Genome-wide screening for highly discriminative SNPs for personal identification and their assessment in world populations

Li, Liming; Wang, Yi; Yang, Shuping; Xia, Mingxu; Yang, Yajun; Wang, Jiucun; Lu, Daru; Pan, Xingwei; Ma, Teng; Pei, Jun‐Peng; Yu, Ge; Zhao, Ziqin; Ping, Yuan; Zhou, Heng; Zhao, Xueying; Sun, Hui; Liu, Bing; Jia, Dongtao; Li, Chengtao; Hu, Rong; Lu, Hongzhou; Liu, Xiaoyang; Chen, Wenqing; Qin, Man; Xue, Fuzhong; Su, Yongdong; Jin, Li; Li, Shilin

doi:10.1016/j.fsigen.2017.02.005

Cited by 19 publications

(15 citation statements)

References 41 publications

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“…Lou et al [ 48 ] reported the performance of a 44 SNPs individual identification assay for Chinese. In addition, studies indicated considerable potential of high throughput platforms for SNP detection which could increase unprecedented discriminative power for human identification [ 49 – 51 ]. These panels are all based on DNA profiles and mostly contain intragenic SNPs which disqualify them for RNA-based genotype calling.…”

Section: Discussionmentioning

confidence: 99%

A SNP panel for identification of DNA and RNA specimens

et al. 2018

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BackgroundSNP panels that uniquely identify an individual are useful for genetic and forensic research. Previously recommended SNP panels are based on DNA profiles and mostly contain intragenic SNPs. With the increasing interest in RNA expression profiles, we aimed for establishing a SNP panel for both DNA and RNA-based genotyping.ResultsTo determine a small set of SNPs with maximally discriminative power, genotype calls were obtained from DNA and blood-derived RNA sequencing data belonging to healthy, geographically dispersed, Dutch individuals. SNPs were selected based on different criteria like genotype call rate, minor allele frequency, Hardy–Weinberg equilibrium and linkage disequilibrium. A panel of 50 SNPs was sufficient to identify an individual uniquely: the probability of identity was 6.9 × 10− 20 when assuming no family relations and 1.2 × 10− 10 when accounting for the presence of full sibs. The ability of the SNP panel to uniquely identify individuals on DNA and RNA level was validated in an independent population dataset. The panel is applicable to individuals from European descent, with slightly lower power in non-Europeans. Whereas most of the genes containing the 50 SNPs are expressed in various tissues, our SNP panel needs optimization for other tissues than blood.ConclusionsThis first DNA/RNA SNP panel will be useful to identify sample mix-ups in biomedical research and for assigning DNA and RNA stains in crime scenes to unique individuals.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4482-7) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

A SNP panel for identification of DNA and RNA specimens

et al. 2018

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“…Conversely, these BMPs are downregulated in models of atrophic nonunion compared to standard healing controls [30, 31]. Increased VEGF expression after EPC application may help to stimulate BMP-2 expression in local endothelial cells [13, 14, 32]. Synergistically, BMP-2 also stimulates VEGF expression in osteoblasts, further suggesting the coupling of angiogenesis and osteogenesis [33].…”

Section: Discussionmentioning

confidence: 99%

“…Synergistically, BMP-2 also stimulates VEGF expression in osteoblasts, further suggesting the coupling of angiogenesis and osteogenesis [33]. Thus, EPC-induced expression of VEGF and BMP-2 [13, 14], even after significant delay, may help to overcome the deficient signalling present in fracture nonunion and may initiate the inflammatory and endochondral phases of bone repair through regulation of angiogenesis and osteogenesis. Alternatively, the secondary surgical procedure is likely to cause an inflammatory reaction, which may stimulate EPC activity via IL-1 and IL-6 signalling [24–26].…”

Section: Discussionmentioning

confidence: 99%

“…Accordingly, angiogenic cell populations, such as EPCs, have recently been investigated, and our research group [13–16], as well as others [17–19], has successfully demonstrated the ability of EPCs to affect the repair of segmental bone defects in animal models when the cells are applied acutely to freshly created defects. However, the timing of intervention plays a significant role in the efficacy of both cellular and molecular therapies [20, 21] as a result of the differing inflammatory environments at different time points following trauma.…”

Section: Introductionmentioning

confidence: 99%

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Delayed Endothelial Progenitor Cell Therapy Promotes Bone Defect Repair in a Clinically Relevant Rat Model

Bates

Godbout

Ramnaraign

et al. 2017

Stem Cells International

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The repair of segmental bone defects remains a significant challenge for orthopaedic surgeons. Endothelial progenitor cells (EPCs) have successfully promoted the repair of acute defects in animal models; however, the ability of EPCs to induce the repair of chronic nonhealing defects, such as those often encountered clinically, has not been investigated. Therefore, the purpose of this study was to investigate the ability of EPCs delivered in delayed fashion to induce the repair of nonhealing defects in a clinically relevant model. In order to simulate delayed treatment, 5 mm segmental defects in Fischer 344 rat femora were treated with bone marrow-derived EPCs on a Gelfoam scaffold at 3 weeks post creation of the defect. At ten weeks posttreatment, 100% of EPC-treated defects achieved union, whereas complete union was only achieved in 37.5% of defects treated with Gelfoam alone. Furthermore, significant increases in ultimate torque (p = 0.022) and torsional stiffness (p = 0.003) were found in EPC-treated defects compared to controls. Critically, no differences in outcomes were observed between acute and delayed EPC treatments. These results suggest that EPCs can enhance bone healing when applied in an acute or delayed fashion and that their use may represent a clinically translatable therapy for bone healing in humans.

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“…A most recent study by Li et al . 21 also performed a genome-wide screening by selecting SNPs with Fst ≤0.01 and heterozygosity ≥0.40, based on HapMap r24, which includes 4 populations. It proposed a final panel encompassing 175 SNPs, compiled based on 26 populations (four in HapMap r24, thirteen in 1000 Genomes phase 1, nine Chinese populations including five Han).…”

Section: Discussionmentioning

confidence: 99%

Genome-wide screen for universal individual identification SNPs based on the HapMap and 1000 Genomes databases

Huang

Liu²,

Zheng

et al. 2018

Sci Rep

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Differences among SNP panels for individual identification in SNP-selecting and populations led to few common SNPs, compromising their universal applicability. To screen all universal SNPs, we performed a genome-wide SNP mining in multiple populations based on HapMap and 1000Genomes databases. SNPs with high minor allele frequencies (MAF) in 37 populations were selected. With MAF from ≥0.35 to ≥0.43, the number of selected SNPs decreased from 2769 to 0. A total of 117 SNPs with MAF ≥0.39 have no linkage disequilibrium with each other in every population. For 116 of the 117 SNPs, cumulative match probability (CMP) ranged from 2.01 × 10–48 to 1.93 × 10–50 and cumulative exclusion probability (CEP) ranged from 0.9999999996653 to 0.9999999999945. In 134 tested Han samples, 110 of the 117 SNPs remained within high MAF and conformed to Hardy-Weinberg equilibrium, with CMP = 4.70 × 10–47 and CEP = 0.999999999862. By analyzing the same number of autosomal SNPs as in the HID-Ion AmpliSeq Identity Panel, i.e. 90 randomized out of the 110 SNPs, our panel yielded preferable CMP and CEP. Taken together, the 110-SNPs panel is advantageous for forensic test, and this study provided plenty of highly informative SNPs for compiling final universal panels.

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Genome-wide screening for highly discriminative SNPs for personal identification and their assessment in world populations

Cited by 19 publications

References 41 publications

A SNP panel for identification of DNA and RNA specimens

A SNP panel for identification of DNA and RNA specimens

Delayed Endothelial Progenitor Cell Therapy Promotes Bone Defect Repair in a Clinically Relevant Rat Model

Genome-wide screen for universal individual identification SNPs based on the HapMap and 1000 Genomes databases

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