Use of Polymorphic Markers for Human
Identification
• Ancestry / anthropology studies
• Paternity testing
 Individual identification
• Maternity testing
 Typically only in cases of war / natural disasters
• Forensics
 Gender identification
 Individual identification
Ancestry Testing
Three general approaches
• Maternal lineage – Mitochondrial DNA testing
• Paternal lineage – Y chromosome testing
• General lineage – Admixture testing
Maternal Lineage: mtDNA
Polymorphisms
• Mitochondria are maternally
inherited
• All maternal relatives will have
the same mitochondrial
sequences
• Mitochondrial typing can be used
for legal exclusion of individuals
or confirmation of maternal
lineage
http://www.forumbiodiversity.com/showthread.php/43295-23andme-results
Maternal Lineage: mtDNA
Polymorphisms
• Sequence differences in the
hypervariable (HV) regions and
throughout the mitochondrial
genome are used in mtDNA
analysis
Paternal Lineage: Y-STR Analysis
• The Y chromosome is inherited in a
block without recombination
• Simple tandem repeat (STR)
sequences are analyzed on the Y
chromosome
• Y chromosome STRs are inherited
paternally as a haplotype
http://www.promega.com/resources/profiles-in-dna/2012/variability-of-new-str-loci-and-kits-in-us-population-groups/
Paternal Lineage: Y-STR Analysis
• Allelic ladders for YSTR loci in a multiplex
format – the Y-Plex 6
system.
• A single haplotype for
the Y-STR loci
M1
M2
M4
M3
M5
M6
Paternal lineage: Y-STR
analysis
Admixture Testing
• Does not use mitochondrial DNA or Y
chromosome analysis
• Focuses on analysis of the 22 pairs of
autosomes
• This is also called autosomal DNA
(atDNA) testing
• Analyzes STR and/or SNP
http://blogs.discovermagazine.com/gnxp/2010/07/really-fine-grained-genetic-maps-of-europe/#.VSVG7eEyg5o
Admixture Testing
http://www.dailymail.co.uk/sciencetech/article-2931700/The-rise-rise-family-historyDNA-tests-AncestryDNA-s-kit-latest-launch-UK-relatives-SECONDS.html
Paternity Testing
• Used to legally exclude a male as a potential father of a child
• Can use many techniques
• Most common technique is now STR analysis
http://www.ctdrugtest.com/?p=107
Paternity Testing– RFLPs
• RFLP genotypes are inherited.
• For each locus, one allele is
inherited from each parent.
Thought question:
 What if both parents were
homozygous for same allele
at locus A?
Paternity Testing– RFLPs
• Which man’s genotype does not exclude him from being the father?
STR Analysis for Parental Testing
• STR genotypes are inherited, one allele is inherited from each parent
• STR is PCR amplified then resolved by electrophoresis (gel or capillary)
 NOTE: AMEL loci is
not an STR
Thought question:
 Why is the TPOX loci
in the child’s sample
not labeled with
parental origin?
STR Analysis for Parental Testing
Which of the potential father’s genotype is consistent with the child’s alleles?
 Not informative
 Supports #1
 Not informative
 Not informative
 Supports #1
 Not informative
 Not informative
 Not informative
Forensics
• Human remains
• Criminal suspects
 Gender identification
 Individual identification
http://www.fayetteville-crime-scene-cleanup.com/
http://blog.illumina.com/blog/illumina/2013/10/17
/next-generation-sequencing-technologies-andforensic-dna-analysis
Gender Identification
• The amelogenin locus is not an STR; it is a gene.
• The human AMEL gene codes for amelogenin-like protein.
• The gene is located at Xp22.1–22.3 and on the Y chromosome.
X allele = 212 bp
Y allele = 218 bp
Males (X, Y) - heterozygous
Females (X, X) - homozygous
RFLPS in Crime Scene Evidence
Locus A
1 = suspect 1
2 = suspect 2
C = child victim
P = parent of child victim
E = Evidence from crime scene
 Why include child and parent?
 Which suspect is consistent with
the evidence?
Locus B
STR Analysis in Crime Scene Evidence
http://www.forensicsciencesimplified.org/dna/img/SInglesourcematch.png
CODIS: Combined DNA Index System
 Local DNA Index System (LDIS)
 State DNA Index System (SBIS)
 National DNA Index System (NDIS)
•
•
•
•
CODIS, launched by the FBI, is now the largest DNA database in the world
Requires specific STR loci to be analzyed
Kits are commercially available for the CODIS STR alleles.
The data generated data are digital which can be banked more readily (i.e. creating a
national database).
• In 2007, CODIS contained almost 200,000 forensic profiles and over 5 million offender
profiles
• As of the end of 2012, CODIS had produced over 200,000 matches or “hits”
 This aided in over 190,000 investigations
CODIS
http://en.wikipedia.org/wiki/File:Codis_profile.jpg
Interpreting Polymorphism Analysis
Results for ID
• Probability of ‘unique’ match with STR and/or haplotype (SNP) analysis
increases with each loci added to the analysis.
 Use likelihood ratios to determine probability of unknown
being a match to a sample in the database
THE END