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Lecture 1

BIOLOGY 1A03 Lecture 1: THEME 5

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Rosa Da Silva

Module 1 – Genetic Variation UNIT I: GENETIC VARIATION TANDEM REPEATS: presented next to each other in multiple identical/near identical copies up to several thousand nucleotides long SIMPLE-SEQUENCE REPEATS: repeats as short as 2 nucleotides repeated over and over again throughout the strand DNA POLYMORPHISMS • One of two or more alternative forms/alleles at a chromosomal region/locus that differs in a single nucleotide or a variable number of tandem repeats • Large number across the genome which reside in non-coding DNA regions • Also referred to as DNA Markers for they allow for high-density genetic maps used for identification and relatedness • Detectable using microarray analysis, PCR, Southern blot, or DNA sequencing UNIT II: DETECTING VARIATION DETECTING SNPs • Most common type of genetic variation • Single nucleotide base changes/substitutions in a sequence • Contained in both coding/non-coding regions, although more common in non- coding • May be used as DNA markers if found close to a particular gene • Inherited in offspring if close/linked to a particular gene DNA MICROARRAY ANALYSIS • Commonly used to detect SNP • Single-stranded oligonucleotides containing a center nucleotide base complementary to the common allele/all variant SNPs, are attached to the glass on the microarray chip • Fragments of the single-stranded fluorescently-labelled DNA of an individual are also contained on the chip • It is possible to match the fluorescent pattern based on which SNPs are contained by an individual due to known location of all oligonucleotides • In this case, the C-G and A-T alleles are being detected • Each SNP genome reveals a distinct pattern of fluorescence, indicating where an individual is homozygous/heterozygous for C-G/A-T • Genome of each individual contains own SNP pattern, resulting in unique SNP profiles 
 VARIABLE NUMBER TANDEM REPEATS (VNTRs) • Repeated, adjacent patterns of one or more nucleotides • Tandem repeat sites are targeted
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