Diagnostic molecular exam 1

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single nucleotide polymorphism (SNP)

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Terms in this set (88)

Structure of short tandem repeatsunit of two to thirteen nucleotides repeated several to dozens of times in a row on the DNA strandCombined DNA Index System (CODIS)the FBI's computerized criminal DNA databases as well as the software used to run these databases; includes the National DNA Index System (NDIS)Amelogenin locusis not an STR. -It is used to identify distinguish between males and females. -It is a sequence of nucleotides on both X and Y chromosomes. -The X-chr has a 6-bp deletion within this gene: X amelogenin allele = 212 bp Y amelogenin allele = 218 bp -Females (X, X) - homozygous -Males (X, Y) - heterozygousY-STRsshort tandem repeats located on the human Y chromosomeY-STR typing is useful...when one is confronted with a DNA mixture containing more than one (male, female) contributormitochondrial DNA polymorphismsSequence differences in the hypervariable regions of the mitochondrial genome. Maternally inheritedmitochondrial DNA polymorphisms used fordetects various diseases such as parkinsons disease, alzheimer disease, bipolar disorder and cancer.mtDNAMitochondrial DNA. Evolve rapidly. Maternally inherited only so trace the maternal line of inheritance through timeIt is important to microbiological specimens for molecular testing to be collected becausecontaminated specimens can yield false-positivesFor molecular testing minimum organisms to be detected successfully?50 organismssingle nucleotide polymorphisms (SNPs)is a substitution of a single nucleotide that occurs at a specific position in the genome, where each variation is present at a level of more than 1% in the populationCommon targets of molecular testsBordetella, Legionella, Mycobacteria, Chlamydia and Streptococcus species.What Condition is associated with trisomy 21? A. Down syndrome B. Tuner syndrome C. Hunter Syndrom D. Chronic myelocytic leukemiaA. Down syndromeWhich situation illustrates a homozygous locus? A. No alleles B. Multiple alleles C. Two Identical Alleles D. Two non identical allelesC. Two Identical allelesIn one type of DNA fingerprinting, 13 pairs of primers are used to amplify 13 repeated regions of DNA in the human genome. When more than one sequence is amplified in a PCR reaction using multiple pairs of primers, what is the reaction referred to as? A. Multiplex PCR B. Hot-start PCR C. poly-PCR D. Combinatorial PCRA. Multiplex PCRWhich Class of bioterrorism agents is considered to pose the greatest risk to national security? A. Yellow B. E C. Tango D. AD. AWhich of the following is a gender marker? A. Amelogenin B. D8S1179 C. PentaDA. AmelogeninWhat polymorphisms may impact warfarin dosing?2C9 or VKORC1What polymorphisms are used to compare DNA from males but nor from females? A. Short tandem repeats (STR) B. Y-short tandem repeats (Y-STR) C. Variable number tandem repeats (VNTR) D. Restriction fragment length polymorphisms (RFLP)B. Y-short tandem repeats (Y-STR)You are asked to select a target sequence so your laboratory can screen all clades (Strains) of HIV. You go to GenBank to select a sequence. What kind of sequence is best for this analysis? A. Conserved sequences present in several viral species B. Sequences specific to HIV and no other organisms C. Sequences with variability for all retroviruses D. HIV drug-resistance sequencesB. Sequences specific to HIV and no other organismsWhat molecular mechanism accounts for the emergence of methicillin resistance in staphylococcus aureus? A. Mutation of the mip gene in the DNA that codes for 55 rRNA B. Mutation of mecA gene that alters penicillin binding protein C. Presence of genes vanA, vanB, vanC1 and vanC2 D. Mutations in the gag geneB. Mutation of mecA gene that alters penicillin binding proteinOnce HIV is detected and measured, why would you go on to perform genotyping? A. Confirm the infection B. Quantitate the viral load C. Determine the source of the HIV D. Detect antiretroviral drug resistanceD. Detect antiretroviral drug resistanceA virus does not need as much nucleic acid for the production of protein as bacteria do because: A. Viruses use the DNA of the cells that they infect to produce protein. B. Viruses contain high sequence variation C. There are no introns in the viral genome D. Viruses use plasmids to synthesize protein instead of DNAA. Viruses use the DNA of the cells that they infect to produce protein.Which one of the following is NOT considered a difference when comparing genomes between bacterial organisms and humans? A. The number of chromosomes B. The structure of chromosomes C. The presence of double-stranded DNA D. The number of genesC. The presence of Double-stranded DNAWhich of the following laboratory methods is use most often to screen for overexpression of HER2/neu in breast cancer cells? A. PCR B. Microarray C. Sequencing D. ImmunohistochemistryD. ImmunohistochemistryMinimal residual disease is... A. The residual symptoms observed in a patient following a bone marrow transplant. B. The smallest number of mutated cells that can exist without causing disease symptoms C. A small clonal population of malignant cells characteristic of a neoplasia that cannot be detected by standard methods.C. A small clonal population of malignant cells characteristic of a neoplasia that cannot be detected by standard methods.Mutations in BRCA1 and BRCA2 A. Are identified in most cases of breast cancer in women of the Western B. Require additional environmental and genetic factors for the development of breast cancer in mutation-positive patientsB. Require additional environmental and genetic factors for the development of breast cancer in mutation-positive patientsThe fusion of chromosomes 9 and 22 producing a BCR-ABL hybrid that occurs in CML forms a chromosome referred to as the A. Indianapolis chromosome B. Pennsylvania chromosome C. Philadelphia chromosome D. CML chromosomeC. Philadelphia chromosomeYou develop a quantitative PCR method to assay Gram negative organisms and include a number of controls. One such control is a "housekeeping" organism that helps identify a false negative test result. What is this control called?Detection of Gene MutationsMatix-assisted laser desorption/ionization (MALDI) - Time of flight > MALDI TOFAllele definitionDifferent forms of a geneLocus definitionLocation of a gene on a chromosomePCR primers allow forMultiplexingFragile X Syndrome (Mental Retardation)FMR-1 gene mutation -CGG repeats -Carrier 56-200 repeats Full Mutation- >200 repeatsHuntington Disease (Neurological degenerative disorder)Huntingtin Gene -50% chance of inheriting from affected parent. -Manifests in 40's to 50'sTrinucleotide Repeatshuntington disease, myotonic dystrophy and fragile x syndromeMajor Histocompatibility Complex (MHC)located on chromosome 6Polymorphisms and tissue rejectiondetermined on HLA on chromosome 6Ampliconsproduct of the amplification of DNA or RNAViral LoadNumber of viruses per ml of fluid, helps determine how the virus is progressingAutosomal recessivecystic fibrosisAutosomal dominantFactor V leidenSex-linked disorder (X linked recessive)hemophilia ANon-Mendelian InheritanceA type of inheritance that does not follow Mendelian laws of inheritanceGonadal mosaicismsomatic mutation in germ-line cells (gonads)genomic imprintingnucleotide or histone modifications that do not change the DNAHistoneprotein molecule around which DNA is tightly coiled in chromatinNucleotide repeat expansionIncreased allele sizes disrupt gene functionMitochondrial InheritanceMaternal inheritance of mitochondrial genesList 4 Non-Mendelian Transmission Patterns1. Gonadal Mosaicism 2. Genomic imprinting 3. Nucleotide repeat expansion 4. Mitochondrial inheritanceThe central dogma of molecular biology with respect to genetic information is best depicted by which of the following? A. DNA → transcription → protein → RNA → DNA B. DNA → transcription → RNA → translation → protein C. DNA → translation → RNA → transcription → DNAB. DNA > Transcription > RNA > translation > ProteinPurines are double-ring structures and include: A. Adenine and Guanine B. Cytosine and thymine C. Adenine and thymineA. Adenine and GuaninePyrimidines are single ring structures and includeThymine and CytosineOf the three pyrimidines-thymine, cytosine, and uracil. Which one is only found in DNA and which one is only found in RNADNA- Thymine RNA- UracilExamples of DNA Isolation?1. Protein Digestion 2. Cell lysis 3. PrecipitationIn organic DNA extraction methodsIncubation, lysis, phenol chloroform extraction, ethanol precipitation and washing steps Often used in laboratories because it is cheap and yields large quantities of pure DNAQuantiitating DNA concentration can be performed by which of the following? A. Microfluidics technology B. UV spectrophotometry C. Gel electorphoresis D. All are correctD. All are correctPolymerasean enzyme that brings about the formation of a particular polymer, especially DNA or RNA.restriction endonucleasesrecognize specific sequences of DNA and break phosphodiester bonds between adjacent nucleotidesRestriction endonucleases are characterized by1. Occurring only in microorganisms 2. Recognizing sequences of 4-15 bp in length 3. Cleaving phophodiester bondsDNA has what net charge?negativeWhat enzyme generates single stranded DNA from ribosomal or messenger RNA? A. Ligase B. Helicase C. DNA polymerase D. Reverse TranscripaseD. Reverse TranscripaseAgarose and polyacrylamide gel matrices differ with respect to A. Gel polymerization B. Resolution of fragment sizes C. Gel casting D. All are correctD. All are correctHow does oligo-dT select from mRNA from a mixture of nucleic acids? A. Adds a signal to the 5' end of mRNA B. Attaches mRNA to ribosomal RNA C. Binds the poly-A 3' tail of mRNAC. Binds the poly-A 3' tail of mRNADuring the transfer of DNA for Southern blotting, larger fragments of DNA: A. Transfer more quickly than smaller fragments B. Transfer more efficiently than smaller fragments of DNA C. Transfer more slowly than smaller fragmentsC. Transfer more slowly than smaller fragmentsStringent hybridization for Southern blotting would includeHigh temperature with low salt concentrationWhat does helicase do?Unzips DNAWhat does ligase do?joins Okazaki fragmentsThe conversion of mRNA nucleotide sequences and the transfer RNA (tRNA) -attached amino acids into a polypeptide is referred to as which of the following? A. replication B. Restriction C. Translation D. TranscriptionC. translationWhat determines the specificity in terms of the gene that is detected in the Southern blot? A. Nitrocelluslose membrane B. Agarose gel C. Restriction enzyme D. labeled probeD. labeled probeWhich of the following molecules polymerize to form a support medium through which nucleic acids move?polyacrylamideDNA is the tempalte for heterogenous nuclear RNA (hnRNA). What is the term for hnRNA production? A. Transcription B. Translation C. Replication D. SplicingA. TranscriptionDuring replication the addition of bases occurs....in the 5' to 3' directionIn contrast to liquid-phase DNA extraction procedures, protocols based on solid-phase are generally: A. Less amenable to automation B. more labor intensive C. more time consuming D. Less adaptable to extract large DNA yields per sample volumeD. Less adaptable to extract large DNA yields per sample volumeDetection of Gene MutationsAn "exon" is defined as:a region of DNA present in a mature strand of mRNA and can be translated into proteinAn intron is a sectionof an RNA that gets spliced out.A codon isthree-nucleotide sequence on messenger RNA that codes for a single amino acid