Genetics:

Genome and chromosome structure + characteristics:

-46 chromosomes in all somatic (non germ line cells): ------contain 22 pairs of autosomes (non sex chromosomes), 1 pair of allosomes (sex chromosomes) Allosomes: XX (women) vs XY (men) Anatomy of individual chromosomes: 1) Centromere: connects the 2 sister chromatids -each chromatid composed of the p (short arm) + q (long arm) -both ends capped via telomeres -Sister chromatids: tandem copies of a 6 nucleotide-long sequence (ex: TTAGGG)

p53 gene mutations:

-50% of all cancers have these mutations, which prevents necessary gene repair or cellular apoptosis -p53 pathway (in normally functioning cells): is activated after S stage when the checkpoint occurs only IF incorrect replication or genomic damage is present -this pathway directs the production of gene repair enzymes or cellular apoptosis **when there is a mutation, this does not happen!

Hypertrophic CM:

-Abnormal thickening of cardiac muscle w/out secondary cause (1/500 adults=common) -50% associated w/germline mutation (affecting b-myosin heavy chain, cardiac myosin-binding protein C, or cardiac troponin T protein synthesis); the rest=sporadic + mosaic mutations -Inheritance risk: 50% of affected individuals demonstrate autosomal dominant patterns of inheritance Pathogenesis: thickening of ventricular walls, including IV septum often-->causes diastolic dysfunction-->dec reserve capacity of heart Phenotype: SXS start 20-40 yrs -SXS: DOE, CP (d/t reduced CO capacity + inc O2 demand of abnormality thickened myocardium), sometimes palps -Sudden death d/t V fib

Definitions:

-Allele: alternate form of a gene -Karyotype: picture depicting the # and morphology of a set of chromosomes -Locus: position of a gene on a chromosome -Gene map: comprehensive depiction of all of the genes on a chromosome and their loci -Cytogenics: study of chromosomes, structures + inheritance -Gamete: germ line cell (spermatocyte and ovum) -Homologues: members of a chromosome pair which carry mostly matching genetic info, but which may have slightly diff forms of specific genes -Chromosome: structure consisting of chromatin + carrying genetic info in form of DNA -Chromatin: the complex of DNA + protein; chromosomes are composed of this -Chromatids: 2 parallel strands of chromatin connected at the centromere (which constitutes a chromosome)

Recurrence risk of Down's Syndrome:

-Any Trisomy: 1% -Mother's <30 have 1.4% risk: this inc in risk is thought to be d/t unrecognized mosaicism in one of the parents -Mothers >30 years: no inc risk beyond that of maternal age IN general: risk of Down's recurrence in second child to a mom and dad w/normal genotypes is essentially same as general risk in the population (if elevated, barely) Translocations: have much higher risk of recurrence which is dependent upon the specific type of translocation

Transcription:

-Begins at the 5' untranslated region (UTR) and moves in the 5' to 3' direction -Hydrogen bonds: found between DNA base pairs, and are broken by polymerase enzymes -Transcription uses the anti-sense (3' to 5') strand in order to create an RNA molecule (which corresponds in polarity + base sequence to the sense (which is 5' to 3') strand -SO: Anti-sense strand is 3' to 5', and is the one used to create an RNA molecule - sense strand is 5' to 3' (which is the original DNA strand) After transcription, a few things happen before translation: 1) introns are spliced out 2) 5' end and 3' end are both chemically modified to increase the stability of the molecule **Now: the RNA molecule is termed mRNA->leaves the nucleus!

Polycystic Kidney Disease: etiology + pathogenesis

-Both autosomal dominant (ADPKD) + recessive varieties (ARPKD) -ADPKD caused by mutations in PKD1 gene (some from PKD2 mutations) -ADPKD=common (1/300) -ARPKD=1/10,000 (much less common) Pathogenesis: PKD1 and PKD2 genes encode proteins polycystin 1 and 2 (respectively) -ADPKD: loss of function of either of these-->causing surface proteins to be mis-located -ARPKD: mutations in PKHD1 gene-->leading to abnormal fibrocystin protein production **Cause cysts to form!

MEN-1: (Multiple Endocrine Neoplasia-1)

-Caused by loss of function mutations on the tumor-suppressor gene MEN1 -Rare (between 2-20 per 100,000) -Pathogenesis: MEN1 gene encodes a nuclear protein ("menin") which is involved in transcription regulation; abnormalities impair the normal production of this and affect transcription Phenotype: -Hyperparathyroidism (most common manifestation b/c penetrance=almost 100%) -Pancreatic tumors (penetrance=50%) -Anterior pituitary adenomas (30% = malignant) DX: made by DNA analysis MGMT: case by case (some best RX=medical; some = surgery) Other MEN syndromes: 1) MEN 2a: medullary thyroid carcinoma, hyperparathyroidism, pheochromocytoma 2) MEN 2b: medullary thyroid carcinoma, pheochromocytoma, mucosal neuromas, intestinal ganglioneromatosis, marfanoid features

Chromosome Disorders:

-Change in the number or structure of chromosomes 1) Aneuploidy: the most common chromosome disorder; is an abnormal number of chromosomes. -In general, these are ALL often not compatible w/life -Exceptions: Trisomies 21, 18, and 13; and Monosomy Turner syndrome **These exceptions=all compatible w/life! Note: euploid genome=46 chromosomes Different types: 1) Trisomies: triplet set of chromosomes: -From paternal set=result is partial hydatidiform -From maternal=most result in first trimester abortions 2) Monosomies: (lack of a chromosome)=less common; these are usually not compatible with life -Exception: Turners syndrome (X chromosome lacks homologous pair, so they have 45 X chromosome genome); b/c one of the X chromosomes in a normal female is inactivated anyway, thought that this it not a fatal syndrome for this reason

MELAS syndrome:

-Common mitochondrial encephalomyopathy; unique in that only affected females can transmit them -MELAS stands for the SXS of the dz: mitochondrial myopathy, encephalopathy, lactic acidosis, strokelike episodes -caused by point mutation in mitochondrial chromosome coding for mitochondrial tRNA Phenotype: SXS begin b/4 30 years -First sxs: seizures -Others: stroke like episodes causing hemiparesis + hemianopia (strokes in general in <40 yrs without stroke on CT-->look for this) -Other sxs: hearing loss, DM, hormone deficiencies, undeveloped secondary sex characteristics -Serum lactic acid=elevated DX: muscle biopsy + neuroimaging -BX shows: ragged red fibers -MRI: basal ganglia calcifications

Frameshift Mutations:

-Deletions + insertions are another class of mutations occurring in the replication + transcriptional period 1) If a deletion or insertion of 3 nucleotides occur: a protein is produced minus or plus the one amino acid deleted or inserted, respectively 2) If there is an insertion or deletion of nucleotides NOT in a multiple of 3: frameshift will occur, leading to either: -A premature stop codon, or -Completely abnormal protein **Frameshift mutations are detrimental to the ultimate polypeptide produced!

Cell Cycle:

-Divided into: 1) Time during which cell division occurs 2) Time during which it does not occur -Interphase: the term for the stages of the lifecycle between active cell division -Interphase contians: Gap0, Gap1, S, Gap2 Gap0: most pertinent to neurons, RBCs, and liver cells -Note that neurons + RBCs do not normally leave Gap0 to enter the other interphase stages (b/c do not normally divide) -Note: liver cells enter Gap0, but can escape to Gap1 after a damage event to undergo cell division Gap 1: no DNA synthesis occurs, but cellular prep for replication begin -Ended by "checkpoint": which halts the cell cycle if the cell is inadequately prepared for replication (or if genome damage is detected) -Cancers are caused by genetic lesions that affect the action of Gap1 checkpoint (which permits cellular replication despite genome damage) S Phase:DNA replication occurs in prep for upcoming cell division 1) 2n cell of Gap 1 becomes 4n cell, with 2 complete copies of the genetic code 2) Each chromosome is copied, producing sister chromatids 3) S-Stage checkpoint then follows: if incorrect replication or genetic damage is detected-->p53 pathway is activated -p53 pathway directs the production of gene repair enzymes or cellular apoptosis Gap2: the cell prepares for division by synthesis of the mitotic spindle

Mosaicism and genetic testing:

-Further complicates S+S of genetic testing -If an individual has 2 diff genotypes in their body, then testing can easily produce false negatives -Ex: if a pt has somatic mosaicism for familial adenomatous polyposis (their blood is negative for the genetic abnormality, but their colonic tissue is positive) then a genetic screening based upon serum blood could result in false negatives

From Genome to Individual: how we get there

-Genes produce proteins, which act to coordinate + carry out cellular functions-->which affect anatomy, physiplogy, behavior -Every step in this process, however, is affected by environmental factors (which have huge impact) -The process of moving from genome-->proteome in itself is an extremely fluid process w/many potential confounders (which often result in genetic d/o's) From genome-->individual: 1) Genome--> Proteome Gene Network Cellular Functions Anatomy/Physiology 6) Behavior **Environmental factors affecting all along this pathway too

Hereditary Breast + Ovarian cancer:pathogenesis + etiology

-Genetic causes account for 3-10% of all cases -BRCA1 and 2=most common ones; BRCA1=1/500; BRCA2=1/250 prevalence--->together account for up to 80% of all familial breast cancers (though familial breast cancers is low in prevalence compared to sporadic breast cancers) Pathogenesis: BRCA1 and 2 function as tumor-suppressors; loss of their function=inc likelihood of mutation in the genome -As mutations accumulate, cells degenerate into malignancies -Heterozygotes: wild-type allele frequency loses function d/t replication errors (may indicate that haploinsufficiency exists w/only 1 normal allele)---->leads to somatic cmpd heterozygosity for abnormal functioning alleles

Diagnosis based upon SXS: genetic testing

-If a genetic d/o is suspected based upon signs + SXS, then genetic testing is indicated -In this case: what must be done is to try + identify the suspected genetic d/o (or at least a differential DX) so that correct genetic testing modalities can be employed

Oogenesis:

-Initiated once in prenatal life -at and after sexual maturity the oocytes undergo meiosis 1 -oocytes only undergo meiosis II if and when they are fertilized Differences between this and sperm creation: -This is initiated once (vs cont process) -Initiated prenatally + produces several million oocytes, which are capable of continued development at birth -Over time...majority of those^degenerate and women will only ovulate 400 oocytes in lifetime -Meiosis 1: distinctly diff from spermatogenesis: the 4n cell divides to become 1 ovum (w/the majority of cytoplasm + organelles), while the other cell becomes the polar body encapsulated by the ovum -Meiosis II: only occurs if fertilization occurs and involves the formation of a diploid zygote, which undergoes mitosis as an embryo

Preimplantation Genetic DX:

-Is a method by which parents at high risk of passing a severe genetic abnormality to their children can conceive w/out risking passing it on to the fetus -Oocyte fertilization is performed ex vivo in a lab, then genetic testing for the dz in question is performed on the zygotes ---Those found to NOT have the dz are then implanted via IVF Select + implant unaffected embryos: -single gene d/o's -CF, Tay Sachs, sickle cell anemia, thalassemia -Chromosome abnormalities -Parent w/a balanced translocation -Aneuploidy screening in AMA

What genetic tests look at: Chromosomes

-Looks for gross abnormalities in chromosome # or structure (best seen in karyotyping cultured leukocyte DNA) -Cells grown until max chromosomal condensation occurs (either prometaphase or metaphase) -What can be seen: gross changes in chromosome size, p or q arm size, or # -Best for: aneuploidies (Turner's, Downs, etc) When do you order a chromosome analysis? 1) Pediatric indications: clinical suspicion of a chromosomal d/o, the pt fails to go into puberty, when multiple anomalies/dysmorphic features/and or developmental problems occur 2) Adult indications: when individual reports a hx consistent w/infertility, or during a pregnancy at high risk of aneuploidy

Rett syndrome:

-Loss of function mutation in MECP2 gene (1/10,000 Females) -If in males: typically leads to spontaneous fetal death d/t lack of functional X chromosome (if in males that live: 47XXY w/only 1 X affected) -Inheritance risk: most have low reproductive fitness (and therefore most mutations=sporadic) Pathogenesis: MECP2 encodes nuclear protein involved in epigenetic gene regulation + DNA methylation -Mutation=inappropriate gene activation Phenotype: SXS=develop progressively after 6-18 months of age -Earliest signs: dec growth + head circumference trajectory -Next: rapid loss of speaking ability + loss of purposeful hand movements -As it becomes more severe: seizures, ataxia, resp irregularities MGMT: DX=DNA testing for most; the rest=DX clinically -RX: pharm for seizures, agitation, rigidity, sleep disturbance

Carrier screning: genetic testing

-Many genetic dz's are found w/a higher prevalence in certain ethnic groups. -Carrier screening can help couples understand the risks of having a child w/a genetic dz which they are heterozygous carriers for Carrier Screening based on ethnicity: -Carrier rates for certain dz's depend on ethnicity: 1) African American: sickle cell anemia (1/10) 2) Caucasian (Cystic fibrosis=1/25) 3) French canadian: Tay Sachs dz (1/50) 4) Mediterranean, Asian, Southeast Asian, Middle Eastern: -thalassemias, hemoglobin variants Ashkenazi Jewish Screening: have a very large carrier screening panel, d/t a large # of dz which afflict this community -Examples: CF, bloom syndrome, Fanconi anemia, familial hyerinsulinism, Tay Sachs, Gaucher dz, etc

Alzheimer's: pathogenesis, multifactorial inheritance discussion

-Most common cause of dementia (20%=familial-->of that, 90% multifactorial inheritance and 10% is autosomal dominance) Pathogenesis: 1) Autosomal dominant dz of it: 3 gene loci=beta-amyloid APP, PSEN1, PSEN2 2) All Alzheimer's affected pts: have abnormally high levels of neurotoxic peptide A-Beta 42/43-->causes premature death of cholinergic neurons in hippocampus, neocortical region, limbic region too--->all causes: -cortical atrophy, neural plaque, neurofibrillary tangles Multifactorial inheritance: represents majority of dz w/genetic cmpts that are identified by findings of inc prevalence of dz in identical twins or fam pedigrees, but w/out predictable heritability pattern -act as predispositions to a d/o which can occur in the presence of specific environmental circumstances, as well as are r/t >1 gene

Down's Syndrome:

-Most common genetic cause of mental retardation (IQs typically between 30 and 60) -20-25% of Trisomy 21s survive to birth; 1/800 live births -Associated w/inc maternal age (>30) -1/3 have congenital heart dz (fatal in 25% b/4 first birthday) -15x inc risk for comorbid leukemia + premature alzheimer's-like dementia Phenotype: newborn hypotonia, short stature, brachycephaly w/flat occiput, short neck w/loose skin on nape, flat nose bridge, low set ears, brushfield spots on iris, furrowed protruding tongue, upslanting palpebral fissures, clindodactyly, feet w/wide gap between 1st and 2nd toes, short broad hands w/single palmar crease

Meiotic Non Disjunction summary:

-Most common mutational mechanism in our species -Typically affects every cell in the organism, causing uniform abnormality -EX: meiotic non-disjunction leads led to 3, instead of the normal 2, copies of chromosome 21 (Down syndrome)

Why transcription + translation are important in medical genetics:

-Most new genetic mutations are caused by aberrant DNA replication, transcription + translation -Most hereditary genetic disorders are caused by the copying of an abnormal gene Processes w/the potential to produce abnormal gene structure, function, and expression: 1) Replication -If replication occurs aberrantly, then genetic mutations can enter the genome 2) Transcription: -Can be affected by genetic mutations or epigenetic factors, such as DNA methylation -A change in transcription rate can result in an overabundance of a certain protein, or a deficit 3) Translation **We must understand both transcription + translation in order to fully understand phenotypic implications of even small changes to the genome

Cystic Fibrosis: Etiology, pathogenesis, inheritance risk

-Multi-system d/o caused by mutations in CFTR gene (mostly in Northern Europe descent, but not always--1/3200) -Inheritance risk: 1/19 (NA Whites) carrier status; 1/3200 affected child **if already have first child affected: risk=25% Pathogenesis: normal CFTR gene codes for chloride-channel regulatory protein (which increases hydration + dec sodium content of mucus) -this pathology in this gene affects all mucous-secreting organs--esp: those in lung, pancreas, and GI tract 1) Lungs: inc local inflammation d/t thick secretions not well cleared, inc infx and obstructing airflow -scarring + fibrosis of pulm parenchyma 2) pancreas: thick secretions impair exocrine digestive enzyme export into SI; leads to fibrosis + dec function 3) GI tract: chronic constipation + intestinal obstruction

Cell Division: Meiosis

-Production of gametes (germline cells) requires that the genetic info be halved to produce 4 haploid (containing 23 chromosomes, or n) cells -These haploid cells are then able to combine w/other gametes (n) through fertilization to produce a novel diploid (2n) organism w/a unique combo of genes **This 2n is NEW (and not just copied, like it is in mitosis) 2 phases: 1) Meiosis 1: contains 5 stages; essentially the same as mitosis, except for: -Prophase: alignment of homologous chromosomes in tetrads-->p and q arms of the aligned homologous chromosomes exchange genes ("crossing over") 2) Meiosis 2: -proceeds after meiosis 1, without an "S" phase: thus a 2n genome proceeds through a second division resulting in 4 haploid (n) daughter cells w/non-identical genomes **b/c there is no S phase/no replication again, there is only division

Cell Division: Mitosis

-Production of new somatic diploid (containing 46 chromosomes, or 2n) -This requires that all of the genetic info in the mother cell is copied + transmitted to the daughter cell -The result: 2 diploid (2n) cells **Dividing a 4n genome in a single mother cell-->2n genome in 2 daughter cells At the beginning of mitosis: there is duplicate chromatid in the cell (b/c in S-stage of interphase, each chromatid doubled). 5 phases: 1) Prophase: condensation of the chromosomes, formation of the mitotic spindle + centrosomes, and migration of centrosomes to antipolar sides of cell 2) Prometaphase: breakdown of the nuclear membrane, condensation of chromosomes, migration of the condensin chromosomes towards midpoint of cell 3) Metaphase: max chromosomal condensation (best time to karyotype a genome!) + arrangement of the chromosomes at equatorial plane of cell 4) Anaphase: chromosomes separated at the centromere and sister chromatids separate, becoming daughter chromosomes 5) Telophase: chromosomes decondense and new nuclear membranes form around 2 nuclei 6) Cytokinesis: process by which the cytoplasm of the cell (now containing 2 nuclei) cleaves, forming 2 distinct cells

Summary of Meiosis:

-Reduces chromosome number from 2n to n -Shuffles genetic material by randomly assorting homologues -Ensures great genetic variegation d/t crossing over -Produces gametes

Hereditary Deafness:

-Relatively common, 1/500 to 1/000 infants; 50% of congenital deafness caused by genetics (75% of which no other phenotypic presentation comes w/it, aka non-syndromic) Pathogenesis: GJB2 codes for connexin26, protein involved in formation of "gap-junctions" between cells (which permit propagation of action potentials)-->expressed in the cochlea! -Loss of this function in cochlea=loss of action potential propagation Phenotype: -autosomal recessive=congenital (hearing impairment degree varies) -autosomal dominant=not congenital (but onset is young w/progressively worsening high frequency hearing loss)

Post-translational processing:

-Required to produce a bioactive polypeptide -Examples: 1) Hemoglobin: post-translational combos of 2 alpha and 2 beta subunits is required to produce a tetrameric hgb molecule 2) Insulin: product of the opposite modification (cleavage): Proinsulin is an 82aa polypeptide which is cleaved-->into bioactive 21 + 30aa mature insulin proteins

Velocardiofacial Syndrome:

-Segmental Aneusomy -22q11.2 -Phenotype: Tetralogy of Fallot -This is not a "whole" chromosome d/o (diff than aneuploidy, which IS whole chromosome d/o) -This is a d/o caused by a small deletion of Chromosome 22 arm q at position 11.2 -This is termed "segmental aneusomy"=results in loss of approx 30-40 genes Abnormalities: -Cardiac: numerous cyanotic congenital heart abnormalities (most commonly = ToF) -Neuro -Primary immunoinsufficiency: b/c of poor T-cell production + function

Turner's Syndrome phenotype:

-Short stature, ovarian dysgenesis (and therefore typically absence of secondary sex characteristics) -webbed neck, low nuchal hairline, broad chest -cardiac abnormalities (coarctation, hypoplastic L heart, bicuspid AV 50%) -Renal abnormalities (60%) -Hearing deficits, dysplastic nails, edema of hands + feet -Intellectual development=normal in most (10% show delay/low IQ) Complications: -Osteoporosis, thyroiditis, DM, IBD, premature CVD **CVD + osteoporosis d/t estrogen deficiency

Chromatin:

-Single, continuous DNA double-helix packaged w/proteins -For majority of the cell life cycle, it is not organized into chromatids + visible as discrete chromosomes -Compaction of chromatin into this^^ only occurs in: 1) Late prometaphase and 2) Metaphase of cell division

Nucleic acid Hybridization:

-Technique in which DNA strands are "screened" for particular known DNA sequence -The process: 1) DNA is heated to break hydrogen bonds, and the known DNA sequence in the solution is tagged w/radioactive tracer/fluorescent dye 2) When it couples w/complementary sequence, the tag identifies it easily **Depends on finding a specific nucleic acid sequence, it is SPECIFIC but not sensitive (thereby it is not very good when many diff mutations occur that inactivate or activate one gene) Southern Blotting: -when recombinant DNA technique is combined w/DNA electrophoresis-->allows for mutations which affect sequence length to be identified -Clinical utility: limited to identifying mutations which sig change length of a coding sequence (but are too small to be seen on karyotype) ASO Probe: -synthetic single stranded tagged DNA sequence made to pair w/ specific length of DNA of known nucleotide -this ASO is hybridized w/individual's DNA: can be either good for ruling in the abnormality OR ruling out (based on how the ASO probe is polyermized: to either the abnormal sequence or the normal sequence) **BEST METHOD to evaluate for suspected dz of single or very few nucleotide substitutions or deletion FISH: (see other slide)

Newborn screening: genetic testing

-The most common genetic testing performed in the US -Intended to detect + DX genetic and metabolic dz in which early intervention CAN affect clinical outcomes, OR the decision to have a second child

Somatic/Mitotic Translocations:

-Unlike meiotic translocations, this does not affect the whole genome -This does predispose to certain cancers -Ex: break in chromosomes affect expression of genetic material at the break point-->leading to a loss of function mutation which causes chronic myelogenous leukemia **This somatic translocation between chromosome 9 and 22 produces a chromosome 22 (Philadelphia chromosome)

Prenatal Diagnosis: Genetic testing

-Very common reason for it. Almost all pregnancies will have either screening or diagnostic tests to evaluate for genetic or congenital abnormalities of the fetus Prenatal testing: 1) Screening: -Non invasive prenatal testing: combines the use of 1st + 2nd trimester maternal serum testing for free B-hCG, AFP, unconjugated estriol, inhibin A, and PAPP-A in conjunction w/nuchal translucency by US **these are the most commonly used prenatal testing^^; can be used to detect aneuploidies AND congenital neural tube defects -First trimester risk assessment -Maternal serum screening -US **Screening tests=NOT associated w/any inc fetal risk 2) Diagnostic testing: -Chorionic villus sampling -Amniocentesis -Percutaneous umbilical blood sampling **These ARE associated w/ a small inc in fetal demise (so usually only utilized when the risk of abnormality is higher than baseline risk) ----higher risk (which is the reason we do these tests) is determined by: -Screening tests, OR -Other risk factors present: advanced maternal age, previous child w/aneuploidy, structural chromosomal abnormality in a parent, fam hx of genetic d/o, or increased risk of neural tube defects d/t fam hx

Fragile X Syndrome:

-X linked d/o caused by unstable triplicate expansion of CGG sequence of the FMR1 gene on X chromosome -25/100,000 people in male population; 50/100,000 in female population Pathogenesis: FMR1 largely expressed in neural tissue (codes for FMRP: responsible for movement of mRNA from nucleus into cytoplasm for translation -Normal CGG repeat: 6-50 repeats; premutation=51 to 100; full mutation=>200 repeats (full repeat can only come from maternal transmission of X chromosome) Phenotype: mental retardation (females less severe), hand flapping, biting, poor eye contact, aggressive behavior -All males who inherit abnormal X FMR1 gene are affected; 50% of females are (d/t X inactivation)

Duchenne Muscular Dystrophy:

-X linked myopathy caused by mutations in the DMD gene (1/3500 males); SXS dz can occur in females (but rare) Pathogenesis: DMD encodes for intracellular protein dystrophin (found in all types of muscle + some areas of brain) -Dystrophin assists in sacrolemma stability (so abnormality or absence=instabile sarcolemma) Phenotype: presents at 3-5 years of life w/muscle weakness + is progressive -Weakness pattern: hip girdle + cervical flexors-->eventual distal muscles -Gower maneuver (classic finding) -Most develop dilated CM, w/dec IQs -By 12 yrs: most confined to wheelchair, and most die in 20-30s d/t pulm complications (from dec chest wall strength + movement) DX: confirmed by DNA analysis or muscle biopsy RX: corticosteroid therapy can slow dz progression, but no RX

Down's Syndrome: specific chromosome abnormalities

1) 95% Trisomy 2 2) 4% Translocation 3) 2% Mosaic: -is a MITOTIC abnormality (rather than meiotic); associated w/more mild phenotypic abnormalities 4) <1% Partial trisomy: -These are very rare -With these, if the genes on the partial trisomy are mapped for which are expressed + which are not, and phenotypes of the affected individuals are compared w/those of full trisomy-->the actual phenotypic affect of specific gene overexpressions can be determined **90% (most) d/t non-disjunction in maternal meiosis 1 (during fetal development) -remaining 10% occur in paternal meiosis II (after fertilization by paternal sperm)

Allosome Abnormalities: Overview

1) Almost always associated w/advanced maternal age (>30 years) -Exception: parental translocation carriers, in which abnormalities are independent of maternal age 2) 1/400 births 3) Less severe phenotypes than autosome abnormalities: -B/C in XX: for trisomies + tetraploidies: all but one X are inactivated -B/C in XY: Y chromosome has relatively low gene content (reducing the # of abnormally expressed proteins in Y aneuploidy therefore_) Phenotypic similiarities between most allosome abnormalities: -reduced psych adaptation, reduced educational achievement, reduced occupational performance, slightly lower IQ

The 5 Pedigree Patterns:

1) Autosomal Dominant 2) Autosomal Recessive 3) X Linked Dominant 4) X Linked Recessive **However, dominance is rarely pure dominance, and being heterozygous for a recessive allele does not result in "complete dz free carrier state"-->the pedigree shows genotypes, and we care about the phenotypes Penetrance: -Refers to the probability that a gene will have any phenotypic expression (ex: 100% penetrance means that 100% of individuals w/a given genotype express a specific phenotype) -If <100%, penetrance=reduced -X percent of individuals w/Y genotype will express Z phenotype **Population based metric Expressivity: the severity of expression of a phenotype among individuals w/a given genotype -Person X w/Allele Z has a cough, while person Y w/allele Z has resp failure) **Measure of the relative severity of phenotypes among individuals w/the same gneotype

Classification of genetic disorders:

1) Chromosome disorders: the most well known classification of these -Ex: Down Syndrome (trisomy 21), Turner syndrome, etc -Structural chromosome d/o's result from breakages w/in a chromosome; this is an abnormal condition d/t something unusual in an individual's chromosomes 2) Single Gene Defect: usually associated w/characteristic heritability patterns (autosomal dominant, recessive, etc) -Any genetic d/o caused by a change affecting only one gene -Marfan's, Sickle Cell Dz, Cystic Fibrosis; others Huntington's, etc -Usually associated w/characteristic heritability pedigrees 3) Multifactorial Inheritance Disorders: -By definition, means there are many factors involved in causing a birth defect. Usually both genetic + environmental, combo of genes from both parents, etc. Key here: combo of genes with lifestyle + environmental factors (b/c complex) -Examples: Cleft palate/lip, congenital heart dz, Alzheimer's DM (other than monogenic type), and HTN

Non-DNA based genetic tests:

1) Gene transcription products: some genetic d/o's do not require DNA analysis b/c their gene transcription products are easily detected + tested for. Examples: -Proteins -Enzymes ---Often, d/o's caused by abnormal proteins (hemoglobinopathies, etc) can be dx by protein electrophoresis 2) Metabolites: not gene transcription products, but are rather readily testable molecules which accumulate d/t a loss of function in a gene regulating their degradation or excretion -Ex: PKU

Pedigree Nomenclature:

1) Kindred: extended fam which is visually represented in a pedigree -so the pedigree is the image, but the kindred is the FAMILY 2) Proband/propositus: the first member of a fam w/genetic d/o to be brought to medical attention. Typically the index around making pedigree for the fam 3) Consultand: first person in a kindred to bring genetic d/o to medical attention 4) Sibship: all the brother's and sisters in a family 5) Second degree relation: grandparents, grandchildren, uncles/aunts/nephews/nieces/half brothers + sisters of the proband 6) Third degree relation: first cousins of the proband 7) Cosanguineous: couples w/more than 1 ancestor in common. The closer the familial relationship of reproductive couple=greater # of alleles likely to have in common 8) Isolated case: probands whom are the only affected member in a fam -Not sporadic cases! B/c sporadic cases are found to result from a new mutation 9) FItness: # of offspring who survive to reproductive age that an individual w/a genetic abnormality is capable of having -Fitness of 0: must always be sporadic (meaning: no affected individual is able to pass the mutation to a 2nd generation b/c the abnormality leaves them incapable of reproduction)

Nomenclature: Single Gene D/O's

1) Locus: segment of DNA occupying a particular position on a chromosome ("position" designation) 2) Allele: variation of a gene or "code" designation -Specific allele can be at a particular locus (but not the other way around) -Many types of alleles 3) Normal (wild-type) are present in the majority of the pop 4) Variant (mutant) are less common. Does not indicate pathology, but rather diff than the norm -EX: change of a codon from AUU to AUC does not change the amino acid sequence transcribed, but does make the allele a mutant 5) Polymorphism: >1 relatively common alleles occurring particular locus in the pop 6) Homozygous: If genes are the same on each of the homologous chromosomes (from mom + dad) 7) Heterozygous: 2 diff genes at a single locus (allele of mom + dad are not same) 8) Compound heterozygote: if pt has abnormal alleles at one locus 9) Hemizygous: when an abnormal allele exists on one of the X or Y alleles in boys; describes genotypes for most all X-linked d/o's in men ---Note: when have homologous allosomes so does not apply to them (but men do not, so need special name for abnormality) 10) Haplotype: set of alleles found at a specific locus; describes the complex of genes at a particular locus (instead of a single gene) 11) Haplosufficiency: abnormal genotype, but expresses the normal gene enough to not have symptoms 12) Haploinsufficiency: also has the abnormal genotype, but it is insufficient in quantity to hide all phenotypic symptoms of the dz 13) Pleiotropic: when a specific genotype is phenotypically expressed in myriad ways in different individuals w/ the SAME specific abnormal allele -can be difficult to track in family hx 14) Pedigree: graphic representations of a fam tree; useful to determine inheritance pattern of a dz Genotype + Phenotype: an abnormal genotype does not necessarily mean an abnormal phenotype -Phenotypes are what bring pts in clinically-->and the genotype may or may not be the cause of that abnormality

Point Mutations:

1) Missense mutation: the most common point mutation -A change in the nucleotide sequence leads to an amino acid substitution -This does not always lead to a diff amino acid than normal being encoded (d/t the genome being degenerate); though it frequently does -50% of dz causing point mutations are Missense 2) Nonsense mutations: premature stop codons, which impede the proper transcription of genes -10% of dz causing mutations 3) RNA processing mutations: are post-transcriptional events in which the processing + production of a mature mRNA molecule is abnormal -This leads to an incorrect code translated into a polypeptide 4) Frameshift mutations: when a single nucleotide is added or deleted -Changes the frame of reading by the tRNA -Usually: leads to a premature stop codon early in the translational process, but if it does not-->a completely abnormal protein can be created -10% of point mutations causing dz

S+S in genetic testing by Type of Test:

1) Protein testing: highly sensitive, variable specificity -looking at the translational products of genes, not the gene itself (so they test for biochemical phenotype of the individual, and NOT for a specific codon sequence in DNA) -high sensitivity b/c can detect most all individuals that produce ab abnormal protein -variable specificity in that they cannot always accurately predict the cause of the abnormal production **so can predict presence of the abnormality, but not always what causes it -Uses: only able to diagnose the dz if it is already present 2) Enzyme assay: same as^^ 3) DNA test: variable sensitivity, highly specific -Identifies the specific abnormalities in the genome itself, and therefore can r/o that a dz state exists -sensitivity is low (b/c DNA probes require that an individual have a previously defined mutation for which the probe was made, and therefore will not accurately diagnose new/novel mutation sequences) -Ex: cystic fibrosis:each mutation of the CFTR gene is diff (w/unpredictable expressivity + penetrance), which complicates genetic dx of CF, however-->testing for the end-result of a phenotypically significant mutation in the CFTR (sweat chloride conc) allows for sig affected individuals to be diagnosed **Basically, DNA testing can be hard to look for CFTR in general b/c there are so many diff abnormalities that could be shown, and the DNA test is so specific that it won't detect that, BUT b/c we know that chloride conc in sweat is a specific dx of it-->we CAN detect for this specifically

Allosome Aneuploidy syndromes

1) Turner Syndrome: one of the only survivable whole-chromosome deletion syndromes (45X genotype) 2) Klinefelter syndrome: results in an additional X chromosome in a male, resulting in 47XXY genotype Allosomes (sex chromosomes) in general: -produce less severe phenotypic abnormalities than autosome aneuploidies -This is bc: Y chromosome is relatively gene poor (only 50 genes), so having an extra Y chromosome has relatively little effect on the proteome compared to autosomes (which code for thousands of genes) -Aneuploidy of X chromosome: results in less severe phenotype than autosomal aneuploidy b/c only 1 X chromosome is active in any given cell anyway

Genome organization:

3 billion base pairs 1.5% encodes protein 5% acts as regulatory proteins 50% of genome=composed of unique DNA; 50% genome=repetitive DNA Unique DNA: genetic code is not repeated throughout the genome Repetitive DNA: sequence is repeated throughout genome (these are often implicated in genetic dz, b/c insertion of a repetitive sequence can alter the exprssion of a gene or turn it off)

Turner's Syndrome:

Allosomal aneuploidy: 50% have 45X karyotype; 25% have a second X w/structural abnormalities; 25% are mosaic for the loss of the second X chromosome **So regardless, they all only result in ONE functional X -Recurrence rate is NOT > than that in normal pop (b/c is a sporadic abnormality) Caused by: vast majority (70%) = by failure to transmit a paternal chromosome to the gamete -Phenotypic abnormalities are relatively mild; though up to 99% are fatal prenatally (so the vast majority are spontaneously aborted) -Abnormal phenotype is d/t insufficiency of the genes on the normal 2nd X chromosome (lacking in these people), which are NOT inactivated in normal genotype people Treatment: -Screened via US for cardiac + renal abnormalities -Growth hormones: given if pt falls <5th percentile of growth (and continued until 15 yrs) -Estrogen therapy: starts between 14-15 yrs to promote dvlpment of secondary sex characteristics + reduce osteoporosis risk -Progesterone: added later on too -IVF: if complete ovarian dsygenesis + desire children (if incomplete dysgenesis, most can still reproduce)

Klinefelter Syndrome:

Allosome aneuploidy resulting in a 47XXY genotype -Tall, thin, long leg males w/pubertal hypogonadism -Caused by: deficiency of expressed androgens compared to estrogens (leads to late closure of bony physeal plates) -Relatively common (1/1000 live male births); may be undetected b/c more mild phenotypes (associated w/only 1 extra X chromosome) pts can live normal lives generally -Presentation: often are dx when come in later in life d/t frequent infertility or oligospermia (low sperm count) -Classic (yet variable) phenotype Causes: -Most: caused by non-disjunction in maternal meiosis I -15% are mosiac for this condition: these pts tend to have inc testicular development and therefore are often fertile (and so go undiagnosed) Consequences w/condition: -Psychosocial development is often abnormal; affected individuals have dec IQs and verbal comprehension, w/increased learning disability incidence

Autosome vs Allosome Loci: Single Gene D/O's----X linked disorders

Allosomes: behave as if the genome is haploid instead of diploid -Reminder: men only have 1 X chromosome, and women only EXPRESS 1 X (d/t X inactivation) -Pseudoautosomal: loci/region on the allosomes in men (so between X and Y chromosomes) in which crossing over can occur; b/c these are not homologous chromosomes they do not cross over as much or in other regions than this X Linked D/Os: known to be associated w/abnormal loci on the X chromosome. -Men: only have 1 X chromosome, so if an abnormality exists at an X locus-->they will express it (whether it is dominant or recessive) -Women: even dominant d/o's which are X linked are not always phenotypically expressed, b/c abnormal X chromosomes are selectively inactivated during early embryologic development Classifications: dominant vs recessive-->based on their presence or absence of phenotypic expression in female carriers -If female carriers consistently have a dz phenotype: d/o= X linked dominant -If female carriers do not express the phenotype: d/o=X linked recessive **Note: impossible to determine dominant vs recessive in males (b/c they are hemizygous for the X chromosome and will express it regardless) Passing on X-Linked Dominant vs Autosomal Dominant d/o's in men: -Distinguish X Linked dominance from autosomal via a LACK of male-male transmission (affected father does not possess an X to pass on-->so can never pass an X-linked dz to a son); but CAN in autosomal

Diagnostic Tests in Prenatal DX: AMniocentesis VS CVS

Amniocentesis: -16-18 weeks gestation -0.5% risk of complications -chromosomes, DNA, biochemical tests **preferable (compared to CVS) d/t its lower rate of fetal loss CVS (Chorionic villus sampling): -10-12 weeks gestation **performed at much earlier gestational age (which is often preferable to worried parents) -1% complication rate -Chromosomes, DNA, biochemical tests

Nucleosome:

An octamere of histones and the associated DNA molecule

Chromosomal Disorders:

Aneuploidy: -Down's Syndrome -Turner's Syndrome -Velocardiofacial Syndrome Allosome Aneuploidy: -Turner's Syndrome -Klinefelter syndrome These are d/o's of entire chromosomes, and therefore are detectable by metaphase or prometaphase karyotyping + imaging the chromosomes

Marfan Disease: pathogenesis + phenotype

Autosomal dominant connective tissue d/o from mutations in a fibrillin 1 gene -1/10,000 individuals; most are inherited defects (but 25-35% are de novo mutations) Pathogenesis: Fibrillin 1=glycoprotein in EC matrix-->polymerizes to form structural foundation in many diff tissues (blood vessels, muscles, tendons, ligaments) -Inheritance is dominant (b/c single wild-type allele carriers=haploinsufficient) Phenotype: skeletal, ocular, CV, pulm, and cutaneous abnormalities -Skeletal: taller than normal, arachnodactyly, pectus deformities, scoliosis, joint laxity -Ophthalmic: ectopia lentis, flat corneas, hypoplastic irises -CV: mitral valve prolapse, aortic regurg, aortic dilatation-->dissection (often cause early mortality) -Pulm: spontaneous pneumothorax -Cutaneous: hernia + striae

Autosomal dominant vs recessive d/o's.; d/o's with both recessive and dominant variants; X linked disorders; different ones in each category

Autosomal dominant: -Neurofibromatosis I -Hereditary Colon Cancer -Marfan Syndrome -Thrombophilias -Hereditary breast + ovarian cancer -Multiple Endocrine Neoplasia 1 -Hypertrophic CM Autosomal recessive: -Hereditary hemochromatosis -Cystic fibrosis -PKU D/O's w/both recessive + dominant variants: -Hereditary deafness -Polycystic kidney dz X linked disorders: -Duchenne Muscular Dystrophy -Fragile X Syndrome -Rett syndrome Mitochondrial d/o's: -MELAS syndrome Multifactoral inheritance d/o's: -Alzheimer's

Phenylketonuria (PKU): etiology + pathogenesis

Autosomal recessive d/o of amino acid metabolism: failure to convert Phenylalanine-->tyrosine, resulting in deficiency of phenylalanine hydroxylase enzyme -1/14,000 to 1/20,000 Pathogenesis: phenylalanine = essential amino acid (must get from diet) + excess is usually degraded to tyrosine via that enzyme ^; in this there is abnormality in that enzyme-->accumulation of phenylalanine -Impedes import of other amino acids required for normal brain function; once >20 mg/dl **Result: super high conc of phenylalaline, very low conc of tyrosine + tryptophan

Balanced vs Unbalanced translocations:

Balanced: do not involve the loss of genetic material (just that the material is on the incorrect chromosome) Unbalanced: -occurs when a parent w/balanced (and phenotypically normal therefore) translocation reproduces -during chromosomal segretation in the zygote, the translocated material is either: 1) included as a partial trisomy, or 2) the genome lacks the translocated material **In 5% of Rob

Nucleotides:

Basic building blocks of the DNA molecule. Each composed of: 1) Pentacarbon sugar 2) Phosphate group 3) One of four potential nitrogenous bases -Purines: adenine + guanine -Pyrimidines: thymine + cytosine Pairing: A with T, C with G **DNA is double stranded, so 2 nucleotides always bond in the center of 2 parallel sugar-phosphate backbones -Starting end: starts w/free phosphate (5' end) -Terminal pentacarbon sugar: contains free -OH (3- end) **One strand of nucleotide chain begins at 5' end, the other begins at 3' end

Reproductive Embryology:

Bipotential gonads: all zygotes after cellular differentation have this until 6 weeks of embryologic development -Then, by default, gonadal cells develop into ovaries (unless the Y-linked gene (testis determining factor (TDF) is present) 1) 46XX genotypes: gonads differentiate into ovaries by 8 weeks of fetal development -Oogonia (proto-oocytes) develop w/in ovarian follicles -At 12 weeks: oogonia undergo meiosis I up to the dictyotene stage (which includes crossing over) **This means: chromosomal abnormalities of meiosis I non-disjunction in females occurs PRE-natally! -In absence of androgens: mesenteric ducts regress, paramesonephric ducts develop-->into female genital tract -External female genitalia develop 2) 46XY genotypes: presence of TDP causes gonads to develop seminiferous tubules + Leydig cells -Androgen secretion: via Leydig cells; this secretion stimulates production of mesonephric cells (which suppress paramesonephric duct formation) -External genitalia begin to develop into testes + penis **Crossing over + meiosis I does not occur until sexual maturity in males!

Crossing over in the 46XY genotype, and sex reversal disorders:

Crossing over: occurs only at Xp and Yp arms (pseudoautosomal regions of the X + Y chromosomes) specifically -This is b/c the chromosomes are not homologous (since one is Y and one is X) and therefore crossing over could cause detrimental changes to the X or Y chromosomes, which would ultimately alter phenotypic expression of normla sexual characteristics Sex reversal d/o's: a phenotypic male has a 46XX or phenotypic woman has 46XY genotype -These occur when abnormal allosome (sex chromosome) crossing over occurs at the SRY gene (sex determining region of the Y) **This moves the testes determining factor gene to the X chromosome, and removes it from the Y chromosome

Hereditary Hemochromatosis: pathogenesis, incidence, etiology

D/o of iron overload, caused by homozygous or compound heterozygous point mutation on HFE gene (cysteine gets substituted for tyrosine) -Carrier status=11-27% (b/c it is an autosomal recessive condition, carrier status is high chance) Pathogenesis:iron is absorbed in intestines by enterocytes + recycled from the breakdown of RBCs via macrophages (regulated via hepcidin hormone) -normal regulation: hepcidin decreases iron release when stores are adequate -mutation of HFE gene=stimulates unregulated release of iron from enterocytes + macrophages-->iron overload Inheritance risk: 25% (chance of being affected w/2 carrier parents), penetrance is variable (so not all clinically affected)

From Genome to Proteome:

DNA-->RNA-->Protein-->DNA: -DNA contains genes which code for proteins -Proteins are created in the cytoplasm by ribosomes -Intra-nuclear DNA communicates the genetic code to the cytoplasm via RNA -RNA: ribose sugar, single stranded, and base uracil (instead of thymine) 1) Transcription: -The production of RNA from DNA (in the nucleus is where this occurs) 2) Translation: -In the cytoplasm is where this occurs -ribosomes create proteins based upon the genes encoded in the RNA

X Chromosome Inactivation: and what happens in Abnormal female XX inactivation

Definition: process by which most genes on 1 or 2 X chromosomes are silenced epigenetically -What occurs in females normally: early in zygote before cellular differentiation, one of the 2 X chromosomes is deactivated to prevent over-expression of the genes on the chromosome (b/c got 1 from mom and 1 from dad, but only keep 1) -This is diff from autosomes: in autosomes, genes are expressed either dominantly, recessively, or co-expressed at each locus from BOTH mom and dad Abnormal female genotype X inactivation: -The abnormal X is ALWAYS inactivated, and the process is not random or mosaic in the diff cell lines 1) IN a balanced X-autosome translocation, the normal X is inactivated: consequences: -----decreases risk of abnormal phenotype expression in the affected individual, but ----increases risk of the individual's offspring 2) In a non-balanced X autosome translocation: the abnormal (translocated) X is always deactivated

What genetic tests look at: DNA

Different types: 1) Recombinant DNA -Restriction enzymes: bacterial proteins which cleave DNA molecules at specific at specific codon sequences, leaving predictable "tails" of single stranded DNA **Called recombinant DNA technology -Can study the action of specific DNA sequences b/c each length of DNA can be grown + replicated attached to a different bacterial artificial chromosome plasmid inserted into a cell -allows for: specific actions of a length of DNA to be analyzed (thus the gene products it encodes can be determined) -used less clinically but used frequently for genetics research 2) Nucleic acid hybridization: -Southern blotting -ASO probe -FISH (see other slide) 3) Comparative Genome -see other slide

Single Gene Disorders:

Disorders determined by the alleles at a SINGLE locus, are much smaller in terms of size of abnormality on the genome (though can be just as devastating clinically depending) Epidemiology: critical in primary care (esp PEDS) -Incidence=0.36% overall, hospitalized children=6-8% -Usually these disorders are detected in the prenatal/postnatal + pediatric years b/c these single gene d/o's are typically present in the genome at birth -<10%: manifest after puberty (as endocrine signals can change the degree of gene expression) 2 general factors affect expression of single gene d/o's: 1) Dominant vs recessive 2) Allosome vs autosome

Dominance vs Recessiveness: Single Gene D/O's:

Dominant: -Expressed when heterozygous for the allele; the abnormality is therefore expressed regardless of the presence + normal activity of the unaffected allele 1) Pure dominant: affected individual either has all or none -Homozygotes + heterozygotes are affected w/equal severity 2) Codominant: the vast majority are this. 2 diff alleles at the same loci on homologous chromosomes are equally expressed -Ex: ABO blood groups (heterozygous AB) 3) Incomplete dominance Dominant heterozygotes: has a second normal allele, which makes 50% of the gene product (so as long as that results in haplosufficiency, there will be no phenotypic dz) -If haploinsufficient state (if that 50% is insufficient to prevent all sxs of dz), then usually very mild or even subclinical dz manifests **Demonstrates that the pure dominance is not the reality (not all-or-nothing) Recessive: -The individual must be homozygous to express it -If in a male pt on the X chromosome: must be hemizygous for the allele -These mutations typically result in loss of function of a particular gene (b/c does not have a "normal" allele to combat)

Gene function:

Encode + regulate the production of proteins -Proteins=the way in which the genome acts in the biologic world -There are more proteins + greater variability than the 25,000 genes in the body, b/c 1 gene can produce a # of diff proteins (posttranslation) -Proteins behave differently depending upon the other proteins being produced in temporal + physical proximity, as well as environmental factors **allows for greater complexity than would be if only 25,000 proteins were encoded

Neurofibromatosis I: etiology, incidence + pathophys:

Etiology: caused by autosomal dominant mutation in the Neurofibromin gene (NF1) -1/2 are de denovo mutations Incidence: pan-ethnic (equal incidence in ethnicities); 1/3500 people Pathogenesis: NF1=a large gene expressed in many tissues, but expressed most in CNS + PNS -NF1: acts as a tumor suppressor -What happens: there are >500 causative mutations at the NF1 gene, and they ALL cause loss of tumor suppressor function-->causing fleshy growths of the nervous tissue -Lots of pleiotropic phenotypic changes + great differentiation (no certain connection between the specific mutation + phenotypic expression) Associated malignancies: optic nerve gliomas, grain tumors, myeloid disorders **B/c the loss of tumor suppressor ability in the gene increases likelihood of malignancy -Also at inc risk of multiple vessel stenoses + HTN

Hereditary Colon Cancer: Hereditary Nonpolyposis Colon cancer (HNPCC):

Etiology: results from a mutation in a DNA mismatch repair gene Pathogenesis: mutations in any of 6 known DNA mismatch repair genes occur, which increases the likelihood of inaccurate replication 1000x-->predisposes to oncogenesis -Autosomal dominant means that heterozygous for the allele confers "autosomal dominant" transmission Natural hx: not as dramatic colonic appearance as FAP -affected individuals have the same number of lifetime polyps as a normal individual -However, HNPCC polyps begin much earlier-->develop 10-15 yrs before colonic polyps in unaffected people -Lifetime risk of cancer=80% and tend to be in ascending + transverse colon (most unaffected people colon cancer=sigmoid + descending) Management: -Colonoscopy begins at 25 years in high risk -Prophylactic removal of colon at 25 **Both of these inc life expectancy dramatically Inheritance risk:50% for each offspring **B/c expressivity can be <100%, not all affected are guaranteed cancer; however, those w/disease genotypes develop in up to 90%

FTRA:

First trimester risk assessment screening: for detecting Down Syndrome prenatally. Most pregnant women are offered this, regardless of personal or familial risk for this condition -Combo of msmts of 2 placental hormones from maternal blood sample: 1) HcG 2) Pregnancy associated plasma protein type A -Also includes: US of first trimester measuring accumulation of fluid around neck of the fetus (abnormally large amount of nuchal fluid=associated w/aneuploidy) -Detects 90% of Down's fetuses when performed between 10.5-13.5 weeks of pregnnacy -There are a fair amount of false positives **This is NOT DIAGNOSTIC for Down's: this is a reason for MORE specific testing!

Histone proteins:

Found within chromatin; 5 varieties H2A, H2B, H3, and H4: -2 each of these 4 histone proteins combine to form an OCTAMERE (a bead-like structure) 1) DNA strand winds around each octamere twice, approx the length of 140 base pairs 2) Then, a 20-40 base pair "spacer" of DNA connects one octamere to another 3) At this "spacer" region: the 5th histone (H1) binds and is integral to the folding and compacting abilities of the molecule 4) Together, an octamere of histones and the associated DNA molecule is referred to as a nucleosome **SO: the 4 histone varities (H2A, H2B, H3, and H4) all combine in the first steps; and the 5th variety (H1) binds at the end

Gene Structure and different parts of it:

From 5' to 3' end, in the following pieces: 1) Promoter: this area initiates transcription, helps regulate gene expression, and controls which proteins are made in each tissue -Untranslated! So it never is expressed in terms of RNA 2) Initiator codon: sequence which turns on the actual translation process 3) Introns: non-coding sequences in the genome. While they are transcribed, they are removed in post-transcriptional processes (RNA splicing) and are not present in mature mRNA that exits the nucleus 4) Exons: gene segments which DO encode proteins (think: Exons Encode) 5) Termination codon: stops transcription -usually is followed by a "poly-Adenosine" tail which is not transcribed

Why genetics are important:

Genes affect susceptibility, severity, prognosis + sequelae of essentially every clinical dz entity -It is not a matter of whether or not a dz is genetic, but rather what proportion of every clinical d/o does genetics play on it's natural history (along w/environmental + other factors)

NF 1: Management + Inheritance Risk

Genetic testing: not routinely done b/c w/the many genetic diff abnormalities of the NF1 gene that can cause the d/o, there is no genotype linked to a specific allelic genotype -Diagnosis=made clinically therefore Treatment: no definitive rx; main things=mitigating sxs and early detection/intervention for prevention of debility -All pts: should receive annual physical exam -Childhood pts: receive ophthalmologic evals annually to detect optic gliomas early -BP monitoring regularly to screen for HTN Inheritance risk: 50% risk in offspring (B/c it is an autosomal dominant d/o)

Limitations of genetic testing (and predicting phenotype in general):

Genotype does not necessarily predict phenotype d/t many things (X-inactivation, DNA methylation, variable expressivity, variable penetrance, etc)-->confounds the ability to DX someone w/a genetic dz with only a DNA test (b/c DNA tests predict genotype NOT phenotype) ---genetic testing + counseling is similar in this! there are many limitations

Genotype vs Phenotype:

Genotype: 1) Gene expression 2) Gene regulation Phenotype -While translation/transcription also determine cell function, the regulation of which genes are expressed, which are suppressed, and to what degree each of them occur determines the actual function of the genetic code in the real world -These differences are caused by: environmental cues/stimuli and developmental cues/stimuli -Genotype: what is coded in the genes -Phenotype: what is expressed at the biological level

Hereditary Colon Cancer: Familial Adenomatous Polyposis (FAP) -Pathogenesis + etiology

Hereditary Colon Cancer in general: 50% of all people w/this develop a colon tumor by age 70; but only small portion are malignant -15% of colon carcinomas=familial FAP: etiology=heritable mutation in the APC gene -Accounts for <1% of all colon cancer -De novo somatic mutations in the APC gene account for 80% of all colorectal cancers (are NOT FAP, and are somatic mosaicism-->so are not heritable) Pathogenesis of FAP: -APC=multifunctional protein involved in transcription, cellular apoptosis + cell proliferation; contains tumor-suppressor functions within the cell -Loss of APC function causes inappropriate gene expression in the affected cell--->over time causes multiple compounding genetic abnormalities-->malignancy -B/C it is autosomal dominant, the person is either heterozygote (functionally " affected w/haploinsufficiency) or homozygous abnormal for APC alleles

Why are histones important?

Histone code affects gene expression: -While DNA codes for proteins, but histone code affects gene expression 1) Histone substitutions: -H3 and H2A can be substituted for a variety of specialized proteins to affect the degree to which DNA around the associated nucleosomes are transcribed 2) Post-translational changes -H3 and H4: can be altered by environmental chemicals to affect transcription **post translational b/c it is environmentally affected and are protein structure changes that happens after translation of mRNA into amino acid sequence **These changes do not change actual genetic code, just gene expression (Which can affect things such as neurons + epidermal cells)Mi

Pedigree Symbols:

Important: notate stillbirths + miscarriages when getting fam hx to make a pedigree, b/c many d/o's affect the fitness of an affected individual (and these occasionally come to medical attention d/t multiple spontaneous abortions)

Marfan Disease: management and inheritance risk

MGMT: -Diagnosis: clinically -Genetic testing not routine b/c of the allelic heterogenity of the fibrillin 1 gene -No dz modifying treatment available; mgmt=prevention of morbidity + mortality--->examples: 1) Aortic dilatation progression prevented w/beta blockade 2) Ortho bracing + ophthalmic lens replacement 3) Aortic root replacement when aortic regurg=severe Inheritance risk: 50%

Punnett square example:

Mendelian Probability: Autosomal Dominance vs Autosomal Recessiveness: both produce a predictable ratio of affected to unaffected individuals in single-gene d/o's AUTOSOMAL DOMINANT: 1) Dd with dd (crossing heterozygote for autosomal dominant allele w/homozygote normal individual): -Dd, Dd, dd, dd=50% affected offspring 2) DD with dd (crossing homozygous for autosomal dominant allele w/homozygote normal individual) -Dd, Dd, Dd, Dd=100% affected offspring AUTOSOMAL RECESSIVE: 1) DD with Dd (heterozygote carrier for an autosomally recessive allele crossed w/normal individual) -DD,DD,Dd,Dd=0% affected offspring 2) Dd with Dd (2 heterozygote carriers for autosomally recessive alleles): -DD, Dd, Dd, dd=25% affected offspring NOTE: autosomal recessive is much less common to present in the phenotype of a patient, but it is common for people to be carriers (since heterozygous people will not express the dz)

The 5th Pedigree Pattern: Mitochondrial Inheritance

Mitochondrial genome: -Circular chromosome -37 genes -13 polypeptides encoded, mostly affect CNS and muscular function Recall: every mitochondria in every cell is from the mitochondria present in oocyte at conception, w/none from the paternal mitochondria from the spermatocyte ---What this means functionally: all children of affected mothers will be affected; no children of affected fathers will be

Non-Disjunctions: Mitotic vs Meiotic

Mitotic Non Disjunctions: failures of proper genome separation AFTER conception -therefore: only affect the progeny of the cells in the particular lineage of the affected cell, while leaving other cells to divide normally w/a normal genome-->MOSAICISM -results in: 2 genotypes being present within an individual w/the possibility of expression as 2 distinct phenotypes -EX: abnormal body proportions; malignant growth Meiotic Non Disjunctions: during gametogenesis -therefore: this occurs during preconception -these non disjunctions are a common source of aneuploidies (abnormal # of chromosomes) -Translocations involve the movement of chromosomal info from one chromosome to another

Is the process of X chromosome inactivation complete?

NO! Incomplete process Process of X inactivation: not fully complete, b/c if it were then there would be no phenotypic affect at all (which is not the case) -15% of genes on the inactive X escape deactivation-->expressed on both X chromosomes ----Most are on Xp arm (not Xq) meaning that imbalance in the Xp expression would be more clinically significant than the other

X Chromosome inactivation: what happens in normal female XX inactivation

Normal females w/2 normal X chromosomes: this process is randomly completed in each undifferentiated cell (the normal female has a different X chromosome expressed in different cell lines) -Mosaic for "X" gene expression 1) The inactivated X expresses the XIST gene-->which leads to production of a non-coding RNA molecule which epigenetically methylates the promoter region-->causing increased macroH2A histone-->which makes up backbone of chromatin 2) The active X does NOT express XIST gene **Note: if there is more than 2 X chromosomes present in a female (or >1 X in a male) this is abnormal, and so ALL of the X chromosomes other than the active one are inactivated via this XIST process ----Note: this is also why X aneuploidy is less phenotypically severe than autosome aneuploidy

Crossing over:

Occurs during prophase of Meiosis 1: genes are exchanged among homologous chromosomes, producing novel/new genetic sequences in each chromatid -crossing over ensures that none of the resultant gametes are genotypically identical

Translation:

Occurs in ribosomes w/in the cytoplasm: -The mRNA now enters cytoplasm, carrying a nucleotide recipe for a particular polypeptide -mRNA consists of: codons: which are sequences of 3 base pairs, each which code for a particular amino acid -The genetic code= "degenerate", b/c there are only 20 potential amino acids but are 64 potential nucleotide combos (meaning that most amino acids are coded for by more than 1 codon) **Exception: methionine + tryptophan = encoded by unique codons -RIbosomes: composed of rRNA (ribosomal) -tRNA: the physical connection between the mRNA and the amino acid it encodes Translation initiation: AUG codon (codes methionine)

Factor V Leiden:

Pathogenesis of Factor V Leiden -Result of a gain of function mutation in the FV gene (unlike protein C mutations) -Active factor V accelerates conversion of prothrombin-->thrombin (causing thrombus formation); broken down by protein C **What goes wrong here: FV gene mutations disrupt breakdown of Factor V via protein C, thus more active factor V persists in population, overwhelming the normal anticoag protein actions -Homozygous: 80% lifetime thrombosis risk -Heterozygous: 10% risk Treatment: if homozygous=require lifetime anticoag; heterozygous it is strongly considered if have had >1 episode of thrombus -Penetrance: 10%

Protein C deficiency:

Pathogenesis of Protein C: -Protein C mutations=caused by a loss of function mutation of the PROC gene, impairing normal function of protein C + slows deactivation of Factor V -Homozygous: results in neonatal death -Heterozygous: haploinsufficient w/20-75% lifetime risk of venous thrombus -Penetrance: 20-75% (diff than Factor V Leiden, and thus they have diff natural hx's)

PCKD: MGMT + phenotype

Phenotype: 1) Autosomal dominant (ADPKD): 3rd or 4th decades of life: UTIs, hematuria, urinary obstruction, nocturia, flank pain from mass effect of the kidneys -HTN (d/t RAAS activation) -hepatic, pancreatic, ovarian, splenic cysts; MV prolapse, colonic diverticula, intracranial aneurysms 2) Autosomal recessive (ARPKD): congenital abdominal distention d/t enlarged kidneys, intrauterine renal failure (oligohydramnios is the cause), pulm hypoplasia DX: based upon pedigree fam hx + renal US showing it MGMT: 1) ADPKD: aggressive rx of HTN and UTIs, with drainage + chemical sclerosis of the cysts 2) ARPKD: more complex (b/c most pts present w/congenital renail failure) -neonatal + infant mortality rate=high of ARPKD

Hereditary Breast + Ovarian cancer: phenotype, MGMT, inheritance risk

Phenotype: BRCA1 and 2 also predispose to cancers other than breast + ovarian): -BRCA1: prostate + colon cancer -BRCA2: prostate, pancreatic, bile duct, gallbladder, male breast cancers -Penetrance: BRCA1=80%; BRCA2 40% MGMT: -Frequent + early screening exams=recommended -Males: frequent + early biochemical phys exams of prostate + of breast -Bilateral prophylactic mastectomy + salpingo-oophorectomy: prophylactic therapeutic options (reducing cancer up to 90%) Inheritance: b/c germ line heterozygotes often become compound heterozygotes, inheritance of the d/o occurs in an autosomal dominance pattern

PKU: phenotype + MGMT

Phenotype: appear normal at birth, but as they accumulate phenylalaline in diet over first few months of life-->developmental delay becomes clear w/in first few months -Untreated infants: faint complexions, rashes, unpleasant odor d/t ketone breakdown products of phenylalanine excretion in urine -Developmental delay, spasticity, hyperreflexia, widely spaced teeth, hypoplastic dental enamel -Untreated: IQs <35 (rarely >65) MGMT: clinical syndrome rarely seen in developing world d/t neonatal screening -RX: strict initiation of phenylalaline restricted diet (not exclusion)

CF: phenotype, MGMT

Phenotype: childhood disease mainly -most present at birth w/meconium ileus, or shortly after w/resp + growth problems -pancreatic dz causes malnutrition -males: sterile -morbidity + mortality: determined by rate of progression + severity of lung dz -RV Hypertrophy-->Cor pulmonale -Most common cause of death=resp failure -Median age of survival=33 yrs MGMT: -DX=made w/correlation of sxs with abnormal sweat chloride conc (or transepithelial diff msmts) -Mgmt focuses on improving nutrition by caloric supplementation PLUS pancreatic exocrine enzyme + fat soluble vitamin supplementation -prevent intestinal obstrcution -increase clearance of resp secretions + control pulm infx -lung transplant can be done

FAP: phenotype + natural history + diagnosis + mgmt + inheritance risk:

Phenotype: colon is affected in its entirety w/loss of function; so they can have up to thousands of polyps (unlike when it is somatic mosaicism and NOT familial APC mutations) Diagnosis: 100 colorectal polyps, or >10 in a person w/known affected fam member Natural hx: -By 21 years: 7% develop cancer -By 45 years: 87% have developed cancer -By 50 years: 93% have developed cancer Management: -Screening w/colonoscopy yearly from 10-12 yrs of age onward (in high risk) -If polyps are found: total colectomy is recommended Inheritance risk: 50% of offspring of affected people

Hereditary Hemochromatosis: phenotype, MGMT

Phenotype: homozygous (or compound heterozygous) likely will manifest sxs of iron overload: fatigue, joint pains, dec sex drive, abd pain -Men: 40-60 yrs of age -Women: asymptomatic until after meopause -Late complications (if not dx early): cirrhosis, hepatic cancer, DM, CM, hypogonadisim, arthritis, skin bronzing **Prognosis=good if DX b/4 cirrhosis; if not=high risk for HCC MGMT: 1) If homozygous or compound heterozygous but no biochemical evidence of dz yet: yearly ferritin screening, until levels >50 ng/ml--> 2_ At that point: therapeutic phlebotomy performed + repeated until normal ferritin levels achieved 3) Then: regular phlebotomy q3-4 months 4) Liver BX required to evaluate for cirrhosis if ferritin >1,000 and symptomatic

Alzheimer's: Phenotype + Inheritance risk

Phenotype: progressive cognitive function loss -early onset dz: 40-60 years; caused by autosomal dominant variety usually -Late onset dz: multifactorial inheritance -SXS: loss of recent memory first, progressing-->to impaired reasoning, concentration, language, visual perception, visual-spatial reasoning -Late stage dz: sxs=rigidity, mutism, incontinence, complete social withdrawal -Fatal w/in 10 yrs (causes=malnutrition, infx, heart dz, and many more) Inheritance risk: -Risk factors for multifactorial varieties: fam hx, old age, female, down's syndrome -baseline risk for development (w/no fam hx)=5% -w/first degree relative affected=increased risk to 15-30%

Neurofibromatosis I: Phenotype + natural history and diagnosis

Phenotype: widespread in this d/o (which makes sense b/c there is a wide range of tissues that express NF1, leaving room for variation) -Main characteristics: neuro + MSK abnormalities; also ophthalmologic + cutaneous abnormalities Neuro phenotype: neurofibromas (benign growths of the peripheral nerves), plexiform neurofibromas (involve multiple nerves) MSK phenotype: -thinning of the cortex of long bones-->can cause pseudoarthrosis -sphenoid dysplasia Ophthalmologic phenotype: optic gliomas, + lisch nodules on the iris Cuaneous phenotype: "cafe au lait" spots, cutaneous neurofibroma nodules + axillary and/or inguinal freckling Diagnosis: 1) made clinically if 2 or more of the classic findings (listed above) are present, OR 2) if 1 finding in a first degree relative of a known NF-affected individual

Diagnosis of Down's Syndrome:

Prenatal Screening Test: 1) NIPT: non-invasive prenatal testing -this is usually done if: -FTRA or quad screen come back positive; or abnormal US result, or -mom is advanced maternal age, or -there is a personal or fam hx of aneuploidy, or ----This test: examines non-cellular fetal blood circulating in maternal blood -99% sensitive (false positive 1/500) **Also NON diagnostic! Must be followed by amniocentesis or chorionic villus sampling 2) FTRA: see other slide 3) Quad screen: can be triple, quad, or penta-hormone screen; done during second trimester. Some or all of the following: AFP, beta HcG, Inhibin-A, estroil, h-hCG -81% sensitivity if performed between weeks 15-18 of gestation; 5% false positive rate 4) US **80% of dx happens prenatally Prenatal diagnostic test: -amniocentesis or CVS Phenotype after birth

DNA Replication:

Process by which new chromosomes are made 1) DNA helicase enzymes unwind the double-helix 2) DNA polymerases form continuous 5' to 3' direction nucleotide strand connected to the leading strand, and a segmental strand on the lagging strand 3) What is left after this process: 2 DNA double-helices from what was previously 1 Determinants: numerous biochemical "tools" are utilized to ensure the accuracy of the DNA replication process

Thrombophilias:

Refers to a propensity to generate thrombi within the vascular system, and in this instance genetic causes of inc risk (25% w/thrombus get diagnosed w/genetic predisposition) Factor V Leiden: accounts for 12-14% of these Prothrombin gene mutation: 6-18% Antithrombotic protein deficiency (genetic): 5-15% Variable penetrance: seen in this d/o's largely d/t environmental factors that inc or dec predisposition to thrombus Phenotype: most form in the calf; causes PE In 5-20% of affected people -Often recurrence in same, or diff, site in lifetime (if genetic abnormality exists) MGMT: -Diagnosis of DVT: US -Genetic thrombophilias: direct DNA analysis, or show Factor V Leiden or Protein C deficiency Inheritance risk: 50%

Genetics testing: things to consider

Results of genetic testing: 1) Not always easy to interpret (as they do not always predict dz): -variability in expression, penetrance, and allele heterogeneity-->tests are not always 100% accurate (and are not always able to predict dz phenotype) 2) May not allow for treatment or intervention: -For dz's w/no rx, the best possible outcome of testing is to have a definitive dx (and pts need to be aware of these limitations) 3) Can carry psych burden 4) Affect numerous individuals

Genetics testing: sensitivity + specificity

Sensitivity: the frequency w/which a test result is positive when the d/o is present -however, it does not define whether a positive result is caused by any particular pathology -ex: a fasting glucose=highly sensitive in detecting the presence of DM2, but incapable of determining whether they have DM2 as a primary dz OR secondary one (like Cushing's, etc) -SCREENING TESTS: b/c highly sensitive tests pick up all individuals w/the given dz-->highly sensitive tests are best for screening Specificity: frequency w/which a test result is negative when the dz is absent -ex: if trying to r/o Cushing's dz as the cause of DM2, then would use specific test (dexamethasone suppression test) and b/c it is highly specific-->it will be negative in almost all of those individuals in which Cushing's is NOT the cause of DM -Good diagnostic testing!

Presymptomatic/predisposition: genetic testing

Some genetic dz/s have late onset of SXS -in individuals w/a concerning family pedigree, presymptomatic/predisposition testing can be used to determine whether or not they are at risk of developing a late-onset genetic dz, or whether they are at increased risk of a multifactorial genetic dz Examples: -Huntington Dz -Breast/Ovarian cancer (BRCA1, BRCA2) -Colon Cancer (FAP, HNPCC) -Multiple cancers: Li-Fraumeni syndrome -Other syndromes in which cancer is a part: Neurofibromatosis, Cowden syndrome **When used in familial cancer syndromes, can help determine if prophylactic surgery or increased screening recommendations are appropriate

Spermatogenesis:

Spermatogenesis: occurs throughout a male's sexually mature life. Basically: the production of 4 haploid spermatids (2 w/ only X chromosomes, 2 w/only Y chromosomes) Primary spermatocyte (46xy)--> 1) Meiosis 1: -Forms secondary spermatocyte (23X) and secondary spermatocyte (23Y) 2) Meiosis II: -Each of the products from Meiosis 1 form 2 spermatids: ---Secondary spermatocyte (23X)-->forms 2 spermatid (23X) ----Secondary spermatocyte (23Y)-->forms 2 spermatid (23Y) **Final product=4 haploid spermatids

Aneuploidy:

Term used to describe the karyotype of a genome suffering from non-disjunction -describes a genome w/an abnormal # of chromosomes (whether they be additions, subtractions, incomplete or complete copies of entire chromosomes) Aneuploidies: common causes of genetic d/o's: 3 types commonly occur: 1) Mitotic Non Disjunction 2) Meiotic Non Disjunction: the most common cause of all forms of aneuploidy. Defined as: failure of a pair of chromosomes to disjoin during 1 of the 2 meiotic divisions (typically the first) -Too few recombinations is the issue; originates next to centromere or telomere 3) Translocation

Down's Syndrome d/t Translocation:

The common=Robertsonian Translocations (one parent had 21Q arm translocated onto one of the acrocentric chromosomes); the parent is unaffected but if the offspring inherits the affected acrocentric chromosome they will have trisomy of 21Q -NOT associated w/maternal age -B/c in this case, one of the parents is a translocation carrier-->risk of recurrence in subsequent zygotes is high Translocation 21Q21Q: the Q arm of the 21st chromosome is double the length d/t a splicing of a second Q arm

Genetic mosaicism:

The presence of 2 or more different genotypes in an individual which developed from a single fertilized egg. The individual as a result has 2 or more genetically different cell lines derived from 1 single zygote

Translocation in general:

Translocation: is a pathological process by which a dividing genome moves a piece of one of its chromosomes from 1 chromosome to another NON-homologous chromosome 1) Reciprocal translations: exchanging pieces of chromosomes between non-homologues 2) Robertsonian translocations (chromosomes 13,14,15,21,22=acrocentric chromosomes) -5% result in Down's Syndrome -In other translocations-->causes genetically non-viable fetuses 3) Balanced translocations: 4) Unbalanced translocations: Note: b/c people w/meiotic translocations have full genome technically (just w/out the genes on the correct chromosome), many are phenotypically normal -occasionally, can lead to cancer -b/c the chromosomes segregate into chromatids during gametogenesis, this can result in aneuploidy in the offpsring of the affected individuals

Trisomy 18 and 13:

Trisomy 18: Edward's syndrome: -Severe + usually fatal genetic aneuploidy -Occurs in 1/7500 live births, but is much more common in miscarriages (b/c only 5% of Trisomy 18s survive to birth) -Phenotypic abnormalities: severe + myriad (many): includes severe dysmorphic features, severe congenital heart dz, hypertonia, mental retardation -Associated w/maternal non-disjunction in 80% of cases -Only known risk factor: increased maternal age Trisomy 13: very rare condition -Affects 1/25,000 live births -Phenotypic abnormalities: severe anomalies, including devastating neuro + cardiac congenital defects -Caused by maternal meiosis I in 80% of cases

Allosome Aneuploidy vs Autosome Aneuploidy:

Typically, Autosome Aneuploidy (whether deletion or insertion) results in much more phenotype consequences, d/t the fact that each of these chromosomes encodes for many thousands of genes -The Y allosomes (sex chromosomes), by contrast, encode for only 50 genes roughly -The X allosomes: have less severe phenotype for diff reason than the Y--->only 1 of the X chromosomes is active in any given cell

Mitochondrial DNA:

Unique +independent DNA sequence d/t evolutionary origins as endosymbiotic bacteria 1) Maternal origin: -The majority of mitochondria in sperm are in the tail (which does not enter the ovum) and the ones in the head are tagged w/ubiquitin + destroyed later y embryo -Result: only maternal mitochondrial chromosome is represented in zygote and eventually the body cells -Therefore: only d/o's associated w/abnormal mitochondria are heritable if mom is affected (not dad) -Only one exception (mitochondrial myopathy) 2) 37 genes 3) Resultant proteins act only in the mitochondria Disorders associated w/mitochondria DNA: -Myoclonic epilepsy w/ragged-red fibers -Leber hereditary optic neuropathy

Genetic testing: summary

Used for: -Newborn screening -Carrier screening -DX based upon SXS -prenatal diagnosis -Presymptomatic/predisposition -Susceptibility testing Types of genetic testis: -Tests at the chromosomal level -DNA testing -Non DNA based genetic tests

Susceptibility testing: genetic testing

Used to determine susceptibility for a disease for which the inheritance is multifactorial -Somewhat controversial: presence or absence of such predisposing alleles does not guarantee dz progression, and so the results are difficult to counsel pts about -What it is: the identification of genetic changes that have been shown to be seen in inc frequency in individuals w/a given phenotype. Things to note: 1) Presence of allele does not guarantee dz 2) Gives a relative risk 3) Also seen in normal pop 4) Absence of allele does not r/o dz 5) May not be known causative mechanism Examples: -Non autosomal dominant familial Alzheimer's to determine presence or absence of the Apolipoprotein E allele (associated w/ development of the dz, but does not guarantee the dz)

Chorionic villus sampling vs Amniocentesis:

Utilized for diagnosis of Down's Syndrome: Chorionic villus sampling: -Sampling of placental tissue. Can be performed either trans-cervically or trans-abdominally -Main drawback: risk of inducing fetal loss=0.5-1% (much higher risk than amniocentesis) -Main utility: can be performed much earlier than amniocentesis (10-12 weeks gestation) and can therefore offer timely diagnostic info in event of abnormal first timester screening Amniocentesis: -Much lower risk of inducing fetal loss than ^^ -However, is performed much later in gestation (15-20 weeks); so not as timely These two are the DIAGNOSTIC tests that can actually diagnose Down's (which are only performed if the other types of testing suggest abnormality)

Comparative Genome Hybridization (CGH): what it is, and when to order

What is it: -Evaluates for changes in DNA segment copy number -How it works: the pt's DNA and a control genome are tagged w/diff fluorescent dyes, and they look to see if there is an area in which the two colors do not overlap, meaning either: 1) there is more of a particular sequence seen in the control compared to the patient (thereby pt is missing stuff), OR 2) there is more seen in the pt (indicating pathologic increase in sample copy number) **CGH is useful for identifying chromosomal structure abnormalities that are too small to be seen on karyotyping, but too large or undefined to perform a FISH When to order: indicated in individuals with -dysmorphic features -congenital abnormalities -intellectual disability and/or autism spectrum -after a normal or non-diagnostic karyotype has been performed -oncologic pathology to evaluate gene dosage in cancer compared to normal tissues **basically: ordered when any of these exist but when there is no specific microdeletion or substitution syndrome suspected

FISH study: when to order, and limitations:

What it is: -more recent: using ASO probe for which specific fluorescent-labeled antibodies have been made -chromosome is incubated w/the fluorescent labeled antibodies (after DNA hybridization + probe polymerization)-->and then can visualize the chromosome under microscope When to order it: -Suspected diagnosis of a microdeletion or a single-nucleotide substitution d/o, such as: 1) Prader-Willi syndrome 2) Angelman syndrome 3) Velocardiofacial syndrome 4) X linked icthyosis 5) Kallman One of the limitations of ASO and FISH probes: you must have a suspected DX so that the correct probes can be utilized during hte FISH (will be NON diagnostic if an unknown or previously unstudied mutation is responsible for the d/o)

Trisomies: 21, 18, 13

While they are all compatible w/life, they are associated w/ growth retardation, mental retardation, congenital anomalies, and distinctive phenotypes (which usually permit diagnosis, or at least suspicion) based on appearance at birth or prenatally