Comparative analysis of allele variation using allele frequencies according to sample size in Korean population

Park Hyun-Chul,Ahn Eu-Ree,Shin Sang-Cheul 한국유전학회 2021 Genes & Genomics Vol.43 No.11

Background Allele frequency using short tandem repeats (STRs) is used to calculate likelihood ratio for database match, to interpret DNA mixture and to estimate ethnic groups in forensic genetics. In Korea, three population studies for 23 STR loci have been conducted with diferent sample size for forensic purposes. Objective We performed comparative analysis to determine how the diference of sample size afects the allele frequency and allele variation within same ethnic population (i.e. Korean). Furthermore, this study was conducted to check how the sampling group and multiplex kit also afect allele variation such as rare alleles and population specifc alleles. Methods To compare allele variation, we used allele frequencies of three population data published from three Korean forensic research groups. Allele frequencies were calculated using diferent sample sizes and multiplex kits: 526, 1000, and 2000 individuals, respectively. Results The results showed the diferent distribution of allele frequencies in some loci. There was also a diference in the number of rare alleles observed by the sample size and sampling bias. In particular, an allele of 9.1 in the D2S441 locus was not observed in population study with 526 individuals due to multiplex kits. Conclusion Because the allele frequencies play an important role in forensic genetics, even if the samples are derived from the same population, it is important to consider the efects of sample size, sampling bias, and selection of multiplex kits in population studies.

대립유전자 특이 시퀀싱으로 분리한 Aw10 대립유전자를 가진 2예

원은정,조덕,신명근,권소영,조남선,양동욱 대한수혈학회 2011 大韓輸血學會誌 Vol.22 No.1

We separated an Aw10 allele by allele-specific sequencing in two Aw10/B101 samples that had the AweakB phenotype. Two samples with the A102/B101 genotype were also tested as a control. The reverse primers using position 930 at exon7 were designed for allele-specific sequencing. The differential positions were a total of 52 points for distinguishing the A-allele from the B-allele. Although overlaps with another haplotype allele that showed a minor chromatographic peak were observed in almost all the points, the specific allele-separation rate was 100% (52/52) by assessing the dominance in the chromatographic peak height. Based on the separation rate in the two cases with Aw10/B101 and the two AB controls, allele-specific sequencing is a convenient and reliable method for the separating the A-allele and B-allele in a clinical laboratory.

Henoch-$Sch{\ddot{o}}nlein$ Purpura 신염에서 Interleukin 1 Receptor Antagonist(IL-1ra) 유전자 다형성

황필경,이정녀,정우영,Hwang, Phil-Kyung,Lee, Jeong-Nye,Chung, Woo-Yeong 대한소아신장학회 2005 Childhood kidney diseases Vol.9 No.2

목 적 : IL-1ra는 항염증반응을 가지고 있는 인자로서 IL-1 수용체와 결합하여, IL-l$\alpha$와 IL-1$\beta$의 결합을 경쟁적으로 억제시킴으로써, IL-1에 의해 매개되는 다양한 질환에서 중요한 내인성 조절인자로 작용한다. 이 유전자의 intron 2 부위에 86 bp 크기를 가지는 tandem repeat 에 의한 유전자 다형성이 존재하는데, 다양한 자가면역질환에서는 allele 2형의 빈도가 정상 인구군에 비해 유의하게 높다는 사실이 밝혀져 있다. 이에 저자들은 Henoch-$Sch{\ddot{o}}nlein$ Purpura 환자들을 대상으로 IL-1ra 유전자의 variable number tandem repeats(VNTR) 다형성을 검사하여 정상 대조군과 비교하였으며, 신장 침범 여부 및 중증의 경과에 $IL1RN^{*}2$가 어떤 영향을 미치는 지를 조사하였다. 방 법.: 1998년 1월부터 2002년 12월까지 부산 백병원 .소아과를 방문하여 Henoch-$IL1RN^{*}2$ purpura로 진단된 74명의 환자와 정상 대조군 43명을 대상으로 하였다. EDTA 처리된 전혈에서 상품화된 DNA 추출키트($QIAamp^{\circledR}$ DNA Blood Mini kit, Quiagen, USA)를 사용하여 DNA를 추출하였다. IL-1ra 유전자 다형성(polymorphysm)은 86 bp의 2, 3, 4, 5번의 반복횟수에 따라 각각 240 bp, 325 bp, 410 bp 또는 500 bp 크기의 밴드를 확인하여 결정하였다. 결 과 : HSP 환자군과 정상 대조군 모두에서 $IL1RN^{*}1$의 allele 빈도가 각각 $93.9\%,\;93.2\%$로 가장 높았으며, carriage rate도 각각 $98.6\%,\;97.9\%$로 가장 높았다. $IL1RN^{*}2$의 allele 빈도는 HSP 군에서 4.7$\%$로 대조군의 2.5$\%$에 비해 높았으나, 통계적으로 유의하지 않았다(P=0.794). Carriage rate도 HSP군에서 8.1$\%$로 대조군의 6.8$\%$에 비해 높았으나, 통계적으로 유의하지 않았다(P=0.915). $IL1RN^{*}2$의 allele 빈도는 신장 침범군에서 6.3$\%$로 비침범군의 2.9$\%$에 비해 높게 나타났으나 통계적으로 유의하지 않았다(P=0.356). Carriage rate는 신장 침범군에서 10.0$\%$, 비침범군에서 5.9$\%$였으며, 양군 사이에는 유의한 차이가 관찰되지 않았다(P=0.523). 24시간 채집뇨에서 측정한 총단백량이 1,000 mg 이상이었던 경우가 13명이었는데, 이들의 allele형은 $IL1RN^{*}1$이 11명이었으며, $IL1RN^{*}2와\;IL1RN^{*}4$형이 각각 1명씩 있었다. 마지막 추적관찰 시점까지 단백뇨가 지속되었던 환자는 4명이었으며 이들은 모두 $IL1RN^{*}1$형 이었다. 결 론 : HSP 환자군과 정상 대조군 모두에서 $IL1RN^{*}1$의 allele 빈도와 carriage rate가 가장 높았다. $IL1RN^{*}2$ allele 빈도와 carriage rate는 HSP 환자군에서 대조군과 비교하여 유의한 차이가 관찰되지 않았다. 또한 HSP 환자군에서도 $IL1RN^{*}2$ allele 빈도와 carriage rate는 신장 침범의 정도와도 유의한 관련성이 발견되지 않았다. Purpose : Interleukin 1 receptor antagonist(IL-1ra) is an endogenous antiinflammatory agent that binds to IL-1 receptor and thus competitively inhibits the binding of IL-1$\alpha$ and IL-1$\beta$. Allele 2 in association with various autoimmune diseases has been reported. In order to evaluate the influence of IL-1ra gene VNTR polymorphism on the susceptibility to HSP and its possible association with disease severity, manifested by severe renal involvement and renal sequelae, we studied the incidence of carriage rate and allele frequency of the 2 repeats of IL-1ra allele 2($IL1RN^{*}2$) of the IL-1ra gene in children with HSP with and without renal involvement. Methods : The IL-1ra gene polymorphisms were determined in children with HSP with(n=40) or without nephritis(n=34) who had been diagnosed at Busan Paik Hospital and the control groups(n=163). Gene polymorphism was identified by PCR amplification of the genomic DNA. Results : The allelic frequency and carriage rate of $IL1RN^{*}1$ were found most frequently in patients with HSP and in controls. The allelic frequency of $IL1RN^{*}2$ was higher in patients with HSP compared to that of controls($4.7\%\;vs.\;2.5\%$, P=0.794). The carriage rate of $IL1RN^{*}2$ was higher In patients with HSP compared to that of controls($8.1\%\;vs.\;6.8\%$, P=0.916). The allelic frequency of $IL1RN^{*}2$ was higher in patients with HSP nephritis compared to that of HSP($5.3\%\;vs.\;2.9\%$, P=0.356). The carriage rate of $IL1RN^{*}2$ was higher in Patients with HSP nephritis compared to that of HSP($10.0\%\;vs.\;5.9\%$, P=0.523). Among 13 patients with heavy proteinuria(>1.0 g), 11 had $IL1RN^{*}1$, 1 had $IL1RN^{*}2$ and the others had $IL1RN^{*}4$. At the time of last follow up 4 patients had sustained proteinuria and their genotype was $IL1RN^{*}1$. Conclusion : The allelic frequency and carriage rate of $IL1RN^{*}1$ were found most frequently in patients with HSP and in controls. Our study suggests that the carriage rate and allele frequency of the 2-repeats of IL-1lra allele 2($IL1RN^{*}2$) of the IL-1ra gene may not be associated with susceptibility and severity of renal involvement in children with HSP (J Korean Soc Pediatr Nephrol 2005;9:175-182)

Correlations between Janus Kinase 2 V617F Allele Burdens and Clinicohematologic Parameters in Myeloproliferative Neoplasms

하정숙,김유경,정순일,정혜라,정인성 대한진단검사의학회 2012 Annals of Laboratory Medicine Vol.32 No.6

Background: This study evaluated potential correlations between the allele burden of the Janus kinase 2 (JAK2) V617F mutation and clinicohematologic characteristics in patients with myeloproliferative neoplasms (MPN). Methods: Clinical and hematologic features were reviewed for 103 MPN patients, including patients with polycythemia vera (PV, 22 patients), essential thrombocythemia (ET, 64 patients), and primary myelofibrosis (PMF, 17 patients). JAK2 V617F allele status and allele burdens were measured by allele-specific PCR and pyrosequencing, respectively. Results: The JAK2 V617F mutation was detected in 95.5%, 68.8%, and 52.9% of PV, ET, and PMF patients, respectively. JAK2 V617F-positive ET patients were significantly older and exhibited higher neutrophil fractions, a higher frequency of thrombotic events, and a higher myelofibrosis rate than JAK2 V617F-negative patients (P <0.05). PV patients carried the highest mean T allele burden (66.0%±24.9%) compared with ET (40.5%±25.2%) and PMF patients (31.5%±37.0%) (P =0.00). No significant correlations were detected between V617F allele burden and patient age, white blood cell count, Hb, Hct, or the platelet count for PV, ET, or PMF patients. ET patients with organomegaly had a higher JAK2 V617F allele burden (53.4%±23.7%) than patients without organomegaly (35.6%± 24.3%) (P =0.03). Conclusions: The JAK2 V617F mutational status and its allele burden correlate with the clinicohematologic phenotypes of ET patients, including older age, higher neutrophil count, and greater rates of organomegaly, thrombotic events, and myelofibrosis. For PV and PMF patients, larger-scale studies involving more MPN patients are needed. Background: This study evaluated potential correlations between the allele burden of the Janus kinase 2 (JAK2) V617F mutation and clinicohematologic characteristics in patients with myeloproliferative neoplasms (MPN). Methods: Clinical and hematologic features were reviewed for 103 MPN patients, including patients with polycythemia vera (PV, 22 patients), essential thrombocythemia (ET, 64 patients), and primary myelofibrosis (PMF, 17 patients). JAK2 V617F allele status and allele burdens were measured by allele-specific PCR and pyrosequencing, respectively. Results: The JAK2 V617F mutation was detected in 95.5%, 68.8%, and 52.9% of PV, ET, and PMF patients, respectively. JAK2 V617F-positive ET patients were significantly older and exhibited higher neutrophil fractions, a higher frequency of thrombotic events, and a higher myelofibrosis rate than JAK2 V617F-negative patients (P <0.05). PV patients carried the highest mean T allele burden (66.0%±24.9%) compared with ET (40.5%±25.2%) and PMF patients (31.5%±37.0%) (P =0.00). No significant correlations were detected between V617F allele burden and patient age, white blood cell count, Hb, Hct, or the platelet count for PV, ET, or PMF patients. ET patients with organomegaly had a higher JAK2 V617F allele burden (53.4%±23.7%) than patients without organomegaly (35.6%± 24.3%) (P =0.03). Conclusions: The JAK2 V617F mutational status and its allele burden correlate with the clinicohematologic phenotypes of ET patients, including older age, higher neutrophil count, and greater rates of organomegaly, thrombotic events, and myelofibrosis. For PV and PMF patients, larger-scale studies involving more MPN patients are needed.

한국인의 아포지단백 E 유전형과 혈청 지질 성분과의 관련성

전사일,김종원,송정한,김진규 대한임상병리학회 1996 대한임상병리학회지 Vol.16 No.5

Growth Behavior of Additional Offspring with a Beneficial Reversal Allele in the Asymmetric Sharply-peaked Landscape in the Coupled Discrete-time Mutation-selection Model

길원평 한국물리학회 2013 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.62 No.1

The probability of additional offspring with a beneficial reversal allele for growing to a size <i>NC</i> for a range of population sizes <i>N</i>, sequence lengths <i>L</i>, selective advantages <i>s</i>, and measuring parameters <i>C</i> was calculated for a haploid, asexual population in the coupled discrete-time mutation-selection model in an asymmetric sharply-peaked landscape with a positive selective advantage of the reversal allele over the optimal allele. The growing probability in the stochastic region was inversely proportional to the measuring parameter when C < 1/<i>Ns</i>, bent when C ≒ 1/Ns and saturated when C > 1/<i>Ns</i>. The crossing time and the time dependence of the increase in relative density of the reversal allele in the coupled discrete-time mutation-selection model was approximated using the Wright-Fisher two-allele model with the same selective advantage and corresponding effective mutation rate. The growth behavior of additional offspring with the reversal allele in the asymmetric sharply-peaked landscape in the coupled discrete-time mutation-selection model was controlled by the selective advantage of the reversal allele compared to the optimal allele and could be described by using the Wright-Fisher two-allele model, in spite of there being many other alleles with lower fitness, and in spite of there being two alleles, the optimal and reversal allele, separated by a low-fitness valley with a tunable depth and width.

Genotyping of Citrus Accessions with S<SUB>9</SUB> and/or S<SUB>10</SUB> Alleles for Self-incompatibility and Their Allelic Distribution

Jung-Hee Kim,Mayumi Sato,Akira Wakana,Fuka Takamatsu,Kaori Sakai,Masayoshi Shigyo,Jun-ichiro Masuda 한국원예학회 2021 원예과학기술지 Vol.39 No.6

Gametophytic self-incompatibility, one of the key characteristics for breeding seedless Citrus cultivars, occurs in pummelo (Citrus maxima), mandarin (Citrus reticulata), and their hybrid cultivars. Allelic variation in Citrus was reported for the self-incompatibility gene (S); however, S allele frequencies and S genotypes of full- and semi-self-incompatible cultivars have been reported for a small number of alleles. To extend our knowledge of S alleles, we tested 146 Citrus accessions, including 82 pummelo accessions, for S9 and S10 alleles. Each accession was pollinated with homozygous S₁ seedlings of ‘Hirado Buntan’ pummelo (S9S9 and S10S10). The pollen tube growth arrest in the lower styles of their pollinated pistils indicated that four accessions, including ‘Hirado Buntan [Citrus maxima (Burm.) Merr.]’, have the S9 allele and five accessions, including ‘Hirado Buntan’, have the S10 allele. The percentage of accessions with the S9 allele was 3.2% (4 of 126 accessions examined), and the S9 allele frequency was 1.8% (4 of 217 alleles, excluding the Sf allele). The percentage of accessions with the S10 allele was 3.9% (5 of 127 accessions examined), and the S10 allele frequency was 2.3% (5 of 217 alleles, excluding the Sf allele). Japanese mandarin (another sources of S alleles) and its relatives had neither the S9 nor the S10 allele. Pummelo accessions had S9 and S10 alleles at higher rates of 2.9% (2 of 70 accessions examined) and 7.0% (5 of 71 accessions examined), respectively. ‘Kabusu’ sour orange (a pummelo-mandarin hybrid; Citrus aurantium) and ‘Kikudaidai’ (a sour orange relative; Citrus canaliculata) had S9 alleles. These results suggested that the two alleles originated from pummelo (the main sources of S alleles). The S genotypes with S9 and/or S10 alleles were fully determined in ‘Hirado Buntan’ (S9S10), ‘Kabusu’ sour orange (SfS9), the ‘Kikudaidai’ (S9S11) sour orange hybrid, and two local pummelo plants. The results of our study suggest that in comparison with the other S alleles reported, the pummelo plants with low frequencies of S9 and/or S10 alleles contributed to very low rates of evolution and development of Citrus species and cultivars during the long history of citrus cultivation, except for those generating sour oranges (Citrus auratinum), which are used as root stocks, and for flesh and rind processing and ornamental plants. Finally, we examined the degree of self-incompatibility between S9 and S10 alleles in the lower part of styles of S₁ seedlings of ‘Hirado Buntan’ and Citrus accessions with S9 and/or S10 alleles. The result indicated no difference in the self-incompatibility reaction between the two alleles.

실시간 반정량 PCR, JAK2 MutaScreenTM kit를 이용한 JAK2 V617F 유전자 변이 선별검사의 유용성

채효진1,이제훈,임지향,김명신,김용구,한경자,이종욱,민우성,정승원,조병식,조석구 대한진단검사의학회 2009 Annals of Laboratory Medicine Vol.29 No.3

Background : Real-time PCR for quantification of JAK2 V617F has recently been introduced and used to evaluate the importance of mutant allele burden in both diagnosis and disease progression in myeloproliferative diseases (MPDs). We evaluated the usefulness of JAK2 MutaScreenTM kit that uses a real-time semiquantitative PCR method and has been designed to screen JAK2 V617F mutant allele burden. Methods : Forty MPD patients were included in this study. We screened JAK2 V617F and determined the mutant allele burden using JAK2 MutaScreenTM kit. The mutant allele burden was estimated by six-scaled standards of JAK2 V617F mutant allele (2%, 5%, 12.5%, 31%, 50%, and 78%). For evaluation of test performance, an allele-specific PCR (AS-PCR) was carried out in all samples by using Seeplex JAK2 Genotyping kit. We assessed the clinical differences in distinct disease entities of MPDs according to JAK2 V617F mutant allele burden. Results : JAK2 V617F mutation was detected in 30 cases, including 10 of 11 cases (91%) of polycythemia vera (PV), 13 of 20 cases (65%) of essential thrombocythemia (ET), and 2 of 3 cases (67%) of chronic idiopathic myelofibrosis (CIMF). The concordance rate between the two tests was 95% (38/40). JAK2 V617F mutant allele burden was greater than 50% in 17 cases, and 10 of them (59%) were PV. In contrast, mutant allele burden was less than 50% in 13 cases and 11 of them (85%) were ET. Conclusions : JAK2 MutaScreenTM kit that utilizes a real-time semi-quantitative PCR method is a useful tool for diagnosing MPDs precisely. It can be used to assess the grade of mutant allele burden as well as to screen JAK2 V617F simultaneously. 배경 : 최근 JAK2 V617F 유전자 변이에 실시간 정량 PCR법 을 이용한 검사법이 소개되어 MPDs의 진단과 질환의 진행에 있어 유전자 변이량 측정의 중요성 평가에 사용되고 있다. 저자 들은 JAK2 V617F 유전자 변이 선별을 위해 새로이 고안된 실 시간 반정량 PCR법인 JAK2 MutaScreenTM kit의 유용성을 평 가하였다. 방법 : 40예의 MPDs 환자를 대상으로 JAK2 MutaScreenTM kit를 이용하여 JAK2 V617F 선별 및 유전자 변이량을 측정하 였다. JAK2 V617F 유전자 변이량 측정에는 6단계의 표준물질 을 사용하였다(2%, 5%, 12.5%, 25%, 31%, 50%, 78%). 검사 수 행능의 평가를 위하여 동일한 모든 검체에 대하여 Seeplex JAK2 Genotyping kit을 이용한 AS-PCR법으로 시행한 검사 결과와 비교하였다. 또한 각 MPDs의 질환군과 유전자 변이량에 따른 임상적 특성의 차이를 분석하였다. 결과 : 30예에서 JAK2 V617F 유전자 변이가 검출되었으며 각 질환별 양성률은 PV 91% (10/11), ET 65% (13/20), CMIF 67% (2/3)였다. 두 검사방법 간의 일치율은 95%였다(38/40). JAK2 V617F 유전자 변이량이 50% 이상인 17예 중 10예가 PV였으며, JAK2 유전자 변이량이 50% 이하인 13예 중에서는 11예가 ET였 다(85%). 결론 : 실시간 반정량 PCR법을 이용한 검사법인 JAK2 V617F MutaScreenTM kit는 유전자 변이 검출 및 유전자 변이량의 동 시 측정이 가능하므로 보다 정밀한 MPDs의 진단에 유용한 검 사방법으로 생각된다.

ABO 유전자 검사 결과 보고시 고려사항: ABO*AW.10 대립유전자 증례에서의 교훈

박동진,임찬수,임지향 대한수혈학회 2023 大韓輸血學會誌 Vol.34 No.1

We would like to introduce domestic subscribers of the Korean Journal of Blood Transfusion to the important aspects to be considered while selecting a reference allele and reporting a new allele candidate. ABO*A1.02 has only a single nucleotide substitution of c.467C>T in ABO*A1.01, and when ABO*A1.01 is used as the reference allele, the ABO*AW.10 allele should be marked as having both c.467C>T and c.784G>A variants. Unfortunately, it has not been modified as such in the ISBT database. For this reason, in the journal Transfusion (2020), the official journal of the Association for the Advancement of Blood Biotherapies, there was a report of a new allele with c.467C>T and c.784G>A variants. Cases of ABO*AW.10 allele with a weak A phenotype are not uncommon in Koreans, and it is necessary to accurately mark the reference allele. The blood type A reference allele of the International Society of Blood Transfusion (ISBT) database currently used for ABO alleles reporting is based on ABO*A1.01. Therefore, it should be considered that the ABO*AW.10 allele has both the c.467C>T and c.784G>A variants together. (Korean J Blood Transfus 2023;34:39-42)

Allelic Variation of Rht-1, Vrn-1 and Ppd-1 in Korean Wheats and Its Effect on Agronomic Traits

( Eun Jin Cho ),( Chon Sik Kang ),( Ji Ung Jung ),( Young Mi Yoon ),( Chul Soo Park ) 한국육종학회 2015 Plant Breeding and Biotechnology Vol.3 No.2

The allelic variations at the Rht-1, Vrn-1 and Ppd-1 of 410 Korean wheat cultivars, including 111 Korean experimental lines, 238 Korean landraces and 61 North Korean collections, were investigated to provide the information of plant height and heading date and to elucidate the relationship between those traits and allelic variation of these genes because earliness is major consideration in Korean wheat production. All Korean wheats displayed vrn-A1 and Ppd-A1b alleles, while Rht-B1a, Rht-D1a, vrn-B1, Vrn-D1, Ppd-B1b and Ppd-D1a alleles were also predominantly found. Most Korean wheats carried both Rht-B1a and Rht-D1a alleles, both vrn-B1 and Vrn-D1 alleles, or both Ppd-B1b and Ppd-D1a alleles. The Rht-B1a, vrn-D1, Ppd-B1b and Ppd-D1b alleles were found to exhibit longer culm and spike length than their counterpart alleles. The Rht-B1a allele also showed longer spike length than Rht-B1b. Vrn-B1b and vrn-D1 alleles exhibited longer days to heading date than their counterpart alleles at the Vrn-B1 and Vrn-D1 loci. Lines carrying both Rht-B1b and Rht-D1b alleles displayed shorter culm and longer spike length and days to heading date than any other combination of alleles at the Rht-B1 and Rht-D1 loci. In contrast, lines carrying both Ppd-B1b and Ppd-D1b alleles exhibited longer culm and spike length than any other combination of alleles at the Ppd-B1 and Ppd-D1 loci.