By Dixie Peters, Kelly Grisedale, Lisa Schade,
Jonathan Tabak and James Anstead
How new technologies are getting results from challenging DNA samples
In a typical crime laboratory operating today, what are the chances of obtaining an informative nuclear DNA profile from a rootless hair shaft? Or from extremely degraded skeletal human remains? The answer, as many forensic DNA analysts will attest, is somewhat discouraging—it is not likely at all. The
reality is—despite misleading Hollywood depictions as well as a number of significant real-world advances
in the sensitivity, robustness and discrimination power of DNA profiling kits—there remains a significant
percentage of biological evidence samples that stubbornly refuse to yield probative results. In fact, estimates show that as much as 25 to 35 percent of all evidence samples submitted to crime laboratories fail to
produce an informative DNA result with standard methods.1
Of course, this failure rate varies significantly depending on each laboratory’s sample submission and
screening policies, validated methods and protocols. The true culprit, however, is not the laboratory, but
the samples themselves which frequently suffer from severe DNA degradation and/or low DNA quantity.
These challenging samples not only hamper investigations, they frequently require labor-intensive re-pro-cessing before being abandoned, which can contribute to increased costs, lengthy turnaround times, and
casework backlogs. Moreover, due to these challenges, a number of sample types commonly found at crime
scenes, such as shed hairs, are frequently not accepted by laboratories for DNA testing due to the low
likelihood of obtaining a usable result.
Until recently, there have been limited technological alternatives for analyzing the most challenging
samples. A small minority of forensic laboratories, such as those proficient in processing human remains,
have validated specialized methods like mitochondrial DNA (mtDNA) sequencing. However, mtDNA
sequencing, while extremely sensitive, is labor intensive, expensive, offers limited discrimination power,
and cannot differentiate offspring of the same maternal lineage.
There appears to be strong potential in massively parallel sequencing—sometimes called “next generation sequencing” or simply “NGS”—systems that can perform whole mtDNA genome sequencing and
analyze large numbers of small amplicon markers such as SNPs (single nucleotide polymorphisms) simultaneously. However, these systems require laboratories to implement completely new instrumentation and
“coding” DNA regions. This is no small feat for typically resource-strapped forensic laboratories.
Therefore, there is a strong need for innovative technologies such as those described here, which expand DNA testing capabilities for extremely challenging samples, while remaining fully compatible with
the current PCR and capillary electrophoresis (CE) platforms commonly used and validated within most
Retrotransposable Elements (REs), are non-coding genomic sequences of repetitive DNA, which comprise
approximately 40% of the human genome. 2 REs are well characterized, but until now their practical utility
as informative biomarkers have been severely limited due to the large size of the insertions which has led
to difficult multiplexing challenges and poor PCR efficiency. A novel “mini-primer” design invented by InnoGenomics reduces the overall amplicon size as well as the difference in amplicon sizes between the two
allelic states, insertion or null insertion (Figure 1). The resulting allelic amplicons can now be designed