Exploring of rare differences in mtGenomes between MZ twins using massively parallel sequencing

Ming, Tianyue; Wang, Mengge; Zheng, Mingrui; Zhou, Yanping; Hou, Yiping; Wang, Zheng

doi:10.1016/j.fsigss.2019.09.028

Cited by 3 publications

(3 citation statements)

References 6 publications

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“…Significantly, however, the existence of heteroplasmy can affect the interpretation of mtDNA evidence in forensic investigations (Just, Irwin, & Parson, 2015;. However, on the other hand, the presence of heteroplasmy between monozygotic (MZ) twins makes it possible to distinguish one from the other Ming et al, 2019;Pfeiffer et al, 2004). The genetic diversity of mitochondrial genomes (mitogenomes) was formed by the sequential accumulation of mutations through maternal lineages.…”

Section: Mitochondrial Genetic Variationsmentioning

confidence: 99%

Perspective and Opportunity for forensic integrative genomics in the Human Pangenome Reference sequence era

Huang

Chen

et al. 2023

Preprint

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Human Pangenome Reference Consortium (HPRC) and Chinese Pangenome Consortium (CPC) have pronounced the finish of the pilot work of the Human Pangenome Project, which aimed to build worldwide population-representative high-quality haplotype-resolved reference graph genomes. Graph-based gapless pangenome reference genomes with enriched genomic diversity and higher completeness and contiguity possessed the potential for a new beginning for third-generation sequencing (TGS)-based genomic research and high-performance mapping rate and variant genotyping for traditional short-read sequencing platforms. With the new pangenome reference coordinates and corresponding computation algorithms and methods, forensic integrative genomics fields will benefit in new-marker identification, highly-accurate marker genotyping, high-resolution panel development and corresponding statistical algorithm updates. Here, we discussed the past advances and new challenges of pangenome-based genomic research and their integrative genomics applications for variant identification and new forensic genomic, epigenetic, transcriptomic, and microbiome practices. We highlighted the necessity and importance of including the forensic TGS-based platforms, pangenome-based entire landscape of genomic diversity, pangenome-based study design and graph-based pangenome reference in short-read NGS mapping and TGS-based innovations to achieve forensic precision medicine.

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Section: Mitochondrial Genetic Variationsmentioning

confidence: 99%

Perspective and Opportunity for forensic integrative genomics in the Human Pangenome Reference sequence era

Huang

Chen

et al. 2023

Preprint

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“…Researchers have reported that there may be differences in these genomic biomarkers between MZTs. However, due to the nearly identical nuclear and mitochondrial genome information shared by MZTs, such differences are infrequent (McRae et al, 2015 ; Ming et al, 2019 ) and genome-wide sequencing is typically necessary to differentiate MZTs. Another MZT identification strategy involves the investigation of various biomarkers from the perspective of epigenetics, including DNA methylation (Stewart et al, 2015 ; Xu et al, 2015 ) and microRNA (Fang et al, 2019 ; Xiao et al, 2019 ).…”

Section: Introductionmentioning

confidence: 99%

Feature selection with a genetic algorithm can help improve the distinguishing power of microbiota information in monozygotic twins' identification

Fu¹,

Ma²,

Dou³

et al. 2023

Front. Microbiol.

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IntroductionPersonal identification of monozygotic twins (MZT) has been challenging in forensic genetics. Previous research has demonstrated that microbial markers have potential value due to their specificity and long-term stability. However, those studies would use the complete information of detected microbial communities, and low-value species would limit the performance of previous models.MethodsTo address this issue, we collected 80 saliva samples from 10 pairs of MZTs at four different time points and used 16s rRNA V3–V4 region sequencing to obtain microbiota information. The data formed 280 inner-individual (Self) or MZT sample pairs, divided into four groups based on the individual relationship and time interval, and then randomly divided into training and testing sets with an 8:2 ratio. We built 12 identification models based on the time interval ( ≤ 1 year or ≥ 2 months), data basis (Amplicon sequence variants, ASVs or Operational taxonomic unit, OTUs), and distance parameter selection (Jaccard distance, Bray-Curist distance, or Hellinger distance) and then improved their identification power through genetic algorithm processes. The best combination of databases with distance parameters was selected as the final model for the two types of time intervals. Bayes theory was introduced to provide a numerical indicator of the evidence's effectiveness in practical cases.ResultsFrom the 80 saliva samples, 369 OTUs and 1130 ASVs were detected. After the feature selection process, ASV-Jaccard distance models were selected as the final models for the two types of time intervals. For short interval samples, the final model can completely distinguish MZT pairs from Self ones in both training and test sets.DiscussionOur findings support the microbiota solution to the challenging MZT identification problem and highlight the importance of feature selection in improving model performance.

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“…This library preparation kit, with 162 amplicons that target the whole mtDNA, is mostly used for forensic samples, achieving reliable results in often degraded samples [ 26 , 27 , 28 , 29 ] and with low DNA input (usually 0.1 ng of genomic DNA, but 6.25 pg [ 30 ] and, very recently, 0.6 pg [ 31 ] have been reported). Despite its most common use in forensic sciences, it has also been used in a range of other applications, from worldwide lineage studies [ 32 ], to rare mtDNA differences in monozygotic twins [ 33 ].…”

Section: Introductionmentioning

confidence: 99%

From Forensics to Clinical Research: Expanding the Variant Calling Pipeline for the Precision ID mtDNA Whole Genome Panel

Cortes-Figueiredo

Carvalho

Fonseca

et al. 2021

IJMS

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Despite a multitude of methods for the sample preparation, sequencing, and data analysis of mitochondrial DNA (mtDNA), the demand for innovation remains, particularly in comparison with nuclear DNA (nDNA) research. The Applied Biosystems™ Precision ID mtDNA Whole Genome Panel (Thermo Fisher Scientific, USA) is an innovative library preparation kit suitable for degraded samples and low DNA input. However, its bioinformatic processing occurs in the enterprise Ion Torrent Suite™ Software (TSS), yielding BAM files aligned to an unorthodox version of the revised Cambridge Reference Sequence (rCRS), with a heteroplasmy threshold level of 10%. Here, we present an alternative customizable pipeline, the PrecisionCallerPipeline (PCP), for processing samples with the correct rCRS output after Ion Torrent sequencing with the Precision ID library kit. Using 18 samples (3 original samples and 15 mixtures) derived from the 1000 Genomes Project, we achieved overall improved performance metrics in comparison with the proprietary TSS, with optimal performance at a 2.5% heteroplasmy threshold. We further validated our findings with 50 samples from an ongoing independent cohort of stroke patients, with PCP finding 98.31% of TSS’s variants (TSS found 57.92% of PCP’s variants), with a significant correlation between the variant levels of variants found with both pipelines.

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Exploring of rare differences in mtGenomes between MZ twins using massively parallel sequencing

Cited by 3 publications

References 6 publications

Perspective and Opportunity for forensic integrative genomics in the Human Pangenome Reference sequence era

Perspective and Opportunity for forensic integrative genomics in the Human Pangenome Reference sequence era

Feature selection with a genetic algorithm can help improve the distinguishing power of microbiota information in monozygotic twins' identification

From Forensics to Clinical Research: Expanding the Variant Calling Pipeline for the Precision ID mtDNA Whole Genome Panel

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