New Standardized Whole Genomes Released to Improve Quality Control

Researchers have expanded the set of tools for more accurate next generation sequencing (NGS) analysis of genomes by developing 4 additional reference materials (RMs) to run as controls for assessing performance of the equipment, chemistry, and data analysis being used.

With the addition of genome RMs to a growing collection of “measuring sticks” for DNA sequencing, the National Institute of Standards and Technology (NIST; Gaithersburg, MD, USA) can now provide laboratories with even more capability to map DNA for genetic testing, medical diagnoses, and development of customized drug therapies. The new RMs feature human genomes for 1 Asian and 3 Ashkenazic Jewish individuals, as well as one RM made up of four microbes commonly used in research.

RMs are critical to properly evaluate NGS and genetic testing methods to increase reliability and effectiveness of precision medicine (personalized medicine). The NIST RMs provide well-characterized, whole genome standards that can help a laboratory evaluate how well its DNA sequencing processes are working.

Biases and "blind spots” for certain sequences contribute to uncertainties or errors in the sequence analysis. These biases can lead to hundreds of thousands of disagreements about the same genome. To better understand these biases, laboratories can now compare their results to the information provided by NIST. The RMs have been extensively characterized with multiple techniques, with the results weighted and analyzed to eliminate as much bias and error as possible.

In 2015, the NIST issued the first genome RM (NIST RM 8398) —detailing the genetic makeup for a woman with European ancestry. The 4 new RMs are: NIST RM 8391: male of Eastern European Ashkenazic Jewish ancestry; NIST RM 8392: son (same as NIST RM 8391), father, and mother who are a family of Eastern European Ashkenazic Jewish ancestry; NIST RM 8393: male of East Asian (Chinese) ancestry; and NIST RM 8375: genomes for 4 bacterial species: Salmonella typhimurium LT2, Staphylococcus aureus, Pseudomonas aeruginosa, and Clostridium sporogenes.

The individual human RMs provide a baseline for comparing and contrasting genes from distinctly different lineages, while the trio mother-father-son RM aids analysis of genetic links between family members. The bacterial genomes come from species that challenge the technical performance of sequencing methods and have been determined by the US Food and Drug Administration (FDA) to have significant relevance to the research of public health issues such as food contamination, antibiotic resistance, and hospital-acquired infections.

The RMs can help increase the ability of DNA sequencing laboratories to be more confident in their reporting of true vs. false positives, and true vs. false negatives, and therefore significantly improve genetic tests used for disease risk prediction, diagnosis, and progression tracking. They also can be used with tools developed by the “Global Alliance for Genomics and Health Benchmarking Team” to further raise confidence level.

Similarly, the standardized microbial genomes in NIST RM 8375 can be used to assess performance of high-throughput methods for microbial DNA sequencing.

The RMs were created by NIST and its partners in the Genome in a Bottle consortium, a group that includes members from the federal government, academia, and industry. The consortium is managed by the Joint Initiative for Metrology in Biology (JIMB), a collaboration between NIST and Stanford University. Through its effort to develop, produce, and distribute a suite of genome RMs, the consortium is providing medical and research laboratories with tools to advance clinical applications of whole genome sequencing, and the FDA with better capability to conduct science-based regulatory oversight of the technology.

All five RMs are available for purchase from the NIST Standard Reference Material program. Each RM sample is characterized for homogeneity (to ensure that each vial contains similar DNA) and stability (to ensure comparability to future batches). The original sources for the RMs are from the “Personal Genome Project,” whose cell lines are hosted at the Coriell Institute for Medical Research.

Next additions to the RM collection may include whole genomes from persons with Hispanic, African, and mixed ancestries, as well as a set containing sequenced genes of both malignant tumor and normal cells from the same individual.

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National Institute of Standards and Technology