• Title, Summary, Keyword: Allele Frequencies

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Genotypic Variation of Esterase Isozyme in Breeding Lines of Two-rowed Barley by Electrophoretic Banding Pattern (전기영동 패턴에 의한 2조보리 계통의 Esterase 동위효소 유전자형 변이분석)

  • 박광근;최홍집;이종호;서세정;김재철;남중현;김상효
    • KOREAN JOURNAL OF CROP SCIENCE
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    • v.47 no.6
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    • pp.465-470
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    • 2002
  • This study presents results of electro-phoretically detectable isozyme variation in Crossing Block (CB) lines of two-rowed barley maintained by the National Crop Experiment Station. The specific objectives were to determine allelic frequencies at the four Est loci(Est1, Est2, Est4, and Est5) and their distribution over 380CB lines of two-rowed barley. A total of 17 alleles were detected over the four Est loci in these lines. There were 4 alleles (Pr, Al, Ca, and Af at the Est1 locus and their frequencies were 69.7, 1.1, 28.4, and 0.8%, respectively. At the Est2 locus, 5 different alleles (Dr, Fr, Sp, Un and a recessive null allele) were detected and their frequencies were 2.9,84.5,0.5,2.1, and 10%, respectively. four alleles (Nz, Su, At, and null were detected at the Est4 locus and the allelic frequency of Su was about 84%. Four alleles(Mi, Pi, Te, and a null allele(od)) were detected at the Est5 locus and their frequencies were 34.2, 61.0, 2.4, and 2.4%, respectively. Based on the allelic frequencies over the four Est loci, 380 CB lines were classified into 25 genotypes. The most frequent genotypes were G1(Pr-Fr-Su-Mi) and G2(Pr-Fr-Su-Pi), and their frequencies were 28.1 and 39.5%, respectively. The frequencies of other genotypes were less than 10%.

Controlling Linkage Disequilibrium in Association Tests: Revisiting APOE Association in Alzheimer's Disease

  • Park, Lee-Young
    • Genomics & Informatics
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    • v.5 no.2
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    • pp.61-67
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    • 2007
  • The allele frequencies of markers as well as linkage disequilibrium (LD) can be changed in cases due to the LD between markers and the disease allele, exhibiting spurious associations of markers. To identify the true association, classical statistical tests for dealing with confounders have been applied to draw a conclusion as to whether the association of variants comes from LD with the known disease allele. However, a more direct test considering LD using estimated haplotype frequencies may be more efficient. The null hypothesis is that the different allele frequencies of a variant between cases and controls come solely from the increased disease allele frequency and the LD relationship with the disease allele. The haplotype frequencies of controls are estimated using the expectation maximization (EM) algorithm from the genotype data. The estimated frequencies are applied to calculate the expected haplotype frequencies in cases corresponding to the increase or decrease of the causative or protective alleles. The suggested method was applied to previously published data, and several APOE variants showed association with Alzheimer's disease independent from the APOE ${\varepsilon}4$ variant, rs429358, regardless of LD showing significant simulated p-values. The test results support the possibility that there may be more than one common disease variant in a locus.

CYP2E1*5B, CYP2E1*6, CYP2E1*7B, CYP2E1*2, and CYP2E1*3 Allele Frequencies in Iranian Populations

  • Shahriary, Ghazaleh Mohammadzadeh;Galehdari, Hamid;Jalali, Amir;Zanganeh, Fatemeh;Alavi, Seyed Mohammad Reza;Aghanoori, Mohammad Reza
    • Asian Pacific Journal of Cancer Prevention
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    • v.13 no.12
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    • pp.6505-6510
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    • 2012
  • Background: CYP2E1 encodes an enzyme which is mainly involved in bioactivation of potential carcinogens such as N-nitrosamines. Polymorphisms in the gene have been reported to be associated with cancer. The aim of this study was to evaluate genotype distributions and allele frequencies of five CYP2E1 polymorphisms in Iran Materials and Methods: Two hundred healthy individuals of an Iranian population from the southwest were included in this study. PCR-restriction fragment length polymorphism and Tetra-ARMS PCR methods were applied for CYP2E1 genotyping. Results: The allele frequencies for $^*5B$, $^*6$, $^*7B$, $^*2$, and $^*3$ were calculated to be 1.5%, 16%, 28.5%, 0%, and 2.75% respectively. Results of this study showed that no significant differences in genotype and allele frequencies of five single nucleotide polymorphisms with respect to the gender and tribes. The chi-square test showed that the genotype frequencies of $CYP2E1^*5B$ were similar to Caucasians, but the distribution of $CYP2E1^*6$ genotypes was similar to Asians. The frequencies of $CYP2E1^*2$ (0%) and $CYP2E1^*3$ (2.75%) alleles were within the range for Caucasians and Orientals. In the case of $CYP2E1^*7B$, the data werelimited. Accordingly, the results were only compared with Europeans and the comparison showed significant differences. Conclusions: In conclusion, ethnic and geographic differences may explain discrepancies in the prevalence of CYP2E1 polymorphisms.

Allele Frequencies of the Single Nucleotide Polymorphisms Related to the Body Burden of Heavy Metals in the Korean Population and Their Ethnic Differences

  • Eom, Sang-Yong;Lim, Ji-Ae;Kim, Yong-Dae;Choi, Byung-Sun;Hwang, Myung Sil;Park, Jung-Duck;Kim, Heon;Kwon, Ho-Jang
    • Toxicological Research
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    • v.32 no.3
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    • pp.195-205
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    • 2016
  • This study was performed to select single nucleotide polymorphisms (SNPs) related to the body burden of heavy metals in Koreans, to provide Korean allele frequencies of selected SNPs, and to assess the difference in allele frequencies with other ethnicities. The candidate-gene approach method and genome-wide association screening were used to select SNPs related to the body burden of heavy metals. Genotyping analysis of the final 192 SNPs selected was performed on 1,483 subjects using the VeraCode Goldengate assay. Allele frequencies differences and genetic differentiations between the Korean population and Chinese (CHB), Japanese (JPT), Caucasian (CEU), and African (YIR) populations were tested by Fisher's exact test and fixation index ($F_{ST}$), respectively. The Korean population was genetically similar to the CHB and JPT populations ($F_{ST}$ < 0.05, for all SNPs in both populations). However, a significant difference in the allele frequencies between the Korean and CEU and YIR populations were observed in 99 SNPs (60.7%) and 120 SNPs (73.6%), respectively. Ten (6.1%) and 26 (16.0%) SNPs had genetic differentiation ($F_{ST}$ > 0.05) among the Korean-CEU and Korean-YIR comparisons, respectively. The SNP with the largest $F_{ST}$ value between the Korean and African populations was cystathionine-${\beta}$-synthase rs234709 ($F_{ST}$: KOR-YIR, 0.309; KOR-CEU, 0.064). Our study suggests that interethnic differences exist in SNPs associated with heavy metals of Koreans, and it should be considered in future studies that address ethnic differences in heavy-metal concentrations in the body and genetic susceptibility to the body burden of heavy metals.

Protein Polvmorphisms and llariations of Wild House Rat (Rattus norueRicus) Population in Korea (한국산 야생집쥐(Rattus nowegicus) 집단의 단백질 다형과 유전적 변이)

  • 김남근;이하규이정주
    • The Korean Journal of Zoology
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    • v.36 no.2
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    • pp.193-199
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    • 1993
  • The protein po;vmorphisms and allele frequencies of wild house rat (Rattus norvegicus) population in Korea were studied. The studied proteins and enzymes were transferrin (Tf), albumin (Alb), fumarate hvdratase (FH), phospho!loucomutase (PGM), lactate dehvdrogenase A (LDHA) and lactate dehvdrogenase B (LDHB). There were two transferrin alleles, TP and Tf in Korean wild house rat popu1ation. The Tf2 allele was found for the first time by a starch gel, and confirmed by a polvacrvlamide gel isoelectric focusing and immunoblotting. The allele frequencies of TP and TF were 0.985 and 0.015, respectively. Two common alleles fumarate hydratase, FHa and FHb were found, and frequencies of FHa and FPP were calculated to be 0.714 and 0.286, respectively. The kequenw of FH in Korean wild house rat was higher than that of Finnish and Czechoslovakian population. Alb, PGM, LDHA and LDHB are only one phenotype each and all. Therefore, these proteins seem to be monomorphic in Korean wild house rat population.

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Identifying the polymorphisms in the thymic stromal lymphopoietin receptor (TSLPR) and their association with asthma

  • Yu, Ji-In;Kang, In-Hong;Chun, Sang-Woo;Yun, Ki-Jung;Moon, Hyung-Bae;Chae, Soo-Cheon
    • BMB Reports
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    • v.43 no.7
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    • pp.499-505
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    • 2010
  • The present study aimed to investigate whether the polymorphisms in the TSLPR gene are associated with atopic and asthmatic disease in the Korean population. We identified eleven single nucleotide polymorphisms (SNPs) and two variation sites in the TSLPR gene, including the promoter region. The genotype and allele frequencies of g.33G>C of the TSLPR gene in asthma patients were significantly different from the respective frequencies of the control group (P = 0.006 and 0.003, respectively). Our additional analysis showed that the genotype and allele frequencies of the g.33G>C and g.19646A>G of the TSLPR gene were significantly associated in the atopic asthma patients rather than in the non-atopic asthma patients (genotype frequencies; P = 0.0001 and 0.0003 respectively, allele frequencies; P = 0.0005 and 0.0001 in that order). Our results suggest that the SNPs of the TSLPR gene could be associated with the susceptibility to atopic asthma in the Korean population.

Significant Genotype Difference in the CYP2E1 PstI Polymorphism of Indigenous Groups in Sabah, Malaysia with Asian and Non-Asian Populations

  • Goh, Lucky Poh Wah;Chong, Eric Tzyy Jiann;Chua, Kek Heng;Chuah, Jitt Aun;Lee, Ping-Chin
    • Asian Pacific Journal of Cancer Prevention
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    • v.15 no.17
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    • pp.7377-7381
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    • 2014
  • CYP2E1 PstI polymorphism G-1259C (rs3813867) genotype distributions vary significantly among different populations and are associated with both diseases, like cancer, and adverse drug effects. To date, there have been limited genotype distributions and allele frequencies of this polymorphism reported in the three major indigenous ethnic groups (KadazanDusun, Bajau, and Rungus) in Sabah, also known as North Borneo. The aim of this study was to investigate the genotype distributions and allele frequencies of the CYP2E1 PstI polymorphism G-1259C in these three major indigenous peoples in Sabah. A total of 640 healthy individuals from the three dominant indigenous groups were recruited for this study. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) at G-1259C polymorphic site of CYP2E1 gene was performed using the Pst I restriction enzyme. Fragments were analyzed using agarose gel electrophoresis and confirmed by direct sequencing. Overall, the allele frequencies were 90.3% for c1 allele and 9.7% for c2 allele. The genotype frequencies for c1/c1, c1/c2 and c2/c2 were observed as 80.9%, 18.8%, and 0.3%, respectively. A highly statistical significant difference (p<0.001) was observed in the genotype distributions between indigenous groups in Sabah with all Asian and non-Asian populations. However, among these three indigenous groups, there was no statistical significant difference (p>0.001) in their genotype distributions. The three major indigenous ethnic groups in Sabah show unique genotype distributions when compared with other populations. This finding indicates the importance of establishing the genotype distributions of CYP2E1 PstI polymorphism in the indigenous populations.

Genetic Variants of the Blood Proteins and Enzymes in Beef Cattle (육우의 혈액단백질 및 효소의 유전적 변이체)

  • Sang, Byung Chan;Ryoo, Seung Heue;Sang, Byung Don
    • Korean Journal of Agricultural Science
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    • v.22 no.1
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    • pp.69-81
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    • 1995
  • This study was conducted to examine the genetic variants of the blood proteins and enzymes in beef cattle breeds, Hereford, Angus and Sharolais reared at the Daekwanryuong Branch of the National Livestock Research Institute. Genetic polymorphisms of transferrin(Tf), post-transferrin2(pTf-2), albumin(Alb), post-albumin (pAlb), ceruloplasmin(Cp), amylase-I(Am-I) and hemoglobin(Hb) in blood were analyzed by the methods of PAGE(polyacrylamide gel electrophoresis) and STAGE(starch gel electrophoresis). The results obtained from this study were summarized as follows: 1. Tf and pTf-2 locus assumed to be controlled by codominant alleles, A. $D_1$, $D_2$ and E allele for Tf, F and S allele for pTf-2. In genotype frequencies, 25% and 90% for Tf $D_1D_2$ and pTf-2 SS in Hereford, 25% and 100% for Tf $AD_1$ and pTf-2 FF in Angus, 50% for Tf $D_1D_1$ and pTf-2 FS in Sharolais were found to have the highest frequency, respectively. In gene frequencies, 0.400 and 0.900 for Tf E and pTf-2 S allele in Hereford, 0.678 and 0.607 for Tf $D_1$ and pTf-2S in Sharolais were appeared to have the highest frequency. 2. Alb and pAlb locus assumed to be controlled by codominant alleles, only A allele for Alb, F and S allele for pAlb. In genotype frequencies, 70% for pAlb SS in Hereford, 90% for pAlb FF in Angus and 57.15% for pAlb SS in Sharolais were found to have the highest frequency. In gene frequencies, 0.825 and 0.750 for pAlb S in Hereford and Charolais, 0.900 for pAlb F in Angus were found to have the highest frequency. 3. Cp and Am-I locus appeared to be controlled by two alleles, F and S allele for Cp, B and C allele for Am-I. In genotype frequencies, 100% and 65% for Cp FF and Am-I BB in Hereford, 45% and 85% for Cp FF, and Am-I CC in Angus, 50% and 64.29% for Cp FF and Am-I BC in Sharolais were found to have the highest frequency. Gene frequencies were 1,000, 0.600 and 0.750 for Cp F in Herehord, Angus and Sharolais, 0.800, 0.875 and 0.680 for Am-I B, C and C allele in Hereford, Angus and sharolais, respectively. 4. Hb locus assumed to be controlled by codominant alleles, only A allele in Hereford and Angus, A and B allele in Sharolais. Genotype frequencies were 57.14% and 42.86% for Hb AA and AB in Sharolais, and gene frequencies were 0.785 and 0.215 for Hb A and B in Sharolais.

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Genotype and Allelic Frequencies of a Newly Identified Mutation Causing Blindness in Jordanian Awassi Sheep Flocks

  • Jawasreh, K.I.Z.;Ababneh, H.;Awawdeh, F.T.;Al-Massad, M.A.;Al-Majali, A.M.
    • Asian-Australasian Journal of Animal Sciences
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    • v.25 no.1
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    • pp.33-36
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    • 2012
  • A total of 423 blood samples were collected (during 2009 and 2010) from all the ram holdings at three major Jordanian governmental Awassi breeding stations (Al-Khanasry, Al- Mushairfa and Al-Fjaje) and two private flocks. All blood samples were screened for the presence of mutations at the CNGA3 gene (responsible for day blindness in Awassi sheep) using RFLP-PCR. The day blindness mutation was detected in all studied flocks. The overall allele and genotype frequencies of all studied flocks of the day blindness mutation were 0.088 and 17.49%, respectively. The genotype and allele frequencies were higher in station flocks than the farmer flocks (0.121, 24.15 and 0.012, 2.32, respectively). Al-Mushairfa and Al-Khanasry stations have the highest genotype and allele frequencies for the day blindness mutation that were 27.77, 30.00% and 0.14, 0.171, respectively. The investigated farmer flocks have low percentages (0.03, 5.88% at Al-Shoubak and 0.005 and 1.05%, at Al-Karak, respectively for genotype and allele frequencies) compared with the breeding stations. Ram culling strategy was applied throughout the genotyping period in order to gradually eradicate this newly identified day blindness mutation from Jordanian Breeding station, since they annually distribute a high percentage of improved rams to farmer's flocks.

Ethnic Differences in Allelic Frequencies of Two (CA)n Microsatellite Markers Located on Chromosome 5q

  • Hong, Sung-Soo;Chae, Jae-Jin;Goh, Sung-Ho;Yong, Koong-Nam;Lee, Chung-Choo
    • Animal cells and systems
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    • v.1 no.1
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    • pp.123-128
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    • 1997
  • The characteristics of allelic polymorphisms of the two (CA)n microsatellite (p599 and ㅅ599) markers spanning the long arm of chromosome 5 were studied in 52 DNA samples from unrelated inhabitants of Seoul (Korea) by using the polymerase chain reaction (PCR) to investigate differences in allele frequencies between Korean and Caucasian populations. The 6 alleles were observed for p599 (CA)n with a polymorphism informative content (PIC) value of 0.71 and 9 alleles for ㅅ599 (CA)n with a PIC value of 0.82. The observed heterozygote frequencies of the loci were estimated to 0.730 and 0.846, respectively. Several allele frequencies of two loci showed significant differences between Korean and Caucasian populations. Genotype data from the two loci were consistent with the Hardy-Weinberg equilibrium by x2 test. Linkage disequilibrium between p599 (CA)n and ㅅ599 (CA)n loci was observed in x2 test between the observed and expected frequency of allelic association. The probability of matching calculated at each locus was 0.104 for p599 (CA)n and 0.043 for ㅅ599 (CA)n, respectively. These results demonstrate the need to determine populationspecific allele frequency distributions for polymorphic markers when performing genetic linkage studies in racially defined several populations.

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