How to Read an Electropherogram for DNA Fingerprinting

A DNA match statistic is calculated by dividing the chance of an actual match by the chance of a coincidence (random match). Population databases, developed by the FBI and NIST, contain genetic data from hundreds of people to calculate the chance of coincidence. A match statistic of 1 means no information (like matching faces, which everyone has), while a statistic of 1 million means the match is a million times stronger than coincidence. Different databases may yield slightly different statistics (typically within a factor of ten).

A DNA match is determined by comparing evidence sample data to standard sample data. If all numbers align, it is considered a match. The product rule is used to calculate match probability by multiplying frequencies across 21 different DNA locations. Statistical databases contain genetic marker frequencies across all population types. A threshold of one in 320 billion (approximately 1,000 times the US population) is used to determine if a match is statistically significant and unreasonable to attribute to anyone other than the matching individual.

Forensic DNA profiling requires attaching specific statistical weights to profile matches rather than merely stating they are rare. The Random Match Probability (RMP) quantifies how rare a DNA profile is within a given population—the chance that a randomly chosen unrelated person would share the same profile. This concept is essential for distinguishing coincidental matches from meaningful identifications. The mathematical foundation uses the product rule: for heterozygous loci (two different alleles), the formula is 2 × P × Q; for homozygous loci (same allele twice), it is P². These formulas, combined across all loci, enable forensic scientists to calculate the probability of finding someone with an identical DNA profile. The FBI established allele frequency databases in the late 1980s using approximately 200 recruits, primarily Caucasians including Mormons from Salt Lake City. Two critical population genetics assumptions underlie these calculations: Hardy-Weinberg equilibrium (independence of alleles within loci) and linkage equilibrium (independence across loci). Laboratories typically report statistics for three major U.S. racial groups: Caucasians, African Americans, and Hispanics. Using allele frequencies from different populations introduces significant errors, similar to using Utah voting data to estimate North Carolina preferences.

Random match probability calculates how common a DNA profile is in a population: (1) Population frequencies are determined for each allele at each locus, (2) Statistical calculations combine these frequencies across all tested loci, (3) Results indicate the probability of randomly selecting an unrelated individual with the same DNA profile, (4) For full profiles, probabilities exceed 1 in quadrillion, demonstrating extreme uniqueness.

This segment covers DNA profile matching and statistical significance. When DNA profiles match known standards, the analyst provides the random match probability for that profile. This probability is calculated based on population databases and the product rule. The statistical analysis shows how rare the DNA profile is in different ethnic populations (Caucasian, African-American, Hispanic). This provides the scientific relevance of the DNA match. When DNA profiles match known standards, the analyst provides the random match probability for that profile. This probability is calculated based on population databases and the product rule. The statistical analysis shows how rare the DNA profile is in different ethnic populations (Caucasian, African-American, Hispanic). This provides the scientific relevance of the DNA match.

The laboratory's CODIS terminal displayed a green light indicating the system was ready to receive the new genetic profile. CODIS, the Combined DNA Index System, had grown exponentially since its creation in the 1990s, now containing millions of profiles from convicted offenders, crime scenes, and missing persons. The database had solved thousands of cold cases through both direct matches and familial searches that could identify suspects through their relatives' DNA. Walsh watched the computer screen as Dr. Romano uploaded Sarah's genetic evidence, officially designated as Wyoming cold case 1990-127A.

In missing persons investigations, CODIS (Combined DNA Index System) is not a universal database that contains all individuals in the US; it only includes samples from people who have had prior interactions with the criminal justice system. When CODIS yields no results, investigators must turn to investigative genetic genealogy, which uses DNA samples to create family trees through open-source DNA databases to identify potential relatives and help locate missing individuals.

The Combined DNA Index System (CODIS) is a national database containing over 19 million offender profiles, 6 million arrestee profiles, and 1.45 million forensic profiles from unsolved crimes, which law enforcement uses to match DNA evidence from crime scenes to known profiles or connect unrelated crimes; in the Nancy Guthrie investigation, the FBI collected 16 gloves near her home, with one glove's DNA profile being processed and prepared for entry into CODIS to help identify the suspect.

After the initial investigation went cold, the crime lab collected a DNA sample from a semen stain on Sharita's pants. Police collected samples from a few male suspects, but neither matched. They ran the DNA sample through CODIS, which is an acronym for Combined DNA Index System—a computer software program that operates local, state, and national databases of DNA profiles from convicted offenders, crime scene evidence, and missing persons.

CODIS (Combined DNA Index System) is a national DNA database system established in 1990 and became operational in 1994. It allows criminal justice agencies such as the FBI to input DNA profiles into a centralized database. The National DNA Index System (NDIS) is the program where these DNA profiles are sorted and processed. For unidentified remains to be matched through DNA, their families must submit DNA profiles as evidence in missing persons reports. In this case, the Klaus and Lynn families were unable to file successful missing persons reports because local authorities did not believe them, which prevented their DNA from entering the system for decades.

Next Generation Sequencing (NGS) offers significant advantages over traditional capillary electrophoresis for forensic DNA analysis, providing increased discriminatory power (approximately 30% more alleles revealed as heterozygous), better handling of degraded and mixed samples, and the ability to simultaneously analyze SNPs for ancestry and physical trait prediction alongside STR typing; however, successful implementation requires optimized amplicon sizes (typically 75-80 base pairs), careful primer design, comprehensive database development, and standardized nomenclature systems to handle the additional information generated.

Next Generation Sequencing (NGS) transforms forensic genomics by consolidating multiple traditional DNA tests (autosomal STRs, Y-STRs, X-STRs, SNPs, and mitochondrial DNA) into a single streamlined workflow, enabling simultaneous analysis of approximately 230 markers including 94 identity SNPs, 24 phenotyping SNPs, and 56 ancestry SNPs; this approach addresses key forensic challenges including low-input samples, mixed DNA samples, and degraded DNA by providing sequence-level resolution that enhances mixture analysis, increases discrimination power for complex relationship cases, and enables phenotyping and ancestry estimation alongside traditional DNA profiling.

Massively parallel sequencing (NGS) offers forensic DNA laboratories a transformative approach by consolidating multiple traditional analysis methods (autosomal STRs, X&Y STRs, SNPs, indels, micro-haplotypes, and mitochondrial DNA) into a single integrated workflow, thereby increasing discrimination capabilities, enhancing data resolution, and improving operational efficiency while reducing processing time, effort, and cost compared to conventional capillary electrophoresis-based methods.

SNP (Single Nucleotide Polymorphism) profiling represents a revolutionary advancement over traditional STR (Short Tandem Repeat) DNA analysis. While STR profiles examine only 13-20 genetic markers and have been used for decades in forensics, SNP profiles analyze hundreds of thousands of genetic markers, dramatically increasing identification capabilities. This technology enables investigators to find distant cousins, identify unknown remains without first-degree relatives, and even distinguish between identical twins—tasks impossible with traditional methods. Medical examiners are increasingly accepting SNP-based identification reports for legal closure. The Golden State Killer case demonstrated this power, proving that SNP profiling can solve cases that had remained unsolved for decades.

Next Generation Sequencing (NGS) enables forensic laboratories to generate megabases to gigabases of genetic data in hours to days, vastly expanding human identification capabilities. The Ion Torrent PGM system uses semiconductor chip technology with 1.2 million ion-sensitive sensors detecting pH changes caused by hydrogen ion release during nucleotide incorporation. Key forensic applications include analyzing multiple polymorphisms (STRs, SNPs, indels) from degraded DNA samples, conducting identity/kinship analysis with fragments as short as 60-70 nucleotides, and employing ancestry-informative SNPs for investigative leads. The workflow involves library preparation through DNA fragmentation, adapter attachment, and clonal amplification onto beads, followed by sequencing on semiconductor chips. Ion AmpliSeq technology enables high-multiplex targeted resequencing with as little as 10 nanograms of DNA, progressing from DNA to annotated variants in approximately 10 hours. HID (Human Identification) SNP panels combine SNPs optimized for high heterozygosity and low population heterogeneity, including ID SNPs, Ken Kid SNPs, Y-SNPs, and unlinked SNPs achieving high genotype match probabilities. Mitochondrial DNA offers significant forensic advantages: high copy numbers enable analysis of challenging samples like hair shafts lacking nuclear DNA, maternal inheritance enables lineage tracing across generations, and lack of recombination preserves genetic history.