Ancestry Informative Marker (AIM)

 

Ancestry informative markers (AIMs) can be used to trace the origin of individuals who have differential genetic background and have been applied to various study fields such as population genetics, medical genetics, forensic sciences, and animal sciences.

AIMs that have a significant difference of allele frequency (AF) among the studied populations in a continent and among the five-continent ancestry groups, i.e., Africa (AFR), Americas (AMR), East-Asia (EAS), South-Asia (SAS), and Europe (EUR)), are identified.

Page “AF” provides allele frequency and adjusted p-value of genetic association.

Page “Pharmacogenomics (AIM)” provides a catalog of AIMs associated with drugs and their related biological and pharmacogenetics information for global continents and populations.

Description of columns

Column

Column name

Content

Range or category
of variable

Remark

1

RSID

 RS number based on NCBI 37   The SNP information is available in the 1KG Project

2

ACB

 Minor allele frequency (minor allele) of
African Caribbean in Barbados		 [0, 0.5] (A, C, G, T) The minor allele and the corresponding allele frequency are
provided and calculated from the 1KG Project data, respectively

3

ASW

 Minor allele frequency (minor allele) of
Africa Ancestry in Southwest US		 As above As above

4

ESN

 Minor allele frequency (minor allele) of
Esan in Nigeria		 As above As above

5

GWD

 Minor allele frequency (minor allele) of
Gambian in Western Division, Mandinka		 As above As above

6

LWK

 Minor allele frequency (minor allele) of
Luhya in Webuye, Kenya		 As above As above

7

MSL

 Minor allele frequency (minor allele) of
Mende in Sierra Leone		 As above As above

8

YRI

 Minor allele frequency (minor allele) of
Yoruba in Ibadan, Nigeria		 As above As above

12

CLM

 Minor allele frequency (minor allele) of
Colombian in Medellin, Colombia		 As above As above

13

MXL

 Minor allele frequency (minor allele) of
Mexican Ancestry in Los Angeles, California		 As above As above

14

PEL

 Minor allele frequency (minor allele) of
Peruvians in Lima, Peru		 As above As above

15

PUR

 Minor allele frequency (minor allele) of
Puerto Rican in Puerto Rico		 As above As above

19

CDX

 Minor allele frequency (minor allele) of
Chinese Dai in Xishuangbanna, China		 As above As above

20

CHB

 Minor allele frequency (minor allele) of
Han Chinese in Bejing, China		 As above As above

21

CHS

 Minor allele frequency (minor allele) of
Southern Han Chinese, China		 As above As above

22

JPT

 Minor allele frequency (minor allele) of
Japanese in Tokyo, Japan		 As above As above

23

KHV

 Minor allele frequency (minor allele) of
Kinh in Ho Chi Minh City, Vietnam		 As above As above

27

CEU

 Minor allele frequency (minor allele) of
Utah residents with Northern and Western European ancestry		 As above As above

28

FIN

 Minor allele frequency (minor allele) of
Finnish in Finland		 As above As above

29

GBR

 Minor allele frequency (minor allele) of
British in England and Scotland		 As above As above

30

IBS

 Minor allele frequency (minor allele) of
Iberian populations in Spain		 As above As above

31

TSI

 Minor allele frequency (minor allele) of
Toscani in Italia		 As above As above

32

BEB

 Minor allele frequency (minor allele) of
Bengali in Bangladesh		 As above As above

36

GIH

 Minor allele frequency (minor allele) of
Gujarati Indians in Houston, TX, USA		 As above As above

37

ITU

 Minor allele frequency (minor allele) of
Indian Telugu in the UK		 As above As above

38

PJL

 Minor allele frequency (minor allele) of
Punjabi in Lahore, Pakistan		 As above As above

39

STU

 Minor allele frequency (minor allele) of
Sri Lankan Tamil in the UK		 As above As above

43

AFR

 Minor allele frequency (minor allele) of
African populations		 As above As above

44

AMR

 Minor allele frequency (minor allele) of
American populations		 As above As above

45

EAS

 Minor allele frequency (minor allele) of
East-Asia populations		 As above As above

46

EUR

 Minor allele frequency (minor allele) of
European populations		 As above As above

47

SAS

 Minor allele frequency (minor allele) of
South-Asia populations		 As above As above

9, 16, 24, 33, 40, 48

Type

 Types of SNVs wg/common, wg/rare, or wg/common×rare SNVs are categorized into common and rare variants by populations

10, 17, 25, 34, 41, 49

FDRp

 FDR adjusted p-values from Fisher’s exact tests across whole genome [0,1] Ancestry informative markers (AIMs) were identified by using Fisher’s exact test

11, 18, 26, 35, 42, 50

FDRp

 FDR adjusted p-values from Fisher’s exact tests according to one of Types [0,1] Ancestry informative markers (AIMs) were identified by using Fisher’s exact test
RSID AFR   AMR   EAS   EUR   SAS   Continent
MAF Type FDRp MAF Type FDRp MAF Type FDRp MAF Type FDRp MAF Type FDRp MAF Type FDRp
ACB ASW ESN GWD LWK MSL YRI     CLM MXL PER PUR     CDX CHB CHS JPT KHV     CEU FIN GBR IBS TSI     BEB GIH ITU PJL STU     AFR AMR EAS EUR SAS    
Description of columns

Column

Column name

Content

Range or category of variable

Remark

1

RSID

 RS number based on NCBI 37   The SNP information is available in the 1000 genomes Project

2

Nucleotide
Change

 Nucleotide change (genotype) of SNV 12 types:
A>C, A>G, A>T, C>A, C>G, C>T, G>A, G>C, G>T, T>A, T>C, and T>G		 For example, A>C indicates that A is a reference allele and C is an alternative allele. The information is available in the 1000 genomes Project

3

Gene
Symbol

 The gene that SNV is located   Official symbol provided by HGNC

4

Functional
Annotation

 Types of genomic SNV
(Variant Effect Predictor)		 35 types:
Refer to here		 The functional annotation was collected from the ftp site of the 1000 Genomes Project

5

Gene
Regulation

 Types of gene regulations
(Ensembl Regulatory Build)		 5 types:
ctcf insulator, distal enhancer, promoter region, proximal enhancer, and unannotated tfbs		 The gene regulation information was collected from the ftp site of the 1000 Genomes Project

6

Bio-
transformation

 The classes of genes CYP endogenous substrates, CYP exogenous substrates, CYP unkown substrates, non-CYP Phase I Metablizing Enzyme, Phase II Metabolizing Enzyme, Transcription factor, Transporter, and Other The information was from Maisano Delser, P. and S. Fuselli (2013) Human Genetics 132(5): 563-577

7

ADME
Class

 The classes of genes associated with drug metabolism Phase I, Phase II and Transporter The information was from PharmaADME.org

8

Drug

 SNV-associated drugs   The information was from DrugBank and PharmGKB

 

RSID Nucleotide
Change		 Gene
Symbol		 Functional
Annotation		 Gene
Regulation		 Bio-
transformation		 ADME
Class		 Drug

Ancestry Informative Gene (AIG)

 

Ancestry informative genes (AIGs) that have a significant difference of homozygosity intensity (HI) among the studied populations in a continent and among the five-continent ancestry groups are identified.

Page “HI” provides average HI and adjusted p-value of genetic association.

Page “Pharmacogenomics (AIG)” provides a catalog of the AIGs associated with drugs and the related biological and pharmacogenetics information for global continents and populations.

Description of columns

Column

Column name

Content

Range or category
of variable

Remark

1

Gene Symbol (Gene ID)

 Entrez Gene symbol (id)   The SNP information is available in the 1KG Project

2

ACB

 Gene-based median (average) of homozygosity intensity of
African Caribbean in Barbados		 [0, 1] ([0, 1]) The median (average) of homozygosity intensity across population/continent

3

ASW

 Gene-based median (average) of homozygosity intensity of
Africa Ancestry in Southwest US		 As above As above

4

ESN

 Gene-based median (average) of homozygosity intensity of
Esan in Nigeria		 As above As above

5

GWD

 Gene-based median (average) of homozygosity intensity of
Gambian in Western Division, Mandinka		 As above As above

6

LWK

 Gene-based median (average) of homozygosity intensity of
Luhya in Webuye, Kenya		 As above As above

7

MSL

 Gene-based median (average) of homozygosity intensity of
Mende in Sierra Leone		 As above As above

8

YRI

 Gene-based median (average) of homozygosity intensity of
Yoruba in Ibadan, Nigeria		 As above As above

10

CLM

 Gene-based median (average) of homozygosity intensity of
Colombian in Medellin, Colombia		 As above As above

11

MXL

 Gene-based median (average) of homozygosity intensity of
Mexican Ancestry in Los Angeles, California		 As above As above

12

PEL

 Gene-based median (average) of homozygosity intensity of
Peruvians in Lima, Peru		 As above As above

13

PUR

 Gene-based median (average) of homozygosity intensity of
Puerto Rican in Puerto Rico		 As above As above

15

CDX

 Gene-based median (average) of homozygosity intensity of
Chinese Dai in Xishuangbanna, China		 As above As above

16

CHB

 Gene-based median (average) of homozygosity intensity of
Han Chinese in Bejing, China		 As above As above

17

CHS

 Gene-based median (average) of homozygosity intensity of
Southern Han Chinese, China		 As above As above

18

JPT

 Gene-based median (average) of homozygosity intensity of
Japanese in Tokyo, Japan		 As above As above

19

KHV

 Gene-based median (average) of homozygosity intensity of
Kinh in Ho Chi Minh City, Vietnam		 As above As above

21

CEU

 Gene-based median (average) of homozygosity intensity of
Utah residents with Northern and Western European ancestry		 As above As above

22

FIN

 Gene-based median (average) of homozygosity intensity of
Finnish in Finland		 As above As above

23

GBR

 Gene-based median (average) of homozygosity intensity of
British in England and Scotland		 As above As above

24

IBS

 Gene-based median (average) of homozygosity intensity of
Iberian populations in Spain		 As above As above

25

TSI

 Gene-based median (average) of homozygosity intensity of
Toscani in Italia		 As above As above

27

BEB

 Gene-based median (average) of homozygosity intensity of
Bengali in Bangladesh		 As above As above

28

GIH

 Gene-based median (average) of homozygosity intensity of
Gujarati Indians in Houston, TX, USA		 As above As above

29

ITU

 Gene-based median (average) of homozygosity intensity of
Indian Telugu in the UK		 As above As above

30

PJL

 Gene-based median (average) of homozygosity intensity of
Punjabi in Lahore, Pakistan		 As above As above

31

STU

 Gene-based median (average) of homozygosity intensity of
Sri Lankan Tamil in the UK		 As above As above

33

AFR

 Gene-based median (average) of homozygosity intensity of
African populations		 As above As above

34

AMR

 Gene-based median (average) of homozygosity intensity of
American populations		 As above As above

35

EAS

 Gene-based median (average) of homozygosity intensity of
East-Asia populations		 As above As above

36

EUR

 Gene-based median (average) of homozygosity intensity of
European populations		 As above As above

37

SAS

 Gene-based median (average) of homozygosity intensity of
South-Asia populations		 As above As above

9, 14, 20, 26, 32, 38

FDRp

 FDR adjusted p-values from Kruskal-Wallis tests [0,1] Ancestry informative genes were identified by using Kruskal-Wallis test
Gene Symbol
(Gene ID)		 AFR   AMR   EAS   EUR   SAS   Continent
HI FDRp HI FDRp HI FDRp HI FDRp HI FDRp HI FDRp
ACB ASW ESN GWD LWK MSL YRI CLM MXL PER PUR CDX CHB CHS JPT KHV CEU FIN GBR IBS TSI BEB GIH ITU PJL STU AFR AMR EAS EUR SAS
Description of columns

Column

Column name

Content

Range or category of variable

Remark

1

Gene Symbol (Gene ID)

 Entrez Gene symbol (id)    

2

Tumor Suppressor Gene

 Tumor Suppressor Gene
(Tumor Suppressor Gene Database)		 Y (Yes) and N (No)  

3

ADME
Class

 The classes of genes associated with drug metabolism Phase I, Phase II and Transporter The information was from PharmaADME.org

4

Drug

 SNV-associated drugs   The information was from DrugBank and PharmGKB

 

Gene Symbol
(Gene ID)		 Tumor Supressor
Gene		 ADME
Class		 Drug

Authors

Hsin-Chou Yang

Chia-Wei Chen

Yu-Ting Lin

Shih-Kai Chu