diabetes research and clinical practice 108 (2015) e25–e27
Contents available at ScienceDirect
Diabetes Research and Clinical Practice journ al h ome pa ge : www .elsevier.co m/lo cate/diabres
Single nucleotide polymorphisms in type 2 diabetes among Hispanic adults Amanda L. Watson a, Jie Hu b, Norman H.L. Chiu a,c,* a
Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27412, USA School of Nursing, University of North Carolina at Greensboro, Greensboro, NC 27402, USA c Department of Nanoscience, Joint School of Nanoscience and Nanoengineering, Greensboro, NC 27401, USA b
article info
abstract
Article history:
In this pilot study, we explore the genetic variation that may relate to type 2 diabetes (T2D)
Received 5 February 2015
among Hispanic adults. The genotypes of 36 Hispanic adults were analyzed by using the
Accepted 20 February 2015
Cardio-Metabochip. The goal is to identify single nucleotide polymorphisms (SNPs) associ-
Available online 26 February 2015
ated to T2D among Hispanic adults. A total of 26 SNPs were identified to be associated with T2D among Hispanic adults. None of these SNPs have been reported for T2D. By using the
Keywords:
principle components analysis to analyze the genotype of 26 SNPs in 36 samples, the
Single nucleotide polymorphism
samples obtained from diabetic patients could be distinguished from the control samples.
Hispanic adults
The findings support genetic involvement in T2D among Hispanic adults. # 2015 Elsevier Ireland Ltd. All rights reserved.
1.
Introduction
Hispanic Americans suffer disproportionately from diabetes with nearly twice the rate of non-Hispanic adults [1]. Recent studies have identified associations between specific single nucleotide polymorphisms (SNPs) and type 2 diabetes (T2D) [2]. Among those studies, only a few have focused on the Hispanic population despite the fact that SNP genotyping technology has become more robust and commercially available [3]. If specific SNPs can be identified for T2D among Hispanic adults, it would assist the ongoing efforts on improving preventive measures as well as the development of new diagnostic biomarkers and/or treatments for T2D. The aim of this pilot study is to explore the genetic variations among Hispanic adults that are associated with T2D.
2.
Material and methods
Among 36 participants, 18 with and 18 without T2D, from central North Carolina were recruited for this study. The eligibility criteria included self-identification of Mexican origin and age 18 years or older. The HbA1c level of each participant was measured [4]. Participants provided a blood draw for DNA isolation, which was carried out by using the PAXgene blood DNA isolation kit (Qiagen). DNA concentration was determined by using the Quant-iT PicoGreen dsDNA Assay Kit (Invitrogen). The Cardio-Metabochip was designed by consortia of experts in genetic variations of cardiovascular and metabolic diseases including T2D [5]. All 36 samples were genotyped on the Cardio-Metabochip (Illumina) using manufacture’s protocols. The genotypes were determined by using GenomeStudio (Illumina).
* Corresponding author at: UNCG Department of Chemistry and Biochemistry, Joint School of Nanoscience and Nanoengineering, Greensboro, NC 27412, United States. Tel.: +1 336 334 3126. E-mail address: [email protected] (N.H.L. Chiu). http://dx.doi.org/10.1016/j.diabres.2015.02.025 0168-8227/# 2015 Elsevier Ireland Ltd. All rights reserved.
e26
diabetes research and clinical practice 108 (2015) e25–e27
Table 1 – Demographics of case and control participants. Case Number of participants Sex: Male Female Age range Average age Hemoglobin A1c Family history
Controls
18
18
5 13 19–70 51 13 7.61% 1.31 (60 mmol/mol 14.3) 11
4 14 25–62 43 11 5.47% 0.49 (36 mmol/mol 5.4) 8
A total of 36 participants were involved in this study. Their sex, age, hemoglobin A1c, and family history of type 2 diabetes were recorded. The average value standard deviation is reported.
Quality control and association tests were done using PLINK (Version 1.07) [6]. The quality control measures included: (1) removal of SNPs that did not genotype correctly, (2) sex check, (3) missingness statistics and (4) Hardy– Weinberg equilibrium deviations. To perform the association study, the chi-squared algorithm was used to compare the case and control SNP genotypes. The results were visualized and filtered in the
Haploview viewer [7]. To determine the specificity of any SNP candidates to the Hispanic population and T2D, both SNP genotype and case allelic frequency were compared with data from the HapMap Project [8]. The relationships of SNP genotypes in 36 participants were further analyzed by using principle components analysis (PCA), which was carried out by using the XLSTAT software (Addinsoft) (version 2014.2.03).
3.
Results
All participants matched the selection criteria. The case group had an average HbA1c of 7.6% (60 mmol/mol) and the control group had an average HbA1c of 5.5% (36 mmol/mol). The complete demographics of participants are listed in Table 1. The raw data obtained from the Cardio-Metabochip consisted of 197,000 SNP genotypes per sample. After performing the quality control measures, 132,623 SNPs were available for association study. The Haploview filtering yielded 300 SNPs with p-value of
Contents available at ScienceDirect
Diabetes Research and Clinical Practice journ al h ome pa ge : www .elsevier.co m/lo cate/diabres
Single nucleotide polymorphisms in type 2 diabetes among Hispanic adults Amanda L. Watson a, Jie Hu b, Norman H.L. Chiu a,c,* a
Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27412, USA School of Nursing, University of North Carolina at Greensboro, Greensboro, NC 27402, USA c Department of Nanoscience, Joint School of Nanoscience and Nanoengineering, Greensboro, NC 27401, USA b
article info
abstract
Article history:
In this pilot study, we explore the genetic variation that may relate to type 2 diabetes (T2D)
Received 5 February 2015
among Hispanic adults. The genotypes of 36 Hispanic adults were analyzed by using the
Accepted 20 February 2015
Cardio-Metabochip. The goal is to identify single nucleotide polymorphisms (SNPs) associ-
Available online 26 February 2015
ated to T2D among Hispanic adults. A total of 26 SNPs were identified to be associated with T2D among Hispanic adults. None of these SNPs have been reported for T2D. By using the
Keywords:
principle components analysis to analyze the genotype of 26 SNPs in 36 samples, the
Single nucleotide polymorphism
samples obtained from diabetic patients could be distinguished from the control samples.
Hispanic adults
The findings support genetic involvement in T2D among Hispanic adults. # 2015 Elsevier Ireland Ltd. All rights reserved.
1.
Introduction
Hispanic Americans suffer disproportionately from diabetes with nearly twice the rate of non-Hispanic adults [1]. Recent studies have identified associations between specific single nucleotide polymorphisms (SNPs) and type 2 diabetes (T2D) [2]. Among those studies, only a few have focused on the Hispanic population despite the fact that SNP genotyping technology has become more robust and commercially available [3]. If specific SNPs can be identified for T2D among Hispanic adults, it would assist the ongoing efforts on improving preventive measures as well as the development of new diagnostic biomarkers and/or treatments for T2D. The aim of this pilot study is to explore the genetic variations among Hispanic adults that are associated with T2D.
2.
Material and methods
Among 36 participants, 18 with and 18 without T2D, from central North Carolina were recruited for this study. The eligibility criteria included self-identification of Mexican origin and age 18 years or older. The HbA1c level of each participant was measured [4]. Participants provided a blood draw for DNA isolation, which was carried out by using the PAXgene blood DNA isolation kit (Qiagen). DNA concentration was determined by using the Quant-iT PicoGreen dsDNA Assay Kit (Invitrogen). The Cardio-Metabochip was designed by consortia of experts in genetic variations of cardiovascular and metabolic diseases including T2D [5]. All 36 samples were genotyped on the Cardio-Metabochip (Illumina) using manufacture’s protocols. The genotypes were determined by using GenomeStudio (Illumina).
* Corresponding author at: UNCG Department of Chemistry and Biochemistry, Joint School of Nanoscience and Nanoengineering, Greensboro, NC 27412, United States. Tel.: +1 336 334 3126. E-mail address: [email protected] (N.H.L. Chiu). http://dx.doi.org/10.1016/j.diabres.2015.02.025 0168-8227/# 2015 Elsevier Ireland Ltd. All rights reserved.
e26
diabetes research and clinical practice 108 (2015) e25–e27
Table 1 – Demographics of case and control participants. Case Number of participants Sex: Male Female Age range Average age Hemoglobin A1c Family history
Controls
18
18
5 13 19–70 51 13 7.61% 1.31 (60 mmol/mol 14.3) 11
4 14 25–62 43 11 5.47% 0.49 (36 mmol/mol 5.4) 8
A total of 36 participants were involved in this study. Their sex, age, hemoglobin A1c, and family history of type 2 diabetes were recorded. The average value standard deviation is reported.
Quality control and association tests were done using PLINK (Version 1.07) [6]. The quality control measures included: (1) removal of SNPs that did not genotype correctly, (2) sex check, (3) missingness statistics and (4) Hardy– Weinberg equilibrium deviations. To perform the association study, the chi-squared algorithm was used to compare the case and control SNP genotypes. The results were visualized and filtered in the
Haploview viewer [7]. To determine the specificity of any SNP candidates to the Hispanic population and T2D, both SNP genotype and case allelic frequency were compared with data from the HapMap Project [8]. The relationships of SNP genotypes in 36 participants were further analyzed by using principle components analysis (PCA), which was carried out by using the XLSTAT software (Addinsoft) (version 2014.2.03).
3.
Results
All participants matched the selection criteria. The case group had an average HbA1c of 7.6% (60 mmol/mol) and the control group had an average HbA1c of 5.5% (36 mmol/mol). The complete demographics of participants are listed in Table 1. The raw data obtained from the Cardio-Metabochip consisted of 197,000 SNP genotypes per sample. After performing the quality control measures, 132,623 SNPs were available for association study. The Haploview filtering yielded 300 SNPs with p-value of
