Exam 3- Molecular

Herceptin (trastuzumab) therapy works best on what tumors?

Breast cancer with Her2/neu overexpression

The most frequently occurring mutation in the HFE gene results in the replacement of cysteine (C) with tyrosine (Y) at position 282. How is this expressed according to the recommended nomenclature?

C282Y

The 3 frequently observed mutation in HFE protein in hematochromatosis are

C282Y- cysteine to tyrosine substitution at codon 282 H63D- histidine to aspartic substitution at codon 63 S65C- Serine to cystine substitution at codon 65-milder form

Chronic Myelogenous Leukemia (CML)

CML- 6-15% of all adult leukemias Median age of onset- 50 Etiology- unknown- radiation and chemical exposure associated increased risk Philadelphia chromosome; t(9;22); BCRABL fusion; Tx: Gleevec

What mutation is related to poor anti platelet aggregating activity for Clopidogrel?

CYP2C19*2

The genes involved in warfarin metabolism are

CYP2C9 and vitamin K epoxide reductase complex subunit 1 (VKORC1)

Caused by nonlethal genetic mutations affecting certain genes

Cancer

Epithelial

Carcinomas

Hemoglobin M

Causes heme iron to auto-oxidize to ferric state which results in *methemoglobin which cannot carry oxygen* altered oxygen affinity Sulfonamides or Phenacetin (oxidants) cause HbM to form a chocolate brown color Heinz bodies may be seen

bizarre karyotypes, grossly abnormal numbers of chromosomes and structural rearrangements.

Chromosomal instability

The Major Histocompatibility Complex (MHC) is located on and contains

Chromosome 6 human leukocyte antigen (HLA) and other genes.

t(9,22) Philadelphia chromosome BCL/ABL fusion gene- (translocation)

Chronic Myelogenous Leukemia Lymphoblastic Leukemia

polymorphism is concentrated in what exon of class I and II ?

Class I -Exon 2 and 3 Class II - Exon 2

Clonality of Lymphomas

Clonality- DNA in each cell is identical B lymphocytes--Immunoglobulins T lymphocytes-- T-cell receptors (antigen recognizing proteins) Clones identified by detection of predominant antigen-receptor gene rearrangement

Non-BCR-ABL Chronic Myeloproliferative Disorders

Common *mutation (V617F)* has be found in the JAK2 (Janus kinase 2, protein tyrosine kinase)-produces activate JAK2 kinase which makes *erythroid precursors grow without EPO*-resulting in followings diseases: Polycythemia Vera Essential Thrombocythemia Idiopathic Myelofibrosis

Fragile X syndrome type of disease and mutation type

Commonb inherited form of mental retardation-X-linked dominant with reduced penetrance associated with a triplet repeat (CGG) expansion in the noncoding region 5' to the fragile X mental retardation gene, FMR-1

Incidence

Condition that changes over time such as disease

CF transmembrane conductance regulator gene (CFTR)

Conducts chloride and is involved in transport of sodium, potassium and ATP intracellular to extracellular

QC: false +

Contamination Dead or dying organisms Detection of less than clinically significant levels

Types of DNA damage

Covalent modification of DNA bases Mismatches of the normal bases Breaks in the backbone--a single-stranded break, SSB) or (a double-stranded break (DSB) Crosslinks

MHC class I presents to

Cytotoxic T cells

Describe Hemophilia B (Christmas Disease)

Deficiency of Factor IX Prolonged aPTT

Complex diseases

Diabetes Thrombophilia Factor V leiden Prothrombin Gene mutation

What does it mean of Genetic heterogeneity?

Different mutations cause the same phenotype. Often observed in diseases with multiple genetic components

DNA repair

Direct chemical reversal of the damage Excision Repair (Base Excision Repair (BER) Nucleotide Excision Repair (NER) Mismatch Repair (MMR))

Thrombophilia

Disorder in coagulation that shifts hemostasis towards an increased predisposition for thrombosis (clots)

Hemoglobin C-Harlem (HbC-Georgetown)

Double substitution on beta chain -subs. at 6th position of valine for glutamine acid identical to HbS -subs. at 73th position of aspartic acid (-1charge) for aspargine (polar uncharged) same as Korle Bu mutation Pt is asymptomatic Positive solubility test

Which of the following predict efficacy of EGFR tyrosine kinase inhibitors? Overexpression of EGFR protein EGFR-activation mutations

EGFR activating mutations.

vanA, vanB and vanC contributes to what organism's resistance to what medication?

Enterococcus to vancomycin

Mechanisms for Development of Resistance to Antimicrobial Agents

Enzymatic target transport genetic factor

collection and analysis of environmental, microbiological, and clinical data

Epidemiology

Autosomal dominant

Every affected individual has an affected biological parent. There is no skipping of generation. The defective product of the gene is usually a structure *protein*, not an enzyme

MHC II proteins present ____-antigens that originate extracellularly from foreign bodies such as bacteria.

Exogenous

The use of fluorescent DNA probes to detect a chromosomal abnromality in cytogenetic studies is a technique referred to as

FISH

more reliable-detects increased copy numbers of gene

FISH

Which of the following is not a triplet-repeat expansion disorder? Fragile X sydrome Huntington disease Factor V leiden Congenital central hypoventilator syndrome

Factor V leiden

List of single-gene disorders

Factor V leiden *Hemochromatosis* *Cystic fibrosis* Cytochrome P-450 Methylenetetrahydrofolate reductase

Accuracy of measurement of virus regardless of sequence variations

Flexibility

Gene translocation inhibits cell death t(14;18)- most breakpoints in major BCR FISH-red dye probe for IgH locus, green probe for BCL2 gene- normal cell red and green appear on separate chromosomes- abnormal cell signals on same chromosome combine to form yellow signal

Follicular Lymphoma

t(14;18) BcL2 protein (inhibits apoptosis in B lymp)

Follicular Lymphoma

What do the products of the HER2/neu and epidermal growth factor receptor (EGFR) genes have in common?

Found on cell surface and, when bound to their substrate, activate proliferation.

2pq=

Frequency of heterozygous or general population Ex. Aa or JkaJkb

*q2=*

Frequency of homozygous *recessive* Ex. aa or Jkbjkb

p2=

Frequency of homozygous dominant Ex. AA or JkaJka

q=

Frequency of recessive allele Ex. a or Jkb

P=

Frequency of the dominant allele Ex. A or Jka

What is Gene frequency

Frequency w/ which persons in a population possess a particular gene

Which of the following can be detected by PCR? Complex chromosomal abnormalities Full fragile X disorder Mitochondrial point mutations

Full fragile X disorder and Mitochondrial point mutations

Gamma chain mixture: G-gamma A-gamma

G-gamma contains glycine at position 136 A-gamma contains alanine at position 136

Prothrombin Gene Mutation

G20210A Single point muation Gain of function mutation with increased mRNA and increased synthesis of protein

MHC Class III

Gene products: Complement C2, C4, B Location: Plasma Proteins Functions: Defense against extracellular pathogens

Class II

Gene products: HLA -D Location: B lymphocytes,monocytes, macrophage, dendritic cells, activated T cells, activated endothelial cells, skin /Langerhans cells. Professional APC's Functions: Identification of foreign antigen by helper T cells.

Class I

Gene products: HLA-A, HLA-B, HLA-C Location: all nucleated cells Functions: Identification and destruction of abnormal or infected cells by cytotoxic T cells.

Cytokine genes

Gene products: TNFa, TNFb Location: Plasma Proteins Functions: Cell growth and differentiation

__________ may be used to detect leukemias and lymphomas arising from cells that have rearranged their immunoglobulin (Ig) or T-cell receptor (TCR) genes.

Gene rearrangements

Antimicrobial agents are classified by

-static (inhibit growth)/ -cidal (kills organisms) -Mode of action -Chemical structure

reveals the loss of the "good allele" at a locus, uncovering the homologous locus with a recessive mutation.

loss of heterozygosity (LOH)

(guardian of the genome)- function regulation of cell cycle and apoptosis in response to DNA damage- found in most human cancers

p53 gene

Li-Fraumeni syndrome, in which affected patients have an increased predisposition to cancer, is caused by a mutation in which of the following genes?

p53 tumore suppresor gene

Child is type B, mother is type O and Alleged father is type O. Based on the phenotypes of mother and child the B gene must have been inherited from the biologic father and is called_________ What parentage analysis is this example represents?

paternal obligatory gene This called Direct exclusion of paternity-- genetic marker is present in the child but in absent from the mother and alleged father.

Dominant negative in transmission patterns

patterns are observed with loss of function in multimeric proteins

Types of abnormalities in tumor suppressor genes

point mutations, deletions, loss of heterozygosity, microsatellite instability and promoter hypermethylation

Types of oncogenes mutations

point mutations, truncations, amplifications and translocations

Normal lymphocyte populations are ________ with respect to Ig and TCR genes.

polyclonal

Quality control- Sensitive

positive at lower limit of detection Quantitative analysis w/ viral load

demonstrates that an assay system is functioning properly

positive control

CYP450 refers to a family of enzymes found in...

predominantly in the liver. CYP450 enzymes work on a variety of substrates (in this case, drugs), altering their chemical structures to facilitate excretion in the urine and feces.

Public gene vs Private genes

public genes and their resulting traits that are found in most of the population while private genes are exceedingly rare, can be found in few people, often only in a particular race or family

in PCR, a reaction mix with everything except the target ; should always be negative and neg amplication control signal

reagent blank/contamination control

What trait is only observable when the same allele is found on homologous chromosomes (homozygous)?

recessive

PCR-RFLP

requires amplification of specific regions by PCR. The amplicons are then cut with restriction enzymes, yeilding bands of informative size.

Screening test for thalassemia

reverse dot-blot

In a random population, 16% of the people are Rh negative (rr). What percentage of the Rh positive population is heterozygous for r?

rr=q2=16% q2=.16= square root 16--> .4 p+.4=1 p= .6 Hetero=2pq=Rr 2x.6x.4=.48= 48%

Amplification control-

rules out false negatives due to amplification failure- usually housekeeping genes *(omnipresent template)*

demonstrate that the procedure is detecting the target down to the indicated input levels of testing

sensitivity control

Enterobacterial repetitive intergenic consensus (ERIC)

sequences are 126-bp-long genomic sequences found in some bacterial species that are highly conserved, even though they are not in coding regions.

SBT results clarified by

serology

Quality control- Positive

show assay system is functioning correctly *(positive template)*

Replication Error (RER) caused by and occurs in.....

slippage between the replication apparatus and the DNA template. Occurs especially in microsatellites where 1-3 nucleotides are repeated in the DNA sequences.

Altered stability

substitutions that reduce stability of tetramerhemoglobin denatures forms Heinz bodies- congenital Heinz body hemolytic anemias

_______ is a reciprocal translocation between the long arms of chromosomes 14;18 and is found in _________ of ________ cases and 20%-30% of large cell lymphomas.

t(14;18) 90% follicular lymphoma

Which of the following translocations is associated with acute promyelocytic leukemia (APL)?

t(15;17)

Translocations Used in Diagnosis and Monitoring of Hematological Tumors: t(9;22)

t(9;22) found in CML and acute lymphoblastic leukemia This translocation forms a chimeric gene between the *breakpoint cluster region (BCR) gene* on chromosome 22 and the *Abelson leukemia virus (ABL) gene (c-abl)* on chromosome 9.-- BCR and c-abl genes are tyrosine kinase. The translocated chromosome is the *Philadelphia chromosome.* Dx: DNA representing BRL-ABL fusion picked up by Southern blot, mRNA fusion product detected by RT-PCR, RT-PCR detects length of BCR-ABL proteins, FISH

Linkage disequilibrium

tendency of specific combination of alleles at two or more linked loci to be inherited together more frequently than would be expected by chance

DNA-Based Typing Methods: SSOP Sequence-specific oligonucleotide probe hybridization (SSOP, SSOPH)

the HLA region under investigation is amplified by PCR using primers flanking the polymorphic sequences

V(D)J recombination

the normal intrachromosomal rearrangements in B and T lymphocytes as well as the abnl interchromosomal translocations that can occur in any cell type

Autosomal Recessive

trait is characteristically found in siblings, not parents of affected or the offspring of affected trait may appear as an isolated (sporadic) event in small sibships A mutation must be homozygous to show the abnl phenotype It is the most frequently observed transmission pattern

what is it when alleles are positioned on the opposite chromosome of a homologous pair and are capable of independent segregation?

trans (repulsion) position- capable of independent segregation

genes normally arrest cell division.

tumor suppressors

gene mutations are usually a loss of function and recessive.

tumor-suppressors

Consanguineous marriage

two individuals who are related as second cousins or closer, with the inbreeding coefficient (F) equal or higher than 0.0156 (

A positive result of HPV type 16 indicates

High risk for cervical cancer HPV type 12-16 (oncogenes) associated with cervical cancer

looks for genetic differences within a population that explains observed responses to a drug or susceptibility to a health problem

Pharmacogenomics

______is the level of detail with which an allele is determined.

Resolution

Which of the following is a disadvantage of molecular based testing?

Results stay positive longer after treatment than do culture Positive results due to dead or living organism complicates interpretation of treatment efficacy

Which of the following is genotypic method used to compare two isolates in an epidemiological investigation?

Ribotyping Phenotype(by serology and antimicro.suscep patterns Genotype(PFGE and ribotyping

Molecular method use to study RBC membrane in Hereditary Spherocytosis

SDS-PAGE-- reveals the underlying quantitative defect in the majority of HS pts.

SSOP followed by

SSP-PCR

Bone cartilage

Sarcomas

*Lowest* level detected at least 95% of the time

Sensitivity

Advantages of Molecular testing

Sensitivity Specificity Rapidity High Throughput Application to archival material Drug targeting of specific mutations/proteins Better understanding of resistance mechanism

DNA-Based Typing Methods: Sequence-Based Typing

Sequence-based typing (SBT) is high resolution. Polymorphic regions are amplified by PCR and then sequenced.

In order of increasing severity of Alpha thal what are the 4 clinical entities --

Silent carrier state Alpha thal trait-Homo and Hetero Hgb H disease-beta chain tetramers Hydrops Fetalis/Hgb Barts-Homozygous (cord blood)

Positive results are true positives

Specificity

Altered function

Stabilize iron in ferric state-methemoglobin which can't bind oxygen: Hgb M and chesapeake mutations affecting allosteric properties- high oxygen and decreased oxygen affinity

mecA contributes to what organism's resistance to what medication?

Staph aureus to oxacillin

leading cause nosocomial infections

Staphylococcus aureus-

Hemoglobin S

Substitution of *thymine* instead of *adenine* at 20th nucleotide in HBB gene *Valine* (uncharged) substitutes for *glutamine acid* (-1 charge) in the 6th position of the beta chain B6(A3)Glu->Val

Most diseases are polygenic and have complex segregation patterns that include environmental factors ---T or F?

T

Most oncogenes function as dominant gain-of-function mutations. T/F

T

Multiple cell types

Teratocarcinomas

What are the two important checkpoint in the cell division cycle that are crossed when the regulation of the cell division cycle is affected?

The transition from unreplicated to replicated DNA (G1 to S) and from replicated DNA to cell division (G2 to M) are regulated checkpoint in the cell division cycle

Almost all sex-linked disorders involve which chromosome?

X chromosomes

Hemophilia A: Type of disease

X- linked recessive inheritance bleeding disorder-- deficiency of *factor VIII* Females have disease if both genes mutated or skewed X-inactivation aPTT prolonged, mild form of disease test may be nl

Mating of affected females and normal males produce 1/2 the sons affected and 1/2 the daughters affected. This trait may be lethal in males but in general population, females are more likely to be affected than males. What trait is this?

X-linked dominant *Trait can never passed from father to son* rare disorder

Linkage equilibrium

alleles at two loci associate according to the individual frequencies in a population

Transplanted organs are______, in which the donor organ and the recipient are genetically different.

allografts

template sequences that are always present; used to confirm the functional competence of the reaction mix (housekeeping gene)

amplification control

Internal Controls

amplification controls that monitor steps of the amplification method. -Homologous extrinsic(wild-type) -Heterologous extrinsic(add before-non-target template) -Heterologous intrinsic(non-target sequence) Mainly for inhibitors

Cystic Fibrosis Type of disease Gene location Type of mutation Molecular methods

an autosomal-recessive, life threatening disorder that causes severe lung damage and nutritional deficiencies. caused by loss of function of the *CF transmembrane conductance regulator gene (CFTR, 7q31.2)*-- codes for a chloride channel membrane protein

RFLP

analysis by Southern blot This method is involves cutting DNA with restriction enzymes, resolving the resulting fragments by gel electrophoresis and then transferring the separated fragments to a membrane for probing with a specific probe

What is mitochondrial mutation? Describe Homoplasmy from Heteroplamsy mutation?

are inherited maternally of mitochondrial genes (mutation only passed on only by the mother) All mitochondrial of embryo derive from egg Homoplasmy= all are the same Heteroplasmy= some nl and some mutation(low penetrance and extremely variable expression)

If an allelic variant with amino acid substitutions decreases the affinity of CYP to drug, we will observe a) enhanced metabolism, reduced concentration of parent drug b) decreased metabolism, increased concentration of parent drug

b) decreased metabolism, increased concentration of parent drug

Which of these has a broader application? a) pharmacogenetics b) pharmacogenomics

b) pharmacogenomics (although both terms are used interchangeably)

Hemoglobinopathies: Quantitative

genetic defects *reduce synthesis of structural normal globin chains*. Unbalanced synthesis of beta and alpha globin chains. Excess chains precipitate and damage developing erythrocytes Thalassemia

Hemoglobin D and G

group of at least 16 beta chain variants and 6 alpha chain variants that migrate in alkaline pH at the same position as HbS Negative solubility test

HLA alleles are inherited in blocks as_____. A set of particular alleles on the same chromosome

haplotypes

G6PD deficiency gene encoding and molecular detection

has been mapped to Xq28 PCR and labeled probes used to detect mutant alleles

MHC I glycoproteins are present on almost every cell in the body, acting to present ____ antigens that originate from the cytoplasm.

endogenous

Ex. of Autosomal recessive disorders

*Hemochromatosis* *Cystic fibrosis*

Viruses involved in human cancer

*Human T-cell leukemia virus type I*- adult T cell Leukemia and lymphoma and Kaposi-sarcoma *Herpesvirus 8*- primary effusion lymphoma *HPV*- cervical cancer *EBV*-nasopharyngeal cancer, Burkitts Lymphoma *HBV and HCV*-hepatocellular carcinoma

genetic testing limitations

*Intergenic mutations* in splice sites or regulatory regions may be missed by analysis of gene coding regions *Therapeutic targets* are phenotypic (except for gene therapy) *Nonsymptomatic diagnosis* Most disease and nl traits are *multicomponent systems*

Ex of oncogene--translocations or inversions of chromosomes

*Philadelphia chromosome* example of chromosomal rearrangement. (reciprocal translocation) *Burkitt's lymphoma*-- translocation 8q24)c-myc has been mapped) 8:14 translocation

Bordetella pertussis target sequence

*Target sequence IS481* insertion sequence, pertussis toxin gene promoter region, adenylate cyclase gene and specific porin protein structural genes

NAT for Chlamydia Trachomatis and Neisseria Gonorrhoeae

-High sensitivity and specificity -Testing for both pathogens can be done simultaneously on a single specimen -Diagnostic sensitivity varies among specimen types and whether patient is symptomatic or asymptomatic

List 4 types of hemochromatosis caused by mutations in specific gene

*Type 1 hemachromatosis caused by mutations in the HFE gene* Type 2 hemachromatosis caused by mutations in either HFE2 or HAMP gene Type 3 hemachromatosis caused by mutation in the TFR2 gene Type 4 hemachromatosis caused by mutation in the SLC40A1 gene

Molecular epidemiology

*genotypic* analysis targeting genomic or plasmid DNA

mutation results in reduced binding of protein to Beta-lactam agents causing resistance

*mecA* gene codes for *PBP2a* (penicillin binding protein

genetic testing complexities

*variable expressivity* a single genetic mutation results in range of phenotype. *genetic heterogeneity* the same phenotype results from mutations in different genes. *Penetrance* mutation is present without the predicted phenotype

Amplified Mycobacterium tuberculosis Direct Test

- transcription mediated amplification of ribosomal RNA

Limitations of Molecular Tests for Pathogens

-Inability to distinguish live from dead organisms -Cost -Requirement for technical skills -Limited Availability -Lack of National and International Standards-Viral load assays -Parasites

Inherited Cancer Gene Mutations

-Inherited tumor suppressor gene mutations are *recessive* for the malignant phenotype. -Tumor suppressor gene mutations are *dominant* with respect to *increased risk* of malignancy. -*Loss of heterozygosity* exposes the recessive mutant allele in a hemizygous state. -This is explained by the *two-hit hypothesis*.

Genotypic Resistance Testing

-Isolation of HIV 1 RNA from plasma -RT-PCR amplification -Sequencing of reverse transcriptase and protease genes -Analysis: sequence alignment and editing, mutation identification and comparison with wild type sequence and interpretation of clinical significance

Advantages of Molecular Detection of Resistance to Antimicrobial Agents

-Mutated genes are strong evidence of resistance. -Rapid detection without culturing -Direct comparison of multiple isolates in epidemiological investigations

Resistance testing

-Patient not responding to therapy -Phenotypic -Genotypic Resistance Testing

Molecular detection of disease---- Targets

-Tissue-specific markers (antigens, gene rearrangements) -Disease-specific markers (translocations, point mutations, polymorphisms in tumor suppressor or oncogenes) -Viruses (EBV, HCV, HTLV-1)

Hereditary Nonpolyposis Colorectal Carcinoma (HNPCC)

-accounts for about 5% of colon cancer. -most common form of hereditary colon cancer. -associated with mutations in genes encoding components of the MMR system, most frequently *MLH1 and MSH2*.

6 essential capabilities of a malignant tumor

-divide independently -ignore external anti-growth signals -avoid apoptosis -divide indefinitely -stimulate sustained angiogenesis -metastasis

The therapeutic response to which one of the following drugs is affected by CYP2D6 polymorphism?

...Cytochrome P450

In caucasian population, 77% of randomly selected individuals are Jka, what is the frequency of Jka- individuals?

.77+q=1 q=.23 or 23% Jka- individuals If blood is needed for a patient with a anti Jka, 23% or approx. 1 in 4 ABO-compatible units of blood should be compatible

5 classes of CFTR mutations

1- mutations produce defects in protein production 2-associated w/ defective processing of CFTR protein 3-4- CFTR expression at membrane but channel activity is reduced 5-associated w/ abnl splicing of CFR mRNA

What is the recurrence risk to the affected individual offspring, Autosomal dominant?

1/2

What is the recurrence risk to the affected individual offspring, Autosomal recessive?

1/4

BcL2 is dysregulated and overexpressed when moved to chromosome ___

14

Factor V leiden mutations

1691 G>A or R506Q-G to A transition at position 1691 in exon 10 of the factor V gene changing arginine 506 to glutanine Arginine 506 is a cleavage site for activated protein C Activated protein C cannot inactivate Factor Va

fetal hemoglobin

2 alpha/2 gamma HbF comprised 2% of hgb by age 2

Describe mutation occurs in Leber Hereditary Optic Neuropathy

27 mutations associated w/ disease causing oxidative prosphorylation (OXPHOS) deficiency Mutation affects subunit of the nicotinamide adenine dinucleotide

What is the gene location and mutation type of Huntingston disease?

4P16.3- caused by increase in number of CAG (glutamine) Trinucleotide repeats in exon 1 --sequence CAG expands from 9 to 37 repeats to 38 to 86 repeats

A patient is group O, Rh negative with an anti D and anti K in her serum. What percentage of the general Caucasian donor *population* would be compatible with this person? Gene Freq O 46% D 85% K 9%

6% P2=46% AntiD=100-85=15% AntiK=100-9=91% .46x.15x.91=.06=6%

t(__,__) forms a chimeric gene between BCR-ABL

9,22

What does adult hgb consist of?

95-97% HbA 2-3% HbA2 1-2% HbF

Structural Variant Hgb

>900 abnl hgbs-majority are beta-chain mutations

Anticipation disease

? huntington disease

extensive metabolizer (EM)

A person with normal enzyme activity is referred to as wild type. This person should respond to standard dosages of a drug. Most people are EM's. This is the population in which most dosing regimens have been worked out in clinical trials.

Which of these is associated with cytochrome 22? a) CYP2D6 B) CYP2C19 C) CYP3A

A) CYP2D6

Which of the following is a high resolution HLA typing result?

A*02:12 (A*02 low resolution, determined at the serological level)

example of co-dominant trait

ABO system different alleles in homologous chromosomes each produce observable traits

caused by HIV a nontransforming human retrovirus from the lentivirus family

AIDS

- individuals born with one mutant allele develop hundreds to thousands of polyps in the colon in their teens or twenties-

APC (adenomatous polyposis coli) gene Down regulation of growth promoting signals

Beta Thalassemia

Abnlity in the rate of synthesis of the hgb chains Structurally normal, imbalance of 2 types Defects in the rate of beta chains produced Decreased in the amount of nl hgb produced Microcytic, hypochromic anemia Excess alpha chains form precipitate-- ineffective erythropoiesis

Translocation of genes into Ig gene

Abnormal interchromosomal translocations

Ability to determine true value

Accuracy

Factor V leiden

Activated protein C resistance Most common genetic cause of inherited thrombophilia in caucasian population Single-gene disorders Hetero-3-8 increased risk Homo-50-100 fold increase risk

The completion of the gene rearrangement process and expression of the rearranged gene of only one of the two homologous immunoglobulin heavy chain gene alleles is an example of......

Allelic exclusion

What is Alleles?

Alternative forms of genes which occupy a single locus on homologous chromosomes

______ are gene that ______ produce detectable products (silent genes: Bombay, Rh(null), Lu(a-b-)..)

Amorphs do not

Which of the following controls are critical for ensuring that amplification is occuring in a pt sample and that the lack of PCR product is not due to the presence of inhibitors?

Amplification control Ampl. control should always generate a product even in the absence of the target

HPV

Anogenital HPV infections common in men and women: 30 types Classified as cutaneous (keratinizing) or mucosal (nonkeratinizing epithelium) infection HPV-definitive evidence that it causes 90% of all cervical cancer worldwide Low risk (genital warts) and high risk for progression to malignancy Traditional method-viral culture Molecular methods- signal amplification and PCR

is a modified PCR using 10-base-long oligonucleotides of random sequences to prime DNA amplification all over the genome.

Arbitrarily primed PCR or random amplified polymorphic DNA (RAPD) assay

CYP2C9

Associated with metabolism of the sulfonylurea hypoglycemic agent tolbutamide Involved in metabolism of 16% of therapeutic agents and has 12 allelic variants Therapeutic agents metabolized include: nonsteroidal anti-inflammatory medication, irbesartan, naproxen and fluvastatin Proposed dose adjustments based on phenotype for warfarin, tolbutamide and phenytoin

List the patterns of inheritance in single-gene disorders (disease of phenotype)

Autosomal Dominant Autosomal Recessive X-linked or sex-linked recessive

Hereditary Elliptocytosis

Autosomal Dominant Horizontal or lateral interactions in the protein cytoskeleton affected Elliptic shape leading to shortened survival

Huntington disease type of disease

Autosomal dominant late onset neurodegenerative disorder Expansion within huntingtin structural gene

Sickle cell anemia

Autosomal recessive Hgb molecules polymerize under conditions low oxygen and dehydration diminishing deformability

gene DNA repair- inherited carcinomas of male and female breast Tumor- suppressor genes 6174delT

BRCA 2

DNA repair- inherited mutations carcinoma female breast and ovary Tumor-suppressor genes 187delAG 5382insC

BRCA1 gene

What is Hardy-Weinberg law?

Based on the assumption that genotypes are distributed in proportion to the frequencies of individual alleles in a population, and will remain constant from generation to generation if the processes of mutation, migration, natural selection, or non-random mating do not occur

to reduce the variability associated with warfarin dosing response.

Genetic testing for the two most common polymorphisms (CYP2C9*2 and *3) as well as for VKORC1

What is observed on a Southern blot for gene rearrangement in the case of a positive result?

Germline bands plus rearranged bands. The rearranged bands represent the gene rearrangement in the *monoclonal population* of tumor cells

List the single-gene disorders with nonclassical patterns of inheritance (non-mendelian transmission pattern)

Gonadal mosaicism Genomic imprinting Nucleotide repeat expansion Mitochondrial inheritance

HLA-DBR1 Nomenclature according to WHO H, D, R and 1

H= Gene region D= Gene locus R= Sub region 1= alpha or beta-chain polypeptide

The MHC is a polymorphic locus encoding the ______ genes

HLA

the combination of polymorphic sequence or alleles in the HLA gene regions

HLA haplotype

*Lymphocytes* are______ by crossmatching to panel reactive antibodies* (PRA*) using the complement-dependent cytotoxicity *(CDC)* test.

HLA-typed

set of closely linked alleles on a chromosomes that are usually inherited as a block

Haplotype

Beta thal Minor increased

HbF and HbA2

MHC Class II, binds CD4 adhesion molecules on ____

Helper T cells

Methods Analysis Sickle cell anemia

Hemoglobin electrophoresis- Hgb carries electrical charge HgF more resistant to alkali and acid denaturation Isoelectric focusing and HPLC PCR and RFLP

Example of X-linked diseases

Hemophilia A Hemophilia B Duchenne Muscular Dystrophy Fragile X syndrome

involving alpha and beta spectrin or protein 4.1

Hereditary Elliptocytosis mutation

Intrinsic defect RBC membrane 75% Autosomal dominant inheritance Deficiency in spectrin Decreased surface area and spherocytosis

Hereditary Spherocytosis

A patient with abnormally high iron levels is tested to determine if hemochromatosis, specifically the C282Y mutation in the HFE gene, is the cause. The patient's DNA is isolated from whole blood and amplified. Amplicons are then cut with RsaI, and the resulting fragments are separated by gel electrophoresis. There are no RsaI sites in the normal 250 bp PCR product, while the C282Y mutation generates one RsaI site. The lane containing the patient's sample has three bands at 250 bp, 140 bp, and 110 bp. Controls were acceptable. What is the correct interpretation of these results?

Heterogygous mutation

A patient is tested for the presence of the factor V Leiden mutation by PCR-RFLP. The mutation forms a recognition site for the MnlI restriction enzyme. Isolated DNA is amplified by PCR, and the resulting amplicons are cut with MnlI and separated by gel electrophoresis. Two bands are seen in the lane loaded with the patient's sample, one at 153 bp and the other at 67 bp. One band (220 bp) is seen in the normal control. What is the correct interpretation of these results?

Homozygous mutation

are *membrane proteins* that are responsible for rejection of transplanted organs and tissues.

Human leukocyte antigens (HLA), the MHC gene products

Treatment of sickle cell anemia

Hydroxyurea- H2N-CO-NH-OH) stimulates HgbF Hematopoietic Stem cell transplant Gene therapy

What target sequence is use to discriminate B. pertussis from B. holmseii

IS1001

Primer binding in PCR assays detecting B. pertussis is

IS481

PCR test targeting the species-specific sequences detecting M. tuberculosis is

IS6110 and 16S rRNA

Which of the following is used to type molds?

ITS sequencing. Molds/Fungi are typed by PCR and sequencing of Internal Transcribed Spacer (ITS) regions or 28S rRNA

Testing for HER2/neu

Immunohistochemistry using monoclonal and polyclonal antibodies -detects HER2/neu protein CISH-chromogenic in situ hybridization FISH

QC: false =

Improper collection and handling Extraction/amplification failure Technical difficulties

Child is Jk(a+b-) Mother is Jk(a+b-) and alleged father is Jk(a-b+). Describe this paternity analysis

In this case the father is presumably homozygous for Jkb and should be transmitted to his offspring. This is called *Indirect exclusion of paternity*-- when the child lacks of genetic marker that the alleged father must transmit to his offspring which may be due to *silent allele*

Describe Homozygous?

Individuals have identical alleles at a given locus on both chromosomes. Ex. AA

Describe Heterozygous?

Individuals who do not have identical allelles at a given locus on a chromosomes Ex. Aa

Type 1 diabetes

Inherited-sudden onset, immune destruction B cells

Factor V leiden molecular method for detection

Invader assay, PCR coupled with restriction endonuclease digestion and gel electrophoresis and real time PCR with melting analysis are the methods most used for detection

What is a Allele frequency

Is the proportion that the allele contributes to the total pool of alleles at that locus within a given population at a given time. -Calculated from phenotype freq. observed within a population -The sum of allele freq. at a given locus must equal 1

a disease that sweeps across wide geographical areas

Pandemic

CYP2D6

It is estimated that about 25% of common drugs are metabolized by CYP2D6. CYP2D6 accounts for only about 1% of all CYP450 enzymes, but it is important in the metabolism of about 100 drugs (Phase ! enzyme). There are more than 80 genetic variants that have been described in the CYP2D6 gene. The normal, wildtype allele displays normal metabolic activity whereas some of the variant forms have enhanced or diminished activity. The variants can be grouped generally according to the resulting alterations in protein function. The groupings correlate with four major enzyme metabolic capacities (phenotypes): poor, intermediate, extensive (normal), or ultrarapid metabolizers.

Why are K-ras activating mutations and B0raf V600E mutually exclusive in colon cancer?

K-ras and B-raf kinases are on the same signal transduction pathway. Once that pathway is activated through mutations in the KRAS or BRAF gene, there is no selective pressure to generate further mutations in genes in the same pathway

Examples of Mitochondrial Inheritance diseases

Leber Hereditary Optic Neuropathy

A serial dilution of standard curve closely approximates a straight line

Linearity

A trait is observed more frequently than would be expected

Linkage

What type of mutations usually occur in tumor suppressor genes in malignant cells?

Loss of function

katG and inhA contributes to what organism's resistance to what medication?

M.tuberculosis to isoniazid

Present only on antigen-presenting cells (APC)

MCH II

______ consist of one membrane-spanning a chain (heavy chain) produced by MHC genes, and one b chain (light chain or b2-microglobulin) produced by the b2-microglobulin gene. _____ consist of two membrane-spanning chains, a and b, of similar size and both produced by MHC genes.

MHC Class I MHC Class II

resistant to methicillin or oxacillin- hospital and community acquired

MRSA/ORSA

Three distinct genetic groups of HIV-1:

Major (M) group Outlier (O) group N (non-M, non-O) group

Translocation of BCL1 locus on chromosome 11 with IgH gene enhancer locus chromosome14 Causes increased production of normal cyclin D1 dysregulation of the cell cycle

Mantle Cell Lymphoma

Process resulting in 4 cells with 23 chromosome

Meiosis

Genetic diseases caused by single gene disorders obey _____

Mendelian Law

movement of dislodged tumor from primary site to other location

Metastasis

looks for a genetic cause of an unexpected drug response

Pharmacogenetics

testing for genetic imprinting disorders

Methylation specific PCR (mPCR) -Treat DNA w/sodium bisulfide to convert unmethylated cytosine to uracil -Primers are specific to DNA that contains either uracil (unmethylated) or cystosine (methylated) -Positive test f/u w/ FISH testing or uniparental disomy testing

This test is used to determine if the mismatch repair system is functioning normally.

Microsatellite instability

checks on DNA replication accuracy are lost

Microsatellite instability

A process called ______, are genes that are responsible for correcting replicative errors and mismatched bases in DNA.

Mismatch repair (MMR)

Process resulting in 2 daughter cells with 23 pairs of chromosome

Mitosis

Dosage

More antigen expressed on their red cells than persons who are heterozygous for that allele. Ex. Jka have a double dose of the Jka gene than JkaJkb

Pyruvate Kinase Deficiency

Most common form of hereditary nonspherocytic hemolytic anemia worldwide Autosomal recessive Enyzme that catalyze phosphoenolpyruvate to pyruvate forming ATP

Leber Hereditary Optic Neuropathy

Most common mitochondrial disease Subacute loss of ventral vision in both eyes-focal degenaration of retinal ganglion cell layer and optic nerve DNA testing available--PCR amplification w/ restriction endonuclease analysis and gel electrophoresis

Hemoglobinopathies: Qualitative

Mutations in coding region result in deletion or substitution of amino acids in globin protein chain causing *structural variation* in one of globin chains HbS-sickle cell anemia HbC HbE

What patient conditions carries a dominant mutation causing a valine-to-phenylalamine amino acid substitution at position 617 of the JAK2 protein (V617F)

Myeloproliferative disorders such as: Polycythemia Vera Essential Thrombocythemia Idiopathic Myelofibrosis

This assay does not require immune response and it helps close the "window period" for donor blood screening for Hepatitis

NAT based assays NAT reduces window periods by 11 and 57 days respectively

*growth of tissue* that exceeds and is not coordinated with normal tissue.

Neoplasms

Name a genetic storage disease in which sulfatides accumulate inside the lysosomes?

Niemann-Pick

HIV testing-- useful during window period in adults-acute patients will have high HIV viral load and negative ELISA

Nucleic acid testing

Prevelance

Occurence of permanent inherited characteristic at the phenotypic levle Ex. Blood group in any given population

mutations are usually a *gain of function* and dominant.

Oncogene

Genes whose normal activity promotes cell proliferation

Oncogenes (Proto-oncogenes)

What would be observed in the event of loss of heterozygosity (LOH)?

One allele at a heterozygous locus

Hematological tumors are monitored using ___

PCR

SSP-PCR followed by

PCR RFLP

LOH can be detected by

PCR amplification of heterozygous STR or Variable number tandem repeat (VNTR) loci closely linked to the disease gene

Amplicor Mycobacterium tuberculosis Test-

PCR target is 16S ribosomal RNA gene

The factor V leiden mutation can be detected by

PCR-RFLP, SSP-PCR, Invader technology

A molecular-based typing method that has high typing capacity, reproducibility and discriminatory power, moderate ease of performance, and good-to-moderate ease of interpretations is

PFGE

NAT 1 and NAT 2 - N-Acetyl Transferases

Phase II enzymes that catalyze the transfer of acetyl moiety from acetyl CoA to homocyclic and heterocyclic arylamines and hydrazines Substrates- drugs, carcinogens, toxicants Variables that affect NAT phenotyping include substrate or probe drug used, age and disease status of individual, medication, dietary factors, smoking and occupational exposure

TPMT-Thiopurine S-Methyltransferase

Phase II metabolic enzyme that catalyzes the inactivation of 6-MP by S-methylation preventing it from forming thioguanine nucleotides Affects AZA- prodrug metabolized to 6-MP AZA and 6-MP are cytotoxic agents which incorporate TGN into DNA- used to treat leukemia, rheumatic disease and inflammatory bowel TPMT deficient patients at risk for hematological toxicity

Genetic linkage

Phenomenon whereby loci that are close together on a chromosome tend to segregate together in families.

Detectable trait

Phenotype

Which term describes a normally occurring gene that when altered is often associated with cancer?

Photo-Oncogene

Involves isolation and restricted mapping of bacterial plasmids

Plasmid fingerprinting

Reproducibility of independently determined test results

Precision

The detection of mitochondrial mutations is complicated by what circumstance?

Presence of mutated and normal mitochondria in the same cell

HIV Genotyping, 2 groups

Primary resistance mutations (affect drug sensitivity but may slow viral growth) Secondary resistance mutations (compensate for the primary-resistance growth defects)

t(15;17) PML/RARA fusion

Promyelocytic Leukemia

Prions cause Creutzfeldt - Jacob disease consists of only

Protein

may become oncogenic by retroviral transduction (v-oncs) or by influences that alter their behavior in situ there by converting them to oncogenes

Proto-oncogenes

HIV testing-- useful for diagnosing acute infections in neonates- test shortly after birth and at 6 weeks to several months old.

Qualitative proviral DNA tests and viral load assays

Hepatitis C and its use of molecular methods

RNA virus- major cause of chronic liver disease Molecular Methods used to -Diagnose HCV infections -Exclude HCV as etiologic agent of symptoms -Screen blood supply -Monitor response to therapy -Determine Duration of therapy

Test methods used to detect t(15;17)

RT-PCR qRT-PCR

function regulation of cell cycle- associated tumors- Retinoblastoma, osteosarcoma, carcinoma of breast, lung and colon

Rb gene

Traits that must be inherited as a double dose before they can be expressed

Recessive

A pt was tested for HUntington disease. PCR followed by PAGE revealed 25 GAG units.

This pt is normal at the Huntington locus--(the seq. CAG expands from 9 to 37 repeats to 38 to 86 repeats)

If a pt has antiC, antiK, and antiJka how many ABO-compatible units of blood would have to be tested to find 4 units of the appropriate phenotype? Freq: C- 20% K- 91% Jka- 23%

To calculate the frequency of the combined phenotype, the individual frequencies are multiplied as the phenotypes are independent of each other 20-100= 70 antiC 91-100= 8 antiK 23-100= 77 antiJka .70x.08x.77=.04 .04/100=4/x-->cross multiple-->10000 units these calculations allow the blood banker to decide about asking for assistance from local blood supplies or rare donor facilities when trying to find compatible blood

HPV Transforming characteristics

Transforming characteristics of the E6 and E7 gene products- bind tumor suppressors p53 and Retinoblastoma and inactivate them immortalizing epithelial cells--New tests use expression of E6 and E7 mRNA as markers

Promyelocytic Leukemia (PML-FAB M3)

Translocation 17q21 leading to rearrangement of the gene that codes for RARA (nuclear hormone receptor that modulated myelopoiesis) >95% t(15;17) (q22;q12) PML/RARA fusion gene and protein- mutant of one of the retinoic acid receptors. (Class II mutation) affects the cells ability to differentiate

The chimeric gene, BCRABL, produces an abnormal protein that drives the tumor cell phenotype.

Translocations Used in Diagnosis and Monitoring of Hematological Tumors: t(9; 22)

West Nile Virus

Transmitted by transfusion of red cells, platelets or plasma but not plasma derivatives Blood donor questionnaire enhanced-fever and headache preceding week of donation NAT- 6 to 16 donors pooled If pool positive individuals tested

What is Trinucleotide Repeat Expansion Disorders? What are the common diseases for this disorders?

Triplet repeats are short tandem repeats (STRs) with 3-bp repeating units Fragile X syndrome Huntington disease

Fertilization where one gamete contains an extra copy of one chromosome will result in what chromosomal abnormality?

Trisomy

Segregation

Two members of a single gene pair (alleles) are never found in the same gamate but always segregate and pass to different gametes

Fungi typed using

Typed using the *Internal Transcribed Spacer (ITS)* regions or 28s rRNA

fastidious organism, most facultative anaerobes Most infections caused by E. faecalis and E. faecium

VRE

few diseases have transmission pattern due to these---

Variable expressivity Genetic heterogeneity Incomplete penetrance

Y-linked inheritance

Vertical pedigree pattern All sons of affected father are affected--affects males only,females do not have Y Abnormality Y chromosome linked to infertility

Genetic analysis of four generations of a family reveals that about 50% of the males in the family are affected by a mutation and about 50% of the females are unaffected carriers of the mutation that affects the males. What type of inheritance pattern is seen in this family?

X-linked recessive

Males are much more likely to be affected than females. All affected males in the family are related through their mothers. Trait or disease is typically passed from affected grandfather, through his carrier daughters, to half of his grandsons.

X-linked recessive *Trait can never passed from father to son*

Duchenned Muscular Dystrophy

X-linked recessive-- Skeletal muscle wasting disorder Most common sever neuromuscular disorder in humans Grossly elevated CK values electromyography and muscle bx for confirmation Duplication and deletions--multiplex PCR

Duchenned Muscular Dystrophy gene location

Xp21- largest gene in human genome

F9 gene location for Hemophilia B

Xq27.1-q27.2

What is the gene location of Fragile X syndrome?

Xq27.3- Breakpoint or fragile site on X chromosome

What is the F8 gene location associated in Hemophilia A?

Xq28- substitutions, gene deletions, insertions and rearrangements

The first and most frequently observed mutation in CFTR is

a 3-bp deletion that removes a phenylalanine residue from position 508 of the protein *(F508del)* 70% affects processing of CFTR and prevents movements to and insertion in apical membrane

Describe polymorphic?

a population that contains 2 or more phenotypes. At least two of the alleles must occur with a frequency of more than 1%

Minimal Residual Disease is

a small clonal population of malignant cells characteristic of a neoplasia that cannot be detected by standard methods

If an allelic variant with amino acid substitutions increases the affinity of CYP to drug, we will observe a) enhanced metabolism, reduced concentration of parent drug b) decreased metabolism, increased concentration of parent drug

a) enhanced metabolism, reduced concentration of parent drug

For a drug, which of these has a higher chance of adverse effects? a) poor metabolizers b) ultrarapid metabolizers c) intermediate metabolizers d) extensive metabolizers

a) poor metabolizers (drug just sits there)

If a polymorphism causes a markedly reduced synthesis of CYP, which of these categories will the enzyme fall under? a) poor metabolizers b) ultrarapid metabolizers c) intermediate metabolizers d) extensive metabolizers

a) poor metabolizers (less enzyme means reduced metabolism of drug, so increased parent drug concentration)

Traditional method to detect Mycobacterium tuberculosis

acid fast smear, conventional and liquid culture methods AFB smear- rapid, poor sensitivity Culture methods sensitive but long turnaround time Doesn't distinguish MTb from nontuberculosis mycobacterium

If a polymorphism causes an increased synthesis of CYP enzymes, which of these categories will the enzyme fall under? a) poor metabolizers b) ultrarapid metabolizers c) intermediate metabolizers d) extensive metabolizers

b) ultra rapid metabolizers (too much enzyme, so too much metabolism, less parent drug concentration)

Which of these will have less therapeutic effect than desired if parent drug is active form? a) poor metabolizers b) ultrarapid metabolizers c) intermediate metabolizers d) extensive metabolizers

b) ultrarapid metabolism (gets kicked out too fast)

Hemoglobin E

beta chain variant in which lysine is substituted for glutamic acid in the 26th position. B26(B8) Glu->Lys In alkaline medium migrates w/ hemoglobins C, O, and A2. On acid migrates w/ HbA

Hemoglobin O-Arab

beta chain variant-substitution of lysine for glutamic acid at the 121 amino acid Migrates w/ HgbA2, C and E on cellulose acetate, it is the only hemoglobin to move just slightly away from point of application toward cathode on citrate agar at acid pH

Carriers of one functional and one defective allele, or 2 defective alleles for CYP mutations will have a) poor metabolizers b) ultrarapid metabolizers c) intermediate metabolizers d) extensive metabolizers

c) intermediate metabolizers

Human Epidermal Growth Factor Receptor 2 (HER2/neu)

cell membrane protein that adds phosphate groups to tyrosines on itself and other proteins (tyrosine kinase activity)

What is Chimera?

cells are derived from more that one distinct zygotic line

what is it when alleles are positioned on the same chromosome and are inherited together?

cis (coupling) position-inherited together

Negative template control-

contains non-target organisms used for typing and other studies *(negative template)*

Carriers of 2 functional genes with normal CYP activity will have a) poor metabolizers b) ultrarapid metabolizers c) intermediate metabolizers d) extensive metabolizers

d) extensive metabolizers

Factor V leiden increases chance of

deep vein thrombosis

What trait is *observable* even when the alleles are not the same on homologous chromosomes (heterozygous)?

dominant

Ultrarapid metabolizer (UM) will require a...

higher dose than usual since he/she has a polymorphism (mutation) that codes for a more efficient enzyme or more expression of an enzyme. They will eliminate the drug more quickly. A UM may be resistant to standard treatments, and it may take some time to adjust the dosage before therapy is achieved.

Pyruvate Kinase Deficiency mutation and molecular method used

in PKLR gene-180 mutations most missense Sequencing exons, flanking regions and promoter region of PKLR gene

what is nucleotide repeat expansion?

increased allele sizes disrupt gene function

The gene rearrangement process is a series of

intrachromosomal recombination events mediated by recombinase enzymes that recognize specific sequences flanking the gene segments.

Hemachromatosis: Type of disease Diagnostic methods

is an autosomal-recessive condition that causes overabsorption of iron from food. Easily treated by phlebotomy Diagnosis made through measurement of blood iron levels, transferrin saturation, or liver bx

Gene silencing in genomic imprinting

is due to methylation of C residues and other modification

What is Genomic imprinting?

is methylation of DNA (and associated histone modification) responsible for specific expression of genes in different cells and tissues.

DNA-Based Typing Methods: SSP-PCR Sequence-specific PCR more rapid method than SSOP

is performed with allele-specific primers that will amplify only specific alleles the 3' end of a PCR primer must be complementary to the template for recognition and extension by DNA polymerase

What is Gonadal mosaicism?

is the generation of new mutation in germ line cells (gonads)

Microsatellite instability (MSI)

is the production of new alleles from unrepaired replication errors (RER).

Incomplete penetrance

is when the person either expresses the disease phenotype or doesnt--(penetrance is genotype who show the character) -presence of mutation but no abnl phenotype

Viable expressivity

is when the pt is always expresses some of the symptoms of the disease and varies from very mildly affected to very severely affected -range of phenotype from the same genetic mutation

Loss of the normal allele, revealing the mutant allele is called____. Where doe it result from?

loss of heterozygosity or LOH results from somatic (enviromental) mutations or deletions of the nl allele

Gene rearrangements are normal events that occur in________. List antibody genes and T-cell receptor genes rearrange

lymphocytes Antibody genes *(immunoglobulin heavy chain genes, immunoglobulin light chain genes [k, l])* *T-cell receptor genes* (a, b, g, d) rearrange.

Hemoglobin C

lysine (+charge) replaces glutamine acid (-1 charge) at 6 position of the beta chain

Phenotypic Resitance testing

measure viral replication in presence of antiretroviral drugs- concentration of drug reducing replication by 50%

Which of the following genes would be analyzed to determine whether an isolate of Staph. aureus is resistant to oxacillin>

mecA

Homologous extrinsic control

modified version of the target that maintain the target primer binding sites; a PCR template with primer binding sites matching test targets and a non-target insert

Reagent Blank or contamination control

monitors reagents for carry-over contamination; contain everything but target; must have negative result *(no template)*

A leukemia or lymphoma is ________ with regard to Ig or TCR rearranged genes.

monoclonal

Hereditary Spherocytosis mutation

mutation in the ankyrin gene

Gain of function transmission patterns

mutations usually display a dominant phenotype

Loss of function transmission patterns

mutations usually display a recessive phenotype

template sequences that do not match the target sequence ; should have a pos amplication control signal

negative template control

any X-linked traits

never passed from father to son

Describe complex traits or multifactorial inheritance

no distinct inheritance pattern. includes normal traits affected by multiple loci and/or enviromental factors (heights, blood pressure). quantitative traits are complex traits with phenotypes defined by thresholds (obesity and diabetics)

Heterologous intrinsic control

non-target sequences naturally present in a sample such as eukaryotic or endocytosis; controls come from host sequences

Heterologous extrinsic control

non-target templates added to a sample before amplification to assure proper sample purification and amplification;

Altered solubility

nonpolar amino acid substituted for polar near molecules surface-HbS and HbC

Type 2 diabetes

normally a complex disease associated with obesity and inactivity Can be inherited -MODY(maturity onset diabetes in young- Autosomal dominant) -Mutation in mitochondria

Viral load testing

number of virus per mL of fluid determine if tx is working and resistance

Phenotypes

observed expressions of genes Physical characteristics that organism has. So when looking at individual you are looking at their phenotype

Oncogenes encode proteins called_____, which resemble the normal products of proto-oncogenes

oncoproteins

HIV Viral Load Testing

used to maximize effectiveness of therapy -Determine when to initiate antiretroviral therapy (HAART- highly active antiretroviral therapy) -Monitor response to therapy -Predict time to progression to AIDS Goal of therapy ..<50copies/mL

Acquired-transmitted by R-plasmids-resistance genes include

vanA, vanB

Intermediate metabolizer (IM) has one...

wildtype (normal) copy of the gene and one absent or dysfunctional copy. The IM group is very heterogeneous.