Supplementary markers Flashcards
LO
* Learn about the available supplementary markers
* Describe the evolution of the sex chromosomes
* Describe the evolution of the mitochondria
* Discuss the organisation of the mitochondrion
* Understand their forensic applications
What are mini STRs and their use?
* Degraded DNA in small amounts often show an incomplete genetic profile when using standard STR amplicons. The technology of mini-STRs, using reduced-size STR amplicons can help to recover information from these samples.
- Mini STRs are used to identify genetic profiles in samples with small amounts of DNA
- Degraded DNA is often encountered in forensic casework
- Smaller PCR products can be designed by moving the primers closer to the repeat region
- In addition to having kits dedicated to short amplicons, many profiling kits have been redesigned to be able to incorporate more of these markers
What are some different kits for Mini STRs?
*** Different kits: **
o PowerPlex 6C Fusion STR kit
o GlobalFiler STR kit
o MiniFiler STR kit
o ForenSeq Kit identity SNPs
o Investigator DIPplex Kit
o InnoTyper 21 DNA typing kit
What are single nucleotide polymorphisms?
- A compound on the DNA strand with one of four nitrogen containing bases. The sequence of the base’s codes for genetic information
- Single- a single base at a particular position in the genome that may vary between individuals
- Nucleotide- a sugar molecule (deoxyribose) attached to a phosphate group on the DNA backbone with an associated nitrogen-containing base
- Polymorphism- a variation seen in more than 1% of the population (if <1% of population then would be known as a mutation)
- Occur in 5’ to 3’ direction, the reverse just changes in order to pair and match. Check!
What are most SNPs?
How do they vary in populations?
Multiallelic SNPs
* Most SNPs are one of two types- biallelic
- A proportion- around 5%- show more than two types
o Tri-allelic- 3 types
o Tetra-allelic- 4 types - Tri and tetra allelic are rare, so be careful, many in the literature are errors
What are Microhaplotypes and what do they provide?
- Microhaplotypes are found in small regions (less than 200 nucleotides) of the DNA where there are two or more SNPs within a short distance
- Provide three or more different allelic combinations or haplotypes
What are Insertion-deletion (INDEL) polymorphisms?
- Not as common as SNPs which are ‘point’ mutations
- Indels are defined by an** insertion** or deletions of one or more nucleotides in the genome
What is a frame shift mutation?
Give an example of a disease which occurs due to this
- Unless the length of the indel is a multiple of three is cases a frame shift mutation and rare in coding regions
o** Tay-Sachs diseases **
Tay-Sachs disease is a rare genetic disorder passed from parents to child. It’s caused by the absence of an enzyme that helps break down fatty substances. These fatty substances, called gangliosides, build up to toxic levels in the brain and spinal cord and affect the function of the nerve cells.
How common are INDEL polymorphisms?
Widely spread across the genome- 20% of all known genetic variants
The sex chromosomes
Why is the Y chromosome so small?
- The blue areas shown here are mutations
- To keep from getting the SRY gene ‘fixed’, the Y chromosome stopped recombining with most of the X chromosome.
Tell me about the STR region on Y chromosomes
- Pseudo autosomal regions (PAR) are homologous with the X chromosome and recombine
- Genes important in testes development and sperm production on the p arm
- AMELY gene encodes for amelogenin protein
o Demineralisation of tooth enamel
o Paralog on the x chromosome
o First intron differs by 6 bp- used in DNA kits to determine sex - 1998 reports in literature of males without the AMELY deletions- X only in electropherogram
- Amelogenin gene is present on both the x and y chromosome. The locus is different in size in both the X and Y chromosomes. The two bands on a gel electropherogram indicate a male and a single band represent a female
What is Endosymbiogenesis ?
What evidence is there for this?
* Theory of origin of eukaryotes from prokaryotes
* Cyanobacteria and protobacteria closely related to mitochondria
* Theory suggests that prokaryotes engulfed by a proto eukaryote
* Presence of DNA supports prokaryotic origin
* Cell cannot regenerate mitochondria
* Mitochondria has DNA present which suggests came from bacteria originally
What is the function of mitochondria?
- Vital role in cellular respiration
- **Krebs cycle **converts glucose metabolites and oxygen into energy in the form of ATP through the electron transport chain (don’t need to learn the Krebs cycle just the generally production)
- Numbers vary depending on cell function from none (red blood cell- as don’t need energy) to around 2000 (liver cells)
What is the components of the mitochondrial genome?
- Circular double stranded molecule
- Has a control region
- 2-10 copies per cell in each mitochondria
- Approximately 16,569 bases numbered clockwise from point between hypervariable regions and 2 (HVI and
- 37 intron less genes (a characteristic of prokaryotes)
- D-displacement loop (control region) has 3 strands of DNA holding strands apart (16024-576)
Describe homoplasmy and heteroplasmy in mitochondria
*** Homoplasmy- **mitochondria sequences are the same
* Heteroplasmy- some cells might have mutated and lead to mitochondria with different DNA type (via SNP). This will only be visible if there is enough of these changes.
* Heteroplasmy is more common in hair
What are the types of supplementary markers and their forensic applications?
- Mini STRs
- SNPs/Microhaplotypes/ INDELS
- X chromosome markers
- Y chromosome STRs
- Mitochondria DNA
