Short-tandem repeat analysis in seven Chinese regional populations

Song, Xiaoling; Zhou, Yi; Ying, Binwu; Wang, Lanlan; Li, Yisong; Liu, Jianfeng; Bai, Xiaogang; Zhang, Lei; Lu, Xiaojun; Wang, Jun; Ye, Yuanxin

doi:10.1590/s1415-47572010000400002

Cited by 10 publications

(5 citation statements)

References 22 publications

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“…To get a more comprehensive picture of population linkages in Asia, we employed POPTREE v.2 ( Takezaki et al, 2014 ) to build a neighbor-joining tree (NJ) based on F st computation by allele frequency from 13 STRs with publicly accessible data from relevant populations ( Brinkmann et al, 2002 ; Kim et al, 2003 ; Seah et al, 2003 ; De Ungria et al, 2005 ; Dobashi et al, 2005 ; Tie et al, 2006 ; Maruyama et al, 2008 ; Zhu et al, 2008 ; Untoro et al, 2009 ; Song et al, 2010 ; Kutanan et al, 2011 ; Yang et al, 2013 ; Zhai et al, 2014 ; Huang et al, 2015 ; Kutanan et al, 2015 ; Srithawong et al, 2015 ; Zhang, 2015a ; Zhang, 2015b ; Chantakot et al, 2017 ; Guo, 2017 ; Guo et al, 2017 ; Srithawong et al, 2020 ; Mawan et al, 2021 ).…”

Section: Methodsmentioning

confidence: 99%

Genetic Structure and Forensic Utility of 23 Autosomal STRs of the Ethnic Lao Groups From Laos and Thailand

et al. 2022

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The Lao Isan and Laotian are the major groups in the area of present-day northeastern Thailand and Laos, respectively. Several previous genetic and forensic studies indicated an admixed genetic structure of Lao Isan with the local Austroasiatic speaking groups, e.g. Khmer, whereas there is a paucity of reporting Laotian’s forensic short tandem repeats (STRs). Here, we newly generated 451 genotypes of seven Lao Isan and three Laotian populations (two Lao Lum and one Lao Thoeng) using 23 autosomal STRs embedded in VerifilerTM plus PCR Amplification kit. We reported allelic frequency and forensic parameters in different dataset: combined ethnic Lao groups, combined Lao Isan populations and combined Laotians. Overall, the forensic parameter results indicate that this set of STRs is suitable for forensic investigation. The anthropological results revealed the genetic homogeneity of Tai-Kadai speaking Lao groups from Thailand and Laos, consistent with previous studies, while the Austroasiatic speaking groups from southern Laos showed genetic relatedness to both Lao Isan and Khmer. In sum, STRs allelic frequency results can provide the genetic backgrounds of populations which is useful for anthropological research and also strengthens the regional forensic database in both countries.

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Section: Methodsmentioning

confidence: 99%

Genetic Structure and Forensic Utility of 23 Autosomal STRs of the Ethnic Lao Groups From Laos and Thailand

et al. 2022

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“…To obtain a broader picture of population relationships within Southeast Asia, we included publicly available STR frequency from relevant populations [ 15 , 21 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 ] and a neighbor-joining tree (NJ) based on F st computation by allele frequency from 13 STRs of the FBI Laboratory’s Combined DNA Index System (CODIS) was carried out using POPTREE v.2 [ 58 ].…”

Section: Methodsmentioning

confidence: 99%

Autosomal Microsatellite Investigation Reveals Multiple Genetic Components of the Highlanders from Thailand

Mawan

Prakhun

Muisuk

et al. 2021

Genes

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The hill tribes of northern Thailand comprise nine officially recognized groups: the Austroasiatic-speaking (AA) Khmu, Htin and Lawa; the Hmong-Mien-speaking (HM) IuMien and Hmong; and the Sino-Tibetan-speaking (ST) Akha, Karen, Lahu and Lisu. Except the Lawa, the rest of the hill tribes migrated into their present habitats only very recently. The Thai hill tribes were of much interest to research groups focusing on study of cultural and genetic variation because of their unique languages and cultures. So far, there have been several genetic studies of the Thai hill tribes. However, complete forensic microsatellite database of the Thai hill tribes is still lacking. To construct such database, we newly generated 654 genotypes of 15 microsatellites commonly used in forensic investigation that belong to all the nine hill tribes and also non-hill tribe highlanders from northern Thailand. We also combined 329 genotypes from previous studies of northern Thai populations bringing to a total of 983 genotypes, which were then subjected to genetic structure and population relationships analyses. Our overall results indicated homogenous genetic structure within the HM- and Tai-Kadai (TK)-speaking groups, large genetic divergence of the HM-speaking Hmong but not IuMien from the other Thai groups, and genetic heterogeneity within the ST- and AA-speaking groups, reflecting different population interactions and admixtures. In addition to establishing genetic relationships within and among these populations, our finding, which provides a more complete picture of the forensic microsatellite database of the multiple Thai highland dwellers, would not only serve to expand and strengthen forensic investigation in Thailand, but would also benefit its neighboring countries of Laos and Myanmar, from which many of the Thai hill tribes originated and where large populations of these ethnic groups still reside.

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“…Notably, the microsatellite markers employed in the MSA assay must be tailored to the population under scrutiny, as demonstrated by the initially low informativeness of the assay on Chinese patients studied using marker panels that were developed for occidental patient cohorts [ 104 , 105 , 106 , 107 , 108 , 109 , 110 , 111 ]. These studies suggest that as experience with MSA increases and as marker panels expand and become better defined, MSA tests will achieve high sensitivity and specificity, making them an ideal approach for a large clinical trial and, ultimately, for evaluation as a substitute for standard-of-care technology.…”

Section: Use Of Microsatellite Assay For Bladder Cancer Detectionmentioning

confidence: 99%

“…Recent studies performed in China on STR markers have established that the heterozygosity frequencies for many of the STR markers is sufficient for LOH testing in cancer. In their report, Song et al investigated the application of 13 short tandem repeat (STR) loci (D13S317, D7S820, TH01, D16S539, CSFIPO, VWA, D8S1179, TPOX, FGA, D3S1358, D21S11, D18S51, and D5S818) routinely used in forensic analysis for delineating population relationships among seven human populations representing the two major geographic groups, namely the southern and northern Chinese [ 104 ]. The resulting single topology suggested significant geographic and population partitioning, which was in line with the differences in geographic location, languages, and eating habits.…”

Section: Use Of Microsatellite Assay For Bladder Cancer Detectionmentioning

confidence: 99%

Microsatellite Instability Analysis (MSA) for Bladder Cancer: Past History and Future Directions

Moon

Gordon

Moon

et al. 2021

IJMS

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Microsatellite instability (MSI), the spontaneous loss or gain of nucleotides from repetitive DNA tracts, is a diagnostic phenotype for gastrointestinal, endometrial, colorectal, and bladder cancers; yet a landscape of instability events across a wider variety of cancer types is beginning to be discovered. The epigenetic inactivation of the MLH1 gene is often associated with sporadic MSI cancers. Recent next-generation sequencing (NGS)-based analyses have comprehensively characterized MSI-positive (MSI+) cancers, and several approaches to the detection of the MSI phenotype of tumors using NGS have been developed. Bladder cancer (here we refer to transitional carcinoma of the bladder) is a major cause of morbidity and mortality in the Western world. Cystoscopy, a gold standard for the detection of bladder cancer, is invasive and sometimes carries unwanted complications, while its cost is relatively high. Urine cytology is of limited value due to its low sensitivity, particularly to low-grade tumors. Therefore, over the last two decades, several new “molecular assays” for the diagnosis of urothelial cancer have been developed. Here, we provide an update on the development of a microsatellite instability assay (MSA) and the development of MSA associated with bladder cancers, focusing on findings obtained from urine analysis from bladder cancer patients as compared with individuals without bladder cancer. In our review, based on over 18 publications with approximately 900 sample cohorts, we provide the sensitivity (87% to 90%) and specificity (94% to 98%) of MSA. We also provide a comparative analysis between MSA and other assays, as well as discussing the details of four different FDA-approved assays. We conclude that MSA is a potentially powerful test for bladder cancer detection and may improve the quality of life of bladder cancer patients.

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Short-tandem repeat analysis in seven Chinese regional populations

Cited by 10 publications

References 22 publications

Genetic Structure and Forensic Utility of 23 Autosomal STRs of the Ethnic Lao Groups From Laos and Thailand

Genetic Structure and Forensic Utility of 23 Autosomal STRs of the Ethnic Lao Groups From Laos and Thailand

Autosomal Microsatellite Investigation Reveals Multiple Genetic Components of the Highlanders from Thailand

Microsatellite Instability Analysis (MSA) for Bladder Cancer: Past History and Future Directions

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