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A new strategy to confirm the identity of tumour tissues using single-nucleotide polymorphisms and next-generation sequencing

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Abstract

With growing cancer morbidity, forensics cases in which archived tumour tissues can be used as biological samples are increasing, and an effective method to identify the body source of tumour tissues is needed. Single nucleotide polymorphisms (SNPs) may be a promising biomarker to identify the source of tumour tissues because of their low mutation rate and small amplicon size. Next-generation sequencing techniques offers the ability to detect hundreds of SNPs in a single run. The Precision ID Identity Panel (Thermo Fisher Scientific, Waltham, MA, USA) detects 90 autosomal SNPs for individual identification and 34 lineage-informative SNPs on Y chromosome using the Ion PGM system (Thermo Fisher Scientific). In this study, we evaluated performance of the panel for individual identification of tumour tissues. One hundred and fifty pairs of tumour tissues and corresponding normal tissues were analysed. Loss of heterozygosity was detected only in tumour tissues. The identity-by-state (IBS) scoring system was adopted to identify the body source of tumour tissues. The IBS score, as well as the number of loci with 2 alleles (A2), 1 allele (A1) and 0 alleles (A0) shared, were analysed within each tumour-normal pair, unrelated individual pairs, parent–offspring pairs and full-sibling pairs. According to the probability distribution, threshold of A2 in the range of 69 to 89 could achieve accuracy > 99% in identifying the source of tumour tissues. Thus, we developed a new strategy (process and criteria) to identify the source of tumour tissues that could be used in practice.

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References

  1. Li C, Zhao S, Zhang S, Li L (2010) Source identification of gastric cancer tissue with discriminatory analysis. Fa Yi Xue Za Zhi 26:100–103

    PubMed  Google Scholar 

  2. Sun L, Li S, Fu G, Bai M, Dong C, Yang B, Chen P, Wang Z, Fu L, Cong B (2017) Mutation analysis of autosomal and X chromosomal STR in gynecologic and breast cancer. Chin J Forensic Med 32(350–353):358

    Google Scholar 

  3. Sun L, Li S, Fu G, Zhang X, Wang Z, Fu L, Cong B (2018) A study on mutations of autosomal, X and Y chromosomal STR in malignant tumor tissues. Chin J Forensic Med 33:471–475

    Google Scholar 

  4. Sun L, Shi K, Tan L, Zhang Q, Fu L, Zhang X, Fu G, Li S, Cong B (2017) Analysis of genetic polymorphisms and mutations at 19 STR loci in Hebei Han population. Forensic Sci Int Genet 31:e50–e51

    CAS  PubMed  Google Scholar 

  5. Liu Y, Li L, Li C, Zhao Z (2009) Allelic alterations of STRs in archival paraffin embedded tissue as DNA source for paternity testing. Forensic Sci Int Genet Suppl Ser 2:12–13

    Google Scholar 

  6. Hunt JL, Swalsky P, Sasatomi E, Niehouse L, Bakker A, Finkelstein SD (2003) A microdissection and molecular genotyping assay to confirm the identity of tissue floaters in paraffin-embedded tissue blocks. Arch Pathol Lab Med 127:213–217

    CAS  PubMed  Google Scholar 

  7. Reich DE, Schaffner SF, Daly MJ, McVean G, Mullikin JC, Higgins JM, Richter DJ, Lander ES, Altshuler D (2002) Human genome sequence variation and the influence of gene history, mutation and recombination. Nat Genet 32:135–142

    CAS  Google Scholar 

  8. Wang Q, Fu L, Zhang X, Dai X, Bai M, Fu G, Cong B, Li S (2016) Expansion of a SNaPshot assay to a 55-SNP multiplex: assay enhancements, validation, and power in forensic science. Electrophoresis 37:1310–1317

    CAS  PubMed  Google Scholar 

  9. Freire-Aradas A, Fondevila M, Kriegel AK, Phillips C, Gill P, Prieto L, Schneider PM, Carracedo A, Lareu MV (2012) A new SNP assay for identification of highly degraded human DNA. Forensic Sci Int Genet 6:341–349

    CAS  PubMed  Google Scholar 

  10. Einaga N, Yoshida A, Noda H, Suemitsu M, Nakayama Y, Sakurada A, Kawaji Y, Yamaguchi H, Sasaki Y, Tokino T, Esumi M (2017) Assessment of the quality of DNA from various formalin-fixed paraffin-embedded (FFPE) tissues and the use of this DNA for next-generation sequencing (NGS) with no artifactual mutation. PLoS One 12:e0176280

    PubMed  PubMed Central  Google Scholar 

  11. Guyard A, Boyez A, Pujals A, Robe C, Tran Van Nhieu J, Allory Y, Moroch J, Georges O, Fournet J-C, Zafrani E-S, Leroy K (2017) DNA degrades during storage in formalin-fixed and paraffin-embedded tissue blocks. Virchows Arch 471:491–500

    CAS  PubMed  Google Scholar 

  12. Watanabe M, Hashida S, Yamamoto H, Matsubara T, Ohtsuka T, Suzawa K, Maki Y, Soh J, Asano H, Tsukuda K, Toyooka S, Miyoshi S (2017) Estimation of age-related DNA degradation from formalin-fixed and paraffin-embedded tissue according to the extraction methods. Exp Ther Med 14:2683–2688

    CAS  PubMed  PubMed Central  Google Scholar 

  13. Miller JK, Buchner N, Timms L, Tam S, Luo X, Brown AM, Pasternack D, Bristow RG, Fraser M, Boutros PC, McPherson JD (2014) Use of Sequenom sample ID plus(R) SNP genotyping in identification of FFPE tumor samples. PLoS One 9:e88163

    PubMed  PubMed Central  Google Scholar 

  14. Huijsmans R, Damen J, van der Linden H, Hermans M (2007) Single nucleotide polymorphism profiling assay to confirm the identity of human tissues. J Mol Diagn 9:205–213

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Pontes ML, Amigo OM, Fondevila M, Porto MJ, Medeiros R (2015) Analysis of autosomal SNPs in paraffin-embedded tissue samples: two cases. J Forensic Invest 3:1–4

    Google Scholar 

  16. Chen X, Lu D, Zhang J, Song F, Luo H, Ren Z, Wei W, Hou Y (2015) Identification of the mislabeled breast cancer samples by mitochondrial DNA haplotyping. J Forensic Sci Med 1:133–139

    Google Scholar 

  17. Tully G, Sullivan KM, Nixon P, Stones RE, Gill P (1996) Rapid detection of mitochondrial sequence polymorphisms using multiplex solid-phase fluorescent minisequencing. Genomics 34:107–113

    CAS  PubMed  Google Scholar 

  18. Livak K (1999) Allelic discrimination using fluorogenic probes and the 5′ nuclease assay. Genet Anal 14:143–149

    CAS  PubMed  Google Scholar 

  19. Sapolsky RJ, Hsie L, Berno A, Ghandour G, Mittmann M, Fan JB (1999) High-throughput polymorphism screening and genotyping with high-density oligonucleotide arrays. Genet Anal 14:187–192

    CAS  PubMed  Google Scholar 

  20. Pakstis A, Speed W, Fang R, Hyland F, Furtado M, Kidd J, Kidd K (2010) SNPs for a universal individual identification panel. Hum Genet 127:315–324

    PubMed  Google Scholar 

  21. Sanchez J, Phillips C, Børsting C, Balogh K, Bogus M, Fondevila M, Harrison C, Musgrave-Brown E, Salas A, Syndercombe-Court D, Schneider P, Carracedo A, Morling N (2006) A multiplex assay with 52 single nucleotide polymorphisms for human identification. Electrophoresis 27:1713–1724

    CAS  PubMed  Google Scholar 

  22. Karafet TM, Mendez FL, Meilerman MB, Underhill PA, Zegura SL, Hammer MF (2008) New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree. Genome Res 18:830–838

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Guo F, Zhou Y, Song H, Zhao J, Shen H, Zhao B, Liu F, Jiang X (2016) Next generation sequencing of SNPs using the HID-ion AmpliSeq identity panel on the ion torrent PGM platform. Forensic Sci Int Genet 25:73–84

    CAS  PubMed  Google Scholar 

  24. Zhang S, Bian Y, Zhang Z, Zheng H, Wang Z, Zha L, Cai J, Gao Y, Ji C, Hou Y, Li C (2015) Parallel analysis of 124 universal SNPs for human identification by targeted semiconductor sequencing. Sci Rep 5:18683

    CAS  PubMed  PubMed Central  Google Scholar 

  25. Li R, Zhang C, Li H, Wu R, Li H, Tang Z, Zhen C, Ge J, Peng D, Wang Y, Chen H, Sun H (2018) SNP typing using the HID-ion AmpliSeq identity panel in a southern Chinese population. Int J Legal Med 132:997–1006

    PubMed  Google Scholar 

  26. Buchard A, Kampmann ML, Poulsen L, Borsting C, Morling N (2016) ISO 17025 validation of a next-generation sequencing assay for relationship testing. Electrophoresis 37:2822–2831

    CAS  PubMed  Google Scholar 

  27. Liu J, Wang Z, He G, Zhao X, Wang M, Luo T, Li C, Hou Y (2018) Massively parallel sequencing of 124 SNPs included in the precision ID identity panel in three east Asian minority ethnicities. Forensic Sci Int Genet 35:141–148

    CAS  PubMed  Google Scholar 

  28. Gettings KB, Kiesler KM, Vallone PM (2015) Performance of a next generation sequencing SNP assay on degraded DNA. Forensic Sci Int Genet 19:1–9

    CAS  PubMed  Google Scholar 

  29. Bruijns B, Tiggelaar R, Gardeniers H (2018) Massively parallel sequencing techniques for forensics: a review. Electrophoresis 39:2642–2654

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Xi KX, Wen YS, Zhu CM, Yu XY, Qin RQ, Zhang XW, Lin YB, Rong TH, Wang WD, Chen YQ, Zhang LJ (2017) Tumor–stroma ratio (TSR) in non-small cell lung cancer (NSCLC) patients after lung resection is a prognostic factor for survival. J Thorac Dis 9:4017–4026

    PubMed  PubMed Central  Google Scholar 

  31. Wang K, Ma W, Wang J, Yu L, Zhang X, Wang Z, Tan B, Wang N, Bai B, Yang S, Liu H, Zhu S, Cheng Y (2012) Tumor–stroma ratio is an independent predictor for survival in esophageal squamous cell carcinoma. J Thorac Oncol 7:1457–1461

    PubMed  Google Scholar 

  32. Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP (2011) Integrative genomics viewer. Nat Biotechnol 29:24–26

    CAS  PubMed  PubMed Central  Google Scholar 

  33. Thorvaldsdottir H, Robinson JT, Mesirov JP (2013) Integrative genomics viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform 14:178–192

    CAS  PubMed  Google Scholar 

  34. Presciuttini S, Toni C, Tempestini E, Verdiani S, Casarino L, Spinetti I, De Stefano F, Domenici R, Bailey-Wilson JE (2002) Inferring relationships between pairs of individuals from locus heterozygosities. BMC Genet 3:23

    PubMed  PubMed Central  Google Scholar 

  35. Excoffier L, Lischer HE (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10:564–567

    PubMed  Google Scholar 

  36. Holsinger KE, Weir BS (2009) Genetics in geographically structured populations: defining, estimating and interpreting F(ST). Nat Rev Genet 10:639–650

    CAS  PubMed  PubMed Central  Google Scholar 

  37. Danjoux M, Guimbaud R, Al Saati T, Meggetto F, Carrère N, Portier G, Delsol G, Selves J (2006) Contribution of microdissection for the detection of microsatellite instability in colorectal cancer. Hum Pathol 37:361–368

    CAS  PubMed  Google Scholar 

  38. Børsting C, Fordyce SL, Olofsson J, Mogensen HS, Morling N (2014) Evaluation of the Ion Torrent™ HID SNP 169-plex: a SNP typing assay developed for human identification by second generation sequencing. Forensic Sci Int Genet 12:144–154

    PubMed  Google Scholar 

  39. Eduardoff M, Santos C, de la Puente M, Gross TE, Fondevila M, Strobl C, Sobrino B, Ballard D, Schneider PM, Carracedo A, Lareu MV, Parson W, Phillips C (2015) Inter-laboratory evaluation of SNP-based forensic identification by massively parallel sequencing using the ion PGM. Forensic Sci Int Genet 17:110–121

    CAS  PubMed  Google Scholar 

  40. Daniel R, Santos C, Phillips C, Fondevila M, van Oorschot RAH, Carracedo Á, Lareu MV, McNevin D (2015) A SNaPshot of next generation sequencing for forensic SNP analysis. Forensic Sci Int Genet 14:50–60

    CAS  PubMed  Google Scholar 

  41. Zhao S, Zhang S, Zhang N, Sun K, Que T, Zhao Z, Li C (2013) A new strategy for body source identification of tumor sample. Forensic Sci Int Genet Suppl Ser 4:e346–e347

    Google Scholar 

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Acknowledgements

We thank the patients for participating in this study and the Affiliated Fourth Hospital of Hebei Medical University. We thank Louise Adam, ELS(D), from Liwen Bianji, Edanz Editing China (www.liwenbianji.cn/ac) for editing the English text of a draft of this manuscript.

Funding

The study was supported by the National Natural Science Foundation of China (No. 81001351); Natural Science Foundation of Hebei province (No. H2015206454); the Hebei Graduate Student Innovation Fund Programs; Scientific Research and Development Foundation of Hebei Medical University (079).

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Authors and Affiliations

  1. College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Shijiazhuang, China

    Lijuan Sun, Qi Liu, Shujin Li, Guanju Ma, Chunling Ma, Bin Cong & Lihong Fu

  2. Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Forensic Science Center of Jining Medical University, Jining, China

    Qi Liu

  3. Department of Pathology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China

    Zhandong Wang

  4. Department of Pathology, Xuzhou Cancer Hospital, Xuzhou, China

    Zhandong Wang

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  1. Lijuan Sun
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Correspondence to Bin Cong or Lihong Fu.

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Sun, L., Liu, Q., Li, S. et al. A new strategy to confirm the identity of tumour tissues using single-nucleotide polymorphisms and next-generation sequencing. Int J Legal Med 134, 399–409 (2020). https://doi.org/10.1007/s00414-019-02216-9

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  • DOI: https://doi.org/10.1007/s00414-019-02216-9

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