Download Sir Alec Jeffreys minisatellites

CODIS
Sir Alec Jeffreys
minisatellites
CODIS - Repetitive DNA
Repetitive DNA
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Satellite DNA
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Minisatellite DNA
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Microsatellite DNA
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Transposable elements
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LINES, SINES and other retrosequences
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High copy number genes (e.g. ribosomal genes, histone genes)
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Multifamily member genes (e.g. hemoglobin, immunoglobulin)
CODIS - Repetitive DNA
Satellite DNA
Unit Repeat Location Examples -
5-300 bp depending on species.
105 - 106 times.
Generally heterochromatic.
Centromeric DNA, telomeric DNA. There are at
least 10 distinct human types of satellite DNA. A
single type may be more than 1% of the genome
(equivalent to 3 entire E. coli genomes).
CODIS - Repetitive DNA
Human satellite DNA is prone to be multimeric or hierarchical
in structure. Human α satellite DNA (centromeric) is typically
171 bp long present as dimers (342 bp) or up to 16’mers
(2736 bp) as the repeating units. Generally less length
variation than minisatellites or microsatellites.
CODIS - Repetitive DNA
Human β satellite DNA is present as 30,000 - 60,000 copies of
a 68 bp monomer (2,040,000 - 4,080,000 bp) on the
metacentric chromosome 9 and the acrocentric chromosomes
13, 14, 15, 21, and 22. It is a pericentromeric repeat in
humans.
CODIS - Repetitive DNA
Examples of Satellites from Drosophila virilus.
Satellite
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II
III
Primary Copies per Percent of
Sequence
genome
genome
ACAAACT
ATAAACT
ACAAATT
1.1 × 107
3.6 × 106
3.6 × 106
25%
8%
8%
41%
CODIS - Repetitive DNA
Minisatellite DNA
Unit - 15-400 bp (average about 20).
Repeat - Generally 20-50 times (1000-5000 bp long).
Location - Generally euchromatic.
Examples - DNA fingerprints. Tandemly repeated but often in
dispersed clusters. Also called VNTR’s (variable
number tandem repeats).
Human λ33.1 minisatellite (62 bp)
AAGGGTGGGCAGGAAGTGGAGTGTGTGCCTG
CTTCCCTTCCCTGTCTTGTCCTGGAAACTCA
Human λ33.5 minisatellite (17 bp)
YGGGCAGGAGGGGGAGG
CODIS - Repetitive DNA
Microsatellite DNA
Unit Repeat Location Examples -
2-4 bp (most 2).
on the order of 10-100 times.
Generally euchromatic.
Most useful marker for population level studies.
This example is from a water snake . . .
...TCCAGACAAGGTGGTGTGTGTGTGTGTGTG
TGTGTGTGTGTGTTTCTCCAGTGAGATTTA...
CODIS - Repetitive DNA
Other repetitive elements include
Transposable elements - Sequences that have the ability to move
around within and between genomes. Most
eukaryotes have them while prokaryotes have a
different class of mobile elements.
LINES, SINES and other retrosequences - Mobile sequences that
copy themselves within genomes via an RNA
intermediate.
High copy number genes - Examples include ribosomal genes and
histone genes.
Multifamily member genes - Examples include hemoglobin and
immunoglobulin genes.
CODIS - the database
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In 1990 the FBI established a pilot project.
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In 1994 CODIS (Combined DNA Index System) was
established.
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In 1998 it was fully operational.
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In 2007 it contained more than 4.5 × 106 records.
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Records contain specimen numbers and DNA profiles but
nothing else.
CODIS - the markers
From wikipedia (28/11/08).
DNA databases go too far
CODIS and probabilities
Juries get confused by numbers.
CODIS and LCN
In the U.S., to my knowledge, LCN is used only for intelligence and
not for evidence.
what are your relatives up to?
CSI hasn’t picked up on this theme yet.
AFIS and CODIS are Biometrics
Both AFIS and CODIS are examples of biometrics. In today’s
environment, such methods are becoming increasingly used. Other
biometric methods include,
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Ear shape-structure
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Facial recognition
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Hand thermograms
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Digital voice signatures
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Gait
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Hand geometry
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Iris scans
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Retinal scans
NCBI
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Science is based on the production and the
exchange of knowledge
NCBI
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Science is based on the production and the
exchange of knowledge
Strong need for places were data could be freely
available
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to verify results
to facilitate the progress of research
NCBI
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Science is based on the production and the
exchange of knowledge
Strong need for places were data could be freely
available
I
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to verify results
to facilitate the progress of research
Submission to databases is mandatory prior to
article publication
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sequences (GenBank, EMBL, DDBJ,
SWISSPROT)
gene expression (Gene Expression Omnibus,
Array Express)
NCBI
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Welcome-Trust Sanger Institute
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The Institute of Genome Research (TIGR)
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Celera
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The Craig Venter Institute
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Genome sequencing center of Washington University at Saint
Louis
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The Broad Institute in Cambridge Mass.
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Riken Institute in Japan