NIPT extended to small deletions and duplications—but many false positives

A research team based in China and California has used a rapid semiconductor sequencing platform to identify small chromosomal deletions and duplications in fetal DNA from a noninvasive prenatal test (NIPT) blood draw. Analyzing plasma from 1,476 pregnant women who had been identified by ultrasound as having potential fetal structural abnormalities, the new method detected 69 of 73 (94.5%) of abnormalities greater than 1 Mb in size. The women also had conventional invasive fetal DNA analysis. The report, published November 2015 in Proceedings of the National Academy of Sciences, also noted that the NIPT test generated 55 false positives, of which 35 were attributed to maternal chromosomal abnormalities. According to the researchers, as the cost of NIPT with semiconductor sequencing goes down, it has the potential to be less expensive (in addition to being, of course, safer) than conventional, invasive prenatal testing methods. However, implementing the technology could introduce a whole raft of complications, not the least of which is that, as more variations are detected, they are likely to flag chromosomal deletions or duplications of unknown clinical significance. “If our NIPT extension is put into clinical practice, great care must be taken in presenting results and providing appropriate counseling to patients,” said principal investigator Kang Zhang, professor of ophthalmology and chief of ophthalmic genetics at UC San Diego School of Medicine and founding director of the school’s Institute for Genomic Medicine in a statement accompanying the research article. —Karyn Hede, News Editor

Extreme-scale analysis produces the 8.4-minute human genome

Supercomputers at Lawrence Berkeley National Laboratories can now churn out a completely assembled human genome sequence in 8.4 minutes, raising expectations that real-time whole-genome testing may be coming sooner than we thought. The announcement was made in November 2015 at the SC15 conference, where supercomputing insiders gather to show off their latest achievements. A research team from Berkeley Labs’ Joint Genome Institute and UC–Berkeley presented HipMer, which they characterized as “the first high-quality end-to-end de novo assembler designed for extreme scale analysis.” For those not well versed in high-end computing, the research team explained that the speed and efficiency of the algorithm exceed the capability of all the world’s current sequencers combined. The HipMer technology, they say, could usher in a new era of genome analysis. It could, for instance, be used to rapidly identify all the species in a microbial community or to compare genetic variants in hundreds of tumor cells from a single biopsy. For now, the technology will be used by researchers interested in testing hypotheses that involve rapidly assembling multiple genomes. Because current genome-assembly programs are unable to keep pace with the flood of genomic data, the new technology may help speed analysis and break up logjams of data. The researchers note that HipMer is “adaptable and scalable,” allowing it to be used in a variety of computing environments. After additional testing, the team plans to release it as publicly available open-source code. —Karyn Hede, News Editor