Technical note: Efficiency of total demineralization and ion‐exchange column for DNA extraction from bone

Seo, Seung Beom; Zhang, Aihua; Kim, Hye Yeon; Yi, Jin Wook; Lee, Hye Young; Shin, Dong Hoon; Lee, Soong Deok

doi:10.1002/ajpa.21193

Cited by 41 publications

(34 citation statements)

References 17 publications

(20 reference statements)

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“…Recent articles demonstrated that calcium ions inhibit Taq DNA polymerase (Opel et al, 2010) and demineralization improved DNA typing (Loreille et al, 2007;Seo et al, 2010). By increasing the digestion volume from 1.0 ml to 1.5 or 2.0 ml and using the Investigator kit Large Volume protocol, there was a resultant 60 and 38%, respectively, increase in DNA recovery over the buffer ATL 1 EDTA using the Trace protocol.…”

Section: Study 1: Selection Of Digestion Componentsmentioning

confidence: 99%

Technical note: Bone DNA extraction and purification using silica‐coated paramagnetic beads

Dukes¹,

Williams

Massey

et al. 2012

American J Phys Anthropol

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The goal of this study was to develop a simple method to improve DNA recovery from challenging bone samples. To this end, an optimized procedure was developed that combined the demineralization and DNA extraction into a single step, followed by DNA purification using an automated silica-coated paramagnetic bead procedure. This method replaced a previous silica-membrane-based procedure, which was able to recover sufficient DNA to obtain full autosomal and Y chromosome STR profiles from greater than 90% of the samples, including samples greater than 20 years old. The development process began with the evaluation of buffer and demineralization systems to determine the best reagent combination. During the developmental process, we observed that the addition of EDTA and DTT affected silica-based DNA purification methods by raising the pH of the digest buffer. The protocols with buffer ATL, PK, EDTA, and DTT followed by lowering the pH with sodium acetate just before purification resulted in the best yields. The method reduced the extraction volume from 10 to 1.5 ml and used commercially available reagents already being utilized in forensic DNA casework. Because of the simplicity and small volume needed for the procedure, many steps where contamination could be introduced have been eliminated or minimized. This study demonstrated a new method of recovering DNA from bone samples capable of extracting trace quantities of DNA, removing potential inhibitors, and minimizing the potential for exogenous DNA contamination.

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Section: Study 1: Selection Of Digestion Componentsmentioning

confidence: 99%

Technical note: Bone DNA extraction and purification using silica‐coated paramagnetic beads

Dukes¹,

Williams

Massey

et al. 2012

American J Phys Anthropol

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“…The bones had been kept underground for several decades and thereafter stored at room temperature until analysis followed by the cleaning procedure [11]. Conventional autosomal STR and Y-STR analysis using commercial kits along with mitochondrial DNA typing were performed but failed to generate full STR profiles for the bone DNA samples.…”

Section: Case Reportmentioning

confidence: 99%

“…DNA was extracted using the QuickGene DNA Whole Blood Kit S with the QuickGene-Mini80 instrument (Kurabo, Osaka, Japan). Bone DNA was isolated from the chopped fragment of two femur bones through a phenol/chloroform extraction method [11]. The DNA concentration was measured using NanoDrop™ 2000 Spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA).…”

Section: Case Reportmentioning

confidence: 99%

Kinship Testing Based on SNPs Using Microarray System

Cho¹,

Seo²,

Lee³

et al. 2016

Transfus Med Hemother

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Background: Kinship testing using biallelic SNP markers has been demonstrated to be a promising approach as a supplement to standard STR typing, and several systems, such as pyrosequencing and microarray, have been introduced and utilized in real forensic cases. The Affymetrix microarray containing 169 autosomal SNPs developed for forensic application was applied to our practical case for kinship analysis that had remained inconclusive due to partial STR profiles of degraded DNA and possibility of inbreeding within the population. Case Report: 169 autosomal SNPs were typed on array with severely degraded DNA of two bone samples, and the kinship compared to genotypes in a reference database of their putative family members. Results: Two bone samples remained unidentified through traditional STR typing with partial profiles of 10 or 14 of 16 alleles. Because these samples originated from a geographically isolated population, a cautious approach was required when analyzing and declaring true paternity only based on PI values. In a supplementary SNP typing, 106 and 78 SNPs were obtained, and the match candidates were found in each case with improved PI values than using only STRs and with no discrepant SNPs in comparison. Conclusion: Our case showed that the utility of multiple SNPs on array is expected in practical forensic caseworks with an establishment of reference database.

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“…Skeletal remains are able to preserve DNA for a long time . For that reason, they are often utilized for ancient archeological or anthropological DNA analysis or for identification of missing persons in, for example, mass disasters in forensic genetics . Mostly, short tandem repeats (STRs) are used for DNA typing.…”

mentioning

confidence: 99%

Forensic SNP Genotyping with SNaPshot: Development of a Novel In‐house SBE Multiplex SNP Assay,

Zar

Shahid

Shahzad

et al. 2018

Journal of Forensic Sciences

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This study introduces a newly developed in-house SNaPshot single-base extension (SBE) multiplex assay for forensic single nucleotide polymorphism (SNP) genotyping of fresh and degraded samples. The assay was validated with fresh blood samples from four different populations. In addition, altogether 24 samples from skeletal remains were analyzed with the multiplex. Full SNP profiles could be obtained from 14 specimens, while ten remains showed partial SNP profiles. Minor allele frequencies (MAF) of bone samples and different populations were compared and used for association of skeletal remains with a certain population. The results reveal that the SNPs of the bone samples are genetically close to the Pathan population. The findings show that the new multiplex system can be utilized for SNP genotyping of degraded and forensic relevant skeletal material, enabling to provide additional investigative leads in criminal cases.

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Technical note: Efficiency of total demineralization and ion‐exchange column for DNA extraction from bone

Cited by 41 publications

References 17 publications

Technical note: Bone DNA extraction and purification using silica‐coated paramagnetic beads

Technical note: Bone DNA extraction and purification using silica‐coated paramagnetic beads

Kinship Testing Based on SNPs Using Microarray System

Forensic SNP Genotyping with SNaPshot: Development of a Novel In‐house SBE Multiplex SNP Assay,

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