A comprehensive profile of DNA copy number variations in a Korean population: identification of copy number invariant regions among Koreans
To examine copy number variations among the Korean population, we compared individual genomes with the Korean reference genome assembly using the publicly available Korean HapMap SNP 50 k chip data from 90 individuals. Korean individuals exhibited 123 copy number variation regions (CNVRs) covering 2...
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| Published in | Experimental & molecular medicine Vol. 41; no. 9; pp. 618 - 628 |
|---|---|
| Main Authors | , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
London
Nature Publishing Group UK
30.09.2009
Springer Nature B.V Korean Society of Medical Biochemistry and Molecular Biology 생화학분자생물학회 |
| Subjects | |
| Online Access | Get full text |
| ISSN | 1226-3613 2092-6413 2092-6413 |
| DOI | 10.3858/emm.2009.41.9.068 |
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| Abstract | To examine copy number variations among the Korean population, we compared individual genomes with the Korean reference genome assembly using the publicly available Korean HapMap SNP 50 k chip data from 90 individuals. Korean individuals exhibited 123 copy number variation regions (CNVRs) covering 27.2 mb, equivalent to 1.0% of the genome in the copy number variation (CNV) analysis using the combined criteria of
P
value (
P
< 0.01) and standard deviation of copy numbers (SD ≥ 0.25) among study subjects. In contrast, when compared to the Affymetrix reference genome assembly from multiple ethnic groups, considerably more CNVRs (
n
= 643) were detected in larger proportions (5.0%) of the genome covering 135.1 mb even by more stringent criteria (
P
< 0.001 and SD ≥ 0.25), reflecting ethnic diversity of structural variations between Korean and other populations. Some CNVRs were validated by the quantitative multiplex PCR of short fluorescent fragment (QMPSF) method, and then copy number invariant regions were detected among the study subjects. These copy number invariant regions would be used as good internal controls for further CNV studies. Lastly, we demonstrated that the CNV information could stratify even a single ethnic population with a proper reference genome assembly from multiple heterogeneous populations. |
|---|---|
| AbstractList | To examine copy number variations among the Korean
population, we compared individual genomes with the
Korean reference genome assembly using the publicly
available Korean HapMap SNP 50 k chip data from 90
individuals. Korean individuals exhibited 123 copy
number variation regions (CNVRs) covering 27.2 mb,
equivalent to 1.0% of the genome in the copy number
variation (CNV) analysis using the combined criteria of
P value (P ＜ 0.01) and standard deviation of copy
numbers (SD ≥ 0.25) among study subjects. In contrast,
when compared to the Affymetrix reference genome
assembly from multiple ethnic groups, considerably
more CNVRs (n = 643) were detected in larger
proportions (5.0%) of the genome covering 135.1 mb
even by more stringent criteria (P ＜ 0.001 and SD ≥
0.25), reflecting ethnic diversity of structural variations
between Korean and other populations. Some
CNVRs were validated by the quantitative multiplex
PCR of short fluorescent fragment (QMPSF) method,
and then copy number invariant regions were detected
among the study subjects. These copy number invariant
regions would be used as good internal controls
for further CNV studies. Lastly, we demonstrated
that the CNV information could stratify even a single
ethnic population with a proper reference genome assembly
from multiple heterogeneous populations. KCI Citation Count: 5 To examine copy number variations among the Korean population, we compared individual genomes with the Korean reference genome assembly using the publicly available Korean HapMap SNP 50 k chip data from 90 individuals. Korean individuals exhibited 123 copy number variation regions (CNVRs) covering 27.2 mb, equivalent to 1.0% of the genome in the copy number variation (CNV) analysis using the combined criteria of P value (P<0.01) and standard deviation of copy numbers (SD>or= 0.25) among study subjects. In contrast, when compared to the Affymetrix reference genome assembly from multiple ethnic groups, considerably more CNVRs (n=643) were detected in larger proportions (5.0%) of the genome covering 135.1 mb even by more stringent criteria (P<0.001 and SD>or=0.25), reflecting ethnic diversity of structural variations between Korean and other populations. Some CNVRs were validated by the quantitative multiplex PCR of short fluorescent fragment (QMPSF) method, and then copy number invariant regions were detected among the study subjects. These copy number invariant regions would be used as good internal controls for further CNV studies. Lastly, we demonstrated that the CNV information could stratify even a single ethnic population with a proper reference genome assembly from multiple heterogeneous populations. To examine copy number variations among the Korean population, we compared individual genomes with the Korean reference genome assembly using the publicly available Korean HapMap SNP 50 k chip data from 90 individuals. Korean individuals exhibited 123 copy number variation regions (CNVRs) covering 27.2 mb, equivalent to 1.0% of the genome in the copy number variation (CNV) analysis using the combined criteria of P value (P < 0.01) and standard deviation of copy numbers (SD ≥ 0.25) among study subjects. In contrast, when compared to the Affymetrix reference genome assembly from multiple ethnic groups, considerably more CNVRs (n = 643) were detected in larger proportions (5.0%) of the genome covering 135.1 mb even by more stringent criteria (P < 0.001 and SD ≥ 0.25), reflecting ethnic diversity of structural variations between Korean and other populations. Some CNVRs were validated by the quantitative multiplex PCR of short fluorescent fragment (QMPSF) method, and then copy number invariant regions were detected among the study subjects. These copy number invariant regions would be used as good internal controls for further CNV studies. Lastly, we demonstrated that the CNV information could stratify even a single ethnic population with a proper reference genome assembly from multiple heterogeneous populations. To examine copy number variations among the Korean population, we compared individual genomes with the Korean reference genome assembly using the publicly available Korean HapMap SNP 50 k chip data from 90 individuals. Korean individuals exhibited 123 copy number variation regions (CNVRs) covering 27.2 mb, equivalent to 1.0% of the genome in the copy number variation (CNV) analysis using the combined criteria of P value ( P < 0.01) and standard deviation of copy numbers (SD ≥ 0.25) among study subjects. In contrast, when compared to the Affymetrix reference genome assembly from multiple ethnic groups, considerably more CNVRs ( n = 643) were detected in larger proportions (5.0%) of the genome covering 135.1 mb even by more stringent criteria ( P < 0.001 and SD ≥ 0.25), reflecting ethnic diversity of structural variations between Korean and other populations. Some CNVRs were validated by the quantitative multiplex PCR of short fluorescent fragment (QMPSF) method, and then copy number invariant regions were detected among the study subjects. These copy number invariant regions would be used as good internal controls for further CNV studies. Lastly, we demonstrated that the CNV information could stratify even a single ethnic population with a proper reference genome assembly from multiple heterogeneous populations. To examine copy number variations among the Korean population, we compared individual genomes with the Korean reference genome assembly using the publicly available Korean HapMap SNP 50 k chip data from 90 individuals. Korean individuals exhibited 123 copy number variation regions (CNVRs) covering 27.2 mb, equivalent to 1.0% of the genome in the copy number variation (CNV) analysis using the combined criteria of P value (P<0.01) and standard deviation of copy numbers (SD>or= 0.25) among study subjects. In contrast, when compared to the Affymetrix reference genome assembly from multiple ethnic groups, considerably more CNVRs (n=643) were detected in larger proportions (5.0%) of the genome covering 135.1 mb even by more stringent criteria (P<0.001 and SD>or=0.25), reflecting ethnic diversity of structural variations between Korean and other populations. Some CNVRs were validated by the quantitative multiplex PCR of short fluorescent fragment (QMPSF) method, and then copy number invariant regions were detected among the study subjects. These copy number invariant regions would be used as good internal controls for further CNV studies. Lastly, we demonstrated that the CNV information could stratify even a single ethnic population with a proper reference genome assembly from multiple heterogeneous populations.To examine copy number variations among the Korean population, we compared individual genomes with the Korean reference genome assembly using the publicly available Korean HapMap SNP 50 k chip data from 90 individuals. Korean individuals exhibited 123 copy number variation regions (CNVRs) covering 27.2 mb, equivalent to 1.0% of the genome in the copy number variation (CNV) analysis using the combined criteria of P value (P<0.01) and standard deviation of copy numbers (SD>or= 0.25) among study subjects. In contrast, when compared to the Affymetrix reference genome assembly from multiple ethnic groups, considerably more CNVRs (n=643) were detected in larger proportions (5.0%) of the genome covering 135.1 mb even by more stringent criteria (P<0.001 and SD>or=0.25), reflecting ethnic diversity of structural variations between Korean and other populations. Some CNVRs were validated by the quantitative multiplex PCR of short fluorescent fragment (QMPSF) method, and then copy number invariant regions were detected among the study subjects. These copy number invariant regions would be used as good internal controls for further CNV studies. Lastly, we demonstrated that the CNV information could stratify even a single ethnic population with a proper reference genome assembly from multiple heterogeneous populations. To examine copy number variations among the Korean population, we compared individual genomes with the Korean reference genome assembly using the publicly available Korean HapMap SNP 50 k chip data from 90 individuals. Korean individuals exhibited 123 copy number variation regions (CNVRs) covering 27.2 mb, equivalent to 1.0% of the genome in the copy number variation (CNV) analysis using the combined criteria of P value (P < 0.01) and standard deviation of copy numbers (SD greater than or equal to 0.25) among study subjects. In contrast, when compared to the Affymetrix reference genome assembly from multiple ethnic groups, considerably more CNVRs (n = 643) were detected in larger proportions (5.0%) of the genome covering 135.1 mb even by more stringent criteria (P < 0.001 and SD greater than or equal to 0.25), reflecting ethnic diversity of structural variations between Korean and other populations. Some CNVRs were validated by the quantitative multiplex PCR of short fluorescent fragment (QMPSF) method, and then copy number invariant regions were detected among the study subjects. These copy number invariant regions would be used as good internal controls for further CNV studies. Lastly, we demonstrated that the CNV information could stratify even a single ethnic population with a proper reference genome assembly from multiple heterogeneous populations. |
| Author | Oh, Bermseok Nam, Hye-Young Jung, Jongsun Han, Bok-Ghee Jeon, Jae-Pil Kimm, Kuchan Kim, Hyung-Lae Shim, Sung-Mi Lee, Hye-Jin |
| AuthorAffiliation | 2 Center for Genome Science, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Seoul 122-701, Korea 1 Division of Biobank for Health Sciences, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Seoul 122-701, Korea |
| AuthorAffiliation_xml | – name: 1 Division of Biobank for Health Sciences, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Seoul 122-701, Korea – name: 2 Center for Genome Science, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Seoul 122-701, Korea |
| Author_xml | – sequence: 1 givenname: Jae-Pil surname: Jeon fullname: Jeon, Jae-Pil organization: Division of Biobank for Health Sciences, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Seoul 122-701, Korea – sequence: 2 givenname: Sung-Mi surname: Shim fullname: Shim, Sung-Mi organization: Division of Biobank for Health Sciences, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Seoul 122-701, Korea – sequence: 3 givenname: Jongsun surname: Jung fullname: Jung, Jongsun organization: Center for Genome Science, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Seoul 122-701, Korea – sequence: 4 givenname: Hye-Young surname: Nam fullname: Nam, Hye-Young organization: Division of Biobank for Health Sciences, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Seoul 122-701, Korea – sequence: 5 givenname: Hye-Jin surname: Lee fullname: Lee, Hye-Jin organization: Division of Biobank for Health Sciences, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Seoul 122-701, Korea – sequence: 6 givenname: Bermseok surname: Oh fullname: Oh, Bermseok organization: Center for Genome Science, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Seoul 122-701, Korea – sequence: 7 givenname: Kuchan surname: Kimm fullname: Kimm, Kuchan organization: Center for Genome Science, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Seoul 122-701, Korea – sequence: 8 givenname: Hyung-Lae surname: Kim fullname: Kim, Hyung-Lae organization: Center for Genome Science, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Seoul 122-701, Korea – sequence: 9 givenname: Bok-Ghee surname: Han fullname: Han, Bok-Ghee email: bokghee@yahoo.com organization: Division of Biobank for Health Sciences, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Seoul 122-701, Korea |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/19478558$$D View this record in MEDLINE/PubMed https://www.kci.go.kr/kciportal/ci/sereArticleSearch/ciSereArtiView.kci?sereArticleSearchBean.artiId=ART001376600$$DAccess content in National Research Foundation of Korea (NRF) |
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| CitedBy_id | crossref_primary_10_1016_j_neuroscience_2020_04_051 crossref_primary_10_1186_s12864_016_2754_7 crossref_primary_10_4070_kcj_2011_41_7_385 crossref_primary_10_2217_pgs_11_24 crossref_primary_10_1111_j_1742_7843_2012_00904_x |
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| SubjectTerms | Asian Continental Ancestry Group - genetics Biomedical and Life Sciences Biomedicine DNA Copy Number Variations Genetics, Population Genome, Human Humans Medical Biochemistry Molecular Medicine Original Polymorphism, Single Nucleotide Stem Cells 생화학 |
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| Title | A comprehensive profile of DNA copy number variations in a Korean population: identification of copy number invariant regions among Koreans |
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