiasm for completing human genome
4) NIH policy that human genome sequences are freely available
- > 2 models: public (free) & commercial (user pay)
In connection w/ omics, what happened during the ff timelines:
1) 2000
2) 2003
3) 2007
4) 2010
1) 1st draft of human genome sequence publicly announced
- > complete sequences for fruit fly and a plant are published
2) Annotated final version of human genome sequence are now available
- > beginning of genomics era
3) 1st diploid human genome published
- > beginning of next generation DNA sequencing
4) Alternative fuels & artificial bacterium
- > synthetic biology on the march
What are the 2 most common forms of DNA variations in the human genome?
1) Single-nucleotide polymorphisms (SNPs)
2) Copy number variations (CNVs)
What is the purpose of SNPs?
They represent variation at single nucleotide positions
What are CNVs?
These are form of genetic variation consisting of diff #s of large contiguous stretches of DNA
Approx 50% of CNVs are involve in what?
Gene-coding sequences
Since approx 50% of CNVs involve gene-coding sequences, what is the result of this?
CNVs may underlie a large portion of human phenotypic diversity
What are the characteristics of SNPs?
1) Disease-causing mutations
2) Susceptibility variants
3) Disease modifiers
4) Determinants of response to therapy
5) Neutral variants
How many SNPs are present across humankind?
30M
How many SNPs are present bet any 2 people?
3M
What is epigenetics?
It is defined as heritable changes in gene expression that are not caused by alterations in DNA sequence
What is proteomics?
It concerns itself w/ the measurement of all proteins expressed in a cell or tissue
What is bioinformatics?
It is computer-based techniques that can manage vast collections of data
*What is the function of microRNA and gene silencing?
*Modulate the translation of target mRNAs into their corresponding proteins
Who discovered microRNA?
Andrew Fire and Craig Mello
What is the award of Andrew Fire and Craig Mello?
Nobel prize in Physiology and Medicine
When did Andrew Fire and Craig Mello received their prize?
2006
True or False
A large # of genes do not encode proteins but rather functions in gene regulation
True
*What is the function of the most recently discovered genes?
Code for microRNA
What is the characteristic (in terms of structure) of microRNA?
It is 21 - 30 nucleotides long
What is the function of microRNA?
It do not code for protein but it inhibits gene expression
What are hereditary disorders?
These are derived from one’s parents and are transmitted in the germ line through the generations therefore are familial
What does congenital imply?
It simply implies “born with”
True or False
Genetic disorders are far more common than is widely appreciated
True
What is the estimated frequency of genetic diseases?
670 per 1,000
50% of spontaneous abortuses during the early mos of gestation have a what?
Demonstrable chromosomal abnormality
What are mutations?
These are defined as a permanent change in the DNA
What are the characteristics of mutations?
1) In germ cells, these are transmitted to the progeny
2) In somatic cells, these do not cause hereditary diseases but are important in the genetics of cancers and some congenital malformations
Since in the germ cells, mutations are transmitted to the progeny, hence, mutations can give rise to what?
Inherited diseases
Mutations can result in what?
In partial or complete deletion of a gene or, more often, affect a single base
What are the diff types of mutations?
1) Point mutations within coding sequences
2) Mutations within noncoding sequences
3) Deletions and insertions
4) Trinucleotide-repeat mutations
What are the diff types of point mutations within coding sequences?
1) Missense mutations
2) Nonsense mutations
What are the diff types of missense mutations?
1) Concervative missense mutations
2) Nonconcervative missense mutations
Both deletions and insertions can cause what?
Occurrence of frameshift mutations
What is the characteristic of trinucleotide-repeat mutations?
These mutations are characterized by amplification of a sequence of 3 nucleotides
What are the categories of genetic disorders?
1) Disorders related to mutations in single gene w/ large effects
2) Chromosomal disorders
3) Complex multigenic disorders (polymorphisms)
Mutations and their associated disorders are what?
Highly penetrant
In connection to disorders w/c are related to mutations in single gene, diseases are caused by what?
Single gene mutations
*What is the pattern of inheritance that diseases caused by single gene mutations follow?
The classic Mendelian pattern of inheritance = Mendelian disorders
What are the diff transmission patterns of Mendelian disorders?
1) Autosomal dominant
2) Autosomal recessive
3) X-linked disorders
What are the autosomal dominant disorders that are present in the nervous system?
1) Huntington disease
2) Neurofibromatosis
3) Myotonic dystrophy
4) Tuberous sclerosis
What is the autosomal dominant disorder present in the urinary system?
Polycystic kidney disease
*What is the autosomal dominant disorder present in the gastrointestinal system?
Familial polyposis coli
What are the autosomal dominant disorders present in the hematopoietic system?
1) Hereditary spherocytosis
2) von Willebrand disease
What are the autosomal dominant disorders present in the skeletal system?
1) Marfan syndrome
2) Ehlers-Danlos syndrome (some variants)
3) Osteogenesis imperfecta
4) Achondroplasia
*What are the autosomal dominant disorders present in the metabolic system?
1) Familial hypercholesterolemia
2) Acute intermittent porphyria
*What are the autosomal recessive disorders present in the metabolic system?
1) Cystic fibrosis
2) Phenylketonuria
3) Galactosemia
4) Homocystinuria
5) Lysosomal storage diseases
6) Alpha(sign)1-Antitrypsin deficiency
7) Wilson disease
8) Hemochromatosis
9) Glycogen storage diseases
What are the autosomal recessive disorders present in the hematopoietic system?
1) Sickle cell anemia
2) Thalassemias
What is the autosomal recessive disorder present in the endocrine system?
Congenital adrenal hyperplasia
What are the autosomal recessive disorders present in the skeletal system?
1) Ehlers-Danlos syndrome (some variants)
2) Alkaptonuria
What are the autosomal recessive disorders present in the nervous system?
1) Neurogenic muscular atrophies
2) Friedreich ataxia
3) Spinal muscular atrophy
What is the X-linked recessive disorder present in the musculoskeletal system?
Duchenne muscular dystrophy
What are the X-linked recessive disorders present in the blood system?
1) Hemophilia A and B
2) Chronic granulomatous disease
3) Glucose-6-phosphate dehydrogenase deficiency
What are the X-linked recessive disorders present in the immune system?
1) Agammaglobulinemia
2) Wiskott-Aldrich syndrome
What are the X-linked recessive disorders present in the metabolic system?
1) Diabetes insipidus
2) Lesch-Nyhan syndrome
What is the X-linked recessive disorder present in the nervous system?
Fragile-X syndrome
What are the categories of Mendelian disorders based on pathogenesis?
1) Enzyme defects
2) Defects in membrane receptors
3) Alterations in structure, function, or quantity of non-enzyme proteins
4) Mutations resulting in unusual rxns to drugs
*slide 31: not complete
Answer the ff regarding the given protein type / function:
- 1) What is / are the ex/s
- 2) What is / are the molecular lesions
- 3) What is / are the disease/s
Given protein type / function: Enzyme
(all *)
1) Phenylalanine hydroxylase
2) Splice-site mutation: reduced amount
3) Phenylketonuria
1) Hexosaminidase
2) Splice-site mutation or frameshift mutation w/ stop codon: reduced amt
3) Tay-Sachs disease
1) Adenosine deaminase
2) Point mutations: abnormal protein w/ reduced act
3) Severe combined immunodeficiency
Answer the ff regarding the given protein type / function:
- 1) What is / are the ex/s
- 2) What is / are the molecular lesions
- 3) What is / are the disease/s
Given protein type / function: Enzyme inhibitor
1) Alpha(sign)1- Antitrypsin
2) Missense mutations: impaired section from liver to serum
3) Emphysema and liver disease
Answer the ff regarding the given protein type / function:
- 1) What is / are the ex/s
- 2) What is / are the molecular lesions
- 3) What is / are the disease/s
Given protein type / function: Receptor
1) Low-density lipoprotein receptor
2) Deletions, point mutations: reduction of synthesis, transport to cell surface, or binding to low-density lipoprotein
3) Familial hypercholesterolemia
Answer the ff regarding the given protein type / function:
- 1) What is / are the ex/s
- 2) What is / are the molecular lesions
- 3) What is / are the disease/s
Given protein type / function: Transport
1) NA
2) NA
3) NA
Answer the ff regarding the given protein type / function:
- 1) What is / are the ex/s
- 2) What is / are the molecular lesions
- 3) What is / are the disease/s
Given protein type / function: Oxygen
1) Hemoglobin
2) Deletions: reduced amt
3) Alpha(sign)-Thalassemia
Answer the ff regarding the given protein type / function:
- 1) What is / are the ex/s
- 2) What is / are the molecular lesions
- 3) What is / are the disease/s
Given protein type / function: Oxygen
1) NA
2) Defective mRNA processing: reduced amt
3) Beta(sign)-Thalassemia
Answer the ff regarding the given protein type / function:
- 1) What is / are the ex/s
- 2) What is / are the molecular lesions
- 3) What is / are the disease/s
Given protein type / function: Oxygen
1) NA
2) Point mutations: abnormal structure
3) Sickle cell anemia
Answer the ff regarding the given protein type / function:
- 1) What is / are the ex/s
- 2) What is / are the molecular lesions
- 3) What is / are the disease/s
Given protein type / function: Ions
1) Cystic fibrosis transmembrane conductance regulator
2) Deletions and other mutations: nonfunctional or misfolded proteins
3) Cystic fibrosis
Answer the ff regarding the given protein type / function:
- 1) What is / are the ex/s
- 2) What is / are the molecular lesions
- 3) What is / are the disease/s
Given protein type / function: Structural
1) NA
2) NA
3) NA
Answer the ff regarding the given protein type / function:
- 1) What is / are the ex/s
- 2) What is / are the molecular lesions
- 3) What is / are the disease/s
Given protein type / function: Extracellular
1) Collagen
2) Deletions or point mutations cause reduced amt of normal collagen or normal amts of defective collagen
3) Osteogenesis imperfecta: Ehlers-Danlos syndromes
Answer the ff regarding the given protein type / function:
- 1) What is / are the ex/s
- 2) What is / are the molecular lesions
- 3) What is / are the disease/s
Given protein type / function: Extracellular
1) Fibrillin
2) Missense mutations
3) Marfan syndrome
Answer the ff regarding the given protein type / function:
- 1) What is / are the ex/s
- 2) What is / are the molecular lesions
- 3) What is / are the disease/s
Given protein type / function: Cell membrane
1) Dystrophin
2) Deletion w/ reduced synthesis
3) Duchenne / Becker muscular dystrophy
Answer the ff regarding the given protein type / function:
- 1) What is / are the ex/s
- 2) What is / are the molecular lesions
- 3) What is / are the disease/s
Given protein type / function: Cell membrane
1) Spectrin, ankyrin, or protein 4.1
2) Heterogenous
3) Hereditary spherocytosis
Answer the ff regarding the given protein type / function:
- 1) What is / are the ex/s
- 2) What is / are the molecular lesions
- 3) What is / are the disease/s
Given protein type / function: Hemostasis
1) Factor VIII
2) Deletions, insertions, nonsense mutations, and others: reduced synthesis or abnormal factor VIII
3) Hemophilia A
Answer the ff regarding the given protein type / function:
- 1) What is / are the ex/s
- 2) What is / are the molecular lesions
- 3) What is / are the disease/s
Given protein type / function: Growth regulation
1) Rb protein
2) Deletions
3) Hereditary retinoblastoma
What is the principle and connection bet somatic cells, autosomes, and chromosomes in an individual?
Human somatic cells contain 46 chromosomes, comprise 22 homologous pairs of autosomes and 2 sex chromosomes, XX in the female and XY in the male
What is karyotyping?
It is the study of chromosomes
What is the characteristic of karyotyping?
It is the basic tool of the cytogeneticist
What are the components of short notation for karyotypes?
1) Total # of chromosomes
2) Sex chromosome complement
3) Description of abnormality
What is the short notation (in terms of karyotypes) of male w/ trisomy 21?
47, XY, +21
What are the causes of occurrence of cytogenetic disorders?
1) Due to an abnormal # of chromosomes
2) Due to alterations in the structure of 1 or more chromosomes
What is the normal # of chromosomes?
46, XX or 46, XY
What is euploid?
It is the exact multiple of a haploid
What is aneuploidy?
It not a multiple of 23
What are the exs of cytogenetic disorders?
1) Monosomies
2) Trisomies
What are the diff types of alterations in the structure of 1 or more chromosomes?
1) Deletions
2) Ring chromosome
3) Inversion
4) Isochromosome
5) Translocation
What are the causes of complex multigenic disorders?
1) Interaction bet variant forms of genes and environmental factors
2) Environmental influences modify the phenotypic expression of complex traits
What is polymorphism?
It is a genetic variant that has at least 2 alleles
What is the percentage of population where polymorphisms occur?
These occurs in at least 1% of the population
True or False
DNA-based analysis has become the least powerful tool for the dx of human disease
False, because DNA-based analysis has become a powerful tool for the dx of human disease
Due to the principle of molecular dx of genetic disorders, what are the actions that can be done (benefits)?
1) It is now possible to identify mutations at the DNA lvl and offer diagnostic tests for an increasing # of genetic disorders
2) Molecular tools have become extremely important in discovery of the genetic basis of common complex disorders such as DM, atherosclerosis, and cancer
What are the advantages of molecular dx of inherited diseases at the NA lvl?
1) Molecular assays are remarkably sensitive
2) DNA-based tests are not dependent on a gene product that may be produced only in certain specialized cells
Provide an ex w/ regards to the concept of molecular assays being remarkably sensitive
The use of PCR allows several million-fold amplification of DNA or RNA, making it possible to use as few as 1 or 100 cells for analysis. 0.1 uL of blood or cells scraped from buccal mucosa can supply sufficient DNA for PCR amplification
Provide an ex w/ regards to the concept of DNA-based tests being not dependent on a gene product that may be produced only in certain specialized cells
(E.g. brain) or expression of a gene that may occur late in life. Because the defective gene responsible for inherited genetic disorders is present in germ line sxs, every postzygotic cell carries the mutation
What are the situations where pt may request prenatal genetic analysis?
1) A mother of advanced age (35 yrs >) because of greater risk of trisomies
2) A parent who is a carrier of a balanced reciprocal translocation, robertsonian translocation, or inversion (in these cases the gametes may be unbalanced, and hence the progeny would be at risk for chromosomal disorders)
3) A parent w/ a previous child w/ a chromosomal abnormality
4) A fetus w/ ultrasound-detected abnormalities
5) A parent who is a carrier of an X-linked genetic disorder (to determine fetal sex)
6) Abnormal lvls of AFP, beta(sign)HCG, and estriol performed as the triple test
What are the situations where the pt may request postnatal genetic analysis?
1) Multiple congenital anomalies
2) Unexplained mental retardation and/or developmental delay
3) Suspected aneuploidy (e.g. features of Down syndrome)
4) Suspected unbalanced autosome (e.g. Prader-Willi syndrome)
5) Suspected sex chromosomal abnormality (e.g. Turner syndrome)
6) Suspected fragile-X syndrome
7) Infertility (to rule out sex chromosomal abnormality)
8) Multiple spontaneous abortions (to rule out the parents as carriers of balanced translocation; both partners should be evaluated)
*What are the indications for analysis of germ line genetic alterations (in connection w/ identifying sp molecular genetic signatures for acquired diseases)?
1) Dx and management of cancer
2) Dx and management of infectious disease
What are the mechanisms that are related w/ dx and management of cancer?
1) Detection of tumor-specific acquired mutations and cytogenetic alterations
2) Determination of clonality as an indicator of a neoplastic (e.g. nonreactive) condition
3) Identification of sp genetic alterations that can direct therapeutic choices (e.g. HER2 / Neu in breast cancer or EGFR mutations in lung cancer)
4) Determination of treatment efficacy (e.g. minimal residual disease detection of BCR-ABL1 by PCR in CML)
5) Detection of Gleevec-resistant forms of CML and gastrointestinal stromal tumors
What are the hallmarks of sp tumors?
*Cytogenetic alterations
Provide an ex of hallmark of sp tumors
BCR-ABL1 in chronic myeloid leukemia (CML)
What is the official name of HER2 / Neu?
ERBB2
What are the mechanisms that are related w/ dx and management of infectious disease?
1) Detection of microorganism-specific genetic mat for definitive dx (e.g. HIV, mycobacteria, HPV, herpes virus in CNS)
2) Identification of sp genetic alterations in the genomes of microbes that are associated w/ drug resistance
3) Determination of treatment efficacy (e.g. assessment of viral loads in HIV and hepatitis C virus infection)
True or False
Though DNA replication is conceptually simple, the process is also simple and involves a # of accessory proteins and enzymes
False, because though DNA replication is conceptually simple, the process is complex and involves a # of accessory proteins and enzymes
What are the components that can unwind the DNA?
1) Extreme heat
2) Hydrogen bond disrupters
3) pH outside 4 - 9
What is often used to unwind DNA?
Temp
What is melting?
It is the process of unwinding DNA via the use of temp
What is melting point?
It is the temp at w/c 50% of dsDNA is converted into single stranded DNA
The melting point depends on the amt of what?
Adenine-to-thymine (AT) pair vs the cytosine-to-guanine (CG) pair in the DNA strand
What is the comparison bet AT pair and CG pair?
The AT pair has a weaker bond compared to the CG pair
Since the AT pair has a weaker bond compared to the CG pair, more CG pairs means what?
Higher melting point
What is the function of thermocycler?
It is an equipment that raises and lowers the temp of the sx in cycles w/c is very important in the process of unwinding the DNA
What are the 3 main steps of PCR?
1) Denaturation
2) Annealing
3) Extension
What is denaturation?
It is the unwinding of strands through heat
What is annealing?
It is the attachment of primer to the target segment through a cooler temp
What is extension?
It is the addition of nucleotides to the primer w/ a warm temp
What are the time durations w/ corresponding temp used for each step in PCR?
1) Denaturation: 1 min at 94 DC
2) Annealing: 45 secs at 54 DC
- > forward and reverse primers are used
3) Extension: 2 mins at 72 DC
- > only deoxynucleotide triphosphates (dNTPs) are used
*What are the indirect methods that can be utilized for the detection of DNA mutations?
1) Via the use of restriction enzymes
2) Via the use of fluorescently-labeled nucleotides
3) PCR analysis for short gene segments
4) Via the use of southern blot w/c is used for mutations involving large segments of genetic mat
*What are the molecular methods that can be used for the molecular analysis of genomic alterations?
1) Southern Blotting
2) FISH
3) Array-based Comparative Genomic Hybridization (Array CGH)
What is sickle cell anemia?
It is an inherited RBC disorder
What is the principle of sickle cell anemia?
Normal RBCs are round like doughnuts, and they move through small blood tubes in the body to deliver O2. If these normal RBCs become sickle, these become hard, sticky, and shaped like sickles used to cut wheat. When these hard and pointed RCs go through the small blood tube, they clog the flow and break apart. This can cause pain, damage, and a low blood ct, or anemia
What is the characteristic of sickle cell anemia?
It is a common hereditary hemoglobinopathy that occurs primarily in individuals of African descent
What is the cause of sickle cell disease (or sickle cell anemia)?
It is caused by a point mutation in the 6th codon of beta(sign)-globin that leads to the replacement of a glutamate residue w/ a valine residue
What is the change that is the cause of sickle cell anemia?
The abnormal physiochemical properties of the resulting sickle hgb (HbS)
What are the major pathologic manifestations that underlies the presence of HbS?
1) Chronic hemolysis
2) Microvascular occlusions
3) Tissue damage
In connection to dx, what are the lab findings that are present in CBC and PBS if a pt has sickle cell anemia ?
1) Irreversible sickled cell
2) Reticulocytosis
3) Target-cells
4) Howel-jolly bodies
In connection to dx, what are the other lab findings that are present if a pt has sickle cell anemia?
1) Bone marrow hyperplasia
2) Bone marrow resorption leads to new bone formation
3) Hyperbilirubinemia / pigmented gallstones formation
In connection to dx, what are the lab findings that are present in hgb electrophoresis if a pt has sickle cell anemia?
Presence of HbS
*What are the characteristics of bone resorption leading to new bone formation?
1) “Crew cut” lesions in X-ray of skull
2) Prominent cheek bones
