In 2018, James Casey, president of Casey’s Seafood Inc. of Virginia, pleaded guilty in federal court to fraudulently labeling thousands of pounds of foreign crabmeat as a “Product of the USA.”[1] A significant decline in Atlantic blue crab harvests beginning in 2010 meant it was increasingly difficult for the company to process sufficient quantities to meet customer demand. In order to meet demand, Casey and collaborators supplemented the Atlantic blue crab meat with meat purchased from the Indo-West Pacific and Central America, while maintaining a “Product of the USA” label.

Critical evidence for the prosecution included DNA analysis of the processed crab meat by the National Oceanic and Atmospheric Administration (NOAA).[2] NOAA’s DNA analysis identified numerous species of crab in Casey’s meat that do not live in the continental waters of the United States.

The NOAA investigators used a type of targeted gene sequencing called DNA barcoding to identify the species of crab and their geographic origin.[3] The term “barcoding” refers to the idea that the species can be quickly identified just by sequencing a single gene. Only certain genes are useful for this method, since they need to vary enough to distinguish species or geographic populations, but remain similar within a specific population. Reference databases are built by sequencing the same gene for multiple different populations. A sample of unknown origin can then be sequenced and searched against these databases to determine the sample’s identity.

Generally, cases that use DNA sequencing or genotyping should include a review of the sample DNA quality and quantity. Chemistry-based methods (PCR amplification) are often used to increase the amount of DNA sampled from a specimen in order to have a sufficient quantity for sequencing or genotyping. This amplification can artificially introduce new variants into the DNA and cause sequencing errors. When evaluating sequencing data, it is useful to determine both if DNA amplification was performed, and whether steps were taken to minimize the introduction of errors.

Careful sample collection, storage, and labeling are also important to limit contamination of the DNA sample or mix-ups in the labeling of DNA sample containers. Regular training, internal validation, and replicate testing can prevent human and technical errors when performing DNA sequencing or genotyping.

In cases that specifically use DNA barcoding, it is important to review which gene or genes were used for barcoding and if a useful database exists for identification. Some databases are designed to have high resolution for a narrow geographic region, for example, differentiating Northeast Artic cod from Baltic cod. Other databases may contain a broader geographic survey but with less resolution, for example, differentiating Atlantic from Indo-West Pacific crab.

In the NOAA investigation, the crab samples were sequenced at the COI gene. This is one of the most common genes used for DNA barcoding and is used for the Fish Barcode of Life (FISH-BOL) database, a global initiative which has been DNA barcoding all 31,000 known marine species in the world.[4] In addition to sequencing, genome-wide SNP genotype data may also be used for species or population identification, making use of population-informative SNPs and comparing unknown samples against reference databases.[5]

Lastly, in cases where DNA sequence data are presented, it is important to consider what sequencing platform was used: short-read, long-read, or Sanger. Different sequencing platforms differ in their sequencing error rates.

In the instance of Casey’s Seafood, the sequencing was performed with short-read sequencing, which has a relatively low error rate. However, in the future, the same process could be done with long-read nanopore sequencers that are more mobile.[6] For example, small nanopore sequencers could be used on site as part of a mobile lab, testing at processing plants, or at retailers. Nanopore sequencers tend to carry higher error rates, but continued technical development may address that. Alternatively, rapid DNA test results from a mobile nanopore sequencer that suggest a product is mislabeled could be verified using a complementary technology with a lower error rate, like short-read or Sanger sequencers.