Development of a forensic identity SNP panel for Indonesia.

Augustinus, D; Gahan, ME; McNevin, D

Development of a forensic identity SNP panel for Indonesia.

Augustinus, D Gahan, ME McNevin, D

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Publisher:: SPRINGER
Publication Type:: Journal Article
Citation:: Int J Legal Med, 2015, 129, (4), pp. 681-691
Issue Date:: 2015-07

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Field	Value	Language
dc.contributor.author	Augustinus, D
dc.contributor.author	Gahan, ME
dc.contributor.author	McNevin, D https://orcid.org/0000-0003-1665-3367
dc.date.accessioned	2023-02-15T05:33:23Z
dc.date.available	2014-07-28
dc.date.available	2023-02-15T05:33:23Z
dc.date.issued	2015-07
dc.identifier.citation	Int J Legal Med, 2015, 129, (4), pp. 681-691
dc.identifier.issn	0937-9827
dc.identifier.issn	1437-1596
dc.identifier.uri	http://hdl.handle.net/10453/166150
dc.description.abstract	Genetic markers included in forensic identity panels must exhibit Hardy-Weinberg and linkage equilibrium (HWE and LE). "Universal" panels designed for global use can fail these tests in regional jurisdictions exhibiting high levels of genetic differentiation such as the Indonesian archipelago. This is especially the case where a single DNA database is required for allele frequency estimates to calculate random match probabilities (RMPs) and associated likelihood ratios (LRs). A panel of 65 single nucleotide polymorphisms (SNPs) and a reduced set of 52 SNPs have been selected from 15 Indonesian subpopulations in the HUGO Pan Asian SNP database using a SNP selection strategy that could be applied to any panel of forensic identity markers. The strategy consists of four screening steps: (1) application of a G test for HWE; (2) ranking for high heterozygosity; (3) selection for LE; and (4) selection for low inbreeding depression. SNPs in our Indonesian panel perform well in comparison to some other universal SNP and short tandem repeat (STR) panels as measured by Fisher's exact test for HWE and LE and Wright's F statistics.
dc.format	Print-Electronic
dc.language	eng
dc.publisher	SPRINGER
dc.relation.ispartof	Int J Legal Med
dc.relation.isbasedon	10.1007/s00414-014-1055-4
dc.rights	info:eu-repo/semantics/closedAccess
dc.subject	0399 Other Chemical Sciences, 0699 Other Biological Sciences, 1103 Clinical Sciences
dc.subject.classification	Legal & Forensic Medicine
dc.subject.mesh	DNA Fingerprinting
dc.subject.mesh	Databases, Nucleic Acid
dc.subject.mesh	Gene Frequency
dc.subject.mesh	Genetic Markers
dc.subject.mesh	Genetics, Population
dc.subject.mesh	Heterozygote
dc.subject.mesh	Homozygote
dc.subject.mesh	Humans
dc.subject.mesh	Indonesia
dc.subject.mesh	Likelihood Functions
dc.subject.mesh	Polymorphism, Single Nucleotide
dc.subject.mesh	Humans
dc.subject.mesh	Genetic Markers
dc.subject.mesh	Likelihood Functions
dc.subject.mesh	DNA Fingerprinting
dc.subject.mesh	Genetics, Population
dc.subject.mesh	Gene Frequency
dc.subject.mesh	Heterozygote
dc.subject.mesh	Homozygote
dc.subject.mesh	Polymorphism, Single Nucleotide
dc.subject.mesh	Databases, Nucleic Acid
dc.subject.mesh	Indonesia
dc.title	Development of a forensic identity SNP panel for Indonesia.
dc.type	Journal Article
utslib.citation.volume	129
utslib.location.activity	Germany
utslib.for	0399 Other Chemical Sciences
utslib.for	0699 Other Biological Sciences
utslib.for	1103 Clinical Sciences
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Strength - CFS - Centre for Forensic Science
pubs.organisational-group	/University of Technology Sydney/Faculty of Science/School of Mathematical and Physical Sciences
utslib.copyright.status	closed_access	*
dc.date.updated	2023-02-15T05:33:22Z
pubs.issue	4
pubs.publication-status	Published
pubs.volume	129
utslib.citation.issue	4

Abstract:

Genetic markers included in forensic identity panels must exhibit Hardy-Weinberg and linkage equilibrium (HWE and LE). "Universal" panels designed for global use can fail these tests in regional jurisdictions exhibiting high levels of genetic differentiation such as the Indonesian archipelago. This is especially the case where a single DNA database is required for allele frequency estimates to calculate random match probabilities (RMPs) and associated likelihood ratios (LRs). A panel of 65 single nucleotide polymorphisms (SNPs) and a reduced set of 52 SNPs have been selected from 15 Indonesian subpopulations in the HUGO Pan Asian SNP database using a SNP selection strategy that could be applied to any panel of forensic identity markers. The strategy consists of four screening steps: (1) application of a G test for HWE; (2) ranking for high heterozygosity; (3) selection for LE; and (4) selection for low inbreeding depression. SNPs in our Indonesian panel perform well in comparison to some other universal SNP and short tandem repeat (STR) panels as measured by Fisher's exact test for HWE and LE and Wright's F statistics.

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http://hdl.handle.net/10453/166150