This document discusses a study that analyzed 23 Y-STR loci in a sample of 132 unrelated Bangladeshi males to generate a Y-STR allele frequency database for the Bangladeshi population. DNA was extracted from blood samples and amplified via PCR. Capillary electrophoresis was used to generate DNA profiles of the 23 Y-STR loci. Allele frequencies were calculated and all 132 samples had unique haplotypes. The most and least polymorphic loci were identified. Comparisons were made to a previous study on the Bangladeshi population and a study of Bosnia and Herzegovina. The study aimed to characterize Y-STR polymorphisms in Bangladeshis and create a forensic database.

1. Presented by
Niaz Faisal
Examination Roll No. : 1515
Reg. No. : HA-2061
M. S. Session: 2013-14

2. Backgrounds
 STRs or microsatellite based DNA typing; powerful tool
 Human identification
 Relationship testing
 Population genetics studies
 Y-STRs and mitochondrial DNA markers; known as ‘lineage markers’.
 15-23 Y-STR markers are appear in commercial kits.
 PCR amplification of 23 Y-STR loci in multiplex approach, followed by
capillary electrophoresis.
 Y-STR allele frequency database represent the studied population
where the tested individuals belong.

3. Y Chromosome Short Tandem Repeats
(Y-STRs)
 2-6 bp long.
 Highly polymorphic.
 Easily amplified by PCR
 Small size allows multiplexing tagged with fluorescence
detection.
 Repeat motifs may be simple, complex or compound.
 Y chromosomes are passed down from generation-to-generation
(except mutation).

4. Objectives of the Study
 To detect the polymorphisms of 23 Y-chromosomal short tandem
repeat (STR) loci.
 To generate a population data.
 To create a database for calculating forensic efficiency parameters
utilized in the judiciary systems.
 To robust the assay for accurate characterization of Y markers.

5. Importance of the Study
 Y-STRs; powerful forensic tools
 Paternity testing
 Sexual assault cases
 Superior to autosomal systems.
 To determine the biogeographical ancestry of human
population.
 For genealogy analysis.
 Identification of missing persons or mass disaster
investigations (i.e. Rana Plaza Tragedy, BDR Revolution).

6. Overview of 23 Y-STR loci
Markers Repeat Motifs Allele Range
DYS576 AAAG 13-21
DYS389I (TCTG) (TCTA) 9-17
DYS448 AGAGAT 17-24
DYS389II (TCTG) (TCTA) 24-34
DYS19 TAAT (CTAT) 9-12
DYS391 TCTA 6-14
DYS481 CTT 20-30
DYS549 AGAT 10-14
DYS533 ATCT 9-14
DYS438 TTTTC 6-14
DYS437 TCTA 13-17
DYS570 TTTC 12-23
DYS635 TSTA compound 17-27
DYS390 (TCTA) (TCTG) 17-28
DYS439 AGAT 9-14
DYS392 TAT 6-17
DYS643 CTTTT 7-15
DYS393 AGAT 9-17
DYS458 GAAA 13-20
DYS385a/b GAAA 7 - 28
DYS456 AGAT 13-18
YGATAH4 TAGA 8-13 (25-30)

7. Relative positions of 23 Y-STR Markers

8. Methods & Materials
Study Population
Blood samples were collected from 132 randomly selected,
unrelated Bangladeshi male.

9.  Centrifuged at 10,000-15,000g for 3 minutes
 Removed supernatant
 5% Chelex (pH 9-11) was added up to final volume 200μl
 Mild vortexing and spinning
 Centrifuged at 10,000-15,000g for 3 minutes
100-120μl supernatant was transferred
DNA in solution
Precipitated protein
& Chelex-100 resin
ssDNA in solution
Precipitated
lymphocytes (~20μl)
Genomic DNA Extraction
1.0ml of TE buffer containing 1.5ml eppendorf tube with 300.0μl of whole blood
 Incubated at room temperature for 30 minutes
Quantitation by NanodropTM 1000 Spectrophotometer

10. Workflow
PCR Setup
• For amplification of DNA, PCR setup was done according
to the protocol provided by the Promega Corporation.
PCR
Amplification
of STR Loci
• PCR Amplification was done by Veriti® 96-Well Thermal
Cycler & GeneAmp® PCR System 9700 thermal cycler.
Veriti® 96-Well Thermal Cycler

11. Workflow
3500 Genetic Analyzer
Data Collection Software V 1.0
GeneMapper ID-X Software V 1.2
Capillary Electropherogram
(Graphical Output)
Y-STR DNA Profile
Locus
DYS576
DYS389I
DYS448
DYS389II
DYS19
DYS361
DYS549
DYS533
DYS438
DYS437
DYS570
DYS635
DYS390
DYS439
DYS392
DYS643
DYS393
DYS458
DYS385a/b
DYS456
YGATAH4
Allele
18
14
19
30
15
10
11
12
9
14
17
22
22
13
11
11
12
17
16,17
15
12

12. Calculation
Allele Frequency
Gene or Haplotype Diversity
No. of allele at a particular locus/N, Where N = Total no. of
individuals.
D = n/ (n-1) (1-∑Pi2), Where Pi is the frequency of the i’th
allele, n indicates the total no. of individuals and D for gene
or haplotype diversity (Hardy-Weinberg equilibrium).

17. Discussion
 Y-STRs are referred to as a haplotype rather than a genotype.
 Forensic DNA laboratories rely on Y-STR analysis
 Identification of male-specific DNA
 Ambiguous cases
 This project established a database (YHRD Accession # YA003445;
Population ID: YP000509) of Bangladeshi population.
 Y-STR database will provide a greater evaluation parameters
 To solve the forensic caseworks
 Future research works.

18. Comparative Study with Previous
Relevant Investigations
211 different haplotypes identified on a previous Y-STR study (17 loci )
on Bangladeshi population
 216 samples
 206 were individual specific
 5 were found in two individuals
In this study (17 loci + 6 additional loci )
 All 132 were unique haplotypes
“By increasing the number of STR loci, the number of unique haplotypes
increases and the number of repetitions decreases”

19. Comparative Study with Previous
Relevant Investigations
Furthermore, in that previous study,
 Highest gene diversity: DYS385 (0.9315)
 Lowest gene diversity: DYS391 (0.4105)
In our study,
 Highest gene diversity: DYS385 (0.9453)
 Lowest gene diversity: DYS391 (0.3027)

20. Comparative Study with Previous
Relevant Investigations
A recent Y-STR study on Bosnia and Herzegovina (23 loci),
 100 samples
 98 unique haplotypes
 Only one repetition
 Most polymorphic loci: DYS481
 Least polymorphic loci: DYS391, DYS389I, DYS437 and DYS393
In our study (23 loci),
 All 132 were unique haplotypes
 Most polymorphic loci: DYS385a/b
 Least polymorphic loci: DYS 391, DYS437

21. Conclusion
Number of total different alleles: 64 alleles
Polymorphisms:
 Most polymorphic loci: DYS385a/b (35 alleles)
 Least polymorphic loci: DYS 391, DYS437 (4 alleles)
Allele Frequency:
 Highest allele frequency: Allele 10 for DYS391 locus (0.8258)
 Lowest allele frequency: DYS385a/b (0.0076)
Gene or Haplotype diversity:
 Highest gene diversity: DYS385a/b locus (0.9453)
 Lowest gene diversity: DYS391 locus (0.3027)

22. Thank You All