UTSW genetics

Description:	UTSW school of medicine 2009 genetics class
Category:	Genetics
Created by:	rbxbrown on 2009-10-21

Question	Answer
What is Q-banding?	Stain with quinacrine mustard (fluorescent). Bright Q bands correspond to dark G bands. Detects heteromorphisms of satellite repeats.
What is G-banding?	Giemsa black stain most commonly used in karyotyping
What is R-banding?	Heat the DNA before staining to improve resolution of bands. Reversed banding patterns.
Metacentric Chromosome	arms are approximately equal length
Submetacentric Chromosome	Centromere is off-center
Acrocentric chromosome	Centromere near one end (13, 14, 15, 21, 22)
Telocentric chromosome	only one arm (occurs sometimes w/chromosome rearrangements)
What is C banding?	Stains centromere and constitutive heterochromatin only
What is SKY?	Spectral karyotyping (uses 24 different colored fluorescent probes simultaneously)
Heteroploid	any chromosome number other than 46
Euploid	Exact multiple of 23 chromosomes
Aneuploid	Any chromosome number that is not a multiple of 23. Usually caused by nondisjunction.
Triploidy & Tetraploidy	Embryonic Lethal, results from failure of complete cleavage of the zygote at an early stage
Isochromosome	one arm is missing & the other is duplicated (haploinsufficiency of one arm and partial trisomy of the other). e.g. i(Xq)
Paracentric Inversion vs. Pericentric Inversion	Para = 2 breaks occur in one arm to one side of the centromere, usually no change in phenotype. Peri = 2 breaks occur in one arm around the centromere, can lead to duplication and deficiency during meiosis.
Balanced Reciprocal Translocation	Reciprocal exchange of broken-off segments between 2 different chromosomes. Very common, risk of abnormal progeny. Forms quadrivalent during meiosis.
Robertsonian Translocation	2 acrocentric chromosomes fuse near the centromere and lose short arms. (all acrocentric short arms contain repeats of ribosomal genes, so usually not deleterious). Risk of unbalanced progeny.
Isodisomy vs. Heterodisomy	(= uniparental disomy), Isodisomy = 2 identical chromosomes from same parent, Heterodisomy = 2 nonidentical chromosomes from same parent
Mole	When sperm fertilizes egg w/out nucleus. Develops into disorganized mass, can cause choriocarcinoma.
Ovarian Teratoma	46, XX containing only maternal chromosomes. Paternal --> extraembryonic devel. and maternal --> fetal devel.
Supernumerary chromosome derived from a paracentromeric region	Typically has clinical repercussions
Name the potential causes of Down Syndrome:	1. Trisomy 21, 2. Robertsonian Translocation (46 chromosomes), 3. 21q21q Translocation (isochromosome origin), 4. Mosaic Down Syndrome, 5. Partial Trisomy 21
Marker Chromosome	Supernumerary chromosome, very small, risk of clinical disorder depend on genes in marker
What are the 3 genetic disorders showing complete trisomy of an autonomic chromosome?	21 (Down Syndrome), 18, and 13
47 XXY	Klinefelter syndrome (male). More X's = still Klinefelter, but more severe phenotype. paternal nondisjunction of meiosis 1.
45 X	Turner syndrome (female), very uncommon (1/4000) short, webbed neck, cardiovascular abnormalities, normal intelligence
What is the region of the sex chromosomes that undergoes recombination?	Pseudoautosomal. When recombination extends beyond this region, XX males and XY females can occur.
X inactivation	X inactivation center at proximal Xq and XIST gene (only expressed from inactive X). X inactivation is usually random, but a damaged X is always inactivated.
47 XYY	normal male phenotype (paternal nondisjunction at meiosis). slightly lower IQ, greater risk of ADHD & hyperactivity. paternal nondisjunction of meiosis 2.
47 XXX	Trisomy X. Lower IQ, learning disabilities. 48XXXX & 49 XXXXX are more severe.
Segmental Aneusomy	microdeletions producing haploinsufficiency for key genes
What is the cell cycle in which most chromosome analysis is conducted?	Metaphase
Name the 6 common indications for chromosome evaluation:	1. Problems with early growth and development, 2. stillbirth and neonatal death, 3. fertility problems, 4. family history, 5. Neoplasia, 6. Pregnancy in woman of advanced age
Which cell types are used in cell culture for FISH analysis?	Leukocytes & Lymphoblastoids (peripheral blood), fibroblasts (skin biopsy), bone marrow, fetal amniocytes or chorionic villus biopsy
What are 3 identifying features of each chromosome?	1. position of the centromere, 2. banding pattern, 3. size
What are the chromosomal features & types of genetic testing available for fragile X?	1. expose cells to chemicals that inhibit DNA synthesis, or 2. detect expansion of the CGG repeat in the FMR1 gene
What are the 3 types of FISH probes?	1. Locus-specific probes (look for presence/absence of particular genes), 2. repetitive DNA probes (detect satellite DNA/centromeres/telomeres), 3. whole chromosome probes (bind segmentally along length of chromosome: painting)
What are the limitations of microarray CGH?	Measures relative copy number of DNA sequences, but not whether they have been translocated/rearranged
What is the incidence of...(1) sex chromosome aneuploidy, (2) autosomal aneuploidy, (3) structural abnormalities ?	(1) sex chromosome aneuploidy 1/350 male -- 1/550 female, (2) autosomal aneuploidy 1/700, (3) structural abnormalities 1/375. TOTAL = 1/150
What are the chromosomal abnormalities leading to spontaneous abortion?	1. Autosomal trisoym (0.52), 2. Autosomal monosomy (<0.01), 3. Triploidy (0.16), 4. Tetraploidy (0.06)
Describe the difference between Prader Willi & Angelman Syndrome:	Prader Willi = lacking chromosome 15 from FATHER, Angelman = lacking lacking chromosome 15 from MOTHER
What are the clinical features of Trisomy 18, 13, and 21 (besides mental retardation)?	Down Syndrome = loose neck skin, protruding tongue, heart disease. Patau Syndrome (Trisomy 13) = cleft palate, microcephaly, clenched hands, rocker-bottom feet, polydactyly. Trisomy 18 = cleft palate, clenched hands, receding jaw.
Name two cytogenetic mechanisms for mosaicism:	mitotic event: 1. nondisjunction in an early postzygotic mitotic division, 2. trisomy of zygote that is lost in an early postzygotic division
What is the mechanism of XX males and XY females?	SRY gene in sex determining region of Y chromosome (P11.3) is located right next to pseudoautosomal region
What is the difference between recombination and sister chromatid exchange?	Meiosis recombination = exchange of different codes, Mitosis sister chromatid exchange = exchange of identical genetic code
How can autosomal dominant be distinguished from X-linked dominant and pseudoautosomal dominant mutations?	X-linked dominant cannot be passed from father to son (son have an autosomal dominant-like pattern if recombination transfers X-linked genes to the Y chromosome (mostly female transmission with a few male)
What is anticipation?	When a disease phenotype is expressed at earlier and earlier ages as it is passed from generation to generation. Common in unstable repeat expansion diseases.
Fragile X Syndrome	fragile site on the q arm fails to condense during mitosis. 50% penetrance in females. Caused by an unstable repeat expansion.
Mitochondrial genetic bottleneck	# mitochondria in the oocyte is severely reduced before being exponentially multiplied. This can allow a mutant mitochondrial DNA to dominate the gamete.
Mitochondrial DNA mutations	each mitochondrion has multiple copies of DNA, but mutations can be propogated amongst daughter cells, and eventually produce homozygous cells. Inheritance is only from the mother.
Obligate Heterozygote	Phenotypically normal, but on the basis of pedigree must contain the mutant allele
Compound Heterozygote	2 different mutant alleles of the same gene are present (no normal allele)
What is the transmission pattern for X-linked recessive mutations?	Generally restricted to males (but not all males), rarely seen among females.
Locus Heterogeneity	Same disease phenotype caused by mutation of different genes
Name 3 autosomal dominant diseases	Familial Hypercholesteremia (incomplete), Achondroplasia (incomplete), Huntington Disease
What is incompletely dominant inheritance?	More severe clinical outcome when homozygote vs. heterozygote in autosomal dominant disease.
Differentiate Consanguinity from Inbreeding:	Inbreeding = isolated population that tends to choose partners from within population. Consanguinity = 2 partners inherit a mutant allele from a single distant common ancestor
pleiotropy	multiple, often seemingly unrelated, clinical disorders related to a single mutation
Name 2 X-linked recessive disorders:	Hemophilia A, Androgen Insensitivity Syndrome
Relative Risk Ratio (RRR)	Prevalence of disease in relatives of an affected person/Prevalence in general population
Difference in the likelihood of relatives of diseased individuals to report a genetic condition vs. relatives of normal individuals:	Ascertainment Bias
Greater likelihood to know of other family members experiencing the same condition in diseased vs. control groups (due to knowledge of the disease):	Recall Bias
Qualitative vs. Quantitative trait:	Quantitative = follows Gaussian distribution in population (e.g. large tonsils), Qualitative = present/absent in disease state (e.g. fibroxanthoma)
Situations in which monozygotic twins do not have identical genotypes:	1. somatic rearrangements in T-cell receptor & IgG, 2. X-chromosome inactivation
Volunteer-Based vs. Population-Based Ascertainment	Volunteer-Based = one twin signs on, then recruits other twin. Population-Based = twins sign up for study and their health is subsequently assessed.
Heritability (h^2)	0 if genes contribute nothing to the phenotypic variance. 1 if genes contribute 100%. = (Variance in DZ - Variance in MZ pairs)/(Variance in DZ pairs)
Multigenic trait disorders	e.g. digenic inheritance in Retinitis Pigmentosa, e.g. Idiopathic Cerebral Vein Thrombosis (2 genetic, 1 environmental factor), 3. Hirschprung Disease, 4. Type 1 Diabetes, 5. Alzheimer's
Which inheritance pattern shows linear, diagonal, or horizontal inheritance?	Linear = autosomal dominant, Diagonal = X-linked recessive, Horizontal = autosomal recessive
Sarcoma	Tumor arises in mesenchyme (bone/muscle/connective/nervous system)
Carcinoma	Tumor originates in epithelial tissue (intestine/bronchi/mammary)
Gatekeeper Tumor Suppressor Genes	Control cell growth (regulate checkpoint transitions = gates)
Caretaker Tumor Suppressor Genes	Protect the integrity of the genome (prevent propogation of mutations)
What is the mechanism of oncogenesis for ABL?	Cytoplasmic Tyrosine Kinase, causing Chronic Myelogenous Leukemia. BCR-ABL protein has constitutive tyrosine kinase activity. (bone marrow leukocyte stem cells)
What is the mechanism of oncogenesis for CMYC?	Transcription factor causing Burkitt Lymphoma. MYC gene translocates from 8q to 14q -> unregulated gene expression (B-cells)
What is the mechanism of oncogenesis for BCL2?	Antiapoptotic mitochondrial protein causing Chronic Lymphocytic Leukemia (Bcells). BCL2 translocated from 18q to 14q -> unregulated expression via heavy chain promoter.
What is the mechanism of oncogenesis for telomerase?	Not a primary oncogenic factor, but likely plays a role in maintenance of the cancerous cell proliferation
2-hit hypothesis for cancer	genotypic heterozygous for one mutation undergoes second somatic mutation to knock out function of the other allele, OR epigenetic changes shut down other allele
Loss of heterozygosity (LOH)	When tumor cells contain two identical mutant alleles at an oncogene locus instead of heterozygous alleles.
Mechanisms for LOH	1. Interstitial deletion (allele loss), 2. Mitotic recombination (allele loss), 3. Mitotic nondisjunction (chromosome loss), 4. Mitotic nondisjunction + duplication (chromosome loss + new copy of chromosome w/mutant gene)
What is the difference between genome, chromosome, and gene mutations?	Genome Mutations = change in # chromosomes, Chromosome Mutations = change structure of single chromsome, Gene Mutation = change in individual gene
What are the consequences of missense mutations?	one codon is replaced with another -> altered protein funtion or altered rate of transcription
What are the consequences of Chain Termination Mutations?	nonsense mutations (inserted/deleted stop codon) -> unstable mRNA leading to decay or unstable protein leading to degradation.
What are the consequences of RNA Processing Mutations?	Alternative RNA splicing sites generated
Mutation Hotspot	Single NT mutations can be transitions (pyrimidine for pyrimidine & purine for purine), or transversions. Hotspots = spontaneous deamination of methylated CpG -> thymidine. Very common mutation.
mechanism for large deletions/insertions	LINE RNA is reverse transcribed into DNA, and can insert randomly into the genome
c.365g>a	cDNA mutation in which a guanine was mutated into an adenine at position 365
g.IVS365+2T>A	genomic DNA mutation in which the invariant T of the GT 5' splice donor site has been mutated to an A, adjacent to an intervening sequence (used when gene sequence not fully known)
g.IVS365-1G>C	genomic DNA mutation in which the highly conserved G of the 3' AG splice acceptor site is mutated to C.
m.365_369delACAC	deletion of 4 nucleotides of mitochondrial DNA beginning at position 365
m.365_369insACAC	insertion of 4 nucleotides of mitochondrial DNA beginning at position 365
Glu365X	nonsense mutation substituting a stop codon for Glutamate 365
dynamic mutation	variable repeat mutations that accumulate over multiple generations of cells/people
Calculating Mutation Rate	Take # affected individuals from a large n of an autosomal dominant mutation. Mutation rate = # affected/(2 alleles x n)
Mutation Rate	# new mutations/locus/generation (typically in the range of 10^-4 to 10^-6)
Genetic Polymorphism	mutation found in >1% of a population
short tandem repeat polymorphisms (STRP's)	microsatellites = repeats of 2-5 NT's, multiple repeat lengths (alleles) in the population, readily genotyped. 5-25 copies.
variable number tandem repeats (VNTR's)	minisatellites = repeats of 10-100 NT's. Thousands of copies.
Copy Number Polymorphism	Repeated segments of DNA, tested by array comparative genome hybridization
Rh	+ have antigen RhD, - lack antigen. (-) mothers w/(+) fetuses make Ab's that attack fetal blood = hemolytic disease. Greater risk for subsequent pregnancies. Treatment = Rh antibodies (RhoGam) to mother to reduce exposure to fetal antigens.
HLA genes	human leukocyte antigen genes, class I (A, B, C) and II (DP, DQ, DR) encode proteins that present antigens to the lymphocytes. chromosome 6p, part of MHC, order = class II, then III, then I.
HLA inheritance	clustered on single choromosomal segment 6p (HLA Haplotype), so inherited in entirety from a single chromosome from each parent. Linkage Disequilibrium.
Ankylosing Spondilitis	autoimmune disease of the spine, caused by HLA B27 polymorphism
Linkage Disequilibrium	Occurence of specific combinations of alleles @ linked loci more frequently than predicted. Due to low recombination & closely located genes of a common function.
SNP	2 alleles only corresponding to 2 different bases @ particular site. Occur 1/1000 base pairs.
Assumptions in calculating mutation rate:	1. ascertained cases due to new mutation, 2. full penetration, 3. all new mutations are carried to term, 4. Only 1 mutation can cause the disease
Stratification	Different subpopulations do not interbreed. Increases frequency of autosomal recessive & dominant disease, only minor effect on X-linked disease.
Assortative Mating	positive = people choose mates with similar characteristics to themselves (including disease). Increases frequency of autosomal recessive disease.
Consanguinity and Inbreeding	Consanguinity increases frequency of autosomal recessive disease.
Linkage Analysis	Compares inheritance of particular stretches of DNA with disease incidence within a family tree
Association Analysis	Compare frequency of a particular allele between diseased individuals and controls from the same population
=genes located on the same chromosome	syntenic
recombination frequency (theta)	between 0 (no recombination)and 1/2 (independent assortment) (proportion, not percentage)
phase	knowing which alleles are syntenic in the case of an AaBb individual. On same chromosome homologue = in coupling (cis), on different homologues = in repulsion (trans)
LOD score (logarithm of the odds)	(Z) statistical measure of accuracy per n for recombination events. = [log(10) (likelihood if linked/likelihood if unlinked)]. higher Z = better estimate of theta max. LOD > +3 = odds better than 1000:1 for linkage.
linkage equilibrium	Equilibrium = frequency of allele within a haplotype is the same as the frequency of the allele within the whole population.
linkage disequilibrium	Disequilibrium = genes surrounding disease allele inherited at higher than expected rates.
D'	measure of linkage disequilibrium. 0 = equilibrium, up to 1 = intense disequilibrium.
Ancestry Informative Markers	SNP's that distinguish different ethnicities
LD blocks	clusters of SNPs in high linkage disequilibrium
Disease Odds Ratio	odds of an allele carrier developing a disease = (# diseased allele carriers/# nondiseased carriers)/(# diseased noncarriers/# undiseased noncarriers)
Relative Risk Ratio	measures strength of an odds ratio: (# diseased carriers/all allele carriers)/(# diseased noncarriers/all noncarriers)
Limitations of Association Studies	1. in population stratification, it may be that a particular alleles is associated with a higher risk of disease because multiple alleles are associated with the stratified group (consanguinity), 2. linkage disequilibrium
tag SNP's	minimum set of SNP alleles necessary for defining a haplotype in a LD block
What's the best method for mapping short genetic distances?	linkage disequilibrium (D')
How do you calculate the number of possible haplotypes with complete linkage equilibrium?	2^n (where n = # SNP's)
Contiguous Gene Syndrome	poly-phenotypic disorder caused by deletion of contiguous genes along a chromosome.
balanced translocation meiotic assortment	adjacent 1 (1 of each type of of centromere), adjacent 2 (2 of one type of centromere), alternate = normal/balanced
pseudohermaphrodite vs. hermaphrodite	pseudohermaphrodite = internal sex organs match karyotype. true hermaphrodite = both testes and ovaries are present.
Indications for Prenatal Diagnosis by Invasive Testing	1. Older women, 2. previous child w/ aneuploidy, 3. structural chromosomal abnormality in parent, 4. family history of single-gene disorder, 5. relatives w/neural tube defect, 6. family history of X-linked disorder, 7. + maternal serum/ultrasound screen
Amniocentesis	1. invasive, 2. 2nd trimester 15-16 weeks, 3. amniotic fluid contains fetal cells & urine, 4. test AFP, metabolites, chromosomes, enzyme activity, DNA sequencing
alpha fetoprotein as indicator	immunoassay in maternal serum (MSAFP) or amniotic fluid (AFAFP). high [AFP] indicates anencephaly, spina bifida. (also blood in AF, death, twins, overestimated age
chorionic villus sampling	1. invasive biopsy (tertiary villi), 2. 1st trimester (early advantage) 10-12 weeks, 3. cells derived from fetus, 4. test chromosomes, enzyme activity, DNA sequencing (NOTE: too early for AFP, some mosaicism ambiguity)
MSAFP	catches Down Syndrome (1st trimester) & neural tube defects (2nd trimester)
1st trimester MSAFP screening	11-13 weeks, measures PAPP-A (low in Down Syndrome) & hCG (high in Down syndrome but low in trisomy 13 & 18)
ultrasonography	2nd trimester & later, look for edema of fetal neck (trisomy marker), other physical abnormalities, growth rate
2nd trimester MSAFP screening	AFP, hCG, estriol (triple screen). sometimes also inhibin A. All low in all trisomies (except hCG high in Down S)
types of mosaicism	true = detected in multiple colonies from multiple primary cultures, pseudo = seen only in single cell or derived from single primary culture (usually false positive)
if unexpected adverse findings from prenatal chromsomes analysis	karyotype the parents (especially for balanced vs. unbalanced structural rearrangements, and for uniparental disomy in region containing imprinted genes)
Prenatal disease treatment & prevention	termination of pregnancy, metabolic disorder treatment, glucocorticoids for CAH, relief of bladder obstruction, bone marrow transplantation
preimplantation genetic diagnosis	in vitro fertilization, single blasttomere tested (8-16 cells), DNA analysis for single disorder, only conducted if parents/other child has a disorder
Genetic screening	public health initiative to identify individuals at increased risk for genetic disease. screen all members of a large population, regardless of family history.
clinical validity vs. utility	validity = predictive of disease, utility = will cause change to treatment
sensitivity vs. specificity	sensitivity = fraction individuals w/disease who have the tested-for genotype, specificity = fraction of individuals w/out disease who do not have the tested-for genotype
positive predictive value	= % chance of developing the disease given a particular genotype, OR % of people with a genotype that actually have the disease
heterozygote screening	when a high frequency of carriers (e.g. Ashkenazi jews & Tay-Sachs), inexpensive tests, genetic counseling & prenatal diagnosis available,
gene flow	slow diffusion of genes across large populations
genetic drift	in small populations, random effects cause a change in allele frequeny
nondirective counseling	patients provided with information, but are not told what to do regarding testing & managment options
conditional probabilities	depend on whether the individual in question is a carrier
What are the odds of 13 successive male births? What are the odds of 13 successive births of a single-sex?	1. (1/2)^13, 2. 2*(1/2)^13
How are genetic vs. allelic diseases treated?	genetic = treat symptoms, identify risk for family. allelic = replace defective protein/minimize consequences, genetic counseling, carrier testing, prenatal diagnosis. increasing protein expression only works when mutant protein is partially functional.
Diversion Therapy	use of alternative metabolic pathways to reduce concentration of a harmful metabolite.
Treatment of Enzymopathies	Improve enzyme folding (2-3% improvement, but enough to restore homeostasis). Doesn't work when protein 100% dysfunctional.
small molecules therapy for skipping over mutant stop codons	nonsense mutation = 11% of defects in human genome. experimental therapy, as yet not fully tested.
ERT (enzyme replacement therapy)	1. proteins can be chemically modified (e.g. PEG) to improve pharmacotherapy, 2. intracellular enzymes can be administered extracellularly if substrate is in equilibrium w/extracellular fluid, 3. don't cross BBB, expensive
best candidates for ERT	CNS not involved, only alternative therapies are high risk, human enzyme available in abundance, biology very well understood
How are enzymes for Gaucher's Disease targeted to particular cell types & organelles?	modification of the carbohydrates normally decorating the glycoprotein enzyme: terminal sugars are removed & core alpha mannosyl residues target macrophages (then delivered to lysosomes intracellularly)
What gene expression targeted treatments are appropriate for sickle cell anemia?	DNA hypomethylation increases expression of fetal Hb
Nuclear Transplantation	= nuclear cloning, transfer of diploid nucleus from adult donor somatic cell into an oocyte cytoplasm
Therapeutic cloning	uses embryonic stem cells generated by nuclear trnsplantation to form mature differentiated cell types in culture, for transplantation into the donor w/no immune rejection
reproductive cloning	reimplanting an embryo obtained by nuclear trnsplantation into the uterus of a surrogate mother -> clone of donor human
What are some examples of genetic disorders treated by hematopoietic stem cell transplantation?	cancer, severe combined immunodeficiency (e.g. beta-thalassemia). Transplanted stem cells release enzymes that are taken up by native cells containing the k/o mutation. Brain perivascular microglia come from marrow. homozygous normal best.
source of hematopoietic stem cells	bone marrow, placental cord blood (more tolerable for histoincompatibility, widely available, risk of graft-vs.-host disease is reduced)
what are the essential requirements of gene therapy for an inherited disorder?	1. known gene identity, 2. cDNA clone, 3. known disease pathophysiology, 4. good risk-to-benefit ratio, 5. low consequences of over/underexpression, 6. target cell w/ long half-life or replicative, 7. successful animal studies, 8. governmental oversight
ex vivo vs. in vivo gene therapy	ex vivo = gene injected into cells in vitro that are then introduced into the body. in vivo = gene introduced directly into the patient via viruses
episome	circular viral DNA containing a normal copy of a gene to replace a mutant allele. good for long-lived cells
Uses for gene therapy	1. replace mutant gene, 2. inactivate dominant allele, 3. administer pharmacotherapy in vivo
ex vivo vs. in vivo gene therapy
retrovirus DNA transfer	= RNA viruses, incapable of replication, non-cytotoxic, up to 8kb DNA, low copy number inserted. Usually target cell must undergo mitosis, but Lentiviruses (eg. HIV) work in non-dividing cells.
adeno-associated viruses in DNA transfer	no adverse effects in humans, infect all cells. Inserts only up to 5 b.
adenoviruses in DNA transfer	easy to produce (high titer), infect all cells, inserts of 30 to 35 kb. Associated w/death due to immune reaction.
nonviral vectors for DNA transfer	naked DNA, DNA in liposomes, protein-DNA conjugates (where protein binds receptor for transport, etc.), artificial chromosomes.
limited success of nonviral vectors	DNA tends to be degraded by lysosomes, remaining DNA mostly does not enter the nucleus, inefficient delivery