Lecture 13

University of Strathclyde Science BM210 Lecture 1: Human Genetic Variation - and its uses

Lecture Overview

  • Lecturer: Dr. Ben Pickard

  • Learning Outcomes: By the end of the lecture, students should:

    • Be confident in understanding various genetics terms frequently encountered in the course.

    • Appreciate the range of DNA polymorphisms in the genome and the methods used for their detection.

    • Understand how polymorphisms function as genetic markers.

Important Genetic Terminology

  • Locus: A place or location in the genome. (Plural: nuclei)

  • Polymorphism: Variations of a particular DNA sequence, including a single nucleotide difference (SNP) or changes that span multiple bases.

  • Allele: A specific version of a polymorphism; types include T and C in a given example.

  • Variant: A broader term that encompasses different forms of genetic sequence.

  • Mutation: A change in the DNA sequence, which may result in phenotypic effects.

  • Copy Number: Refers to the number of copies of particular segments of DNA.

  • Genotype: The genetic constitution, specifically at a locus; can be homozygous (CC, TT) or heterozygous (CT).

  • Homozygous: A genotype with two identical alleles.

  • Heterozygous: A genotype with two different alleles.

  • Marker: A specific locus or sequence that can be identified and used in genetic analysis.

  • Linkage: The tendency of genes located close to each other on a chromosome to be inherited together.

  • Recombination: The process by which chromosomes exchange genetic material during meiosis, leading to genetic variation.

  • Contig: A set of overlapping DNA segments that together represent a consensus region of DNA.

  • Phase: Refers to the arrangement of alleles on the two homologous chromosomes.

  • Haplotype: A group of alleles in an organism that are inherited together from a single parent.

  • De novo vs. Inherited: De novo mutations are new mutations not inherited from either parent, while inherited mutations are passed down through generations.

Definitions and Clarifications

  • Polymorphisms: Defined as "many forms", these can include simple alterations such as single nucleotide polymorphisms (SNPs) or extensive alterations involving thousands of bases. Variation can occur among individuals and chromosomes.

  • Example Visualization: Example of sequence difference given:

    • C allele: AAGCCTA

    • T allele: AAGCTTA

    • Genotype possibilities from alleles: CC, CT, TT.

Double-stranded DNA Sequence Presentation

  • Directionality: DNA has a 5’-3’ direction and includes both positive and negative strands. The positive strand has its 5’ end on the left.

  • Visualization of Sequence: Illustrations use Courier font to present double-stranded DNA sequences clearly.

  • Polymorphism Example: A specific change in the sequence indicated (C-to-A polymorphism) at a specified position.

Polymorphism versus Mutation

  • Phenotypic Effects: Polymorphisms may have phenotypic outcomes but they often are neutral and passed through generations; rare variants (less than 1-2% frequency) might indicate new mutations.

  • Mutation Context: Described as having a possible link to disease and phenotypes.

Human Variation

  • Structural Differences: On average, individuals differ by approximately 0.1% sequence, translating to ~6 million differences overall.

Main Types of Polymorphic DNA Sequences

  • SNP (Single-nucleotide Polymorphism): A sequence change where a single base pair changes (e.g., A to G).

  • Microsatellites: Short tandem repeats (STR, SSR) consisting of 2-7 base pairs (e.g. [CAG]n).

  • Minisatellites: Variable number tandem repeats (VNTR) with units ranging from 8 to over 50 base pairs (e.g., [CGT…TAG]n).

  • CNV (Copy Number Variant): Indicates zero, one, or multiple copies of a large DNA stretch (1000 base pairs > Mb).

Repetitive DNA

  • Tandem Repeats:

    • Microsatellites: Repeated units of size 2-7 base pairs occurring multiple times in individuals, useful for genetic fingerprinting.

    • Vary between individuals, can have 5-200 repeats in a genome.

    • Minisatellites: Larger variations with units between 10-100 base pairs, repeated tens to thousands of times.

    • Usually clustered homogeneously in the genome.

Applications of Polymorphisms

  • RFLPs (Restriction Fragment Length Polymorphisms): A technique used for profiling polymorphisms prior to the advent of sequencing.

  • Forensic Identification: RFLPs can assist in criminal identifications, biodiversity studies, food quality control, ancestry determinations, and disease gene mapping.

RFLPs Explained

  • Definition: Restriction enzymes from bacterial origins cut specific DNA sequences, effectively used to profile individuals.

  • Molecular Tool: Utilizes the specificity of restriction enzymes, such as those from E. coli, to identify polymorphisms.

  • Detection: Indicates genomic differences visible through changes in restriction fragment sizes due to point mutations or microsatellite variations.

Inheritance and RFLPs

  • Genotype Transmission: Inheritance pattern of RFLP markers showcases variations within families; denoted by allele sizes (big, quite big, small).

DNA Fingerprinting Applications

  • Broad Applications: Used in crime scene analysis, paternity tests, identifying disaster victims, and establishing unique genetic profiles based on polymorphisms identified through techniques originally pioneered in the 1980s.

    • Example: Prof. Sir Alec Jeffreys first used DNA for establishing innocence and guilt in criminal cases.

Modern Techniques vs. Historical Techniques

  • Today’s Approach: PCR-based methods now replace restriction digests (RFLPs) for amplifying DNA segments of interest.

Example of PCR Methods

  • SGM+ Markers: Include multiple loci such as FGA, TH01, VWA, and others aimed at generating a unique genetic fingerprint for comparison against crime scene DNA.

  • Sex Markers: Analysis of the AMEL gene locus can also determine biological sex based on differences in allele size.

Ancestry and Origins

  • Polymorphisms Reflect Origins: Genetic variations inherited from ancestors can be discerned, demonstrating human migration and population structures.

Additional DNA Features

  • Repetitive DNA: Contains sequences that are often inert but sometimes vary, also referred to as 'junk DNA'.

  • Types of Repetitive DNA:

    • Highly Repetitive DNA: Found in arrays near chromosome ends and centromeres, including alpha satellite DNA with repeats essential for chromosome stability.

    • Middle Repetitive DNA: Includes transposons and mobile genetic elements that may impact gene expression and evolutionary changes in species.

Important Notes

  • Viral and parasitic behavior of transposons highlights their evolutionary significance and potential risks.

  • Variations in transposable elements can contribute to genetic diversity but may also lead to deleterious effects due to gene inactivation.

Summary

  • Key Takeaways:

    • Repetitive and mobile DNA are crucial sources of genetic polymorphism.

    • Understanding these components enhances genetic analysis capabilities and applications in DNA fingerprinting.

    • Mastery of genetic terminology is vital for success in the field of genetics.