New Tools for Old Evidence: How Advanced Sequencing Is Revolutionizing Forensic Genomics

Nearly four decades ago, DNA analysis was introduced into forensic practice, transforming the criminal investigation process. The first methods were labor-intensive, requiring large amounts of high-quality biological material. The emergence of polymerase chain reaction (PCR), which amplifies tiny quantities of DNA into detectable amounts, made routine forensic testing practical. Today, short tandem repeat (STR) profiling via capillary electrophoresis (CE) is the mainstay of forensic DNA analysis. STRs are short, repetitive DNA sequences scattered throughout the genome that vary in length between people. CE separates these fragments by size, generating a genetic profile that can be compared against reference samples or searched against national databases. The approach is well-validated, courtroom-tested, and capable of confident identification.¹

But CE-based STR typing has real limits. It resolves only length variation at a restricted set of loci, typically 13 to 20 markers. It struggles with degraded or low-input samples. And when no reference profile exists for direct comparison, its utility is limited to close familial relationships.¹ Massively parallel sequencing (MPS) processes millions of DNA fragments simultaneously, and single nucleotide polymorphism (SNP) analysis examines variation at specific DNA base positions across the genome. These technologies are now expanding what STR-based methods cannot achieve, across forensic and applied genomics, from criminal investigation and legal proceedings to disaster victim identification, missing persons cases, and the analysis of degraded biological material.

Cold cases are now being solved with samples that would have been unworkable a decade ago. This article examines how the sequencing technologies behind this shift are reshaping forensic and applied genomics, what they can do that traditional methods cannot, and where the field is headed.

Sequencing STRs at higher resolution

MPS, also referred to as next-generation sequencing (NGS), enhances rather than displaces STR analysis. Where CE detects only the length of STR alleles, MPS reads the underlying nucleotide sequence, revealing variation that length-based methods miss entirely. This increases discriminatory power between people and improves performance in populations where certain allele lengths are common.²

MPS is also compatible with much shorter DNA fragments than CE, making it effective on highly degraded samples such as skeletal remains, aged touch DNA, and samples exposed to environmental insult. And it can better separate the DNA of multiple people present in a single sample, resolving mixtures that CE may struggle to interpret.¹

MPS extends further still, typing SNPs simultaneously alongside STRs in a single assay, something CE cannot do. The leading forensic platforms supporting this combined approach are the Verogen MiSeq FGx, now distributed by Qiagen, a purpose-built forensic sequencing system, and Thermo Fisher's Ion Torrent system, a general-purpose platform with forensic-validated kits. The ForenSeq kit on the MiSeq FGx was the first forensic MPS assay approved by the FBI for upload to CODIS, the national DNA database system. Workflow complexity, cost, and a lack of specialized bioinformatics expertise have slowed adoption, driving a hybrid approach: CE for routine casework, MPS for cases where greater resolution is needed.¹

Mitochondrial DNA (mtDNA) analysis is another area where MPS excels. Unlike nuclear DNA, which exists in just two copies per cell, mtDNA is present in hundreds to thousands of copies, making it far more likely to survive in difficult samples such as hair shafts without roots and heavily degraded skeletal remains. Because mtDNA is maternally inherited, it cannot distinguish between maternal relatives, but it can place an unknown sample within a maternal lineage and is especially useful for excluding candidates.

Traditional forensic mtDNA analysis targeted only the control region, a short, highly variable stretch representing roughly 7% of the mitochondrial genome. MPS makes whole-genome sequencing (WGS) practical, revealing more variable positions to distinguish between unrelated people and reducing the chance of coincidental matches.¹ Qiagen's ForenSeq mtDNA Whole Genome Kit on the MiSeq FGx and Thermo Fisher's Precision ID mtDNA Whole Genome Panel on the Ion Torrent system both enable sensitive sequencing from minimal input.

SNPs and microarrays expand the toolkit

SNP profiling offers a core complement to STR analysis. NGS-based targeted panels and SNP microarrays serve different needs. Targeted panels typically analyze between a few dozen and around 10,000 loci in a single assay and perform well on low-quality or degraded samples. Microarrays, on the other hand, can interrogate 600,000 or more markers cost-effectively, but require good-quality DNA, making them better suited to kinship testing and forensic investigative genetic genealogy when sample quality permits. SNPs are particularly resilient on degraded samples because they represent variation at single base positions, which are more likely to survive DNA fragmentation than the longer repetitive sequences targeted by STR analysis.¹

SNP datasets open forensic DNA analysis beyond identification. Many fall within or near genes associated with traits such as eye and hair color or population ancestry, allowing inference of appearance and geographic origin from biological evidence. These capabilities are most useful when investigators are working without a known suspect, using DNA evidence alone to generate leads. SWGDAM, the Scientific Working Group on DNA Analysis Methods, recognized the growing role of SNP analysis in January 2024 with dedicated interpretation guidelines covering human identification, ancestry inference, phenotypic prediction, and kinship testing.¹

Forensic investigative genetic genealogy

Forensic investigative genetic genealogy (FIGG) is changing cold case investigation by generating a genome-wide SNP profile from crime scene DNA, searching opt-in genealogical databases for genetic matches, and using genealogical research to reconstruct family trees and narrow the suspect pool.

In 2021, FIGG was used for the first time in Europe to solve the murders of an eight-year-old boy and a 56-year-old woman, a case that had gone unsolved for 16 years. SNP profiling of crime scene DNA generated leads that conventional STR analysis could not have produced, ultimately identifying the perpetrator.³

Sweden subsequently passed FIGG-enabling legislation in early 2025. In the United States, no federal law currently governs FIGG use. A 2019 FBI interim policy, however, restricts it to violent crimes and unidentified remains cases after other investigative methods have been exhausted.

The effectiveness of FIGG depends heavily on data quality. A 2024 study found that kinship inference held up well with at least 164,000 SNPs but fell off as marker count declined.⁴ This matters because most targeted forensic panels generate far fewer markers, and crime scene DNA is rarely pristine. FIGG profiles can be generated through SNP microarrays or whole-genome sequencing. As noted earlier, microarrays require good-quality DNA, while WGS handles difficult samples more effectively—recent work demonstrated accuracy comparable to high-quality reference DNA from inputs as low as 0.5 nanograms, or fragment lengths as short as 200 base pairs.⁵

Predicting appearance from DNA

While FIGG uses SNP profiles to trace biological relatives, forensic DNA phenotyping (FDP) takes a different approach, using SNPs to predict the physical appearance and geographic ancestry of an unknown person. A 2025 review catalogued dozens of panels developed for geographic ancestry inference, externally visible characteristics, or both.⁶ Predicted traits span eye color, hair color, skin pigmentation, freckling, male-pattern baldness, and elements of facial morphology.⁷ DNA methylation patterns, which change predictably with age, are also being explored as a way to estimate an individual’s age from biological evidence alone.

But all FDP outputs are estimates, used to generate investigative leads rather than as standalone evidence in court.⁶ Standardization across panels and platforms remains incomplete, and accuracy varies by trait and by population. Most reference datasets are enriched for people of European descent, which can skew predictions for underrepresented groups and produce unreliable results.¹

Long-read sequencing on the horizon

Where standard MPS generates short DNA reads, third-generation long-read sequencing (LRS) platforms work with fragments thousands of base pairs in length. This enables assembly of genomic regions that short-read platforms struggle to resolve, including highly repetitive sequences, direct methylation analysis from native DNA, and the ability to determine which variants occur together on the same chromosome.⁸ In clinical genomics, LRS has already resolved rare disease cases that standard short-read methods could not.⁹

Forensic adoption of LRS has lagged behind, reflecting the extensive validation requirements for any technology used in legal proceedings. Potential applications include improved analysis of complex STR regions and portable field deployment.⁸ Oxford Nanopore Technologies, for example, offers a handheld device suited to on-site DNA analysis, while Pacific Biosciences provides high-accuracy LRS for laboratory settings. The technology is not yet validated for casework.

Looking ahead

Guidelines for newer applications such as FIGG and WGS-based SNP analysis are still incomplete, and no binding federal law governs their use in the United States.¹ The field also faces unresolved questions about equity and privacy. Non-European populations continue to be underrepresented in forensic reference databases, affecting the reliability of results for a significant portion of the global population. The use of consumer genealogical data for law enforcement purposes raises questions about consent, privacy, and the rights of people who never chose to participate in a criminal investigation.

These challenges exist alongside practical ones. Adoption of MPS in forensic laboratories is accelerating but uneven globally. In many jurisdictions, cost, limited training opportunities, and the absence of consistent international standards continue to slow implementation. The path forward is incremental, but the case for moving faster is clear. Closing these gaps is as essential as the underlying science.

References

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About the author: Lauren Tanabe has a Ph.D. in pharmacology and molecular signaling from Columbia University. She completed her postdoctoral work at the University of Michigan as a Dystonia Medical Research Foundation Fellow and at Wayne State University as an American Cancer Society Fellow.