Improvement of short tandem repeat analysis of samples highly contaminated by humic acid

Seung Bum Seo; Hong Xuan Jin; Hye Young Lee; Jianye Ge; Jonathan L. King; Sung Hee Lyoo; Dong Hoon Shin; Soong Deok Lee

doi:10.1016/j.jflm.2013.08.001

Improvement of short tandem repeat analysis of samples highly contaminated by humic acid

Seung Bum Seo, Hong Xuan Jin, Hye Young Lee, Jianye Ge, Jonathan L. King, Sung Hee Lyoo, Dong Hoon Shin, Soong Deok Lee

Research output: Contribution to journal › Article › peer-review

10 Scopus citations

Abstract

We investigated several methods for obtaining successful short tandem repeat (STR) results from high-humic acid (HA)-content samples. DNA purification efficiency was tested for QIAquick® PCR Purification, QIAamp® DNA Investigator and Prepfiler™ Forensic DNA Extraction kits. HA-removal capacity of Inhibitor Remover and InhibitEX® Tablet was tested. Experiments on overcoming HA effects on STR amplification were conducted using an AmpliTaq Gold® DNA Polymerase and a TaKaRa Ex Taq™ Hot Start Version (Ex Taq HS) with BSA addition. QIAquick kit was most efficient in HA removal and Ex Taq HS showed high resistance to HA. Increasing the amounts of Taq polymerases and BSA addition were shown to be efficient in overcoming PCR inhibition, but BSA addition was superior to the former method. Inhibitor Remover and InhibitEX® Tablet did not positively affect the STR results. This study will help achieve better STR results with high-HA-content samples.

Original language	English
Pages (from-to)	922-928
Number of pages	7
Journal	Journal of Forensic and Legal Medicine
Volume	20
Issue number	7
DOIs	https://doi.org/10.1016/j.jflm.2013.08.001
State	Published - 2013

Keywords

DNA recovery
Forensic DNA typing
Humic acid
Inhibitor
Short tandem repeat

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10.1016/j.jflm.2013.08.001

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title = "Improvement of short tandem repeat analysis of samples highly contaminated by humic acid",

abstract = "We investigated several methods for obtaining successful short tandem repeat (STR) results from high-humic acid (HA)-content samples. DNA purification efficiency was tested for QIAquick{\textregistered} PCR Purification, QIAamp{\textregistered} DNA Investigator and Prepfiler{\texttrademark} Forensic DNA Extraction kits. HA-removal capacity of Inhibitor Remover and InhibitEX{\textregistered} Tablet was tested. Experiments on overcoming HA effects on STR amplification were conducted using an AmpliTaq Gold{\textregistered} DNA Polymerase and a TaKaRa Ex Taq{\texttrademark} Hot Start Version (Ex Taq HS) with BSA addition. QIAquick kit was most efficient in HA removal and Ex Taq HS showed high resistance to HA. Increasing the amounts of Taq polymerases and BSA addition were shown to be efficient in overcoming PCR inhibition, but BSA addition was superior to the former method. Inhibitor Remover and InhibitEX{\textregistered} Tablet did not positively affect the STR results. This study will help achieve better STR results with high-HA-content samples.",

keywords = "DNA recovery, Forensic DNA typing, Humic acid, Inhibitor, Short tandem repeat",

author = "Seo, {Seung Bum} and Jin, {Hong Xuan} and Lee, {Hye Young} and Jianye Ge and King, {Jonathan L.} and Lyoo, {Sung Hee} and Shin, {Dong Hoon} and Lee, {Soong Deok}",

note = "Funding Information: This research was supported by the Bio & Medical Technology Development Program of the National Research Foundation (NRF) funded by the Korean Government (MEST) (No. 2011-0027729 ). Copyright: Copyright 2013 Elsevier B.V., All rights reserved.",

year = "2013",

doi = "10.1016/j.jflm.2013.08.001",

language = "English",

volume = "20",

pages = "922--928",

journal = "Journal of Forensic and Legal Medicine",

issn = "1752-928X",

publisher = "Churchill Livingstone",

number = "7",

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AU - Seo, Seung Bum

AU - Jin, Hong Xuan

AU - Lee, Hye Young

AU - Ge, Jianye

AU - King, Jonathan L.

AU - Lyoo, Sung Hee

AU - Shin, Dong Hoon

AU - Lee, Soong Deok

N1 - Funding Information: This research was supported by the Bio & Medical Technology Development Program of the National Research Foundation (NRF) funded by the Korean Government (MEST) (No. 2011-0027729 ). Copyright: Copyright 2013 Elsevier B.V., All rights reserved.

PY - 2013

Y1 - 2013

N2 - We investigated several methods for obtaining successful short tandem repeat (STR) results from high-humic acid (HA)-content samples. DNA purification efficiency was tested for QIAquick® PCR Purification, QIAamp® DNA Investigator and Prepfiler™ Forensic DNA Extraction kits. HA-removal capacity of Inhibitor Remover and InhibitEX® Tablet was tested. Experiments on overcoming HA effects on STR amplification were conducted using an AmpliTaq Gold® DNA Polymerase and a TaKaRa Ex Taq™ Hot Start Version (Ex Taq HS) with BSA addition. QIAquick kit was most efficient in HA removal and Ex Taq HS showed high resistance to HA. Increasing the amounts of Taq polymerases and BSA addition were shown to be efficient in overcoming PCR inhibition, but BSA addition was superior to the former method. Inhibitor Remover and InhibitEX® Tablet did not positively affect the STR results. This study will help achieve better STR results with high-HA-content samples.

AB - We investigated several methods for obtaining successful short tandem repeat (STR) results from high-humic acid (HA)-content samples. DNA purification efficiency was tested for QIAquick® PCR Purification, QIAamp® DNA Investigator and Prepfiler™ Forensic DNA Extraction kits. HA-removal capacity of Inhibitor Remover and InhibitEX® Tablet was tested. Experiments on overcoming HA effects on STR amplification were conducted using an AmpliTaq Gold® DNA Polymerase and a TaKaRa Ex Taq™ Hot Start Version (Ex Taq HS) with BSA addition. QIAquick kit was most efficient in HA removal and Ex Taq HS showed high resistance to HA. Increasing the amounts of Taq polymerases and BSA addition were shown to be efficient in overcoming PCR inhibition, but BSA addition was superior to the former method. Inhibitor Remover and InhibitEX® Tablet did not positively affect the STR results. This study will help achieve better STR results with high-HA-content samples.

KW - DNA recovery

KW - Forensic DNA typing

KW - Humic acid

KW - Inhibitor

KW - Short tandem repeat

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AN - SCOPUS:84883360783

SN - 1752-928X

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EP - 928

JO - Journal of Forensic and Legal Medicine

JF - Journal of Forensic and Legal Medicine

IS - 7

ER -

Improvement of short tandem repeat analysis of samples highly contaminated by humic acid

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