Determining a DNA match between two samples requires examining and comparing DNA markers from each sample. The number of DNA markers examined can vary considerably depending on the type of DNA test being conducted and the degree of discrimination needed. Generally, examining more DNA markers allows for a higher degree of confidence in declaring a match.
DNA Profiling for Forensic Identification
In forensic DNA profiling, sometimes referred to as DNA fingerprinting, 13 specific DNA markers known as Short Tandem Repeats (STRs) are examined. These 13 genetic markers are areas of the genome that tend to differ greatly between individuals, making them useful for human identification purposes.
The Federal Bureau of Investigation (FBI) has standardized a set of 13 core STR loci that are used by crime labs across the United States when generating DNA profiles for the FBI’s National DNA Index System (NDIS) database. They include markers on chromosomes 13, 18, 21, X and Y. By examining and comparing the alleles present at each of these 13 STR regions, DNA analysts can determine whether two samples came from the same individual or from different individuals.
So in standard forensic DNA profiling using the FBI core STR loci, 13 DNA markers are examined.
Expanded DNA Profiling
While examining 13 core STR loci is the standard for generating DNA profiles for criminal justice purposes, many forensic labs have expanded their DNA profiling panels so they are looking at 20 or more STR markers rather than just the 13 CODIS core loci.
For example, the UK national database uses 10 core STR loci plus 6 additional ones. And various US labs have implemented expanded DNA typing panels with 15, 18, 20 or more STR markers.
Examining additional loci provides more genetic information and allows analysts to generate more discriminating DNA profiles and better estimate match probabilities. With more STR markers in an expanded panel, the chance of two unrelated people having the same DNA profile becomes extremely unlikely.
So while 13 core STRs are the standard, many labs use expanded panels with 15-20+ DNA markers for increased statistical power and more conclusive identifications.
Y-STR Testing
Y-STR testing examines DNA markers on the male Y-chromosome and is often used in sexual assault cases when a sample contains a mixture of male and female DNA. By targeting only markers on the Y-chromosome, Y-STR testing can isolate and generate a profile from just the male contributor(s) in a mixed sample.
Standard Y-STR testing kits typically look at 12-17 different Y-STR genetic markers. So in Y-STR profiling, generally around 12-17 Y-chromosome specific DNA markers are examined.
Mitochondrial DNA Testing
Mitochondrial DNA (mtDNA) testing analyzes DNA found inside mitochondria, the energy-producing structures within cells. mtDNA is passed down directly from a mother to her children. Unlike nuclear DNA, mtDNA remains relatively undiluted over generations, so it can be useful for analyzing older biological evidence and remains.
For forensic mtDNA testing, the control region (CR) of the mitochondrial genome is examined. This hypervariable non-coding region tends to accumulate mutations more rapidly than other areas of mtDNA, providing variation that can distinguish maternal lineages.
Typically, the full control region comprising 1,100 base pairs is sequenced and examined for mtDNA testing. However, forensic labs will often focus their comparisons on key regions of hypervariability within the control region that are known to provide the most discrimination.
So in mtDNA testing, analysts will sequence and compare around 1,100 base pairs comprising the full control region, focusing on the key hypervariable segments.
Autosomal SNP Profiling
Newer DNA profiling methods based on autosomal single nucleotide polymorphisms (SNPs) are increasingly being used, often in combination with standard STR testing. SNP profiling examines thousands or even hundreds of thousands of SNP markers distributed across the 22 pairs of non-sex chromosomes.
Comparing known reference SNPs to SNPs in DNA evidence can provide more statistical power for matching and ancestry analysis compared to standard STR testing alone.
The number of SNP markers examined can vary greatly depending on the platform. The Illumina ForenSeqTM DNA Signature Prep Kit profiles 231 autosomal SNPs. Other expanded SNP profiling kits may look at ~600 SNPs, ~9500 SNPs, ~24000 SNPs or over 100,000 SNP loci depending on the specifics of the test.
So SNP profiling examines anywhere from hundreds to hundreds of thousands of SNP DNA markers distributed across the autosomal chromosomes, depending on the platform.
Whole Genome Sequencing
In whole genome sequencing, as the name implies, the aim is to sequence and analyze almost the entire genome of over 3 billion base pairs. While not routinely performed for forensic work today, whole genome sequencing has been demonstrated for identification in select forensic casework applications.
Whole genome sequencing provides the maximum genetic information and definitive DNA matching. However, forensic DNA testing currently focuses more on standardized profiling of specific highly informative loci rather than sequencing the entire genome which remains costly and generates enormous datasets. But whole genome analysis may become more routine in the future as the technology continues advancing.
So in summary, the number of DNA markers examined to determine a match can range from just 13 core STR loci for standard NDIS DNA profiling up to the full ~3.2 billion base pairs comprising the entire genome in whole genome sequencing. More extensive DNA testing panels and emerging SNP profiling provide additional statistical power for difficult cases involving mixed or degraded samples and when standard STR results are inconclusive. While standard DNA profiling relies on just 13 highly informative STR markers, expanded genetic analysis provides more definitive results by examining a much greater number of genomic loci.
Factors in Selecting DNA Markers for Forensic Testing
When selecting which DNA markers to include in forensic identification testing, scientists look for genomic regions with certain desirable characteristics:
– High variation between individuals (high heterozygosity) – This provides more statistical power to discriminate between people
– Shorter DNA fragments – These are more likely to be recovered from degraded samples
– Repeat sequences that can be easily amplified and analyzed with PCR and capillary electrophoresis
– Low mutation rates – Mutations can create false exclusions, so markers with greater stability are preferred
– Located on nuclear DNA rather than mitochondrial DNA – Important for kinship analysis
– Distinct peaks and robust signal on detection platforms – Provides clear alleles for straightforward interpretation
– Minimal overlap or linkage with other markers – Ensures markers provide independent information
By selecting markers with these favorable genetic properties, forensic scientists can assemble DNA profiling panels optimized to be highly informative for human identification purposes. All standard forensic DNA markers like STRs, Y-STRs and SNPs are specifically chosen using these criteria.
Minimum DNA Markers Required for Identification
While expanded DNA profiling panels provide more statistical certainty, matches can sometimes be declared with fewer markers.
For a single source sample, some European labs will declare a full DNA match with as few as 6 matching STR markers. Standard U.S. protocol requires 10-13 matching core CODIS STR loci for a confirmed identity match.
With mixed DNA samples, the presence of alleles from two different individuals can complicate interpretation. In these trickier cases, relaxed match criteria may be needed depending on the data quality. A partial match might be declared with as few as 5-8 matching alleles.
So while 13 core STR loci provide the accepted standard, under certain circumstances identification can be achieved with as few as 5-6 concordant DNA markers when sample conditions limit the available data. But more matching markers gives greater statistical certainty. Expanding beyond the standard 13 markers to 20, 100 or more loci provides the most power for definitive DNA-based identification.
Conclusion
In conclusion, the number of DNA markers examined during forensic DNA profiling can range considerably from just 13 core STR loci to expanded panels with 20-100+ STRs and SNPs up to complete whole genome sequencing. While standard 13 STR marker analysis remains the accepted baseline, examining additional genetic loci provides more statistical discrimination, especially with challenging samples. When selecting DNA markers for forensic identification, scientists choose regions providing high variability between unrelated individuals while avoiding excessive mutations or overlap with other markers. By comparing more concordant DNA markers, analysts can better assess match significance and provide more definitive conclusions regarding the common identity source of two samples. While minimum thresholds exist to potentially declare matches with fewer than 13 loci in special cases, examining more DNA markers gives the greatest evidential power for conclusive human identification.
