Pedigree, Mendelian inheritance, Genome organization Flashcards
Proband
“index case,” the affected member through whom a family with a genetic disorder is brought to attention
consanguinous matings
couples that have >1 known ancestor in common
mendelian disorders
a disorder caused by a single gene (oversimplification)
Phenotype
the observable expression of a genotype as a morphological, clinical, cellular or biochemical trait
Genotype
the set of alleles that make up his or her genetic constitution
Mendelian inheritance
the transmission of inherited characters from generation to generation through the transmission of genes
genes come in ____, with one from each ____
pairs, parent
genes come in different ____, which result in different observed ______
alleles, phenotypes
Mendel’s first law
Law of segregation: at meiosis, alleles separate from each other such that each gamete receives one copy from each allele pair
Mendel’s second law
Law of independent assortment: at meiosis, the segregation of each pair of alleles is independent
Dominant
expressed when only one chromosome of a pair carries the mutant allele (in a heterozygous state)
recessive
expressed when both paired chromosomes carry a mutant allele at a locus (expressed in a homozygous or compound heterozygous state)
codominant
when both traits (alleles) are expressed in a heterozygous state
How many chromosomes do humans have?
46
each chromosome is believed to consists of a _______ continuous _____ _____ _____
single, DNA double helix
Retroposed gene
a gene without introns
______ + ______=phenotype
genotype, environment
Is chromosome 19 gene rich or gene poor?
gene rich
are genes 13, 18, 21 gene rich or gene poor
gene poor
Euchromatic
more relaxed regions of DNA
Heterochromatic
more condensed regions of DNA
Minisatellites
tandemly repeated 10-100bp blocks of DNA, VNTR(variable number of tandem repeats)
Microsatellites
di, tri, tetra nucleotide repeats, 5X10^4 per genome, STRPs (short tandem repeat polymorphisms)
______ are PCR detectable markers that are easy to store and are widely distributed, 1/1000bps
Single Nucleotide Polymorphisms (SNPs)
Copy Number variations
variations in segments of genome from 200bp-2Mp, can range from one copy to many, array comparative genome hybridization
Many human genes are members of _____ _____
gene families
Gene families are composed of genes with ______ _______ ______. Do they carry out similar or distinct functions?
high sequence similarity. They carry out both similar and distinct functions
Gene families arise through _____ _____, a mechanism of evolutionary change
gene duplication
Limitation of Nextgen DNA sequencing
no mammalian genome has been completely sequenced and assembled, it relies on short read sequences, complex, highly duplicated regions are typically unexamined and can be implicated in diseases (1q21)
Limitations of Genome wide association studies (GWAS)
“missing heritability” for complex diseases: many large scale studies implicate loci that account for only a small fraction of the expected genetic contribution. Many regions of the genomes are unexamined by available “genome-wide” screening technologies
bivalents
maternal and paternal homologs of each chromosome that pair along their entire lengths
synaptonemal complex
a proteinaceous structure which promotes inter-homolog interactions
Chiasmata
Crossovers between homologs
When does the synaptonemal complex disassemble? What holds the bivalents together?
at the end of prophase I, and the bivalents are held together by the chisamata only
What is the most error prone step of meiosis
Meiosis 1-chromosome nondisjunction at this stage is the most frequent mutational mechanism in humans
Genetic consequences of meiosis
1) reduction in chromosome number from diploid to haploid, 2) random segregation of homologous chromosomes, 3) random shuffling of genetic material due to crossover events
Metacentric
the centromere of chromosome is located in the middle of the chromosome such that 2 chromosome arms are apprx. equal in length
Submetacentric
the centromere is slightly removed from center
Acrocentric
the centromere is near one end of the chromosome
Aneuploidy
condition where wells contain an abnormal chromosome number
nondisjunction
missegregation of chromosomes at metaphase in either mitosis or meiosis such that daughter cells receive extra or fewer than the normal number of chromosomes
Monosomy
when a cell lacks one copy of a chromosome
trisomy
when a cell has an extra copy of an entire chromosome
Are monosomies compatible with life?
No. Except for Turner’s syndrome (monosomy for X chromosome)
Are trisomies compatible with life
yes, although some result in spontaneous abortion
What phase is the implicated most commonly in trisomy 21
maternal meiosis 1
Trisomy 18
Edward’s syndrome-intrauterine growth retardation, characteristic faces, severe intellectual disability, characteristic hand positioning, valvular heart disease, posterior fossa CNS maldevelopment, diaphragmatic hernias, renal anomalies
Trisomy 13
Patau syndrome, characteristic facies, intellectual disability, holoprosencephaly, facial clefts, polydactyly, renal abnormalities
XXY
Kleinfelter syndrome. Tall stature, hypogonadism, elevated frequency of gynecomastia, commonly sterile, language impairment
X0
Turner syndrome- short stature, webbed neck, edema of hands and feet, narrow hips, broad chest, renal and cardio anomalies, gonadal dysgenesis
Mosaicism
presence of at least 2 genetically different cells in a tissue arising from a single zygote
heteroploid
a chromosome complement with any chromosome number other than 46
eupoloid
An exact multiple of the haploid chromosome number
What are the 2 basic types of structural chromosome rearrangements?
Balanced and unbalanced
Chromosome inversion
when one chromosome undergoes two double strand breaks of the DNA backbone and the intervening sequence is inverted prior to the rejoining of the broken ends
Paracentric inversion
a chromosome inversion that excludes the centromere
Pericentric inversions
a chromosome inversion that includes the centromere
Reciprocal translocation
Results from the breakage and rejoining of non-homologous chromosomes, with a reciprocal exchange of the broken segments
Robertsonian translocation
the fusion of 2 afrocentric chromosomes within their centromeric regions, resulting in the loss of both short arms (containing rDNA repeats). Reduction in chromosome number but are balanced rearrangements
Deletion
Loss of genetic info that can arise by simple chromosome breakage and rejoining, unequal crossing over between misaligned homologous chromosomes or sister chromatids, or by abnormal segregation of a balanced translocation or inversion
Duplication
gain of genetic information, which is generally less harmful than deletion, but can lead to abnormalities. Can also result from unequal crossing over or by abnormal segregation during meiosis in a carrier of a translocation or inversion
Ring chromosome
a chromosome fragment that circularizes and acquires kinetochore activity for stable transmission to daughter cells. Sample karyotype: 46, XY, r(13)(p11q34)
Isochromosome
A chromosome in which one arm is missing and the other duplicated in a mirror-image fashion, possibly occurring through an exchange involving one arm of a chromosome and its homolog at the proximal edge of the arm, adjacent to the centromere
Continuous gene syndromes
abnormal phenotypes caused by over-expressoin of loss (haploinsufficiency) of neighboring genes
Imprinting
Allele-specific methylation of CpG dinucleotides on the promotor region of imprinted genes
Characteristics of imprinted genes
- they tend to be clustered, 2. These clusters contain both maternally and paternally imprinted genes, 3. The imprinted genes encode both proteins and non-coding RNAs
What is a common finding in childhood B-cell acute lymphoblastic leukemia (ALL)?
high hyper-diploidy revealed by chromosome and FISH analyses
What is diagnostic for chronic myelogenous leukemia (CML)?
t(9;22)
What can CML be treated with?
tyrosine kinase inhibitors
What is diagnostic for a specific acute promyeloid leukemia (PML)?
t(15;17)
What can PML be treated with?
Retinoic Acid
FISH: Centromere Probe-name and function, example
cen, used for Enumeration – leukemias, ex: Cen 4, 8, 10, 17, 21
FISH: Locus Specific-name and used for, examples
LSI, Deletion, leukemias, p53
FISH
fluorescent in-situ hybridization. Uses labelled probes to detect and localize the presence or absence of specific DNA sequences on chromosomes
Chromosomal Microarray (CMA)
Compares patient DNA to control to detect gains and losses using fluorescent hybridization
Can CMA detect balanced rearrangements?
No
What test is used for children with children with developmental delays?
CMA
What are FISH panels used for?
for initial differential diagnosis, and as a means to monitor treatments or disease progression
How many regions are interrogated in a single CMA?
180,000
Database of Genomic Variants
contains published literature as well as the mapping of the variants and known disease regions.
Name the 3 ways to get Down Syndrome
(95%) Trisomy 21 from nondisjunction, (3-4%) Unbalanced translocation between chromosome and another acrocentric chromosome, (1-2%) Mosaic Tri
What are the 1st semester screening tests for Down Syndrome? What is the detection rate?
Detection rate 82-87%. US measurement of nuchal folds, Beta-hCG, PAPP-A (pregnancy-assocaited plasma protein A)
What does 2nd trimester screening consist of? What is the detection rate?
80% detection rate. Quad screen: Beta-hCG, AFP (alpha-fetoprotein), unconjugated estradiol, inhibin level
What is the detection rate of 1st trimester + second trimester?
95%
How can the suspicion of Down Syndrome be confirmed?
Chromosome analysis via amniocentesis or CVS
Comment on the growth parameters of DS babies
growth parameters are usually normal
Common facial features of DS
midface hypoplasia, upslanting palpebral fissures, epicanthal folds, small ears, large appearing tongue
Comment on the muscle tone and joints of babies with DS
low muscle tone, increased joint mobility
hand features of DS
short fingers, transverse plamar crease, Vth finger incurving (clinodactyly), increased space between toes 1 and 2
Cardiac issues with DS
all types of anomalies can be present, but AV canal is most common. EKG as a newborn recommended.
GI issues with DS
Structural: esophageal and duodenal atresia, Hirschsprung’s.
Functional: feeding problems, constipation, GERD, celiac disease
Opthalmic issues with DS
blocked tear ducts, myopia, lazy eye, nystagmus, cataracts
ENT issues with DS
chronic ear infectons, deafness (neuro and conductive), chronic nasal congestion, enlarged tonsils and adenoids-apnea
Endocrine issues (autoimmune) with DS
thyroid disease (hypothyroidism-congenital or acquired), insulin dependent diabetes, alopecia atreata, reduced fertility
Do individuals with DS experience puberty normally?
yes
orthopedic problems with DS
hip problems, joint subluxation, atlantoaxial subluxation
Hematological issues with DS
myeloproliferative disorder in newborn, increased risk of leukemia, iron deficient anemia
Developmental issues with DS
hypotonia affects gross motor development, mild to moderate intellectual disability, speech problems
Neurological problems associated with DS
hypotonia mild-severe, seizures, infantile spasms
Psychiatric issues with DS
depression, early AD, 1/10 Autistic
How does a newborn with PW present?
hypotonia, dysmorphic features, undescended testicles
What test can be used to diagnose PW?
FISH, methylation testing
Describe feeding of PW
early on failure to thrive, difficult feeding, preschool age they develop hyperphagia and gain weight
hyperphagia
Excessive hunger, characteristic of PW
Describe the developmental delay of PW
mild-moderate to intellectual disability
Opthalmic problems associated with PW
strabismus and nystagmus
What causes PW?
missing information on paternal chromosome 15q11-q13
List the ways PW may occur
- Paternal deletion, 2.UPD of maternal allele, 3. Imprinting error-“virtual” maternal UPD
What common orthopedic issues exist for PW patients
scoliosis
What else can cause problems on chromosome 15?
linkage disequilibrium between patients with autism and polymorphisms on the GABAa-b3 locus
What is the most common cytogenetic abnormality in patients with autism?
Maternal mutation 15q11-q13
Phenotype of Angleman’s Syndrome
mildly dysmorphoc facial features, hypotonia as a chilf that turns to spasticity, intellectual disability, seizures, autism
4 Characteristics of epigenetic phenomena
1) Different gene expression pattern/phenotype, identical genome, 2) Inheritance thru cell division, even through generations, 3) Like a switch ON/OFF, 4) Erasable (therapeutic?)
Waddington’s epigenetic landscape
Each cell state is a “low energy” state
3 examples of epigenetic phenomena
1) sweden famine/feast (diabetes/CV issues), 2) Father smoking during slow growth period (BMI). 3) High and low methyl donor diet (AGOUTI gene: coat color and feeding habits)
Why is erasure and resetting of methylation patterns of imprinted genes during gametogenesis essential?
Embryos with no active copies or 2 active copies of imprinted genes would be produced at high frequencies
DNA methylation lock DNA in what state?
repressed
Where does DNA methylation occur
only on cytosines of CpG
Does DNA methylation affect the base pairing of 5-meC with G?
NO
_______, _______, and _____ are examples of epigentetic phenomena
x inactivation, imprinting, and herterochromatin domains
Examples of non-nuclear inheritance
cytosolic epigenetic inheritance in cancer
How could methylation lead to cancer?
Normally, a tumor suppressor gene (TSG) is ON. If it gets methylated and turns off, this can lead to cancer
Population genetics
quantitative study of the distribution of genetic variation in populations and how the frequencies of genes and genotypes are maintained or change.
What evolutionary forces affect allele frequencies?
natural selection, genetic drift, mutation and gene flow
Polymorphism
A genetic variant (mutation) which is common (>1%) in the populations
Founder effects
a high frequency of a mutant allele in a population founded by a small ancestral group when one or more of the original founders was a carrier of the mutant allele
Genetic drift
random fluctuation of allele frequencies, usually in small populations
Selection:
active selection of favorable alleles over non-favorable ones
fitness
a measure of the chance an allele will be transmitted to the next generation (Scale is 0-1).
Hardy-Weinberg principle
describes the frequency of two alleles in a population in terms of allele frequency and genotype frequency
Hardy-Weinberg assumptions
random mating, no mutation, no selection for/against any allele, no migration/drift, large population
Stratification
refers to populations containing 2 or more subgroups which tend preferentially
mate within their own subgroup. Mate selection is not dependent on the trait/disease or interest. (Example: sickle cell anemia in African Americans (AAs) has higher incidence social stratification favoring mating of AAs with other AAs, than is predicted by HWE)
Assortive mating
when the choice of mate is dependent (in part) on a particular trait (or sometimes a disease). This occurs because people tend to choose mates who resemble themselves for (language, intelligence, height, skin color, etc.). This has been observed for congenital short stature (previously called ‘dwarfism’), blindness, and deafness.
Eye characteristics of Turner syndrome
Inner canthal folds, blue sclerae, ptosis
ENT of someone with Turner syndrome
prominent auricles, low set ears, high narrow palate, small mandible
Neck of Turner syndrome
low posterior hairline, webbing
Chest of someone with Turner Syndrome
broad, shield like chest, wide spaced nipples, pectus excavatum
Skeleton of someone with Turner syndrome
cubitus valgus, short 5th metacarpal/metatarsal, made lung deformity, scoliosis
What are the heart conditions common to Turner syndrome?
(Prenatal) cystic hygroma, (newborn) neck webbing
bicuspid aortic valve, coartation of the aorta, systemic hypertension, EKG abnormalities
what other systems are affected by Turner syndrome?
Lymphatics, urinary, vision and hearing
Sexual probs-turner syndrome:
infertility, sexual development, no menstruation
Common pitfalls in disclosure of Turner Syndrome
secret keeping, difficulty communicating an infertility diagnosis, perceived negative experiences with physicians
What is at the root of Gaucher’s disease?
not making enough of the enzyme “glucocerebrosidase”to break down the lipid “glucocerebroside” so it accumulates in the lysozomes of macrophages
How many RBCs are produced (and destroyed) every second?
2.4 million new red blood cells
How long is an RBC in circulation?
120 days
What happens to old RBCs?
they are recycled by macrophages
How are RBCs broken down?
90% removed from the circulation by the phagocytic macrophages in liver, spleen and lymph nodes.
2. 10% hemolyze in the circulation. Fragments of engulfed by macrophages.
Where are the chemical components of the RBC broken down?
within vacuoles of the macrophages due to the action of lysosomal enzymes
Hemoglobin is degraded into ______, ________, and ______
globin, heme, iron
macrophages convert ____ into ____ and then ____ that is released into the blood where it forms a complex with blood albumin (bound bilirubin).
heme, bilverdin, bilirubin
In the liver cells (hepatocytes) ______ reacts with glucuronic acid to form ______.
Bound bilirubin, conjugated bilirubin
Most of the _______ is secreted into the small intestine with the bile. In the large bowel, bacteria convert _____ into the yellow-brown pigment (urobilinogen)
conjugated bilirubin, bilirubin
_____ is removed from heme molecules in the phagocytes. In the plasma, it binds to the protein ______ and is carried to the bone marrow where the iron can be used to synthesize new hemoglobin.
Iron, transferrin
What % of the RBC membrane is lipid?
30%
Where are the typical Gaucher cells stored?
mainly in liver, spleen and bone marrow.
What is the most common first symptom of Gaucher’s disease and what can it be attributed to?
A swollen stomach. This is because the spleen has swollen.
Why is anemia common?
When the spleen enlarges, sometimes to 25 times its normal size, it weeds out too many blood cells, including good ones.
Difference between Type I, II, and III Gaucher’s disease
type 2 and 3 have neurological symptoms
How can gaucher’s disease be diagnosed?
- blood test to check glucocerebrosidase levels, 2. Genetic testing: N370S, L444P, 84gg and IVS2
What type of mendeilan disease is Gaucher’s?
Autosomal recessive
Imiglucerase (Cerezyme)
recombinant DNA-produced analogue of human β-glucocerebrosidase. It is given intravenously after reconstitution as a treatment for Type 1 Gaucher’s disease
Miglustat
inhibitor of the enzyme glucosylceramide synthase, reduced the substrate to treat Gaucher’s disease
Taliglucerase alfa
recombinant glucocerebrosidase enzyme produced in a slurry of carrot cells.
Characteristics of diseases demonstrating multifactorial inheritance
- cluster in families, 2. do not follow simple Mendelian inheritance, 3. Likely due to variants in multiple genes and non-genetic factors interacting, 4. No simple relationship b/w genetic variant and trait
Heterogeneity (allele and locus)
allele-cystic fibrosis, locus-alzheimer’s disease
Phenocopies
tahildomide-induced limb malformation
define heterogeneity at an allele or locus
the “same” disease can be caused by different alleles at one location or by alleles at different locations in the genome
Define phenocopy
disease traits that manifest like the disease, but have a different cause other than primary genetics.
Multifactorial inheritance
indicated when there is an increased risk to relatives, but there is no consistent pattern of inheritance within families
Heritability
the proportion of total variance in a trait that is due to variation in genes.
A ____ heritability implies that differences among individuals with respect to a trait such as blood pressure in a population can be attributed to differences in the genetic make-up.
high
A ____ heritability does not imply that non-genetic factors are not important
high
What are the most common polymorphic DNA markers?
Microsatellites, SNPs, and CNVs
Each SNP occurs in local context (_______) of surrounding SNPs
haplotype
haplotype
Groups of SNPs that can be inherited
haplotype block
Alleles that are in linkage disequilibrium, and therefor are inherited together. Smaller in african populations
How often do CNVs contribute to human disease?
It is uncertain
Are candidate gene association studies hypothesis driven or hypothesis free? Consequence?
Hypothesis driven, false positives. Hypotheses are often wrong
What are candidate gene association studies most powerful for?
common risk alleles with small to moderate effects
i.e. “complex”, polygenic traits
Do candidate gene association studies depend on Linkage disequilibrium
yes
How does candidate gene association work?
- Genotype marker in candidate gene in cases and in controls
- Compare allele frequencies in cases versus controls
Advantages of candidate gene association studies
simple, reasonable number of controls (hundreds), simple stats
Genetic linkage studies: hypothesis driven or no?
hypothesis free!
What do genetic linkage studies do?
Search genome for segments disproportionately co-inherited along with disease through “multiplex families” (families with multiple cases of a disease)
What does a genetic linkage study assume?
affected relatives share the disease (not phenocopies)
What is a disadvantage of genetic linkage study?
less powerful for complex traits
What types of traits does a genetic linkage study work best for?
Mendelian traits (uncommon alleles with strong effects)
What is the unit of genetic distance in linkage studies?
centiMorgan (cM)
1 cM = 1% recombination between two loci per meiosis
What is the statistical measure of genetic linkage analysis?
LOD (log of odds) score
Significance level of LODs for Mendelian and polygenic traits
LOD >3.0 for Mendelian trait
LOD >3.3 for Polygenic trait
What does GWAS stand for?
Genome wide association study
How are GWAS different from candidate gene association studies?
GWAS tests hundreds of thousands or millions of markers (SNPs) across entire genome
What is a disadvantage of GWAS?
must use more than a thousand cases and 1000 controls
What is GWAS most effective for?
Most effective for common alleles with small to moderate effect sizes
What are exomes and what % of the genome do they make up?
Gene coding regions; ~ 3 Mb (1% of genome)
What are the 3 steps of sexual differentiation?
- establishment of genetic sex thru X and Y chromosomes, 2. Formation of sex specific gonads (testes and ovaries), 3. development of internal and external reproductive organs
Genetic sex is determined by______
the presence or absence of Y chromosome
All diploid somatic cells in both males and females have a single ______ __ ______regardless of the total number of X and Y chromosomes present.
active x chromosome
X inactivation is normally _____ so that females are _____ for expression of their x chromosomes.
random, mosaic
How is the x chromosome inactivated?
DNA methylation and modification of histone proteins
XIST gene
encodes noncoding RNA, which is expressed in the nucleus where it associates in cis as a part of an XIST RNA/barr body complex
What percentage of genes on the X chromosome escape inactivation? Where are they located?
10-15%, many are located on Xp
Where do the X and Y chromosomes pair for recombination during meiosis?
pseudoautosomal region
Nonrandom X inactivation. How might this present clinically?
when an X chromosomes is abnormal or there is an X-autosome translocation. Might present as a female with an x linked recessive phenotype
Gonadal sex is determined by
expression of genes that induce the development of testes (SRY)
SRY
principal determinant of testicular differentiation. Without SRY–> ovaries
Germ cells develop in 2 stages:
- sexually independent pregonadal stage where they migrate from yolk sac->developing gonads
- gonadal dependent stage-they mature
Mutations at autosomal loci on chromosomes ___, ___, and ___ can lead to sex reversal in the presence of ____ gene
9, 11, 17, SRY
WT gene
directs differentiation of the mesonephros and genital ridge (precede gonadal development)
Loss of ____ gene can lead to adrenal hypoplasia and gonadal agenesis
SF1
DAX1 is a nuclear hormone receptor. It’s presence leads to the development of ____ even in the presence of ___, a disorder called ____
ovaries, SRY, Dosage Sensitive Sex Reversal (DSS)
Anatomic sex is determined by:
the action of growth factors and sex steroid hormones
Testes contain two non-germ cells:
- Sertoli cells (MIF), 2. Leydig cells (testosterone)
What do sertoli cells produce?
Mullerian Inhibitory factor
What do leydig cells produce?
testosterone
What does MIF do?
Prevents formation of the mullein duct derivatives (would be fallopian tubes, uterus, and upper vagina)
What does testosterone stimulate the development of? What does it become?
Wolffian (mesonephric) duct, becomes epidydimal duct and ductus deferens.
In the absence of testosterone, what structure degenerates in women?
wolffian (mesonephric duct)
The male external genitalia develop in response to what?
testosterone
In many androgen sensitive tissues, testosterone must be converted to ____
dihydrotestosterone
The genital tubercle becomes what in M/F?
M: glans and shaft of penis
F: glans and shaft of clitoris
The definitive urogenital becomes what in M/F?
M: penile urethra
F: vestibule of vagina
The urethral fold becomes what in M/F?
M: Penis surrounding penile urethra
F: Labia miora
Labioscrotal fold becomes what in M/F?
M: Scrotum
F: Labia majora
Sex reversal
whe gonadal sex is the opposite of what is predicted from karyotype (genetic sex)
XX males
translocation of Y chromosome material (SRY) to another chromosome. Translocation to an autosome is most common.
XY females
insertion of SRY gene on a chromosome
pseudohermaphroditism
abnormal development of genital sex. External phenotype and sex assignment can be different than genetic sex.
How can pseudohermaphroditism occur for males and females?
masculinized females-exposure to androgens during development
males-failure to produce or respond to testosterone
Loss-of-Function Mutations:
Caused by genetic mutations that eliminate (or reduce) the function of the protein.
Of the four major mechanisms, which is the most common genetic mechanism leading to human genetic disease?
loss of function mutation
Examples of loss of function mutations:
Duchenne Muscular dystrophy (loss of protein), alpha-thalassemia (reduction of protein), Turner syndrome (loss of entire chromosome), hereditary retinoblastoma (loss of a TSG). Also: Hereditary neuropathy with liability to pressure palsies (HNPP), Osteogenesis imperfecta type I. MANY METABOLIC DISORDERS
Gain of function mutations
caused by genetic mutations (often missense or sometimes promoter mutations) that enhance one or more normal functions of a protein (e.g. increased protein expression, increased half- life, decreased degradation, increased activity)
Examples of gain of function mutations
Hemoglobin Kempsey, Achrondroplasia, Alzheimer, Charcot-Marie-Tooth
Novel property mutations
Caused by genetic mutations (often missense) that confer a novel property on the protein, without necessarily altering its normal functions. Although the introduction of a novel property has sometimes been advantageous from an evolutionary standpoint, the majority of such changes result in a novel protein property that reduces fitness (i.e. can lead to disease).
Are novel property mutations common or uncommon?
uncommon
Examples of novel property mutations
Sickle cell anemia, Huntington disease
Ectopic or Heterochronic expression mutations are seen in what kind of conditions?
Cancers. Also hereditary persistance of fetal Hb
Ectopic or Heterochronic expression mutations
Caused by genetic mutations that alter regulatory regions of a gene and alter either the timing (wrong time = heterochronic) or location (wrong place = ectopic) of expression.
Unstable Repeat Sequences
These genes contain tri, or tetra-nucleotide repeats that make the genes susceptible to slipped mispairing during DNA replication. The repeat numbers for each allele are prone to change from parent to offspring. An expansion of repeat numbers can lead to disease.
Example of unstable repeat sequence disease
Huntington disease
Genetic anticipation
the observation that disease severity worsening in subsequent generations.
What explains genetic anticipation?
tri/tetra nucleotide repeat number expansions occurring from parent to offspring. The offspring inheriting an expanded disease allele is more likely to present earlier and progress faster
Consequences of expansion of noncoding repeats and loss of function:
- Impaired transcription
- Mutant RNA not made
- Mutant protein not made
Consequences of expansion of noncoding repeats conferring novel properties
- RNA has novel property (abnormal RNA binds and soaks up RNA-binding proteinsàaffects other gene products)
- Mutant RNA is made
- Mutant protein not made
Consequences of expansion of codons in exons
- Novel property on expressed protein
- Mutant RNA is made
- protein is made and is toxic
Where do the majority of mutant alleles exist for a given autosomal recessive disease?
Carriers
Allelic heterogeneity
existence of multiple mutant alleles for a single gene
Compound heterozygote
one who carries 2 different mutant alleles on the same gene
What enzyme is missing in PKU?
phenylalanine hydroxylase
What happens in PKU?
high levels of Phe accumulate and damage CNS
Describe the risks for a pregnant PKU woman
miscarriage, baby might have deformities, mental retardation, growth impairment REGARDLESS OF BABY’S GENOTYPE
What is the treatment for PKU?
Diet low in phenylalanine
What tests can screen for PKU?
Guthrie test (bacteria will grow in presence of Phe when they normally would’t), Mass spectrometry.
Why is timing important for PKU screening?
Can screen at birth, but have to be careful because levels might be normal. PKU levels will increase in the first few days
How can you imagine a1-antitrypsin?
A lung protector
What are some characteristics of a1-antitrypsin deficiency? (ATD)
- late onset
- common among norther Europeans
- 20X risk of emphysema, high risk of cirrhosis and liver cancer
- smoking makes it much worse
What does a1-antitrypsin do on a molecular level?
Inhibits elastase, which is a protease that breaks down lung tissue. When a1-antitrypsin is not present in sufficient amounts, emphysema results.
Why can a1-antitrypsin deficiency cause cirrhosis?
because misfolded a1-antitrypsin aggregates in the liver where it is produced
Which mutant allele of a1-antitrypsin deficiency is most severe? Why?
Z allele so most severe and most common. Improperly folded protein sticks in the liver (potential for cirrhosis)
Which mutant allele is less severe? why?
S allele, makes a protein unstable but is not misfiled so no liver disease.
What gene is mutated in Tay-Sachs?
HEXA
What gene is mutated in Sandhoff disease?
HEXB
What gene is mutated in AB-variant of Tay Sachs?
GM2AP
What are the substrates involved in Tay-sachs?
GM2 gangliosides
What are the substrates involved in Sandhoff disease?
globosides
What does the enzyme test for tay-sachs show?
HEXA defective, HEXB normal
What does the enzyme test show for Sandhoff disease?
HEXA and HEXB both defective
What does the enzyme test show for AB-variant of tay sachs
Normal HEXA and HEXB
What group is at a high risk for tay-sachs?
central/eastern europeans and Ashkenazi Jews
What causes tay sachs?
HEXA mutation=defective hexosaminidaseA, can’t degrade ganglioside=progressive CNS destruction
What type of hemoglobin is present in embryos?
Zeta2epsilon2
Hb in fetal development
a2y2 (HbF)
Adult Hb
a2B2 (HbA) and a2d2 (HbA2)
What Hb’s are present in an adult?
HbA, HbA2, and HbF
Locus control region
upstream of the coding regions for the alpha and B globin clusters. Controls timing and levels of the globin proteins
Sickle cell anemia results from a switch between ___ and ___ in codon ____ of exon____
Glu, Val, 6, 1
In low O2, HbS is ______ soluble than HbA
less
Hemoglobin C Disease results from a change from ___ to ___ in exon ___ and codon ___
Glu, Lys, 1, 6
In low O2, HbC is ____ soluble than HbA and tends to ______ causing _____
less, crystalize, lysis
How can sickle cell anemia be diagnosed?
PCR using MstII to tell between HbA and HbS (cannot tell between HbA and C)
How many total copies of the alpha globin gene do people have
4 (2 on each chromosome)
How many total copies of beta globin gene do people have?
2 (1 on each chromosome)
What is the genotype for a silent carrier of a-thalassemia? What % a-globin level?
aa/a-
75%
What is the genotype for a-thalassemia 1 trait? What % a-globin level? Where is it common?
aa/–
50%
common in SE asia
What is the genotype for a-thalassemia 2 trait? What % a-globin level? Where is it common?
a-/a-
50%
Africa, mediterranean, asia
What is the genotype for HbH disease? What % a-globin level? What forms?
a-/–
25%
B4 clusters form
hydrops fetais
–/– y4 clusters, results in fetal death
locus heterogeneity
mutation in more than one locus that causes the same clinical condition
trinucleotide repeat disorders work by a _____ ______ mechanism
slipped mispairing
______ and _______ ________ _____ are characteristics of trinucleotide repeat disorders
anticipation, parental transmission bias
Are trinucleotide repeat disorders AD, AR, or X linked?
They can be autosomal dominant, autosomal recessive, or x linked
Parental transmission bias
trinucleotide expansion more prone to occu in gametogenesis of male or female
Where do mtDNA disorders typically cause dysfunction
repiratory chain
How many genes are coded for in the mitochondrial genome?
37
Pharmacogenetics
Study of differences in drug response due to allelic variation in genes affecting drug metabolism, efficacy, toxicity
Pharmacogenetics is variable due to _____
individual genes
Pharmacogenomics
the genomic approach to pharmacogenetics, concerned with assessment of common genetic variants in the aggregate for their impact on the outcome of drug therapy.
Pharmacogenomics has a variable response due to _______
multiple loci across the genome
What are the two major elements of response to drugs?
Pharmacokinetics and pharmacodynamis
Pharmacokinetics
ADME: Absorption, Distribution, Metabolism, and Excretion of drugs
Pharmacodynamics
Describes the relationship between the concentration of a drug at its site of action, observed biological effects.
Drug metabolism: Phase I
polar group added (exposed)–>solubilize
Drug metabolism: Phase II
conjugation rxn (sugar/acetyl group)–>detoxify
Where are the gene products of CYP450 complex active?
liver, intestinal epithelium
What are the 3 main families of CYP450 complex
CYP1, CYP2, CYP3
Most CYPs function to _______ drugs. Is this always the case?
inactivate, not always the case, sometimes they are needed for activation
What converts codeine to morphine?
CYP2D6
What inactivates 40% of common drugs?
CYP3A4
What types of mutations are expected for a poor metabolizer?
Frameshift, splicing, nonsense, missence (some)
What types of mutations are expected for an ultrafast metabolizer?
increased copy number, missense (some)
10 % of females are affected in which x linked recessive disorder?
hemophilia a
1/3 of females are affected by what trinucleotide repeat, x linked disorder
Fragile X, but much less severely
Cooley’s thalassemia is another name for what?
B thalassemis major
What might be observed for a patient with B thalassemia
osteopenia, dense marrow expansion, enlarged spleen, short stature
homoglobin S variant: (ethnic group)
15 % African Americans carriers
hemoglobin E varient: (region)
7% SE asians
Treatment for Multiple Endocrine Neoplasia (MEN)
Thyroid removal after early testing
Treatment for Aplha-1AT
recombinant enzymen therapy
Treatment for Fabry disease
recombinant a-galactose (stabilizes the protein so it can fold correctly) intreacellular protein
Treatment for hemophilia A
replace factor VIII
informative result
definitively diagnoses or excludes the disease
non-informative
result is normal, but not possible to exclude disease risk
genetic heterogeneity
multiple genes (when mutated) are associated with the same phenotype
example of genetic heterogeneity
HCM
a SNP occurs every ____/_____ bp
1/1000
Number of base pairs in human genome
3X10^9
More AT or GC rich regions?
AT rich, 54%
what % of genome is protein coding?
1.5%
what % of genome is genes?
20-25%
Number of human genes
20-30k
gene duplication
major mechanism of evolutionary change. When it duplicates, it frees up one copy to very while the other copy continues to carry out function
