• Genomics & Informatics
• /
• 제5권2호
• /
• pp.61-67
• /
• 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.

• 한국동물학회지
• /
• 제25권3호
• /
• pp.123-129
• /
• 1982

한국산 초파리집단의 유전적 특성을 생화학적으로 분석하여 분자유전학적 측면에서 집단 유전학적 체계를 확립하기 위하여 한국산 노랑초파리 (Drosophila melanogaster)의 11개 지역의 자연집단 (청량리, 등촌동, 신촌, 용산, 부천, 춘천, 대전, 대구, 광주, 나주 및 노화도)의 $\\alpha$-glycerophosphate dehydrogenase (\\alpha-GPDH) 인자형을 agarose gel 전기영동법에 의하여 조사 분석한 결과는 다음과 같다. 1. 한국산 노랑초파리 11가지 자연집단에서 $\\alpha$-GPDH allele는 상당한 다형현상을 이루고 있다. 2. $\\alpha$-GPDH allele의 heterozygosity는 $45\\sim50%$로서 상다히 높은 값을 보여주고 있다. 3. $\\alpha$-GPDH allele의 FF 인자형의 빈도는 SS인자형과 비슷하나 FS 인자형보다는 낮은 값을 보이고 있다. 4. $\\alpha$-GPDH allele의 F, S 두인자가 거의 비슷한 빈도를 보이고 있다.

• Asian-Australasian Journal of Animal Sciences
• /
• 제21권4호
• /
• pp.471-477
• /
• 2008

The porcine PRKAG3 (RN) gene encodes the regulatory gamma subunit of adenosine monophosphate-activated protein kinase (AMPK), which is a good candidate gene affecting meat quality. In this study, the effects of two missense mutations A595G (Ile199Val) and G154A (Gly52Ser) in porcine PRKAG3 gene on meat quality traits were studied in M. Longissimus dorsi (LD), M. Semispinalis capitis (SC) and M. Biceps femoris (BF) from different populations of 326 pigs. The PRKAG3 alleles 199I, 199IV, 52S and 52G were identified with PCR-RFLPs and all genotypes - 199I/199I, 199I/199V, 199V/199V, 52S/52S, 52S/52G and 52G/52G - were found. The frequency of V allele was larger than that of I allele in all populations. I allele frequency was zero in Chinese Meishan pigs (population D) especially. G allele frequency was larger than that of S allele in all populations except Large White (population A). Both variations at the PRKAG3 locus significantly affected these meat quality traits. The pork meat quality has not previously been established in Meishan or crosses thereof. The results suggested that generally pH of LD, SC and BF was higher in Meishan pigs than that in other populations. Moreover, Meishan pigs showed higher water-holding capacity and intramuscular fat (IMF), lower water content and water loss percentage compared to other populations in terms of the two variations. The results present here supply new evidence that alleles V199I and G52S at the PRKAG3 locus affect pork meat quality and provide useful information on pork production.

• Journal of Periodontal and Implant Science
• /
• 제35권2호
• /
• pp.299-310
• /
• 2005

The severe form of chronic periodontitis(CP) has been reported to be strongly associated with the presence of allele 2 of composite IL-1B(+3954) and IL-1A(+4845) genetic polymorphisms(genotype positive). However, other studies have reported conflicting findings. These might have resulted from differences in ethnic background and disease entities. The aim of this study was to determine the distribution of IL-1A(+4845), IL-1B(+3954), IL-1B(-511), and IL-1 RN(VNTR) genetic polymorphisms in children as a future Korean population. The study population consisted of 92 children from the Dept. of Pediatric Dentistry, Chonnam National University Hospital. Genomic DNA was obtained from buccal swab. The IL-1A(+4845), IL-1B(+3954), and IL-1B(-511) genes were genotyped by amplifying the polymorphic region using multiplex polymerase chain reaction(PCR), followed by restriction enzyme digestion and gel electrophoresis. IL-1 RN(VNTR) polymorphism were then evaluated by PCR amplification and fragment size analysis in agarose gel. The allele 2 frequency was 41.3%, 4.3%, 47.8%, and 9.9% for IL-1A(+4845), IL-1B(+3954), IL-1B(-511), and IL-1 RN respectively. The frequency of genotype with allele 2 carriage for IL-1A(+4845), IL-1B(+3954), IL-1B(-511), and IL-1 RN was 77.1%, 7.6%, 63.0%, and 15.2% respectively. The allele 2 frequency in IL-1B(+3954) was significantly higher in female than in male population(p<0.05). The negative association was shown between the presence of allele 2 in IL-1B(-511) and in IL-1B(+3954), and the carriage rate of IL-1B(+3954) allele 2 tended to lower in IL-1B(-511) allele 2(P=0.056). Only 7.3% of children carried the composite genotype of IL-1A(+4845) and IL-1B(+3954). These results suggest that the polymorphism of IL-1B(+3954) and the positive composite genotype was relatively rare in Korean population.

• 생명과학회지
• /
• 제19권2호
• /
• pp.174-178
• /
• 2009

본 연구는 2006년 8월경에 어획된 서해, 남해 및 동해 멸치집단을 분석하기 위하여 6종류의 microsatellite로 하였다. 서해멸치의 경우, 샘플수 72마리에 대한 allele 범위가 19-41로 평균 28.5를 보였다. 특히 EJ9 locus에서 평균보다 약 1.4배 많은 41를 나타내었다. 남해멸치의 평균 allele는 24.5로 서해보다는 적었고, EJ2, EJ9, EJ27.1 loci는 평균보다 높은 29-37의 범위를 보였다. 동해멸치는 평균 allele가 25.0으로 EJ35를 제외하면 대부분의 loci에서 평균 이상을 보였다. 그러나 서해, 남해 및 동해멸치의 allele 빈도율은 대부분 0.24 이하로 나타났다. 또한 Hobs보다 Hexp에서 0.5 정도 높은 값을 보였으나 유의성은 없었다(p>0.05). 유전적 다양성도 0.9 이상으로 매우 높은 값을 보였다. 6종류의 microsatellite에 대한 지역간의 유전적 차이 및 거리는 0.258과 0.019로 유의적으로 차이는 없었다 (p>0.05). 따라서 서해, 남해 및 동해 멸치계군은 유전적으로 동일한 집단을 형성하고 있는 것으로 판단된다.

• Asian-Australasian Journal of Animal Sciences
• /
• 제17권6호
• /
• pp.733-736
• /
• 2004

The study was carried out on eight Bos indicus cattle breeds namely, Sahiwal, Tharparkar, Nimari, Khilari, Deoni, Amritmahal, Hariana and Hilly cattle; two Bos taurus cattle breeds namely, Jersey and Holstein Friesian and Indicine${\times}$Taurine crossbred cattle to find out the polymorphic pattern of beta-lactoglobulin gene. The polymorphism at beta-lactoglobulin gene was detected by conducting PCR-RFLP studies on 398 bp fragment spanning over 104 bases of exon IV and 294 bases of intron IV. Two alleles A and B and three genotypes AA, AB and BB were observed in all the cattle breeds. The frequency of B allele was comparatively higher than that of A allele. The allelic frequency of A varied from 0.20 to 0.30 in Bos indicus cattle breeds and 0.19 to 0.34 in Bos taurus breeds while in crossbred cattle the frequency was estimated as 0.21. The weighted frequency of A allele was highest in Indian cattle and lowest in crossbred cattle while the frequency in taurine cattle was found to be in between indicus and crossbred cattle. The non-significant differences of allelic frequency amongst Bos indicus, Bos taurus and crossbred cattle was observed. The effect of genotype on fat percentage was also found to be non-significant in cattle.

• Asian Pacific Journal of Cancer Prevention
• /
• 제16권14호
• /
• pp.6155-6158
• /
• 2015

Background: The human leukocyte antigen-G (HLA-G) gene is highly expressed in cancer pathologies and is one strategy used by tumor cells to escape immune surveillance. A 14-bp insertion/deletion (InDel) polymorphism of the HLA-G gene has been suggested to be associated with HLA-G mRNA stability and the expression of HLA-G. The aim of present study was to assess any genetic association between this polymorphism and breast cancer among Iranian-Azeri women. Materials and Methods: In this study 227 women affected with breast cancer, in addition to 255 age-sex and ethnically matched healthy individuals as the control group, participated. Genotyping was performed using polymerase chain reaction and electrophoresis assays. The data were compiled according to the genotype and allele frequencies, compared using the Chi-square test. Statistical significance was set at P<0.05. Results: In this case-control study, no significant difference was found between the case and control groups at allelic and genotype levels, although there is a slightly higher allele frequency of HLA-G 14bp deletion in breast cancer affected group. However,when the stage I subgroup was compared with stage II plus stage III subgroup of affected breast cancer, a significant difference was seen with the 14 bp deletion allele frequency. The stage II-III subgroup patients had higher frequency of deletion allele (57.4% vs 45.8%) than stage I cases (${\chi}^2=4.16$, p-value=0.041). Conclusions: Our data support a possible action of HLA-G 14bp InDel polymorphism as a potential genetic risk factor for progression of breast cancer. This finding highlights the necessity of future studies of this gene to establish the exact role of HLA-G in progression steps of breast cancer.

• 한국응용곤충학회지
• /
• 제33권3호
• /
• pp.141-147
• /
• 1994

Deosophila melanogadter 자연집단재 alcohol dehydrogenase(ADH) allele 의 polymorphism 및 두 ADH allele 유전자형간의 적응도와 ethanol 의 상관 관계를 조사하였다. D. meanogaster의 자연집단내 ADH는 polymorphic 하였으며, FF,FS그리고 SS형의 유전자 빈도는 47.66,42.18 및 10.16%로 나타나 F 유전자의빈도가 S 유전자에 비하여 높게 분포하였다. 산란력과 우화율에서는 FF 유전자형이 SS 유전자형에 비하여 모두 약간 높게 나타났다. 자연집단에서 유래된 인공 소집단에서는 세대의 흐름에 따라 {{{{ { Adh}^{F } }}}} 유 전자형의 빈도증가와 상대적 {{{{ { Adh}^{S }}}}} 유전자형의 감소를 보였고, etha-nol은 ADH locu 상의 selective factor로서 작용함을 시사하여 주었다.

• 생명과학회지
• /
• 제13권4호
• /
• pp.412-415
• /
• 2003

제주마의 Es유전적 다형은 F, G, H, I, M, $I^o$ 의 6개의 대립유전자가 분포되어 있으며, 대립유전자 II가 22두(30.1%), FI 16두(21.9%), FF 9두(12.3%), GI 9두(12.4%) 순으로 높은 분포를 보였다. 또한 특이적인 silent 대립유전자로 추정되는 $I^oI^o$가 1두(1.4%)에서 관찰되었다. Es의 유전자 빈도는 대립유전자 I가 47.9%로 가장 높은 빈도를 보였으며 그 다음은 F (27.4%), G (19.2%), H (2.7%), M과 $I^o$가 각각 1.4% 순으로 분포하였다.

• Asian Pacific Journal of Cancer Prevention
• /
• 제15권6호
• /
• pp.2747-2751
• /
• 2014

Background: DNA repair pathways play a crucial role in maintaining the human genome. Previous studies associated DNA repair gene polymorphisms (XPD Lys751Gln, XRCC1 Arg280His and XRCC1 Arg399Gln) with nasopharyngeal carcinoma. These non-synonymous polymorphisms may alter DNA repair capacity and thus increase or decrease susceptibility. The present study aimed to determine the genotype distribution of XPD codon 751, XRCC1 codon 280 and codon 399 polymorphisms and haplotype associations among NPC cases and controls in the Malaysian population. Materials and Methods: We selected 157 NPC cases and 136 controls from two hospitals in Kuala Lumpur, Malaysia for this study. The polymorphisms studied were genotyped by PCR-RFLP assay and allele and genotype frequenci es, haplotype and linkage disequilibrium were determined using SNPstat software. Results: For the XPD Lys751Gln polymorphism, the frequency of the Lys allele was higher in cases than in controls (94.5% versus 85.0%). For the XRCC1 Arg280His polymorphism, the frequency of Arg allele was 90.0% and 89.0% in cases and controls, respectively and for XRCC1 Arg399Gln the frequency of the Arg allele was 72.0% and 72.8% in cases and controls respectively. All three polymorphisms were in linkage disequilibrium. The odds ratio from haplotype analysis for these three polymorphisms and their association with NPC was 1.93 (95%CI: 0.90-4.16) for haplotype CGC vs AGC allele combinations. The global haplotypte association with NPC gave a p-value of 0.054. Conclusions: Our study provides an estimate of allele and genotype frequencies of XRCC1Arg280His, XRCC1 Arg399Gln and XPD Lys751Gln polymorphisms in the Malaysian population and showed no association with nasopharyngeal cancer.