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Major Components of a Gene. Promoter: The DNA region that signal initiation of transcription 5’-Untranslated Region: A short DNA sequence rich in GC pairs present in the 5’-flanking region of the gene Exon : Segment of a gene which is decoded to give an mRNA product or a mature mRNA product.

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Major Components of a Gene

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Major components of a gene l.jpg

Major Components of a Gene

  • Promoter:The DNA region that signal initiation of transcription

  • 5’-Untranslated Region:A short DNA sequence rich in GC pairs present in the 5’-flanking region of the gene

  • Exon:Segment of a gene which is decoded to give an mRNA product or a mature mRNA product


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Major Components of a Gene

  • Intron:Noncoding DNA which separates neighboring exons in a gene

  • 3’-Untranslated Region:A short DNA sequence in the 3’-flanking region of the gene that contains polyadenylation signal

  • Codon:A nucleotide triplet which specifies an amino acid or a signal for terminating the synthesis of a polypeptide


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The Genetic Code

  • Three-nucleotide sequences (codons) control selection of amino acids for protein synthesis

  • Four kinds of Nucleic acids in mRNA: Adenine, Guanine, Uracil, Cytosine

  • Commaless and nonoverlapping within a reading frame


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The Genetic Code

  • Non-ambiguous (no codon is specific for two different products)

  • Redundant (or Degenerate)

  • Code degeneracy usually in the third position of the codon


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Major Components of a Gene

  • Open reading frame (ORF): A long sequence of DNA in which there are no termination codons

  • Example:

    5’…TGTCCCGGCATGGATATCCGGAACAACCTCACTAGG…3'

    …CysProGlyMetAspIleArgAsnAsnLeuThrArg…


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Gene Transcription

  • 5’-Capping

  • 3’-Polyadenylation

  • Intron Splicing


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Basic Concepts in Gene Mapping

  • genomic DNA:the entire complement of genetic material

  • mRNA:RNA that is transcribed from the genomic DNA of a gene

  • cDNA:DNA which is synthesized by the enzyme reverse transcriptase using mRNA as a template


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Genomic DNA

Transcription

mRNA

Reverse Transcription

cDNA

Basic Concepts in Gene Mapping


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Basic Concepts in Gene Mapping

Genomic DNA

Transcription

Pre-mRNA

Splicing

Mature mRNA

Reverse Transcription

cDNA


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Basic Concepts in Modern Genetic Epidemiology

  • Allele:Alternative forms of a gene or DNA sequence at a specific chromosomal location

  • Allelic association:Any significant association between specific alleles at two or more neighboring loci

  • Allelic heterogeneity:Different mutations at the same locus cause the same phenotype


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Basic Concepts in Modern Genetic Epidemiology

  • Locus:The physical location of a gene

  • Locus heterogeneity:A phenotype may be caused by mutations at more than one gene locus


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Basic Concepts in Modern Genetic Epidemiology

  • Mutation: A change in the DNA

  • Polymorphism: A locus with more than one allele, each of which occurs with at least 1% frequency


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Point Mutations

  • Base substitutions

    • Change in a single nucleotide

    • Transitions: changes from purine-purine or pyrimidine-pyrimidine.

      • Examples: AG, TC

    • Transversions: changes from purine to pyrimidine or vice versa.

      • Examples: AT, GC


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Point Mutations

  • Synonymous substitutions:A substitution which replaces one codon by another without changing the amino acid that is specified

    =silent mutation

  • Non-synonymous substitutions: A substitution which replaces one codon by another with changing the amino acid that is specified

    =missense mutation


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Mutations

  • Deletions - small and large

    • Example: insulin receptor gene

    • TTCAAGAGATgATTCAGATGG (small)

    • Entire gene (large)


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Mutations

  • Insertions

    • Example: ACE Gene

      • Intron 16 D/I (289-bp Alu-I repeat sequence)

  • Inversions

    • Example: IDS Gene

      • Inversions of Exons 8 and 9


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Point Mutations

  • Missense mutation: A codon change can occur, such that a new amino acid is coded for.

  • Nonsense mutation: A stop codon can be created, causing termination of synthesis.

  • Silent mutation: If no change in product is observed, because of the redundancy of the genetic code.

  • Frameshift Mutation: Change in reading frame, usually by deletion or insertion of one or more nucleotides.


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Point Mutations

  • Splicing mutation: Changes in the splice donor/acceptor site or branch site that cause aberrant splicing

    • Example: Insulin receptor gene

      • Intron4 AG  GG (splice acceptor site)

  • Regulatory mutation: Changes in promoter site sequences that can affect the rate of transcription

    • Example: IL1 alpha gene

      • GGCAACA(CT)CATTGAAGGC (-889 relative to the transcription initiation site)


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Mitosis and Meiosis

  • Mitosis: A type of nuclear division that results in two daughter cells identical to the original cell

  • Meiosis: The process of two successive nuclear divisions resulting in cell with 1/2 the genetic complement of the original cell


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Hardy-Weinberg Equilibrium

  • Hardy and Weinberg discovered that for a given population, under certain stable conditions, gene frequencies tended to remain constant


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Hardy-Weinberg Equilibrium

  • Let p = freq. Of one allele (A)

  • Let q = freq. Of the alternative allele (a)

  • p +q =1

  • HWE predicts that proportion in the next generation will be:

    • p2 + 2pq + q2 =1, where

    • p2, 2pq, q2 represent allele freq. of AA, Aa, and aa


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Hardy-Weinberg Assumptions

  • Population is definitely large

  • Each genotype is equally likely to mate with any other

  • All genotypes produce viable offspring with same frequency - have equal genetic fitness

  • No mutation occurs

  • No migration in or out of population occurs


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Mendel’s First Law

  • The law of segregation

  • During gamete formation each member of the allelic pair separates from the other member to form the genetic constitution of the gamete


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Mendel’s Second Law

  • The law of independent assortment

  • During gamete formation the segregation of the alleles of one allelic pair is independent of the segregation of the alleles of another allelic pair


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Basic Concepts in Modern Genetic Epidemiology


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Autosomal Dominant Inheritance


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X-Linked Inheritance


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Autosomal Recessive Inheritance


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Basic Concepts in Gene Mapping

  • Genetic Linkage Map: Measures the amount of recombination between two loci; quantified by either recombination fraction or centiMorgans

  • Physical Map: Quantifies the actual amount of DNA, usually in base pairs, between two loci


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Genetic Map (Distribution of Cross-Overs)

A

C

A

B

B

D

C

D

Physical Map (Number of DNA Base Pairs)

A-B:Suppression of recombination

Genetic Distance Shorter than Physical Distance

B-C:Increase of recombination

Genetic Distance Larger than Physical Distance

Genetic Map and Physical Map


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Basic Concepts in Gene Mapping

  • Sequence-tagged site (STS): any piece of DNA whose sequence is known and for which a specific PCR assay has been designed

  • Example:

    • 273-bp STS (Genebank: G54567)

    • TGACTCCAATGACCGTCTGTCTATTTCACTGTATCCAGGCCAGTCTCTTTGAAGCTCTTTAAAAACATAATCCTTTAAGGTATATGAGAGGTCCTTAGAATTCAGATTGGCTACCTAGTATGAGGTATAAAAACAGAGCATTAGGTATTTTTACTATCATCTCCTAACCTAAAACAGGCAACCTTTAGGATTTACACTGAAAATAATTACATCAATTGGCCCCAAAGGGACTGCTAGTTTTGTATTATATGCCAGATCTCAATAAATGCCATT


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Basic Concepts in Gene Mapping

  • Expressed sequence tag (EST): A short sequence of a cDNA clone for which a PCR assay is available

  • Example:

    187-bp cDNA (Genebank: AL110360)

    • AAAAAAGGCAGCAGCTACCAAGAAACCAGCCCCTGAAAAGAAGCCTGCAGAGAAGAAACCTACTACAGAGGAGAAGAAGCCTGCTGCATAAACTCTTAAATTTGATTATTCCATAAAGGTCAAATCATTTTGGACAGCTTCTTTTGAATAAAGACCTGATTATACAGGCAAAAAAAAAAAAAAAAAA


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Basic Concepts in Gene Mapping

  • Recombination:The process during meiosis by which homologous chromosomes exchange material

  • Crossover:The physical process that results in the exchange of genetic materials between two paired chromosomes during a recombination event

  • Recombination fraction:The frequency of crossing over between two loci


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Crossover


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Basic Concepts in Gene Mapping

  • Marker:A polymorphic DNA or protein sequence derived from a single chromosomal location

  • Primer:A short nucleic acid sequence which specifically binds to a single strand of a targeted nucleic acid sequence


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Basic Concepts in Modern Genetic Epidemiology

  • Genotype: The observed alleles at a locus in an individual

  • Haplotype: A series of alleles found at linked loci on a single chromosome


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Basic Concepts in Gene Mapping

  • Heterozygous:The alleles at a genetic locus are different from one another

    • Example: Aa

  • Homozygous:The alleles at a genetic locus are identical

    • Examples: AA and aa


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Basic Concepts in Gene Mapping

  • Single nucleotide polymorphism (SNP): a substitution, deletion, or insertion of a single nucleotide

    • Examples: AG, AC

  • cSNP: A SNP that occurs in the coding sequence of a gene

    • Example: CTC (Leu)TTC (Phe)


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Basic Concepts in Gene Mapping

  • Microsatellite DNA: small array of tandem repeats of a very simple sequence, often between 1-4 bp (often < 0.1 kb)

    Example: A tetranucleotide repeat microsatellite

    …GAAAGAAAGAAAGAAAGAAAGAAAGAAA...

  • Minisatellite DNA: An intermediate size array of short tandemly repeated DNA sequences

    Example: A minisatellite (Genebank: AF157691)

    …(AGGGGGTGAGGGTGGGTGTGCTGG)n...


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Basic Concepts in Modern Genetic Epidemiology

  • Polymorphism Information Content:A measure of marker informativeness that reflects the fraction of matings in which a particular parent is expected to be fully informative

  • Heterozygosity:The fraction of individuals that are likely to be heterozygous at that locus


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Basic Concepts in Gene Mapping

  • Identity by descent (IBD):Two alleles are IBD which it can be determined with certainty that they have been inherited from a common ancestor

  • Identity by state (IBS):Two alleles are IBS when they share the same state


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AB

CD

AC

AC

IBD sharing: 2

IBS sharing: 2

IBD and IBS

AB

AC

AB

AC

IBD sharing: 0

IBS sharing: 1


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Basic Concepts in Gene Mapping

  • Linkage: The tendency of genes or other DNA sequences at specific loci to be inherited together as a consequence of their physical proximity on a single chromosome

  • Linkage Disequilibrium: Nonrandom associations of alleles at linked loci


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LOD Score

  • a two-point LOD score defined by Morton (1955)

  • L(pedigree|=x): the likelihood of observing a particular configuration of a disease and a marker locus in a family assuming a selected range of  (00.5)


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Basic Concepts in Modern Genetic Epidemiology

  • Morgan:A unit of genetic distance corresponding to a length of DNA which, on average, undergoes one crossover per individual chromatid strand

  • centiMorgan (cM):A unit of genetic distance equivalent to a 1% probability of recombination during meiosis


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Aa

Bb

Aa

Bb

Aa

Bb

aa

bb

aa

bb

aa

bb

Basic Concepts in Modern Genetic Epidemiology

Phase Unknown

Phase Known


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Basic Concepts in Gene Mapping

  • Penetrance: The probability of expressing a phenotype given a genotype

  • Phenocopy: A trait that appears to be identical to a genetic trait but is caused by non-genetic factors

  • Pleiotropy: One gene loading to many different phenotypic expressions.


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Basic Concepts in Gene Mapping

  • Bacterial artificial chromosomes (BAC): A recombinant plasmid which permits propagation of very large inserts (up to 300kb) in bacterial cells

  • Yeast artificial chromosomes (YAC): An artificial chromosome produced by combining large fragments of foreign DNA with small sequence elements necessary for chromosome function in yeast cells


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