Skip to main content
Key Specialties
Cardiology Diabetology Endocrinology Gastroenterology Geriatrics and Gerontology Gynecology and Obstetrics Hematology Infectious Disease Internal Medicine Nephrology Neurology Oncology Pediatrics Respiratory Medicine Rheumatology Surgery
Congress Coverage
2024 ACC Congress 2023 ESMO Congress 2023 EASD Congress 2023 ERS Congress 2023 ESC Congress
Clinical Collections
Advances in Alzheimer’s

At a glance: The ONWARDS insulin icodec trials

A round-up of the ONWARDS phase 3 clinical trials evaluating the novel weekly insulin icodec in people with diabetes.
ADVANCED SEARCH
Log in
Top
International Journal of Legal Medicine
Published in: International Journal of Legal Medicine 6/2019

01-11-2019 | Original Article

Ancestry informative markers (AIMs) for Korean and other East Asian and South East Asian populations

Authors: Ju Yeon Jung, Pil-Won Kang, Eungsoo Kim, Diego Chacon, Dominik Beck, Dennis McNevin

Published in: International Journal of Legal Medicine | Issue 6/2019

Login to get access

Abstract

Inference of ancestry from biological evidence can provide investigative information, especially for unknown DNA donors. Although tools for predicting ancestry have been developing, ancestry research focusing on populations relevant for South Korea is not common and markers are seldom chosen specifically to differentiate Koreans from other East Asian and South East Asian populations. Here, we report ancestry informative markers (AIMs) for distinguishing six East/South East Asian regional populations: China, Japan, Indonesia, Philippines, South Korea and Thailand. Individual genotypes from these six populations were available in PanSNPdb: The HUGO Pan-Asian SNP Database. To select AIMs, we calculated four population divergence metrics for each SNP: Nei’s FST, Rosenberg’s Informativeness (In), the average absolute allele frequency difference between populations (δFmean) and the maximum allele frequency difference between populations (δFmax). Based on these values, we selected 100 single nucleotide polymorphisms (SNPs) for distinguishing the six populations, 13 of which exhibited large allele frequency differences between Koreans and non-Koreans. To assess the performance of the AIMs, we performed principal coordinates analysis (PCoA) on the individuals from all six populations and inferred ancestral population clusters using the STRUCTURE program. In conclusion, we found that the selected AIMs can be applied to distinguish the six East/South East Asian groups and we suggest the markers in this study will be helpful to establish ancestry panels for Korea and neighbouring populations.
Appendix
Available only for authorised users
Literature
1.
2.
Yuasa I, Akane A, Yamamoto T, Matsusue A, Endoh M, Nakagawa M, Umetsu K, Ishikawa T, Iino M (2018) Japaneseplex: A forensic SNP assay for identification of Japanese people using Japanese-specific alleles. Leg Med (Tokyo) 33:17–22
3.
Yang N, Li H, Criswell LA, Gregersen PK, Alarcon-Riquelme ME, Kittles R, Shigeta R, Silva G, Patel PI, Belmont JW, Seldin MF (2005) Examination of ancestry and ethnic affiliation using highly informative diallelic DNA markers: application to diverse and admixed populations and implications for clinical epidemiology and forensic medicine. Hum Genet 118(3):382–392PubMed
4.
Ziv E, John EM, Choudhry S, Kho J, Lorizio W, Perez-Stable EJ, Burchard EG (2006) Genetic ancestry and risk factors for breast cancer among Latinas in the San Francisco Bay Area. Cancer Epidemiol Biomark Prev 15(10):1878–1885
5.
Barnes KC (2010) Ancestry, ancestry-informative markers, asthma, and the quest for personalized medicine. J Allergy Clin Immunol 126(6):1139–1140PubMed
6.
Li CX, Pakstis AJ, Jiang L, Wei YL, Sun QF, Wu H, Bulbul O, Wang P, Kang LL, Kidd JR, Kidd KK (2016) A panel of 74 AISNPs: Improved ancestry inference within Eastern Asia. Forensic Sci Int Genet 23:101–110PubMed
7.
Cheung EYY, Gahan ME, McNevin D (2017) Prediction of biogeographical ancestry from genotype: a comparison of classifiers. Int J Legal Med 131(4):901–912PubMed
8.
Al-Asfi M, McNevin D, Mehta B, Power D, Gahan ME, Daniel R (2018) Assessment of the Precision ID Ancestry panel. Int J Legal Med 132(6):1581–1594PubMed
9.
Phillips C, Salas A, Sánchez JJ, Fondevila M, Gómez-Tato A, Alvarez-Dios J, Calaza M, de Cal MC, Ballard D, Lareu MV, Carracedo A, SNPforID Consortium (2007) Inferring ancestral origin using a single multiplex assay of ancestry-informative marker SNPs. Forensic Sci Int Genet 1(3):273–280PubMed
10.
Cheung EYY, Gahan ME, McNevin D (2018) Prediction of biogeographical ancestry in admixed individuals. Forensic Sci Int Genet 36:104–111PubMed
11.
Butler JM, Coble MD, Vallone PM (2007) STRs vs. SNPs: thoughts on the future of forensic DNA testing. Forensic Sci Med Pathol 3(3):200–205PubMed
12.
Phillips C, Parson W, Lundsberg B, Santos C, Freire-Aradas A, Torres M, Eduardoff M, Børsting C, Johansen P, Fondevila M, Morling N, Schneider P, EUROFORGEN-NoE Consortium, Carracedo A, Lareu MV (2014) Building a forensic ancestry panel from the ground up: the EUROFORGEN global AIM-SNP set. Forensic Sci Int Genet 11:13–25PubMed
13.
Kidd KK, Speed WC, Pakstis AJ, Furtado MR, Fang R, Madbouly A, Maiers M, Middha M, Friedlaender FR, Kidd JR (2014) Progress toward an efficient panel of SNPs for ancestry inference. Forensic Sci Int Genet 10:23–32PubMed
14.
Soundararajan U, Yun L, Shi M, Kidd KK (2016) Minimal SNP overlap among multiple panels of ancestry informative markers argues for more international collaboration. Forensic Sci Int Genet 23:25–32PubMed
15.
Rosenberg NA, Li LM, Ward R, Pritchard JK (2003) Informativeness of genetic markers for inference of ancestry. Am J Hum Genet 73(6):1402–1422PubMedPubMedCentral
16.
Londin ER, Keller MA, Maista C, Smith G, Mamounas LA, Zhang R, Madore SJ, Gwinn K, Corriveau RA (2010) CoAIMs: a cost-effective panel of ancestry informative markers for determining continental origins. PLoS One 5(10):e13443PubMedPubMedCentral
17.
Vongpaisarnsin K, Saengkaeotrakul P, Rasmeepaisarn K (2017) Ancestry informative markers for Asian subcontinent. Forensic Sci Int Genet Suppl Ser 6:e260–e262
18.
International HapMap Consortium (2003) The International HapMap Project. Nature 426(6968):789–796
19.
1000 Genomes Project Consortium, Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA (2010) A map of human genome variation from population-scale sequencing. Nature 467(7319):1061–1073
20.
Wang Y, Lu D, Chung YJ, Xu S (2018) Genetic structure, divergence and admixture of Han Chinese, Japanese and Korean populations. Hereditas 155:19PubMedPubMedCentral
21.
Qin P, Li Z, Jin W, Lu D, Lou H, Shen J, Jin L, Shi Y, Xu S (2014) A panel of ancestry informative markers to estimate and correct potential effects of population stratification in Han Chinese. Eur J Hum Genet 22(2):248–253PubMed
22.
Vongpaisarnsin K, Listman JB, Malison RT, Gelernter J (2015) Ancestry informative markers for distinguishing between Thai populations based on genome-wide association datasets. Leg Med (Tokyo) 17(4):245–250
23.
Santos HC, Horimoto AVR, Tarazona-Santos E, Rodrigues-Soares F, Barreto ML, Horta BL, Lima-Costa MF, Gouveia MH, Machado M, Silva TM, Sanches JM, Esteban N, Magalhaes WCS, Rodrigues MR, Kehdy FSG, Pereira AC, The Brazilian EPIGEN Project Consortium (2015) A minimum set of ancestry informative markers for determining admixture proportions in a mixed American population: the Brazilian set. Eur J Hum Genet 24(5):725–731PubMedPubMedCentral
24.
Santos C, Phillips C, Fondevila M, Daniel R, van Oorschot RAH, Burchard EG, Schanfield MS, Souto L, Uacyisrael J, Via M, Carracedo Á, Lareu MV (2016) Pacifiplex: an ancestry-informative SNP panel centred on Australia and the Pacific region. Forensic Sci Int Genet 20:71–80PubMed
25.
Yahya P, Sulong S, Harun A, Wan Isa H, Ab Rajab NS, Wangkumhang P, Wilantho A, Ngamphiw C, Tongsima S, Zilfalil BA (2017) Analysis of the genetic structure of the Malay population: ancestry-informative marker SNPs in the Malay of Peninsular Malaysia. Forensic Sci Int Genet 30:152–159PubMed
26.
Kim JJ, Verdu P, Pakstis AJ, Speed WC, Kidd JR, Kidd KK (2005) Use of autosomal loci for clustering individuals and populations of East Asian origin. Hum Genet 117(6):511–519PubMed
27.
Brissenden JE, Kidd JR, Evsanaa B, Togtokh AJ, Pakstis AJ, Friedlaender F, Kidd KK, Roscoe JM (2015) Mongolians in the genetic landscape of Central Asia: exploring the genetic relations among Mongolians and other world populations. Hum Biol 87(2):73–91PubMed
28.
Kim SM, Yoo SY, Nam SH, Lee JM, Chung KW (2016) Identification of Korean-specific SNP markers from whole-exome sequencing data. Int J Legal Med 130(3):669–677PubMed
29.
Ngamphiw C, Assawamakin A, Xu S, Shaw PJ, Yang JO, Ghang H, Bhak J, Liu E, Tongsima S, the HUGO Pan-Asian SNP Consortium (2011) PanSNPdb: the Pan-Asian SNP genotyping database. PLoS One 6(6):e21451PubMedPubMedCentral
30.
Holsinger KE, Weir BS (2009) Genetics in geographically structured populations: defining, estimating and interpreting FST. Nat Rev Genet 10(9):639–650PubMedPubMedCentral
31.
Nei M (1977) F-statistics and analysis of gene diversity in subdivided populations. Ann Hum Genet 41:225–233PubMed
32.
Boca SM, Rosenberg NA (2011) Mathematical properties of Fst between admixed populations and their parental source populations. Theor Popul Biol 80(3):208–216PubMedPubMedCentral
33.
Phillips C (2015) Forensic genetic analysis of bio-geographical ancestry. Forensic Sci Int Genet 18:49–65PubMed
34.
Collins-Schramm HE, Chima B, Morii T, Wah K, Figueroa Y, Criswell LA, Hanson RL, Knowler WC, Silva G, Belmont JW, Seldin MF (2004) Mexican American ancestry-informative markers: examination of population structure and marker characteristics in European Americans, Mexican Americans, Amerindians and Asians. Hum Genet 114(3):263–271PubMed
35.
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155(2):945–959PubMedPubMedCentral
36.
Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164(4):1567–1587PubMedPubMedCentral
37.
Falush D, Stephens M, Pritchard JK (2007) Inference of population structure using multilocus genotype data: dominant markers and null alleles. Mol Ecol Notes 7(4):574–578PubMedPubMedCentral
38.
Hubisz MJ, Falush D, Stephens M, Pritchard JK (2009) Inferring weak population structure with the assistance of sample group information. Mol Ecol Resour 9(5):1322–1332PubMedPubMedCentral
39.
Jakobsson M, Rosenberg NA (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23(14):1801–1806PubMed
40.
Team RC (2015) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria
41.
Paradis E, Claude J, Strimmer K (2004) APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20(2):289–290PubMed
42.
Clarke L, Fairley S, Zheng-Bradley X, Streeter I, Perry E, Lowy E, Tassé AM, Flicek P (2017) The International Genome Sample Resource (IGSR): a worldwide collection of genome variation incorporating the 1000 Genomes Project data. Nucleic Acids Res 45(D1):D854–D859PubMed
43.
Yuasa I, Umetsu K, Adachi N, Matsusue A, Nakayashiki N, Fujihara J, Akane A, Harihara S, Jin F, Ishikawa T (2015) Investigation of Japanese-specific alleles: most are of Jomon lineage. Leg Med (Tokyo) 17(1):52–55
44.
Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38(6):1358–1370PubMed
45.
Wahlund (1928) Composition of populations and correlation appearances viewed in relation to the studies of inheritance. Hereditas 11:65–106
46.
Cox MP, Karafet TM, Lansing JS, Sudoyo H, Hammer MF (2010) Autosomal and X-linked single nucleotide polymorphisms reveal a steep Asian–Melanesian ancestry cline in eastern Indonesia and a sex bias in admixture rates. Proc Biol Sci 277(1687):1589–1596PubMedPubMedCentral
47.
Karafet TM, Hallmark B, Cox MP, Sudoyo H, Downey S, Lansing JS, Hammer MF (2010) Major east–west division underlies Y chromosome stratification across Indonesia. Mol Biol Evol 27(8):1833–1844PubMed
48.
Xu S, Pugach I, Stoneking M, Kayser M, Jin L, HUGO Pan-Asian SNP Consortium (2012) Genetic dating indicates that the Asian–Papuan admixture through Eastern Indonesia corresponds to the Austronesian expansion. Proc Natl Acad Sci U S A 109(12):4574–4579PubMedPubMedCentral
49.
Shi L, Yao YF, Shi L, Matsushita M, Yu L, Lin QK, Tao YF, Oka T, Chu JY, Tokunaga K (2010) HLA alleles and haplotypes distribution in Dai population in Yunnan province, Southwest China. Tissue Antigens 75(2):159–165PubMed
50.
1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR (2015) Nature 526(7571):68–74
51.
Pouyet F, Aeschbacher S, Thiéry A, Excoffier L (2018) Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences. Elife 7:e36317PubMedPubMedCentral
52.
53.
Salas A (2019) The natural selection that shapes our genomes. Forensic Sci Int Genet 39:57–60PubMed
54.
Li H, Borinskaya S, Yoshimura K, Kal’ina N, Marusin A, Stepanov VA, Qin Z, Khaliq S, Lee M-Y, Yang Y, Mohyuddin A, Gurwitz D, Mehdi SQ, Rogaev E, Jin L, Yankovsky NK, Kidd JR, Kidd KK (2009) Refined geographic distribution of the oriental ALDH2∗504Lys (nee 487Lys) variant. Ann Hum Genet 73:335–345PubMedPubMedCentral
55.
Kidd KK (2015) Further development of SNP panels for forensics (Final Technical Report for NIJ Grant# 2010-DN-BX-K225). US National Institute of Justice
56.
Jung JY, Yoon HK, An S, Lee JW, Ahn ER, Kim YJ, Park HC, Lee K, Hwang JH, Lim SK (2018) Rapid oral bacteria detection based on real-time PCR for the forensic identification of saliva. Sci Rep 8(1):10852PubMedPubMedCentral
57.
Zaumsegel D, Rothschild MA, Schneider PM (2013) A 21 marker insertion deletion polymorphism panel to study biogeographic ancestry. Forensic Sci Int Genet 7(2):305–312PubMed
Metadata
Title
Ancestry informative markers (AIMs) for Korean and other East Asian and South East Asian populations
Authors
Ju Yeon Jung
Pil-Won Kang
Eungsoo Kim
Diego Chacon
Dominik Beck
Dennis McNevin
Publication date
01-11-2019
Publisher
Springer Berlin Heidelberg
Published in
International Journal of Legal Medicine / Issue 6/2019
Print ISSN: 0937-9827
Electronic ISSN: 1437-1596
DOI
https://doi.org/10.1007/s00414-019-02129-7

Other articles of this Issue 6/2019

International Journal of Legal Medicine 6/2019 Go to the issue

Original Article

Characterization of new chloroplast markers to determine biogeographical origin and crop type of Cannabis sativa

Original Article

The use of FTA cards to acquire DNA profiles from postmortem cases

Case Report

Sudden unexpected cardiac death and postmortem identification of a novel RYR2 gene mutation

Review

Analysis of RNA in the estimation of post-mortem interval: a review of current evidence

Original Article

Utility of ForenSeq™ DNA Signature Prep Kit in the research of pairwise 2nd-degree kinship identification

Original Article

Novel Y-chromosome short tandem repeat sequence variation for loci DYS710, DYS518, DYS385, DYS644, DYS612, DYS626, DYS504, DYS481, DYS447 and DYS449