SNPS and phenotyping

• define SNPs

  • single nucleotide polymorphisms
  • variation in DNA sequences at single base positions
• different types of SNPS

  2 types

  1. bi-alleic: allele change b/w 2 people and 3 different types for a child
  2. tri-allelic: allele change b/w 3 people and 4 different types for a child
• nomecnulture for SNPS

  1. a/g
  2. a>g
  3. a —>g
  4. tri-allelic: a>g/a>c
  5. chr 8:19956018 <— chromosome:position
  6. rs268 is the most common type and refers to SNP accesion number in dbSNP
• haplotype 


  combines 3 SNPS = block allele ie. ACT
• explore SNPS

  • most abundant type of genetic variation in gnome ~ 10 million
  • 99% of DNA is identical
  • 0.1% over 80% are SNPS and occurs in every 300bp
  • minor allele freq: >1% of pop
• list how SNPS can be infor active

  1. disease
  2. health correlation ie. cancer and migarines
  3. bio genetic ancestory BGA
  4. trait
• why are SNP better than str

  1. small aplicion size b/2 70-150
  2. good for degreaded DNA that is very fragmented
  3. Low mutation rate
  4. more stable over generations
• disadvnatges of SNP

  1. Less polymorphic = low discrimination power
  2. 4 times the nuMyer of SNP required for equivalent random match prob
  3. mixtures are diffcult to read
• describe DNA phenotyping

  • use BGA<- biogentic ancestorY
  • autosomal and linages
  • use for the prediction of visible characteristics
• List theses visible charactersics

  • skin, hair, eye and eyebrow colour
  • freckles
  • hair shape
  • male pattern baldness
  • height
• when is phenotyping useful

  1. large or unknown pool of suspects
  2. offender is not in database
  3. forensic intelligence
• what is a risk of BGA

  can racially target a group, so it is important to use careful context
• compare Y, X and autosomal SNPS

  x: gets info from mum

  y: get info from dad

  auto: male from mum and female from both parent
• how many SNP are required/dependent on 


  they are dependent of how markers are selected

  either

  1. at random
  2. ancestory informative markers
• what are SNPfor ID 34 plex used for

  • 34 markers
  • differentation of: Africa, European, America and south and east Asia
• type of SNP fro BGA

  1. fixed SNP: 1 allele is only expressed in pop
  2. pop specific SNP: where 1 allele is expressed in both pop = equal
  3. skewed freq SNP: where allele in both pop but 1 is more expressed
  4. tri-alleleic SNP: where mutli alleles
• commonly available kits

  1. forenseq DNA signature kit: from illumina, 56 markers and focuses on: africa, Europe, east Asia and admix america

  2. Precision ID ancestry panel: from thermo fihser, 165 markers and focuses on: africa, Europe, southwest asi, Oceania and America
• EVC for eye colour

  • predicts blue, intermediate and brown
  • 93% brown: 91% blue and 73% intermed
• What does the irisplex panel do

  6 SNPs model

  influential SNP for blue brown
• what genes play a role in determining eye colour

  1. HERC2
  2. OCA2
• what does rs12913832 do

  • is on HERC2 gene
  • strongest association with eye pigmentation
  • t-allele acts as on/off switch for brown eyes
  • presence = evaluates OCA2 expression and dark pigmentation
• EVC for hair colour

  • hirisplex panel for hair and eye colour using 24 SNPS
  • mainly european pop
  • focus: blond (69.5%), brown (78.5%), red (80%) and black (87.5%)
• EVC for skin colour

  hirisplex s <— hair, eye and skin with 41 SNP

  75% for very pale and intermediate

  73% for pale

  84% for dark

  98% for dark to balck