NEW YORK (GenomeWeb) – The National Institute of Standards & Technology has released the first DNA reference materials that labs can use to gauge the performance of tests employing whole-genome sequencing, exome sequencing, and targeted panel tests.
For $450, labs can purchase reference material 8398 — described as "Human DNA for Whole Genome Variant Assessment (daughter of Utah/European Ancestry)" — and receive a 10 ug vial of genomic DNA. The DNA is extracted from a human lymphoblastoid cell line from the Coriell Institute for Medical Research.
"The material can be used to obtain estimates of true positives, false positives, true negatives, and false negatives for variant calls," NIST states in a document accompanying the reference material data.
According to the institute, a lab can use the reference material to assess its sequencing library preparation methods, sequencing machines, and bioinformatics processes, such as mapping, alignment, and variant calling. The DNA material "is not intended to assess subsequent bioinformatics steps, such as functional or clinical interpretation," according to NIST.
After sequencing the reference DNA, labs can compare their results to reference values for SNPs, small indels, and homozygous reference genotypes. NIST provides a variant call file that contains information on high confidence SNPs, indels, and regions.
The latest release reflects the work of the Genome in a Bottle Consortium, a group spearheaded by NIST that has been working to develop reference materials for human genome sequencing. "This is the first and only NIST reference material for genome sequencing, though there are more planned," NIST biomedical engineer Justin Zook told GenomeWeb via e-mail.
NIST and Genome in a Bottle are working on characterizing four other genomes into reference materials, including DNA from a mother-father-son trio of Ashkenazi Jewish ancestry and a son from a trio of Asian ancestry. For these genomes, which come from the Personal Genome Project, NIST and Genome in a Bottle have generated short- and long-read sequencing data, Zook said.
There is a group within Genome in a Bottle that will coordinate data analyses for these genomes, he added. NIST plans to release the reference materials by next year.
The development of these reference materials dovetails with the US Food and Drug Administration's efforts to craft a flexible regulatory framework for next-generation sequencing tests that doesn't overburden the agency or labs. The agency has held a number of meetings to discuss regulation of NGS tests and has participated in NIST's effort to develop reference materials for genome sequencing.
NIST representative Michael Newman described the reference materials as a kind of "measuring stick" for the human genome. "This gives someone a chance to tell how well their sequencers are working," Newman said. "The standards are set so if they get the result that we tell them they should be getting, then they know their equipment is working properly and it validates results they're getting."
However, at the moment, it is completely voluntary for labs to assess their sequencing processes using NIST's reference materials and values. "These are not official industry standards," Newman said. "NIST is not a regulatory [body] … we can't tell people they have to use these things."
NIST is hopeful though that regulatory bodies will take these reference materials and raise them up as an official standard. The FDA hasn't issued any guidelines or policies in this regard, but Newman noted that even while these reference materials were under development, the agency used them in their review of next-generation sequencing platforms.
In late 2013, the FDA cleared the first NGS instrument, Illumina's MiSeqDx, along with two cystic fibrosis assays. In announcing this clearance, the agency highlighted that among the data submitted by Illumina, the company compared results from its CF tests against a reference human genome, called Human Genome Build 19, and compared the performance of its instrument and reagent systems to "a publically available quality-weighted human reference genome that was created through collaboration between the FDA and NIST."