online supplemental materials€¦ · figure s5.the ld plot of the gabrb1 gene in the asw sample...

GABRB1, thalamus, IQ

1

Online Supplemental Materials

Supplemental Tables ................................................................................................................................ 2

Table S1. Allele frequencies of 49 candidate SNPs in the GABRB1 gene shown by ethnic groups. Data

were from the present study and the HapMap dataset (www.hapmap.org)........................................ 2

Table S2. Associations between 49 SNPs within the GABRB1 gene and bilateral thalamus volumes after

controlling for age, sex and ICV ........................................................................................................ 4

Supplemental Figures .............................................................................................................................. 6

Figure S1. Freesurfer subcortical segmentation of the thalamus.. ............................................................. 6

Figure S2.The LD plot of the GABRB1 gene in the CHB sample (Han Chinese in Beijing, China) based

on the HapMap data (version 3 released R2) using Haploview 4.2 program .................................... 8

Figure S3.The LD plot of the GABRB1 gene in the CHD sample (Chinese in Metropolitan Denver,

Colorado) based on the HapMap data (version 3 released R2) using Haploview 4.2 program ......... 8

Figure S4.The LD plot of the GABRB1 gene in the CEU sample (Utah residents with Northern and

Western European ancestry from the CEPH collection) based on the HapMap data (version 3

released R2) using Haploview 4.2 program ....................................................................................... 9

Figure S5.The LD plot of the GABRB1 gene in the ASW sample (African ancestry in Southwest USA)

based on the HapMap data (version 3 released R2) using Haploview 4.2 program .......................... 9

Figure S6. Distributions of left and right thalamus volumes, intelligence measured by Wechsler Adult

Intelligence Scale-Revised (city version) and the intracranial volume in the current study. ........... 10

Figure S7. Schematic representation of the GABRB1 gene and linkage disequilibrium map of 49 SNPs

used in the current sample.. .............................................................................................................. 11

Figure S8. Most significant SNPs associated with phenotypes in the current study and previous studies

are marked on the LD plot of the GABRB1 gene in the CHB sample (Han Chinese in Beijing,

China) based on the HapMap data (version 3 released R2) using Haploview 4.2 program.. ........... 12

Supplemental Notes ............................................................................................................................... 13

Supplemental Note 1: Haplotype analysis ........................................................................................... 13

Supplemental Note 2: Additional analyses........................................................................................... 13


2

Supplemental Tables

Table S1. Allele frequencies of 49 candidate SNPs in the GABRB1 gene shown by ethnic

groups. Data were from the present study and the HapMap dataset (www.hapmap.org).

SNP

Base-pair

position

Reference

/other

allele

Reference allele frequencies

Present study

Han Chinese

HapMap data

Chinese European African

CHB CHD CEU ASW

rs10015366 46752516 A / G 0.34 (N = 309) 0.27 (N = 135) 0.31 (N = 109) 0.19 (N = 111) 0.12 (N = 57)

rs4396968 46783941 T / C 0.22 (N = 309) 0.15 (N = 137) 0.26 (N = 109) 0.17 (N = 113) 0.15 (N = 57)

rs1866989 46795862 T / A 0.28 (N = 316) 0.24 (N = 137) 0.25 (N = 109) 0.45 (N = 113) 0.45 (N = 57)

rs971353 46797651 C / T 0.49 (N = 299) 0.50 (N = 137) 0.55 (N = 109) 0.23 (N = 112) 0.22 (N = 57)

rs971354 46797872 A / G 0.50 (N = 316) 0.50 (N = 137) 0.45 (N = 109) 0.77 (N = 113) 0.78 (N = 57)

rs1372494 46813141 G / A 0.29 (N = 316) 0.25 (N = 137) 0.25 (N = 109) 0.45 (N = 113) 0.49 (N = 57)

rs2351299 46838122 T / G 0.32 (N = 310) 0.38 (N = 136) 0.32 (N = 109) 0.16 (N = 111) 0.28 (N = 57)

rs1442101 46838714 A / G 0.21 (N = 306) 0.16 (N = 137) 0.27 (N = 109) 0.08 (N = 113) 0.14 (N = 57)

rs12640095 46839791 G / A 0.32 (N = 316) 0.37 (N = 137) 0.32 (N = 108) 0.16 (N = 113) 0.27 (N = 57)

rs7680321 46839864 C / T 0.22 (N = 316) 0.17 (N = 137) 0.27 (N = 109) 0.08 (N = 113) 0.14 (N = 57)

rs1442097 46845754 C / T 0.49 (N = 316) 0.51 (N = 137) 0.43 (N = 108) 0.81 (N = 113) 0.49 (N = 57)

rs6447535 46849513 G / A 0.20 (N = 309) 0.14 (N = 137) 0.25 (N = 109) 0.13 (N = 113) 0.11 (N = 57)

rs994447 46852458 G / C 0.20 (N = 316) 0.14 (N = 137) 0.25 (N = 109) 0.13 (N = 113) 0.11 (N = 57)

rs7435958 46855766 C / G 0.31 (N = 316) 0.35 (N = 137) 0.32 (N = 109) 0.06 (N = 113) 0.27 (N = 56)

rs989808 46861538 T / G 0.20 (N = 316) 0.15 (N = 137) 0.25 (N = 109) 0.16 (N = 113) 0.10 (N = 57)

rs2351300 46874970 A / G 0.30 (N = 316) 0.31 (N = 137) 0.31 (N = 109) 0.06 (N = 113) 0.25 (N = 57)

rs1442094 46875185 T / C 0.21 (N = 314) 0.18 (N = 136) 0.26 (N = 109) 0.13 (N = 113) 0.14 (N = 57)

rs11728647 46880974 A / G 0.46 (N = 311) 0.46 (N = 137) 0.53 (N = 109) 0.19 (N = 113) 0.53 (N = 55)

rs10938477 46888276 G / T 0.20 (N = 316) 0.18 (N = 137) 0.25 (N = 109) 0.13 (N = 113) 0.14 (N = 57)

rs1023775 46890465 A / G 0.49 (N = 306) 0.49 (N = 136) 0.56 (N = 109) 0.19 (N = 113) 0.48 (N = 57)

rs10002281 46893890 G / A 0.29 (N = 316) 0.31 (N = 137) 0.30 (N = 109) 0.06 (N = 113) 0.26 (N = 57)

rs17600029 46894580 G / A 0.29 (N = 316) 0.31 (N = 137) 0.30 (N = 109) 0.06 (N = 113) 0.26 (N = 57)

rs1596139 46896575 A / G 0.21 (N = 313) 0.18 (N = 136) 0.26 (N = 109) 0.13 (N = 113) 0.20 (N = 57)

rs2044084 46897672 T / G 0.21 (N = 316) 0.18 (N = 137) 0.26 (N = 109) 0.13 (N = 113) 0.20 (N = 57)

rs10025913 46898550 G / A 0.21 (N = 316) 0.18 (N = 137) 0.26 (N = 109) 0.13 (N = 113) 0.14 (N = 57)

rs10016894 46920098 A / G 0.26 (N = 316) 0.25 (N = 137) 0.26 (N = 108) 0.32 (N = 113) 0.48 (N = 57)

rs1372498 46920961 A / G 0.23 (N = 310) 0.23 (N = 136) 0.20 (N = 108) 0.19 (N = 112) 0.25 (N = 57)

rs16860083 46922787 A / G 0.23 (N = 315) 0.23 (N = 137) 0.21 (N = 109) 0.19 (N = 113) 0.30 (N = 57)

rs1442108 46923047 A / G 0.26 (N = 316) 0.25 (N = 137) 0.25 (N = 109) 0.32 (N = 113) 0.48 (N = 57)

rs7666487 46938494 G / C 0.26 (N = 315) 0.24 (N = 136) 0.25 (N = 109) 0.32 (N = 113) 0.52 (N = 57)

rs10026884 46967149 A / G 0.22 (N = 309) 0.20 (N = 136) 0.19 (N = 108) 0.69 (N = 113) 0.42 (N = 57)

rs4695209 46979791 G / C 0.28 (N = 315) 0.24 (N = 136) 0.22 (N = 109) 0.10 (N = 113) 0.02 (N = 57)

rs1076015 46984728 A / G 0.31 (N = 316) 0.28 (N = 137) 0.24 (N = 109) 0.50 (N = 113) 0.37 (N = 57)

rs35744755 47006735 C / T 0.27 (N = 315) 0.25 (N = 137) 0.23 (N = 109) 0.04 (N = 113) 0.09 (N = 57)

rs12331018 47013059 C / T 0.29 (N = 311) 0.27 (N = 137) 0.24 (N = 109) 0.41 (N = 113) 0.37 (N = 57)


3

rs9291305 47031603 A / T 0.29 (N = 309) 0.27 (N = 137) 0.24 (N = 109) 0.41 (N = 113) 0.33 (N = 57)

rs7665508 47042046 G / A 0.29 (N = 311) 0.27 (N = 137) 0.25 (N = 109) 0.40 (N = 112) 0.36 (N = 57)

rs4588429 47045629 G / A 0.23 (N = 313) 0.20 (N = 137) 0.17 (N = 109) 0.39 (N = 113) 0.33 (N = 57)

rs10517184 47061882 G / A 0.13 (N = 316) 0.14 (N = 137) 0.15 (N = 109) 0.50 (N = 113) 0.62 (N = 57)

rs17600511 47062277 G / C 0.11 (N = 316) 0.13 (N = 137) 0.12 (N = 109) 0.05 (N = 113) NA NA

rs4695220 47063437 C / T 0.13 (N = 314) 0.14 (N = 137) 0.15 (N = 109) 0.50 (N = 112) 0.62 (N = 57)

rs4694846 47063555 C / T 0.12 (N = 316) 0.14 (N = 137) 0.15 (N = 109) 0.35 (N = 113) 0.50 (N = 57)

rs10938482 47064514 C / A 0.13 (N = 316) 0.14 (N = 137) 0.15 (N = 109) 0.50 (N = 113) 0.62 (N = 57)

rs7677890 47066346 C / T 0.13 (N = 316) 0.14 (N = 137) 0.15 (N = 109) 0.50 (N = 112) 0.62 (N = 57)

rs11733050 47070069 A / G 0.12 (N = 315) 0.14 (N = 137) 0.15 (N = 109) 0.29 (N = 113) 0.27 (N = 57)

rs6814130 47092415 T / C 0.11 (N = 313) 0.14 (N = 137) 0.12 (N = 109) 0.53 (N = 113) 0.71 (N = 57)

rs13434696 47109976 G / C 0.11 (N = 316) 0.10 (N = 137) 0.06 (N = 109) 0.28 (N = 113) 0.36 (N = 57)

rs7679148 47111576 T / G 0.11 (N = 316) 0.10 (N = 137) 0.06 (N = 109) 0.27 (N = 113) 0.30 (N = 57)

rs10030377 47118537 A / G 0.20 (N = 315) 0.17 (N = 135) 0.14 (N = 109) 0.42 (N = 113) 0.81 (N = 57)

Note: Data for the HapMap samples were from the HapMap Website (HapMap genome

browser Rel 28 [phase II+III]). Population descriptors: CHB: Han Chinese in Beijing, China;

CHD: Chinese in Metropolitan Denver, Colorado; CEU: Utah residents with Northern and

Western European ancestry from the CEPH collection; ASW: African ancestry in Southwest

USA.


4

Table S2. Associations between 49 SNPs within the GABRB1 gene and bilateral thalamus

volumes after controlling for age, sex and ICV

Left thalamus volume Right thalamus volume

SNP Position

Effective

allele N β t p β t p

rs10015366 46752516 A 309 11.16 0.24 .813 -19.33 -0.42 .676

rs4396968 46783941 T 309 39.53 0.76 .447 38.97 0.77 .443

rs1866989 46795862 T 316 -89.22 -1.96 .051 -103.90 -2.33 .020

rs971353 46797651 C 299 115.40 2.62 .009 106.80 2.50 .013

rs971354 46797872 A 316 -108.60 -2.58 .010 -112.30 -2.74 .007

rs1372494 46813141 G 316 -80.44 -1.77 .078 -95.63 -2.15 .032

rs2351299 46838122 T 310 98.42 2.25 .025 109.40 2.58 .010

rs1442101 46838714 A 306 46.00 0.84 .399 18.40 0.34 .730

rs12640095 46839791 G 316 101.60 2.37 .019 114.70 2.74 .007

rs7680321 46839864 C 316 45.25 0.87 .387 34.67 0.68 .498

rs1442097 46845754 C 316 -121.00 -2.94 .004 -129.10 -3.22 .001

rs6447535 46849513 G 309 6.71 0.13 .899 -15.70 -0.30 .761

rs994447 46852458 G 316 -0.99 -0.02 .985 -27.66 -0.54 .590

rs7435958 46855766 C 316 142.20 3.19 .002 173.20 4.01 .000

rs989808 46861538 T 316 -0.99 -0.02 .985 -27.66 -0.54 .590

rs2351300 46874970 A 316 145.20 3.20 .001 167.20 3.79 .000

rs1442094 46875185 T 314 -1.78 -0.03 .973 -14.96 -0.30 .767

rs11728647 46880974 A 311 109.70 2.56 .011 119.20 2.83 .005

rs10938477 46888276 G 316 -14.92 -0.29 .771 -30.56 -0.61 .542

rs1023775 46890465 A 306 114.50 2.75 .006 121.60 2.99 .003

rs10002281 46893890 G 316 149.30 3.26 .001 172.30 3.87 .000

rs17600029 46894580 G 316 149.30 3.26 .001 172.30 3.87 .000

rs1596139 46896575 A 313 -11.86 -0.23 .816 -28.61 -0.58 .565

rs2044084 46897672 T 316 -16.11 -0.32 .750 -28.41 -0.57 .566

rs10025913 46898550 G 316 -15.37 -0.30 .762 -29.56 -0.60 .551

rs10016894 46920098 A 316 108.80 2.23 .026 108.90 2.28 .023

rs1372498 46920961 A 310 100.80 1.97 .050 98.65 1.98 .049

rs16860083 46922787 A 315 116.50 2.33 .021 116.40 2.40 .017

rs1442108 46923047 A 316 108.80 2.23 .026 108.90 2.28 .023

rs7666487 46938494 G 315 111.90 2.32 .021 119.30 2.53 .012

rs10026884 46967149 A 309 -108.20 -2.12 .035 -93.12 -1.87 .062

rs4695209 46979791 G 315 -1.64 -0.03 .973 15.24 0.32 .748

rs1076015 46984728 A 316 1.51 0.03 .974 19.30 0.43 .666

rs35744755 47006735 C 315 13.90 0.28 .776 45.25 0.95 .344

rs12331018 47013059 C 311 14.15 0.30 .761 31.95 0.70 .482

rs9291305 47031603 A 309 18.22 0.38 .701 35.14 0.76 .450

rs7665508 47042046 G 311 15.64 0.33 .739 43.24 0.95 .345

rs4588429 47045629 G 313 19.64 0.38 .705 54.21 1.07 .285


5

rs10517184 47061882 G 316 50.11 0.78 .433 53.13 0.85 .396

rs17600511 47062277 G 316 16.50 0.24 .809 25.69 0.39 .701

rs4695220 47063437 C 314 43.48 0.68 .496 47.53 0.76 .447

rs4694846 47063555 C 316 54.34 0.83 .406 57.10 0.89 .372

rs10938482 47064514 C 316 40.94 0.65 .519 43.71 0.71 .481

rs7677890 47066346 C 316 40.94 0.65 .519 43.71 0.71 .481

rs11733050 47070069 A 315 21.77 0.34 .736 17.34 0.27 .784

rs6814130 47092415 T 313 -38.80 -0.60 .551 -48.48 -0.76 .447

rs13434696 47109976 G 316 15.86 0.24 .807 27.81 0.44 .662

rs7679148 47111576 T 316 15.86 0.24 .807 27.81 0.44 .662

rs10030377 47118537 A 315 -7.23 -0.14 .892 -9.85 -0.19 .851

Note: Individual SNP analysis using Plink revealed significant associations for 16 SNPs with

bilateral thalamus volumes after controlling for age, sex, and ICV (p < 0.05), including

rs7435958, rs10002281, rs17600029, rs2351300, rs1442097, rs1023775, rs11728647,

rs12640095, rs971354, rs2351299, rs7666487, rs971353, rs16860083, rs10016894,

rs1442108, and rs1372498. Four SNPs were still significant after correcting for multiple

testing by max(T) permutation approach in Plink (10000 permutation). SNP rs7435958:

Corrected empirical p-values [max(T) / familywise] = 0.029 and 0.002 for the left and right

thalamus volumes. SNP rs10002281: Corrected empirical p-values [max(T) / familywise] =

0.023 and 0.003 for the left and right thalamus volumes. SNP rs17600029: Corrected

empirical p-values [max(T) / familywise] = 0.023 and 0.003 for the left and right thalamus

volumes. SNP rs2351300: Corrected empirical p-values [max(T) / familywise] = 0.028 and

0.005 for the left and right thalamus volumes. SNP rs7435958 had high linkage

disequilibrium (LD) with the other three SNPs (r2 = 0.90, 0.90, and 0.93 for its LD with

rs10002281, rs17600029 and rs2351300, respectively). Significant p values after correcting

for multiple testing by max(T) permutation approach in Plink (10000 permutation) are shown

in bold.


6

Supplemental Figures

Figure S1. Freesurfer subcortical segmentation of the thalamus. Models are displayed on two

subjects with extremely large thalamus volume (images A and C are for subject 1) and small

thalamus volume (images B and D are for subject 2) in the current sample. Images A and B:

Freesurfer derived subcortical labels in the coronal view of the brains; right thalami of these

two subjects are indicated by red arrows. Images C and D: 3D surface models created with

3D Slicer derived from the Freesurfer subcortical segmentations; thalami (dark green) of

these two subjects presented in the axial view of the brains.


7

The Supplemental Materials Figures S2-S5 present the LD plots of the GABRB1 gene in

different populations based on the HapMap data (http://www.hapmap.org). These populations

include CHB: Han Chinese in Beijing, China (Fig S2); CHD: Chinese in Metropolitan

Denver, Colorado (Fig S3); CEU: Utah residents with Northern and Western European

ancestry from the CEPH collection (Fig S4); ASW: African ancestry in Southwest USA (Fig

S5).


8

Figure S2.The LD plot of the GABRB1 gene in the CHB sample (Han Chinese in Beijing,

China) based on the HapMap data (version 3 released R2) using Haploview 4.2 program

Figure S3.The LD plot of the GABRB1 gene in the CHD sample (Chinese in Metropolitan

Denver, Colorado) based on the HapMap data (version 3 released R2) using Haploview 4.2

program


9

Figure S4.The LD plot of the GABRB1 gene in the CEU sample (Utah residents with

Northern and Western European ancestry from the CEPH collection) based on the HapMap

data (version 3 released R2) using Haploview 4.2 program

Figure S5.The LD plot of the GABRB1 gene in the ASW sample (African ancestry in

Southwest USA) based on the HapMap data (version 3 released R2) using Haploview 4.2

program


10

Figure S6. Distributions of left and right thalamus volumes, intelligence measured by

Wechsler Adult Intelligence Scale-Revised (city version) and the intracranial volume in the

current study.


11

Figure S7. Schematic representation of the GABRB1 gene and linkage disequilibrium map of

49 SNPs used in the current sample. Regions of high LD are shown in dark red. Markers with

lower LD are shown in light red with the intensity decreasing with decreased D’/LOD value.

Regions of low LD are shown in white. SNP (rs7435958) associated with thalamus volume

was marked.


12

Figure S8. Most significant SNPs associated with phenotypes in the current study and

previous studies are marked on the LD plot of the GABRB1 gene in the CHB sample (Han

Chinese in Beijing, China) based on the HapMap data (version 3 released R2) using

Haploview 4.2 program. Finding from the current study was marked with a red arrow

(rs7435958 [bp: 46855766] was associated with thalamus volume). Findings in previous

studies are marked with green and blue arrows (green: rs7680321 [bp: 46839864] was

associated with bipolar disorder [Hamshere et al., 2009]; blue: rs2351299 [bp: 46838122]

was associated with autism in family with a positive history of seizure [Collins et al., 2006],

and its interaction with rs1912960 in the GABRA4 gene also associated with autism [Ma et al.,

2005]). There was a relatively high LD between rs7435958 and rs2351299 (r2 = 0.79), but

there was no LD between rs7435958 and rs7680321 (r2 = 0.07) in the CHB sample (Han

Chinese in Beijing, China) based on the HapMap data (version 3 released R2). Similarly, in

the current study, there was a relatively high LD between rs7435958 and rs2351299 (r2 =

0.75), but there was no LD between rs7435958 and rs7680321 (r2 = 0.07).


13

Supplemental Notes

Supplemental Note 1: Haplotype analysis

As shown in Figure S7, according to the criteria of confidence intervals (Gabriel et al.,

2002), eight haplotype blocks across the GABRB1 gene were revealed from the linkage

disequilibrium (LD) data for these 49 SNPs. The third block contained 12 SNPs rs1442097,

rs6447535, rs994447, rs7435958, rs989808, rs2351300, rs1442094, rs11728647,

rs10938477, rs1023775, rs10002281, rs17600029, which covered 48.8 kb. Haplotype-based

association analysis was performed for the third haplotype block within the GABRB1 gene in

the current sample. We found a haplotype T-A-C-C-G-A-C-A-T-A-G-G (with a frequency of

25%) for rs1442097-rs6447535-rs994447-rs7435958-rs989808-rs2351300-rs1442094-

rs11728647-rs10938477-rs1023775-rs10002281-rs17600029 that showed a significant

association with thalamus volumes (β = 130 and 157, t = 7.08 and 11.1, p = 0.008 and 0.001

for the left and right thalamus volumes, respectively). This association remained significant

after correcting for multiple testing by max(T) permutation (Corrected empirical p-value

[max(T) / familywise] = 0.031 and 0.004 for the left and right thalamus volumes,

respectively). These findings imply that rs7435958 was well tagged by surrounding SNPs

and the causal variant lies within the haplotype block defined by the SNPs above.

Supplemental Note 2: Additional analyses

To examine whether there were potential confounds, we conducted additional analyses.

First, we focused on the SNP rs7435958 in our analysis of gene-brain interaction effect on

intelligence. The main effect of rs7435958 genotype on intelligence was not significant with

age, sex and ICV as covariates (t = 0.57, p = 0.57). To investigate whether any other SNPs

within the GABRB1 gene had significant main effects on intelligence, we conducted

additional analyses using Plink. Results showed no significant direct associations between

any GABRB1 genetic variants and intelligence after correcting for multiple testing by max(T)

permutation (all p’s >.05). As a side note, no significant differences were found across

rs7435958 genotypes in age, sex, handedness, and ICV (all p’s >.05).

Second, to examine potential confounds of subjects’ mental health, we conducted

additional analyses with data from several measures of mental health. Although we did not

administer a systematic battery of objective assessments for neurological diseases and mental

disorders, the larger project included measures of two main mental health issues relevant to

college students: depression and anxiety. They were measured with Beck’s depression and

anxiety inventories: BDI-II and BAI (Beck, 1990; Beck et al., 1996). In addition, Alcohol

Use Disorders Identification Test (AUDIT) (Saunders et al. 1993) was used to measure

alcohol use. Smoking data were also subsequently collected using the Fagerström Tolerance

Questionnaire (FTQ) (Prokhorov et al., 2000), although 78 subjects had missing data (mainly

because the smoking questionnaire was administered during the last wave of data collection).

Therefore, two additional analyses were conducted: one using indices of BDI, BAI, AUDIT,

sex, age, and ICV as covariates for the larger sample, and the other using smoking as an

additional covariate. The results showed that controlling for these covariates did not


14

substantially alter the results. Specifically, for the larger sample (without smoking as a

covariate), the association between GABRB1 rs7435958 and thalamus volume was still the

same (β = 142.4 and 172.1, t = 3.10 and 3.84, p = 0.002 and 0.0001 for the left and right

thalamus volumes, respectively; for both left and right thalamus volumes: G allele < C allele).

Using indices of BDI, BAI, AUDIT, age, and ICV as covariates, the GABRB1 rs7435958

genotype still had significant interactions with lateral thalamus volume on intelligence in

females (t = -2.35 and -2.07, p = 0.02 and 0.04 for its interactions with left and right thalamus

volumes, respectively); the GABRB1 rs7435958 genotype did not have significant interaction

with lateral thalamus volume on intelligence in males (t = -0.84 and 0.23, p = 0.40 and 0.82

for its interactions with left and right thalamus volumes, respectively). Similarly, for the

analysis with all covariates, the association between GABRB1 rs7435958 and thalamus

volume was still the same (β = 137.1 and 167.6, t = 2.63 and 3.27, p = 0.009 and 0.001for the

left and right thalamus volumes, respectively; for both left and right thalamus volumes: G

allele < C allele). Using indices of BDI, BAI, AUDIT, age, ICV, and smoking as covariates,

the GABRB1 rs7435958 genotype still had significant interactions with lateral thalamus

volume on intelligence in females (t = -2.24 and -1.90 , p = 0.027 and 0.048 for its

interactions with left and right thalamus volumes, respectively); the GABRB1 rs7435958

genotype did not have significant interaction with lateral thalamus volume on intelligence in

males (t = -1.08 and -0.54, p = 0.28 and 0.59 for its interactions with left and right thalamus

volumes, respectively).

Third, as we described in the method section, the WAIS-R including two sections (i.e.,

verbal and performance sections) (Gong, 1992). Besides the full scale intelligence score used

in the current study, we also conducted the analysis for verbal intelligence and performance

intelligence, separately. These results using verbal and performance intelligence scores were

similar to those using full scale intelligence score. There were significant positive correlations

between bilateral thalamus volume and verbal intelligence after controlling for age, sex, and

ICV (r = 0.12 and 0.13, p = 0.030 and 0.018, for the left and right thalamus volumes,

respectively); and there were significant positive correlations between bilateral thalamus

volumes and performance intelligence after controlling for age, sex, and ICV (r = 0.15 and

0.15, p = 0.009 and 0.006, for the left and right thalamus volumes, respectively).We also

explored the joint effect of thalamus structure and GABRB1 rs7435958 genotype on verbal

intelligence and performance intelligence. Linear regression analyses were conducted in

female and male subjects using age and ICV as control variables. Verbal intelligence score or

performance intelligence score was the dependent variable, with the GABRB1 rs7435958

genotype, lateral thalamus volume, and their interaction as predictors, and with age and ICV

as control variables. Again, females and males were analyzed separately. For females, both

thalamus volumes (t = 1.99 and 2.04, p = 0.049 and 0.043 for the left and right thalamus

volumes, respectively) and the two-way interaction terms (t = -2.07 and -2.26 , p = 0.040 and

0.025 for the interaction terms of left thalamus*genotype and right thalamus*genotype,

respectively) were significant predictors of verbal intelligence, whereas only thalamus

volumes (t = 2.45 and 2.08, p = 0.015 and 0.039 for the left and right thalamus volumes,

respectively) were significant predictors of performance intelligence. For males, there was no

significant predictor of verbal or performance intelligence (p > 0.05). We further examined

the associations between bilateral thalamus volumes and verbal and performance intelligence

for the three GABRB1 rs7435958 genotypes separately (GG homozygotes, CG heterozygotes,

and CC homozygotes) in female and male subjects, respectively. Age and ICV were again


15

used as covariates. Only for the female GABRB1 rs7435958 GG homozygotes, were

significant positive correlations found between bilateral thalamus volumes and performance

intelligence (r = 0.35 and 0.27, p = 0.001 and 0.014 for left and right thalamus volumes,

respectively). They also showed marginal positive correlations between bilateral thalamus

volumes and verbal intelligence (r = 0.19 and 0.21, p = 0.082 and 0.053 for left and right

thalamus volumes, respectively). However, there was no significant correlation between

bilateral thalamus volumes and verbal or performance intelligence for the other two genotype

groups in females, and no significant correlation between bilateral thalamus volumes and

verbal or performance intelligence for these three genotype groups in males (p > 0.05).

Fourth, we also examined the association between all GABRB1 SNPs and thalamus

volume for males and females separately. Although the sample sizes were smaller, the

associations between SNP rs7435958 and thalamus volumes remained significant for both

genders (i.e., males [N = 129]: β = 234.10 and 128.50, t = 3.77 and 2.00, p = 0.00025 and

0.048 for the right and left thalamus volumes, respectively, with age and ICV as covariates;

females [N = 187]: β = 120.50 and 154.90, t = 2.04 and 2.52, p = 0.042 and 0.013 for the right

and left thalamus volumes, respectively, with age and ICV as covariates). In addition, there

were slightly stronger correlations with different neighboring SNPs for males and females.

For males, the highest association with thalamus volumes was found for the SNP rs10002281

(which has a high linkage disequilibrium [LD] with SNP rs7435958, r2 = 0.90): β = 249.80

and 151.60, t = 3.89 and 2.28, p = 0.00016 and 0.024 for the right and left thalamus volumes,

respectively, with age and ICV as covariates. For females, the highest association with

thalamus volumes was found for the SNP rs971354 (which has only a moderate LD with SNP

rs7435958, r2 = 0.24): β = 162.10 and 180.30, t = 3.13 and 3.32, p = 0.0021 and 0.0011 for

the right and left thalamus volumes, respectively, with age and ICV as covariates. In sum, the

GABRB1 gene and SNP rs7435958 in particular appeared to be associated with thalamus

volumes for both genders, but there was also evidence that the causative locus might be

slightly shifted for the two genders. These results need to be replicated and further explored

with larger samples for each gender.

References for Supplemental Notes:

Beck AT, Steer RA. 1990. Manual for the Beck Anxiety Inventory. San Antonio, TX:

Psychological Corporation.

Beck AT, Steer RA, Brown GK, 1996. Beck Depression Inventory-II. San Antonio, TX: The

Psychological Corporation.

Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel B. et al (2002). The

structure of haplotype blocks in the human genome. Science 296, 2225-2229.

Gong Y. 1992. The manual of Wechsler Adult Intelligence Scale Revised in China. Changsha,

Hunan, China: Hunan Medical University Press.

Prokhorov AV, De Moor C, Pallonen UE, Suchanek Hudmon K, Koehly L, Hu S (2000).

Validation of the modified fagerström tolerance questionnaire with salivary cotinine

among adolescents. Addictive Behaviors 25, 429-433.

Saunders JB, Aasland OG, Babor TF, de la Fuente JR, Grant M (1993). Development of the

Alcohol Use Disorders Identification Test (AUDIT): WHO Collaborative Project on

Early Detection of Persons with Harmful Alcohol Consumption–II. Addiction, 88,791–

804.

online supplemental materials€¦ · figure s5.the ld plot of the gabrb1 gene in the asw sample...

Documents