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Table 1 Optimised panel of identifying SNPs

From: A SNP profiling panel for sample tracking in whole-exome sequencing studies

Chromosome

Positiona

dbSNP rsID

Gene

Alleles

HapMap 3 AF

     

CEU

CHB

JPT

YRI

1

179520506

rs1410592

NPHS2

A/C

0.59

0.62

0.54

0.53

1

67861520

rs2229546

IL12RB2

A/G

0.64

0.36

0.44

0.58

2

169789016

rs497692

ABCB11

A/Gb

0.55

0.65

0.51

0.22

2

227896976

rs10203363

COL4A4

C/T

0.46

0.44

0.36

0.57

3

4403767

rs2819561

SUMF1

A/Gb

0.56

0.73

0.73

0.72

4

5749904

rs4688963

EVC

A/Gb

0.33

0.65

0.67

0.52

5

82834630

rs309557

VCAN

A/Gb

0.49

0.34

0.52

0.50

6

146755140

rs2942

GRM1

C/T

0.54

0.49

0.55

0.47

7

48450157

rs17548783

ABCA13

C/T

0.46

0.72

0.53

0.48

8

94935937

rs4735258

PDP1

C/T

0.40

0.64

0.66

0.46

9

100190780

rs1381532

TDRD7

A/Gb

0.48

0.59

0.50

0.58

10

100219314

rs10883099

HPSE2

A/G

0.52

0.52

0.53

0.62

11

16133413

rs4617548

SOX6

C/T

0.52

0.65

0.61

0.51

12

993930

rs7300444

WNK1

A/G

0.46

0.55

0.48

0.28

13

39433606

rs9532292

FREM2

A/G

0.29

0.41

0.44

0.54

14

50769717

rs2297995

L2HGDH

A/G

0.55

0.65

0.67

0.59

15

34528948

rs4577050

SLC12A6

C/T

0.68

0.75

0.63

0.32

16

70303580

rs2070203

AARS

A/Gb

0.53

0.28

0.51

0.49

17

71197748

rs1037256

COG1

C/T

0.50

0.67

0.65

0.56

18

21413869

rs9962023

LAMA3

A/G

0.67

0.81c

0.75

0.51

19

10267077

rs2228611

DNMT1

C/Tb

0.47

0.73

0.56

0.48

20

6100088

rs10373

FERMT1

G/Tb

0.54

0.31

0.35

0.58

21

44323590

rs4148973

NDUFV3

C/T

0.65

0.33

0.38

0.73

22

21141300

rs4675

SERPIND1

A/C

0.46

0.62

0.51

0.57

  1. aPosition as defined in genome reference assembly GRCh37 (hg19).
  2. bSNP is defined on the negative strand.
  3. cAF marginally outside target range for candidate selection. Selected due to paucity of candidates on chromosome 18.