Legal Medicine 12 (2010) 208–211

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Legal Medicine
journal homepage: www.elsevier.com/locate/legalmed

Brief Communication

A Japanese-speciﬁc allele in the GALNT11 gene
Isao Yuasa a,*, Kazuo Umetsu b, Aya Matsusue c, Hiroaki Nishimukai d, Shinji Harihara e, Yasuo Fukumori f,
Naruya Saitou g, Feng Jin h, Prasanta K. Chattopadhyay i, Lotte Henke j, Jürgen Henke jaDivision of Legal Medicine, Faculty of Medicine, Tottori University, Yonago 683-8503, Japan
Department of Forensic Medicine, Faculty of Medicine, Yamagata University, Yamagata, Japanc
Department of Forensic Medicine, Fukuoka University School of Medicine, Fukuoka, Japand
Division of Legal Medicine, Ehime University School of Medicine, Ehime, Japane
Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japanf
Osaka Red Cross Blood Center, Osaka, Japang
Division of Population Genetics, National Institute of Genetics, Mishima, JapanhInstitute of Psychology, Chinese Academy of Sciences, Beijing, Chinai
Amity Institute of Forensic Sciences, Defence Colony, New Delhi, IndiajInstitut für Blutgruppenforschung, Cologne, Germanyb

a r t i c l e

i n f oArticle history:
Received 15 February 2010
Received in revised form 29 March 2010
Accepted 4 April 2010
Available online 23 May 2010
Keywords:
Ancestry-informative markers (AIMs)
Genotyping
Single nucleotide polymorphism (SNP)
Population-speciﬁc
Population studya b s t r a c t
In this study, ﬁve single nucleotide polymorphisms (SNPs) in the ABCC4, FBN1, CEP152, ZNF804B, and GALNT11 genes were investigated to assess allele frequencies in 14 different populations by a novel pentaplex
PCR method. All SNPs were polymorphic in East Asians, whereas mutant alleles were absent or rare in
non-East Asians. The frequencies of a mutant allele in FBN1 (rs140598) showed a north–south downward
cline in East Asia, whereas those of a mutant allele in ZNF804B (rs1916830) were relatively uniform in
East Asia. The highest frequencies of mutant alleles in ABCC4 (rs3765534), CEP152 (rs2289178), and GALNT11 (rs3778922) were observed in Okinawa. The mutant allele in GALNT11 was found only in Far-East
Asian populations: the frequencies were about 0.153 in Okinawa, 0.076 in the main island of Japan, and
0.017–0.004 in Korea. These ﬁve East Asian- and Japanese-speciﬁc SNPs would be useful markers forforensic individualization, in particular, as ancestry-informative markers.
Ó 2010 Elsevier Ireland Ltd. All rights reserved.

1. Introduction
Inference of the ancestry and population to which an individual
belongs is an important aspect of forensic individualization. Information about the ancestry of the perpetrator of a crime in the absence of eyewitness evidence and of victims in disasters isinvaluable. Genetic markers with a geographically restricted distribution, or with marked allele frequency differences between two
regions, are effective for this purpose. Short tandem repeat (STR)
polymorphisms have successfully been applied to forensic individualization, because they are the most variable types of DNA sequence in the genome. Increases and decreases in repeat number
arise from replication slippage, which can occur in every humanpopulation. Regionally private STR alleles with a frequency above
0.02 have sometimes been detected on autosomal chromosomes.
However, only a few alleles with a frequency above 0.13 have been
observed [1–3]. In contrast, single nucleotide polymorphisms* Corresponding author. Tel.: +81 859 38 6123; fax: +81 859 38 6120.
E-mail address: yuasai@med.tottori-u.ac.jp (I. Yuasa).
1344-6223/$ - see front matter Ó 2010 Elsevier Ireland Ltd. All rights reserved.
doi:10.1016/j.legalmed.2010.04.001(SNPs) sometimes show signiﬁcant differences in allele frequency
among human populations. Such population-speciﬁc alleles are
known as ancestry-informative markers (AIMs) [4,5]. The distribution patterns of allele frequencies are also useful for evolutionary
elucidation of population migration. Some of these alleles havespread by positive selection and are associated with physical traits
such as skin pigmentation [6]. In East Asia, genetic differentiation
between northern and southern populations has been observed
using classic and DNA markers [7]. Japanese from the main islands
and those from Okinawa were distinguished using 140 K SNPs [8].
Japanese-speciﬁc alleles are powerful for the characterization of aforensic sample as being of Japanese origin, but only a few alleles
have been identiﬁed to date. In this study, ﬁve SNPs in the ABCC4,
FBN1, CEP152, ZNF804B, and GALNT11 genes were investigated,which are known to be polymorphic in Japanese and Chinese populations, but are shown to be monomorphic in people of European
descent and the Yoruba people of the international HapMap project. To assess allele frequencies for the ﬁve SNPs in 14 different
populations, a novel simultaneous genotyping method was developed, based on the pentaplex PCR. Of the ﬁve mutant alleles, an allele in the GALNT11 gene was shown to be Japanese-speciﬁc.

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I. Yuasa et al. / Legal Medicine 12 (2010) 208–211

2. Materials and methods

3. Results and discussion

2.1. DNA samples

Fig. 1 shows the band patterns of the products obtained by pentaplex PCR. The nucleotide substitutions were clearly and unambiguously detected as bands of different sizes. The sizes ranged
from 70 bp for GALNT11*G to 119 bp for ABCC4*A. Simultaneous
genotyping by the present pentaplex PCR method is advantageousfor investigating genotypes, because the amplicons at every locus
are obtained by only one ampliﬁcation without sampling errors.
In addition, this method is technically simple and inexpensive
and does not require specialized instruments.
We genotyped ﬁve SNPs in 1541 individuals from the 14 populations. The frequencies of the mutant allele at each locus areshown in Table 1. In each locus, there was no statistically signiﬁcant departure from Hardy–Weinberg equilibrium except for the
CEP152 locus in Han Chinese at Huizhou (p = 0.0356), where theobserved numbers of the homozygous types were increased, but
the reason for this was unknown. The allele frequencies in our African, German, Chinese, and Japanese samples were similar to thosein the SNP database. The results conﬁrmed marked differences infrequency between East Asian and non-East Asian populations.
Some mutations in the FBN1 gene are associated with Marfan
syndrome and aortic aneurysm, but FBN1*G (p.1148A) is innocent
for these diseases [15]. Buryats and Mongolians showed the highest frequencies for this allele among the 14 populations investigated in this study. The frequencies were higher in the northernparts of East Asia than in the southern parts. There was a signiﬁcant correlation between allele frequencies and the degree of latitude in 9 East Asian populations (r = 0.935, p < 0.001), showing anorth–south downward cline in East Asia. ZNF804B is one of thezinc ﬁnger proteins, and its function has not well been characterized. ZNF804B*A showed a relatively uniform distribution in East
Asia, with frequencies ranging from 0.35 in Okinawa to 0.49 in Tottori. Multiple drug resistance protein 4 (MRP4), the product of the
ABCC4 gene, mediates some form of xenobiotic transport and/or
drug resistance. ABCC4*A (p.757 K) exhibits a 10% reduction in
the level of protein expression and 20% higher transporter activities in comparison with the wild type [16]. ABCC4*A was mainly
found in East Asian populations, and its frequency was somewhat
higher in the northern parts of East Asia than in the southern parts.
Interestingly, the highest frequencies were observed in Japan, in

DNA samples were obtained from 1541 unrelated individuals
living in various areas of Eurasia and South America and were used
for a population study. Sub-Saharan African (Nigerian and Ghanaian) and Turkish samples were collected from people residing inGermany (Table 1). Most of these samples were from a set usedin previous studies [9–12], where the geographical locations of
the investigated populations were also shown. This study was approved by the Ethical Committee at the Faculty of Medicine, Tottori
University.
2.2. Genotyping procedure
Five SNPs, rs3765534, rs140598, rs2289178, rs1916830, andrs3778922, were investigated as shown in Table 1. These SNPs
were simultaneously genotyped by pentaplex PCR based on theampliﬁed product length polymorphism (APLP) method [9–12].
The nucleotide sequence and ﬁnal concentration of each primer
are shown in Table 2. The PCR cocktail consisted of 50 ll ofMultiplex PCR Master Mix from a Multiplex PCR Kit (Qiagen,Hilden, Germany), 8.25 ll of 15 primers with a concentration of
100 pmol/ll, and 41.75 ll of water. PCR was performed in a volume of 8 ll containing 7.5 ll of the PCR cocktail and 0.5 ll of asolution containing 10–20 ng of genomic DNA. The cycle conditions were 95 °C for 15 min; then 30 cycles of 94 °C for 10 s,
54 °C for 10 s, 72 °C for 10 s, and a ﬁnal extension step of 15 min
at 72 °C. The products were separated using a polyacrylamide gel(9%T, 5%C) together with positive and negative controls and thenvisualized by ethidium bromide staining.
2.3. Statistical analysis
The estimation of allele and haplotype frequencies and population pairwise FST, and testing of Hardy–Weinberg equilibrium andlinkage disequilibrium were carried out using the Arlequin program ver. 3.11 [13]. The statistics D0 and r2 values were measured
according to Hartl and Clark [14].
Table 1Frequencies of the mutant alleles in 14 populations with data from the HapMap project.
No.

Population

n

ABCC4
3q32
rs3765534
exon 18c.2269GAG>AAG
Glu757Lys

FBN1
15q21.1
rs140598
exon 28
c.3442
CCC>GCC
Pro1148Ala

CEP152
15q21.1
rs2289178
exon 18
c.2378
AGC>ATC
Ser793Ile

ZNF804B
7q21.13
rs1916830
exon 4c.743
TGT>TAT
Cys248Tyr

GALNT11
7q34-q36
rs3778922
exon 5c.589
GAT>TAT
Asp197Tyr

1
2
3
4
5
6
7
8
9
10
11
12
13
14

AfricanGermanTurk
IndianBuryatMongolian
Korean (Seoul)
Korean (Kwangju)
Japanese (Tottori)
Japanese (Okinawa)
Han (Wuxi)
Han (Huizhou)
Thai
ColumbianAfrican (YRI)
Caucasian (CEU)
Japanese (JPT)Han Chinese (CHB)

68
92
109
107
108
120
140
144
131
88
119
111
111
93
53–60
53–60
42–45
42–45

0
0.01090.00920.06070.08330.12920.08930.09030.14120.23300.04200.05410.04500.0215
0
0
0.2
0.067

0.007400.00920.01400.40280.36670.28930.29170.28630.27270.24370.22970.20270.0430
0.009
0
0.393
0.214

0
0
0.00460.00930.13430.08750.11430.12150.29010.36360.1261
0.19820.21620.1935
0
0
0.4
0.133

0.00740.00540.0413
0.09350.38890.42920.47860.44440.48850.35230.4202
0.46850.39640.4140
0.025
0.017
0.489
0.433

0
0
0
0
0
0
0.00360.01740.07630.1534
0
0
0
0
0
0
0.114
0

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I. Yuasa et al. / Legal Medicine 12 (2010) 208–211

Table 2
PCR primers for simultaneous typing of 5 SNPs and their ﬁnal concentrations.

*

SNP

Primer name

Sequence (50 ?30 )*Final concentration (lM)

rs3765534

ABCC4-FA2
ABCC4-FG
ABCC4-R2

tatattATGGAGGAGGAAATGTtACCATGGAGGAGGAAATGTAtCCG
TCATTGTAAGCACCTCAGCC

0.45
0.6
0.6

rs140598

FBN1-F
FBN1-RG
FBN1-RCaCTCTCCTATGCCGAGGTG
tatatTACACGCGGAGATGTTaGC
TACACGCGGAGATGTTtGG

0.5
0.5
0.5

rs2289178

CEP152-F
CEP152-RT
CEP152-RG

ttAAGGAGTGGCAGTCTAAGCTG
tataTGGTTACTTGGTCAGaTTGGATGGTTACTTGGTCAGTTaGGC

0.2
0.2
0.2

rs1916830

ZNF804B-FA
ZNF804B-FG
ZNF804B-R

atatACACAGAAGAAACCCAaGATTAACACAGAAGAAACCCATGtTTG
tCTGCAGCACTTGCACTTATC

0.9
0.6
0.6

rs3778922

GALNT11-FT
GALNT11-FG
GALNT11-R

attaAATTGTGGGACTTTATTTTCtGATT
AATTGTGGGACTTTATTTTCAGtTG
CAGGGAGGTATTTTTGGACAT

1.2
0.6
0.6

Lowercase letters indicate noncomplementary nucleotide.

Fig. 1. Simultaneous genotyping of the ﬁve SNPs by pentaplex PCR based on the
APLP method. Lane M: 25-bp ladder.

particular, in Okinawa where a high frequency of 0.23 was observed. The association between the prevalence of this allele in
Okinawa and the expression level or functional activities of the
MRP4 variant is unknown. CEP152, a centrosomal protein of
152 kDa, is essential for cilia formation [17]. GALNT11, one of the
UDP-N-acetylgalactosamine:polypeptide N-acetylgalactosaminyltransferases, is expressed only in kidney [18]. Although the significance of amino acid substitutions in these proteins is unknown,
CEP152*T and GALNT11*T also showed the highest frequencies in
Okinawa. GALNT11*T was found only in Far-East Asian populations.
The frequencies were about 0.153 in Okinawa, 0.076 in Tottori, and
0.017–0.004 in Korea. Thus, this allele was nearly restricted toJapanese.
The FST values, obtained by comparisons between German andJapanese (Tottori) populations, ranged from 0.437 for ZNF804B to
0.061 for GALNT11. FBN1 and CEP152 are adjacent to each otheron chromosome 15q21.1, and the two polymorphisms were foundto be in signiﬁcant linkage disequilibrium in ﬁve populations,
including Buryat, Korean (Kwangju), Japanese (Tottori and Okinawa), and Han (Huizhou) populations. However, the low r2 values
suggested that linkages between them were relatively weak.
Although both ZNF804B and GALNT11 are located on chromosome
7q, signiﬁcant linkage disequilibrium was not observed between
them in any populations. The haplotype frequencies and D0 andr2 values are shown in Appendix A. The frequencies of people having at least one of ﬁve mutant alleles ranged from 0.029 in Africans
to 0.971 in Japanese (Okinawa) (Appendix A).
There are three different hypotheses regarding the origins ofEast Asian populations: (i) South East Asian origin, (ii) North Asianorigin, and (iii) a combination of northern and southern origins [7].
This suggests at least two main centers of human expansion andmigration in East Asia. East Asian-speciﬁc alleles, rs17822931*A at
ABCC11 and rs3827760*C at EDAR, which are associated with ear
wax type and hair thickness, respectively, are more frequent in
the northern parts of East Asia, where they are nearly ﬁxed
[19,20]. OCA2*481Thr, which exhibits a 70% of the function of thewild type allele in terms of melanogenesis, was also found almost
exclusively in the northern parts of East Asia [10]. A north–south
downward cline of FBN1*G frequency observed in East Asia reﬂects
the migration and expansion of ancient North East Asians. Somemutants in the HERC1 gene have frequencies as high as about 0.9
in East Asians, but only about 0.1 in sub-Saharan African and German populations [12]. Similarly, ZNF804B*A was distributed uniformly in East Asia, with a relatively high FST value between
Japanese in Tottori and Germans. ABCC4*A, CEP152*T, and GALNT11*T showed the highest frequencies in Okinawa. It is suggested
that ABCC4*A and CEP152*T spread into the Japanese archipelago
before the Neolithic Yayoi period (300 BC–300 AD). According toa dual structure model [21], modern Japanese are the result of anintermixture between the upper Paleolithic native population ofJapan (Jomon people) and migrants from northeast Asia who
passed through the Korean peninsula during the Neolithic Yayoi
period. A representative Jomon allele, YAP+(M1) on the Y chromosome, is observed at a frequency of 0.556 in Okinawa, whereas it isobserved at frequencies of 0.257–0.385 in the main islands of Japan. This allele is absent or low in other East Asians except forsome populations including Tibetans [22,23]. The high frequenciesof ABCC4*A and CEP152*T in Okinawa may reﬂect a smaller degreeof migration of Yayoi ancestors to Okinawa. It is also possible thatthese two alleles have been maintained at high frequencies in Japanese populations partly through genetic drift during and after
migration from the Asian continent to Japan.
Only a few Okinawa-speciﬁc alleles have been identiﬁed.
AHSG*5 in the alpha2-HS-glycoprotein gene is polymorphic in Okinawa with a frequency of 0.026, whereas it is quite rare or absent
in other populations [24]. Some Japanese-speciﬁc alleles have beenfound. The fusion gene (sefus) at the ABO-secretor locus (FUT2) was
found in the Japanese populations with relatively high frequencies
ranging from 0.048 to 0.079 in the main islands of Japan to 0.055 in
Okinawa. This allele was found to be rare in a Korean population(0.006) and absent in two Chinese populations. This mutation
was suggested to have arisen in the Japanese archipelago [25]. Recently, we also found a Japanese-speciﬁc allele in the complement
factor I (CFI) gene. CFI*As was detected with a frequency of 0.03 inI. Yuasa et al. / Legal Medicine 12 (2010) 208–211

two main island Japanese populations, whereas it was found to berare in a Japanese population in Okinawa (0.006) and among Korean populations (0–0.007) [11]. The frequency of GALNT11*T in Japanese populations was found to be 0.076–0.153, whereas it was
found to be 0.004–0.017 in Korean populations and absent in otherpopulations. The frequency in the Japanese populations was about
tenfold higher than that in the Korean populations. Evidently,
GALNT11*T is a unique allele showing a high frequency in Okinawa.
These ﬁndings suggest that GALNT11*T emerged in Japanese living
in Okinawa after the divergence of the Japanese–Korean groupfrom other populations and then very recently entered into the
Korean populations. Conversely, GALNT11*T as well as the fusion
gene (sefus) may have arisen in the Korean peninsula. This new
mutation could have spread to the Japanese islands through a phenomenon called allelic surﬁng [26]. However, GALNT11*T could
show an irregular distribution in Asia in a fashion similar to thatof the YAP+(M1) allele [22,23]. Further studies are needed to investigate the frequencies of GALNT11*T in other populations, including
Central Asians.
In conclusion, genetic markers with a geographically restricteddistribution, or with marked allele frequency differences between
two regions, are useful to infer the ancestry of an individual. The
distribution of the ﬁve SNPs investigated in this study was restricted to East Asia. One of them, GALNT11*T, was observed only
in Far-East Asians, and the highest frequency was observed in Japanese living in Okinawa. These SNPs would be useful AIMs forforensic individualization, and also help to decipher the migration
patterns of East Asians.
Acknowledgement
This study was supported in part by a Grant-in-Aid for ScientiﬁcResearch (20590678 to IY) from the Japan Society for the Promotion of Science.
Appendix A. Supplementary data
Supplementary data associated with this article can be found, inthe online version, at doi:10.1016/j.legalmed.2010.04.001.
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