Skip Navigation
Skip to contents

Diabetes Metab J : Diabetes & Metabolism Journal

Search
OPEN ACCESS

Search

Page Path
HOME > Search
2 "Exome"
Filter
Filter
Article category
Keywords
Publication year
Authors
Funded articles
Original Article
Genetics
Exome Chip Analysis of 14,026 Koreans Reveals Known and Newly Discovered Genetic Loci Associated with Type 2 Diabetes Mellitus
Seong Beom Cho, Jin Hwa Jang, Myung Guen Chung, Sang Cheol Kim
Diabetes Metab J. 2021;45(2):231-240.   Published online July 28, 2020
DOI: https://doi.org/10.4093/dmj.2019.0163
  • 6,158 View
  • 195 Download
  • 6 Web of Science
  • 6 Crossref
Graphical AbstractGraphical Abstract AbstractAbstract PDFSupplementary MaterialPubReader   ePub   
Background

Most loci associated with type 2 diabetes mellitus (T2DM) discovered to date are within noncoding regions of unknown functional significance. By contrast, exonic regions have advantages for biological interpretation.

Methods

We analyzed the association of exome array data from 14,026 Koreans to identify susceptible exonic loci for T2DM. We used genotype information of 50,543 variants using the Illumina exome array platform.

Results

In total, 7 loci were significant with a Bonferroni adjusted P=1.03×10−6. rs2233580 in paired box gene 4 (PAX4) showed the highest odds ratio of 1.48 (P=1.60×10−10). rs11960799 in membrane associated ring-CH-type finger 3 (MARCH3) and rs75680863 in transcobalamin 2 (TCN2) were newly identified loci. When we built a model to predict the incidence of diabetes with the 7 loci and clinical variables, area under the curve (AUC) of the model improved significantly (AUC=0.72, P<0.05), but marginally in its magnitude, compared with the model using clinical variables (AUC=0.71, P<0.05). When we divided the entire population into three groups—normal body mass index (BMI; <25 kg/m2), overweight (25≤ BMI <30 kg/m2), and obese (BMI ≥30 kg/m2) individuals—the predictive performance of the 7 loci was greatest in the group of obese individuals, where the net reclassification improvement was highly significant (0.51; P=8.00×10−5).

Conclusion

We found exonic loci having a susceptibility for T2DM. We found that such genetic information is advantageous for predicting T2DM in a subgroup of obese individuals.

Citations

Citations to this article as recorded by  
  • Polygenic Risk Score, Lifestyles, and Type 2 Diabetes Risk: A Prospective Chinese Cohort Study
    Jia Liu, Lu Wang, Xuan Cui, Qian Shen, Dun Wu, Man Yang, Yunqiu Dong, Yongchao Liu, Hai Chen, Zhijie Yang, Yaqi Liu, Meng Zhu, Hongxia Ma, Guangfu Jin, Yun Qian
    Nutrients.2023; 15(9): 2144.     CrossRef
  • Celebrities in the heart, strangers in the pancreatic beta cell: Voltage‐gated potassium channels Kv7.1 and Kv11.1 bridge long QT syndrome with hyperinsulinaemia as well as type 2 diabetes
    Anniek F. Lubberding, Christian R. Juhl, Emil Z. Skovhøj, Jørgen K. Kanters, Thomas Mandrup‐Poulsen, Signe S. Torekov
    Acta Physiologica.2022;[Epub]     CrossRef
  • Substitution of Carbohydrates for Fats and Risk of Type 2 Diabetes among Korean Middle-Aged Adults: Findings from the Korean Genome and Epidemiology Study
    Hye-Ah Lee, Hyesook Park
    Nutrients.2022; 14(3): 654.     CrossRef
  • Ethnic-Specific Type 2 Diabetes Risk Factor PAX4 R192H Is Associated with Attention-Specific Cognitive Impairment in Chinese with Type 2 Diabetes
    Su Fen Ang, Serena Low, Tze Pin Ng, Clara S.H. Tan, Keven Ang, Ziliang Lim, Wern Ee Tang, Tavintharan Subramaniam, Chee Fang Sum, Su Chi Lim, Nagaendran Kandiah
    Journal of Alzheimer's Disease.2022; 88(1): 241.     CrossRef
  • TrustGWAS: A full-process workflow for encrypted GWAS using multi-key homomorphic encryption and pseudorandom number perturbation
    Meng Yang, Chuwen Zhang, Xiaoji Wang, Xingmin Liu, Shisen Li, Jianye Huang, Zhimin Feng, Xiaohui Sun, Fang Chen, Shuang Yang, Ming Ni, Lin Li, Yanan Cao, Feng Mu
    Cell Systems.2022; 13(9): 752.     CrossRef
  • Sex Differences in the Effects of CDKAL1 Variants on Glycemic Control in Diabetic Patients: Findings from the Korean Genome and Epidemiology Study
    Hye Ah Lee, Hyesook Park, Young Sun Hong
    Diabetes & Metabolism Journal.2022; 46(6): 879.     CrossRef
Brief Report
Genetics
Identification of Two Cases of Ciliopathy-Associated Diabetes and Their Mutation Analysis Using Whole Exome Sequencing
Min Kyeong Kim, Soo Heon Kwak, Shinae Kang, Hye Seung Jung, Young Min Cho, Seong Yeon Kim, Kyong Soo Park
Diabetes Metab J. 2015;39(5):439-443.   Published online October 22, 2015
DOI: https://doi.org/10.4093/dmj.2015.39.5.439
  • 4,391 View
  • 47 Download
  • 5 Web of Science
  • 5 Crossref
AbstractAbstract PDFPubReader   
Background

Alström syndrome and Bardet-Biedl syndrome are autosomal recessively inherited ciliopathies with common characteristics of obesity, diabetes, and blindness. Alström syndrome is caused by a mutation in the ALMS1 gene, and Bardet-Biedl syndrome is caused by mutations in BBS1-16 genes. Herein we report genetically confirmed cases of Alström syndrome and Bardet-Biedl syndrome in Korea using whole exome sequencing.

Methods

Exome capture was done using SureSelect Human All Exon Kit V4+UTRs (Agilent Technologies). HiSeq2000 system (Illumina) was used for massive parallel sequencing. Sanger sequencing was used for genotype confirmation and familial cosegregation analysis.

Results

A 21-year old Korean woman was clinically diagnosed with Alström syndrome. She had diabetes, blindness, obesity, severe insulin resistance, and hearing loss. Whole exome sequencing revealed a nonsense mutation in exon 10 of ALMS1 (c.8776C>T, p.R2926X) and a seven base-pair deletion resulting in frameshift mutation in exon 8 (c.6410_6416del, p.2137_2139del). A 24-year-old Korean man had Bardet-Biedl syndrome with diabetes, blindness, obesity, and a history of polydactyly. Whole exome sequencing revealed a nonsynonymous mutation in exon 11 of the BBS1 gene (c.1061A>G, p.E354G) and mutation at the normal splicing recognition site of exon 7 of the BBS1 gene (c.519-1G>T).

Conclusion

We found novel compound heterozygous mutations of Alström syndrome and Bardet-Biedl syndrome using whole exome sequencing. The whole exome sequencing successfully identified novel genetic variants of ciliopathy-associated diabetes.

Citations

Citations to this article as recorded by  
  • Genotype–phenotype associations in Alström syndrome: a systematic review and meta-analysis
    Brais Bea-Mascato, Diana Valverde
    Journal of Medical Genetics.2024; 61(1): 18.     CrossRef
  • Whole exome sequencing identifies rare biallelic ALMS1 missense and stop gain mutations in familial Alström syndrome patients
    Naglaa M. Kamal, Ahmed N. Sahly, Babajan Banaganapalli, Omran M. Rashidi, Preetha J. Shetty, Jumana Y. Al-Aama, Noor A. Shaik, Ramu Elango, Omar I. Saadah
    Saudi Journal of Biological Sciences.2020; 27(1): 271.     CrossRef
  • Established and emerging strategies to crack the genetic code of obesity
    V. Tam, M. Turcotte, D. Meyre
    Obesity Reviews.2019; 20(2): 212.     CrossRef
  • Identifying Pathogenic Variants of Monogenic Diabetes Using Targeted Panel Sequencing in an East Asian Population
    Seung Shin Park, Se Song Jang, Chang Ho Ahn, Jung Hee Kim, Hye Seung Jung, Young Min Cho, Young Ah Lee, Choong Ho Shin, Jong Hee Chae, Jae Hyun Kim, Sung Hee Choi, Hak C Jang, Jee Cheol Bae, Jong Cheol Won, Sung-Hoon Kim, Jong-Il Kim, Soo Heon Kwak, Kyong
    The Journal of Clinical Endocrinology & Metabolism.2019; 104(9): 4188.     CrossRef
  • Whole exome sequencing as a diagnostic tool for patients with ciliopathy-like phenotypes
    Sheila Castro-Sánchez, María Álvarez-Satta, Mohamed A. Tohamy, Sergi Beltran, Sophia Derdak, Diana Valverde, Anand Swaroop
    PLOS ONE.2017; 12(8): e0183081.     CrossRef

Diabetes Metab J : Diabetes & Metabolism Journal