Understanding the Y chromosomevariation by haplogroup andhaplotype analyses in a Koreanpopulation
Myung Jin Park
December 2012
I. Introduction
non-recombining portion of the Y chromosome= (NRY)
Two classes of markers on the NRY, single nucleotide polymorphism (SNP) and short tandem repeat (STR), are widely used.
Due to their low mutation rate, Y chromosome SNPs are useful genetic markers for reconstructing male lineages through hierarchically arranged allelic sets known as haplogroups, whereas the high mutation rates of Y-chromosomal STRs make them valuable for differentiating between unrelated males and inferring affinities among related populations.
There are several regional Y-STR haplotype databases currently in use globally, such as the Y-Chromosome Haplotype Reference Database (YHRD)16-18.
In particular, the phylogeny of haplogroup O-M175 has recently been revised to include the phylogenetic positions of redefined markers, L127, KL1, KL2, P164 and PK4
The haplogroup O-M175 is one of the major clades in the Korean population and the haplogroup O3a-M324 accounts for 43.9% of Korean males31, 32
31. Kim SH, Han MS, Kim W, Kim W.
Y chromosome homogeneity in the Korean population. Int J Legal Med 2010;124:653-7.
32. Kim SH, Kim KC, Shin DJ, Jin HJ, Kwak KD, Han MS, et al.
High frequencies ofY-chromosome haplogroup O2b-SRY465 lineages in Korea: a genetic perspectiveon the peopling of Korea.
Investig Genet 2011;2:10.
II. MATERIAL AND METHODS
DNA samples from 300 unrelated Korean males were obtained from the National Biobank of Korea for validation of the developed multiplex PCR systems
【サンプルを新たに集めたわけではない。300人分について韓国バイオバンク利用】
I analyzed DNA samples from 1006 unrelated Korean males, which include 706 individuals who have been typed for 19 or 22 Y-STRs33, 34.
【残りの706名については既発表の33、34の論文を利用としている。肝心のサンプルについては詳しくは書いていない。】
III. RESULTS
2. Y chromosome haplogrouping of Koreans
DNA samples from 1006 Korean males were analyzed using the multiplex allele-specific PCR assays.
A set of 16 Y-SNPs (M7, M9, M95, M117, M119, M134, M174, M175, M122, M231, P31, P201, JST002611, RPS4Y711, SRY465 and 47z) was initially analyzed in all samples using multiplex AS-I to determine the haplogroups frequent in East Asians.
A total of 21 different haplogroups were identified (when M117 was used alone to designating haplogroup O3a2c1a);
haplogroup O2b*-SRY465 was most frequently observed (24.2%), followed by haplogroups C3-M217 (xC3c, C3d, C3e) (13.4%) and O3a2c1a-M117 (12.3%) (Figure 18). The haplogroup diversity was 0.8830, and the discriminatory capacity was 2.1%.
By typing of the newly defined or relocated SNPs KL2, JST002611, P164 and PK4 in Korean haplogroup O-M175 samples, their phylogenetic positions were confirmed.
Meanwhile, O2b-SRY465 and its derived sublineage O2b1-47z were found frequent (37.7%) in the Korean population, but they were nearly absent in the Han Chinese population.
The subhaplogroups were concentrated in Korean and Japanese populations32 and the results of this current study are consistent with those findings
32. Kim SH, Kim KC, Shin DJ, Jin HJ, Kwak KD, Han MS, et al. High frequencies of Y-chromosome haplogroup O2b-SRY465 lineages in Korea: a genetic perspective on the peopling of Korea. Investig Genet 2011;2:10.
37. Xue Y, Zerjal T, Bao W, Zhu S, Shu Q, Xu J, et al. Male demography in East Asia: a north-south contrast in human population expansion times. Genetics 2006;172:2431-9.
38. Zhong H, Shi H, Qi XB, Xiao CJ, Jin L, Ma RZ, et al. Global distribution of Y-chromosome haplogroup C reveals the prehistoric migration routes of African exodus and early settlement in East Asia. J Hum Genet 2010;55:428-35
Myung Jin Park
December 2012
ハマーの論文ではOー47Z変異=O2b1は、日本人以外には1%以下の頻度であり、ほぼ日本人男性固有。これに対して、この論文では9.54%もキチガイどもで検出されたことになる。あまりにも差が大きい。ハマーの論文のサンプルは少なく、この論文では計1000名以上であるが、サンプル差でこれほどの差が出ることはあり得ない。この論文が引用しているHigh frequencies ofY-chromosome haplogroup O2b-SRY465 lineages in Korea: a genetic perspectiveon the peopling of Korea.
でもO2b1を8.89%としている。恐らくは、ハマーとの分析能力の差=間違いである。ハマーの場合には直接サンプルを集めている。Y染色体の非組み換え領域の分析は、組み換えのある常染色体と異なり難しいことは明らかである。
下に掲げたのは、この論文ではなく、High frequencies ofY-chromosome haplogroup O2b-SRY465 lineages in Korea: a genetic perspectiveon the peopling of Korea.からである
ハプログループOに焦点を当てた論文であり、よくできた図であり、もし間違えでなければ、参考にはなる
でもO2b1を8.89%としている。恐らくは、ハマーとの分析能力の差=間違いである。ハマーの場合には直接サンプルを集めている。Y染色体の非組み換え領域の分析は、組み換えのある常染色体と異なり難しいことは明らかである。
下に掲げたのは、この論文ではなく、High frequencies ofY-chromosome haplogroup O2b-SRY465 lineages in Korea: a genetic perspectiveon the peopling of Korea.からである
ハプログループOに焦点を当てた論文であり、よくできた図であり、もし間違えでなければ、参考にはなる
I. Introduction
non-recombining portion of the Y chromosome= (NRY)
Two classes of markers on the NRY, single nucleotide polymorphism (SNP) and short tandem repeat (STR), are widely used.
Due to their low mutation rate, Y chromosome SNPs are useful genetic markers for reconstructing male lineages through hierarchically arranged allelic sets known as haplogroups, whereas the high mutation rates of Y-chromosomal STRs make them valuable for differentiating between unrelated males and inferring affinities among related populations.
There are several regional Y-STR haplotype databases currently in use globally, such as the Y-Chromosome Haplotype Reference Database (YHRD)16-18.
In particular, the phylogeny of haplogroup O-M175 has recently been revised to include the phylogenetic positions of redefined markers, L127, KL1, KL2, P164 and PK4
The haplogroup O-M175 is one of the major clades in the Korean population and the haplogroup O3a-M324 accounts for 43.9% of Korean males31, 32
31. Kim SH, Han MS, Kim W, Kim W.
Y chromosome homogeneity in the Korean population. Int J Legal Med 2010;124:653-7.
32. Kim SH, Kim KC, Shin DJ, Jin HJ, Kwak KD, Han MS, et al.
High frequencies ofY-chromosome haplogroup O2b-SRY465 lineages in Korea: a genetic perspectiveon the peopling of Korea.
Investig Genet 2011;2:10.
II. MATERIAL AND METHODS
DNA samples from 300 unrelated Korean males were obtained from the National Biobank of Korea for validation of the developed multiplex PCR systems
【サンプルを新たに集めたわけではない。300人分について韓国バイオバンク利用】
I analyzed DNA samples from 1006 unrelated Korean males, which include 706 individuals who have been typed for 19 or 22 Y-STRs33, 34.
【残りの706名については既発表の33、34の論文を利用としている。肝心のサンプルについては詳しくは書いていない。】
III. RESULTS
2. Y chromosome haplogrouping of Koreans
DNA samples from 1006 Korean males were analyzed using the multiplex allele-specific PCR assays.
A set of 16 Y-SNPs (M7, M9, M95, M117, M119, M134, M174, M175, M122, M231, P31, P201, JST002611, RPS4Y711, SRY465 and 47z) was initially analyzed in all samples using multiplex AS-I to determine the haplogroups frequent in East Asians.
A total of 21 different haplogroups were identified (when M117 was used alone to designating haplogroup O3a2c1a);
haplogroup O2b*-SRY465 was most frequently observed (24.2%), followed by haplogroups C3-M217 (xC3c, C3d, C3e) (13.4%) and O3a2c1a-M117 (12.3%) (Figure 18). The haplogroup diversity was 0.8830, and the discriminatory capacity was 2.1%.
By typing of the newly defined or relocated SNPs KL2, JST002611, P164 and PK4 in Korean haplogroup O-M175 samples, their phylogenetic positions were confirmed.
Meanwhile, O2b-SRY465 and its derived sublineage O2b1-47z were found frequent (37.7%) in the Korean population, but they were nearly absent in the Han Chinese population.
The subhaplogroups were concentrated in Korean and Japanese populations32 and the results of this current study are consistent with those findings
32. Kim SH, Kim KC, Shin DJ, Jin HJ, Kwak KD, Han MS, et al. High frequencies of Y-chromosome haplogroup O2b-SRY465 lineages in Korea: a genetic perspective on the peopling of Korea. Investig Genet 2011;2:10.
37. Xue Y, Zerjal T, Bao W, Zhu S, Shu Q, Xu J, et al. Male demography in East Asia: a north-south contrast in human population expansion times. Genetics 2006;172:2431-9.
38. Zhong H, Shi H, Qi XB, Xiao CJ, Jin L, Ma RZ, et al. Global distribution of Y-chromosome haplogroup C reveals the prehistoric migration routes of African exodus and early settlement in East Asia. J Hum Genet 2010;55:428-35