International Journal of Legal Medicine

, Volume 127, Issue 2, pp 369–372

Mutation rates at 16 Y-chromosome STRs in the South China Han population

Authors

  • Weixia Weng
    • Institute of Forensic MedicineSouthern Medical University
  • Hong Liu
    • Guangzhou Forensic Institute
  • Shuanglin Li
    • Guangzhou Forensic Institute
  • Jianye Ge
    • Institute of Applied Genetics, Department of Forensic and Investigative GeneticsUniversity of North Texas Health Science Center
  • Huijun Wang
    • Institute of Forensic MedicineSouthern Medical University
    • Institute of Forensic MedicineSouthern Medical University
    • Guangzhou Forensic Institute
Short Communication

DOI: 10.1007/s00414-012-0786-3

Cite this article as:
Weng, W., Liu, H., Li, S. et al. Int J Legal Med (2013) 127: 369. doi:10.1007/s00414-012-0786-3
  • 301 Views

Abstract

Nine hundred eighteen DNA-confirmed father–son pairs were typed for 16 Y-chromosomal short tandem repeat (Y-STR) markers by AmpFLSTR® Yfiler™ PCR Amplification kit. In a total of 15,606 allele transmissions, 36 mutations were detected. The average mutation rate across all 16 Y-STR markers was 0.0023 (95 % confidence interval, 0.0016–0.0032). One two-step mutation was found at DYS389II, and all other mutations were single steps. The losses and gains were balanced at all other loci, excluding DYS385 and DYS458, where losses were more frequent than gains. Mutation rates among different Y-STR loci were significantly different (Χ2 = 69.05, P = 0.000). Mutation rates were correlated with the lengths of the alleles. Alleles with higher number of repeats were more likely to mutate. Mutation rates were also correlated with the gene diversity of the locus (r2 = 0.565, P = 0.023). Loci with higher gene diversity had higher mutation rates. In addition, the mutation rate of the older father was found to be notably higher than that of the younger father.

Keywords

Y-STRsMutation ratesSouth China Han population

Introduction

Y-chromosomal short tandem repeat (Y-STR) loci are inherited from fathers to sons and have been widely used in forensic investigations to test the paternal lineages [1, 2]. AmpFLSTR® Yfiler™ PCR Amplification kit is one of the most commonly used kits for Y-STR typing, which includes 16 Y-STR markers or 17 Y-STR loci (i.e., DYS19, DYS385a/b, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, and Y-GATA-H4). Because of relatively high mutation rates of Y-STR loci, Y-STR profiles with a few mismatched may be still from the same paternal lineage. Thus, the interpretation of Y-STR profiles matching depends on accurate estimation of the mutation rates. Y-STR mutation rates have been reported for the 16 Y-STR markers in Yfiler™ for many different populations [14], but very few studies have been done for the Chinese populations. In this study, we report the mutation rates of the 16 Y-STRs in Yfiler™ for China Han population by investigating 918 father–son pairs which were collected from South China.

Materials and methods

Blood samples and saliva swabs of 918 father–son pairs were collected from the Verification Centre of Forensic Medicine in the Southern Medical University, China. All father–son pairs were confirmed by autosomal STRs testing with a minimum paternity probability of 99.95 %. Written informed consent forms were signed by all participants involved in the study. The samples were amplified using 17 loci by AmpFLSTR® Yfiler™ PCR Amplification kit following manufacturer’s recommendations. Allele separation and detection were performed in an ABI 3130xl with GeneMapper 3.2 software.

Result and discussion

In this study, 918 meiosis from fathers to sons were observed, in which 36 mutations were found at DYS458, DYS439, DYS385a/b, DYS389II, DYS390, DYS635, and DYS456 (Table 1). Only one father–son pair had two mutations at two different markers (i.e., 30→29 at DYS389II; 13→12 at DYS385a/b). Except one double-step mutation occurred at DYS389II, all remaining mutations were single step, namely, 97.2 % mutations were one step. Among these 36 mutations, 11 mutations (i.e., 30.6 %) gained repeats, and 25 mutations (i.e., 69.4 %) lost repeats. The ratio of repeat gains and losses was different from some previous literatures [2, 3, 5], which was mainly due to unbalanced losses and gains at DYS385 and DYS458. Excluding these two loci, the proportions of losing and gaining repeats were balanced, namely, 47.4 % and 52.6 %, respectively.
Table 1

The mutations and mutation rates of the 16 Y-STR markers

 

No. of meiosis

No. of mutations

No. of mutations with repeat gains

No. of mutations with repeat losses

No. of single-repeat mutations

No. of two-repeat mutations

Mutation rate

95 % confidence interval

Y-STR locus

 DYS19

918

     

0.0000

0.0000–0.0004

 DYS389I

918

     

0.0000

0.0000–0.0004

 DYS389II

918

5

2

3

4

1

0.0054

0.0018–0.0127

 DYS390

918

3

2

1

3

 

0.0033

0.0007–0.0095

 DYS391

918

     

0.0000

0.0000–0.0004

 DYS392

918

     

0.0000

0.0000–0.0004

 DYS393

918

     

0.0000

0.0000–0.0004

 DYS385a/b

1,836

9

1

8

9

 

0.0049

0.0022–0.0093

 DYS438

918

     

0.0000

0.0000–0.0004

 DYS439

918

7

3

4

7

 

0.0076

0.0031–0.0156

 DYS437

918

     

0.0000

0.0000–0.0004

 DYS448

918

     

0.0000

0.0000–0.0004

 DYS456

918

2

1

1

2

 

0.0022

0.0003–0.0078

 DYS458

918

8

1

7

8

 

0.0087

0.0045–0.0185

 DYS635

918

2

1

1

2

 

0.0022

0.0003–0.0078

 Y-GATA-H4

918

     

0.0000

0.0000–0.0004

Total

15,606

36

11

25

35

1

0.0023

0.0016–0.0032

The average mutation rate across these 16 Y-STR markers was 0.0023 (95 % confidence interval (CI), 0.0016–0.0032), which was close to the mutation rates of the Texas populations (i.e., 0.0021) by Ge et al. [5] and the Rotterdam population (i.e., 0.0025) by Goedbloed et al. [3]. The mutation rates of the 16 Y-STR markers ranged from 0.0000 (95 % CI, 0.0000–0.0004) at DYS19 to 0.0087 (95 % CI, 0.0045–0.0185) at DYS458. The mutation rates of the individual loci were significantly different (χ2 = 69.059, df = 15, P values (two tailed) = 0.000). Gene diversity of the 16 Y-STR markers ranged from 0.3723 (DYS391) to 0.9549 (DYS385a/b). The gene diversity and the locus-specific mutation rate were positively correlated (r2 = 0.565, P value = 0.023), which means that the loci with higher polymorphism are prone to mutate. These mutation rates and their 95 % confidence intervals were also compared with the cumulative mutation rates from multiple studies in YHRD [4] (Table 2). All confidence intervals were overlapped, and no significant difference (P values (two tailed) = 0.398) was found.
Table 2

Comparison between the mutation rates of this study and the cumulative mutation rates in YHRD

Y-STR locus

This study

95 % confidence interval

YHRD

95 % confidence interval

DYS19

0.0000

0.0000–0.0040

0.0023

0.0016–0.0032

DYS389I

0.0000

0.0000–0.0040

0.0025

0.0017–0.0035

DYS389II

0.0054

0.0018–0.0127

0.0036

0.0027–0.0048

DYS390

0.0033

0.0007–0.0095

0.0021

0.0014–0.0030

DYS391

0.0000

0.0000–0.0040

0.0026

0.0018–0.0036

DYS392

0.0000

0.0000–0.0040

0.0004

0.0002–0.0009

DYS393

0.0000

0.0000–0.0040

0.0010

0.0006–0.0018

DYS385a/b

0.0049

0.0022–0.0093

0.0021

0.0016–0.0028

DYS438

0.0000

0.0000–0.0040

0.0003

0.0000–0.0009

DYS439

0.0076

0.0031–0.0156

0.0052

0.0039–0.0068

DYS437

0.0000

0.0000–0.0040

0.0012

0.0006–0.0021

DYS448

0.0000

0.0000–0.0040

0.0016

0.0007–0.0029

DYS456

0.0022

0.0003–0.0078

0.0042

0.0028–0.0062

DYS458

0.0090

0.0045–0.0185

0.0064

0.0046–0.0087

DYS635

0.0022

0.0003–0.0078

0.0035

0.0022–0.0051

Y-GATA-H4

0.0000

0.0000–0.0040

0.0024

0.0014–0.0038

P values (two tailed) = 0.398

To estimate the relationship between the sizes of alleles and the corresponding mutation rates, the alleles of each locus were categorized into short, moderate, and long alleles (roughly 25, 50, and 25 %, respectively) according to the number of repeats of the alleles, using the method described in Ge et al. [5] (Table 3). The mutation rates of the long alleles (0.0130; 95 % CI, 0.0067–0.0225) were significantly higher than those of the short (0.0010; 95 % CI, 0.0000–0.0058) and moderate (0.0019; 95 % CI, 0.0012–0.0028) alleles. Therefore, the longer alleles are more likely to mutate, compared with the shorter alleles at each locus, which is consistent with the findings in previous studies [3, 6, 7].
Table 3

Mutation counts and rates by allele repeat size (the number of repeats)

 

Short

Moderate

Long

Y-STR locus

 DYS19

   

 DYS389I

   

 DYS389II

 

4

1

 DYS390

  

3

 DYS391

   

 DYS392

   

 DYS393

   

 DYS385a/b

 

6

3

 DYS438

   

 DYS439

1

5

1

 DYS437

   

 DYS448

   

 DYS456

 

1

1

 DYS458

 

5

3

 DYS635

 

2

 

 Y-GATA-H4

   

No. of mutations

1

23

12

No. of alleles

966

12,277

925

Mutation rate

0.0010

0.0019

0.0130

95 % CI

0.0000–0.0058

0.0012–0.0028

0.0067–0.0225

We also observed one sample with two alleles (i.e., 30 and 32) at DYS389II, seven samples with tri-allele patterns at DYS385a/b [i.e., (13, 18, and 19) in three samples; (13, 17, and 18) in one sample; (13, 18, and 20) in one sample; (12, 13, and 18) in one sample; (13, 17, and 19) in one sample], and one sample with four alleles (i.e., 11, 13, 17, and 18) at DYS385a/b. Off-ladder alleles were also observed at seven different loci (i.e., DYS458, DYS448, DYS438, DYS391, DYS456, DYS385a/b, and Y-GATA-H4) in 24 different samples (Table 4). In Table 4, the alleles that exceed the boundaries of the allelic ladders were designated by extrapolation using the nomenclature recommended in the ISFG guideline [8]. It would be better to have wider allelic ladders to fit in these newly observed alleles.
Table 4

Off-ladder alleles found in the South China Han population

ID

Locus

Allele of father

Allele of son

Ladder

A11-86

DYS458

13

13

14~20

FS105

DYS458

13

13

14~20

A11-186

DYS458

21

21

14~20

FS317

DYS458

21

21

14~20

FS61

DYS458

21

21

14~20

A10-1029

DYS458

21

21

14~20

A11-1060

DYS458

21

21

14~20

FS15

DYS458

21

21

14~20

A11-749

DYS458

21

21

14~20

A11-686

DYS458

21

21

14~20

A11-894

DYS458

21

21

14~20

A11-726

DYS458

18.2

18.2

14~20

A11-622

DYS458

22

22

14~20

FS167

DYS448

13

13

17~24

A10-0910

DYS448

18.2

18.2

17~24

A11-1059

DYS448

19.2

19.2

17~24

A11-67

DYS438

6.3

6.3

8~13

A11-716

DYS438

9.2

9.2

8~13

FS16

DYS391

6

6

7~13

A11-455

DYS391

6

6

7~13

A11-627

Y-GATA-H4

15

15

8~13

A11-859

Y-GATA-H4

14

14

8~13

A10-1076

DYS385

13,27

13,27

7~25

FS255

DYS456

12

12

13~18

Further, the correlation between the mutation rate and the age of the father when the child was born was investigated. Among the 918 fathers, the ages of 625 fathers were known. The mean age of the fathers in the father–son pairs with mutation was 32.69 years, which was slightly higher than the mean age of the fathers without mutation at 32.05 years. However, the mutation rate of the older father was notably higher than that of the younger father (Table 5), which is consistent with a previous study [9].

This is the first study to provide the mutation rates of the 16 Y-STR markers included in AmpFLSTR® Yfiler™ kit for the Han population in South China, which can be very useful in kinship analysis and familial searching for the forensic investigations in China.
Table 5

Father’s age and mutation rates

Age of fathers

Allele transmission

No. of mutation

Mutation rate

95 % CI

17–29

4,777

7

0.0015

0.0006–0.0030

30–70

5,848

19

0.0032

0.0020–0.0051

Conflict of interest

None.

Copyright information

© Springer-Verlag Berlin Heidelberg 2012