Molecular Diagnostics Exam 3 Flashcards
Definition:
All the genes found in a single individual
Human genome
TRUE or FALSE:
Humans have 2 copies of every gene with the exception of some on the X and Y chromosomes
TRUE
Definition:
Genetic DNA composition of an individual
Genotype
Definition:
Physical characteristics of an individual resulting from genotype
Phenotype
Definition:
A change in the sequence of nucleotides in DNA present in a small percentage of the population; usually used to describe rarer genetic changes
Mutation
Definition:
A variance in DNA found in a small percentage of the population. Considered mutations that do not severely affect phenotype.
Polymorphism
Definiton:
Having the proper number of chromosomes per nucleus
Euploid
Definition:
Having other than two of each chromosome, caused by genome mutations.
Aneuploidy
Definition:
The complete set of metaphase chromosomes in a cell
Karyotype
DNA coils up, wraps around proteins called __________
Histones
DNA keeps coiling up and creates ________ and exists as this most of the time.
Chromatin
When do we see chromosomes?
During cell division
What is done to confirm or predict phenotype?
Genotypic analysis
TRUE or FALSE:
Mutations and polymorphisms will always result in a phenotypic change
FALSE
What are the 3 categories of DNA mutations?
-Gene mutation
-Chromosome mutation
-Genome mutation
Definition:
DNA mutation that affects single genes; often small changes in DNA.
Gene mutation
Definition:
DNA mutation that affects the structures of entire chromosomes.
Chromosome mutation
Definition:
DNA mutation that changes the number of chromosomes.
Genome mutation
Label the picture:
1: Telomere
2: p arm
3: Centromere
4: q arm
Definition:
The site of attachment of the chromosome to the spindle
Centromere
Definition:
The end of a chromosome composed of repeated DNA sequences and associated proteins
Telomere
Definition:
The long arm of a chromosome
q arm
Definition:
The short arm of a chromosome
p arm
Chromosome Morphology:
Centromere is in the middle of the chromosome; arms are the same length
Metacentric
Chromosome Morphology:
One arm is longer than the other
Sub-metacentric
Chromosome Morphology:
Centromere is located at one end of the chromosome where the telomere is located
Telocentric
Chromosome Morphology:
One arm is extremely small or missing altogether
Acrocentric
Visualizing Chromosomes:
This stain results in Q band pattern
Fluorescent
Visualizing Chromosomes:
This stain results in G band pattern
Chemical
Visualizing Chromosomes:
Stain that results in R banding; pattern that is opposite of G/Q banding
Giemsa
Visualizing Chromosomes:
Results in C banding
Alkali treatment of chromosomes
Visualizing Chromosomes:
Alkali treatment of chromosomes is used to visualize which part of a chromosome?
Centromere
Basis for genetic nomenclature:
Determine the (?)
17p11.5
Chromosome 17
Region 1
Band 1
Subband 5
Definition:
A method to detect genome mutations, or aneuploidy
Karyotyping
Detection of Chromosomal Mutations:
The exchange of genetic material between chromosomes - may be reciprocal or balanced
Translocation
Detection of Chromosomal Mutations:
Loss of chromosomal material - may be micro/smaller and not easily detected by karyotyping
Deletion
Detection of Chromosomal Mutations:
Gain of chromosomal material
Insertion
Detection of Chromosomal Mutations:
Excision, flipping, and reconnecting chromosomal material within the chromosome
Inversion
Detection of Chromosomal Mutations:
Chromosome containing two copies of the same arm and loss of the other arm
Isochromosome
Detection of Chromosomal Mutations:
Results from deletion of genetic regions from ends of the chromosome and a joining of the ends to form a ring
Ring chromosome
Which of the following is a normal female karyotype result?:
-23, XX
-23, XY
-46, XX
-46, XY
-46, XX
A male patient with down syndrome would have what karyotype analysis result?
47,XY+21
Definiton:
A method used to detect protein, RNA, and DNA structures in place in the cell
FISH - fluorescence in situ hybridization
FISH targets specific sequences of ___________ with fluorescent probes
chromosomes
This type of FISH is commonly used to test prenatal samples, tumors, and hematological malignancies. It is more sensitive than metaphase FISH.
Interphase FISH
Types of probes used in interphase FISH (4)
-Dual-fusion
-Break-apart
-Centrometric
-Telomeric
This type of FISH is commonly used to detect abnormalities that affect multiple chromosomes, detecting small or complex rearrangements.
Metaphase FISH
This type of FISH requires sample prep of 72 hour cell culture
Metaphase FISH
Definition:
A permanent alteration in DNA sequence that affect single genes; usually small changes in DNA sequence but can range from 1 bp to large segments
Gene mutation
Defintion:
Alteration of a single base pair or a few base pairs
Point mutations
Types of point mutations (5)
-Silent
-Conservative
-Non-conservative
-Nonsense
-Frameshift
Types of Point Mutations:
An alteration in the DNA sequence that does not change the amino acid sequence
Silent
Types of Point Mutations:
An alteration in DNA sequence that substitutes and amino acid with one of similar biochemical properties
Conservative
Types of Point Mutations:
An alteration in DNA sequence that results in the substitution of an amino acid with dissimilar biochemical properties
Non-conservative
Types of Point Mutations:
Alteration in DNA sequence that results in the substitution of a stop codon for an amino acid codon
Nonsense
Types of Point Mutations:
Insertion or deletion in DNA sequence that throws the triplet codon out of frame
Frameshift
Types of Point Mutations:
Which point mutations affect the phenotype? (3)
Frameshift
Nonsense
Non-conservative
TRUE or FALSE:
Finding a mutation does not guarantee an altered phenotype
TRUE
4 methods of detection for gene mutations
-Biochemical
-Hybridization based
-Sequencing based
-Enzymatic & chemical cleavage
Detection of Gene Mutations:
Method used to directly analyze the change in protein structure or function rather than searcher point mutations; useful for metabolic defects
Biochemical method
Detection of Gene Mutations:
This type of biochemical method is uses specific antibodies to detect the presence of target molecules.
Enzyme immunoassays (EIA)
Detection of Gene Mutations:
This type of biochemical method detects antigens in cells in tissue specimens using labeled antibodies specific for target antigen
Immunohistochemistry (IHC)
Detection of Gene Mutations:
Labels for this biochemical method may be chromogenic or fluorescent
Immunohistochemistry (IHC)
Detection of Gene Mutations:
This biochemical method measures migration rates of different molecules
High-Performance Liquid Chromatography (HPLC)
Detection of Gene Mutations:
-Molecules are separated
-Bead or particulate solid trap smaller particles
-Separated particles then measured by detector
High-Performance Liquid Chromatography (HPLC)
Detection of Gene Mutations:
Similar to HPLC but the samples are vaporized
Gas Chromatography (GC)
Detection of Gene Mutations:
Molecules are converted to ions that can be moved in a magnetic field based on charge and mass
Mass spectrometry (MS)
Detection of Gene Mutations:
Molecules are identified based on characteristic peaks
Mass spectrometry (MS)
Detection of Gene Mutations:
Method that produces ions by shooting a sample with a laser. The ion flies to the detector at a speed based on charge and mass (“time of flight”).
Matrix-Assisted Laser Desorption/Ionization (MADLI)
Detection of Gene Mutations:
Used to identify high-molecular weight molecules. Used in the micro lab for microorganism identification, sub typing, and antibiotic susceptibility testing. Responsible for decreasing turn-around times in many areas of micro
MALDI-TOF
Detection of Gene Mutations:
Method that includes methods such as Single-Strand Conformation Polymorphism (SSCP)m Allele-Specific Oligomer (ASO) hybridization, Melt-Curve Analysis (MCA), Heteroduplex Analysis, and Array Methods
Hybridization-Based Methods
Detection of Gene Mutations:
Method that includes Sequence-Specific PCR (SSP-PCR)
Sequencing-Based method
Detection of Gene Mutations:
Method that includes Restriction Fragment Length Polymorphisms and Nonisotopic RNAse Cleavage Assay (NIRCA)
Enzymatic and Chemical Cleavage Methods
A system to consistently describe mutations and polymorphisms
Gene Variant Nomenclature
Gene or Protein:
Names are capiltalized and set in italics, no hyphens
Genes
Gene or Protein:
Names are not italicized nor completely capitalized
Proteins
Mutations in germ cells result in (inherited disease/cancer and some congenital malformations)
Inherited disease
Mutations in somatic cells result in (inherited disease/cancer and some congenital malformations)
cancer and some congenital malformations
What can be within genes or outside of genes? Also, when benign, these can be useful for mapping disease genes, identity testing, and determining parentage.
Polymorphisms
Change in phenotype without change in genotype. Do not change primary DNA sequence. Heritable changes in gene expression.
Epigenetic alterations
3 forms of epigenetic alterations
-DNA methylation
-Genomic imprinting
-Chromatic remodeling
Epigenetic alterations:
methyl groups added to DNA which can change the activity of a DNA segment without changing the sequence
DNA methylation
Epigenetic alterations:
Selectively inactivates chromosomal regions
Genomic imprinting
Epigenetic alterations:
Sequesters large regions of chromosomal DNA
Chromatin remodeling
Chromosomal Abnormalities:
Abnormalities in chromosome number
Genome mutations
Chromosomal Abnormalities:
How are genome mutations detected? (3)
Karyotyping, policy analysis by flow cytometry, and FISH
Chromosomal Abnormalities:
Down syndrome and Edward syndrome are examples of which type of chromosomal abnormality?
Genome mutation
Chromosomal Abnormalities:
Abnormalities in chromosome structure. Structural mutations require breakage and reunion of DNA.
Chromosome mutation
Chromosomal Abnormalities:
How are chromosome mutations detected? (3)
Karyotyping, high-resolution FISH, and MicroArray
Chromosomal Abnormalities:
DiGeorge syndrome and Cri du chat syndrome are examples of which type of chromosomal abnormality?
Chromosome mutation
Patterns of Inheritance in Single-Gene Disorders:
Transmission patterns = ?
Transmission patterns = patterns of inheritance
Patterns of Inheritance in Single-Gene Disorders:
A diagram of the inheritance pattern of a phenotype f family members
Pedigree
Patterns of Inheritance in Single-Gene Disorders:
The frequency of expression of disease phenotype in individuals with a gene lesion
Penetrance
Patterns of Inheritance in Single-Gene Disorders:
The expression of the disease phenotype in every individual with the mutated gene; common in homozygous recessive phenotypes.
Complete penetrance
Patterns of Inheritance in Single-Gene Disorders:
A range of phenotypes in individuals with the same gene lesion
Variable expressivity
Patterns of Inheritance in Single-Gene Disorders:
What are the 3 main Mendelian transmission patterns?
-Autosomal dominant
-Autosomal recessive
-X-linked or Sex-linked
Patterns of Inheritance in Single-Gene Disorders: (Mendelian transmission patterns)
A child of an infected individual + unaffected mate has a 50% to 100% risk of expressing disease phenotype
Autosomal dominant
Patterns of Inheritance in Single-Gene Disorders: (Mendelian transmission patterns)
-A child of an affected individual + unaffected carrier has a 50% change of being affected
-A child of two affected individuals has a 100% probability of being affected
-More often observed as a result of two individuals heterozygous for the same mutation producing offspring
Autosomal recessive
Patterns of Inheritance in Single-Gene Disorders: (Mendelian transmission patterns)
-Having genetic components located on the X chromosome
-Almost always recessive
-Carried by females, manifested most often in males
X-linked/Sex-linked
This type of disorder can affect structural proteins, enzymes, cell surface receptor proteins, and growth regulators.
Single-gene disorders
This disorder affects DNA sequence in one gene
Single-Gene disorder
How are single-gene disorders transmitted?
Mendelian fashion (autosomal recessive/dominant or X-linked)
Cystic fibrosis is an example of what type of disorder?
Single-gene disorder
Cystic fibrosis is caused by the loss of function of what gene?
CF transmembrane conductance regulator (CFTR)
Cystic fibrosis can be detected by what molecular test methods? (4)
-PCR-RFLPs, SSP-PCR, Bead Array Technology, and Direct Sequencing
Single-Gene Disorders:
Hemoglobinopathies are detected using which molecular methods? (2)
Sequencing and PCR-RFLP
Single-Gene Disorders:
Connective tissues disorders are detected using which molecular method? (1)
Sequencing
Single-Gene Disorders:
Cell membrane-associated protein dysfunction can be detected using which molecular methods? (3)
Southern Blot, RFLP, Multiplex PCR
The most frequent mutation for Cystic Fibrosis
3 bp deletion that removes a phenylalanine residue from position 508 of the protein (F508del)
3 categories of Single-Gene Disorders with Non-Classical Patterns of Inheritance
-Gonadal mosaicism
-Mitochondrial mutations
-Genomic Imprinting
TRUE or FALSE:
Single-gene disorders with non-classical patterns of inheritance do not follow Mendelian rules of inheritance
TRUE
Single-Gene Disorders with Non-Classical Patterns of Inheritance:
-Generation of new mutations in germ cells
-Mutated cells give rise to eggs/sperm carrying the mutation, which can lead to a heritable phenotype
-phenotypically normal parents can have more than one affected child
Gonadal mosaicism
Single-Gene Disorders with Non-Classical Patterns of Inheritance:
Testing methods for this category include Next-generation sequencing, Sanger sequencing, and Southern Blot
Gonadal mosaicism
Single-Gene Disorders with Non-Classical Patterns of Inheritance:
Osteogenesis imperfecta is an example of this category
Gonadal mosaicism
Single-Gene Disorders with Non-Classical Patterns of Inheritance:
-Inherited from mother
-Mitochondria contain their own genome with 37 genes
-Disease manifests in energy-demanding organs (muscles, nervous system)
Mitochondrial mutations
Single-Gene Disorders with Non-Classical Patterns of Inheritance:
Testing methods include Southern Blot, PCR, PCR-RFLPs, and sequencing
Mitochondrial mutations
Single-Gene Disorders with Non-Classical Patterns of Inheritance:
Kearns-Sayre syndrome is an example of this category
Mitochondrial mutations
Single-Gene Disorders with Non-Classical Patterns of Inheritance:
-Inherit only one working copy of a gene instead of two
-Uniparental disomy: inheritance of chromosomal material from only one parent due to abnormal chromosome separation during meiosis
Genomic imprinting
Single-Gene Disorders with Non-Classical Patterns of Inheritance:
Testing methods include cytogenetics, Karyotyping, FISH, PCR-RFLPs, STR analysis
Genomic imprinting
Single-Gene Disorders with Non-Classical Patterns of Inheritance:
Chromosome 15:
-Prater-Willi syndrome: deletion from paternal chromosome
-Angelman syndrome: deletion from maternal chromosome
Genomic imprinting
Label the following on the chromosome: Telomere (2), centromere, p arm, q arm, gene region
A-Telomere
B-Centromere
C-Telomere
D-Gene region
E-p arm
F-q arm
If the location of a certain part of Chromosome 17 is located on the q arm, region 1, band 1, subbed 2, how would that be written?
17q11.2
Fill in the blank:
_________ is the exchange of genetic material between chromosomes
Translocation
Fill in the blank:
________ is the loss of chromosomal material
Deletion
Fill in the blank:
__________ is the gain of chromosomal material.
Insertion
Fill in the blank:
___________ is the excision, flipping, and reconnecting of chromosomal material within the chromosome.
Inversion
Fill in the blank:
____________ is a chromosome containing two copies of the same arm and a loss of the other arm.
Isochromosome
Fill in the blank:
__________ results from a deletion of genetic regions from ends of the chromosome and a joining of the ends to form a ring.
Ring chromosome
Karyotyping analysis results are expressed as the number of chromosomes per nucleus, followed by sex chromosomes, followed by any genetic abnormalities. How would a normal male and female karyotype be expressed?
Male: 46,XY
Female: 46,XX
If a male had an extra chromosome 21, how would that karyotype be written?
47,XY+21
If a female had a deletion in the q arm of chromosome 7 at region 1, band 3, how would her karyotype be written?
46,XX,del(7)(q13)
