Haplotype diversity in mitochondrial genome in a Chinese Han population

Ma, Ke; Li, Hui; Cao, Yu; Zhao, Xuejun; Liu, Wen-Bin; Zhao, Xueying

doi:10.1038/jhg.2016.74

Cited by 7 publications

(2 citation statements)

References 28 publications

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“…Figure 4A showed the PCA for the first two principal components, which together explained 49.42% of the total variance based on top-level haplogroup frequencies from 13 mitogenome dataset ( Supplementary Table S3 ). Herein, African (African American [ 42 ] and Zambian [ 54 ]) were clustered to the 4th quadrant, distinguishing from Westeurasian, East and Southeast Asian by PC1, whereas East and Southeast Asian (Xibe, Eastern Han Chinese [ 55 ], Northern Chinese Han [ 8 ], Tibetan [ 44 ] and Filipino [ 56 ]) were clustered to the 2nd quadrant, distinguishing from Westeurasian (U.S. Caucasian [ 42 ], Armenian, Azeri, Georgian, Iranian and Turk [ 49 ]) in the 3rd quadrant by PC2. This distribution mirrored the geographical background of populations compared.…”

Section: Resultsmentioning

confidence: 99%

RETRACTED Mitochondrial Genome Sequencing with Short Overlapping Amplicons on Miseq FGx System

Yang

Jia

Zhang

et al. 2021

Forensic Sciences Research

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With the development and maturation of massively parallel sequencing (MPS) technology, the mitochondrial genome (mitogenome) sequencing is increasingly applied in the forensic field. In this study, we employed the strategy of short overlapping amplicons for the whole mitogenome, library preparation with tagmentation using the Nextera® XT DNA Library Preparation Kit, sequencing on the MiSeq FGx TM Forensic Genomics System and analyzing data using the mitochondrial(mtDNA) MSR Plug-in and the mtDNA Variant Analyzer. A total of 27 libraries and 56 libraries were sequenced in a run using MiSeq Reagent Kit v2 and v3, respectively. Results showed more than 1800 × of averaged depth of coverage (DoC) at each position. Concordant haplotypes of 9947 A and 2800 M were obtained at 32 variants. Cross-reactivity was observed with 1 ng primate DNA and 10 ng non-primate DNA but could be easily distinguished. Full and accurate variants were obtained from at least 50 pg input DNA and from minor contributors between 19:1 and 1:19 mixed ratios with known reference profiles. More than 86% variants were detected from ≥200-bp degraded samples but its haplotype was assigned to more ancestral haplogroup. Further, a total of 3 962 variants were observed at 613 nucleotide positions from 103 Xibe mitogenomes with 25:1 ratio of transitions to transversions. Two new transversions (C13735A and A14755C) and two tri-alleles at nps 9824 and 16092 were identified. There were 103 unique mitogenome haplotypes from 103 Chinese Xibe that were assigned to 79 haplogroups. Haplogroup D was the preponderant top-level haplogroup in Xibe followed by F, B, M, A, N, G, C, Z, Y, HV and J. Random match probability (RMP) and haplotype diversity (HD) of the whole mitogenome was calculated as 0.0097 and 1.0000, respectively. Compared with HVS-I only, RMP decreased 33.56%, while the number of haplotypes and HD increased 15.73% and 0.49%, respectively. Principal component analysis (PCA) showed that Xibe was clustered to East and Southeast Asian. As a whole, this MPS strategy is suitable for the whole mitogenome sequencing especially for degraded samples and can facilitate generating mitogenome data to support the routine application in forensic sciences. EMP00726 is the first whole mitogenome dataset from Xibe contributed to the EMPOP. Supplemental data for this article are available online at.

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Section: Resultsmentioning

confidence: 99%

RETRACTED Mitochondrial Genome Sequencing with Short Overlapping Amplicons on Miseq FGx System

Yang

Jia

Zhang

et al. 2021

Forensic Sciences Research

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“…Two publications were identified after filtering using the terms Homo sapiens, sampling method, and sequencing strategy. The two published population studies included 145 Han individuals from southern Shanghai were identified as CHSH [14], and 107 Han individuals from northern Liaoning province were identified as CHLN [15]. The variant call format (VCF) file of all Chinese data from the phase 3 data of the 1000 Genomes Project were downloaded ( ftp://ftp.ncbi.nlm.nih.gov/1000genomes/ ) [16,17], which included individuals from Beijing who identified as CHBJ, Hunan province was identified as CHHN and Fujian province was identified as CHFJ, and the Dai population from Yunnan was identified as CDX.…”

Section: Methodsmentioning

confidence: 99%

Whole Mitochondrial DNA Sequencing Analysis in 47 Han Populations in Southwest China

Yao

Wan

2019

Med Sci Monit

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BackgroundMitochondrial DNA (mtDNA) sequencing has been used in many areas, including forensic genetics. Due to the rapid development of sequencing technology, whole mtDNA sequencing is now possible and may be used in epidemiological and forensic studies. This study aimed to use whole mtDNA sequencing to investigate 47 Chongqing Han populations in southwest China and the diversity in the mtGenome reference data.Material/MethodsThe mtDNA of 47 Chongqing Han populations was generated using the Ion Torrent Personal Genome Machine (PGM) system. The extent of the effects of the mtDNA on the subpopulations was investigated and compared with six other populations from published studies. Pairwise fixation index (FST), a measure of population differentiation due to genetic structure, were calculated. Analysis of molecular variance (AMOVA) was performed, and 1257 hypervariable region data sets were added to the principal component analysis (PCA).ResultsThe whole mtDNA sequencing data of 47 southwest Chinese Han populations were successfully recovered. Expanding the sequencing rage increased the discrimination power of mtDNA from three-times to 25-times based on different populations. The subpopulation effects showed 20 times the differences in match probability when compared with south China regions.ConclusionsWhole mtDNA sequencing distinguished between individuals from 47 Chongqing Han populations in southwest China and has potential applications that include high-quality forensic identification.

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Massive parallel sequencing of mitochondrial DNA genomes from mother-child pairs using the ion torrent personal genome machine (PGM)

Ma¹,

Zhao²,

Li³

et al. 2018

Forensic Science International: Genetics

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Haplotype diversity in mitochondrial genome in a Chinese Han population

Cited by 7 publications

References 28 publications

RETRACTED Mitochondrial Genome Sequencing with Short Overlapping Amplicons on Miseq FGx System

RETRACTED Mitochondrial Genome Sequencing with Short Overlapping Amplicons on Miseq FGx System

Whole Mitochondrial DNA Sequencing Analysis in 47 Han Populations in Southwest China

Massive parallel sequencing of mitochondrial DNA genomes from mother-child pairs using the ion torrent personal genome machine (PGM)

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