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Forensic Application of Newly Suggested Y Chromosome Variation

Kyoung-Jin Shin, Ph.D.

Department of Forensic Medicine

Yonsei University College of Medicine

Value of Y chromosome markers

Application Advantage

Forensic case work on sexual assault evidence

Male-specific amplification (can avoid differential extraction to separate and epithelial cells)

Paternity testing Male children can tied to fathers in motherless cases

Missing persons investigations

Patrilineal male relatives may be used for reference samples

Y

Non-Recombination Portion of Y chromosome

(NRY)

Human migration and evolutionary studies

Lack of recombination enables comparison of male individuals separated by large periods of time

Historical and genealogical research

Surnames usually retained by males; can make links where paper trail is limited

Y-STRs (short tandem repeats)

Y-SNPs (single nucleotide polymorphisms)

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Thomas Jefferson II

Field Jefferson Peter Jefferson

President Thomas Jefferson

Eston Hemings Thomas Woodson

Different Y Haplotype

Same Y Haplotype

Jefferson Y Haplotype

Jefferson Y Haplotype

?

Figure 9.10, J.M. Butler (2005) Forensic DNA Typing, 2nd Edition © 2005 Elsevier Academic Press

Historical Investigation of Jefferson-Hemings DNA

Genetic Genealogy Companies

SOURCE: Foster et al. (1998) Nature 396:27-28

http://www.cstl.nist.gov/div831/strbase/training.htm

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Representative commercial Y-STR kit

http://www.cstl.nist.gov/div831/strbase/training.htm

Schematic diagram of Kplex Y17 system

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Electropherogram of Kplex Y17

2800M standard DNA

500 pg 250 pg 125 pg

100 pg 62.5 pg

Sensitivity test using serially diluted DNA

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[1:1] 100pg of 007 DNA + 100pg of female DNA [1:10] 100pg of 007 DNA + 1ng of female DNA

[1:100] 100pg of 007 DNA + 10ng of female DNA [1:1000] 100pg of 007 DNA + 100ng of female DNA

Specificity test using mixed samples

Newly suggested Y-STR loci

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DYS576DYS391DYS481DYS549DYS533DYS570DYS643DYS385a/b

DYS627*DYS576DYS391DYS460DYS518*DYS449*DYS385a/bDYS570DYS533DYF387S1*DYS481* RMY-STR

DYS460

DYS627

DYS518

DYS449

DYF387S1

DYS391

DYS385a/b

New commercial Y-STR kits

http://www.cstl.nist.gov/div831/strbase/training.htm

Schematic diagram of Kplex Yplus

New Y-STRs Yfiler

RMY-STRs New Y-STRs

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Electropherogram of Kplex Yplus

2800M standard DNA

Focusing on Y-SNPs

n Increasing requests for information regarding ethnic andgeographical origin from specimens left at a crime scene.

n Globalization of crime suspects and victims

n Increase of movement from East-southern population

n Increase of excavation of Korean War victims and ancient mummies

n Individual identification in mass disaster such as airplane crashes,tsunamis or terrorist attacks where people from various geographicalareas are involved

n Y-haplogroup ß combination of allelic states at SNPs

n Set of haplotypes defined by slowly mutating markers (mainly SNPs)which have more phylogenetic stability

n Unique event polymorphisms (UEP) record history of Y chromosome

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Y chromosome haplogroup

Y chromosome phylogenetic tree

n In 2008, Karafet TM et al.- Genome Res 2008;18:830-838

n 20 major clades

n 311 haplogroups based on 599 binary markers

n In 2011, Yan et al. - Eur J Hum Genet 2011;19:1013-1015

n An updated tree of haplogroup O

n Redefined marker KL2, JST002611, PK4 and P164

A

B

C

D

E

FGH

I

J

K

L

MN

O

P

Q

R

S

T

Need for development of Y-SNPtyping method according to therevised tree

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SNP detection methods in forensics

Multiplex SBE reaction

Multiplex PCR

5’ AT3’ 5’

3’

5’ GC3’ 5’

3’

5’ TA3’ 5’

3’

CG3’ 5’

5’ 3’

T

ddATPA

3’ 5’

ddGTP

CG

3’ 5’

A3’ 5’

ddTTPT G3’ 5’

ddCTPC

GA T C

SAP treatment ElectrophoresisExo-SAP purification

SBE reaction

Multiplex allele-specific PCR

M17478

C

81

T

M9127

G

130

C

M231153

A

156

T

PCR Size

SNP

5’ 3’

F primer

R primer

T

A

GF primer

R primer

C

CF primer

R primer

T

Multiplex PCR

C T G CA

Electrophoresis

Multiplex SBE reactions

DE

C

K

NO

O

Multiplex I

O1a

O2

O2b

O2b1

O3

Multiplex IIMultiplex III

O3a

O3a3

O3a3b

O3a3c

O3a3c1

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n Multiplex AS-I

Multiplex ASP systems

Y haplogroup distributions in Koreans

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Y haplogroup tree update

Y-STR Haplotype Reference Database

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Y chromosome STR manager

Y-STR haplotype search

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Kinship index calculation

n This research was supported by the Bio & MedicalTechnology Development Program of the NationalResearch Foundation (NRF) funded by the Koreangovernment (MEST)

n This work was supported by the research project forpractical use and advancement of forensic DNA analysisof Supreme Prosecutors' Office, Republic of Korea

n Most of this presentation material was prepared byMyung Jin Park in the course of her doctoraldissertation.

Acknowledgements