Genomic Variation & Single Nucleotide Polymorphisms (SNPs) PDF
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Uploaded by ArtisticCharoite7173
University of North Texas Health Science Center
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Summary
This document provides an overview of genomic variation and single nucleotide polymorphisms (SNPs). It covers different mutation types, including gene, chromosome, and genome mutations. The document also discusses the impact of mutations on protein structure and function, along with regulatory elements and non-coding DNA mutations.
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GENOMIC VARIATION & SINGLE NUCLEOTIDE POLYMORPHISMS(SNPs) MUTATION CLASSIFICATIONS ◦ Gene mutations ⁃ most common of genetic disorders ⁃ Types: point mutations and single nucleotide substitutions ◦ Chromosome mutations ⁃ Rearrangement of chromosomal material ◦ Genome mutations ⁃ Los...
GENOMIC VARIATION & SINGLE NUCLEOTIDE POLYMORPHISMS(SNPs) MUTATION CLASSIFICATIONS ◦ Gene mutations ⁃ most common of genetic disorders ⁃ Types: point mutations and single nucleotide substitutions ◦ Chromosome mutations ⁃ Rearrangement of chromosomal material ◦ Genome mutations ⁃ Loss or gain of whole chromosomes NATURE OF NUCLEOTIDE SUBSTITUTION ◦ Substitution location affects impact ◦ Diff. Selective Contraints: ⁃ Structural genes: if mutated affects physical structure of organism ⁃ Synonymous variant: no change in amino acid sequence ⁃ Example: UCU, UCC, UCA,UCG all codons for serine even w/ alter ⁃ Non-synonymous variant: change in amino acid (AA) sequence ⁃ Example: AUC - Isoleucine to AUG - methionine altered the AA ⁃ Noncoding regions: when and how often a gene will be transcribed CODING POINT MUTATIONS ◦ Nucleotide change at one point in genome ◦ Transition: purine to purine, pyrimidine to pyrimidine (changing like to like) ⁃ 2x more frequent in coding regions ⁃ Single ring structure substitution - more likely ◦ Transversion: Purine to pyrimidine or vice versa (changing into opposite) ◦ Ratio of transition to transversion can tell if you’re looking at coding region CONSEQUNCES OF POINT MUTATIONS ◦ Missense: AA sequence changes (look at chart below for groups/properties) ⁃ Conservative: replacing AA with another AA that has the same qualities ⁃ Non-conservative: replacing AA with another AA that has diff. qualities ⁃ Example: AUC - Isoleucine changed to AUG - Methionine (diff. qualities) ◦ Nonsense: makes STOP codons ◦ Silent: AA sequence stays the same (like synonymous nucleotide variant) CODON USAGE BIAS ◦ Codons that appear frequently ◦ Synonymous condons occur at different frequencies INSERTIONS AND DELETIONS ◦ Large section of chromosomes can be duplicated or deleted ◦ Larger changes than copy number variations (CNVs) ⁃ Observable under microscope (karyotype) ◦ Cytogenetics: study of chromosomes under different colors “chromosome paint” FRAME SHIFT INDEL ◦ Removal or addition of nucleotide(s) that change codon reading frameshift ⁃ Results in large change in protein structure and/or function INSERTIONS AND DELETIONS ◦ Accounts for >15% of human genetic polymorphism ⁃ Microindels: indels that are
