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Research article| Volume 1, ISSUE 1, P105-106, August 2008

Population data for MiniNC01 in a population sample from North-eastern Italy and their use in neoplastic tissues fixed in formalin and embedded in paraffin

DOI:https://doi.org/10.1016/j.fsigss.2007.10.088
Population data for MiniNC01 in a population sample from North-eastern Italy and their use in neoplastic tissues fixed in formalin and embedded in paraffin
Previous ArticlePrinciples of STR multiplex amplification
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      Abstract

      To establish a database for the three MiniNC01 loci D10S1248, D14S1434, D22S1045 in a population sample from North-eastern Italy, 102 unrelated individuals were typed. DNA was amplified in a multiplex reaction with subsequent automatic detection using capillary electrophoresis. The obtained data give a contribution to the definition of Italian population miniSTRs allele frequencies for the three analysed loci. These three MiniSTRs were tested on 21 neoplastic tissues and the obtained genotypes were compared to those obtained from normal tissue. Only 3 cases (14.28%) gave a different genotype suggesting a better performance of these markers than traditional STRs.

      Keywords

      1. Introduction

      A number of studies demonstrated that successful analysis of degraded DNA specimens from mass disaster or forensic evidence improves with smaller sized PCR products (MiniSTRs) [
      • Coble M.D.
      • Butler J.M.
      Characterization of new miniSTR loci to aid analysis of degraded DNA.
      J. Forensic Sci. 2005; : 43-53
      ].
      Because of the few population data regarding MiniNC01 loci in Italy, 102 unrelated individuals from North-eastern Italy were typed for the three MiniNC01 loci D10S1248, D14S1434 and D22S1045. To verify the value of these markers in neoplastic tissues, they were tested on different neoplastic specimens fixed in formalin and embedded in paraffin (8 breast cancer, 7 gastric cancer, 6 primary colorectal cancer and their metastasis) that sometimes are used for forensic purposes. For each case the genetic profile obtained from the neoplastic specimen was compared to that obtained from normal tissue.

      2. Materials and methods

      Genomic DNA was extracted using the Chelex-100 procedure from whole blood, buccal swabs or from neoplastic tissue and their normal counterpart. PCR was performed in a GeneAmp PCR System 2400 (PE) using the protocol suggested by Coble (www.cstl.nist.gov./biotech/strbase/miniSTR). The amplification products were loaded on the ABI Prism 310 Genetic Analyser and analysed by GeneMapperID V3.2.

      3. Results and discussion

      This work provides a picture of allele frequencies for three mini-STRs loci in a population sample from North-eastern Italy (Table 1). As expected the distribution of the allele frequency in our population sample is close to that found in the Caucasian population; no microvariants previously described were found [
      • Coble M.D.
      • Butler J.M.
      Characterization of new miniSTR loci to aid analysis of degraded DNA.
      J. Forensic Sci. 2005; : 43-53
      ,
      • Martin P.
      • Garcia O.
      • Albarran C.
      • Garcia P.
      • Yurrebaso I.
      • Alonso A.
      Allele frequencies of six miniSTR loci (D10S1248, D14S1434, D22S1045, D4S2364, D2S441 and D1S1677) in a Spanish population.
      Forensic Sci. Int. 2007; : 252-254
      ].
      Table 1Allele frequencies and statistical evaluation
      AlleleD10S1248D14S1434D22S1045
      90.1225
      100.0049
      110.00490.0147
      120.00980.0441
      130.02450.3873
      140.25980.21570.2941
      150.32840.07350.1275
      160.20590.04900.0049
      170.13730.3088
      180.02450.2941
      190.00490.0392
      200.0049
      210.0147
      N102102102
      Observed H0.78430.77450.7451
      Expected H0.7620 ± 0.04210.7620 ± 0.04210.7300 ± 0.0440
      PE0.57030.55270.5014
      PD0.89980.89720.8791
      PI2.31812.21741.9615
      PIC0.72380.72420.6877
      H: Rate of heterozygosity, PE: power of exclusion, PD: power of discrimination, PI: paternity index, PIC: polymorphic information content.
      Neoplastic tissues show a great variety of genetic alterations, such as allelic deletions (loss of heterozygosity LOH), allelic insertions (microsatellite instability, MSI) or chromosomal instability [
      • Lengauer C.
      • Kinzler K.W.
      • Vogelstein B.
      Genetic instability in human cancers.
      Nature. 1998; : 643-649
      ]. In this study the typing of the neoplastic tissues was found incorrect in 3 cases on 21 (14.28%), 2 of which regarding colon tumors and 1 regarding a gastric cancer; no differences were found in breast cancer cases (Table 2). Locus D14S1434 has been the most prone to alterations (2 cases on 21, 9.52%) while D10S1248 gave no differences. Although STRs alterations in neoplastic tissues seem to be higher then those found in this study (Vauhkonen et al. reported a rate of 68% [
      • Vauhkonen H.
      • Hedman M.
      • Vauhkonen M.
      • Katja M.
      • Sipponen P.
      • Sajantila A.
      Evaluation of gastrointestinal cancer tissues as a source of genetic information for forensic investigations by using STRs.
      Forensic Sci. Int. 2004; : 159-167
      ]; Ceccardi et al. reported a rate of 54.4% [
      • Ceccardi S.
      • Alù M.
      • Lugaresi F.
      • Ferri G.
      • Bini C.
      • Balbi T.
      • Ingravallo F.
      • Pelotti S.
      Evaluation of reliability of STR typing in different types of cancerous tissues used for identification purpose.
      in: Progress in Forensic Genetics. vol. 11. Elsevier, 2006: 672-675
      ]) tumor tissues should only be used in forensics with great care, since any exclusion in identification or paternity testing may be due to alteration events in the tumor.
      Table 2Genotypes observed in neoplastic tissues regarding 21 individuals (In bold the observed alterations)
      TissueD10S1248D14S1434D22S1045
      Gastric 1N11–1414–1510–13
      Gastric 1P11–1414–1410–13
      Gastric 2N15–1712–1414–14
      Gastric 2P15–1712–1414–14
      Gastric 3N14–1514–1711–15
      Gastric 3P14–1514–1711–15
      Gastric 4N15–1518–1813–14
      Gastric 4P15–1518–1813–14
      Gastric 5N15–1518–1813–13
      Gastric 5P15–1518–1813–13
      Gastric 6N13–1616–1713–13
      Gastric 6P13–1616–1713–13
      Gastric 7N16–1617–1813–14
      Gastric 7P16–1617–1813–14
      Colon 8N15–1615–179–13
      Colon 8P15–1615–179–13
      Colon 8met15–1615–179–13
      Colon 9N14–1617–1813–14
      Colon 9P14–1617–1813–14
      Colon 9met14–1617–1813–13
      Colon 10N14–1414–1414–15
      Colon 10P14–1414–1414–15
      Colon 10met14–1414–1414–15
      Colon 11N16–1714–1714–14
      Colon 11P16–1714–1714–14
      Colon 11met16–1714–1714–14
      Colon 12N15–1715–1812–13
      Colon 12P15–1715–1512–13
      Colon 12met15–1715–1512–13
      Colon 13N13–1514–1414–15
      Colon 13P13–1514–1414–15
      Colon 13met13–1514–1414–15
      Breast 14N14–1814–1712–14
      Breast 14P14–1814–1712–14
      Breast 15N15–1714–1613–15
      Breast 15P15–1714–1613–15
      Breast 16N15–1517–1812–12
      Breast 16P15–1517–1812–12
      Breast 17N14–1616–1814–14
      Breast 17P14–1616–1814–14
      Breast 18N15–1617–1813–14
      Breast 18P15–1617–1813–14
      Breast 19N14–1515–1713–14
      Breast 19P14–1515–1713–14
      Breast 20N14–1416–1713–14
      Breast 20P14–1416–1713–14
      Breast 21N15–1517–189–14
      Breast 21P15–1517–189–14
      N: Normal tissue; P: pathological tissue, met: metastasis.

      Conflict of interest

      None

      References

        • Coble M.D.
        • Butler J.M.
        Characterization of new miniSTR loci to aid analysis of degraded DNA.
        J. Forensic Sci. 2005; : 43-53
        View in Article
        • Martin P.
        • Garcia O.
        • Albarran C.
        • Garcia P.
        • Yurrebaso I.
        • Alonso A.
        Allele frequencies of six miniSTR loci (D10S1248, D14S1434, D22S1045, D4S2364, D2S441 and D1S1677) in a Spanish population.
        Forensic Sci. Int. 2007; : 252-254
        View in Article
        • Lengauer C.
        • Kinzler K.W.
        • Vogelstein B.
        Genetic instability in human cancers.
        Nature. 1998; : 643-649
        View in Article
        • Vauhkonen H.
        • Hedman M.
        • Vauhkonen M.
        • Katja M.
        • Sipponen P.
        • Sajantila A.
        Evaluation of gastrointestinal cancer tissues as a source of genetic information for forensic investigations by using STRs.
        Forensic Sci. Int. 2004; : 159-167
        View in Article
        • Ceccardi S.
        • Alù M.
        • Lugaresi F.
        • Ferri G.
        • Bini C.
        • Balbi T.
        • Ingravallo F.
        • Pelotti S.
        Evaluation of reliability of STR typing in different types of cancerous tissues used for identification purpose.
        in: Progress in Forensic Genetics. vol. 11. Elsevier, 2006: 672-675
        View in Article

      Article info

      Publication history

      Accepted: October 9, 2007
      Received: August 20, 2007

      Identification

      DOI: https://doi.org/10.1016/j.fsigss.2007.10.088

      Copyright

      © 2008 Elsevier Ireland Ltd. Published by Elsevier Inc. All rights reserved.

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