NBDC Research ID: hum0042.v1

 

SUMMARY

Aims: To identify susceptibility genes associated with degenerative bony changes of the temporomandibular joint (TMJ) and third molar agenesis.

Methods: Illumina HumanOmniExpress BeadChip was used for genotyping.

Participants/Materials: (1) 146 cases with TMJ and 374 controls (non-TMJ) in the Japanese and Korean populations

                  (2) 149 cases with at least one-third molar agenesis and 338 controls in the Japanese and Korean populations

 

Data Set IDType of DataCriteriaRelease Date
hum0042.v1.TMJ.v1

GWAS in TMJ (105 Japanese cases, 41 Korean cases) and

non-TMJ (193 Japanese controls, 181 Korean controls)

Controlled Access (Type I) 2016/03/02
hum0042.v1.3MA.v1

mandibular third molar agenesis (40 Japanese cases, 40 Korean cases),

maxillary third molar agenesis (62 Japanese cases, 63 Korean cases),

at least one-third molar agenesis (78 Japanese cases, 71 Korean cases)

Controlled Access (Type I) 2016/03/02

*Release Note

* Data users need to apply the Form 2 (Application Form for Using NBDC Human Data) to reach the Controlled Access Data. Learn more

 

MOLECULAR DATA

hum0042.v1

Participants/Materials:

(1) TMJ

  TMJ: 146 cases (105 Japanese cases, 41 Korean cases)

  non-TMJ: 374 controls (193 Japanese controls, 181 Korean controls)

(2) third molar agenesis

(2-1) mandibular third molar agenesis

   with third molar agenesis (40 Japanese cases, 40 Korean cases)

   without third molar agenesis (224 Japanese controls, 183 Korean controls)

(2-2) maxillary third molar agenesis

   with third molar agenesis (62 Japanese cases, 63 Korean cases)

   without third molar agenesis (202 Japanese controls, 160 Korean controls)

(2-3) at least one-third molar agenesis

   with third molar agenesis (78 Japanese cases, 71 Korean cases)

   without third molar agenesis (186 Japanese controls, 152 Korean controls)

Targets GWAS
Target Loci for Capture Methods -
Platform Illumina [HumanOmniExpress BeadChip]
Source gDNAs extracted from saliva
Cell Lines -
Library Construction (kit name) Illumina HumanOmniExpress BeadChip kit
Genotyping Call Methods (software) GenCall software (GenomeStudio)
Filtering Methods Sample Call rate ≤ 0.98, SNP call rate ≤ 0.98, MAF ≤ 3%, HWE P < 1 x 10^-6
Marker Number (after QC)

(1) Japanese: 550,005 SNPs, Korean: 545,797 SNPs

(2) Japanese: 547,727 SNPs, Korean: 545,945 SNPs

Japanese Genotype-phenotype Archive Data set ID

(1) hum0042.v1.TMJ.v1

(2) hum0042.v1.3MA.v1

Dictionary file

Total Data Volume

(1) 198 MB (zip [xlsx])

(2) 589 MB (zip [xlsx])

Comments (Policies) NBDC policy

This study was supported by “Genome Science”. “Genome Science” is a part of the “Support Programs for Three Fields in Life Sciences (cancer, genome and brain sciences)” established by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) under the Grant-in-Aid for Scientific Research on Innovative Areas.

 

DATA PROVIDER

Principal Investigator: Tetsutarou Yamaguchi

Affiliation: Showa University School of Dentistry

Project / Group Name:

Funds / Grants (Research Project Number):

NameTitleProject Number

Ministry of Education, Culture, Sports, Science and Technology (MEXT) KAKENHI

Grant-in-Aid for Scientific Research on Innovative Areas

Genome Science 221S0002

 

PUBLICATIONS

TitleDOIData ID
1 Genome-wide association study of degenerative bony changes of the temporomandibular joint. doi:10.1111/odi.12141 hum0042.v1.TMJ.v1
2 A genome-wide association study of third molar agenesis in Japanese and Korean populations. doi:10.1038/jhg.2013.106 hum0042.v1.3MA.v1

 

USERS (Controlled-Access Data)

Principal Investigator: Affiliation: Data in Use (Data Set ID)Period of Data Use