title: Highly effective DNA extraction method for nuclear short tandem repeat testing of skeletal remains from mass graves.
abstract: OBJECTIVE
  To quantitatively compare a silica extraction method with a commonly used phenol/chloroform extraction method for DNA analysis of specimens exhumed from mass graves.
  
  
  METHODS
  DNA was extracted from twenty randomly chosen femur samples, using the International Commission on Missing Persons (ICMP) silica method, based on Qiagen Blood Maxi Kit, and compared with the DNA extracted by the standard phenol/chloroform-based method. The efficacy of extraction methods was compared by real time polymerase chain reaction (PCR) to measure DNA quantity and the presence of inhibitors and by amplification with the PowerPlex 16 (PP16) multiplex nuclear short tandem repeat (STR) kit.
  
  
  RESULTS
  DNA quantification results showed that the silica-based method extracted on average 1.94 ng of DNA per gram of bone (range 0.25-9.58 ng/g), compared with only 0.68 ng/g by the organic method extracted (range 0.0016-4.4880 ng/g). Inhibition tests showed that there were on average significantly lower levels of PCR inhibitors in DNA isolated by the organic method. When amplified with PP16, all samples extracted by silica-based method produced 16 full loci profiles, while only 75% of the DNA extracts obtained by organic technique amplified 16 loci profiles.
  
  
  CONCLUSIONS
  The silica-based extraction method showed better results in nuclear STR typing from degraded bone samples than a commonly used phenol/chloroform method.
authors: International Commission on Missing Persons, Sarajevo, Bosnia and Herzegovina.
authors: Jon
authors: J
authors: Davoren
authors: Daniel
authors: D
authors: Vanek
authors: Rijad
authors: R
authors: Konjhodzić
authors: John
authors: J
authors: Crews
authors: Edwin
authors: E
authors: Huffine
authors: Thomas J
authors: TJ
authors: Parsons
mesh_terms: D001842:Bone and Bones / Q000737:chemistry*; D004247:DNA / Q000302:isolation & purification*; D018732:Forensic Anthropology / Q000379:methods*; D006801:Humans; D018895:Microsatellite Repeats
chemical_list: D004247:DNA
references: Croat Med J. 2005 Aug;46(4):540-8
references: 16100756
references: Croat Med J. 2001 Jun;42(3):271-5
references: 11387637
references: Biotechniques. 1995 Apr;18(4):670-7
references: 7598902
references: Electrophoresis. 1999 Jun;20(8):1712-6
references: 10435436
references: Croat Med J. 2001 Jun;42(3):260-6
references: 11387635
references: Proc Natl Acad Sci U S A. 2005 Sep 27;102(39):13783-8
references: 16162675
references: Methods Mol Biol. 2005;297:13-30
references: 15570097
references: Croat Med J. 2003 Jun;44(3):264-72
references: 12808717
references: Forensic Sci Int Genet. 2007 Jun;1(2):175-9
references: 19083751
references: Genet Anal. 1997 Jul;14(2):41-4
references: 9349938
references: Forensic Sci Int. 1995 Nov 30;76(1):7-15
references: 8591839
references: Croat Med J. 2007 Aug;48(4):486-93
references: 17696303
references: Forensic Sci Rev. 2004 Jan;16(1):63-90
references: 26256813
references: Biotechniques. 2007 Mar;42(3):343-52
references: 17390541
references: Forensic Sci Int Genet. 2007 Jun;1(2):191-5
references: 19083754
references: Science. 2005 Nov 18;310(5751):1122-3
references: 16293742
references: Nucleic Acids Res. 1993 Aug 11;21(16):3913-4
references: 8396242
references: Forensic Sci Int. 2001 Dec 1;123(2-3):215-23
references: 11728750
references: Croat Med J. 2003 Jun;44(3):259-63
references: 12808716