Single-Nucleotide Polymorphisms and Haplotype Analysis inβ-Defensin Genes in Different Ethnic Populations

Abstract A significant number of hereditary breast or ovarian cancers are caused by germline variants, mostly BRCA1/BRCA2 genes. Because genetic predispositions vary by ethnicity, several studies have reported founder variants of BRCA1/BRCA2 genes. Such founder variants were reported primarily based on their relevant population frequencies. We reviewed the variant data relating to BRCA1 and BRCA2 genes from January, 2012 to March 2019 at Samsung Medical Center, Seoul, Korea. Among the cases with pathogenic variants (PVs) or likely pathogenic variants (LPVs), we defined recurrent variants as those found in more than five unrelated patients. Using single nucleotide polymorphisms, we analyzed patient haplotypes. There were 14 recurrent variants in the BRCA1 gene and seven variants in the BRCA2 gene. Of note, three variants in each gene were primarily detected in Korean populations. Among them, the c.5339T > C BRCA1 variant had a long block sized 74.5 kb. In BRCA2, the c.1399A > T variant had a long block sized 35.5 kb. We suggest that BRCA1 c.5339T > C and BRCA2 c.1399A > T are founder variants of the Korean population. These two recurrent variants were ethnicity-prevalent, primarily found in Korean populations, and the sizes of the linkage disequilibrium blocks are longer than others.

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High-throughput molecular haplotype analysis (allelic assignment) of single-nucleotide polymorphisms by fluorescent polymerase chain reaction

Analytical Biochemistry ◽

10.1016/j.ab.2004.08.025 ◽

2004 ◽

Vol 335 (1) ◽

pp. 165-167 ◽

Cited By ~ 7

Author(s):

Dmitri Proudnikov ◽

K. Steven LaForge ◽

Mary Jeanne Kreek

Keyword(s):

Polymerase Chain Reaction ◽

Single Nucleotide Polymorphisms ◽

High Throughput ◽

Haplotype Analysis ◽

Nucleotide Polymorphisms ◽

Chain Reaction ◽

Single Nucleotide ◽

Polymerase Chain ◽

Fluorescent Polymerase Chain Reaction

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Single Nucleotide Polymorphisms of the Pregnane X Receptor Gene in Han Chinese and a Comparison with Other Ethnic Populations

Pharmacology ◽

10.1159/000123687 ◽

2008 ◽

Vol 81 (4) ◽

pp. 350-354 ◽

Cited By ~ 8

Author(s):

Xue-Ding Wang ◽

Xiao-Ying Deng ◽

Jie Chen ◽

Jia-Li Li ◽

Xiao Chen ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Receptor Gene ◽

Pregnane X Receptor ◽

Han Chinese ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Ethnic Populations

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CD44, IL-33, and ST2 Gene Polymorphisms on Hepatocellular Carcinoma Susceptibility in the Chinese Population

BioMed Research International ◽

10.1155/2020/2918517 ◽

2020 ◽

Vol 2020 ◽

pp. 1-11

Author(s):

Xiaolan Pan ◽

Meiqin Li ◽

Lei Huang ◽

Dan Mo ◽

Yihua Liang ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Single Nucleotide Polymorphisms ◽

Chinese Population ◽

Haplotype Analysis ◽

Control Group ◽

Case Group ◽

Nucleotide Polymorphisms ◽

Cancer Stemness ◽

Single Nucleotide ◽

The Relationship

The interleukin- (IL-) 33/ST2 axis plays a pivotal role in tumorigenesis through influencing cancer stemness and other mechanisms. CD44 is one of the critical markers of hepatocellular carcinoma (HCC) among the cancer stem cells (CSCs). There is still a lack of CD44 gene single-nucleotide polymorphisms (SNPs) combined with IL-33/ST2 pathway single-nucleotide polymorphisms in HCC susceptibility analysis literature, although CD44 and IL-33/ST2 have been reported separately in human cancers. This study is aimed at investigating the relationship between CD44, IL-33, and ST2 SNPs and HCC susceptibility and clinicopathological features. We analyzed 565 HCC patients and 561 healthy controls in the Chinese population. The genes for CD44rs187115A>G, IL-33 rs1929992A>G, and ST2 rs3821204G>C were typed using the SNaPshot method. We found that the distribution frequencies of CD44 and ST2 alleles and genotypes in both the HCC case group and the control group were statistically significant ( p < 0.05 ). The results showed that individuals carrying at least one G allele of the CD44 rs187115 gene were at a higher risk than the AA genotype carriers ( p = 0.007 , odds ratio OR = 1.429 , 95% confidence interval (CI): 1.102–1.854). Similarly, individuals with at least one C allele of ST2 rs3821204 had a higher risk of HCC than those with GG genes ( p ≤ 0.001 , OR = 1.647 , 95% CI: 1.296-2.093). Combining the haplotype analysis of the 3 loci suggested that CD44 rs187115, IL-33 rs1929992, and ST2 rs3821204 are associated with the risk of HCC and could potentially serve as useful genetic markers for HCC in some populations of China.

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Linkage disequilibrium and haplotype analysis among eight novel single-nucleotide polymorphisms in the human tissue-type plasminogen activator (t-PA) gene

Journal of Human Genetics ◽

10.1007/s100380170055 ◽

2001 ◽

Vol 46 (7) ◽

pp. 367-371 ◽

Cited By ~ 4

Author(s):

I. Nakazawa ◽

T. Nakajima ◽

T. Ishigami ◽

S. Umemura ◽

M. Emi

Keyword(s):

Linkage Disequilibrium ◽

Single Nucleotide Polymorphisms ◽

Plasminogen Activator ◽

Human Tissue ◽

Haplotype Analysis ◽

Tissue Type ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Tissue Type Plasminogen Activator ◽

Type Plasminogen Activator

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Association between single nucleotide polymorphisms in CDKAL1 and HHEX and type 2 diabetes in Chinese Population

10.21203/rs.3.rs-63444/v1 ◽

2020 ◽

Author(s):

Chuanyin Li ◽

Keyu Shen ◽

Man Yang ◽

Ying Yang ◽

Wenyu Tao ◽

...

Keyword(s):

Type 2 Diabetes ◽

Insulin Secretion ◽

Single Nucleotide Polymorphisms ◽

Chinese Population ◽

Haplotype Analysis ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Genotype Frequencies ◽

Inheritance Model

Abstract Background: Type 2 diabetes mellitus (T2DM) has a high global prevalence, and the interaction of environmental factors and genetic factors may contribute to the risk of T2DM. We aimed to investigate the association between T2DM and the single nucleotide polymorphisms (SNPs) in genes associated with insulin secretion is necessary. Methods: T2DM (1169) and nondiabetic (NDM) (1277) subjects were enrolled and the eight SNPs in CDKAL1 and HHEX associated with insulin secretion were genotyped in a Chinese population.Results: Our result revealed that four SNPs (rs4712524, rs10946398, rs7754840 in CDKAL1 and rs5015480 in HHEX) showed significantly different genotype frequencies in the T2DM and NDM groups (P<0.00625). The G allele of rs4712524(P=0.004, OR=1.184; 95%CI: 1.057-1.327) , C allele of rs10946398(P<0.001, OR=1.247; 95%CI: 1.112-1.398) and C allele of rs775480 in CDKAL1 (P<0.001, OR=1.229; 95%CI: 1.096-1.387) functioned as risk allele in incidence of T2DM. The C allele of rs5015480 in HHEX (P<0.001, OR=1.295; 95%CI: 1.124-1.493) was risk factor for the development of T2DM. The haplotype analysis revealed that rs4712524-rs10946398-rs7754840-rs9460546GCCG (P=0.001, OR=1.210; 95%CI: 1.076-1.360) was associated with a greater risk of T2DM development. Moreover, The HHEX rs1111875-rs5015480 haplotype analysis with D’>0.9 showed that rs1111875-rs5015480CC was associated with development of T2DM(P=2.63×10-5, OR=1.364; 95%CI:1.180-1.576). In the inheritance models analysis, the best fit inheritance model for rs4712524, rs10946398, and rs7754840 in CDKAL1 and rs5015480 in HHEX were all log-additive. Conclusion: Our results revealed that genetic variations in CDKAL1 and HHEX were associated with T2DM susceptibility in a Chinese population.

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