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Study Report
Comment on Study | View All Comments on Study |
Reference | Fan, J., 2010 PMID: 19308960 |
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Citation | Fan, J., I. Ionita-Laza, et al. (2010). "Linkage disequilibrium mapping of the chromosome 6q21-22.31 bipolar I disorder susceptibility locus." Am J Med Genet B Neuropsychiatr Genet 153B(1): 29-37. |
Disease Type | Bipolar I Disorder |
Study Design | case-control and family-based |
Study Type | Candidate-gene association study |
Sample Size | 530 cases, 534 controls, 256 nuclear families, 1,301 individuals |
SNP/Region/Marker Size | 3047 SNPs in initial stage and 151 SNPs for replication |
Predominant Ethnicity | Caucasian |
Population | American |
Sample Diagnosis | DSM-IV, Diagnostic Interview for Genetic Studies |
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Sample Status | complete affected parent-proband trios for family sample. |
Replication Size | 622 cases, 1,181 controls |
Technique | genotyping using two Oligo Pool Arrays (OPAs) by the Illumina BeadArray platform (San Diego, CA) at the Broad Institute. All SNPs in our follow-up tests were genotyped by an allelespecific primer extension of amplified products with detection by matrix-assisted laser desorption ionization time-of-flight mass spectroscopy using the Sequenom iPLEX genotyping platform (San Diego, CA) at the Broad Institute. |
Statistical Method | Genetic quality control analyses were performed using the PLINK software package. Single-marker association analyses were conducted using PLINK for the case-control sample, and FBAT for the family based sample. For gene-based analysis, The set-based test implemented in the PLINK software package was performed in case-control samples. The min-p test implemented in the FBAT software was performed in family-based samples. |
Result Summary | SNP-wise and gene-based test results in the three samples provided convergent evidence for association with SLC22A16. |
SNP | Related Gene(s) | Allele Change | Risk Allele | Statistical Values | Author Comments | Result Category |
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rs9400393 | SLC22A16 | C | P-value = 0.00097 in STEP1 sample; | showed evidence of association in the STEP1 sample showed evidence of association in the STEP1 sample | Positive | |
rs9401352 | G | P-value = 0.00025 in STEP1 sample; | showed evidence of association in the STEP1 sample showed evidence of association in the STEP1 sample | Positive | ||
rs9491388 | C | P-value = 0.0015 in STEP1 sample; | showed evidence of association in the STEP1 sample showed evidence of association in the STEP1 sample | Positive | ||
rs1190053 | PREP | A | P-value = 0.00046 in NIMH sample; | showed evidence of association in the NIMH sample showed evidence of association in the NIMH sample | Positive | |
rs10944288 | HTR1E | G | P-value = 0.12 in STEP1 sample; P-value = 0.013 in NIMH sample; P-value = 0.0045 in STEP1 and NIMH sample; | showed evidence of association in the NIMH sample showed evidence of association in the NIMH sample | Positive | |
rs12198581 | T | P-value = 0.00052 in NIMH sample; | showed evidence of association in the NIMH sample showed evidence of association in the NIMH sample | Positive | ||
rs12213914 | PREP | T | P-value = 0.00039 in NIMH sample; | showed evidence of association in the NIMH sample showed evidence of association in the NIMH sample | Positive | |
rs1204787 | NT5DC1 | C | P-value = 0.21 in STEP1 sample; P-value = 0.0035 in NIMH sample; P-value = 0.0032 in STEP1 and NIMH sample; | showed evidence of association in the NIMH sample and pooled...... showed evidence of association in the NIMH sample and pooled sample. More... | Positive | |
rs12153828 | CEP85L | G | P-value = 0.039 in STEP2 sample; | showed evidence of association in the replication sample showed evidence of association in the replication sample | Positive | |
rs1339197 | PTPRK | A | P-value = 0.0026 in NIMH sample; | showed evidence of association in the NIMH sample showed evidence of association in the NIMH sample | Positive | |
rs1688615 | A | P-value = 0.015 in STEP2 sample; | showed evidence of association in the replication sample showed evidence of association in the replication sample | Positive | ||
rs13191605 | G | P-value = 0.00088 in NIMH sample; | showed evidence of association in the NIMH sample showed evidence of association in the NIMH sample | Positive | ||
rs13196925 | BVES | C | P-value = 0.002 in NIMH sample; | showed evidence of association in the NIMH sample showed evidence of association in the NIMH sample | Positive | |
rs17282486 | G | P-value = 0.0037 in STEP1 sample; P-value = 0.29 in NIMH sample; P-value = 0.0052 in STEP1 and NIMH sample; | showed evidence of association in the STEP1 sample and poole...... showed evidence of association in the STEP1 sample and pooled sample More... | Positive | ||
rs17447037 | EPHA7 | A | P-value = 0.0034 in STEP1 sample; | showed evidence of association in the STEP1 sample showed evidence of association in the STEP1 sample | Positive | |
rs17071713 | SLC22A16 | G | P-value = 0.0011 in STEP2 sample; | showed evidence of association in the replication sample showed evidence of association in the replication sample | Positive | |
rs17071722 | SLC22A16 | T | P-value = 0.0021 in NIMH sample; P-value = 0.02 in STEP2 sample; | showed evidence of association in the NIMH sample and replic...... showed evidence of association in the NIMH sample and replication sample More... | Positive | |
rs2428190 | SLC22A16 | C | P-value = 0.0017 in STEP2 sample; | showed evidence of association in the replication sample showed evidence of association in the replication sample | Positive | |
rs2496353 | CEP85L BRD7P3 | A | P-value = 0.0099 in STEP2 sample; | showed evidence of association in the replication sample showed evidence of association in the replication sample | Positive | |
rs2244924 | SEC63 | A | P-value = 0.0029 in STEP1 sample; | showed evidence of association in the STEP1 sample showed evidence of association in the STEP1 sample | Positive | |
rs2428168 | T | P-value = 0.0027 in STEP1 sample; | showed evidence of association in the STEP1 sample showed evidence of association in the STEP1 sample | Positive | ||
rs3823447 | SLC22A16 DDO | A | P-value = 0.047 in STEP1 sample; P-value = 0.055 in NIMH sample; P-value = 0.0058 in STEP1 and NIMH sample; | showed evidence of association in the STEP1 sample and poole...... showed evidence of association in the STEP1 sample and pooled sample. More... | Positive | |
rs3798366 | ROS1 | A | P-value = 0.24 in STEP1 sample; P-value = 0.005 in NIMH sample; P-value = 0.0052 in STEP1 and NIMH sample; | showed evidence of association in the NIMH sample and pooled...... showed evidence of association in the NIMH sample and pooled sample. More... | Positive | |
rs3734381 | CEP85L PLN | A | P-value = 0.03 in STEP2 sample; | showed evidence of association in the replication sample showed evidence of association in the replication sample | Positive | |
rs2892767 | GJA1 | T | P-value = 0.0017 in NIMH sample; | showed evidence of association in the NIMH sample showed evidence of association in the NIMH sample | Positive | |
rs6932749 | A | P-value = 0.014 in STEP2 sample; | showed evidence of association in the replication sample showed evidence of association in the replication sample | Positive | ||
rs6931341 | A | P-value = 0.0003 in NIMH sample; | showed evidence of association in the NIMH sample showed evidence of association in the NIMH sample | Positive | ||
rs6922074 | T | P-value = 0.00021 in STEP1 sample; | showed evidence of association in the STEP1 sample showed evidence of association in the STEP1 sample | Positive | ||
rs4946138 | COL10A1 NT5DC1 | G | P-value = 0.04 in STEP1 sample; P-value = 0.007 in NIMH sample; P-value = 0.0009 in STEP1 and NIMH sample; | showed evidence of association in STEP1 sample, NIMH sample ...... showed evidence of association in STEP1 sample, NIMH sample and pooled sample. More... | Positive | |
rs7768422 | SLC22A16 | G | P-value = 0.0053 in STEP2 sample; | showed evidence of association in the replication sample showed evidence of association in the replication sample | Positive | |
rs7765860 | PKIB | C | P-value = 0.0016 in STEP1 sample; | showed evidence of association in the STEP1 sample showed evidence of association in the STEP1 sample | Positive | |
rs6938431 | SLC22A16 DDO | T | P-value = 0.0000672 in STEP1 sample; P-value = 0.79 in NIMH sample; P-value = 0.0027 in STEP1 and NIMH sample; P-value = 0.04 in STEP2 sample; | showed evidence of association in STEP1 sample, pooled sampl...... showed evidence of association in STEP1 sample, pooled sample and replication sample. More... | Positive | |
rs6935739 | G | P-value = 0.0013 in NIMH sample; | showed evidence of association in the NIMH sample showed evidence of association in the NIMH sample | Positive | ||
rs871746 | A | P-value = 0.04 in STEP1 sample; P-value = 0.013 in NIMH sample; P-value = 0.0014 in STEP1 and NIMH sample; | showed evidence of association in the STEP1 sample, NIMH sam...... showed evidence of association in the STEP1 sample, NIMH sample and pooled sample. More... | Positive | ||
rs846950 | C | P-value = 0.0026 in STEP1 sample; | showed evidence of association in the STEP1 sample showed evidence of association in the STEP1 sample | Positive | ||
rs794854 | CEP85L | C | P-value = 0.0076 in STEP1 sample; P-value = 0.033 in NIMH sample; P-value = 0.0007 in STEP1 and NIMH sample; | showed evidence of association in the STEP1 sample, NIMH sam...... showed evidence of association in the STEP1 sample, NIMH sample and pooled sample. More... | Positive | |
rs783419 | AIM1 | T | P-value = 0.17 in STEP1 sample; P-value = 0.009 in NIMH sample; P-value = 0.005 in STEP1 and NIMH sample; | showed evidence of association in the NIMH sample and pooled...... showed evidence of association in the NIMH sample and pooled sample. More... | Positive |
Gene | Statistical Values/Author Comments | Result Category |
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BVES | For gene-based test, P-value = 0.22 in STEP1; P-value = 0.01 in NIMH; P-value = 0.016 in STEP1 and NIMH. nominally significant in NIMH sample and pooled sample, but not survive Bonferroni correction test. nominally significant in NIMH sample and pooled sample, but not survive Bonferroni correction test. | Positive |
SERINC1 | For gene-based test, P-value = 0.017 in STEP1. nominally significant in STEP1 sample, but not survive Bonferroni correction test. nominally significant in STEP1 sample, but not survive Bonferroni correction test. | Positive |
CEP85L | For gene-based test, P-value = 0.036 in STEP2. nominally significant in STEP2 sample, but not survive Bonferroni correction test. nominally significant in STEP2 sample, but not survive Bonferroni correction test. | Positive |
FAM184A | For gene-based test, P-value = 0.043 in STEP1. nominally significant in STEP1 sample, but not survive Bonferroni correction test. nominally significant in STEP1 sample, but not survive Bonferroni correction test. | Positive |
GJA1 | For gene-based test, P-value = 0.24 in STEP1; P-value = 0.01 in NIMH; P-value = 0.017 in STEP1 and NIMH. nominally significant in NIMH sample and pooled sample, but not survive Bonferroni correction test. nominally significant in NIMH sample and pooled sample, but not survive Bonferroni correction test. | Positive |
NT5DC1 | For gene-based test, P-value = 0.29 in STEP1; P-value = 0.02 in NIMH; P-value = 0.05 in STEP1 and NIMH. nominally significant in NIMH sample and pooled sample, but not survive Bonferroni correction test. nominally significant in NIMH sample and pooled sample, but not survive Bonferroni correction test. | Positive |
HSF2 | For gene-based test, P-value = 0.007 in STEP1; P-value = 0.93 in NIMH; P-value = 0.043 in STEP1 and NIMH. nominally significant in STEP1 sample and pooled sample, but not survive Bonferroni correction test. nominally significant in STEP1 sample and pooled sample, but not survive Bonferroni correction test. | Positive |
FAM26F | For gene-based test, P-value = 0.038 in STEP1. nominally significant in STEP1 sample, but not survive Bonferroni correction test. nominally significant in STEP1 sample, but not survive Bonferroni correction test. | Positive |
POPDC3 | For gene-based test, P-value = 0.021 in STEP1. nominally significant in STEP1 sample, but not survive Bonferroni correction test. nominally significant in STEP1 sample, but not survive Bonferroni correction test. | Positive |
KPNA5 | For gene-based test, P-value = 0.33 in STEP1; P-value = 0.02 in NIMH; P-value = 0.048 in STEP1 and NIMH. nominally significant in NIMH sample and pooled sample, but not survive Bonferroni correction test. nominally significant in NIMH sample and pooled sample, but not survive Bonferroni correction test. | Positive |
TSPYL4 | For gene-based test, P-value = 0.041 in STEP1. nominally significant in STEP1 sample, but not survive Bonferroni correction test. nominally significant in STEP1 sample, but not survive Bonferroni correction test. | Positive |
DDO | For gene-based test, P-value = 0.00079 in STEP1; P-value = 0.46 in NIMH; P-value = 0.0033 in STEP1 and NIMH. leading gene-based results, but not survive Bonferroni correction test. leading gene-based results, but not survive Bonferroni correction test. | Positive |
SLC22A16 | For gene-based test, P-value = 0.0013 in STEP1; P-value = 0.034 in NIMH; P-value = 0.00048 in STEP1 and NIMH; P-value = 0.03 in STEP2. nominally significant in all three samples nominally significant in all three samples | Positive |
CNR1 | For gene-based test, P-value = 0.063 in STEP1. non-significant in any samples. non-significant in any samples. | Negative |
RFPL4B | For gene-based test, P-value = 0.036 in STEP1; P-value = 0.066 in NIMH; P-value = 0.017 in STEP1 and NIMH. nominally significant in STEP1 sample and pooled sample, but not survive Bonferroni correction test. nominally significant in STEP1 sample and pooled sample, but not survive Bonferroni correction test. | Positive |
PREP | For gene-based test, P-value = 0.22 in STEP1; P-value = 0.0089 in NIMH; P-value = 0.014 in STEP1 and NIMH. nominally significant in NIMH sample and pooled sample, but not survive Bonferroni correction test. nominally significant in NIMH sample and pooled sample, but not survive Bonferroni correction test. | Positive |
PKIB | For gene-based test, P-value = 0.047 in STEP1. nominally significant in STEP1 sample, but not survive Bonferroni correction test. nominally significant in STEP1 sample, but not survive Bonferroni correction test. | Positive |
SCML4 | For gene-based test, P-value = 0.106 in STEP1. non-significant in any samples. non-significant in any samples. | Negative |
FIG4 | For gene-based test, P-value = 0.16 in STEP1; P-value = 0.03 in NIMH; P-value = 0.032 in STEP1 and NIMH. nominally significant in NIMH sample and pooled sample, but not survive Bonferroni correction test. nominally significant in NIMH sample and pooled sample, but not survive Bonferroni correction test. | Positive |
SEC63 | For gene-based test, P-value = 0.018 in STEP1. nominally significant in STEP1 sample, but not survive Bonferroni correction test. nominally significant in STEP1 sample, but not survive Bonferroni correction test. | Positive |
Copyright: Bioinformatics Lab, Institute of Psychology, Chinese Academy of Sciences Feedback
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Last update: March 31, 2016