颜林林 (2022-06-01 07:41):
#paper doi:10.1101/2022.05.29.493900 bioRxiv 2022, Cost-efficient whole genome-sequencing using novel mostly natural sequencing-by-synthesis chemistry and open fluidics platform. 这是来自MIT的一家创业公司Ultima Genomics的新作品,它从设计原理上对当前“边合成边测序”的方法进行突破创新。通过在圆形大晶片上设计流控和光学系统,使相应的试剂耗材更加便宜。相对于Illumina测序在每个cycle进行可逆阻断的碱基追加方法,本文通过使用非阻断的方法,使碱基追加过程更加快速,同时配合一套CNN算法,来实现准确的base calling。实测下来,该测序方法可以做到在20小时以内、300bp长读长、Q30>85%高质量的高通量测序,且每Gb数据成本低于1美元。本文还使用GIAB及千人基因组的样本进行了基准测试,验证了测序结果的准确度。我们很多人天天都在围绕高通量测序做研究,早已把Illumina测序原理当做习以为常且理所当然的技术,默认了它的垄断和天花板地位,很少去考虑它还有什么可以进一步改善的地方。这篇文章是个拓展这方面眼界的机会。
Cost-efficient whole genome-sequencing using novel mostly natural sequencing-by-synthesis chemistry and open fluidics platform
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Abstract:
We introduce a massively parallel novel sequencing platform that combines an open flow cell design on a circular wafer with a large surface area and mostly natural nucleotides that allow optical end-point detection without reversible terminators. This platform enables sequencing billions of reads with longer read length (~300bp) and fast runs times (<20hrs) with high base accuracy (Q30 > 85%), at a low cost of $1/Gb. We establish system performance by whole-genome sequencing of the Genome-In-A-Bottle reference samples HG001-7, demonstrating high accuracy for SNPs (99.6%) and Indels in homopolymers up to length 10 (96.4%) across the vast majority (>98%) of the defined high-confidence regions of these samples. We demonstrate scalability of the whole-genome sequencing workflow by sequencing an additional 224 selected samples from the 1000 Genomes project achieving high concordance with reference data.
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