- Occurs when the chromosomes don't properly separate

- Can occur in meiosis I, mieosis II, or mitosis

- Results in unbalanced distribution of genetic material in offspring

- Occurs between the chromatids of sister chromosomes during meiosis

- Results in an exchange of genetic material between chromatids

- Differing genotypes for each different phenotype

- Results in normal, mild and severe cases

- Multiple alleles work together to create a specific phenotype

- Ex. blood type

- Phenotype presents itself in varying degrees 

- Ex. Rb factor has a 75% penetrance --> Only presents itself 75% of the time

- The other 25% are genotypically positive for Rh factor but do not actually express the phenotype

- Spontaneous mutation in a gene that leads to a clinical condition

- This may be incorrectly interpreted as inheritance of a familial germ line mutation

- Mutations in a specific gene or area of a chromosome can effect multiple different organ systems

- Ex. CFTR in cystic fibrosis --> Affects GI, respiratory system, etc.

- Also SOX9 is a main master transcription factor in proper development of male internal genitalia

- Some characteristics are affected by multiple genes

- Ex. height

- Environmental influence and modifier genes can contribute to the spectrum of clinical presentations

- Areas rich in CG pairing

- Usually associated with the promoter region of a gene

- Performed by DNA methylases

- Helps modify the activity of a gene --> Methylated (off)

- Can be passed down from cell replication to cell replication

- Can also pass down "imprinted" genes to offspring via methylation patterns

- Specific genes are imprinted and passed down to offspring from maternal or paternal gametes

- Maternal and paternal genes passed down are different

- Imprints and methylation patterns probably initiated via histone modification of the histone tails

- Short (p) arm

- Long (q) arm

- Specific based on their banding patterns --> Giemsa staining (heterochromatin vs. euchromatin) --> More bands present in early metaphase

- Centromere in between the two --> Acrocentric, metacentric, and submetacentric

- Acrocentric chromosomes are particularly susceptible for translocation events

1. Problems in early growth and development

2. Stillborn and neonatal death

3. Infertility

4. Family history

5. Neoplasia --> Cancers

6. Pregnancy for mother of advanced age

- Occurs when non-disjunction occurs

- Furrow regression possible --> Moves backwards to recreate single cell

- Cell now has 2 nuclei and double the genetic material   --> Tetraploid offspring

- Can also occur with multiple fertilizations of one oocyte

- 1-2% spermatocytes

- 20% oocytes

- Pre-implantation embryos --> 20%

- Spontaneous abortion --> 35% 

- Stillborns --> 4%

- Livebirths --> 0.3%

- Much more likely in older women who are pregnant (<35 years old)

- Occurs when nondisjuction occurs during mitosis

- Only some of the cell population has aneuploidy

- Edward's Syndrome

- 3 copies of chromosome 18

- Individuals usually don't live past 1 year old

- Clenched fist with overlapping 2nd and 3rd digits

- Rocker-bottom feet

- Low set, malformed ears

- Mental retardation

- Patau's Syndrome

- Bilateral cleft lip

- Polydactyly

- Growth retardation

- Mental retardation

- CNS issues

- Severe midline defects

- Congenital heart and UG defects

- Down's Syndrome

- Occurs either from a true trisomy nondisjuction or due to acrocentric translocation (Robertsonian translocation)

- q arm of Chromosome 21 attaches to the q arm of chromosome 14 --> 46 XY, t (14;21) +21

- Classic Features: Hypotonia, short stature, flat nasal bridge, open mouth with protruding tongue, palmar crease in hands

- Symptoms: Mental retardation, congenital heart defects, leukemia risk, early Alzheimer's risk, and generally cannot be self-sufficient

- Specific type of translocation

- q arm of one acrocentric chromosome binds to the q arm of another acrocentric chromosome

- Occurs in every cell of a female

- Occurs randomly with two normal copies of the X-chromosome

- One can be selectively inactivated in abnormal

- Must protect two things: 

1. Retain x-chromosome equivalent

2. Maintain autosomal functioning

- Some genes escape from inactivation --> Located primarily on p arm

- This is why aneuploidy of X chromosomes does create pathology

- X-autosome unbalanced translocation can create much milder symptoms through the process of non-random x-inactivation

- XO --> Monosomy of X chromosome

- Characteristic features: Webbed neck, short stature, lymph edema at birth in hands and feet

- Other Symptoms: Amenorrhea, streak gonads, and infertility

- Usually only diagnosed around puberty when female does not undergo menstruation

- Possible Genetic Causes: 46, XX, i(Xq) isochromosome --> 3 copies of q arm, 45, XO --> 1 copy of q arm

- In either case no p arm is present --> No presence of 2 copies of the genes that escape x-inactivation

-XXY --> Disomy of x-chromosome

- Most symptoms are eliminated due to x-inactivation

- Symptoms produced by the genes that escape inactivation

- Symptoms: Long limbs, hypogonadism, gynecomastia, infertility and learning issues (learning, social, and IQ disabilities) 

- Paracentric --> Around by not containing the centromere

- Pericentric --> Including the centromere

- Improper pairing results in a characteristic loop structure forming during metaphase

- Once mitotic spindle splits chromatids genes split off to each daughter cell

- Can result in both balanced or unbalanced offspring

- Balanced offspring can also end up with varying numbers in centromeres in chromosomes

- Upon further division chromatids either wont attach or can attach twice to the spindle 

- Chromatids that attach twice --> Chromatids ripped apart during cell division

- Paracentric --> Possible result has one chromosome with two centromeres and the other with none

- Balanced --> Correct number of chromatids, chromosomes, and genes just in different order

- Unbalanced --> Incorrect number of chromatids, chromosomes, and genes between daughter cells

- Technique that is especially good at determining which chromosome translocated or inverted

- Different color for each specific chromosome

- Translocation of a kinase gene to another chromosome

- Chromosomes 9 and 22 --> bcr-abl (Philadelphia) chromosome

- Results in an uncontrolled kinase

- Causes chronic myelogenous leukemia (bcr-abl chromosome)

- Forms a characteristic cruciform structure

- Alternative splitting occurs

- Can either result in balanced or unbalanced offspring

- Alternative splitting causes balanced offspring

- Adjacent (Type 1 and Type 2) splitting causes unbalanced offspring

- Terminal deletion

- Interstitial deletion

- Unequal crossing over

- Ring

- Isochromosome --> 2 q arms bind together or 2 p arms bind together

- 5p15 deletion --> 46, XX, del(5p15)

- Symptoms: 

1. Characteristic cry like a cat

2. Mental retardation

3. Microencephaly

4. Epicanthal folds

5. Low set ears

6. Heart defects

- Angelman Syndrome --> Deletion of maternally imprinted gene (gene 1) --> Causes characteristic holding of arms

- Prader-Willi Syndrome --> Deletion of the same sequence --> Pathology caused by a deletion in a paternally imprinted gene (gene 2) --> Causes massive trunkal obesity

- Caused by a deletion of the SAME chromosomal sequence

- Symptoms caused by different genes within sequence based on whether the individual inherited the maternally or paternally imprinted copy

- Occurs in either the 1st or 2nd position of the codon

- B-globulin 6: Glu --> Val

- Causes sickle cell shape in deoxy state of RBCs

- Occludes blood vessels

- Symptoms: Jaundice, leg ulcers, splenomegaly, and abnormal blood smear

- Sickle Cell Trait: Heterozygous normal --> Heterozygous advantage --> Resistance to malarial infection

- Sickle Cell trait patients can still show symptoms at low oxygen states

- Due to a non-sense mutation --> Produces early stop codon

- Symptoms caused a truncated NF1 protein (29 codons instead of the normal 60)

- Truncated protein is unable to properly inactivate Ras

- Ras being permanently on --> Lots of tumors throughout the body due to Schwann cell proliferation

- 3-5% of these tumors are malignant --> Most are benign

- Lisch nodules in the eyes and cafe-au-lait spots on the skin are also common signs of this condition

- Caused by a deletion/insertion frameshift mutation

- Exon frameshift mutation --> Single gene mutation

- Extremely high predisposition to breast cancer (~80% by the age of 70)

- Bilateral breast cancers, young presentation, and other organ cancers (ovarian) 

- Majority caused by a Delta F508 Deletion (2/3 of cases) --> Full amino acid deletion

- This particular amino acid is actually very important

- Absence of amino acid prevents correct folding and causes protein to be sequestered in the ER

- Protein never travels properly to the cell membrane

- Causes faulty transport via the CFTR channel

- Symptoms: Extremely viscous mucous secretions in the lungs and pancreas, susceptibility to opportunistic infections, and heart arrythmias possible also

- Loss-of-function recessive trait

- Over 1600 known mutations of the CFTR gene

- Change in splice junction --> Incorrect splicing and inability to remove proper intronic sequences

- Inabilty to properly breakdown Phe

- Due to an abnormal phenylalanine hydroxylase (PAH) protein structure --> Build up of Phe --> Toxic

- Causes mental retardation if left untreated 

- Can be treated by a life-long dietary change

- Prevalence: 1/8000 caucasians --> Every newborn is tested for PKU

- Same phenotype and pathology caused by multiple different mutations

- Mutations can be present in any region of the gene as long as an abnormal protein is created

- Can either cause a loss of function or a gain of function

- Sickle cell is an exception --> Only one single gene mutation is the cause

- Splice junction mutation --> Allelic heterogeneity

- Multiple different abnormal proteins possible depending on mutation present

- B-globin is abnormal and therefore unable to bind properly to A-globin

- Causes a decrease in the normal hemoglobin in RBCs

- Excess A-globin (unbound to B-globin) precipitates out of solution --> RBC death and anemia

- Presents almost exactly like sickle cell, but a loss of function instead of a gain of function mutation

- Symptoms: Jaundice, splenomegaly, abnormal blood smear, etc. 

- CAG trinucleotide repeat in exon region of huntingtin gene (40-200 repeats)

- Causes an excess of glutamine residues in protein --> Abnormal folding

- Protein precipitates in nucleus --> Abberant protein interactions --> Apoptosis results

- Causes basal ganglia degeneration

- Symptoms: Chorea, dementia, and seizures

- Paternal transmission has a much higher probabilty and more severe anticipation

- Diagnostic Genetic Test: PCR and gel electrophoresis

- Caused by a mutation in the promoter region/transcription binding site

- Increase in CG pairs in promoter region --> Get methylated

- Methylated CG pairs silence the gene

- Causes the lack of transcription of factor IX

- Factor IX lowers to <5% of normal

- Symptoms: Excessive bleeding after normal events

- Treatment: Factor IX injection --> Effective but VERY expensive

- Diagnostic Genetic Test: Southern blot --> large repeats

- Caused by a CGG promoter repeat

- Fragile-X --> >200 repeats --> Becomes methylated and causes genes to not be expressed anymore

- Most common cause of inherited mental retardation

- Called fragile-X because chromosome has a fragile area at the bottom that is susceptible to breakage --> Not the cause of mutation

- Loss of function recessive gene

- More common and severe in males due to the one X-chromosome

- Characteristics: Mental retardation, long faces, long ears, prominent jaw, irregular teeth, and macroorchidism

- Diagnostic Genetic Test: Southern blot

- Intronic GAA repeat --> 200-900 repeats in FRDA1 (frataxin) gene

- Results in improper splicing

- Symptoms: Loss of muscle control, incoordinated limb movements, loss or diminished tendon reflexes and enlarged hearts

- Diagnostic Genetic Test: Southern Blot

- CTG expanded repeat in the 3'-untranslated region

- 200-2000 repeats can be present

- Shows signs of severe amplification between subsequent generations

- Symptoms: Myotonia, muscular dystrophy, cataracts, hypogonadism, frontal balding, and arrhythmias

- High maternal anticipation

- Diagnostic Genetic Test: Southern Blot

- Multiple disorders that result from abnormal tRNA and mRNAs of the circular mitochondrial genome

- Varying penetrance due to the fact that mitochondria are divided assymetrically to daughter cells

- Specific cells can be more or less affected

- Maternally inherted --> 100,000 mitochondria transferred from oocytes and only 100 from spermatocytes

- Mitochondrial Encephalomyopathy with Lactic Acidosis and Stroke-Like Episodes (MELAS)

- Clinical manifestations: Many systemic issues including strokes, ataxia, mygraine, psychosis, depression, renal tubular defects, myopathy, diabetes, hypoparathyroidism, hypothyroidism, cataracts, etc

- Symptoms are extremely variable between patients

1. Determine whether the trait is dominant or recessive based on broken-unbroken descent. 

2. Determine the sex of individuals affected

3. Determine the sex of the individuals who are transmitting the trait

-100000 and 200000 --> Autosomal loci or phenotypes (entered before May 15,1994)

- 300000 --> X-linked traits

- 400000 --> Y-linked traits

- 500000 --> Mitochondrial

- 600000 --> Autosomal loci (entered after May 15, 1994)

- An individuals with a disease allele that does not actually manifest with the disease pathology

- Multiple genes may be responsible for the same disease pathology

- Clinical heterogeneity or the phenotypic spectrum can vary from person to person

- Even with the same underlying mutation

- Conditions may not manifest, manifest differently, or may even lead to lethality depending on the gender of the affected individual

- If a disease gene is imprinted, it will only contribute to the phenotype if it is designated as active by the transmitting parent

- This describes why maternally imprinted gene mutations are only transmitted by men and visa versa

- Usually imprinted genes are methylated and therefore silenced

- p(affected)= p(parents are carriers) x p(transmission)

- Unbroken transmission between generations

- Affects both males and females equally

- Unbroken transmission from generation to generation

- Affects both males and females equally

- Anticipation occurs --> Earlier age of onset

- Broken descent --> Skips generations

- Affects both males and females equally

- Maternal Transmission Only

- Affects both males and females equally

- Unbroken descent between generations

- Males effected more often than females

- Male to male transmission not seen

- Broken descent between generations

- Affects both males and females but males affected more often than females

- Male to male transmission not seen

- Unbroken descent between generations

- Only males affected

- Male to male transmission

- Maternally imprinted --> Never transmitted by mother to offspring

- Paternally imprinted --> Never transmitted by father to offspring

- Human body has 10^14 cells and about 210 different cell types

- Initial zygote is totipotent

- Cell differenatiation occurs through a sequential activation of genes and signaling pathways

- Many transcripton factors act as master genes that help to initate differentiation in multiple cell lines

- Some fate decisions are made autonomously based on the surrounding cells or neighborhood of cells

- Environmental factor that leads to a birth/congenital defect

- Social Drugs: Alcohol, cocaine and cigarettes

- Environmental Agents: Organic solvents, chemicals, lead, mercury, anesthetic gases

- Infection Diseases: Chicken pox, rubella, and CMV

- Others: Maternal diabetes, lupus, epilepsy, radiation and hyperthermia

- Androgenic drugs --> Alter the testosterone levels of the fetus --> Interfers with proper development of genitalia

- Retinoids --> CNS, cranifacial, and cardiovascular defects

- Thalidomide --> Severe limb defects

- Statins --> Holoprosencephaly (forebrain and midline facial defects) 

- Prescribed for morning sickness for women in the 1960's

- Causes severe limb defects when ingested during the critical period for limb development

- Day 30: Defects in both upper and lower limbs

- Day 35: Only lower limb defects

- FGF normally initiates proper proliferation and differentiation of mesenchymal cells of the limb bud

- Cells exposed to FGF levels for a longer period of time form distal regions of the limb

- Only distal regions of the limb form at the shoulder because these regions are exposed to FGF for a longer period of time

- Proximal limb structures not formed in these individuals

- Most common cause of dwarfism

- Autosomal dominant trait

- 1/15,000 births

- Caused by a mutation in the FGFR3 gene (inactive FGF receptor)

- >99% of mutations due to mutation of 1138 base pair mutation: Arg --> Gly shift in protein

- ~80-90% of mutations occur de novo in sperm

- Mutation paternally inherited (through sperm)

- Characteristics: Rhizomelic shortening of the arms and legs with relatively long and narrow trunk comparatively, macrocephaly with midface hypoplasia and prominent forehead, spinal cord compression, and normal but delayed intelligence

- Normal population: 1/15,000 even if one child has already been born with the disorder

- One parent affected: 50% affected

- Both parents affected: 50% affected (Rr), 25% lethality (RR), and 25% normal (rr)

- Gly380Arg mutation --> ligand independent receptor activation

- Results in a gain of function mutation

- Normally FGFR3 activation inhibits chondrocyte proliferation

- Normally helps to coordinate the cycle between proliferation and differentiation that is necessary for proper bone growth

- FGFR3 mutation --> Inhibits chondrocyte proliferation and therefore endochondral ossification

- 1/13,000 births (50x greater prevalence in spontaneous abortions)

- Complex etiology: Chromosomal anomalies, single-gene mutations (autosomal dominant, recessive, and X-linked), teratogens

- Causative teratogens: Maternal diabetes, hypocholesterolemia, or cyclopamine ingestion

- Mutations: SHH, TGIF, SIX3, or ZIC2 --> All master gene transcription factors

- An example of genetic/locus heterogeneity

- Characteristics: Defects in midline formation of the forebrain, craniofacial abnormalities, developmental delay, seizures, and pituitary dysgenesis

- Varying severity of disease based on the genetic background

- Both due to the same mutation in SHH but entirely different appearances

- Mutation in sonic hedgehog (SHH) gene

- Mutation in gene leaves receptor and down stream genes inactivated

- SHH is necessary and sufficient to cause proper formation of the forebrain

1. SHH is mutated in 30-40% of autosomal dominant nonsyndromic HPE

2. Other mutations are non-coding mutations (15-265 kb pairs from gene) 

- "Position-effect" mutations affect the levels of SHH gene transcription --> Improper gene dosage for normal development

- Cyclopamine: Blocks the action of SHH

- Maternal hypocholesterolemia: Caused by maternal ingestion of statins --> SHH normally bound to cholesterol in order to travel throughout the brain

- SHH normally modifies multiple cells and travels extracellularly between neighboring cells

- SHH as a morphogen: Movement of SHH creates a concentration gradient where some cells receive higher levels and higher activation compared to others --> Promotes growth in certain areas

- De novo gene deletion of 11p13

- Includes PAX6 and WT1 genes

- Characteristics: Wilm's tumor, aniridia, genitourinary anomalies, and mental retardation

- About 1/3 of patients with anirida have WAGR syndrome

- Complete or partial loss of the iris

- Autosomal dominant trait

- Can either be sporadic (arising de novo) or familial

- Caused by a PAX6 mutation

- PAX6: Master gene involved with many organ systems, including CNS development as well as eye formation

- Nephroblastoma

- 1/100,000 births

- Accounts for ~8% of pediatric tumors --> Mean diagnosis of 3.5 years old

- Genetic/locus heterogeneity

- Most cases are sporadic --> ~5% due to germline mutation

- Mutations in the WT1 gene in both cases

- WT1 Gene:

1. Zinc finger that binds to DNA and RNA --> Acts as a negative and positive transcription factor

2. WT1 gene also involved in RNA splicing

3. Necessary for kidney differentiation and nephron and glomeruli formation

- Primary: Internal genitalia does not match genotype

- Secondary: External genitalia does not match the genotype and the internal genitalia

- ~1 in 1000 newborns

- Phenotypically heterogeneous: Extreme being XX or XY complete sex reversal

- Genetically heterogenous: SRY, SOX9, WT1, SF1 and DAX1 mutations possible

- Varying degrees of phenotype due to the mutations of different genes --> Each gene represents a different step in the sex differentiation pathway

- Degree of protein dysfunction caused by each mutation will determine the severity of the phenotype expressed

- XY sex reversal --> Often leads to gonadoblastoma

- Translocation of SRY gene from the Y-chromsome to the X-chromosome during meiotic crossing over

1. 46, XX Sex Reversal: 1 in 20,000 males --> 80% with SRY translocation

- Sterile due to the two X-chromosomes (gene dosage issue) and no Y-chromosome genes for spermatogenesis

2. XY females: 10-15% have mutated SRY genes --> Inactive SRY gene

- XY females are infertile due to only one X-chromosome (gene dosage issue)

- Very susceptible to gene dosage issues

1. Heterozygous mutations in SOX9, WT1, and SF1 --> XY females

2. Duplication of DAX1 --> XY females

3. Duplication of SOX9 --> XX males

4. Imbalance of WT1 splice isoforms --> XY females

5. SRY mutation can be passed from father to XY daughter

1. Deamination of cytosine --> Uracil

2. Double stranded breaks due to UV radiation

3. Single stranded breaks

1. Gain of function in oncogenes

2. Loss of function in tumor suppressor genes

3. Loss of function in apoptotic genes

4. Gain of function in anti-apoptotic genes

- Mutations result in gain of function

- Activates pathways that promote cell growth

- Mutations can occur anywhere along the pathway

- Different mutations and syndromes result from different mutations in the same pathways

- Types of Mutations: Deletion, point mutation, gene amplification, and chromosome rearrangement

- Epigenetic Changes: Demethylation of normally silenced gene results in the gene being abnormally active

- Resulting chromosome due to a translocation of chromosome 9 to chromsome 22

- bcr-abl gene fusion --> Chronic Myelogenous Leukemia

- Easily treated with Gleevac --> Targets the Philadelphia Chromosome

- Specific miRNAs that regulate the activity of oncogenes

- Each miRNA can modify >200 genes

- Mutation in one of these mRNAs can cause lots of systemic problems

- Act to properly repair the mutations that occur naturally in cells due to radiation and other external factors

- Nucleotide excision, double stranded breaks and single stranded breaks need to be repaired

- Mutations in these genes leave cells susceptible to further mutation

- Also leads to chromosomal instabilty that is charactertistic of neoplasms

- Caused by a defect in nucleotide excision repair

- Individuals have acute sensitivity to sunlight

- Normally develop skin cancer by the age of 10 or younger

- Mutation causes chromosomal instability

- Mutation in double stranded repair protein ATM

- Symptoms usually present by the age of 2

- Symptoms: Loss of balance and slurred speech

- Progressive disease of degeneration, radiosensitivity, immunodeficiency, and predisposition to cancer

- Ultimately leads to chromosomal instability

- Chromosomes do not arrange into the normal structures --> Have very odd shapes upon karyotyping

- Mutation in double stranded break repair --> Similar to AT but not specifically an ATM mutation

- Characteristics: Physical abnormalities, bone marrow failure, and increased predisposition to cancer

- Physical abnormalities: Short stature, skeletal malformations, thumb malformations, and abnormal pigmentation

- Very similar in presentation to Fanconi Anemia

- Mutation in genes that interact with the genes involved in Fanconi Anemia

- Symptoms: Severe growth deficiency, repeated otis media and pneumonia, early menopause (women), infertility (men), and wide susceptibility to cancer

- AKA gatekeeper genes

- Regulate the progression of a cell into each of the different cell cycle stages

- Knudson's Two Hit Hypothesis --> Both copies of the gene need to be mutated for cancer to develop

- Possible Genetic Alterations: Chromosome loss, gene deletion, unbalanced gene translocation, loss or duplication of a gene, miotic recombination, and point mutation

- Epigenetic Alterations: Normally active supressor gene becomes methylated and therefore inactive

- Mutated oncogene or tumor suppressor gene transmitted to offspring

- Two Hit Hypothesis is still necessary

- Second mutation happens much more frequently in this population --> High frequency mutation

- Cancer still occurs pretty often in this population

- Should be recessive traits but actually passed along in a dominant fashion since the 2nd mutations occur at such high frequency

- Familial mutation in p53

- Susceptible to breast cancer, sarcomas and other types of cancer

- p53 is involved in MANY processes --> DNA repair, apoptosis, cell cycle arrest, and senescence

- Critical gene for cancer development --> Mutation in about 50% of cancers

- DNA repair genes --> Involved in the same pathway as ATM

- Genes are very similar but not identical

- BRCA1 --> Breast, prostate, ovarian, pancreatic and colon cancer

- BRCA2 --> Breast, ovarian, prostate, pancreatic and male breast cancer

- Genetic tests allow for patients to undergo preventative surgery or simply undergo increased surveillance measures

1. Self-sufficiency in growth signals

2. Insensitivity to anti-growth signals

3. Evading apoptosis

4. Limitless replicative potential

5. Sustained angiogenesis

6. Tissue invasion and metastasis

- Microarray analysis of cDNA produced from mRNA of tumor and normal samples

- Color of each well determines the composition of gene expression between both samples

- Helps determine which genes are over and under expressed

- Allows determination of cancer subtype

- Each subtype has different treatments and responds differently to treatment plans

- Some cancers are more agressive and more susceptible to relapse episodes

- Faster, more comprehensive DNA diagnostics

- More accurate, objective diagnosis

- Better prognostic ability

- Identification of biomarkers for specific illness/individual

- Better understanding of disease processes involved

- One base pair mutations that are particularly common in the population

- Indentified through the Human Genome Project

- Equivalent to variations in 10^7 base pairs

- SNPs found at about 3 every kb

- 80-85% of SNPs are within the coding region

- Performed by spliceosomes

- Creates multiple proteins from one mRNA product

- The amount of gene produced is different for each specific gene

- Can cause gene dosage issues

- Individual genes are duplicated

- Can end up with multiple copies of each gene

- Can cause gene expression variations

- 1,500 CNVs in genome

- Phenotypes could be modulated by gene dosage 

- Mother eating a diet high in methyl donors can cause offspring to have a different colored coat

- High presence of methyl donors --> Genes more methylated

- More methylated --> More silenced

- Compares the risk of an individual of an affected relative with the general population

- Gives the increased risk ratio for affected families vs. general population

- Compares monozygotic and dizygotic twins

- Disadvantages: Most twins live together, so unable to determine what is genetic vs environmental influence

- Helps differentiate between genetic causes and environmental causes of disease/syndrome

- Allows monozygotic twins who have been separated at birth and grew up in different households to be studied

- Useful to properly determine what is genetic vs. environmental

- Very hard to find individuals to enroll in the study

- Law of Independent Assortment during Meiosis --> Chromatids are inherited independently of one another

- Used to determine if two sections of DNA are linked

- If linked --> Genes will be inherited together even if recombination occurs

- Unlinked: Genes recombine independently --> Could either be inherited together or separately with equal frequency

- Tries to find a silent DNA marker allele that is associated with the disease gene that is inherited with the diseased gene in a family

- Requires both large extended families as well as large collections of silent DNA markers

- Subjects: Large, multi-case families

- Complications: Requires specific, hard to find family structure and can only detect strong genetic contributions

- Restriction Fragment Length Polymorphism (RFLP): These markers bind to different lengths of DNA sequences after being cut by restriction enzymes

- Simple Sequence Length Polymorphism (SSLP): These marerks beind to different lengths of doublet repeat sequences --> Generally have more alleles

- Single Nucleotide Polymorphism (SNP)

- Markers can be present in different alleles themselves

- Follow the inheritance of the markers with respect to disease phenotype --> Determines whether the marker is linked or unlinked to disease gene

- Unlinked --> No specific relationship between the marker allele and disease gene

- Tightly linked --> Marker allele directly related to disease gene

- Linked --> Marker allele is inherited with disease gene

- One recombination even can still occur with a linked gene to change the results --> Very uncommon though

- Also, the lack of presence of disease with marker allele could mean the individual is non-penetrant

1. If a marker is linked to the disease gene it will be transmitted at a higher rate that normal in affected individuals --> Almost 100%

2. If marker is not linked to disease gene --> Will be inherited 50% of the time due to law of independent assortment

- Combination of alleles at different loci of one chromosome that are inherited together

- Size of the haplotype depends on the number of recominbation events that occur during meiosis

- Analyzing the size of a particular haplotype including the diseased gene can help narrow down which genes it is linked with

- Searches for changes in sequences that correlate with the known disease pathology

- Identifies if individual has the mutation necessary for a particular disease

- Look for proteins that are known to have relevant functions in the pathology of a disease

- Must know the pathways involved in disease pathogenesis

- Also must already know something about the disease and its biochemical properties

- Hunting for gene or protein families that are involved in similar diseases

- This provides a good starting point

- Run BLAST search on already identified genes/proteins

- Use knock out animals to study disease pathways

- Statistical test used to estimate the probability that a marker is actually linked to the disease gene

- Essential in linkage analysis studies

- Must know something about the mode in inheritance first

- Need to be able to make assumptions about the disease gene in order to move forward

- Takes into account non-penetrance, co-dominance, etc

- Study of affected siblings

- By chance siblings can share 0,1, or 2 alleles --> If the allele is linked to disease gene than it is more likely to be inherited by both siblings

- Sharing of alleles near the disease locus is more common in affected siblings

- These alleles would be linked to the disease gene so should be inherited together

- Can be hard to distinguish identity by state vs identity by descent in these studies

- Autosomal dominant trait: Overrepresentation of siblings sharing at least one allele of a marker for disease gene

- This pattern shows a deviation from expected allele sharing

- In this case siblings would share 1 or more allele at a much higher frequency than normal

- Normal is 50% for one allele and 25% for two alleles shared

- Without the phenomena of non-penetrance, codominance or incomplete dominance

- Identity by state: Same allele inherited from mother and one from father

- Identity by descent: Two different alleles from either mother or father

- Only way to weed out state vs. descent is by obtaining parental DNA samples --> Often not possible

- When not possible to obtain parental DNA --> select markers that have multiple low frequency alleles (SNPs not SSLPs)

- Allows lots of people to be observed and enrolled in the study

- Case control study

- Assumes that there is one common ancestor at some point who contributed the disease gene to the population

- Linkage disequilibrium: Occurs in the affected group due to the common ancestor who provided disease gene

- Can get very skewed results if the control group is not properly determined and selected

- Requires the presence of an isolation population with a small group of founders

- Subjects: Population samples

- Frequency of an allele is different in an affected child compared to their parents

- Disease allele seems to be passed on more frequently to offspring than wild type allele

- Evident through observation of a pedigree

- Shows a special charactertistic of that particular disease allele

- Built in familial controls rule out the issue of controls in association studies

- Subjects: Trios of parents and affected offspring

- Often times a disease is not caused by just one mutation in one gene

- Varying degrees of severity and alterations in phenotype can occur

- Thought to be due to the interplay of modifier genes

- Ex. Cystic fibrosis

1. Always due to a deletion of the CFTR gene

2. Varying degrees of severity in CF due to modifier genes --> some cases are very severe and the patient dies rather quickly while other do not

3. Caused by gene-gene interactions

- Determined through affected sib pair analysis of syntenic human DNA region

- 40-50% twin concordance --> Risk for twins

- Weak linkage to multiple genes throughout the genome

- Diagnostic tools: Schizoid personality only or also some bipolar personalities within the family

- Very subjective diagnosis by physicians --> hard to diagnose, so hard to properly study the genetic basis

- Interphase FISH --> Need to know exactly what you're looking for --> Need probe already but faster

- FISH --> Does not require specific probe but not as fast as interphase FISH

- Spectral karyotyping

- PCR is used to determine the specific mutation involved 

- Only detects size differences in segments cut by restriction endonucleases

- Detects moderate size changes

- Only detected if the size is big enough to change the migration in the gel

- Great for determining the length of exonic repeats --> CAG repeat of Huntington's

- Intronic and promoter repeats are too large to be detected through this method

- Used to detect large size changes --> Intron and promoter regions

- If size is too large PCR won't work because Taq polymerase won't fully amplify sequence

1. Digest with restriction endonuclease

2. Run on gel

3. Add filter paper to bind DNA

4. Add specific DNA probe for sequence

5. Bands light up when exposed to x-rays

- Caused by a huge CTG repeat in the intronic region

- Presents as >10 kb pair segments on gel after EcoR1 cleavage

- Normal protein presents with 8 or 9 kb pair segments after EcoR1

- Maternal transmission causes severe amplification or anticipation of trinucleotide repeat

- Also through southern blot

- Expanded CGG repeat in promoter region

- Expanded region is prone to methylation --> Increased methylation with increased expansion of repeat

- Methylation causes inactivation of gene

1. Digest sequence with EcoR1 and then EclXI

2. EclXI will not cleave if sequence is methylated

3. Run on gel to observe segment sizes

- Some methylation is normal due to X-inactivation in females so segment lengths are normally rather long

- Allows the determination of small mutations, even single nucleotide changes

1. Uses ddNTP nucleotides as well as normal dNTP nucleotides

2. Incorportation of ddNTP at any position causes the termination of the DNA sequence

3. These chains can then be run on a special gel that can separate out chains by single nucleotide size changes

4. ddNTP nucleotides are radiolabeled so each specific one can be tracked

5. DNA is sequenced through laser analysis of the colors on the gel

- Comparing the patient's sample to a control sample allows for determination of mutations

- High sequencing burden of DNA sequencing --> Infromatics issue

- Looks for a specific known mutation or set of possible mutations

- Hybridize a specific probe to an individual gene

- Dot blot examination: Used to see if the probe binds to each individual sample --> Determines the presence of the allele in question

- Generally only looks at one possible allele --> Misses any other mutations that cause the same condition

1. PKU has multiple mutations and genes that can cause the same condition (locus and allelic heterogeneity)

2. CF has multiple mutations as well --> DF508 causes 2/3 of CF cases but 1/3 not caused by this

- Good for conditions with high allelic heterogeneity within one gene

- Allows determination of single nucleotide changes causing gene mutation

- Looks for a small number of mutations

- Good for limited allelic heterogeneity

- Need to know the most common and specific mutations

1. Restriction Fragment Length Polymorphisms: Digest and probe for sequence or PCR first to amply before digesting

2. Simple Sequence Length Polymorphisms: Probes for sequences outside gene sequences for PCR amplification

3. Single Nucleotide Polymorphisms: DNA sequencing and look at changes

- Pick markers on both sides of the gene in order to look at how it is passed down through generations

- Determines how it is passed down

- X-linked recessive disease --> More males affected

- Follow markers to help determine who is affected and who is a carrier

- Always possible that recombination event occurred and marker is no longer linked to disease gene

- This could cause the presence of a carrier when allele not present or not carrier when allele is present

- Eliminate probabilty of recombination by choosing markers that are as close to the disease gene as possible

- When both copies of a chromosome are inherited from either mom or dad

- Results from a non-disjuction even

- Can result in the appearance of a recessive disorder from one parent carrier or disease arising in unbalanced imprinting (Prader-Willi or Angelmann's Syndrome) 

- Only poses an issue when the gene is imprinted from the parent they inherited it from

1. Maternal deletion or paternal disomy --> Same symptoms

- Ex. Angelmann's Syndrome: Gene 1 of chromsome 15 is paternally imprinted so no active copy of gene 1 is present

2. Paternal deletion or maternal disomy --> Same symptoms

- Ex. Prader-Willi's Syndrome: Gene 2 of chromosome 15 is maternally imprinted so no active copy present

- Genetic Testing Methods: FISH analysis for gene 1 or gene 2 or haplotype analysis

- Compares the loci of each chromosome that are generally inherited together

- Compares the genes present in each locus between offspring and parent

- Needs both parents DNA for comparison

- Can determine where the chromosomes were inherited from

- Looks for homozygosity between chromosomes then determine whether it is from mom or dad

- Sometimes you can even detect a carrier with these tests

1. Sweat test for CF

2. Phe blood test for PKU at birth

3. Isoelectric Focusing: Gel electrophoresis analysis of HbA and HbS subunits for hemaglobinopathies --> Catches sickle cell and sickle cell trait individuals

4. High Performance Liquid Chromatography: Can determine the quantity of HbA and HbS present --> Good for B-thalasemia and other similar diseases

- More costly than isoelectric focusing

- Allows preventative or early treatment options

- May aid in reproductive decision making

- Confirm diagnosis and suitability of medical treatment

- Give prognostic information

- Not diagnostic

- Must be an important health problem with known genetics and course of the disease

- Test must be inexpensive

- Test must be relatively accurate, quick, and easy to interpret

- Test must be safe and voluntary

- Patients or their family must benefit from test --> Available diagnosis and treatment or ability to change the clinical course (preventative measures)

- Sensitivity: Probability that a person carrying the disease will present with a positive test (true positive)

- Positive Predictive Value (PPV): Probability that people who test positive will actually have disease

- Specificity: Probability that a person not carrying the disease will test negative (true negative)

- Negative Predictive Value (NPV): Probability that people who test negative will actually not have the disease

- Population Screening: Not currently available for genetic testing, tests for things like hypertension, diabetes, etc

- Newborn Screening: Tests for conditions like PKU, hypothyroidism, inborn errors of metabolism, and hearing loss

- Carrier Screening: Test for carrier status of conditions such as CF, Sickle Cell, or Ashkenazi Jewish panels

- Prenatal Screening: Performed before birth but during a pregnancy --> Maternal serum screening and ultrasounds

- Currently there is a panel of 29 conditions and an additional 25 conditions associated with the first 29 conditions

- Ex. PKU testing for high phenylalanine levels

- Conditions must:

1. Be able to be identified at a certain time after birth

2. Tests must have appropriate sensitivity and specificity

3. There must be demonstrated benefits of early detection, time intervention and efficacious treatment of the condition

- NBS Core Panel: For Organic acids, fatty acid oxidation, amino acids, hemoglobinopaties, and other conditions

- 50-62% of hearing loss is actually genetic

- Most are autosomal recessive in transmission

- Usually due to a mutation in the connexin-26 gene --> 50-80% of non-syndromic AR deafness and 37% of sporadic deafness

- Connexin-26 --> Chromosome 13q

- 1 in 31 individuals of European descent are carriers

- Common Caucasian mutation: 35 delG in 90% of cases

- 1 in 25 Ashkenazi Jews have 167 delT mutation

- Single gene --> CF

- Mutliplex panels --> 5-12 diseases tested at once

- Chip-based assay --> Can test for >100 diseases

- Sequencing-based assay --> 100's to 1000's of diseases at once

- Certain ancestral groups are more likely to be carriers of certain recessive conditions

- Tests for disease alleles with a frequency of 0.1% in the gene population

- The sensitivity of specific DNA carrier screenings depends on the individual's ancestry --> 80% for some while 30% for others such as Asians

- Common conditions tested: Hemoglobinopathies, cystic fibrosis, Tay-Sachs disease and other diseases common in Ashkenazi Jewish populations

- Cystic Fibrosis Testing: Commonly offered for Caucasians and Ashkenazi Jews --> Pan-ethnic mutation panel of 25 common mutations

- 7% of people in the world are carriers

- Types: Sickle cell, HbSC disease, Beta-thalassemia, Alpha-thalassemia, and other variants

- Testing: Complete Blood Count and hemoglobin electrophoresis

- Features: Progressive neurodegeneration, weakness, loss of motor skills, seizures, blindness, and eventual death

- Carrier Screening: Enzyme anaylsis of hexosaminidase A enzyme --> Simple, inexpensive and accurate --> Use leukocytes for women who are pregnant or taking oral contraceptives to avoid false positives

- Molecular Analysis: Indentifies specific mutations in the HEXA gene

- Causes hemolytic anemia and neonatal jaundice

- X-linked recessive --> More severe in males

- Symptoms can be induced by certain medications (sulfa drugs), fava beans, and certain infections

- Genetic testing is often performed in families with histories of the disease

- Recurrent attacks of fever, inflammation, and pain

- Also associated with amyloidosis, renal failure, and reduced fertility

- Carrier screening is usually only offered once a mutation has been identified in the family

- Caucasian: Cystic fibrosis (1:25)

- African American: Sickle Cell (1:12) and Beta-thalassemia (1:10)

- Mediterranean: Beta-thalassemia (1:20)

- East Asian/Southeast Asian: Alpha-thalassemia (1:6 in some areas)

- French-Canadian: Tay-Sachs Disease (1:30)

- Ashkenazi Jews: Tay-Sachs Disease, Canavan disease, cystic fibrosis, familial dysautonomia, Bloom syndrome, Fanconi Anemia, Gaucher Disease, Mucolipidosis IV, Niemann-Pick Disease, Maple-Syrup Urine Disease (Type 1B), and Glycogen Storage Disease (Type 1A) --> 1:4 or 1:5 are carriers of something

- Causes progressive muscle weakness

- Onset of disease ranges from birth to young adulthood --> Varying phenotypes

- SMN1 gene on chromosome 5 mutation

- Carrier frequency is 1:41 --> 95% have homozygous deletions or truncations of exon 7 of SMN1 gene

- 5% are compound heterozygotes (1 deletion/truncation and 1 mutation)

- 2% of cases will have 1 de-novo mutation

- ACMG recommended that SMA carrier screening be offered to all pregnant couples in 2008

- X-linked disorder caused by expanded CGG repeat in promoter region --> Expanded repeat is methylated and inactivates gene

- Features: Moderate intellectual disabilities in males and mild ID in females due to heterozygosity

- Properly catches patients with >200 repeats and allows them to make decisions about reproduction

- Also catches people in the pre-mutation range (59-200 repeats) --> These people do not have ID but women may develop premature ovarian insufficiency and males may develop late-onset tremor-ataxia

- What is the cut-off for "abnormal results?" 

- Is it good that pre-mutation individuals are caught in this screening?

-Counsyl: Allows 100 of genes to be tested for only about $100 dollars --> Very low cost and wide screening

- GoodStart Genetics: Advanced DNA sequencing screening for patients --> Provides higher detection rate and improved clinical performance

1. Ancestry-based vs. Pan-ethnic? --> Quality vs. quantity

2. Preconception vs. Prenatal testing?

3. Couples of mixed ancestral background?

4. Informed Consent? --> Does patient really understand all of what they are being screened for?

5. Testing patient and partner sequentially or in tandem?

- First Trimester Screen: 10-13 weeks, tests PAPP-A and hCG, also nuchal translucency --> 80% detection of Down's and 90% for trisomy 18

- Second Trimester Screen: 15-21 weeks, tests for AFP, hCG, uE3, and inhibin-A --> 80% for Downs, trisomy 18 and open neural tube defects

- Mothers can only go through either 1st or 2nd trimester screening --> 2nd trimester gets results later but does estimate risk of open tube defects

- First Trimester

1. Trisomy 21: Increased hCG and decreased PAPP-A

2. Trisomy 18: Decreased hCG and PAPP-A

- Second Trimester

1. Neural Tube Defects: Very high AFP

2. Trisomy 21: Decreased AFP and uE3 and increased hCG and inhibin-A

3. Trisomy 18: Decreased AFP, hCG, uE3, and inhibin-A

- Observing the amount of lymphatic fluid present in the nuchal area during ultrasound

- Increased nuchal translucency --> Increased risk of genetic diseases

- Combination of 1st and 2nd trimester screenings

- Reported after 2nd trimester

- Eliminates the option of CVS

- Initial measurement of nuchal translucency, PAPP-A and hCG in first trimester screening

- Divide pregnancy into low, moderate or high risk group

- Low risk requires no further testing

- Moderate risk usually receives 2nd trimester screening and potentially diagnostic testing

- High risk group is offered diagnostic testing

- First trimester: Dating scan and nuchal translucency

- Second trimester: Fetal survey

- Third trimester: Pregnancy complications and observe whether the baby continues to grow

- Fetal survey ultrasound findings: 

1. Soft-signs/Markers: Choroid plexus cysts, echogenic bowel, echogenic intracardiac foci, two-vessel cord, and increased nuchal translucency

2. Anomalies: Heart defects, cleft lip/palate, spina bifida, brain abnormalities, clubfeet, and diaphragmatic hernia

1. Cytogenetic Analysis

- Maternal age >35

- Known balanced translocation in one of the parents

- Previous pregnancy with aneuploidy

- Abnormal ultrasound

- Abnormal MSS

2. Molecular Genetic Analysis

- One or both parents is a confirmed carrier of a genetic condition

- Abnormal ultrasound

- Paternity testing

3. Biochemical Analysis

- Open neural tube defects and abdominal wall defects (AFAFP)

- Metabolic conditions

- Fetal lung maturity

4. Test for Intrauterine infections

- Cytomegalovirus, toxoplasmosis, etc

- Amniocentesis: 99.9% accurate, sampling of amniotic fluid --> Can only diagnose ONTDs w/AFP and AChE

- Chorionic Villus Sampling (CVS): 98% accurate --> Possible to have maternal cell contamination vs. true mosaicism --> Can be performed earlier in pregnancy

- This testing only detects specific conditions --> Need hypothesis

- Risk of miscarriage for both of these procedures --> More likely in CVS

- Non-invasive Prenatal Testing --> Very promising due to its high detection rates and decreased risk of miscarriage

- There are ~20 fetal cells in 20cc of maternal blood --> VERY scarce

- 10-15% of DNA in maternal plasma is fetal --> Can be isolated out

- Mother's blood may contain cells of child up until child is 20 years old

- Can detect aneuploidy

- Can provide reassurance for parents that their child is unaffected

- Can allow parents to prepare psychologically and practically for the birth of their child

- Can allow for physicians to plan delivery, management and special care

- Can allow for the option of termination if wanted

- Rapid, high resolution screening of the entire genome that allows for the detection of losses and gains in DNA copy number

- Future applications: 3-5% hit rate for clinically significant CNV with abnormal ultrasound

- Could produce variants of unknown significance (VUS) --> Would provide little knowledge about their prognosis

- Pros: Can ask multiple genetic questions, less expensive, shorter timeframe, better for individuals who are adopted, information provided directly to patient

- Cons: May not test the common mutations of the non-majority and genetic counselor not involved

- Incidental findings could either be a pro or con depending on the mutation and depending on the beliefs of the individual

- Pros: Only one genetic question in question and information is interpreted through a professional

- Cons: Only asks one genetic question normally, more expensive, long wait for appointments, anxiety involved with the doctor, not optimal for making time-sensitive clinical decisions

- Autosomal dominant trait

- Mutation in 1 of 3 genes: presenilin 1,2, and amyloid precursor protein (APP)

- Presenilin protein 1 and 2 are part of the gamma-secretase complex that cleaves beta amyloid from APP

- These mutations have been down in 50 families now

- Met146Leu in PSEN1 gene mutation --> 100% penetrant for Early-onset Alzheimers Disease

- 1=p2 +2pq+ q2

- 1= p+q

- Only if population is large and only if inheritance of alleles is random

- Repository for genetic information

- Registrants can select their preferences and can change them over time so they can learn certain things about their genome at different times

- Loss of genetic diversity within a particularly small population

- See an abnormally high incidence of certain alleles

- Common in populations with lots of inbreeding

- AKA high throughput sequencing

- Crucial in refined linkage studies

- Over 98% of genes are within 5 kb of a SNP

- Over 10 million SNPs identified --> Density of about 3 per kb

- Previously used 200-300 markers at a density of one marker per 10-15 megabase

- Microarrays used to identify SNP alleles --> DNA tagged with flourescents --> Resulting color are identified in each well

- Once micrarray analyzed --> SNP sequened via DNA sequencing

- Microarray analysis of SNPs can be as specific as differentiating what single nucleotide is in a position

- Also use microarrays

- Wells specified for different viral DNA sequences

- Take samples from affected individuals and run microarray analysis

- Helped determine the virus responsible for the SARS outbreak

- Then sequence gene after microarray completed

- Detects amplifications and deletions in genomic loci

- Allows for the determination of copy changes in SNPs and other small genomic loci

- Can be used to determine which genes are upregulated or downregulated in diseases/cancers

- May also eventually replace karyotypes

- Cannot detect translocations --> Can only detect copy variants

- SKY still good for translocations

- Used for individuals with undiagnosed diseases

- Generally used for people when they are desperate

- Diagnosed 15% of the cases it has taken on during the NIH project

- Allows physicians to create treatment plans for otherwise untreatable cases

- Requires alot of scientists involved --> bioinfromaticians, sequencing techs, physicians, genetic counselors, and ethicists 

1. Activation of paralog gene to compensate --> Not always possible

2. Non-viral --> naked DNA enclosed in liposomes

- Very non-specific and ineffecient --> Can't distinguish specific cell types

3. Replication deficient virus --> Much more efficient and can target specific cell types

- Risk of activating oncogenes --> Cancer

- Also risk of severe inflammatory/immune reactions

- Ex. SCID with IL2RgC and Hemophilia B with Factor IX gene

4. RNAi: RNA interference --> Silence abnormal genes

- Use pluripotent or totipotent cells

- Introduce treatment gene

- Administer to patient to re-colonize specific cell type

- Can potential turn mature fibroblasts back into pluripotent/totipotent stem cells --> Introduce treatment gene and administer to patient

- This is the future of gene therapy!!

- Individuals with certain genes tend to have different reactions to specific medications

- Responses: No response, therapeutic response or adverse response

- Allows physicians to determine factors that influence drug specificity, metabolism and toxicity

- Can use this information to develop individualized treatments that are more effective with fewer side effects

- Ex. 6-Mercaptopurine for Acute Lymphoblastic Leukemia --> Stops the transition of 6-MP to 6-MeMP

- Ex. Gleevac for Bcr-Abl translocated CML

- Began after the human genome project sequenced the entire DNA sequence

- Soon genetic testing will account for 1/3 of all diagnostic testing costs

- Most specialize in clincal areas --> Most in prenatal, cancer, pediatric, and adult testing

- Non-clinical areas --> Laboratory areas, research coordinators, marketing, legislation, sales, administration, etc

- Personal/family history of cancer diagnosed <45 years

- 3 or more first/second degree relatives diagnosed with the same type of cancer

- Constellation of colon and endometrial cancers within a family

- Constellation of breast and ovarian cancers within a family

- Multiple types of primary cancers

- Male breast cancers and other rare cancers

- Previously identified cancer-predisposing gene mutation in the family

- Birth defects --> Cleft palate, etc

- Developmental delay

- Prenatal exposures

- Dysmorphic features

- Behavioral concerns --> Autism, etc

- Unexplained cognitive impairment

- Gathering and Intepreting Information: Creating a detailed pedigree, examining pictures, etc 

- Education: Explaining all treatment options, reproductive options, and details of syndrome

- Counseling: Discuss the patients concerns, lifestyle choices, etc

- Care coordination and follow-up: Write a detailed letter to the patient detailing the topics discussed and for any specialists the patient will be referred to

- Mendelian Risk: Looking only at the inheitance pattern and the degree of relationship between affected individuals and the patient

- Bayesian Risk Analysis: Takes Mendelian risk assessment one step further --> Takes into account age of onset, other affected relatives, testing results, etc

- Empiric Risk: Uses population statistics --> Can be specified by ethnicity, age, sex, etc. 

- Positive Results: Can allow a family to learn about the natural history and prognosis of disorder and can allow preventive measures to be undertaken

- Negative Results: Can offer a sense of relief and in some cases rigorous surveillance can be avoided

- Allows patients to make informed decisions about the future, including reproduction

- Loss of privacy for other family members

- Inability to predict severity of disease

- Discrimination --> Employment and insurance

- Endless emotional response possibilities

- Autosomal dominant --> 93% de novo and 7% inherited

- 22q11.2 chromosome deletion --> Detectable by FISH

- Features: heart defects, cleft palate, learning disabilities, immune deficiency, hypocalcemia, renal anomalies, and hearing loss

- Variable expression within families

- Study of the bio-social movement that supports practices that improve and change the genetic make up of a population

- Previous examples are sterilization programs

- Modern day trends are familial balancing

- Modern Eugenics: Preimplanation screening, prenatal screening and cloning

- Family balancing is NOT a feared modern eugenics movement

- Standard karyotyping is recommended

- Mother could have a balanced translocation --> Robertsonian translocation

- Any non-disjunction even could cause a fatal aneuploidy in the fetus

- Ex. 14/21 translocation --> Trisomy 14 is not compatible with life

- Procedure begins  by extracting oocytes from mother

- Injecting sperm via intracytoplasmic sperm injection (ICSI)

- In vitro fertilization then occurs where embryo is left to grow in an incubator for a couple days until the blastocyst stage

- Then about 2 of the totipotent cells of the embryo at this point are extracted and DNA analyzed

- This allows for specific genetic testing of fetus at a very early age

- Genetic Test: FISH, microarray, comparative genomic hybridization, and PCR for particular gene sequences

- Can filter 91% x-chromosome or 74% y-chromosome sperm

- Currently used to prevent or decrease transmission of x-linked diseases

- Also used for family balancing --> Wanting to have a particular sex baby

- Only tests for the most frequent mutations

- Often need samples from other family members

- If frequent mutations are not identified, only full exon sequencing is performed --> Some mutations will go undetected

- In a situation where parents need to gain access to the resources needed to care for a special needs child before the child is born

- There is a social stigma against special-needs children so some parents want to know

- Illness of a child is a major cause of divorce

- Allows for parents to make decisions about selective abortions

- Question about whether to test prenatally for late onset diseases

- Also always the issue of eugenics

- Privacy is always an issue for people

- Don't want insurance company or employers to know their genetic status

- New genetic testing privacy law prohibits people from being discriminated against based on their genetic status

- Genetic Information Nondiscrimination Act (GINA)

- Genetic test are often very expensive

- Sometimes insurance doesn't completely cover

- Insurance should cover testing if there is a documented presence of the gene in question within the family

- Insurance will cover if:

1. Technology is FDA approved

2. Scientific evidence must demonstrate positive effect on health outcomes

3. Technology is at least as beneficial as any established alternatives

- Caused by uniparental disomy or imprinting

- del15q11-13

- Maternal deletion and paternal disomy

- No active copy of gene 1 --> Paternally imprinted

- Both copies of gene 1 are imprinted or only copy is imprinted

- Causes characteristic stance with arms outstretched, "marching walk" and perpetually smiling face

- del15q11-13

- Caused by maternal disomy or paternal deletion

- No active copy of gene 2 present 

- Gene 2 is normally maternally imprinted --> So either both copies or only copy is imprinted

- Causes severe trunkal obesity

- Principle explaining how the cytoplasm is not equally split between daughter cells during mitosis

- Describes the varying severity of mitochondrial diseases in individuals

- Some cells are more affected than others based on which mitochondria each daughter cell receives

- DNA methylation --> Associated with silencing of gene

- Histone acetylation --> Associated with activation of gene

- Both are heritable from one cell to the next

- Inadequate expression from a single gene causes disease symptoms

- These types of genes are inherited in a dominant fashion

- Ex. Myotonic dystrophy: Decreased expression of the DMPK gene

- Ex. Sex Reversal syndromes with gene dosage issues in SOX9, WT1, or SF1 genes --> A single gene is insufficient to produce proper testis development

- Genomic regions in two organisms containing the same stretch of genes

- Investigated for indentification of a gene that was associated with the severity in disease phenotype

- Standard linkage study

- Affected sib-pair analysis

- Genome-Wide Association Studies

- Twin studies

- Transmission disequilibrium test

- Uses an allele specific oligonucleotide

- PCR amplification will only occur if the anti-sense strand of the specific oligonucleotide is present

- Will only amplify if the one specific allele in question is present

- Will NOT amplify even if one base pair is different