Considerations for the Implementation of Massively Parallel Sequencing into Routine Kinship Analysis

TY - JOUR

T1 - Considerations for the Implementation of Massively Parallel Sequencing into Routine Kinship Analysis

AU - Davenport, Lucinda

AU - Devesse, Laurence

AU - Satmun, Somruetai

AU - Syndercombe Court, Denise

AU - Ballard, David

N1 - Publisher Copyright: © 2025 by the authors.

PY - 2025/2/20

Y1 - 2025/2/20

N2 - Background: Investigating the way in which individuals are genetically related has been a long-standing application of forensic DNA typing. Whilst capillary electrophoresis (CE)-based STR analysis is likely to provide sufficient data to resolve regularly encountered paternity cases, its power to adequately resolve more distant or complex relationships can be limited. Massively parallel sequencing (MPS) has become a popular alternative method to CE for analysing genetic markers for forensic applications, including kinship analysis. Data workflows used in kinship testing are well-characterised for CE-based methodologies but are much less established for MPS. When incorporating this technology into routine relationship casework, modifications to existing procedures will be required to ensure that the full power of MPS can be utilised whilst maintaining the authenticity of results. Methods: Empirical data generated with MPS for forensically relevant STRs and SNPs and real-world case experience have been used to determine the necessary workflow adaptations. Results: The four considerations highlighted in this work revolve around the distinctive properties of sequence-based data and the need to adapt CE-based data analysis workflows to ensure compatibility with existing kinship software. These considerations can be summarised as the need for a suitable sequence-based allele nomenclature; methods to account for mutational events; appropriate population databases; and procedures for dealing with rare allele frequencies. Additionally, a practical outline of the statistical adjustments required to account for genetic linkage between loci, within the expanded marker sets associated with MPS, has been presented. Conclusions: This article provides a framework for laboratories wishing to implement MPS into routine kinship analysis, with guidance on aspects of the data analysis and statistical interpretation processes.

AB - Background: Investigating the way in which individuals are genetically related has been a long-standing application of forensic DNA typing. Whilst capillary electrophoresis (CE)-based STR analysis is likely to provide sufficient data to resolve regularly encountered paternity cases, its power to adequately resolve more distant or complex relationships can be limited. Massively parallel sequencing (MPS) has become a popular alternative method to CE for analysing genetic markers for forensic applications, including kinship analysis. Data workflows used in kinship testing are well-characterised for CE-based methodologies but are much less established for MPS. When incorporating this technology into routine relationship casework, modifications to existing procedures will be required to ensure that the full power of MPS can be utilised whilst maintaining the authenticity of results. Methods: Empirical data generated with MPS for forensically relevant STRs and SNPs and real-world case experience have been used to determine the necessary workflow adaptations. Results: The four considerations highlighted in this work revolve around the distinctive properties of sequence-based data and the need to adapt CE-based data analysis workflows to ensure compatibility with existing kinship software. These considerations can be summarised as the need for a suitable sequence-based allele nomenclature; methods to account for mutational events; appropriate population databases; and procedures for dealing with rare allele frequencies. Additionally, a practical outline of the statistical adjustments required to account for genetic linkage between loci, within the expanded marker sets associated with MPS, has been presented. Conclusions: This article provides a framework for laboratories wishing to implement MPS into routine kinship analysis, with guidance on aspects of the data analysis and statistical interpretation processes.

KW - forensic genetics

KW - kinship analysis

KW - kinship casework

KW - likelihood ratio

KW - massively parallel sequencing

KW - microhaplotypes

KW - next generation sequencing

KW - population databases

KW - sequence allele nomenclature

KW - sequence-based STR analysis

UR - http://www.scopus.com/inward/record.url?scp=105000944539&partnerID=8YFLogxK

U2 - 10.3390/genes16030238

DO - 10.3390/genes16030238

M3 - Article

C2 - 40149390

AN - SCOPUS:105000944539

SN - 2073-4425

VL - 16

JO - Genes

JF - Genes

IS - 3

M1 - 238

ER -