DNA Fingerprinting:

UWC developments on Y-chromosome profiling

Eugenia D’Amato Research Manager Forensic DNA Lab University of the Western Cape

SAASTA-March 2009

DNA Fingerprinting

Genetic individual profiling using highly variable DNA located in our chromosomes

.

DNA utilized in profiling = STR (Short Tandem Repeats or Microsatellites) Sir Alec Jeffreys

SAASTA-March 2009

How a genetic profile is generated

Mother Father The human genome is composed by 22 pair of autosomal chromosomes and 1 pair of sexual chromosomes. The 2 chromosomes of each pair in inherited from our mother and our father.

Large individual variation occurs at microsatellites.

XY

determines

a male XX determines a female SAASTA-March 2009

How a genetic profile is generated..

TAGA Non-sexual chromosomes Maternal chromosome = 4 repeats Paternal chromosome = 7 repeats Millions of copies of several DNA fragments (markers) are obtained in a single tube by the technological procedure called PCR.

The products of the PCR are separated by size in automatic instrumentation. Application: individual identity, e.g. paternity analysis

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(TAGA)3 (TAGA)4 (TAGA)7 (TAGA)8 (TAGA)10 (TAGA)14

In a paternity testing:

Mather Male 1 Male 2 child

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Y-chromosome

• Y-chromosome is a single block of DNA that is fully transmitted from fathers to sons • information in the Y-chromosome is used to define lineages • related men in the same paternal lineage share the same Y-chromosome genetic profile SAASTA-March 2009

Y-chromosome STRs

Forensic application: rape cases   Differential extraction of DNA from sperm PCR targets only male DNA in excess if victim’s DNA

Over 54000 cases/year are reported to SAP

  15% of reported cases result in conviction 41% of victims are children SAASTA-March 2009

Brief history of Y-STR genotyping  1997: 9 markers, the Minimal Haplotype, are recommended for Court use  2000: establishment of the Y-HRD at present: 72 000 profiles MH 16 000 profiles with additional 8 markers  2004, 2006: reviews on all known Y-STRs (~400) SAASTA-March 2009

Developments in forensic Y-genotyping

:

 International standardization of nomenclature (ISFG- NIST)  Commercial developments Promega: 12 markers (MinH + 3) Applied Biosystems: 17 markers (MinH + 8) SAASTA-March 2009

Profiling – the crime scene

1. Is there a match?

2. If so, how rare is this profile??

crime scene suspect 1 victim- female MATCH suspect 2 SAASTA-March 2009

How unique is a profile?

To answer this question we need large amount of data DATABASES Y-HRD Promega Applied Biosystems SAASTA-March 2009

FDL lab studies on Y-STR markers

2004: UWC-genetic diversity studies in local population groups Sampling : buccal swabs Approved by Ethics Committee – UWC

samples are provided by unrelated volunteers who remain anonymous

2005: new Y-STR markers are discovered in the FDL

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UWC data

YHRD Database

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Analysis of population diversity

 Poor genetic diversity in SA low DC , Xhosa = 0.62

European DC ~ 0.75-0.85

Discrimination = No distinct profiles Few profiles in high frequency 13% Xhosa share same profile capacity No profiled individuals Europeans ~ 5 %  Consequences: limited forensic utility of these markers SAASTA-March 2009

The FDL Y-STR project

 Design of a new system to profiling males that is more efficient for the SA population    1. Profiling of 3 population groups at 45 Y-STRs 2. selection of the best markers 3. Optimize the PCR , single reaction.

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DC of commercial systems and UWC system 1 0.95

0.9

0.85

0.8

0.75

0.7

0.65

0.6

0.55

0.5

* *

Indian English Xhosa ALL MH 9 markers

*

European values RG PP 12 markers YF 17 markers

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10-plex

The UWC 10-plex

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Advantages of UWC development    Higher discrimination capacity Lower cost Some markers provide information about population group ( African - Indian ) need for population data !! SAASTA-March 2009

Further studies- research

 Development of statistic tools simulation of Y-profiles match-P and databases Research project with Statistics Dept- UWC Haplogroup Ib2 SAASTA-March 2009 Haplogroup R1b3

The way forward…

 Screening of additional population groups in South Africa and Africa using  Commercial markers  UWC markers  Link-up with interested parties  Offer the service for resolution of rape cases SAASTA-March 2009

Lab members

Staff Sean Davison Mongi Benjeddou PostDoc Eugenia D’Amato Students Tasneem Geduld (MSc) Shafieka Isaacs (MSc) Zainu Abrahams (MSc) Kevin Cloete (MSc) Curtis Cole-Showers (PhD) Khadija Mwema (MSc) Tiro Tau (MSc) www.forensicdnalab.org.za

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THNX !

questions?

SAASTA-March 2009