Forensic Science International Genetics Supplement Series

Publications in this journal

• Article: Synovial fluid: An alternative source for forensic DNA

  Kornkiat Vongpaisarnsin
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  ABSTRACT: In human remains that have undergone decomposition, blood and other biological tissues are recognized as sources for forensic DNA identification, yet the success rate is influenced by the extent of decomposition to the subcellular structures and nucleic acids. Thus, synovial fluid may be considered as an alternative source for forensic DNA recovery, as compared to other decomposed tissues. In this study, 24 samples (12 synovial, 8 blood, and 4 muscle tissue samples) were obtained from 12 decomposed bodies. Our results show that synovial fluid is a suitable source for forensic DNA recovery compared to decomposed blood or muscle tissue. In addition, no mixture or contamination of DNA was detected in synovial sources. Further study is required to determine whether an additional pre-treatment of the synovial sample with hydrolysis can potentially recover more DNA.
  Forensic Science International Genetics Supplement Series 12/2011; 3(1):e323-e324.
• Article: Reliable nuclear and mitochondrial DNA quantification for low copy number and degraded forensic samples

  Fregel R, Almeida M, Betancor E, Suarez NM, Pestano J
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  ABSTRACT: DNA quantification is a prerequisite for both low copy number (LCN) forensic analysis and ancient DNA (aDNA) studies. Moreover, if nuclear quantification is focused on the amelogenin locus, it also allows sex determination. Some of the problems of these techniques are allelic drop-out phenomenon in amelogenin locus and mitochondrial DNA (mtDNA) quantification biases, due to human intraspecific variation affecting the annealing of primers and/or probes. The method presented here combines two multiplex TaqMan® real-time PCR (qPCR) for nuclear and mtDNA quantification in degraded or limited samples. Nuclear DNA detection is based on the independent amplification of X and Y chromosome specific fragments in the amelogenin locus and an internal PCR control (IPC) to recognize inhibition problems. The small length of the fragments (71 bp) favors the quantification of severely degraded DNA, whereas the use of two distinct primer sets for X and Y chromosome amplification is directed to reduce allelic drop-out in LCN analysis. MtDNA quantification is based on the amplification of three PCR fragments located in the mtDNA 16S region. Two of them are amplified with human specific conservative primers and probes, which allows a world-wide application of this technique. Moreover, their length difference (167 and 314 bp respectively), provides information about the DNA degradation level. In order to also recognize non-human DNA an interspecific mtDNA fragment (187 bp) was also designed.
  Forensic Science International Genetics Supplement Series 11/2011; 3(1):e303-304.
• Article: A new algorithm for mtDNA sequence clustering

  Inês Soares, António Amorim, Ana Goios
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  ABSTRACT: We here present a new strategy for mtDNA sequence clustering based on protein coding region analysis and using a new algorithm for a fast calculation of similarities between sequences. The resulting phylogenetic tree showed a good clustering of major haplogroups according to canonical classifications. We propose the use of this method for a first assignment of sequences into major haplogroups, thus avoiding the first step of going through a phylogenetic tree and/or as a quality control for sequences classified manually.
  Forensic Science International Genetics Supplement Series 10/2011; 3(1):e315-e316.
• Article: Efficient DNA extraction from hair shafts

  Almeida M, Betancor E, Fregel R, Suárez NM, Pestano J
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  ABSTRACT: Hairs are common biological samples in crime scene investigation. However, most of this evidence is comprised of hair fragments without the root. As the major part of DNA is located in the root, hair shafts are usually problematic samples in forensic analysis. For these reasons, hair DNA typing is directed at mitochondrial DNA (mtDNA), which is present in high copy number in each cell, instead of nuclear DNA analysis. In our laboratory, we have used the PrepFiler BTA™ extraction method for routinely processing difficult samples such as old bones or cigarette butts, obtaining good quality DNA in all cases. As the use of automatic extraction methods has been progressively introduced in forensic laboratories, we have tested the applicability of the PrepFiler BTA™ extraction method in combination with AutoMate Express™ equipment, to the analysis of hair shafts. In order to determine the efficiency of the method, DNA extractions were quantified using a real-time PCR approach, and mtDNA fragments of different lengths were amplified to determine DNA degradation. We also processed several types of hairs, with different characteristics (thickness, gender, antiquity and hair dyeing) and from diverse ethnical groups. In all cases, the PrepFiler BTA Express™ extraction method showed very reproducible results in obtaining DNA from hair shafts, its application being highly recommendable as a routine protocol in forensic laboratories.
  Forensic Science International Genetics Supplement Series 10/2011; 3(1):e319-e320.
• Article: DNA typing for the identification of eight victims of Spanish Civil War reprisals in the Canary Islands: The case of "the Fuencaliente thirteen" mass graves (Fuencaliente, La Palma)

  Betancor E, Fregel R, Almeida M, Suarez NM, Pestano J
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  ABSTRACT: During the Spanish Civil War (1936–1939), the Canary Islands suffered one of the highest levels of repression by the insurgent side, even though there were no battles in the islands. More than 50 people were killed in the island of La Palma between July 1936 and June 1937. The Association for the Recovery of Historical Memory in La Palma, made up of relatives of people who went missing during the Civil War, located the Fuencaliente mass graves in 2004. The excavation process recovered eight skeletal remains. The aim of this work was the genetic identification of these reprisal victims. In general, obtaining nuclear DNA profiles from old skeletal samples is known to be difficult. Due to the age and conservation conditions, this was the case for the Fuencaliente remains. For these reasons, we firstly attempted to analyze the mitochondrial DNA (mtDNA). Although mtDNA control region sequences were obtained for the eight skeletal remains, the limited number of possible maternal relative donors complicated identification based only on mtDNA. Taking into account the problems in establishing identity by using mtDNA, a few years later we were presented with the possibility of analyzing nuclear DNA using the new PrepFiler Express BTA™ Forensic DNA extraction methodology. This extraction protocol, in combination with the new AmpFℓSTR® NGM™ PCR Amplification Kit (Applied Biosystems), allowed us to obtain full nuclear DNA profiles for the eight victims. In conclusion, the use of specific protocols designed for old DNA samples, such as PrepFiler Express BTA™ Forensic DNA extraction and AmpFℓSTR® NGM™ PCR amplification kit seems to be crucial for obtaining full nuclear profiles that allow statistically significant identification of the putative relatives.
  Forensic Science International Genetics Supplement Series 10/2011; 3(1):e301-e302.
• Article: Complete automated DNA procedure to facilitate DNA database collection

  F. Jaffredo, F. Freund, S. Godichaud, M. Gaboyard, J.P. Moisan
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  ABSTRACT: To address the requirements of DNA database workflow, a complete automated procedure is necessary. Analysis by direct PCR on FTA punches is possible. However, since DNA quantity is highly variable from one sample to another, genotyping STR profiling leads to a very high rate of invalidated genetic profiles (20–25%). In order to be in the best amplification conditions, it is important to isolate good quality DNA in a normalized concentration. To meet this requirement in one step, we used Smart D-N-Adem-kit for profiling (ADEMTECH) containing calibrated magnetic nanoparticles suitable with a fast and completely automated procedure, from DNA extraction to injection plate setup. The DNA extraction and normalization procedure was successfully validated on 2047 FTA cards, leading to 95.5% success rate with av. PHR of 86.5%. DNA quantification is no longer necessary prior to STR typing. Similar results have been shown with buccal sample swabs.
  Forensic Science International Genetics Supplement Series 08/2011; 3:228-229.
• Article: Forensic performance of insertion–deletion marker systems

  Manuel Fondevila, Rui Pereira, Leonor Gusmão, Christopher Phillips, Maria Victoria Lareu, Angel Carracedo, John M. Butler, Peter M. Vallone
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  ABSTRACT: The ability to improve amplification and analysis of degraded DNA extracts has been a long-standing area of research in forensic genetics. One of the latest approaches is the single multiplex typing of insertion–deletions (InDels), short biallelic length polymorphisms. InDels share most of the properties of single nucleotide polymorphisms (SNPs) that makes them ideal markers for forensic analysis of degraded DNA. The short amplicon size ranges, high multiplexing capability, and low mutation rate make them an attractive complement to mini-STRs. In addition, as length polymorphism markers, InDels can be analyzed with the same simple end-labeled PCR primer methods as STRs, thus avoiding the multi-step protocols required of SNP typing single base extension assays, as well as providing a more direct relationship between input DNA and peak height ratios. InDel genotyping should be considered a serious candidate for incorporation into the forensic marker battery. In order to assess the utility of such assays to the forensic community we have conducted a thorough analysis of a set of U.S. population samples with a commercial Indel assay, a 30 marker multiplex ‘DIPplex’ produced by Qiagen.
  Forensic Science International Genetics Supplement Series 01/2011; 3(1):e443-e444.
• Article: Contamination monitoring in the forensic DNA laboratory and a simple graphical model for unbiased EPG classification

  Digréus P, Andersson A-C, Nilsson J, Dufva C, Nordgaard A, Ansell R
  Forensic Science International Genetics Supplement Series 01/2011; 3:e299-e300.
• Article: Discrepancies between forensic DNA databases

  Hedell R, Nordgaard A, Ansell R
  Forensic Science International Genetics Supplement Series 01/2011; 3:e135-e136.