scholarly journals Rapid Pyrosequencing Method for FMO3 Non-Synonymous Genetic Variant Evaluation in A Korean Population

2021 ◽  
Author(s):  
Jin-woo Park ◽  
In-Hwan Park ◽  
Jong-Min Kim ◽  
Kyoung-Ah Kim ◽  
Ji-Young Park
Keyword(s):  
Linkage Disequilibrium ◽  
Single Nucleotide Polymorphisms ◽  
Ethnic Differences ◽  
Japanese Population ◽  
Genetic Variant ◽  
Allele Frequencies ◽  
Korean Population ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Pyrosequencing Method

Abstract Background: The aim of this study was to develop a feasible pyrosequencing method to detect non-synonymous single nucleotide polymorphisms (SNPs) of the flavin-containing monooxygenase 3 (FMO3) gene and compare the ethnic differences in the frequencies of these alleles. Methods and Results: This pyrosequencing method was used to identify four non-synonymous FMO3 SNPs, including c.855C>T (rs909530), c.441C>T (rs1800822), c.923A>G (rs2266782), and c.472G>A (rs2266782). The allele frequencies of these SNPs in 122 unrelated Korean subjects were analyzed, and were as follows: 44.7% for c.855C>T, 23.4% for c.441C>T, 23.0% for c.923A>G, and 27.1% for c.472G>A. Linkage disequilibrium (LD) analysis showed that c.923A>G and c.472G>A were in strong LD (D′ = 0.8289, r2 = 0.5332). Conclusions: The designed pyrosequencing method was successfully applied to identify the c.855C>T, c.441C>T, c.923A>G, and c.472G>A SNPs. The frequencies were similar to those reported previously in a Japanese population. However, in general, large differences between ethnicities were found.

scholarly journals Discovery of BRCA1/BRCA2 Founder Variants by Haplotype Analysis

2021 ◽  
Author(s):  
Won Kyung Kwon ◽  
Hyeok-Jae Jang ◽  
Jeong Eon Lee ◽  
Yeon Hee Park ◽  
Jai Min Ryu ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Single Nucleotide Polymorphisms ◽  
Haplotype Analysis ◽  
Medical Center ◽  
Korean Population ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Pathogenic Variants ◽  
Ovarian Cancers ◽  
Brca1 Brca2

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.

Protein Variation in ADH and ADH-RELATED in Drosophila pseudoobscura: Linkage Disequilibrium Between Single Nucleotide Polymorphisms and Protein Alleles

Genetics ◽  
2001 ◽  
Vol 159 (2) ◽  
pp. 673-687
Author(s):  
Stephen W Schaeffer ◽  
C Scott Walthour ◽  
Donna M Toleno ◽  
Anna T Olek ◽  
Ellen L Miller
Keyword(s):  
Linkage Disequilibrium ◽  
Single Nucleotide Polymorphisms ◽  
Drosophila Pseudoobscura ◽  
Linkage Disequilibrium Mapping ◽  
Nucleotide Polymorphisms ◽  
Neutral Model ◽  
Significant Linkage Disequilibrium ◽  
Single Nucleotide ◽  
Synonymous Sites ◽  
Significant Linkage

Abstract A 3.5-kb segment of the alcohol dehydrogenase (Adh) region that includes the Adh and Adh-related genes was sequenced in 139 Drosophila pseudoobscura strains collected from 13 populations. The Adh gene encodes four protein alleles and rejects a neutral model of protein evolution with the McDonald-Kreitman test, although the number of segregating synonymous sites is too high to conclude that adaptive selection has operated. The Adh-related gene encodes 18 protein haplotypes and fails to reject an equilibrium neutral model. The populations fail to show significant geographic differentiation of the Adh-related haplotypes. Eight of 404 single nucleotide polymorphisms (SNPs) in the Adh region were in significant linkage disequilibrium with three ADHR protein alleles. Coalescent simulations with and without recombination were used to derive the expected levels of significant linkage disequilibrium between SNPs and 18 protein haplotypes. Maximum levels of linkage disequilibrium are expected for protein alleles at moderate frequencies. In coalescent models without recombination, linkage disequilibrium decays between SNPs and high frequency haplotypes because common alleles mutate to haplotypes that are rare or that reach moderate frequency. The implication of this study is that linkage disequilibrium mapping has the highest probability of success with disease-causing alleles at frequencies of 10%.

Twenty­six Novel Single Nucleotide Polymorphisms and their Frequencies of the NR1I3(CAR) Gene in a Japanese Population

2003 ◽  
Vol 18 (6) ◽  
pp. 413-418 ◽  
Author(s):  
Shinobu Ikeda ◽  
Kouichi Kurose ◽  
Shogo Ozawa ◽  
Kimie Sai ◽  
Ryuichi Hasegawa ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Japanese Population ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide
Sign in / Sign up

Export Citation Format

Share Document