Establishing multiple omics baselines for three Southeast Asian populations in the Singapore Integrative Omics Study

被引：40

作者：

Saw, Woei-Yuh ^{[1
,2
]}

Tantoso, Erwin ^{[1
]}

Begum, Husna ^{[2
,3
]}

Zhou, Lihan ^{[4
]}

Zou, Ruiyang ^{[4
]}

He, Cheng ^{[4
]}

Chan, Sze Ling ^{[5
]}

Tan, Linda Wei-Lin ^{[1
]}

Wong, Lai-Ping ^{[1
]}

Xu, Wenting ^{[1
]}

Kyin, Don ^{[1
]}

Moong, Nwe ^{[1
]}

Lim, Yenly ^{[1
]}

Li, Bowen ^{[1
]}

Pillai, Nisha Esakimuthu ^{[2
]}

Peterson, Trevor A. ^{[6
,7
]}

Bielawny, Tomasz ^{[6
,7
]}

Meikle, Peter J. ^{[3
,8
]}

Mundra, Piyushkumar A. ^{[3
]}

Lim, Wei-Yen ^{[1
]}

Luo, Ma ^{[6
,7
]}

Chia, Kee-Seng ^{[1
]}

Ong, Rick Twee-Hee ^{[1
]}

Brunham, Liam R. ^{[5
]}

Khor, Chiea-Chuen

Too, Heng Phon ^{[11
,12
,13
]}

Soong, Richie ^{[14
]}

Wenk, Markus R. ^{[2
,9
,15
,16
,17
]}

Little, Peter ^{[2
]}

Teo, Yik-Ying ^{[1
,2
,9
,10
,15
,18
]}

机构：

[1] Natl Univ Singapore, Saw Swee Hock Sch Publ Hlth, 12 Sci Dr, Singapore 117549, Singapore

[2] Natl Univ Singapore, Life Sci Inst, 28 Med Dr, Singapore 117456, Singapore

[3] Baker IDI Heart & Diabet Inst, 75 Commercial Rd, Melbourne, Vic 3004, Australia

[4] Agcy Sci Technol & Res Singapore, MiRXES, 10 Biopolis Rd, Singapore 138670, Singapore

[5] Agcy Sci Technol & Res Singapore, Translat Lab Genet Med, 8A Biomed Grove, Singapore 138648, Singapore

[6] Univ Manitoba, Dept Med Microbiol, 730 William Ave, Winnipeg, MB R3E 0Z2, Canada

[7] Natl Microbiol Lab, 1015 Arlington St, Winnipeg, MB R3E, Canada

[8] Univ Melbourne, Dept Biochem & Mol Biol, Bio21,30 Flemington Rd, Melbourne, Vic 3010, Australia

[9] Genome Inst Singapore, Agcy Sci Technol & Res Singapore, 60 Biopolis St, Singapore 138672, Singapore

[10] Singapore Eye Res Inst, 20 Coll Rd, Singapore 169856, Singapore

[11] Natl Univ Singapore, Yong Loo Lin Sch Med, Dept Biochem, 8 Med Dr, Singapore 117597, Singapore

[12] Singapore Massachusetts Inst Technol Alliance, Mol Engn Biol & Chem System Chem Pharmaceut Engn, 4 Engn Dr 3, Singapore 117576, Singapore

[13] BioprocTechnol Inst, A STAR Agcy Sci Technol & Res Singapore, 20 Biopolis Way, Singapore 138668, Singapore

[14] Natl Univ Singapore, Canc Sci Inst Singapore, 14 Med Dr, Singapore 117599, Singapore

[15] Natl Univ Singapore, NUS Grad Sch Integrat Sci & Engn, 28 Med Dr, Singapore 117456, Singapore

[16] Chinese Acad Sci, Inst Genet & Dev Biol, State Key Lab Mol Dev Biol, 1 West Beichen Rd, Beijing 100101, Peoples R China

[17] Natl Univ Singapore, Dept Biol Sci, 16 Sci Dr 4, Singapore 117543, Singapore

[18] Natl Univ Singapore, Dept Stat & Appl Probabil, 6 Sci Dr 2, Singapore 117546, Singapore

来源：

NATURE COMMUNICATIONS | 2017年 / 8卷

基金：

新加坡国家研究基金会; 英国医学研究理事会;

关键词：

TYPING IDENTIFIED 2; GENE-EXPRESSION; HYPERSENSITIVITY REACTIONS; POSITIVE SELECTION; HLA ALLELES; DATABASE; PHARMACOGENETICS; CARBAMAZEPINE; ASSOCIATION; DIVERSITY;

D O I：

10.1038/s41467-017-00413-x

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

The Singapore Integrative Omics Study provides valuable insights on establishing population reference measurement in 364 Chinese, Malay, and Indian individuals. These measurements include > 2.5 millions genetic variants, 21,649 transcripts expression, 282 lipid species quantification, and 284 clinical, lifestyle, and dietary variables. This concept paper introduces the depth of the data resource, and investigates the extent of ethnic variation at these omics and non-omics biomarkers. It is evident that there are specific biomarkers in each of these platforms to differentiate between the ethnicities, and intra-population analyses suggest that Chinese and Indians are the most biologically homogeneous and heterogeneous, respectively, of the three groups. Consistent patterns of correlations between lipid species also suggest the possibility of lipid tagging to simplify future lipidomics assays. The Singapore Integrative Omics Study is expected to allow the characterization of intra-omic and inter-omic correlations within and across all three ethnic groups through a systems biology approach.

引用

页数：11

共 62 条

[31] Reducing hypersensitivity reactions with HLA-B*5701 genotyping before abacavir prescription: clinically useful but is it cost-effective in Singapore? [J].

Kapoor, Ritika ;

Martinez-Vega, Rosario ;

Dong, Di ;

Tan, Sharlene Yanying ;

Leo, Yee-Sin ;

Lee, Cheng-Chuan ;

Sung, Cynthia ;

Oon-Tek Ng ;

Archuleta, Sophia ;

Teo, Yik-Ying .

PHARMACOGENETICS AND GENOMICS, 2015, 25 (02) :60-72

[32] The IntAct molecular interaction database in 2012 [J].

Kerrien, Samuel ;

Aranda, Bruno ;

Breuza, Lionel ;

Bridge, Alan ;

Broackes-Carter, Fiona ;

Chen, Carol ;

Duesbury, Margaret ;

Dumousseau, Marine ;

Feuermann, Marc ;

Hinz, Ursula ;

Jandrasits, Christine ;

Jimenez, Rafael C. ;

Khadake, Jyoti ;

Mahadevan, Usha ;

Masson, Patrick ;

Pedruzzi, Ivo ;

Pfeiffenberger, Eric ;

Porras, Pablo ;

Raghunath, Arathi ;

Roechert, Bernd ;

Orchard, Sandra ;

Hermjakob, Henning .

NUCLEIC ACIDS RESEARCH, 2012, 40 (D1) :D841-D846

[33] Interethnic variability of warfarin maintenance requirement is explained by VKORC1 genotype in an Asian population [J].

Lee, SC ;

Ng, SS ;

Oldenburg, J ;

Chong, PY ;

Rost, S ;

Guo, JY ;

Yap, HL ;

Rankin, SC ;

Khor, HB ;

Yeo, TC ;

Ng, KS ;

Soong, R ;

Goh, BC .

CLINICAL PHARMACOLOGY & THERAPEUTICS, 2006, 79 (03) :197-205

[34] Shorthand notation for lipid structures derived from mass spectrometry [J].

Liebisch, Gerhard ;

Vizcaino, Juan Antonio ;

Koefeler, Harald ;

Troetzmueller, Martin ;

Griffiths, William J. ;

Schmitz, Gerd ;

Spener, Friedrich ;

Wakelam, Michael J. O. .

JOURNAL OF LIPID RESEARCH, 2013, 54 (06) :1523-1530

[35] Warfarin pharmacogenetics: a single VKORC1 polymorphism is predictive of dose across 3 racial groups [J].

Limdi, Nita A. ;

Wadelius, Mia ;

Cavallari, Larisa ;

Eriksson, Niclas ;

Crawford, Dana C. ;

Lee, Ming-Ta M. ;

Chen, Chien-Hsiun ;

Motsinger-Reif, Alison ;

Sagreiya, Hersh ;

Liu, Nianjun ;

Wu, Alan H. B. ;

Gage, Brian F. ;

Jorgensen, Andrea ;

Pirmohamed, Munir ;

Shin, Jae-Gook ;

Suarez-Kurtz, Guilherme ;

Kimmel, Stephen E. ;

Johnson, Julie A. ;

Klein, Teri E. ;

Wagner, Michael J. .

BLOOD, 2010, 115 (18) :3827-3834

[36] Differential positive selection of malaria resistance genes in three indigenous populations of Peninsular Malaysia [J].

Liu, Xuanyao ;

Yunus, Yushimah ;

Lu, Dongsheng ;

Aghakhanian, Farhang ;

Saw, Woei-Yuh ;

Deng, Lian ;

Ali, Mohammad ;

Wang, Xu ;

Ghazali, Fadzilah ;

Rahman, Thuhairah Abdul ;

Shaari, Shahrul Azlin ;

Salleh, Mohd Zaki ;

Phipps, Maude E. ;

Ong, Rick Twee-Hee ;

Xu, Shuhua ;

Teo, Yik-Ying ;

Hoh, Boon-Peng .

HUMAN GENETICS, 2015, 134 (04) :375-392

[37] Expression monitoring by hybridization to high-density oligonucleotide arrays [J].

Lockhart, DJ ;

Dong, HL ;

Byrne, MC ;

Follettie, MT ;

Gallo, MV ;

Chee, MS ;

Mittmann, M ;

Wang, CW ;

Kobayashi, M ;

Horton, H ;

Brown, EL .

NATURE BIOTECHNOLOGY, 1996, 14 (13) :1675-1680

[38] High-resolution sequence-based DPA1 typing identified two novel DPA1 alleles, DPA1*010303 and DPA1*0303, from a Kenyan population [J].

Luo, M ;

Bamforth, J ;

Gill, K ;

Cohen, C ;

Brunham, RC ;

Plummer, FA .

TISSUE ANTIGENS, 2005, 65 (01) :120-122

[39] High resolution sequence-based DPB1 typing identified two novel DPB1 alleles, DPB1*9401 and DPB1*9501, from a Kenyan population [J].

Luo, M ;

Ramdahin, S ;

Iqbal, S ;

Pan, Y ;

Jacobson, K ;

Narayansingh, MJ ;

Schroeder, M ;

Brunham, RC ;

Embree, J ;

Plummer, FA .

TISSUE ANTIGENS, 2003, 62 (02) :182-184

[40] UniProt Knowledgebase: a hub of integrated protein data [J].

Magrane, Michele .

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, 2011,

← 1 2 3 4 5 6 7 →