Extended Kinship Inference Part 1: Evaluation of Short Tandem Repeats and Single Nucleotide Polymorphisms Using Likelihood Ratios and Haplotype Matching
Restricted accessResearch articleFirst published online March, 2025
Extended Kinship Inference Part 1: Evaluation of Short Tandem Repeats and Single Nucleotide Polymorphisms Using Likelihood Ratios and Haplotype Matching
Medium- and long-range kinship analysis using single nucleotide polymorphism (SNP) genotyping allows law enforcement to generate investigative leads by identifying an unknown individual through their close and distant genetic relatives. Short-range kinship inference can be conducted through calculation of likelihood ratios (LRs) using population allele frequency data and the degree of similarity between two DNA profiles but has historically been limited to short tandem repeat (STR) profiles. Alternatively, identical by descent (IBD) segment matching algorithms can be used to detect shared DNA haplotypes between two genetically related individuals that have been inherited from a common ancestor. The ForenSeq® Kintelligence Kit enables law enforcement and forensic laboratories to utilize medium-density SNP sequencing technology for extended kinship inference by analyzing 10,230 SNPs. In this study, DNA from two pedigrees was used to compare the ability of STR profiles, identity-informative SNP (iiSNP) profiles, Kintelligence profiles and Kintelligence and direct-to-consumer profiles available on public genetic genealogy databases to detect and classify genetic relationships. The DNA profiles were analyzed using DBLR™ software to calculate kinship LRs or uploaded to GEDmatch PRO™ for IBD segment matching with either database searching or one-to-one comparisons. The LRs calculated for STR and iiSNP profiles were able to correctly infer first degree relationships (i.e., parent, offspring, and full sibling), with the combined discrimination power able to distinguish between second degree relationships. LRs calculated for the Kintelligence profiles exceeded one million for 93% of full sibling to fifth degree relationships tested. IBD segment matching was effective for detecting first to fifth degree relatives when Kintelligence profiles were searched on the GEDmatch PRO™ database. The results of this study demonstrate that the Kintelligence Kit is a valuable tool for law enforcement and forensic investigators, offering an advanced method for medium-range kinship testing using either LRs or IBD segment matching.
Scientific Working Group on DNA Analysis Methods. Recommendations from the SWGDAM Ad Hoc Working Group on Familial Searching. SWGDAM Communications; 2013. Available from: https://www.swgdam.org/publications [Last accessed: January2, 2025].
3.
KlingD. On the use of dense sets of SNP markers and their potential in relationship inference. Forensic Sci Int Genet, 2019; 39:19–31; doi: 10.1016/j.fsigen.2018.11.022
4.
MaguireCN, McCallumLA, StoreyC, et al.Familial searching: A specialist forensic DNA profiling service utilising the National DNA Database® to identify unknown offenders via their relatives—The UK experience. Forensic Sci Int Genet, 2014; 8(1):1–9; doi: 10.1016/j.fsigen.2013.07.004
5.
GeJ, ChakrabortyR, EisenbergA, et al.Comparisons of familial DNA database searching strategies. J Forensic Sci, 2011; 56(6):1448–1456; doi: 10.1111/j.1556-4029.2011.01867.x
KennettD. Using genetic genealogy databases in missing persons cases and to develop suspect leads in violent crimes. Forensic Sci Int, 2019; 301:107–117; doi: 10.1016/j.forsciint.2019.05.016
8.
GeJ, BudowleB, ChakrabortyR. Choosing relatives for DNA identification of missing persons. J Forensic Sci, 2011; 56 Suppl 1:S23–S28; doi: 10.1111/j.1556-4029.2010.01631.x
9.
KlingD, TillmarA. Forensic genealogy—A comparison of methods to infer distant relationships based on dense SNP data. Forensic Sci Int Genet, 2019; 42:113–124; doi: 10.1016/j.fsigen.2019.06.019
10.
GeJ, BudowleB. Forensic investigation approaches of searching relatives in DNA databases. J Forensic Sci, 2021; 66(2):430–443; doi: 10.1111/1556-4029.14615
11.
MorimotoC, ManabeS, FujimotoS, et al.Discrimination of relationships with the same degree of kinship using chromosomal sharing patterns estimated from high-density SNPs. Forensic Sci Int Genet, 2018; 33:10–16; doi: 10.1016/j.fsigen.2017.11.010
12.
KlingD, PhillipsC, KennettD, et al.Investigative genetic genealogy: Current methods, knowledge and practice. Forensic Sci Int Genet, 2021; 52:102474; doi: 10.1016/j.fsigen.2021.102474
13.
GlynnCL. Bridging disciplines to form a new one: The emergence of forensic genetic genealogy. Genes (Basel), 2022; 13(8):1381; doi: 10.3390/genes13081381
14.
GEDmatch. Find DNA Matches for Free | Analyze Your DNA. GEDmatch; 2024. Available from: https://www.gedmatch.com/ [Last accessed: November25, 2024].
15.
FamilyTreeDNA. DNA Testing for Ancestry & Genealogy. FamilyTreeDNA; 2024. Available from: https://www.familytreedna.com/ [Last accessed: November25, 2024].
AntunesJ, WalichiewiczP, ForouzmandE, et al.Developmental validation of the ForenSeq® kintelligence kit, MiSeq Fgx® sequencing system and ForenSeq universal analysis software. Forensic Sci Int Genet, 2024; 71:103055; doi: 10.1016/j.fsigen.2024.103055
SnedecorJ, FennellT, StadickS, et al.Fast and accurate kinship estimation using sparse SNPs in relatively large database searches. Forensic Sci Int Genet, 2022; 61:102769; doi: 10.1016/j.fsigen.2022.102769
Signature Science. SigSci’s Center for Advanced Genomics Validating the Verogen ForenSeq® Kintelligence Workflow for Forensic Genetic Genealogy. Austin, TX; 2021. Available from: https://www.signaturescience.com/press/ngs_fgg/ [Last accessed: March31, 2022].
24.
PeckMA, KoeppelAF, GordenEM, et al.Internal validation of the ForenSeq kintelligence kit for application to forensic genetic genealogy. Forensic Genom, 2022; 2(4):103–114; doi: 10.1089/forensic.2022.0014
25.
WatsonJL, McNevinD, GrisedaleK, et al.Operationalisation of the ForenSeq® kintelligence kit for Australian unidentified and missing persons casework. Forensic Sci Int Genet, 2024; 68:102972; doi: 10.1016/j.fsigen.2023.102972
Department of Justice. Forensic Genetic Genealogical DNA Analysis and Searching. Interim Policy; 2019. Available from: https://www.justice.gov/olp/page/file/1204386/dl [Last accessed: November20, 2024].
Thermo Fisher Scientific. QuantStudio™ 5 Real-Time PCR Instrument for Human Identification User Guide. Life Technologies; 2017. Available from: https://www.thermofisher.com/order/catalog/product/A34322 [Last accessed: January5, 2024].
SpeedD, BaldingDJ. Relatedness in the post-genomic era: Is it still useful? Nat Rev Genet, 2015; 16(1):33–44; doi: 10.1038/nrg3821
43.
Scientific Working Group on DNA Analysis Methods. Recommendations of the SWGDAM Ad Hoc Working Group on Genotyping Resulted Reported as Likelihood Ratios. 2016. Available from: https://www.swgdam.org/publications [Last accessed: January2, 2025].
44.
ZvénigoroskyV, SabbaghA, GonzalezA, et al.The limitations of kinship determinations using STR data in ill-defined populations. Int J Legal Med, 2020; 134(6):1981–1990; doi: 10.1007/s00414-020-02298-w
45.
GeJ, BudowleB. How many familial relationship testing results could be wrong? PLoS Genet, 2020; 16(8):e1008929; doi: 10.1371/journal.pgen.1008929
46.
WatsonJL, GrisedaleK, ChoK, et al.Characterisation of identity-informative genetic markers in the Australian population with European Ancestry. Forensic Sci Int Genet, 2025; 74:103169; doi: 10.1016/j.fsigen.2024.103169
47.
PajničIZ, LeskovarT, ČrešnarM. Improving kinship probability in analysis of ancient skeletons using identity SNPs and MPS technology. Int J Legal Med, 2023; 137(4):1007–1015; doi: 10.1007/s00414-023-03003-3
48.
AndersenMM, KampmannM-L, JepsenAH, et al.Shotgun DNA sequencing for human identification: Dynamic SNP selection and likelihood ratio calculations accounting for errors. Forensic Sci Int Genet, 2025; 74:103146; doi: 10.1016/j.fsigen.2024.103146
49.
GettingsKB, TillmarA, Sturk-AndreaggiK, et al.Review of SNP assays for disaster victim identification: Cost, time, and performance information for decision-makers. J Forensic Sci, 2024; 69(5):1546–1557; doi: 10.1111/1556-4029.15585
HymusCM, TayJW, CoghlanML, et al.Tree vs tree–comparing kinship prediction outcomes for three generations of a family using the Verogen Kintelligence and Infinium Global Screening Array-24 Kit. Aust J Forensic Sci, 2024; 56(Suppl 1):119–122; doi: 10.1080/00450618.2024.2324750
53.
DanielR, RaymondJ, SearsA, et al.It’s all relative: A multi-generational study using ForenSeq™ Kintelligence. Forensic Sci Int, 2024; 364:112208; doi: 10.1016/j.forsciint.2024.112208
54.
WeirBS, AndersonAD, HeplerAB. Genetic relatedness analysis: Modern data and new challenges. Nat Rev Genet, 2006; 7(10):771–780; doi: 10.1038/nrg1960
55.
GreytakEM, MooreC, ArmentroutSL. Genetic genealogy for cold case and active investigations. Forensic Sci Int, 2019; 299:103–113; doi: 10.1016/j.forsciint.2019.03.039
56.
Scientific Working Group on DNA Analysis Methods. Overview of Investigative Genetic Genealogy. SWGDAM Communications; 2020. Available from: https://www.swgdam.org/publications [Last accessed: January2, 2025].
57.
TaylorD, BrightJ-A, McGovernC, et al.Allele frequency database for GlobalFiler™ STR loci in Australian and New Zealand populations. Forensic Sci Int Genet, 2017; 28:e38–e40; doi: 10.1016/j.fsigen.2017.02.012
58.
The International Genome Sample Resource. 1000 Genomes Project. 2021. Available from: https://www.internationalgenome.org/ [Last accessed: October17, 2023].
59.
WatsonJL, GrisedaleK, CoakleyL, et al.Extended kinship inference. Part 2: Evaluation of the impact of information loss on likelihood ratios and haplotype matching. Forensic Genom, 2025; 5(1):32–49; doi: 10.1089/forensic.2025.0002
Supplementary Material
Please find the following supplemental material available below.
For Open Access articles published under a Creative Commons License, all supplemental material carries the same license as the article it is associated with.
For non-Open Access articles published, all supplemental material carries a non-exclusive license, and permission requests for re-use of supplemental material or any part of supplemental material shall be sent directly to the copyright owner as specified in the copyright notice associated with the article.
