Next generation sequencing (NGS): a golden tool in forensic toolkit

Aly, Sanaa M.; Sabri, Dalia

doi:10.5114/amsik.2015.61029

Cited by 23 publications

(24 citation statements)

References 38 publications

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“…Next-generation sequencing (NGS) has become an essential technology in molecular biology research and clinical assessment [1][2][3]. However, the quality of the input biological samples has a critical effect on NGS results.…”

Section: Introductionmentioning

confidence: 99%

DV200 Index for Assessing RNA Integrity in Next-Generation Sequencing

Matsubara

Soh

Morita

et al. 2020

BioMed Research International

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Poor quality of biological samples will result in an inaccurate analysis of next-generation sequencing (NGS). Therefore, methods to accurately evaluate sample integrity are needed. Among methods for evaluating RNA quality, the RNA integrity number equivalent (RINe) is widely used, whereas the DV200, which evaluates the percentage of fragments of >200 nucleotides, is also used as a quality assessment standard. In this study, we compared the RINe and DV200 RNA quality indexes to determine the most suitable RNA index for the NGS analysis. Seventy-one RNA samples were extracted from formalin-fixed paraffin-embedded tissue samples (n = 30), fresh-frozen samples (n = 25), or cell lines (n = 16). After assessing RNA quality using the RINe and DV200, we prepared two kinds of stranded mRNA sequencing libraries. Finally, we calculated the correlation between each RNA quality index and the amount of library product (1 st PCR product per input RNA). The DV200 measure showed stronger correlation with the amount of library product than the RINe (R 2 = 0:8208 for the DV200 versus 0.6927 for the RINe). Receiver operating characteristic curve analyses revealed that the DV200 was the better marker for predicting efficient library production than the RINe using a threshold of >10 ng/ng for the amount of the 1 st PCR product per input RNA (cutoff value for the RINe and DV200, 2.3 and 66.1%; area under the curve, 0.99 and 0.91; sensitivity, 82% and 92%; and specificity, 93% and 100%, respectively). Our results indicate that NGS libraries prepared using RNA samples with the DV200 value > 66:1% exhibit greater sensitivity and specificity than those prepared with the RINe values > 2:3. These findings suggest that the DV200 is superior to the RINe, especially for low-quality RNA, because it is a more consistent assessment of the amount of the 1 st NGS library product per input.

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Section: Introductionmentioning

confidence: 99%

DV200 Index for Assessing RNA Integrity in Next-Generation Sequencing

Matsubara

Soh

Morita

et al. 2020

BioMed Research International

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“…Hlai, which is one important branch of the Tai-Kadai language, is widely spoken by more than 1.51 million Hainan Li for daily communications at present [31,32].In the field of massively parallel sequence (MPS), for the past decade, there are tremendous advances had been made in the aspect of accuracy, speed, read length, and throughput, as well as the substantial cost reduction. Together, these progresses democratized this technology and laid a solid foundation for the future development of abundant applications in basic subjects and translational research areas, such as clinical diagnostics, agrigenomics, and forensic sciences [33][34][35][36][37][38][39]. The ForenSeq™ DNA Signature Prep Kit, as the first commercial MPS-based and forensic related kit formally released in 2015, made full use of the MPS method's advantages by means of the simultaneous and compound amplification of either greater than 150 loci including various types of genetic markers.…”

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confidence: 99%

The forensic landscape and the population genetic analyses of Hainan Li based on massively parallel sequencing DNA profiling

Fan

Wang

et al. 2020

Preprint

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Due to the formation of the Qiongzhou Strait by climate change and marine transition, Hainan island isolated from the mainland southern China during the Last Glacial Maximum. Hainan island, located at the southernmost part of China and separated from the Leizhou Peninsula by the Qiongzhou Strait, laid on one of the modern human northward migration routes from Southeast Asia to East Asia. The Hlai-language speaking Li minority, the second largest population after Han Chinese in Hainan island, is the direct descendants of the initial migrants in Hainan island and has unique ethnic properties and derived characteristics, however, the forensic associated studies on Hainan Li population are still insufficient.Hence, 136 Hainan Li individuals were genotyped in this study using the MPS-based ForenSeq™ DNA Signature Prep Kit (DNA Primer Set A) to characterize the forensic genetic polymorphism landscape, and DNA profiles were obtained from 152 different molecular genetic markers (27 autosomal STRs, 24 Y-STRs, 7 X-STRs, and 94 iiSNPs). A total of 419 distinct length variants and 586 repeat sequence sub-variants, with 31 novel alleles (at 17 loci), were identified across the 58 STR loci from the DNA profiles of Hainan Li population. We evaluated the forensic characteristics and efficiencies of DAPA, it demonstrated that the STRs and iiSNPs in DAPA were highly polymorphic in Hainan Li population and could be employed in forensic applications. In addition, we set up three Datasets, which included the genetic data of (Ⅰ). iiSNPs (27 populations, 2640 individuals), (Ⅱ). Y-STRs (42 populations, 8281 individuals), and (Ⅲ). Yhaplogroups (123 populations, 4837 individuals) along with the population ancestries and language families, to perform population genetic analyses separately from different perspectives.In conclusion, the phylogenetic analyses indicated that Hainan Li, with a southern East Asia origin and Tai-Kadai language-speaking language, is an isolated population relatively. But the genetic pool of Hainan Li influenced by the limited gene flows from other Tai-Kadai populations and Hainan populations. Furthermore, the establishment of isolated population models will be beneficial to clarify the exquisite population structures and develop specific genetic markers for subpopulations in forensic genetic fields. Signature Prep Kit; Massively parallel sequencing. mass landings of the Han (since BC 214 in Qin Dynasty) and Lingao people (about BC 500 during the Spring and Autumn period) compressed the living space of Hainan Li, making Li from the north to the south of Hainan island [1,2,9,29,30]. (Nowadays, the main distributions of Hainan Li minority are shown in Fig. 1C.) In all ages, ever since the primordial settlements in Hainan island, Hlai language was the dominant language for the original migrants and their descendants, and the intangible cultural and spiritual heritages within Hainan Li were preserved by oral transmission without ancient writings to hand down. Hlai, which is one important branch of the Tai-Kadai languag...

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“…Progress in NGS technologies has brought, ethical questions as well [10,11]. Promising applications include detection of pathogenic organisms [12,13] and forensic sciences [14,15]. At present, the cost of the sample library preparation process for NGS is still a significant part of the total cost of genome sequencing.…”

Section: Introductionmentioning

confidence: 99%

Single molecule sequencing of M13 virus genome without amplification

Zhao

Deng

et al. 2017

Preprint

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Third generation sequencing is a direct measurement of DNA/RNA sequences at the single molecule level without amplification. In this study, we report sequencing of the genome of the M13 virus by a new single molecule sequencing platform. Our platform detects single molecule fluorescence by the total internal reflection microscope technique, with sequencing-by-synthesis chemistry. We sequenced the genome of M13 to a depth of 316x and 100% coverage. The consensus sequence accuracy is 100%. We demonstrated that single molecule sequencing has no significant GC bias.

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Next generation sequencing (NGS): a golden tool in forensic toolkit

Cited by 23 publications

References 38 publications

DV200 Index for Assessing RNA Integrity in Next-Generation Sequencing

DV200 Index for Assessing RNA Integrity in Next-Generation Sequencing

The forensic landscape and the population genetic analyses of Hainan Li based on massively parallel sequencing DNA profiling

Single molecule sequencing of M13 virus genome without amplification

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