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Analysis of 22 Y chromosomal STR haplotypes and Y haplogroup distribution in Pathans of Pakistan
Lee, E.Y.,Shin, K.J.,Rakha, A.,Sim, J.E.,Park, M.J.,Kim, N.Y.,Yang, W.I.,Lee, H.Y. Elsevier Science 2014 FORENSIC SCIENCE INTERNATIONAL GENETICS Vol.11 No.-
We analyzed haplotypes for 22 Y chromosomal STRs (Y-STRs), including 17 Yfiler loci (DYS19, DYS385a/b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DY438, DYS439, DYS448, DYS456, DYS458, DYS635 and Y-GATA-H4) and five additional STRs (DYS388, DYS446, DYS447, DYS449 and DYS464), and Y chromosomal haplogroup distribution in 270 unrelated individuals from the Pathans residing in the Federally Administered Tribal Areas and the North-West Frontier Province of Pakistan using in-house multiplex PCR systems. Each Y-STR showed diversities ranging from 0.2506 to 0.8538, and the discriminatory capacity (DC) was 73.7% with 199 observed haplotypes using 17 Yfiler loci. By the addition of 5 Y-STRs to the Yfiler system, the DC was increased to 85.2% while showing 230 observed haplotypes. Among the additional 5 Y-STRs, DYS446, DYS447 and DYS449 were major contributors to enhancing discrimination. In the analysis of molecular variance, the Pathans of this study showed significant differences from other Pathan populations as well as neighboring population sets. In Y-SNP analysis, a total of 12 Y chromosomal haplogroups were observed and the most frequent haplogroup was R1a1a with 49.3% frequency. To obtain insights on the origin of Pathans, the network analysis was performed for the haplogroups G and Q observed from the Pathans and the Jewish population groups including Ashkenazim and Sephardim, but little support for a Jewish origin could be found. In the present study, we report Y-STR population data in Pathans of Pakistan, and we emphasize the need for adding additional markers to the commonly used 17 Yfiler loci to achieve more improved discriminatory capacity in a population with low genetic diversity.
Kwon, S.Y.,Lee, H.Y.,Lee, E.Y.,Yang, W.I.,Shin, K.J. Elsevier Science 2015 FORENSIC SCIENCE INTERNATIONAL GENETICS Vol.19 No.-
Y chromosome single nucleotide polymorphisms (Y-SNPs) are useful markers for reconstructing male lineages through hierarchically arranged allelic sets known as haplogroups, and are thereby widely used in the fields such as human evolution, anthropology and forensic genetics. The Y haplogroup tree was recently revised with newly suggested Y-SNP markers for designation of several subgroups of haplogroups C2, O2b and O3a, which are predominant in Koreans. Therefore, herein we analyzed these newly suggested Y-SNPs in 545 unrelated Korean males who belong to the haplogroups C2, O2b or O3a, and investigated the reconstructed topology of the Y haplogroup tree. We were able to confirm that markers L1373, Z1338/JST002613-27, Z1300, CTS2657, Z8440 and F845 define the C2 subhaplogroups, C2b, C2e, C2e1, C2e1a, C2e1b and C2e2, respectively, and that markers F3356, L682, F11, F238/F449 and F444 define the O subhaplogroups O2b1, O2b1b, O3a1c1, O3a1c2 and O3a2c1c, respectively. Among six C2 subhaplogroups (C2b, C2e, C2e1*, C2e1a, C2e1b and C2e2), the C2e haplogroup and its subhaplogroups were found to be predominant, and among the four O2b subhaplogroups (O2b*, O2b1*, O2b1a and O2b1b), O2b1b was most frequently observed. Among the O3a subhaplogroups, O3a2c1 was predominant and it was further divided into the subhaplogroups O3a2c1a and O3a2c1c with a newly suggested marker. However, the JST002613-27 marker, which had been known to define the haplogroup C2f, was found to be an ancestral marker of the C2e haplogroup, as is the Z1338 marker. Also, the M312 marker for the O2b1 haplogroup designation was replaced by F3356, because all of the O2b1 haplotypes showed a nucleotide change at F3356, but not at M312. In addition, the F238 marker was always observed to be phylogenetically equivalent to F449, while both of the markers were assigned to the O3a1c2 haplogroup. The confirmed phylogenetic tree of this study with the newly suggested Y-SNPs could be valuable for anthropological and forensic investigations of East Asians including Koreans.
Haplotype and mutation analysis for newly suggested Y-STRs in Korean father-son pairs
Oh, Y.N.,Lee, H.Y.,Lee, E.Y.,Kim, E.H.,Yang, W.I.,Shin, K.J. Elsevier Science 2015 FORENSIC SCIENCE INTERNATIONAL GENETICS Vol.15 No.-
In this study, 363 Korean father-son haplotype transfers in 351 families were analyzed using an in-house multiplex PCR system for 14 Y-STRs (DYS385a/b, DYF387S1, DYS391, DYS449, DYS460, DYS481, DYS518, DYS533, DYS549, DYS570, DYS576, DYS627 and DYS643), that included 11 loci newly added to the PowerPlex Y23 system or the Yfiler Plus system. The Y-STRs showed gene diversity values ranging from 0.2499 to 0.9612; the multicopy Y-STR loci DYS385 and DYF387S1 had high gene diversity of 0.9612 and 0.9457, respectively. In addition, DYF387S1, which has two copies, showed three alleles in seven individuals, and micro-variant alleles were observed in 14 individuals at four loci (DYS448, DYS518, DYS570 and DYS627). Among 351 haplotypes for the 11 newly added Y-STRs, 350 different haplotypes were observed, with an overall haplotype diversity of 0.9999 and discrimination capacity of 99.72%. In 363 haplotype transfers from 351 pedigrees, 29 single-step mutations were observed at 11 Y-STRs. Locus-specific mutation rate estimates varied from 0.0 to 1.93x10<SUP>-2</SUP>, with an average estimated mutation rate of 6.66x10<SUP>-3</SUP>. Two father-son pairs had mutations at two different loci in 11 Y-STRs. The number of pairs with mutations at multiple loci increased to five when the mutation event was investigated for haplotype transfer at 28 Y-STRs including 17 Yfiler loci and 11 Y-STRs examined in this study: four father-son pairs had mutations at two loci, and one pair had mutations at three loci. Overall, mutations were frequently observed at DYS449, DYS576 and DYS627 loci, which are known to be rapidly mutating Y-STRs. Mutation rate estimates at most loci were not significantly different from rates in other populations, but estimates for DYF387S1, DYS518 and DYS570 were considerably lower in the Korean population than in other populations.
Lee, E.Y.,Lee, H.Y.,Kwon, S.Y.,Oh, Y.N.,Yang, W.I.,Shin, K.J. ELSEVIER SCIENCE B V AMSTERDAM 2017 FORENSIC SCIENCE INTERNATIONAL GENETICS Vol.26 No.-
<P>In forensic science and human genetics, Y-chromosomal short tandem repeats (Y-STRs) have been used as very useful markers. Recently, more Y-STR markers have been analyzed to enhance the resolution power in haplotype analysis, and 13 rapidly mutating (RM) Y-STRs have been suggested as revolutionary tools that can widen Y-chromosomal application from paternal lineage differentiation to male individualization. We have constructed two multiplex PCR sets for the amplification of 13 RM Y-STRs, which yield small-sized amplicons (<400 bp) and a more balanced PCR efficiency with minimum PCR cycling. In particular, with the developed multiplex PCR system, we could separate three copies of DYF403S1a into two copies of DYF403S1a and one of DYF403S1b1. This is because DYF403S1b1 possesses distinguishable sequences from DYF403S1a at both the front and rear flanking regions of the repeat motif; therefore, the locus could be separately amplified using sequence-specific primers. In addition, the other copy, defined as DYF403S1b by Ballantyne et al., was renamed DYF403S1b2 because of its similar flanking region sequence to DYF403S1b1. By redefining DYF403S1 with the developed multiplex system, all genotypes of four copies could be successfully typed and more diverse haplotypes were obtained. We analyzed haplotype distributions in 705 Korean males based on four different Y-STR subsets: Yfiler, PowerPlex Y23, Yfiler Plus, and RM Y-STRs. All haplotypes obtained from RM Y-STRs were the most diverse and showed strong discriminatory power in Korean population. (C) 2016 Elsevier Ireland Ltd. All rights reserved.</P>
Ock, C. Y.,Oh, D. Y.,Lee, J.,Kim, T. Y.,Lee, K. H.,Han, S. W.,Im, S. A.,Kim, T. Y.,Bang, Y. J. Springer Science + Business Media 2016 Gastric cancer Vol.19 No.2
<P>Weight loss during chemotherapy is a significant prognostic factor for poor survival in patients with advanced gastric cancer (AGC). However, in most studies, weight loss was measured at the end of chemotherapy, limiting its clinical use. In this study, we evaluated whether weight loss during the first month of chemotherapy could predict survival outcomes in patients with AGC. We analyzed 719 patients with metastatic or recurrent AGC who were receiving palliative chemotherapy. We calculated the initial body mass index (BMIi), percent weight loss after 1 month of chemotherapy (Delta W (1)m), percent weight loss after last administration of chemotherapy (Delta W (end)), and average weight loss per month during chemotherapy (Delta W/m). We correlated these data with overall survival (OS) by receiver-operating characteristic (ROC) curves and Kaplan-Meier curves, and performed a subgroup analysis using Cox regression. The probabilities of longer OS had stronger correlations with Delta W/m and Delta W (1)m than with Delta W (end) or BMIi. A significant positive correlation between Delta W (1)m and Delta W/m (r (2) = 0.591, p < 0.001) was observed. Median OS of patients with Delta W (1)m more than 3 % was significantly shorter than in patients with less weight loss (OS: 9.7 vs. 16.3 months, p < 0.001). Subgroup analysis revealed that Delta W (1)m accompanied poor survival irrespective of other clinical characteristics. Weight loss at the very first month of palliative chemotherapy could predict unfavorable survival outcomes in AGC.</P>
1987년 한국에서 발생한 렙토스피라병의 혈청역학적 조사
이증훈,박영수,이우곤,김석용,정선식,우준희,박성광,박경희,송영욱,김선영,기정일,최두혁,강성귀,김주완,최강원,김우열,최명식,최인학,장우현,윤성열 대한감염학회 1988 감염 Vol.20 No.3
Human leptospirosis was an unfamiliar disease in Korea until 1984 that outbreak of leptospirosis occurred among farmers and soldiers after field works for harvesting rice. During that time, Lee and Jo confirmed the first Korean cases of leptospirosis by serological test, isolation of causative agent and autopy findings. Afterward several outbreaks occurred also during autumn especially after flood in every years and some characterisitcs of leptospirosis in Korea such as clinical manifestations, serotypes and seroepidemiological features has been revealed by many investigators. Because of the major mode of transmission between rodents and human is by direct contact with leptospiral urine of rodents or contaminated soil by the urine, leptospirosis in Korea has been primarily a disease of person in occupations heavily exposed to contaminated soil or infected urine such as farmer, army and etc. Therefore it seems that leptospirosis is one of the main communicable diseases to be controlled urgently in Korea, for an agricultural people account for almost half of total Korean people. For clarifying the seroepidemiological patterns of human leptospirosis in Korea by sex, month region and main reacting serovars of L. interrogans among acute febrile disease occurred in 1987, 1,773 patient's sers with acute febrile episodes were tested by microagglutination test using 19 representative strains of leptospiral serogroup as antigen. All of those sera were collected from 10 collaborative clinics located in Kyunggi, Kangwon, Chungbuk, Chungnam, Chonbuk, Chonnam province and Seoul. The results wee summerized as follows. 1) Among 1,773 sera of patients with acute febrile episodes, 219 (12.4%) were seropositive to L. interrogans, 487(27.5%) to R. tsutsugamushi, 241(13.6%) to R.typhi and 160(90.0%) to Hantaan virus. 2) Among seropositives to L.interrogans, the male outnumbered the female, 65% and 35%. 3) For age distribution, 26.9% of seropositives to L.interrogans were fifties, 19.6% were forties, 9.1% were sixties, 5.9% were thirties and 4.1% were twenties. 4) Eighty three percent of seropositives had occurred between September and October in 1987 with a peak in September. 5) Main leptospiral serovars reactive to patient's sera were Icterohaemorrhagiae(54.3%), Canicola(31.0%), CH-48(13.2%), Tarassovi(0.9%)and Cynopteri(0.5%). 6) For regional distribution, 65.8% of seropositives to L.interrogans were residents from Chonbuk, 12.3% were Chonnam, 7.3% were Chungnam, 5.5% were Kyunggi and 1.4% were Kangwon.