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Demonstration of the Mutation Associated with Porcine Stress Syndrome
Published in S. Tsuyoshi Ohnishi, Tomoko Ohnishi, Malignant Hyperthermia, 1994
Xia Zhang, Hua Shen, C. Robert Cory, Peter J. O’Brien
Table 2 and Figure 5 show the results of PSS gene-frequency estimates made using caffeine and halothane sensitivity tests and the DNA-based test for the HAL-1843 mutation. The estimates of allele frequency based on phenotype analysis were highly correlated with genotype analysis (log p>-12).
Forensic features and phylogenetic analyses of the population of Nayagarh (Odisha), India using 23 Y-STRs
Published in Annals of Human Biology, 2022
Muktikanta Panda, Ramkishan Kumawat, Shivani Dixit, Awdhesh Narayan Sharma, Hari Shankar, Gyaneshwer Chaubey, Pankaj Shrivastava
For each Y-STR locus, the allele frequencies and gene diversity (GD) values have been mentioned in Tables 1 and 2, respectively. For the male population of Nayagarh, Odisha, a total of 44 alleles were observed at 23 Y-STR loci. The range of allele frequency was found to be between 0.004 and 0.797. Locus-wise, the number of alleles seen were in the range of 4 (for locus DYS389I, DYS437 and DYS439) to 19 (for locus DYS385a/b). 55 allelic combinations were observed at the multi-copy loci DYS385a/b. A total of 33 allelic micro-variants were observed at 11 markers (Table 3); DYS576 (16.3 in single copy), DYS448 (17.2 in single copy), DYS389II (31.1 in single copy and 28.2 in two copies), DYS437 (13.2 in single copy), DYS570 (18.3 in single copy), DYS635 (23.1 in two copies), DYS392 (11.2 in four copies,10.2 in two copies and 14.1 in single copy), DYS643 (9.2 in two copies and 10.1 in single copy), DYS458 (15.1 in six copies and 19.2 in single copy), DYS385a (15.2, 10.1, and 11.3 in single copy) and DYS385b (15.2 in three copies and 16.2 in single copy). Here no null allele was observed.
Inferring the population structure and admixture history of three Hmong-Mien-speaking Miao tribes from southwest China based on genome-wide SNP genotyping
Published in Annals of Human Biology, 2021
Ting Luo, Rui Wang, Chuan-Chao Wang
To quantify the genetic relationships between our newly reported Guizhou Miao populations and worldwide reference populations, we primarily performed allele frequency-based outgroup-f3-statistics analysis in the form of f3(X, Y; Yoruba) to calculate the shared genetic drift between X and Y since their divergence from the outgroup Yoruba. Higher f3 values indicated more shared genetic drift between X and Y. Cluster patterns in Heatmap (Figure 3(A)) revealed high genetic sharing within the present-day populations belonging to the same language family. Each studied Guizhou Miao group was found to share maximum alleles with Vietnam Hmong, followed by other newly collected Miao groups, Tai-Kadai-speaking CoLao, Hmong-Mien-speaking PaThen, Hunan Miao, and Tai-Kadai-speaking Dong. Hunan Miao shared the most genetic drift with Hmong, followed by Miao_Ziyun, Miao_Xixiu, Miao_Zhenning, and CoLao. When focussed on outgroup-f3 (studied Guizhou Miao, published ancient samples; Yoruba), we observed our studied Guizhou Miao groups presented the top highest f3 values with the historic individuals from Fujian (Chuanyun), Iron Age samples from Taiwan (Hanben, Gongguan), followed by Neolithic-Iron Age Yellow River Basin and Western Liao River Basin-related individuals (Figure 3(B)).
Mutations of DNAJC7 are rare in Chinese amyotrophic lateral sclerosis patients
Published in Amyotrophic Lateral Sclerosis and Frontotemporal Degeneration, 2021
Xiaohan Sun, Ximeng Zhao, Qing Liu, Kang Zhang, Shuangwu Liu, Zhili Wang, Xunzhe Yang, Liang Shang, Liying Cui, Xue Zhang
In this study, we screened DNAJC7 mutations by WES in a Chinese cohort comprising 326 Chinese ALS patients. Two heterozygous missense rare variants were identified in 6 SALS patients. No pathogenic DNAJC7 mutations were identified in FALS and ALS-FTD patients. The p.K137R variant is interpreted as uncertain significance according to ACMG by the following evidences. First, it is absent from control databases (gnomAD and ExAC) and our inhouse controls (PM2). Second, the variant sites are conserved through revolution and the variant was predicted by Mutation Taster to be disease-causing (PP3). As for another variant, p.N369T, was identified in 5 SALS patients. It has a relatively high allele frequency in healthy populations recorded in public databases and our matched controls. According to the interpretation of sequence variants formulated by the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) 2015 guideline, “allele frequency is greater than expected for disorder” is strong evidence for benign variant (6). In this case, the p.N369T variant frequency is greater than the incidence of ALS which ranges from 0.42/100,000 in South Asia to 2.26/100,000 in West Europe (7). We suppose the variant is not pathogenic. Thus, we consider the p.N369T as benign SNP rather than pathogenic missense mutation.