the golden age of forensic y-str typing – new markers, new databases, new technologies lutz...

The golden age of forensic Y-STR typing – new markers, new databases, new technologies

Lutz Roewer, Dept. Forensic GeneticsInstitute of Legal Medicine and Forensic Sciences, Charité – Universitätsmedizin Berlin

©Charité – Universitätsmedizin Berlin, Dept. Forensic Genetics 2014

System Minimal HaplotypePowerPlex Y (12 Loci)

PromegaY-Filer (17 Loci)

Applied BiosystemsPPY23 (23 Loci)

PromegaYFiler plus beta (27 Loci)

Applied BiosystemsCommercial +

add. Y-STRs (45 loci)DYS19 x x x x x x

DYS389I x x x x x xDYS389II x x x x x xDYS390 x x x x x xDYS391 x x x x x xDYS392 x x x x x xDYS393 x x x x x x

DYS385ab (2) x x x x xDYS437 x x x x xDYS438 x x x x xDYS439 x x x x xDYS448 x x x xDYS456 x x x xDYS458 x x x xDYS635 x x x x

YGATAH4 x x x xDYS570 x x xDYS576 x x xDYS533 x x xDYS481 x x xDYS549 x x DYS643 x xDYS460 x xDYS627 x xDYS518 x xDYS449 x x

DYF387S1ab (2) x xDYF399S1 (3) xDYF403S1 (3) xDYF404S1 (2) x

DYS526 xDYS547 xDYS612 xDYS626 x

DYS464 (4) x


Ballantyne KN, Goedbloed M, Fang R, Schaap O, Lao O, Wollstein A, Choi Y, van Duijn K, Vermeulen M, Brauer S, Decorte R, Poetsch M, von Wurmb-Schwark N, de Knijff P, Labuda D, Vézina H, Knoblauch H, Lessig R, Roewer L, Ploski R, Dobosz T, Henke L, Henke J, Furtado MR, Kayser M (2010) Mutability of Y-chromosomal microsatellites: rates, characteristics, molecular bases, and forensic implications. Am J Hum Genet 87(3):341-53.

Really fast mutating Y-STR markers are very rare


Family analysed with 45 markers –patrilineage resolved with 2 mutations

576

389I

448

389II

19

391

481

549

533

438

437

570

635

390

439

392

643

393

458

385ab

456

GATAH4

627

460

518

449

387S1

526a

526b

626

399S1

612

547

404S1

403

F

S

G

DYS626 µ=1.22 x 10-2DYS391 µ=2.54 x 10-3


• Yfiler® Plus• 25 marker, 2 bilocal• 6 dye matrix


Loci Mutation Rate [95% CI] Meioses Position[MutRate] Group[MutRate]dys438 2,96E-04 10122 1 slowdys392 4,04E-04 14867 2 slowdys393 1,09E-03 13713 3 slowdys437 1,19E-03 10101 4 slowdys448 1,65E-03 6678 5 slowdys390 2,06E-03 15061 6 mediumdys385 2,30E-03 25620 7 mediumdys19 2,32E-03 15539 8 medium

ygatah4 2,47E-03 7709 9 mediumdys391 2,54E-03 14935 10 mediumdys389i 2,68E-03 13788 11 mediumdys635 3,72E-03 7525 12 medium

dys389ii 3,78E-03 13759 13 mediumdys456 4,19E-03 6678 14 mediumdys481 4,97E-03 1744 15 mediumdys533 5.01E-03 1730 16 mediumdys439 5,35E-03 10096 17 mediumdys460 6,22E-03 1717 18 mediumdys458 6,74E-03 6677 19 mediumdys518 1,84E-02 1556 20 fast

dyf387S1ab 1,59E-02 1804 21 fastdys576 1,43E-02 1727 22 fastdys570 1,24E-02 1426 23 fastdys627 1,23E-02 1766 24 fastdys449 1,22E-02 1617 25 fast


Ranking of mutation rates (Yfiler® Plus)

Continental proportions of distinct haplotypes determined with slow, middle and fast mutating marker sets

N=18863 N=445 N=2829 N=11830 N=1183 N=2576Overall Africa Asia Europe Latin America North America

0%

10%

20%

30%

40%

50%

60%

70%

80%

90%

100%

continents

fast mut.middle mut.slow mut.


Increased discrimination

n=8066 n=10375 n=10945 n=16130 n=18118 N=18863MHT SWGDAM PPY12 Yfiler PPY23 sample size

0

18863


Local Y-STR diversity differs between continents


0

20000

40000

60000

80000

100000

120000

140000

rele

ase1 r3 r5

r8,9

r11

r13

r15

r17

r19

r21

r23

r25

r27

r29

r31

r33

r35

r37

r39

r41

r43

r45

Growth of the YHRD (2000-2014)

All haplotypes

Haplotypes 17 loci

Haplotypes with Y-SNPs

Haplotypes 23 loci


Choose the most informative haplotype format in the largest available database!

17 loci

0/19,593

0/71,246 1.4 x 10-5

5.1 x 10-5

260/125,700 2.1 x 10-3

23 loci

9 loci

Count frequency

Count EstimatesAugmented

1

1)|(ˆ 00 N

hShTP


Frequency estimation methods

Counting methods

• Augmented counting (1/n+1)

• Counting with database inflation (Brenners κ)

Methods taking evolutionary distance between haplotypes into account

• Surveying method (Krawczak)• Coalescence based

estimation (Caliebe)• Discrete Laplace method

(Andersen)


Case-sensitive workflow (touch DNA, mixture expected)

Autosomal analysis

Mixed female/male profile

Autosomal male profile clearly

identifiable

ReportNational Police

Database

Y chromosomal analysis

Male profile

Report

Direct matching possible?

Database (YHRD) frequency


Charité Pilot study to evaluate the workflow:40 sexual crimes with only „touch“ DNA (2011)

40 cases

8 casesIndividual male

autosomale profile

10 casesInformative

YSTR Profile

22 casesinconclusive

National Police Database

Report withYHRD match statistics Number of

informative profilesdoubled


Casework statistics since implementation of the PPY23 kit (08/2012 bis 02/2014)

160 cases (1038 contact stains)

29% (=14 delicts) with Y-Profil

Single source Y profile

(>20 Y-STRs)39%

Y-chromosomal

No Y profile (11%)

Y profile observed

(89%)

informative Y profile 58%

autosomal

No male admixture observed in the

Amelogenin system30%

Additional Y peak in Amelogenin

70%

37.5% informative for the male component


Case example 1: touch stain on fabric in a sexual assault case

• Vollständiges Y-chromosomales Einzelprofil in 23 loci

• Nur -Komponente, ohne Hinweis auf -♀ ♂

Beimischung im Amelogenin

Autosomale Analyse Y-chromosomale Analyse


- Yfiler + SNaPshot

- 9/16 Y-STRs detectable

- Haplogroup I (M170)©Charité – Universitätsmedizin Berlin, Dept. Forensic Genetics 2014

Case example 2: touch stain on fabric in a child abuse case

Haplogroup I (I2a) can also be reliably predicted from YHRD data


Case example 2 (continuing): Prediction of ancestry

Case example 3: Serial rape - linking 3 crime scenes

DYS389I

DYS448

DYS389II

DYS19

DYS391

DYS438

DYS437

DYS635

DYS390

DYS439

DYS392

DYS393

DYS458

DYS385ab

DYS456

GATAH4

Case1 13 19 29 14 10 12 15 24 22 12 13 13 17 11,14 16 12

Case2 13 19 29 nd 10 nd 15 nd nd nd nd 13 17 11,14 16 nd

Case 3 13+ 19+ 29+ 14+ 10+ 12+ 15+ 24 22+ 12+ 13+ 13 17 11,14+ 16+ 12+

DYS389I

DYS448

DYS389II

DYS391

DYS437

DYS393

DYS458

DYS385ab

DYS456

13 19 29 10 15 13 17 11,14 16

Suspect 12 19 27 11 15 13 16 11,14 14

Exclusion of the suspect

Consensus profile


Is NGS the future for complete resolution of male relatives ?


Next generation sequencing

• 13 generations• 10 Mb (of 24 MB NRY)

sequenced• 67 STRs identical• 4 SNPs different• Potentially long

sequence reads more variable than STRs

Xue Y, Tyler-Smith C 2009


Summary• Wider acceptance of forensic Y chromosome analysis due to a new generation of

diagnostic kits with high discriminative power and much improved performance• Complete resolution of distant relatives in most populations• a proportion of close relatives can be differentiated• Adaptation of the workflow, otherwise you‘re losing evidence!• Necessity to employ statistics (LR) to evaluate the match probability• Haplotype databases accomodate the profiles of the new generation kits (

www.yhrd.org)• Y-STRs are included in different National DNA Databases (USA, Netherlands,

Austria)

For Forensic or Paternity Use Only. Yfiler is a trademark of Thermo Fisher Scientific and its subsidiaries.


http://www.yhrd.org/

Disclaimers

For Forensic or Paternity Use Only. Yfiler is a trademark of Thermo Fisher Scientific and its subsidiaries.

the golden age of forensic y-str typing – new markers, new databases, new technologies lutz...

Documents

dys549 x x dys643 x

medium dys456

medium dys458

medium dys635

medium dys439

medium ygatah4

medium dys460

medium dys481