Microarrays and Sequencing for SNP Profiling of Challenged Skeletal Remains

Source: BioTechniques, written by Maddy Chapman; research by David Mittelman (Othram) (November 10, 2026). AI-generated summary by biochip.com, published November 11, 2026. Not independently reviewed.

David Mittelman of Othram compared microarray genotyping with massively parallel sequencing to profile DNA from difficult skeletal remains. The study used the same DNA extracts from 10 samples, allowing the two methods to be compared directly. Although the microarray performed well on high-quality control DNA, several remains produced poor-quality genetic profiles despite apparently acceptable call rates. The result cautions forensic laboratories against treating a high call rate as proof that a DNA profile is reliable.

Two ways to read genetic variation

A single-nucleotide polymorphism, or SNP, is a one-letter difference in DNA among people. Microarray genotyping works like a checklist: DNA from a sample binds to probes designed to detect selected SNPs, and the platform records which variants it finds. Massively parallel sequencing reads DNA fragments at many locations at once, providing another way to identify genetic variants.

Mittelman’s team compared the methods on DNA from 10 challenging skeletal samples. Each had previously yielded a genome-wide sequencing profile considered suitable for forensic genetic genealogy, which uses genetic matches to help identify people or their relatives. The comparison therefore focused on whether microarray genotyping could produce useful profiles from remains with difficult DNA, rather than only from intact reference samples.

Why a high call rate can mislead

A call rate measures the share of tested genetic positions for which a method reports a result. It can look like a simple score of completeness, but it does not show whether the reported genotypes are accurate or whether the profile will identify relatives reliably. In this comparison, several skeletal samples had poor-quality microarray profiles even though their call rates appeared acceptable.

The microarray performed well with high-quality control DNA, but that performance did not carry over consistently to the challenging remains. Skeletal evidence may contain degraded human DNA or substantial microbial contamination, conditions that differ from those in intact reference DNA. The findings support using sequencing for these challenging samples and show why laboratories should judge methods on evidence resembling actual forensic casework.

Choosing tests while preserving evidence

Forensic samples and laboratory budgets are limited. A test that consumes evidence but fails to produce a dependable profile can leave less material for later analyses. Mittelman said the comparison was intended to help laboratories choose methods based on demonstrated performance and avoid relying on call rate or genotype recovery alone.

He argues that validation should measure how reliably a profile detects both close and distant genetic relatives, while also tracking false matches. Larger prospective studies could connect sample characteristics and laboratory methods to the reliability of resulting profiles. The 10-sample comparison offers a caution about microarray call rates, but broader testing is needed to guide method choices across forensic cases.

Topics: Biochip · Diagnostics & precision medicine

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