With the addition of four new reference
materials (RMs) to a growing collection of "measuring sticks" for gene
sequencing, the National Institute of Standards and Technology (NIST)
can now provide laboratories with even more capability to accurately
"map" DNA for genetic testing, medical diagnoses and future customized
drug therapies. The new tools feature sequenced genes from individuals
in two genetically diverse groups, Asians and Ashkenazic Jews; a
father-mother-child trio set from Ashkenazic Jews; and four microbes
commonly used in research.
NIST issued the world's first genome reference material (NIST RM
8398) -- detailing the genetic makeup for a woman with European ancestry
-- in May 2015. Together, all five RMs serve as a collection of
well-characterized, whole genome standards that can tell a laboratory
how well its DNA sequencing processes are working by measuring the
performance of the equipment, chemistry and data analysis involved.
The latest reference materials are:
- NIST RM 8391 -- male of Eastern European Ashkenazic Jewish ancestry
- NIST
RM 8392 -- male son, father and mother who are a family of Eastern
European Ashkenazic Jewish ancestry (with the son's genome being the
same released as NIST RM 8391)
- NIST RM 8393 -- male of East Asian (Chinese) ancestry
- NIST
RM 8375 -- genomes for four 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 Ashkenazic trio set aids the 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 Food and Drug Administration (link is external) (FDA) to have
significant relevance to the research of public health issues such as
food contamination, antibiotic resistance and hospital-acquired
infections.
The three individual and one family set of standardized human genomes
were created by NIST and its partners in the Genome in a Bottle
consortium (link is external), a group that includes members from the
federal government, academia and industry. The consortium is managed by
the Joint Initiative for Metrology in Biology (link is external) (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 worldwide with
the tools they need to advance clinical applications of whole genome
sequencing, and the FDA with the ability to conduct science-based
regulatory oversight of the technology.
Reference materials are critical to properly evaluate the
next-generation of gene sequencing and genetic testing methods that will
increase the reliability and effectiveness of precision medicine (also
known as "personalized medicine"), in which a person's genetic profile
is used to create treatments and therapies unique to that individual.
Sequencing devices take long strings of a person's DNA and randomly
chop them into small pieces that can be individually analyzed to
determine their sequence of letters from the genetic code (A, C, G and T
representing the four key components of DNA that code for protein
production in living organisms: adenine, cytosine, guanine and thymine).
The sequenced pieces can then be compared to a well-defined "reference
sequence" to identify differences between the two codes. The differences
reveal where mutations may have occurred in specific genes.
However, 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 between different sequencing
results for the same human genome.
To better understand these biases, laboratories can now compare their
DNA sequences to those obtained from the DNA in any or all of the human
genome RMs. The reference materials have been extensively characterized
with multiple techniques, with the results weighted and analyzed to
eliminate as much bias and error as possible.
The new NIST human genome RMs increase the ability of DNA sequencing
laboratories to be more confident in their reporting of true positives,
false positives, true negatives and 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 (link is external) to further raise that confidence level.
Similarly, the standardized microbial genomes in NIST RM 8375 can be
used to assess the performance of high-throughput methods for microbial
DNA sequencing.
All five of the NIST reference materials are available for purchase
from the NIST Standard Reference Material program. Each RM sample is
characterized for homogeneity (ensuring that each vial contains similar
DNA) and stability (ensuring that the DNA ordered now will be comparable
to samples ordered in the future). The original sources for the RMs are
from the Personal Genome Project (link is external), whose cell lines
are hosted at the Coriell Institute for Medical Research.
Future 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.
