A technique for setting analytical thresholds in massively parallel sequencing-based forensic DNA analysis

Brian Young, Jonathan L. King, Bruce Budowle, Luigi Armogida

Research output: Contribution to journalArticleResearchpeer-review

7 Citations (Scopus)

Abstract

Amplicon (targeted) sequencing by massively parallel sequencing (PCR-MPS) is a potential method for use in forensic DNA analyses. In this application, PCR-MPS may supplement or replace other instrumental analysis methods such as capillary electrophoresis and Sanger sequencing for STR and mitochondrial DNA typing, respectively. PCR-MPS also may enable the expansion of forensic DNA analysis methods to include new marker systems such as single nucleotide polymorphisms (SNPs) and insertion/deletions (indels) that currently are assayable using various instrumental analysis methods including microarray and quantitative PCR. Acceptance of PCR-MPS as a forensic method will depend in part upon developing protocols and criteria that define the limitations of a method, including a defensible analytical threshold or method detection limit. This paper describes an approach to establish objective analytical thresholds suitable for multiplexed PCR-MPS methods. A definition is proposed for PCR-MPS method background noise, and an analytical threshold based on background noise is described.

Original languageEnglish
Article numbere0178005
JournalPLoS ONE
Volume12
Issue number5
DOIs
StatePublished - 1 May 2017

Fingerprint

High-Throughput Nucleotide Sequencing
analytical methods
Capillary electrophoresis
DNA
Microarrays
Polymorphism
Mitochondrial DNA
Polymerase Chain Reaction
Nucleotides
methodology
Noise
forensic sciences
high-throughput nucleotide sequencing
DNA Fingerprinting
capillary electrophoresis
Capillary Electrophoresis
DNA fingerprinting
single nucleotide polymorphism
Single Nucleotide Polymorphism
Limit of Detection

Cite this

@article{f2385164c4bb4f68a5ffdeebf672cca7,
title = "A technique for setting analytical thresholds in massively parallel sequencing-based forensic DNA analysis",
abstract = "Amplicon (targeted) sequencing by massively parallel sequencing (PCR-MPS) is a potential method for use in forensic DNA analyses. In this application, PCR-MPS may supplement or replace other instrumental analysis methods such as capillary electrophoresis and Sanger sequencing for STR and mitochondrial DNA typing, respectively. PCR-MPS also may enable the expansion of forensic DNA analysis methods to include new marker systems such as single nucleotide polymorphisms (SNPs) and insertion/deletions (indels) that currently are assayable using various instrumental analysis methods including microarray and quantitative PCR. Acceptance of PCR-MPS as a forensic method will depend in part upon developing protocols and criteria that define the limitations of a method, including a defensible analytical threshold or method detection limit. This paper describes an approach to establish objective analytical thresholds suitable for multiplexed PCR-MPS methods. A definition is proposed for PCR-MPS method background noise, and an analytical threshold based on background noise is described.",
author = "Brian Young and King, {Jonathan L.} and Bruce Budowle and Luigi Armogida",
year = "2017",
month = "5",
day = "1",
doi = "10.1371/journal.pone.0178005",
language = "English",
volume = "12",
journal = "PLoS ONE",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "5",

}

A technique for setting analytical thresholds in massively parallel sequencing-based forensic DNA analysis. / Young, Brian; King, Jonathan L.; Budowle, Bruce; Armogida, Luigi.

In: PLoS ONE, Vol. 12, No. 5, e0178005, 01.05.2017.

Research output: Contribution to journalArticleResearchpeer-review

TY - JOUR

T1 - A technique for setting analytical thresholds in massively parallel sequencing-based forensic DNA analysis

AU - Young, Brian

AU - King, Jonathan L.

AU - Budowle, Bruce

AU - Armogida, Luigi

PY - 2017/5/1

Y1 - 2017/5/1

N2 - Amplicon (targeted) sequencing by massively parallel sequencing (PCR-MPS) is a potential method for use in forensic DNA analyses. In this application, PCR-MPS may supplement or replace other instrumental analysis methods such as capillary electrophoresis and Sanger sequencing for STR and mitochondrial DNA typing, respectively. PCR-MPS also may enable the expansion of forensic DNA analysis methods to include new marker systems such as single nucleotide polymorphisms (SNPs) and insertion/deletions (indels) that currently are assayable using various instrumental analysis methods including microarray and quantitative PCR. Acceptance of PCR-MPS as a forensic method will depend in part upon developing protocols and criteria that define the limitations of a method, including a defensible analytical threshold or method detection limit. This paper describes an approach to establish objective analytical thresholds suitable for multiplexed PCR-MPS methods. A definition is proposed for PCR-MPS method background noise, and an analytical threshold based on background noise is described.

AB - Amplicon (targeted) sequencing by massively parallel sequencing (PCR-MPS) is a potential method for use in forensic DNA analyses. In this application, PCR-MPS may supplement or replace other instrumental analysis methods such as capillary electrophoresis and Sanger sequencing for STR and mitochondrial DNA typing, respectively. PCR-MPS also may enable the expansion of forensic DNA analysis methods to include new marker systems such as single nucleotide polymorphisms (SNPs) and insertion/deletions (indels) that currently are assayable using various instrumental analysis methods including microarray and quantitative PCR. Acceptance of PCR-MPS as a forensic method will depend in part upon developing protocols and criteria that define the limitations of a method, including a defensible analytical threshold or method detection limit. This paper describes an approach to establish objective analytical thresholds suitable for multiplexed PCR-MPS methods. A definition is proposed for PCR-MPS method background noise, and an analytical threshold based on background noise is described.

UR - http://www.scopus.com/inward/record.url?scp=85019393247&partnerID=8YFLogxK

U2 - 10.1371/journal.pone.0178005

DO - 10.1371/journal.pone.0178005

M3 - Article

VL - 12

JO - PLoS ONE

JF - PLoS ONE

SN - 1932-6203

IS - 5

M1 - e0178005

ER -