• Animal cells and systems
• /
• v.5 no.3
• /
• pp.237-241
• /
• 2001

Three STR loci (STRX1[AGAT]$_{n}$, HPRTB[AGAT]$_{n}$ and ARA[AGC]$_{n}$) on X chromosome and three other STR loci (DYS390[CTG(A)T]$_{n}$, DYS392[ATT]$_{n}$ and DYS39［GATA]$_{n}$) on Y chromosome were analyzed in 154 unrelated healthy Korean subjects. Four loci (STRX1, HPRTB, DYS390 and DYS393) were amplified by quadruplex polymerase chain reaction (PCR) using fluorescent labeled primers (FLP). ARA and DYS392 were amplified separately using single PCR, similarly by using FLP. They were then run in an automated DNA sequencer and were analyzed with Genescan software. We found 7 alleles (308-332 bp) in STRX1, 7 alleles (275-299 bp) in HPRTB, 16 alleles (252-315 bp) in ARA, 6 alleles (203-223 bp) in DYS390, 7 alleles (245-263bp) in DYS392 and 5 alleles (116-132 bp) in DYS393. The ＊13(34%), ＊13(5l%), ＊23 (l8%), ＊23(50%), ＊14(39%) and ＊13(40%) alleles were observed to be the highest frequencies of STRX1, HPRTB, ARA, DYS390, DYS392 and DYS393, respectively. The detection of STR loci on sex chromosomes by quadruplex PCR allows simple determination of sex and identification of an individual. individual.

• Asian-Australasian Journal of Animal Sciences
• /
• v.19 no.6
• /
• pp.775-778
• /
• 2006

Sarabi cows (n = 136) from the Sarabi Breeding Station were genotyped at bovine lymphocyte antigen (BoLA)-DRB3.2 locus by a genotyping system that used the polymerase chain reaction and restriction fragment length polymorphism. Genomic DNA was extracted from whole blood samples. A two-step polymerase chain reaction was carried out in order to amplify a 284 base-pair fragment of target gene. Nested-PCR products were digested with three restriction endonuclease enzymes RsaI, BstYI and HaeIII. Digested fragments were analyzed by polyacrylamide gel electrophoresis. Twenty-six BoLA-DRB3.2 alleles were identified with frequencies ranging from 0.4 to 15.1%. Six new allele types observed in this study have not been reported previously. Identified alleles include: BoLA-DRB3.$2^*1$, $^*2$, $^*4$, $^*6$, $^*8$, $^*12$, $^*13$, $^*14$, $^*15$, $^*16$, $^*17$, $^*23$, $^*24$, $^*25$, $^*28$, $^*32$, $^*34$, $^*35$, $^*36$, $^*37$, $^*42$, $^*46$, $^*51$, $^*kba$, $^*laa$ and $^*vaa$. Their frequencies were found to be 0.4, 0.4, 0.7, 11.4, 1.1, 1.8, 2.9, 2.2, 4.4, 9.6, 1.1, 13.6, 0.4, 0.4, 1.1, 0.7, 0.4, 6.2, 2.2, 3.7, 1.1, 7.7, 1.5, 15.1, 2.6 and 7.3% respectively. The six most frequent alleles (DRB3.2 $^*6$, $^*16$, $^*23$, $^*46$, $^*kba$ and $^*vaa$) accounted for 64.7% of the alleles in the population of this herd. Numerous studies on this locus, covering different breeds, has revealed the existence of various alleles in this locus, and new investigations have introduced novel alleles. With respect to the high number of the observed alleles in this survey and the novelty of some alleles with no previous record of reporting, it is plausible to conclude that the BoLA-DRB3.2 locus is highly polymorphic in Iranian native Sarabi cows.

• BMB Reports
• /
• v.43 no.10
• /
• pp.698-703
• /
• 2010

In this study, we characterized two blocks of minisatellites in the 5' upstream region of the BORIS gene (BORIS-MS1, -MS2). BORIS-MS2 was found to be polymorphic; therefore, this locus could be useful as a marker for DNA fingerprinting. We assessed the association between BORIS-MS2 and breast cancer by a case-control study with 428 controls and 793 breast cancers cases. Rare alleles in the younger group (age, <40) were associated with a statistically significant increased risk of breast cancer (odds ratio, 4.84; 95% confidence interval, 1.06-22.22; and P = 0.026). A statistically significant association between the short rare alleles and cancer was identified in the younger group (8.02; 1.01-63.83; P = 0.021). Kaplan-Meier estimates showed that poor prognosis was associated with patients who contained the rare alleles. Our data suggest that the short rare alleles of BORIS-MS2 could be used to identify the risk for breast cancer in young patients.

• Proceedings of the Korean Society of Crop Science Conference
• /
• 2017.06a
• /
• pp.22-22
• /
• 2017

Genetic diversity is one of fundamental parameters for rice cultivar improvement. Rice mutants are also a new source for rice breeding innovation. In this study, ninety-three SSR markers were applied to evaluate the genetic variation among nineteen rice mutant lines. The results showed that a total of 169 alleles from 56 polymorphism markers was recorded with an average of 3.02 alleles per locus. The values of polymorphism information content (PIC) varied from 0.09 to 0.79. The maximum number of alleles was 7, whereas the minimum number of alleles was 2. The heterozygosity values ranged from 0.10 to 0.81. Four clusters were generated using the unweighted pair group method with arithmetic mean (UPGMA) clustering. Fourteen phenotype characteristics were also evaluated. The correlation coefficient values among these phenotye characteristics were obtained in this study. Genetic diversity information of rice mutant lines can support rice breeders in releasing new rice varieties with elite characterisitics.

• Korean Journal of Mathematics
• /
• v.28 no.1
• /
• pp.1-7
• /
• 2020

A partition X describes that there exists α_i kinds of alleles occurring i loci for each i. All genes have multiple alleles, i.e., they exist in more than two allelic forms, although any one diploid organism can carry no more than two alleles. The number of possible genotypes in a multiple allel series depends on the number of alleles. We will deal with an n locus model in which mutation and gene conversion are taken into consideration. In this paper, we firstly find the probability p_n(x) of genotype $$p_{n+1}(x)=p_n(x){\sum\limits_{k=1}^{r}}q_{kx}p_n(k)$$ with the rates of mutation and gene conversion. Also we find the probability of genotype without the rates of mutation and gene conversion and we apply this probability to two examples.

• KOREAN JOURNAL OF CROP SCIENCE
• /
• v.54 no.2
• /
• pp.181-191
• /
• 2009

To investigate the genetic variation of high-and low-molecular-weight glutenin subunits (BMW-GS and LMW-GS), granule-bound starch synthase I (GBSSI) and puroindoline in 24 Korean wheat cultivars. At the BMW-GS compositions, three Glu-A1 alleles, five Glu-B1 alleles and three Glu-D1 alleles were identified. The high frequency of alleles at each locus was Glu-A1c allele (15 cultivars), Glu-B1b allele (16 cultivars) and Glu-D1f allele (16 cultivars). Four alleles were identified at the Glu-A3 and Glu-B3 loci and three at Glu-D3 locus and Glu-A3d, Glu-B3d and Glu-D3a were mainly found at each Glu-3 locus. Glu-A3d, Glu-B3d, Glu-D3b or c (4 cultivars, respectively) and Glu-A3d, Glu-B3d, Glu-D3a and Glu-A3c, Glu-B3d or h, Glu-D3a (3 cultivar, respectively) were predominantly found in Korean wheats. At the GBSS compositions, 2 waxy wheat cultivars, Shinmichal and Shinmichal1, showed null alleles on the Wx loci and other cultivars were wild type in GBSS compositions. At the puroindoline gene compositions, Korean wheat cultivars carried 3 genotypes, which 10 cultivars (41.7%) were Pina-D1a and Pinb-D1a, 11 cultivars (45.8%) had Pina-D1a and Pinb-D1b and 3 cultivars (12.5%) carried Pina-D1b and Pinb-D1a. These genetic variations could present the information to improve flour and end-use quality in Korean wheat breeding programs.

• Korean Journal of Biological Psychiatry
• /
• v.1 no.1
• /
• pp.67-78
• /
• 1994

The author examined the relationship of two markers, D5S39(p105-153Ra), D5S76(p105-599Ha) of chromosome 5 and $D_2$, $D_3$ receptor genes in a Korean schizophrenic pedigree using polymerase chain reaction(PCR). The results were as follows : 1) On D5S39 locus, 5 different alleles(224/226 bp : 4 cases, 218/226 bp : 3 cases, 222/226 bp : 3 cases, 218/230 bp : 1 case, 222/224 bp : 1 case) were produced. 2) On D5S76 locus, 5 different alleles(102/112 bp : 4 cases, 94/112 bp : 3 cases, 108/112 bp 3 cases, 94/94 bp : 1 case, 102/108 bp 1 case) were produced. 3) On $D_2$ receptor gene, 3 different alleles($A_1A_2$ : 8 cases, $A_1A_1$ : 2 cases, $A_2A_2$ : cases) were produced. 4) On $D_3$ receptor gene, 2 different alleles(1/2 : 7 cases, 1/1 : 5 cases) were produced. The author had not find any specific alleles on all four loci in all pedigree nor any specific alleles in the schizophrenic patients. Though the author has not found absolute relationship between the four loci and the onset of schizophrenia, there still remains the possibilities if the more detailed and elaborated pedigree studies are done.

• Asian Pacific Journal of Cancer Prevention
• /
• v.14 no.11
• /
• pp.7007-7010
• /
• 2013

Background: In the literature, data concerning the relationship between breast cancer and HLA class II gene polymorphisms are limited, so the aim of this study was to determine if HLA-DQB1 and HLA-DRB1 MHC class-II alleles may confer susceptibility or resistance to the disease among Jordanian females. Materials and Methods: This case control study enrolled 56 Royal Hospital breast cancer patients and 60 age matched healthy controls, all of whom provided blood samples (2011-2013). A questionnaire was filled after signing a consent form and DNA was extracted, nucleic acids being amplified for assessment of HLA-DQB1 and HLA-DRB1 alleles by muliplex INNO-LiPA and allele typing carried out by reverse hybridization. Comparison of HLA-DQB1 and HLA-DRB1 allele distributions was carried out with paired t-test and chi-square statistics. Risk factors were assessed by odd ratios with 95% confidence intervals. Results: A significant negative correlation was observed between $HLADQB1^*$ 02 alleles and breast cancers (p=0.013). No significant associations were observed among $HLADQB1^*$ 03, 04, 05 and 06 or among $HLA-DRB1^*$ 01, 03, 04, 07, 08, 10, 11, 13, 14 and 15. Conclusions: $HLADQB1^*$ 02 alleles may provide positive protection against breast tumor risk among Jordanians, but not $HLADQB1^*$ 03, 04, 05 and 06 or $HLA-DRB1^*$ 01, 03, 04, 07, 08, 10, 11, 13, 14 and 15 alleles.

• IMMUNE NETWORK
• /
• v.1 no.2
• /
• pp.135-142
• /
• 2001

Background: A large number of diseases occur in association with specific HLA-B or-C alleles. Recently a new gene, termed maj or histocompatibility complex class I chain-related gene A (MICA), has been identified in close proximity to HLA-B. The function of this gene is still unknown. However, it is structurally similar to HLA class I genes. MICA gene is polymorphic and is potentially associated with several diseases. Methods: To evaluate the association of MICA gene in Korean patients with human immunodeficiency virus 1 (HIV-1) infections, Polymerase chain reaction-Sequence specific primer (PCR-SSP) was done for MICA alleles in the extracellular exons, and a microsatellite analysis for GCT repeat polymorphisms in the TM exon was also completed. Results: In 199 Korean healthy controls, 7 alleles were observed and the frequencies for each allele were MICA008 (44.7%), MICA0 10 (34.2%), MICA002 (31.7%), MICA004 (23.6%), MICA0 12 (2 1.6%), MICA009 (19.6%), and MICA007 (6.5%). When 65 HIV seropositive patients were analyzed, MICA007 allele frequency was significantly higher than in controls (15.4% vs 6.5 %, RR=2.6, p<0.04). In contrast, the frequencies of other MICA alleles and microsatellite alleles in the transmembrane region of MICA gene were not significantly different between HIV seropositive patients and controls. The tight linkage between MICA alleles in the extracellular exons and GCT repeat polymorphisms in the TM exon was observed as follows; MICA002/A9, MICA004/A6, MICA007/A4, MICA008/A5.1, MICA0 10/A5, and MICA0 12/A4 in both groups. No significant difference between patients and controls was observed in the haplotype frequencies of MICA alleles in the extracellular exons and GCT repeat polymorphisms in the TM exon. Conclusion: The data suggest that immune functions related with MICA gene may affect a HIV infections.

• Asian Pacific Journal of Cancer Prevention
• /
• v.17 no.5
• /
• pp.2491-2497
• /
• 2016

Background: Human leukocyte antigen (HLA) genes have been implicated in cervical cancer in several populations. Objectives: To study the predispositions of HLA alleles/haplotypes with cervical cancer. Materials and Methods: Clinically diagnosed and PAP smear confirmed cervical cancer patients (n 48) and age matched controls (n 47) were genotyped for HLA-A,-B,-DRB1* and DQB1* alleles by PCR-SSP methods. Results: The frequencies of alleles DRB1*04 (OR=2.57), DRB1*15 (OR=2.04), DQB1*0301 (OR=4.91), DQB1*0601 (OR=2.21), B*15 (OR=13.03) and B*07 (OR=6.23) were higher in cervical cancer patients than in the controls. The frequencies of alleles DRB1*10 (OR=0.22) and B*35 (OR=0.19) were decreased. Strong disease associations were observed for haplotypes DRB1*15-DQB1*0601 (OR=6.56; p< $3.5{\times}10^{-4}$), DRB1*14-DQB1*0501 (OR=6.51; p<0.039) and A*11-B*07 (OR=3.95; p<0.005). The reduced frequencies of haplotypes DRB1*10-DQB1*0501 (OR=0.45), A*03-B*35 (OR=0.25) and A*11-B*35 (OR= 0.06) among patients suggested a protective association. HLA-C* typing of 8 patients who possessed a unique three locus haplotype 'A*11-B*07-DRB1*04' (8/48; 16.66%; OR=6.51; p<0.039) revealed the presence of a four locus haplotype 'A*11-B*07-C*01-DRB1*04' in patients (4/8; 50%). Amino acid variation analysis of susceptible allele DQB1*0601 suggested 'tyrosine' at positions ${\beta}9$ and ${\beta}37$ and tyrosine-non-tyrosine genotype combination increased the risk of cervical cancer. Conclusions: Strong susceptible associations were documented for HLA alleles B*15, B*07, DRB1*04, DRB1*15, DQB1*0301, DQB1*0601 and haplotypes DRB1*15-DQB1*0601 and DRB1*14-DQB1*0501. Further, protective associations were evidenced for alleles B*35 and DRB1*10 and haplotypes A*11-B*35 and DRB1*10-DQB1*0501 with cervical cancer in South India.