New Challenges of Next-Gen Sequencing
By Dan Koboldt,
MassGenomics
| 07. 10. 2014
I first started MassGenomics in the early days of next-gen sequencing, when Illumina was called “Solexa” and came in fragment-end, 35-bp reads. Even so, the unprecedented throughput of NGS and the nature of the sequencing technology brought a whole host of difficulties to overcome, notably:
- Bioinformatics algorithms developed for capillary-based sequencing didn’t scale.
- Sequencing reads were shorter and more error-prone.
- The instruments were expensive, limiting access to the technology
- Most of the genetics/genomics/clinical community had no experience with NGS
All of these are essentially solved problems: new bioinformatics tools and algorithms were developed, the reads became longer and more accurate, benchtop sequencers and sequencing-service-providers hit the market, and NGS was widely adopted by the research community. Mission accomplished!
Yet these victories were short-lived, because we find ourselves facing new challenges. Harder challenges. Here are a few of them.
1. Data storage
You’ve probably seen the plot of Moore’s Law compared to sequencing throughput. In short, the cost of DNA sequencing has plummeted much faster than the cost of disk storage and CPU. A run on the Illumina HiSeq2000 provides enough...
Related Articles
By Megan Molteni and Anil Oza, STAT | 10.07.2025
For two years, a panel of scientific experts, clinicians, and patient advocates had been hammering out ways to increase community engagement in National Institutes of Health-funded science. When they presented their road map to the NIH Director Jay Bhattacharya last...
By Pam Belluck, The New York Times | 10.17.2025
Before dawn on a March morning, Doug Whitney walked into a medical center 2,000 miles from home, about to transform from a mild-mannered, bespectacled retiree into a superhuman research subject.
First, a doctor inserted a needle into his back to...
By Julia Black, MIT Technology Review | 10.16.2025
Consider, if you will, the translucent blob in the eye of a microscope: a human blastocyst, the biological specimen that emerges just five days or so after a fateful encounter between egg and sperm. This bundle of cells, about the size of...
By Deni Ellis Béchard, The Washington Post | 10.07.2025
In 1949, when John Gurdon was a 16-year-old boarding school student at Eton College in England, his teacher described his biology studies as “disastrous” and his scientific ambitions as “ridiculous.”
“If he can’t learn simple biological facts,” his term report...