Vishwajit L. Nimgaonkar, M.D., Ph.D., Principal Investigator

 

 
 

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Supplemental Information Concerning the RGS4 Gene

  • Erratum: we recently discovered an unfortunate error in the snp7 data for the Bipolar sample reported on in the above paper.  This error does not change the association reported in the schizophrenia sample.  Click here to view the erratum to be published in Human Molecular Genetics, along with the relevant  tables omitted from the published erratum.

 

Untranslated Region

 

GTACGCTCAAAGCCGAAGCCACAGCTCCTCCTGCCGCATTTCTTTCCTGCTTGCGAATTCCAAGCTGTTAA
ATAAG

 

mRNA Sequence with Amino Acid Labeled

 

ATG

TGC

AAA

GGG

CTT

GCA

GGT

CTG

CCG

GCT

TCT

TGC

TTG

AGG

AG/T

M

C

K

G

L

A

G

L

P

A

S

C

L

R

S

GCA

AAA

GAT

ATG

AAA

CAT

CGG

CTA

GGT

TTC

CTG

CTG

CAA

AAA

TCT

A

K

D

M

K

H

R

L

G

F

L

L

Q

K

S

GAT

TCC

TGT

GAA

CAC

AAT

TCT

TCC

CAC

AAC

AAG

AAG

GAC

AAA

GTG

D

S

C

E

H

N

S

S

H

N

K

K

D

K

V

GTT

ATT

TGC

CAG

AG/A

GTG

AGC

CAA

GAG

GAA

GTC

AAG

AAA

TGG

GCT

V

I

C

Q

R

V

S

Q

E

E

V

K

K

W

A

GAA

TCA

CTG

GAA

AAC

CTG

ATT

AGT

CAT

GAA

TGT/

GGG

CTG

GCA

GCT

E

S

L

E

N

L

I

S

H

E

C

G

L

A

A

TTC

AAA

GCT

TTC

TTG

AAG

TCT

GAA

TAT

AGT

GAG

GAG

AAT

ATT

GAC

F

K

A

F

L

K

S

E

Y

S

E

E

N

I

D

TTC

TGG

ATC

AGC

TGT

GAA

GAG

TAC

AAG

AAA

ATC

AAA

TCA

CCA

TCT

F

W

I

S

C

E

E

Y

K

K

I

K

S

P

S

AAA

CTA

AGT

CCC

AAG

GCC

AAA

AAG

ATC

TAT

AAT

GAA

TTC

ATC

TCA

K

L

S

P

K

A

K

K

I

Y

N

E

F

I

S

GTC

CAG

GCA

ACC

AAA

GAG

GT/G

AAC

CTG

GAT

TCT

TGC

ACC

AGG

GAA

V

Q

A

T

K

E

V

N

L

D

S

C

T

R

E

GAG

ACA

AGC

CGG

AAC

ATG

CTA

GAG

CCT

ACA

ATA

ACC

TGC

TTT

GAT

E

T

S

R

N

M

L

E

P

T

I

T

C

F

D

GAG

GCC

CAG

AAG

AAG

ATT

TTC

AAC

CTG

ATG

GAG

AAG

GAT

TCC

TAC

E

A

Q

K

K

I

F

N

L

M

E

K

D

S

Y

CGC

CGC

TTC

CTC

AAG

TCT

CGA

TTC

TAT

CTT

GAT

TTG

GTC

AAC

CCG

R

R

F

L

K

S

R

F

Y

L

D

L

V

N

P

TCC

AGC

TGT

GGG

GCA

GAA

AAG

CAG

AAA

GGA

GCC

AAG

AGT

TCA

GCA

S

S

C

G

A

E

K

Q

K

G

A

K

S

S

A

GAC

TGT

GCT

TCC

CTG

GTC

CCT

CAG

TGT

GCC

TAA

        

D

C

A

S

L

V

P

Q

C

A

stop

        

 

Untranslated Region

 

TTCTCACCTGAAGGCAGAGGGATGAAATGCCAAGACTCTATGCTCTGGAAAACCTGAGGCCAAATATTGAT
CTGTATTAAGCTCCAGTGCTTTATCCACATTGTAGCCTAATATTCATGCTGCCTGCCATGTGTGAGTCACT
TCTACGCATAAACTAGATATAGCTTTTGGTGTTTGAGTGTTCATCAGGGTGGGACCCCATTCCAGTCCAAT
TTTCCTAAGTTTCTTTGAGGGTTCCATGGGAGCAAATATCTAAATAATGGCCTGGTAGGTCTGGATTTTCA
AAGATTGTTGGCAGTTTCCTCCTCCCAACAGTTTTACCTCGGGATGGTTGGTTAGTGCATGTCACATGACA
TCCACATGCACATGTATTCTGTTGGCCAGCACGTTCTCCAGACTCTAGATGTTTAGATGAGGTTGAGCTAT
GATATGTGCTTGTGTGTATGTCTATGTGTATATATTATATATACATTAGACACACATATACATTATTTCTG
TATATAGATGTCTGTGTATACATATGTATGTGTGAGTGTATGTATACACACACACACACACACACACACAC
ACTTTTGCAAGAGTGATGGGAAAGACCCTAGGTGCTCATAACTAGAGTATGTGTATGTACTTACATGGGTG
TTTTGATCTCTGTTCTTTCATACTACATTTGAACAGGGCAAAATGAACTAACTGCCATGTAGGCTAAGAAA
GAAATGCTAACCTGTGGAAAGTTGGTTTTGTAAAATTCCATGGATCTTGCTGGAGAAGCATCCAAGGAACT
TCATGCTTGATTTGACCACTGACAGCCTCCACCTTGAGCACTATTCTAAGGAGCAAATACCTTAGCTCCCT
TGAGCTGGTTTTCTCTGATGGCACTTTTGAGCTCCTAAGCTGCCAGCCTTCCCTTCTTTTCCTGGGTGCTC
AGGGCATGCTTATTAGCAGCTGGGTTGGTATGGAGTTGGCAGACAGGATGTTCAACTTAATGAAGAAATAC
AGCTAAGGCCTTGCCAGCAACACCTGCCGTAAGTTACTGGCTGAGTGAGGGCATAGAAGTTAAAGGTTACT
GTTTTTATCCTCTATCCTTTTTTCCTTTCCTGATCAAGGTGCTCTTCTCATTTTTTCCTGAGAACCTTAGC
CATCAGATGAGGCTCCTTAGTTTATTGTGGTTGGTTGTTTTTTCTTTATAATGGCTCTGGGCTATATGCCT
ATATTTATAAACCAGCAGCAGGGGAAAGATTATATTTTATAAGAGGGAACAAATTTTCACAATTTGAAAAG
CCCACATAAGTTTTCTCTTTTAAGGTAGAATCTTGTTAATTTCATTCCAAACATCGGGGCTAACAGAGACT
GGAGGCATTTCTTTTTAGGCTCTGAGACTAAATGAGAGGAAAAGAAAAGAAAAAAAAAATGATTGTCTAAC
CAATTGTGAGAATTACTGTTTGAAACTTTTCAAGGCACATTGAAATACTTGAAAACTTCTCATTTATGTTA
TTTATGATGTTATTTTGTACGTGTTATTATTATTATATTGTTTTATAAATGGAGGTACAGGATATCACCTG
AATTATTAATGAATGCCCAGGAAGTAATTTTCTTCTCATTCTTCTAAAACTACTGCCTTTCAAAGTGCACA
CACACGCGTCCACATACACTGCATTCGTTGCTCCAGTATAAATTACATGCATGAGCACCTTTCTGGCTTTT
AAGCCAATATAATGGGCTGCAAAATGAAGACACCAGAGTGTATGCATACAAATCTCACTGTATTAAAGATG
CAGGTTTTCTAATTGTACCCTTCTTGTCTCTCTGGCAATCTTGCCCTTAATATCCCTGGAGTTCCTCATCA
GTGTCATTTTCTGTTATACACAGTTCCACAATTTTGTCTCTAGTTGACTTCAAATGTGTAACTTTATTGGT
CTTGCCCTATTATAATTGTCATGACTTTCAGATTGTATCTGAACTCACAGACTGCTGTCTTACTAATAGGT
CTGGAAGGTCACGCTGAATGAGAAGTAAATTATTTTATGTAATACATTTTTGAGTGTGTTTTTCAGTTGTA
TTTCCCTGTTATTTCATCACTATTTCCAATGGTGAGCTTGCCTGCTCATGCTCCCTGGACAGAATACTCCT
TCCTTTTGCATGCCTGTTTCTATCATGTGCTTGATAGGCCTCAAAGCTAATGCTTCCAGTGAAACACACGC
ATCTTAATAATAAGGGTAAATAAACGCTCCATATGAAAC

 

Assay Information:

 

SNP

Type

Annealing Temp

PCR Product(bp)

Assay Method

Forward Primer

(5'-3')

Reverse Primer(5'-3')

FP Primer

ddNTP

27859

T/C

500C

386 (277+109)

SphI

aattgccccaatccttctct

gcatctggacaatgtcttgg

90387

G/A

600C

324 (262+62)

MboII

gctagttgtgtgatttgggaca

tgctctcacttagcctgctg

SNP1

G/A

500C

310 (187+123)

BstNI

ggtgtcatggaaagtgcttg

ggcacagaacaggggaaata

    

SNP4

T/G

500C

115

SSCP/FP

cagaagcctccctccttctt

tatacagcatcctccagccc

5' TCT TTG CTT TTT AGT CCT AAA A3'

A/C

SNP7

G/A

600C

191(153+38)

DdeI

agaaagaaagcttgggaggc

gttcacatcctgctgtgtgg

    

SNP14

Ins/Del

600C

150/157

PAGE

ggaccaaaggagggagtagat

ttttctgcctgctctctctc

SNP18

A/G

600C

138

SSCP/FP

tggggcagagagataaggaa

aggtttggctccatcatcag

5' CTC CAT CAT CAG AAA GGC ACT A 3'

C/T

SNP23

C/A

600C

207 (155+52)

BamHI

ctcctctgcttccctgactg

taagcacacttaccccctgc

118740

C/G

600C

341 (215+75+51)

BstNI

tgcctttgagggtgttaaaaa

tgggtatcagatgggagattg

130121

G/C

600C

317 (205+112)

EcoRV

aggcacactgggaagttaca

tccttcctcactttatttctctgg

187688

C/G

600C

399 (273+126)

PvuII

ggcaggggacttgatcttct

cattgcatttgattgtttgga

208899

A/T

600C

345 (227+118)

ApoI

tggtttctcagtggagtgga

ttgaatgagatcactttgggataa

217761

C/T

600C

329 (258+71)

AvaI

tgccataacactgcatgagc

tgaccttgggttagagtgtgc

322448

A/T

600C

344 (247+97)

EcoRI

gcctttcaaaagtgaagagca

tttgccaacaaaaaccatca

 

DNA Sequence Information for RGS4 SNPs

(bold face indicates the SNP and the Primers positions)

 

 

SNP 27859

 

ggattaatcatgacaaaagtaatctaaatctcgttaagactacttaatgatcaatctttc

 

cctctgttttccctgactatagggaagtg aattgccccaatccttctct atcacccccct

 

gcagccatgccaatgccttacctctgttatattcagccataggggaagcttattctcata

 

gaatcaggggttggcatg t/c agtcactagctattcttggtgagactagtgaagatgagtga

 

aggaaaatattgcataggtgaaatctcataggcacaaataggtgtttgtgagagtaacaa

 

taaaagaaagtcattcccatactctagtagatgactcattttctcctcattttttttttt

 

tcaaggcgttctctacaacggttaacctagtaccaaaaatccttctcttttttcttggac

 

aaatcctgttcaagttagcatggcatttactacgt ccaagacattgtccagatgc tgtgg

 

 

 

SNP 90387

 

ataatctcctttcaagtttttatcctgtcactt gctagttgtgtgatttgggaca aatca

 

tttaactccttgtaaagggagagaag g/a aaggctgtaaaaaaattaagtaataaaaagata

 

aactccttgtggtatattttgttattgttcaaaaatatttattgcccctcttaggatgtc

 

ttaggtcattcttgcattgctataaagaaatacccaagtctgggtaatttataaagaata

 

gaggttaaattggctcacagttctgcaggctgcacaggaagcatcccactggcgtctact

 

cacttctggtgaggactcagaaagcttttgcttatga cagcaggctaagtgagagca ggt

 

 

 

SNP 1

 

aggggaagaaaaccttgtttcccaagaaggaggagaaaacccaaaatagccttatcccaaagattaaatc

 

ttttttctgcaacatttagcccaggatagaaacagcagtttcataagagttcatttgcattgtgcaggtg

 

gaaagaaacagtat ggtgtcatggaaagtgcttg aactttacagagaggcagatctggattccaattcta

 

gatcctctaggaaatcttggtaaattagggtaaactttatgacctctagttttgtaacgtgccctg g/a act

 

tcaatttgccctcacattttaaaatctagattccttagcataacattctggtactttcataattcatccc

 

cattccaacttttcatctttcccttccactcttttcttcattatattctactatgtagtcatcccagacc

 

actgaatattcccacacatttatg tatttcccctgttctgtgcc atcaacctgaaatgtcttcacagtac

 

cctgcggtcaagctcttttttctcctgtcgccagtggtaatcaactgctacctcttatgcactctagaag

 

tatggtgtttgagccagacctctgtttcgctcctctttaaatccgatcatgttacatttgccaataacgt

 

 

 

SNP4

 

gagttgcgttctttagttctaccagatattaaatggggcactgatcctccacttgggcaggatgtaggcc

 

aaggctcagccccaggctgtgcttgcaccacttcagatgacaatttcctctcagttgt cagaagcctccc

tccttctt tattgtttactacaatggcctagacatcaatgagagttcagttattga g/t ttttaggactaaa

 

aagcaaagatatg gggctggaggatgctgtata ccaggaaggtaaacagggacttcccagtatgtcttac

 

ttttgggaaatgtgtccaattctttgcaccaagctttgtgggcacatgcaataaatcaggaactccaacc

 

 

 

SNP7

 

Aagaggtagttcaagtacttaagccgatcaggttagcattct agaaagaaagcttgggaggc agagtaaa

 

agaatagattggatatcagagaaactggcaaaaagtttgaaggctattttaagttccttaaattgtaaaa

 

tgctaacatctggaaggtattgttgacaataggctttagaagaactgtttcctactg g/a ggggcagacatt

 

cag ccacacagcaggatgtgaac tatgtgtggtctctaggtaaatttcaaatttttccaacctttgctca

 

gggagaacaaaagaaaacatttctcaaggattgacggtatcaaatgcagggaaataagtcattgtggcag

 

 

 

SNP18

 

tttaagatgagatcttctacaaaactattaactgatttgtaatgatcaatatttctcaaccaaactcata

 

tgagacacttcaagaactagaga tggggcagagagataaggaa gatctggctttaaaactcatatctcat

 

tgtaacattttcttataagaacatagagagtgaaagttactgcaccaccacacggaaagc g/a tagtgcctt

 

t ctgatgatggagccaaacct cattctggggtacctttcctgaaacaagttgtagcatacaatcagaaag

 

cccagagccaggcttctatgtactccagggatgctcaaatagcagtagtaatcacagatggagatattac

 

 

 

SNP23

 

Tcc ctcctctgcttccctgactg atgactgttcaggggatgcaacatcctttttgattataacaagatac

 

aatcctgaatgttagggtgattccaaggtgataatgtaaatatatcatgaagtccaaatagaaacgaatt

 

catatttctatgtgctggatc c/a acctgagatcctagagttattaatcaat gcagggggtaagtgtgctta

 

gcaagtattcttataataaaaccataaaaataaaaaacaaaatgacttcagaagttactggagtcaggaa

 

 

 

SNP118740

 

catggtatttttactacccattgccttctaggaaagggtataacaaataggaaatattaa

 

tatttttaa tgcctttgagggtgttaaaaa gcacaactctaaggactgtttgtaaattc c/g

 

aggtcaaatgttgtttctccttctctatttcctaccttggtgatggcctgatcttatatg

 

gagtcactccaactagaaaccacagaatcatccctagttcctacttctgactcactccat

 

acactcaaaagtcacctgactctgcagaatttctctagaaaaactctatgaaaacctatt

 

cctgcctctccacctgcatagatgtagcttcatccaggctcttatggtgcatggcctcgg

 

ttactgccttatcctttctactggcctct caatctcccatctgataccca ttaatgtact

 

 

 

SNP130121

 

ccaaatacttttt aggcacactgggaagttaca ttgtttcttgcaagtgacaggttgtcc

 

tttaattagttctttctctcaaaaagagactgctgactccaaactgggaagaaacccact

 

caccagcaaaatgctgctgaattcactctgatagttttctaatctctcatcagtagatga

 

caataatgaagccagtattgttaccacaagactcagatat g/c tctatcacccaagatgatt

 

tctctttaagacgcaataaaagggaacttttctccccatttattagcaactaagatgaaa

 

tgagag ccagagaaataaagtgaggaagga aagagaatttactacctttacaagctgaaa

 

 

 

SNP187688

 

tt ggcaggggacttgatcttct tgtaatcctcacaggcaatccagaactcaaggttttcc

 

tcactgaattcagacttcaggaaacttttgaaactggcaagtccatctggaaagaaaaaa

 

acagtca c/g ctggagaaatttattaatttacttaacaaatattgtatccatgagagaaagg

 

gaaagggcttagcaatactcttctatgcacaaagttttagctcattcatgtctagcttcc

 

tttactccttcattcaaatgcagaaggaatgagacagagatggaagatagacagcagaga

 

acacagagctcaagccctgctcatcatgcagagccgtatggaactctagaactagacaga

 

gagatttaccacattgtctt tccaaacaatcaaatgcaatg tctatttaagtgacaaacg

 

 

 

SNP208899

 

gtattccttaaattaacaatctttttctctgtgaagaatat tggtttctcagtggagtgg

a agtatataaacaatcccaaatcaagacatagatttgctctgtcttcaaggagtttacaa

 

acacatcaaagaagagaagatatatttagaccttttta a/t aattttttaaagtaataaagc

 

cacagtgaagaaaatgtaaagaaaagagaaaaatcaacccccaatcccaccactctaaca

 

gtctctggccatgtcttttaataacttatgctgatccctccttttcttgtggattcttaa

 

tgtatcagaacccagggtttggtccttggacttctcatcttttctatcgtttctatcttc

 

ac ttatcccaaagtgatctcattcaa tcttatggctttaaatgctatctgtatgctgatg

 

 

 

SNP 217761

 

atttccagtgttgtatgtaatacagggatatagaattcagattcaaagcctatgcttttt

 

tctcatga tgccataacactgcatgagc cttgagtttgaaattaatttggatttgaagta

 

ataaaaataaatttaggtcc c/t gagtgatttttctttttgcttctcttgctttacagtcaa

 

ttgatgagatctttggatggtttgcatcattttttaatcctatataaatatttgtttctt

 

tcatttgcctattttggctttctttagaaaatggtcttagtttattgaaattatcgccag

 

tgctttaaagagtatgacttccagtcaattcagttccacagttttattgagcaaatatca

 

tggattcaaaattagc gcacactctaacccaaggtca tatagagtggtataaaggacttt

 

 

 

SNP 322448

 

cagttatttgaggacaggtatttcatttta gcctttcaaaagtgaagagca gtattttaa

 

tctattttgctgtgttaagttctgttccagttgaagagcaagaagagttcaagcagcttt

 

cagatgg a/t attcaggagctacaacaatcactaaatcaggattttcatcaaaaaacggtat

 

ctgttgtgaggcaccttaaactttaaaaaataaaatttgtttgtagatgtggtgggacat

 

atagtggaggtaacagcacattgctttctctattaccaaagaaacagaatatatttctgt

 

gcccatttgtgccccttataatggatacatacttctctcaaccatctagaaccg tgatgg

 

tttttgttggcaaa gttttttgttgtcttattgaatagaattttttagggttttcctagg

 

 

dbSNP (NCBI rs#)

SNP not in the manuscript

879719

27859

1507754

90387

not listed

SNP1

951436

SNP4

951439

SNP7

2661319

SNP18

not listed

SNP23

1395967

118740

925128

130121

1354939

187688

976288

208899

1396549

217761

1509022

322448

 

PCR Conditions for RGS4 SNPs

10xPCR buffer 1.0ul

dNTP(5mM) 0.4ul

MgCl2(25mM) 0.6ul (for FP, use 1.2ul)

F-primer(20uM) 0.125ul (for FP, use 0.025ul)

R-primer(20uM) 0.125ul (for FP, use 0.025ul)

Taq Polymerase(5U/ul) 0.05ul

DNA(20ng/ul) 3.0ul

Sterile water ---

Total 10.0ul

 

PCR Reaction Conditions

Initial denaturation

95° C for 4min(if it is AmpliTaq Gold do it for 10min)

35 cycles of

94° C for 45sec

60° C for 45 sec(see table for change in temp)

72° C for 1min

Followed by final extension at 72° C for 7min.

 

SSCP :

MDE gel solution (2X concentration), 10% glycerol,

Run at 10W for 6hrs

3.2ml of water

7.0ml of glycerol

42ml of 1X TBE buffer

17.5ml of MDE2X gel solution

37.5ul of TEMED

375ul of 10% APS

 

FP Method :

SAP Treatment :

10X SAP buffer 1.0ul

Alkaline Phosphatase 2.0ul

Exonuclease I 0.1ul

Sterile water --

Total 10.0ul

37° C for 1hr 30min, followed by 95° C for 15min.

 

FP Labeling :

10uM Detection primer 1.0ul

Thermoseq buffer 1.0ul

25uM ddNTP 0.05ul

Thermoseq (8u/ul) 0.1ul

Sterile water

Total 10ul

 

Reaction Conditions

94° C for 1min

Followed by

94° C for 10sec

55° C for 30sec (for SNP18 at 60° C)

Ror 35 cycles

4° C forever