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Uniqueness of Korean gene

When spring is in the air at Japan and iron storm by Russia are covering Ukraine, author have released several articles in this web site, basing on population genetics papers which clearly indecates uniqueness or strangeness of Korean genetic structure. It is at the heart of genetic research for an isolated and homogeneous ethnic population that analyzing of inherent variants and the frequency shall provide more information for promoting mental and physical health of the population.

Abstructs

According to the following genetics papers, genetic structure of Koreans are very strange and unique in the following four points,

1.Koreans have high percentages of non-synonymous variants compared with other ethnic population (The Japanese, The chinese etc)

2.As opposed to the other ethnic population (The Japanese, The Chinese, etc.), variants which are inherent to Koreans extremely biased to the parts of Koreans.

3.MAF(minor allele frequency) clearly differs from the other ethnic population (The Japanese, The chinese etc), therefore, many genes of Koreans are under more strong negative selection pressure combined with high ratio of non-synonymous variants compared to the other ethnic population.


4. The overwhelming majority of variants which are inherent to Koreans have relation to mental diseases, personality disorders and human mentality. Please visit for details.

Strange phenomenon in South Korea



Though there might be no relation, total fertility rate(birth rate) in South Korea is abnormal and lowest in the world, and suicide rate is the highest on the earth.

2016
2017
2018
2019
2020
2021
1.17
1.05
0.98
0.92
0.84
0.81








I don't know cosmetic surgery expenditure of BTS members(BTS=Bangtan Boys), but it is beyond all doubts that BTS members did plastic surgery.

Gender, Globalizationand Aesthetic Surgeryin South Korea
Ruth Holliday(proffessor in University of Leed) et ai.
[cited]
This article explores the unusually high levels of cosmetic surgery in South Korea – for both women and men.
South Korean’ alleged ‘obsession’ with cosmetic surgery regularly hits headlines both in Asia and the ‘West’ because of its reportedly high take-up rate by both women and men.
Cosmetic surgery and skin treatment clinics are now commonplacein urban shopping malls, viewed much like nail and beauty salons in the UK, and providing procedures such as laser removal ofblemishes to 'walk-in’ customers.






There are no winners of all sixty-three famous scientific prizes in South Korea, despite of high education revel ratio and large population size.

  South Korea Japan
prizes winner 0 at least over 220
population size 50M 125M

Figuratively speaking, South Korea might be "huge mental hospital".
Please visit for details.


From population genetics paper

According to several population genetics papers, it is beyond all doubts that the genetic structure of Koreans is astonishingly unique and strange.
Believe it or not, the variants distribution of Koreans completely differ from The Japanese in spite of same East Asians, and needless to say, differs from other populations too, please see below cited contents.

1.Very large scale analyzing of whole exome region clearly indecates that nonsynonymous variants are a half of SNVs in exome region of human and a great majority of SNVs occurred at a minor allele frequency of ≤1%(=0.01).

Distribution and clinical impact offunctional variants in 50,726 whole-exomesequences from the DiscovEHR Study
Frederick E. Dewey et al.
Science; accepted 16 November 2016
depth in this study : average 80x

SNVs=Single-Nucleotide Variants

[Cited from the above paper]
Deleterious variants are expected to have lower allele frequencies than neutral ones, due to negative selection. This theoretical property has been demonstrated previously in human population sequencing data


2. In the case of The Japanese too, overwhelming majority of of SNVs occurr at a minor allele frequency of ≤1%.

Human genetic variation database, a reference database of genetic variations in the Japanese population
Koichiro Higasa et al.
Nature Published: 25 February 2016
depth in this study :at least 10x

[Cited from the above paper]
The allele frequencies for the majority (88.8%) were lower than 0.5% in allele frequency and predicted to be functionally deleterious.


3. Contrastly, Koreans indecates strange variants distribution.

Findings of a 1303 Korean whole-exome sequencing study
Soo Heon Kwak et al.
nature; Published: 14 July 2017
depth in this study : median103.7X


Please note that the fact that depth is very deep means that one can easily discover the very rare variants.
In other words, the very deep depth implies an increase in variants of less than MAF 1%(or 0.5%) .
Nonetheless, MAF>5% in the above paper is a high percentage.

Recommended Coverage by illumina is Whole genome sequencing=30x-50x, Whole-exome sequencing=100x



[reference (result of very large scale DNA sequencing)]
Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program
Daniel Taliun et al.
Nature Published: 10 February 2021
depth in this study : average 38x

(cited from Main)
[Among the more than 400 million detected variants, 97% have frequencies of less than 1% and 46% are singletons that are present in only one individual (53% among unrelated individuals). (cited from Abstract)
Here we describe high-coverage whole-genome sequencing (WGS) analyses of the first 53,831 TOPMed samples.
Among all variants, we observed 3.17 million nonsynonymous and 1.53 million synonymous variants (a 2.1:1 ratio), but individual genomes contained similar numbers of nonsynonymous and synonymous variants (11,743 nonsynonymous and 11,768 synonymous, on average) (Extended Data Table 4). The difference can be explained if more than half of the nonsynonymous variants are removed from the population by natural selection before they become common.

Could you understand how unique Koreans genetic architecture is?

4. Astonishingly, in the case of Koreans, only 0.6579(65.79%) of of SNVs occurred at a minor allele frequency of ≤1%. In other words, deleterious variants spread over Korean, or Korean are under high negative selection pressure compared with other population.


Korean Variant Archive (KOVA): a reference database of genetic variations in the Korean population
Sangmoon Lee et al.
Nature Published: 27 June 2017
depth in this study : 75x




5.Interestingly, in the case of Koreans, minor allele frequency of ≤10% is a very high ratio compared with Chinese and Japanese as same East Asians.

Whole genome sequencing of 35 individuals provides insights into the genetic structure of Korean population
Wenqian Zhang et al.
Published: 21 October 2014
from Electronic supplementary material in the above paper
12859_2014_6653_MOESM5_ESM.jpg


[Cited from the above paper]
In contrast with the SNVs common to other populations in HapMap and 1KGP, the Korean only SNVs had high percentages of non-silent variants, emphasizing the unique roles of these Korean only SNVs in the Korean population.

Therefore, we inferred that special attention should be made for the Korean population when treated for the above mentioned terms related diseases, since other populations did not carry those Korean only SNVs.

herefore, we rationally conjectured that Korean only SNVs prevalent across many of the individuals would be more important for treating Korean differently from other populations in the personalized medicine

Based on our analysis, we hypothesize that Korean might have different responses to the above mentioned terms-related drugs, when compared to other populations.


6.Variants which are inherent to Koreans extremely biased to the parts of Koreans.

Korean National Standard Reference Variome database of whole genomes with comprehensive SNV, indel, CNV, and SV analyses
Nature Published: 04 April 2018
Jungeun Kim et al.



[Cited from the above paper]
Surprisingly, however, roughly half of the variants in ‘1000GP low frequency’ were classified as ‘frequent in KoVariome’.
This indicates that there exist a significant population specific biases for common and uncommon variants.

1000GP=1000 Genomes Project
KoVariome=Korean National Standard Reference Variome)

Our analyses showed that a high portion of the coding SNVs were enriched in the ‘1000GP rare’ class, while the SNVs in the non-coding regions were similarly distributed in all other variant classes.

The portion of non-synonymous SNVs in the ‘1000GP rare’ class was more than twice what was observed in the other classes.

It is possible that these patterns are associated with purifying selection to rapidly remove deleterious alleles in the population


7.In contrast to other populations, the Koreans only SNVs (=Single-Nucleotide Variants) have high percentages of nonsynonymous variants (=non-silent variants) in low frequency.

Very fortunate thing for Koreans is that Koreans were not subject of 1000 genome project unlike The Japanese, The Chinese and Vietnamese.
Because of the ratio (=NS/S ratio), depth (=Coverage) almost don't effect analyzing results, that is, comparing between papers is possible.

(To my regret, frankly speaking, If we limit it to populations over 50 million, human kinds might consist of three groups i.e. Koreans, Blacks and others.)





Name: Kazuo Ueda
Country: Japan
DNA:The Japanese (Please note that residents whose DNA is Koreans are about 900,000 in Japan)

Please remember that Koreans genetic structure is very strange and unique !. That isn't racism but complete and scientific fact. Again, it is beyond all doubts that Koreans are very unique people from viewing of population genetics. All results and fact of Koreans completely coincide with their unique genetic structure. For instance,

1. Koreans have no winners of any of the 63 international famous science-related academic prizes, not to mention Nobel Prizes!
All humans around the world should know the fact above and should think the reason, maybe the cause would be Koreans unique DNA.

2.variants inherent to Koreans have a strong relation to mental diseases, personality disorders and human personality.
Geneticist except for Koreans should research Koreans very unique genetic architecture with all their might, like FDA(U.S. Food and Drug Administration)


I think that we human being should not deny scientific fact, under the name of racism. As a matter of fact, the ironic thing is that the most racist country in the world surely is South Korea, maybe you can't find a Korean female formally married with Blacks. In the event that you find a Korean female formally married with Blacks, please teach me, to my knowledge, it's very few compared with Japanese and Chinese.

The interaction between Koreans DNA (I. e. genetic factors) and the environment (I. e. sociocultural factors) created evil people in Korean peninsula like Korean movie.

bottleneck effect in the 13th century at Korean peninsula and slavery peculiar to Korean peninsula

The bottleneck effect itself is an extremely large scale of genetic drift that happens when the a population size is drastically decreased, and It is not known at all that bottleneck effect in the 13th century at Korean peninsula caused by invasion of Genghis Khan and his descendants. It is little known that peoples in Korean peninsula in those days resisted the invasion by Mongol for the long period of more than four decades when is the most long periods of resistance to Mongolia in the world at that time. And I infer that population in Korean peninsula decreased at least 85%-90% in the four decades, basing on the number of soldiers who were conscripted by Mongolia in Korean peninsula for invasion to Japan. Although genetic diversity wasn't lost from Koreans, I hypotheses that this historical incident surely and drastically altered Koreans DNA who is genetically isolated for long after the most strong impact to Koreans DNA in the past. And pleiotropic effects by bottleneck effect created the mental personality of Koreans like the examples mentioned hitherto.

Results of official historical records in China are as follows.
 (In the event that you can read and understand old Chinese characters, please visit this website, and please input 高麗, then choose 元史)


1. Genghis Khan Reign : Spring 1206 – August 25, 1227

2. Ögedei Khan : Reign 13 September 1229 – 11 December 1241
3. Möngke Khan Reign 1 July 1251 – 11 August 1259
# meaning of old Chinese characters
#1 Genghis Khan 13year=AD1219, At last, the king of Koreans was surrendered to Mongol and the king of Koreans sent tributes to Mongol.
#2 Ögedei Khan 3year=AD1231, The king of Koreans rebelled and killed emissary of Mongol. Mongol's army started to invade to the Korean peninsula, then Mongol's army attacked and felled more than 40 mountain castle. At last, the king of Koreans was surrendered to Mongol.
#3 Ögedei Khan 4year=AD1232, The king of Koreans rebelled again and killed Mongol supervisor who had been stationed throughout the Korean
Ögedei Khan 4year=AD1232 august, Mongol's army started to invade to Korean peninsula again.
#4 Ögedei Khan 7year=AD1235. Mongols army started to invade to Korean peninsula again.
(I infer that the king of Koreans rebelled again)
#5 Ögedei Khan 13year=AD1241 autumn, The king of Koreans sent his son to Mongolia as a hostage.
(I infer that the king of Koreans rebelled again)
#6 Möngke Khan 2year=AD1252 octover, Mongols army started to invade to Korean peninsula again.
(I infer that the king of Koreans rebelled again)
#7 Möngke Khan 3year=AD1253
Mongols army started to invade to Korean peninsula again.
(I infer that the king of Koreans rebelled again)
#8 Möngke Khan 4year=AD1254
Mongol's army started to invade to Koreann peninsula again.
(I infer that the king of koreans rebelled again)
#9 Möngke Khan 5year=AD1255
Mongols army started to invade to Korean peninsula again. Then mongol invaded the Korean peninsula for three consecutive years.
(I infer that the king of Koreans rebelled again)
#10 Möngke Khan 8year==AD1258
Mongol's army started to invade to Koreann peninsula again.
(I infer that the king of koreans rebelled again)

Thus, the King of Korea repeatedly rebelled and surrendered for about 40 years. At last, AD1260, King of Korea completely surrendered to Mongol.

Please strongly keep in mind that;
1. There is no doubt that repeated rebellions by Koreans led to thoroughgoing carnage by the Mongolian army. So, i infer that at least 85% of the population of the Korean peninsula at those days was lost, and the ratio between male and female was severely disrupted. (Chinese researchers estimate that the population in neighboring Northeast China declined by about 90% during the same period.)

2. There was no large-scale battle between the Korean army and the Mongols, and the Korean army separately resisted the Mongols by methods keeping in a small but many mountain castles where were soldiers for fighting and several hundred residents who escaped from carnage. (For instance, please see #2 historical record.)
According to population genetics, the more smaller of population, the more larger genetic drift.

3. The most important thing from the viewing of population genetics is that the fierce resistance to the Mongolian army lasted as long as 40 years, which are equivalent to about 1.5 generations in population genetics. In short, there was a prolonged genetic drift in the 13th century at Korean peninsula.
According to population genetics, the more longer of population reduction periods, the more larger genetic drift.

Therefore, I think that Mongol invasion to Korean peninsula should be called a bottleneck effect from the viewpoints of population genetics.
However, theoretically speaking, Mongol invasion to Korean peninsula might not be called a bottleneck effect. So, I think that population geneticists should research !.







It is very little known in the West that the number of surnames(=last name) in Korean Peninsula is about 270 only, meanwhile the number of family name(=last name) in Japan is estimated about 50,000, maybe, the number of family name(=last name) in china is at least over 100,000, and Koreans extremely and abnormally hate consanguineous marriages and endogamy as legal provisions that relatives within the 8th kinship cannot marry in Korea. (Until the end of the 20th century, marriage was prohibited in Korea by civil law for people with the same family name and same common ancestor region regardless of current residence.)

Thus, at least there is no doubt that Korean civil law and the number of family names(=last name) in Korean peninsula suggest the bottleneck effect in the past,



And historical records in Korea strongly suggest very large-scale decreasing of population size in Korean peninsula at 13th century.


The Mongol emperor demanded the Korean king that Korean soldiers be sent out to invade Japan with Mongolians at 13th century after complete surrender of Korean king. The above contents in Japanese are a record of the conversation between the Mongolian emperor and the chief vassal of the Korean king.

The Japanese in the red frame above means the following.
[There are many infants and boys, but they can't be soldier because many of them are 9-10 age]



After then, slavery was spread over the Korean peninsula, and it is estimated that 30-50% of the population was slaves called "Nobi" in 16th century Joseon Dynasty (i.e.in medieval Korea), according to Japanese researchers of Korean history. And, slave owner called "Yanban" could leave an overwhelming number of offspring.
This slavery peculiar to Korean peninsula continued until end of the 19th century (1894), and that means that Korean people constantly wasn't "panmictic" population. (Needless to say, please note that random mating is an important assumption of population genetics. )

1. Deleterious variants are expected to have lower allele frequencies.

Analysis of protein-coding genetic variation in 60,706 humans
Monkol Lek et.al
Nature 17 August 2016

[Cited from the above paper]
Deleterious variants are expected to have lower allele frequencies than neutral ones, due to negative selection. This theoretical property has been demonstrated previously in human population sequencing data12,13 and here (Fig. 1d, e).


2. Variants observed at lower frequency in specified population are a genetic indicator of purifying (negative) selection.

Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals
Masao Nagasaki et.al
Nature 21 August 2015

[Cited from the above paper]
Because deleterious mutations are removed from populations faster than neutral mutations, SNVs observed at lower frequency in a population are indicative of purifying (negative) selection, and their selection strength differs among the various functional genomic categories.


3. In the case of Koreans, MAF (=minor allele frequency) completely differs from others.

Whole genome sequencing of 35 individuals provides insights into the genetic structure of Korean population
Wenqian Zhang et al.
Published: 21 October 2014
from Electronic supplementary material in the above paper
12859_2014_6653_MOESM5_ESM.jpg and
[Only the low-frequency part was taken from the figure in the above paper]


Therefore, there are no doubts that The Koreans are under higher negative selection pressure compared with The Chinese and Japanese.

My hypothesis is that most likely, slavery, which is unique to the Korean peninsula at Joseon Dynasty's periods , was the obstructive factor for negative natural selection.
Concretely speaking, the historical fact that "Yanban" in Joseon Dynasty could leave an overwhelming number of offspring by slavery in Korean peninsula are the strong destructive factor for negative natural selection and random mating.

Non-Random Mating are three types, i.e. assortative mating, disassortative mating and unequal sex ratios in a breeding population.
 As for unequal sex ratios in a breeding population, good instance is 'harem' where only one male can mate with many females in Elephant Seals.

During the Joseon Dynasty, "Yanban"=slave owner's property mainly consisted of land and slaves, and it is crucial that a slave child was a slave if mother was a slave whoever the father is. As the natural result, the slave owner's male made many children with his owned slave women, enjoying sex with many slave's females to increasing their property. On the other hand, formal marriage of "Yanban" were made among "Yanban" without exception, in other word, that means a kind of assortative mating.
I infer that this very unique mating structure of Koreans, which has been prevalent for more than 500 years, has certainly had a great impact on the genes of the Korean people.

Genellaly speaking, Non-Random mating decreases heterogeneosity of isolated populations, and calculated effective population size is smaller compared with the normal population, but the gene frequency distribution might not be changed by Non-Random mating.

1.assortative mating, disassortative mating
Lecture Notes in Population Genetics,
Kent E. Holsinger, Department of Ecology & Evolutionary Biology, U-3043 University of Connecticut
[p22]
When there is sexual selection or disassortative mating genotypes differ in their chances of being included in the breeding population. As a result, allele and genotype frequencies will tend to change from one generation to the next.

Population Genetics
H. Richard Johnston et.al

12.3.1.2 Assortative Mating
Assortative mating is the tendency for people to choose mates who are more similar (positive) or dissimilar (negative) to themselves in phenotype characteristics than would be expected by chance. If these characteristics are genetically determined, positive assortative mating may increase homozygosity in the population. An important difference between inbreeding and positive assortative mating is that inbreeding affects all loci, while assortative mating affects only those that play a role in the phenotype characteristics that are similar.

2.unequal sex ratios in a breeding population.
Population genetics Tutorial
Peter Pfaffelhuber and Pleuni Pennings
November 30, 2007

Imagine a zoo population of primates with 20 males and 20 females. Due to dominance hierarchy only one of the males actually breeds.

The loss-of-heterozygosity effective population size is thus much smaller than the census size of 40 due to the fact that all offspring have the same father. Genetic variation will rapidly disappear from such a population. If males and females have equal (and Poisson) distributions of offspring numbers, and the sex ratio is equal, then Nf = Nm = N 2 , and Ne ≈ N; the Wright-Fisher model thus applies with the original census population size N in this respect.

As my hypotheses,
1. Very rapid decreasing of population number in the 13th century at Korean peninsula caused by invasion of Genghis Khan and his descendants extremely increased genetic drift. As the result, non-synonymous variants, which related mental traits increased.
 
2. After then, remarkable, unique mating structure of Koreans at Joseon Dynasty periods prevented the decreasing of non-synonymous variants, which related mental traits, mental diseases, and personality disorders.



1. As the results, I hypothesize that deleterious variants were remaining in a higher ratio than the other ethnic population without being deleted from Koreans by negative selection (purifying selection). And principal component analysis of single nucleotide polymorphism, which is the overwhelming majority of human variants indicates that Koreans and Japanese completely differ each other.

Korean Genome Project: 1094 Korean personal genomes with clinical information
Science Advances 27 May 2020
Sungwon Jeon et al.



2. Researcher of population genetics around the world except for Koreans should read the following paper and analyze the very unique genetic architecture of Koreans DNA like FDA (Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration).

Whole genome sequencing of 35 individuals provides insights into the genetic structure of Korean population
Wenqian Zhang et al.

Published: 21 October 2014

List of data showing the abnormality of South Korea (in Japanese)

The Koreans from population genetics perspective(in Japanese)

Genetic Relationship between Japanese and Koreans(in Japanese)


The following points are scientific facts of Korean DNA, indecating the uniquness of genetic structure.
1. Unusual high ratio of nonsynonymous variants compared with other population.
2.Strange distribution of minor allele of frequency and of Korean only variants.