Genetics Study Guide Problems

homoplasmy wild-type homoplasmy mutant heteroplasmy

"heteroplasmy" or Homoplasmy" for a mtDNA mutation only wild-type mtDNA present- _ only mutant mtDNA present-_ 2 different populations of mtDNA are present in given cell or tissue (wild-type and mutant)-_

locus heterogeneity allelic heterogeneity

***Mutations at multiple loci can cause disease (a,b) Ex: mutations cause DIFFERENT gene products to exist in a pathway that produces same phenotype ***Many different alleles at same locus can cause disease Ex: Mutations cause varying dysfunctions in SAME gene products that produce same phenotype. (a1, a2)

leukemia single low Chronic Myelogenous Leukemia Chromosomal Translocation tyrosine kinase inhibiting tyrosine kinase fusion

*Chromosome Analysis (conventional cytogenic analysis/G banding) is standard of care to detect abnormalities in L_, detecting (single or double) cell abnormalities and (high or low) resolution view of entire genome *CML (give name) is the first C_ abnormality associated with dancer. (Replication or translocation) between chromosomes 9 and 22. The translocation results in the BCR-ABL fusion gene resulting in a (tyrosine kinase inhibitor protein or tyrosine kinase protein) Treated with therapy targeted at (stimulating or inhibiting) tyrosine kinase activity from the F_ gene.

P + Q = 1 = p2 + 2pq + q2 * frequency of males p2 + 2pq + 2pr + 2rq + q2 + r2

*Give Hardy Wienberg Equation for two alleles *For x-linked recessive: q= frequency of (males or females) *Give Hardy-Weinber Equation for three alleles

UPD is when there are 2 copies of a chromosome (or part of a chromosome) come from one parent, and none from the other parent. It occurs as a result of nondisjunction of either homologous chromosomes or sister chromatids and either Monosomy Rescue (where one chromosome is duplicate to yield two) or Trisomy Rescue (where chromosome from parent that contributed to one chromosome is lost). *Gene imprinting is when a gene is identified as either parental or maternal and genes that are imprinted are only expressed from either maternal or paternal chromosome. *DNA methylation *same, same, MUTANT

*What is uniparental disomy (UPD)? It usually occurs as a result of _, and either M_ rescue or T_ rescue. Explain both processes. *UPD can cause disease, when there is an I_ gene on the involved chromosome. What is gene imprinting? What epigenetic factor does imprinting usually occur through? *UPD also can cause a disease, if the two copies from the (same or different) parent are the (same or different) chromosome AND the chromosome contains a (mutant or wild-type) allele.

X-linked RECESSIVE inheritance X-linked Dominant Inheritance, caused by New Mutations

- Hemophilia, what type of inheritance? - Rett Syndrome, what type of inheritance? (most cases of Rett syndrome are caused by

Imprinting, Paternal yes Imprinting, Maternal Yes uniparental disomy Yes No, cannot detect if chromosome is maternal or paternal Methylation specific multiplex ligation-dependent probe amplification (MLPA) Methylation Specific polymerase chain reaction (PCR) Single nucleotide Polymorphism (SNP) array

- Prader-Willi Syndrome - Caused by a deletion on chromosome 15. Also caused by I_ of (paternal or maternal) genes. If you have two maternal chromosome 15, then will a patient have the syndrome? - Angelman Syndrome- caused by a deletion on chromosome 15. Also caused by I_ of (paternal or maternal) genes. If you have two chromosomes inherited from dad, will a patient have this syndrome? *This syndromes are examples of U_ P_ D_ (UPD). Is this a departure from Mendelian inheritance? *Can chromosomal analysis and FISH work to detect UPD? What methods will detect UPD? MLPA, PCR, SNP array (give names)

- gene deletion (copy number change) in the inverted duplication that deletes the SMN1 gene. Point mutations less common - the inverted duplication predisposes to misfiring during meiosis and gene deletion and duplication due to crossing over within the inverted duplication. - The unique structure of the SNM1 region predisposes to new mutation due to gene deletion (rather than point mutation in most other cases) and the high mutation rate results in a significant fraction (2%) in which one parent is not a heterozygous carrier. - If the patient has a new mutation of one of the SMN1 alleles (i.e. parent does not have mutation) then the risk of recurrence is much lower than the typical 25% we would say for autosomal recessive disorders.

- What sort of mutation is most commonly seen in patients with SMA (whether inherited or new mutations)? - What about the gene structure of SMA locus predisposes to this sort of mutation? - How do you explain the high rate of new mutations in patients with SMA compared with other autosomal recessive disorders? - How do the parental genotypes in SMA affect the recurrence risks for future children?

Genome - size of PCR different for mRNA vs genomic DNA. mRNA from an expressing cell is more difficult to obtain. Also, if analyzing RNA, the primers cannot be located within intronic sequences, as these are spliced out of the mature mRNA. - get the complementary of the 5' strand then do the primer strand against this complementary strand. - Do primer strand against 3' strand directly. (keep 5' sequence (its the same), and directly do complement of 3' strand, hybridize it) - NO! sequencing would be required!

- when testing mutations, would you prefer to test for the mutation in mRNA or in the genome? What do you need to consider when formulating your approach? - 5' to 3' DNA strand, how do you make a primer? - Can a size difference of 3 base pairs be easily detected on a gel? if not, what would be required?

ATM is the gene mutated in AT. ATM plays a key role in double-stranded DNA repair. With AT, chromosome irradiation causes more breaks than normal because ATM is no longer functional and cannot fix the breaks. AT cells fail to stop cell cycle to allow repair of the double0-strand breaks generated by radiation. - Autosomal Recessive, 25% - Chemotherapy. Patient is radiosensitive With radiation therapy, the loss of AT causes more breaks in the chromosomes and chromosomal damage. You should minimize your patients exposure to radiation including for diagnostic procedures such as CT scans.

-You suspect a child may have Ataxia Telangiectasia, so you send her blood for radiosensitive assay. Chromosome fragility analysis showed an increased percentage of fragments (5 breaks/cell, normal <1.5). Is this expected if she has AT? Why? - What is the mode of inheritance of AT syndrome? What is the chance of her 3 month old sibling having AT? - You continued to follow this patient. At age 6, she was diagnosed with leukemia. Would you start her on chemotherapy or radiation therapy, and why?

a) likely that child as a "NEW MUTATION" in the RB1 gene in the germ line. Genetic testing for mutations in RB1 gene in the child can provide evidence that a "new germ line" mutation has occurred in child. b) Once germline mutation in RB1 gene is identified in child, parents should be tested to see if they are carriers. The risk of RB developing in second child is almost zero. Not zero because the father can be a germ line mosaic for the child's mutation. (many of his germ line cells have the mutation) -risk determined by degree of mosaicism in sperm of father. c. 50%

A couple has a 1 year old child with bilateral retinoblastoma--a childhood onset ocular tumor. Both parents have normal eye exams and there is no family history of retinoblastoma on either side of the family. a. What is the likely explanation of RB in this child? b. What is the risk of recurrence in other children of this couple? c. What is the chance that a future offspring of this child will be affected with retinoblastoma?

Every person has two alleles for a chromosome. They pass on one allele to their offspring. A 21/21 Robertsonian translocation means that their offspring will be either non-viable (not get chromosome) or that they will end up with a trisomy of chromosome 21. All Live-born children will have down syndrome.

A man has a 21/21 Robertsonian Translocation and is phenotypically normal . What is true regarding his children? Explain.

HNPCC/Lynch Syndrome has a high risk for colon cancer because of inherited mutations that impair DNA MISMATCH REPAIR. **The patient should contact her brother. Her brother should have sections of the brother's tumor block (embedded in paraffin) screened by immunohistochemistry (IHC) for loss of DNA mismatch repair proteins. This method can quickly narrow the focus to a specific gene. The brother should then have a blood sample sent for DNA sequencing, focusing on the MMR proteins absent in the tumor. If a mutation is found in the brother, the patient should then have her blood tested for the same mutation. **They should undergo genetic testing for the mutation. If positive, they should undergo intensive screening, beginning now (all at-risk individuals in their 20s or older.) If negate, they can undergo less intensive screening, as for average risk individuals. **The patient should undergo colonoscopy every 1-2 years, beginning now. She should also undergo yearly screening for uterine and ovarian cancer. (If she didn't carry a MMR gene mutation present in her brother and sister, she could be screened as any other average risk patient, with a colonoscopy every ten years, beginning at age 50.)

A patient has a brother who was recently diagnosed with colony cancer. Her sister had two adenomatoous polyps removed on colonoscopy. The rest of the patient's family is alive and healthy. You advise her and her family to pursue genetic testing for HNPCC/LYNCH Syndrome. **How should the patient go about genetic testing? (first think about what cause Lynch syndrome) **What should you advise the patient regarding her other family members if a mutate his found in her 44 year old mother? **The older brother and sister and the patient are all found to carry an HNPCC-associated mutation. How should the patient be treated?

25% chance

A young woman is pregnant. She and her husband, both healthy, have been diagnosed as carriers of abnormal hemoglobin genes. The husband is a carrier of the sickle cell gene, the woman carrier of a beta-thalassemia mutation. What is the change that the child will be affected with a severe anemia?

autosomal recessive "inborn error of metabolism) - IS, DO NOT

Alkaptonuria Give inheritance - One good copy (is or is not) enough, thus heterozygotes (do or do not) manifest the disease

No. But most importantly it is the specific COMBINATION of regulators factors that bind to the regulatory determinants of a particular gene that leads to a specific transcriptional result (activation, enhancement, or silencing of transcription_, the transcriptional factors (trans-acting proteins) act in a combinatorial manner and NOT as single factors. This allows for these proteins to generate specificity of gene control and economizes the number of transcriptional factors that are necessary to control the multitude of tranctiponal responses in the hundreds of different cell types.

An 8bp sequence occurs at 46,000 sites in the genome. Considering this frequency, would it be reasonable to predict that this single transcription factor would be able to selectively activate and coordinate the expression of a subset of 100 genes in the human genome?

- YES!! Why? B/c with many genes it could signify a pleiotropic issue (many gene mutations with smaller penetrance), also with cardiac disease and/or developmental delay, usually many genes are implicated. - BOTH! this gives you help to determine wheterh or not the deleted gene causes the disease - YES! So that you can understand the underlying mechanism of the gene(s) and what they do for normal cells.

An array cytogenomic test was done on your patient with cardiac disease and developmental delay and an 800kb deletion was identified that contains 10 genes. What factors will help you decide if this deletion is the cause of the patient's problem? Hint: Does the number of genes matter? Why or Why not? Does the number of patients without or with clinical problems or both who have deletions of this gene or genes matter? Should the expression pattern of this gene within the deletion be assayed?

microarray, SNP increased homozygosity

By what methods could incest be identified? M_ analysis if S_ genotypes showed (increased or decreased) (homozygosity or heterozygosity)

transcription, wrong chimeric novel long enhancer

Chromosomal translocations can lead to expression of T_ factors in the w_ cell type, generate C_ transcription factors with (novel or old) activities, and reveal the existence of (close or long) range (promoter or enhancer) elements.

dividing, metaphase Amniotic Chorionic used to detect GERMLINE cytogenic changes bone marrow blood skin do not stimulate leukemic

Conventional cytogenetic analysis requires a source of (senescent or dividing) cells in M_ *In prenatal analysis, use A_ fluid, and C_ villi (placental biopsy) *What is one of the purposes for prenatal and post natal indications (to do) cytogenic studies? *In other analysys, use B_ M_, Peripheral B_, S_, other tissues *Normal white blood cells (do or do not) divide; need to (inhibit or stimulate) the cells with a mitogen. L_ cells in the peripheral blood can divide without stimulation.

histone deacetylases, REPRESSION

Cytosine methylation occurs when (histone deacetylases or histone acetylases) are recruited to targeted promoter causing (activation or repression) of gene activation.

- Conventional G-band analysis: No, need cells to be living (in culture) need during metaphase (dividing cells) - FISH: Yes for enumeration (dosage) or Balanced chromosomal rearrangement (can't use for local chromosomal rearrangement, need to be in metaphase, live culture) - Chromosomal microarray: Yes. It would be possible if you could get DNA of good enough quality.

Do you think it is possible to use cytogenetic/cytogenomic techniques on formalin fixed, paraffin embedded tissue (the tissue remains permeable to allow for staining)? Talk about each and whether or not you can use it - conventional g-band analysis - FISH - chromosomal microarray

No UPD can be associated with a normal phenotype if there are no imprinted genes within the UPD region AND no recessive disorders are uncovered

Does uniparental disomy always result in an abnormal phenotype? explain

Mismatch Repair defect

Examining tumor DNA samples for abnormal patterns of MICROSATELLITES is a test for which type of defect?

Fluorescent in Situ Hybridization. Cytogenic Probes Chromosome High No. Can only be used to identify chromosomes (blocks of genes, many base pairs) not high resolution enough. No! cannot find mutation in gene (only looks at chromosomes) *FISH CANNOT be used for unbalanced rearrangements. - Dosage (amount of chromosomes) - Balanced rearrangements - localization of rearranged material identify POSITION of genes (where on chromosome), identify deletions, duplications, or rearrangements (balanced) Yes- trisomy 21, duplication

FISH (give name) is a C_ technique that uses Fluorescent P_ to that bind only those part of the (SNP or chromosome) with a (high or low) degree of sequence complimentary. Can FISH be used to identify SNPs? Why or Why not? Can FISH be used to find parental origin in child (essential SNP or mutation in gene?) Can FISH be used to for Unbalanced rearrangement? What can it be used to discover? list three Can FISH be used to diagnose Down Syndrome?

telocentric, acrocentric, submetacentric, and metacentric

From left to right, identify as either acrocentric, metacentric, telocentric, or submetacentric

100% make a punned square mother's egg will by E1a and E1a father's sperm will be E1bE1b crossing, all kids will get E1aE1b (thus both alleles will have mutations!) 100 will inherit disorder.

Genetic testing shows that a husband is homozygous for a mutation in the E1 alphas gene and the wife is humorous for a different mutation in the E1 alpha gene, what is the risk that their first child will have this disease, MSUD, an autosomal recess disorder? give reason why

Loss of Heterozygosity (LOH) Ex: Retinoblastoma Hereditary Sporadic

Give term for: Aa (heterozygous) then lose the one good copy (second hit) Ex: _ * _:usually both eyes due to LOH (one somatic mutation, because entire body is heterozygous for rb) *_: usually only in 1 eye because 2 somatic mutations are required.

locus - person who MUST be a carrier - Pleiotropy - Variable Expressivity - Incomplete Penetrance - Incomplete dominant penetrance

Give words or definitions for - location on gene: - Obligate Carrier: - Multiple organs affected by one gene - Affected individuals show different severity in phenotype - no disease phenotype despite having genotype - AA phenotype is more severe than Aa

autosomal recessive inheritance - Heterozygous advantage means that carriers of sickle cell anemia have higher fitness against malaria compared to this wild-type and disease allele carrying - Deletions

Hemoglobinopathies like sickle cell and alpha and beta thalasemmia are what type of inheritance pattern? - How does Sickle Cell Anemia display heterozygote advantage? - The most common form of alpha-thalassemia is the result of (mutation or deletions)

Epigenetic Enzymes that remove acetyl group from lysine residues on Histones, causing compaction of DNA and REPRESSION of transcription.

Histone Deacetylases. Describe function

45 (loss of p arms) fusion of q arms (total 1 less chromosome) 47 if free chromosome, 46 is inherited Robertsonian Translocation FISH chromosome analysis (conventional cytogenic, karyotype, g banding)

How many chromosomes does a carrier of a Robertsonian translocation have? Explain. How many chromosomes does a patient with trisomy 21 have? What cryogenic test can be used to detect trisomy 21 prenatally? Can the origin of trisomy be determined with this test? What test will show origin of trisomy?

Identity by descent matching DNA common recombination FISH or chromosomal analysis (karyotyping) SNP array can detect Identity by Descent single, is not recessive consanguinity R= coefficient of relationship between parents F= Coefficient of inbreeding

IBD stands for _ _ _. *What is IBD? term used to describe a (matching or varying) segment of (DNA or RNA) shared by two or more people inherited from a (different or common) ancestor without any intervening (recombination or cytogentism) *What two cytogenic methods cannot detect IBD? What can? The difference between UPD (uniparental disomy) and IBD (identify by descent) is that UPD typically restricted to (single or many) chromosomes and (is or is not) spread across entire genome. *IBD can uncover regions of potential (dominant or recessive) allele risk. the degree of IBD is the degree of C_ (inbreeding). Equation R= 2F tells us what? What does F stand for? How do you calculate.

reduced (or incomplete) penetrance- person carries disease causing variant but does not show phenotype OR there could be evidence that the variant is not disease causing

If a variant does not completely segregate with the phenotype, what are the possible explanations?

aneuplodies (excess of genes) less Turner Syndrome. 99% Klinefelter SYndrom decreased, infertility, tall - normal male - SRY translocated from Y chromosome to X chromosome - SRY gene is deleted from Y chromosome

In comparison with autosomal aneuploidies (What is this?), sex chromosome aneuploidies result in much (more or less) severe effects on mental and physical development. - Identify disorder 45, X karyotype This genotype results in (99% or 1%) spontaneous abortions. - Identify disorder 48, XXYY or 48, XXXY, or 49, XXXXY This genotype results in (increased or decreased) penis size and testes, (fertility or infertility) and (short or tall) stature. - 47, XYY Results in (normal or abnormal) (male or female) Give reason for 46, XX male _ gene is present, probably translocated from where to where? Give reason for 46, XY female _ gene is deleted from where?

mRNA splicing

In one type of Beta-thalassemia, intronic sequences are found within the mature Beta-Globin mRNA. The mutation which lies at the intron 2/exon 3 boundary blocks normal

- somatic recombination, loss and duplication, chromosome loss, local events

Loss of heterozygosity is usually associated with

Mitochondrial Encephomyelopathy, Lactic Acidosis, and Stroke like episodes mtDNA defect high heteroplasmy levels (like 70 or 80%) to show phenotype low heteroplasmy levels (less than 30%) likely lead to diabetes mellitus

MELAS stands for what? does it result in a mtDNA defect or nDNA defect? What is its heteroplasmy for phenotype expression? Does it have anything to do with diabetes mellitus?

Microdeletion Syndrome too small FISH and/or Microarray analysis Critical Region- Specific portion of chromosome that when deleted causes the syndrome Occurs because of non-allelic homologous recombination. flanking repeat regions surround deleted gene and cause misalignment during meiosis. Williams Syndrome.

M_ S_caused by chromosomal deletion spanning several genes that is (too small or too large) to be detected by conventional cytogenetic methods or high resolution Karyotyping. Detection is done by what? *What is the critical region of a chromosome? *In some cases, the deletion breakpoint are (recurrent or nonrecurrent) with the (same or different) breakpoints seen in patients. Why does this occur? b/c of (allelic or non-allelic) homologous recombination. what is this?

autosomal dominant, autosomal recessive, x-linked

Mendelian patterns of inheritance

50% Harry is a carrier. If the disease is rare, it is most likely only one of his parents is a carrier. The probability that Harry's sister also got it is 50%.

Methylmalonic aciduria is a rare autosomal recessive condition that shows little ethnic predilection. Harry and Sally, who are both healthy, have a child with MMA. The family history is otherwise unremarkable. What is eh best estimate for the probability that Harry's sister is a carrier for MMA?

Probe SOLID - resulting from loss or gain of chromosome high Entire (WHOLE) balanced, not visible

Microarray analysis put P_ on a SOLID surface that bind only those part of the SNP and/or chromosome at (high or low) sequence of Chromosome complimentary. Measure copy number variation-type of change resulting from what? - Can scan/analyze (entire or part) genome (balanced or unbalanced) rearrangements are not visible.

double, circular no introns, no meiosis high mutation rate, no histones haplogourps evolution HOMOPLASMIC (same genes)

Mitochondria (double or single) stranded DNA (linear or circular) DNA Have introns? Undergo homologous recombination (meiosis) Relative to nDNA, mtDNA have (high or low) mutation rate Why? no H_ *Natural mtDNA variation defines H_groups and human E_. The number of fixed, (homoplasmic or heteroplasmic) mtDNA differences between any 2 people indicates the time since they shared a common mother.

abundant, ribosome, post transcriptional Transcriptional

Noncoding RNAs represent a (scarce or abundant) subset of RNAs in the cell, are critical components of the (ribosome or lysosome), can mediate (pre or post transcriptional) controls, and can mediate T_ controls.

POLG the only polymers that function in the replication and repair of mtDNA mitochondrial deficiencies ANY cell type. nuclear

POLG is (one of many or the only one) polymerase that functions in the R_ and R_ of (mtDNA or nDNA) so a POLG defect can cause (lysosomal or mitochondrial) deficiencies in (only one or any) cell type. POLG1 is encoded by (nuclear or mitochondrial) DNA.

more than excess should

Patients with a particular metabolic disease that is inherited as an autosomal recessive, carry two abnormal alleles at this gene locus. They lack a specific enzyme. Their parents who are heterozygotes are clinically normal, but have half the normal level of the enzyme. What does this tell you about the relationship between homeostasis and the pathogenesis of the enzymopathy? In most cases, the basal or inducible amount of an enzyme is in (less than or more than) two fold (excess of in excess) of that needed to cope with metabolic changes. if the basal or inducible amount of enzyme is reduced by one-half, heterozygotes (should or should not) withstand most challenges.

Huntington's disease is caused by expansion of the CAG repeat in exon 1 of the HD gene result in in long poly-glutamine tracts in the mutant protein, Huntington. The mutant protein acquires new properties (gain of function) that affects specific neurons and leads to neuro-degeneration. In the individuals with the deletion, the retained allele is normal and does not compromise the protein function. Thus, individual does not get HD.

Patients with heterozygous and homozygous mutations of HD gene have similar clinical expression of Huntington's disease. However individuals heterozygous for a deletion of one allele of HD gene have a normal phenotype. How can you explain this ?

- autosomal recessive inborn error of metabolism - Loss of function - Allelic Heterogeneity - Compound Heterozygotes- One allele has a mutation that causes dysfunction PAH, the other allele has a different mutation that causes dysfunction PAH (but in a different way than first allele) - a low number of mutations in allelic heterogeneity account for the majority of a population (i.e. high frequency of an allele (can be mutated) in a population) - low protein, low phenylalanine. PKU caused by defect in enzyme that breaks down phenylalanine (accumulate phenylalanine) which causes mental retardation, heart disease, etc in babies of mother who do not stick to diet during pregnancy if they have PKU

Phenylketonuria (PKU) displays what type of inheritance pattern? Is it a gain of function or loss of function of an enzyme, PAH? - What type of heterogeneity? - Most affected individuals carry two different mutations in PAH- they are C_ H_? Explain - PKU displays founder effect, what is founder effect? - Those pregnant with PKU should be on a diet (low or high) in protein which means they are on diet (low or high) in Phenylalanine. Why? Explain what phenylketonuria is

Acrocentric 13, 14, 15, 21, and 22 long Acrocentric short long aren q p

Robertsonian translocation a rare translocation that occurs only in the five A_ chromosomes, which are (give number). - Occur when the (long or short) arms of two A_ chromosomes fuse at the centromere and the two (long or short) arms are lost. - Loss of a (long or short) arm will not hinder someone. - more or fewer than normal (long or short) arm will hinder someone. Long - (p or q) short- (p or q)

do NOT balanced located on a chromosome

State at least one disadvantage of chromosomal microarray (CMA) based testing compared to the cytogenic and molecular cytogenetic techniques (analysis of metaphase chromosome and FISH) - You (do or do not) get positional information so you can't determine ** if there is a (balanced or unbalance) rearrangement present or where a duplicated segment is (located in cell or located on chromosome)

close proximity, Transcription, regulatory, TATA, polymerase

The basal transcription machinery binds in (close or far) proximity to the site of _ initiation, is influenced by _ factors, binds to the _ Box, includes RNA p_.

higher level mtDNA low low mtDNA mtDNA female do not

The child has a (lower or higher) level of (mtDNA or nDNA) deletion present than his mother or likely any siblings, giving him a severe disease phenotype. Most Pearson syndrome cases are de novo (new, begin) in the affected individual. There is a (low or high) risk of recurrence in children of his female siblings (like the current pregnancy); the empiric risk is 1 in 24 (1-4%), but the precise risk cannot be determined since females who many carry the deletion in (high or low) heteroplasmy levels may not be affected. Neither the male pro band nor his brothers can pass on the disease since it is caused by (nDNA or mtDNA) deletion and (nDNA or mtDNA) is only passed on through the (male or female) germ line. Also, most affected individuals with Pearson syndrome (do or do not) survive beyond infancy.

The site of transcription initiation is exactly determined at the TATA-containing promoter. The exact positioning of the start sixte of the TATA-linked promoter is a consequence of the sequence specific binding of a general transcription TO THE TATA box itself. (recognition of the TATA sequence by the TATA binding protein (TBP) subunit of TFIID. PolII assembles with this fixed complex of GTFs to assemble a pre-initiation complex (PIC) at this site and then initiates transcription at a fixed distance 20 to 30 bp downstream, 3' to TATA box. - In contrast, GC rich promoter lacks a well-defined binding site for the PIC. For this reason it tends to generate a cluster of multiple transcriptional start sites for Pol II (usually within a region of 100-200 Bp.

The promoter of gene X lacks a TATA box- instead it contains a G/C rich region in the promoter region. In contrast, the promoter of the Y gene has a TATA box and lacks a C/G region. Which promoter will have a discrete start site (and why) and which will have multiple start sites?

heteroplasmy before age

Threshold effect - Specific (homoplasmy or heteroplasmy) load for a specific mtDNA mutation that any tissue tolerates (before or after) showing signs of pathology. -mtDNA mutations accumulate with (age or youth), increase heteroplasmy (finish writing up mitochondria slides, mitochondria 377)

autosomal dominant HIGHLy entrant with variable penetrance (different phenotype symptoms seen among those with disease)

Type I Neurofibromatosis (NF1) - What type of inheritance pattern? - (incomplete, low, or high) penetrance - If penetrance, (same or different) variable expression

dividing more higher Breakpoint detailed

What are 3 advantages of chromosomal microarray (CMA)-based testing compared to cytogenetic analysis of metaphase chromosomes and fluorescence in situ hybridization (FISH)? - You don't need (dividing or quiescent) cells for CMA, so you can get DNA from (more or less) cells and tissue types - Resolution. CMA allows for scanning of the whole genome at much (higher or lower) resolution than chromosomes (can detect deletions of 50kb with array; need about 5 million base pairs for cytogenics) - B_ Precision. You can get precise breakpoints and (general or detailed) information about gene content

deletion, paternally maternal, 15 15q11

What are 3 mechanism by which Prader-Willi Syndrom occurs and why do these different mechanisms result in the same phenotype? - (deletion or duplication) of (maternally or paternally) inherited genes within 15q11 - (maternal or paternal) uniparental disomy of chromosome (15 or 16) - Mutations in the imprinting center of chromosome (16q11 or 15q11)

two X and Y sequence homology male Darkened region of condensed chromosomes in the nucleus of female cells. This is known as X-inactivation, occurs so that the inactive X chromosome codes for the same amount of genes as the much smaller Y chromosome. This is known as DOSAGE COMPENSATION. *most 75% Mosaics, some, some Skewing of X-activation means purposefully X-inactivating a structurally abnormal or mutant carrying X-chromosome. IF there is a defect in X-inactivation process then X-skewing will also occur. - X-linked Severe Combined Immune Deficiency X-skewing is commonly seen in female carriers. this disease their is selection for white blood cells to only select the non-mutant allele. - non-translocated X-chromosome

What are pseudoautosomal regions? (two or three) regions on the X and (X or Y) chromosome that have sequence (hetero or homo) logy and undergo crossing over in (female or male) meiosis - What is a Barr body? Is it present in male or female? Why? What is dosage compensation? *X-inactivation silences (all or most) genes but not all. _ percent are permanently inactivated - All females are M_. Why? B/c they express alleles from their maternal X in (all or some) cells and express alleles from their paternal X in (all or some) cells. - What is skewing of X-activation? How does X-SCID (give name) explain this concept? With translocation of X-chromosome and autosome, X- inactivation is skewed to occur in (translocated or non-translocated X-chromosome)

Balanced/reciprocal Robertsonian Either constitutional (germ line) or Acquired (somatic) like cancer

What are the two different types of translocations? How do these translocations occur?

Comparative Genome Hybridization genome-wide Single Nucleotide Polymorphism Alleles in different regions Variations: deletions or duplications heterozygosity

What are the two main types of DNA microarray used in practice? Explain how each operates C_ G_ H_ (CGH) detects (genome-wide or small section of genome) copy number losses or gains S_ N_ P_ (SNP array) measures the relative representation and intensity of Alleles in (same or different) regions detects Copy Number V_: D_ and D_ detects absence of H_

heteroplasmy more different

What determines phenotype expression for mitochondrial genetic mutations? The ratio of wild-type (normal) to mutant (alleles). The amount of H_. The higher the amount of heteroplasmy, the (more or less) likely an individual will express diseased phenotype. But different diseases have (same or different) thresholds of heteroplasmy.

Chorion Villus Sampling, look for chromosomal abnormalities in fetus Chromosome 15. Prader Willi's (paternal imprinting) (only express paternal gene to be normal) or Angelman's Syndrome (maternal imprinting) (only express maternal gene to be normal) - Imprinting means that a cells recognizes if a chromosome is paternal or maternal and will only express certain portions of those chromosomes. Recommend to UPD (uniparental disomy) testing to sure sure there wasn't trisomy rescue. - Trisomy rescue is when three chromosomes (two from one parent and one from one parent) combine in a zygote and the cell makes up for this by losing one of the chromosomes, this is trisomy rescue. If one of the chromosomes lost is the only one contributed by one of the parents, then the child will have two same (maternal or paternal) chromosomes, this is known as trisomy rescue leading to UPD (uniparental disomy)

What is CVS? C_ V_ Sampling. What is purpose of the test (look for chromosomal abnormalities in fetus or look for chromosomal abnormalities in germ cells) **You are seeing a patient who showed trisomy 15 at CVS and now has a normal karyotype on amniocentesis. What should be done? First, what is the significance of chromosome 15, what two diseases result as a deletion or imprinting? (hint: choose testing for deletion of chromosome 15q11q13 to determine if the baby has either of the two diseases OR choose to to UPD (U_P_D_) testing to be sure there wasn't a trisomy rescue event in the fetus) Explain. In your answer, explain the terms imprinting, trisomy rescue.

end 13, 14, 15, 21, 22 ribosomal RNA SRY male

What is an acrocentric chromosome and which human chromosomes are acrocentric? Centromere near the (end or middle) with long (q) and Short (P) arms. Short (p) arms of chromosomes (give number) code for (rRNA or tRNA). Short (p) arm of Y chromosomes has _ gene which codes for products involved in (female or male) determination and differentiation.

Occurs because of non-allelic homologous recombination. flanking repeat regions surround gene and cause misalignment during meiosis which results in deletion of gene (region between repeats). Williams Syndrome.

What is cause of William's syndrome?

G banding Cytogenetics Karyotype condensed metaphase ENTIRE WHOLE Chromosomes

What is conventional Cytogenic Analysis? (G or A) banding technique used in C_ to produce a K_ of (condensed or spread out) chromosomes, thus it must occur during (interphase or metaphase) Photographic representation of the (part or entire) chromosome compliment.

chromosomal abnormalities numerical, structural, constitutional (germline), acquired (somatic)

What is cytogenetics?

Genetic problem with gene on the X chromosomes. A permutation are triple nucleotide repeats that under a certain amount to not show any phenotype but above a certain amount show a diseased phenotype. **The male fetus is carrying a permutation with the number of repeats at the lower end of the permutation range. The male fetus will not be affected with Fragile X syndrome. However, males with permutations can have fragile-X-associated TREMOR and ATAXIA SYNDROME (FXTAS) **The female fetus is carrying a permutation with the number of repeats at the lower end of the permutation range The female fetus will not be affected with fragile X syndrome. However, female carriers of permutations are at a 2-% increased risk of premature ovarian failure. - The female fetus is carrying a full mutation with the number of repeats higher than the upper end of the permutation range. The female fetus will have about 50% risk of having fragile X syndrome. The severity of disease will depend on degree of moaiscism defined by skewed X-inactivation

What is fragile X syndrome? What is a permutation? The risk that a woman with a permutation in FMR1 gene will have an affected child is determined by the size of the permutation, sex of the fetus and the family history. How would you counsel a pregnant women about the risk of having an affected child if - The woman is carrying a 46, XY fetus with 60 repeats - The woman is carrying a 46, XX fetus with 60 repeats - The woman is carrying a 46, XX fetus with 300 repeats

more than one type mtDNA in a cell or within an individual.

What is heteroplasmy? the presence of (one or more than one type) of organellar genome (mtDNA or nDNA) within a cell or within an individual (different cells have different genome)

balanced translocation (rearrangement of material) still produces chromosomes with all parts (genes) Unbalanced translocation (rearrangement of material) produces chromosomes missing parts (genes)

What is the difference between a balanced translocation and unbalanced translocation ? Use diagram if you need help - balanced translocation (rearrangement of material) still produces chromosomes with (all or missing) parts (genes) - Unbalanced translocation (rearrangement of material) produces chromosomes with (all or missing parts) (genes)

Variable expressivity- People that have gene(s) implicated in a disorder express phenotype at varying levels. Some express just a little while others express a lot. Incomplete penetrance- People with defective gene(s) do NOT express phenotype at all.

What is the difference between variable expressivity and incomplete penetrance? What five factors cause variable expressivity? 1- variabel expressiveity for deletion, there may be a M_ in one go genes on the non-deleted chromosome and for duplication syndrome, over expression of one A_ might be better or worse for others. 2- Anotehr change knocks out the initial M_, causing less signs 3- There might be E_ effects 4- There might be E_ factors that modified the phenotype 5- There might be (same or different) sized deletions or duplications that are being compared between (different or same) patients, which could involve different genes.

Autosomal dominant - usually seen in every generation with one or two siblings with disease or trait - Vertical transmission. transmission from affected male or affected female

What type of inheritance is this? (mitochondrial, X-linked dominant or X-linked recessive, autosomal recessive, autosomal dominant, or Y-linked) Explain.

Y- linked - ONLY males will consist of pro band because they will always have Y chromosome.

What type of inheritance is this? (mitochondrial, X-linked dominant or X-linked recessive, autosomal recessive, autosomal dominant, or Y-linked) Explain.

autosomal recessive Both parents have to be carriers, skipped generations not autosomal dominant because not seen in every generation.

What type of inheritance is this? (mitochondrial, X-linked dominant or x-linked recessive, autosomal recessive, autosomal dominant, or Y-linked) Explain.

Mitochondrial inheritance is Maternal. - Affected mother will pass on her mitochondrial defect to all of her kids - Disease is NOT transmitted from affected males to his offsprings.

What type of inheritance is this? (mitochondrial, X-linked dominant, or X-linked recessive, autosomal recessive, autosomal dominant, or Y-linked) Explain.

X-linked Recessive (mostly males will consist of the proband)

What type of inheritance is this? (mitochondrial, X-linked dominant, or X-linked recessive, autosomal recessive, autosomal dominant, or Y-linked) Explain.

- regions of DNA more resistant to cleavage by DNAase are those wrapped around histones, these regions mean that the gene is LESS accessible to transcription factors because it is tightly packed in the chromatin fiber. Regions that are more sensitive to DNAase cleavage include enhancers and promotors of genes that are actively expressed or regulated in the cell type examined. - The nucleosome is the structural element of chromatin, composed of DNA wrapped around an octamer of histones. The nucleosome gives relative protection to the DNA with cleavage occurring preferentially between nucleosomes (the "linker" region). Each nucleosome is wrapped in approximately 145 bp of DNA. In a partial DNAase digest you generate monosome, disomes,triremes etc-thus generating a ladder on a a DNA analytic gel prior to running the gel, the chromatin must be stripped of proteins so that the sizing is accurate.

When chromatin is digested in the laboratory by DNAase, some regions prove to be much more resistant than others to cleavage. - How might these differences in resistance to cleavage be related to the in vivo function of a specific gene? - When chromatin is subjected to partial digestion with DNAse and analyzed on a sizing (agarose) gel we often observe a ladder of DNA fragments with a periodicity of approximately 200 bp. What is the basis of these protected regions and what is the basis of the ladder?

both parents should be karytoped (general cytogenic analysis) to determine if imbalance what inherited. - NO! It depends upon what gametes are passed on. This test is just to understand the probability of another offspring having an unbalanced translocation.

When counseling a parent of a child with an unbalanced translocation, what would be appropriate recommendations? should (one or both or none) of the parents be karytotyped? Why? Does this mean that all subsequent pregnancies are likely to be affected?

d. Ataxia Telangiectasia

Which of the following is associated with the greatest degree of radiation sensitivity? a. Lynch Syndrom (hereditary non-polyposis colorectal cancer) b. Ovarian Cancer c. Breast Cancer d. Ataxia Telangiectasia

- conventional cytogenic analysis (routine analysis of G banded proteins by Karytype) taking picture during metaphase (need DIVIDING cells) - FISH studies for localization of a rearranged material Both above need cell culture, need live cells undergoing metaphase - Microarray analysis and FISH studies for enumeration (dosage) can be done with interphase nuclei.

Which of the following requires cell culture? Choose all that apply and explain your answers a) microarray analysis b) conventional cytogenic analysis c) FISH studies for enumeration (dosage) d) FISH studies for localization of of rearranged material

meiotic normal fused THREE monosomy trisomy - Monosomy rescue= gamete has only one chromosome and chromosome is duplicated to give cell two chromosomes. both chromosomes will be either parental or maternal. this is a homozygous rescue (uniparental rescue) - Trisomy Rescue= gamete has three chromosomes and a chromosome is lost (perhaps by nondisjunction) and the remaining chromosomes come from parent. this will lead to heterozygous parental chromosomes (hetero-uniparental rescue)

Why do Robertsonian translocation carriers have an increased risk of having offspring with uniparental disomy? (in your answer define Robertsonian Translocation and trisomy rescue and monosomy rescue) - The (mitotic or meiotic) products of a RObertsonian Translocation include Trisomy (if both the fused chromosome and one of the (normal or abnormal) ones both go into the same cell). Remember that in normal meiosis, each chromosome pairs with and separates from its homologue. But in Robertsonian translocations, the two (fused or unfused) chromosomes will each pair with their normal homologue, so there are (two or three) CENTROMERES in the pairing figure. (normal is two (because only two distinct centromeres/chromosomes)...WHen the separation occurs, there will be two chromosomes going to one cell, and one to the other, which could lead to M_ and T_. - Explain how UPD can occur from a trisomy or monosomy chromosome.

collagen is a triple helix of amino acid strands, made up of three strands, 2 alpha strands and 1 beta strand. Defect in an alpha strand affects 2/3 of the formation of collagen, also if defect is in carboxyl terminal then it is early in the collagen forming (goes from C to N) and entire segment will be messed up. In contrast, a deletion of the alpha 1 pro collagen gene will produce a REDUCTION in collagen formation because the other allele still has a working collagen gene. Here REDUCTION in amount of collagen made is BETTER than producing large amount of DEFECTIVE collagen. - This is called a DOMINANT NEGATIVE EFFECT of the peptide carrying the missense mutation.

Why does a heterozygote for a deletion of the entire alpha-1-procollagen gene have only mild osteogenesis imperfect (brittle bone disease) whereas a heterozygote for a missense mutation in an exon encoding the carboxy-terminal segment of the alpha helical portion of this gene have lethal neonatal osteogenesis imperfecta?

Father 46,XY, t(4;11)(p16;p24) Mother 46, XX` Yes, father's balanced translocation can malsegregate again

You are called to see a male newborn who is severely hypotonic and dysmorphic. You request chromosomal microarray analysis and the results come back indicating a male, with duplication of chromosome 11 from band q24 to qter (the end of the long arm of chromosome 11) and a deletion of chromosome 4 from band p16 to pter (the end of the short arm of chromosome 4). Assuming abnormality is in father. What is the most likely parental karyotype to explain the child's abnormality? - Is this couple at risk for future pregnancies resulting in abnormal outcomes?

- The infant is a male. Only boys are subject to neonatal onset OTC because it is an X-linked disorder that is usually lethal. - Mothers always have 2/3 chance of carrying X-linked mutations. Father's always have 1/3 chance of carrying X-linked mutations. In this case, the father could not carry the mutation because it is lethal. - Yes,

You are caring for a newborn with severe hyperammonemia. You suspect that the child has ornithine transcarbamylase (OTC) deficiency, an X-linked disease. Both parents appear to be healthy. The child became ill at two days of life. Genetic testing of the infant shows a C to T mutation causing a CGA to turn into a TGA (stop) at amino acid 109. This has been previously associated with a very severe phenotype. - What sex is the infant based on the question? - How likely is it that the mother carries the mutation? How likely is it that the father carries the mutation? - Mother has new partner, wants to know risks of having another affected fetus, is there risk for new fetus, what is probability?

x-linked, autosomal recessive, and maternal (mtDNA based disorder) maternal males more severe in X-linked mother consanguinity multiple affected single autosomal recessive POLG1 X-linked PDHA1 gene maternal, MELAS, MERRF

_, _, and _ all apply in this situation. - The difference between an x-linked pedigree and maternal pedigree is that males and females are equally affected in (x-linked or maternal), but males are typically more severely affected in (x-linked or maternal). In both cases, the affected child inherits the disease only from the (mother or father) - Autosomal Recessive either have C_ (inbreeding), (one or multiple) individuals to the same couple who are (affected or unaffected), or possible a (double or single) case with no prior known affected individuals - Nuclear gene mutations cause (x-linked, mitochondrial, or autosomal recessive) such as the recessive forms of POLG1 disorders. - Nuclear gene mutations also cause (x-linked, mitochondrial, or autosomal recessive) such as Pyruvate dehydrogenase deficiency caused by _1 gene mutations. - mtDNA point mutations or small insertions or deletions underlie _ inheritance, as in MELAS and MERRF.

Beta thalessemia means inadequate synthesis of the Beta globin of hemoglobin ** A critical transacting factor binding site in a long-range enhancer (locus control region (LCR) might have been mutated. This mutation would result in loss of expression from the linked (i.e. 'cis'_ target gene. (could result in lower than adequate) level of GTF assembly and PIC) **The function of a chromatin insulator or boundary element might have been lost. This determinant prevents the spread of epigenetic inhibitory factor in a gene region. If its lost then epigenetic inhibitory factors will silence the gene. **characterize histone/chromatin structure of the mutant beta globin allele and compare to normal allele - characterize epigentic factor of histone/chromatin structure (methylation, acetyation). do this by immunoprecipitation of specifically modified histones that are bound to the chromatin, called ChIP (chromatin immunoprecipiation technology. - determine whether 'looping' of the putative long-range enhancer to the promoter has been lost. (3C technology)

a patient diagnosed with Beta thalassemia? (What is this?) has no mutations but deficient levels of mRNA and protein product (50% of usual). You find a deleted region about 20 Kb 5" from one the genes in question. Describe two type of regulatory elements that might be located such a large distance from the target promoter. **What sorts of studies might you consider to further characterize the defective beta-globin allele?

incompletely numerous Y is not mosaic

a) Even though one X- chromosome is inactivated in females, it is (incompletely or completely) inactivated and there are (numerous or few) genes that escape X-inactivation. There are homologues for some of these on the _ chromosome, so complete loss of one sex chromosome (is or is not) seen in normal individuals. b) Could possibly be M_

i've down the problems

do punnet square and allele frequency calculations for problems in problem set 1

I've gotten help

get help for problem set 2, number 7

I've looked over it

look over problem set 6

MRE (microRNA recognition element) in the 3'UTR in the mRNA of a protein that mediates the silencing of a protein's expression via inhibiting translation or direct mRNA destruction. If you lose the MRE sequence, then silencing by mRNA cannot occur. loss of MRE could have occurred by direct mutation or mutation via splicing or alteration in polyA site that eliminates MRE from mature mRNA - protein could have target modification that causes it to be targeted for rapid clearance

look up problem set 2 question 6 what is a post-trancriptional control of a protein?

unbalanced translocation

switch of genes from one chromosome to another (translocation) resulting in LOSS of pieces of chromosomes (gene(s))