NEW YORK – In a highly anticipated webinar on Thursday, Roche offered more technical details about its so-called Sequencing-by-Expansion (SBX) nanopore sequencing technology.

纽约——在周四备受期待的网络研讨会上，罗氏公司提供了更多关于其所谓的扩展测序（SBX）纳米孔测序技术的技术细节。

The platform, which has been in development for over a decade, is scheduled for a 2026 launch, according to the firm.

该公司表示，这个已经开发了十多年的平台计划于2026年推出。

During the event, Roche made clear that the platform is underpinned by two fundamental technologies:

在活动期间，罗氏明确表示，该平台由两项基本技术支撑：

a semiconductor array chip, which Roche obtained through its

一种半导体阵列芯片，罗氏通过其获得

acquisition of Genia

收购Genia

in 2014, and the

2014年，以及

SBX chemistry

SBX化学

that was originally developed by

最初由

Stratos Genomics

平流层基因组学

, which Roche acquired in 2020.

，罗氏在2020年收购了该公司。

In an interview with

在一次采访中

GenomeWeb

基因组网

this week, Mark Kokoris, Roche's head of SBX technology and a cofounder of Stratos, said there has been 'a continual stream of innovation' over the past several years. '[T]his is the coming together of those two technologies.'

本周，罗氏SBX技术主管、Stratos联合创始人马克·科科里斯表示，过去几年来“创新源源不断”。 “[这]是这两种技术的结合。”

Co-invented by Kokoris and Robert McRuer, another Stratos cofounder, the SBX chemistry works by enzymatically converting a DNA molecule into a larger surrogate, dubbed Xpandomer. Four distinct novel molecules called X-NTPs, or High Signal-to-Noise Reporters — one for each DNA base — are used during the Xpandomer synthesis..

由科科里斯和斯特拉托斯公司的另一位联合创始人罗伯特·麦克鲁尔共同发明的SBX化学技术，通过酶促反应将DNA分子转化为更大的替代物，称为Xpandomer。在Xpandomer合成过程中，使用了四种不同的新型分子，称为X-NTP或高信噪比报告分子——每种对应一个DNA碱基。

The Xpandomer, which is more than 50 times longer than the original DNA fragment, then passes through a biological nanopore, creating distinct electrical signals for each X-NTP that are translated back into the original nucleic acid sequence.

Xpandomer 比原始 DNA 片段长 50 多倍，然后通过生物纳米孔，为每个 X-NTP 产生不同的电信号，并将其转译回原始核酸序列。

'Our approach to efficiently sequencing DNA is to not sequence DNA,' Kokoris explained.

“我们高效测序DNA的方法就是不去测序DNA，”科科里斯解释说。

During the presentation, Kokoris delineated some of the technical innovations to optimize the Xpandomers for the nanopore readout. For instance, he noted that the researchers introduced a so-called translocation control element, enabling a 'clean, reproducible, synchronized modulation of the Xpandomer as it moves through the nanopore.'.

在报告中，Kokoris 详细介绍了为优化 Xpandomers 的纳米孔读取而进行的一些技术创新。例如，他指出研究人员引入了所谓的移位控制元件，从而实现“Xpandomer 在穿过纳米孔时的干净、可重复、同步的调制”。

Additionally, since 'most polymerases don't like X-NTPs,' Kokoris said, the team introduced

此外，由于“大多数聚合酶不喜欢 X-NTP，”科科里斯说，团队引入了

enhancer chemistries dubbed Symmetrically Synthesized Reporter Tethers (SSRTs) into the Xpandomer structure.

将增强化学物质称为对称合成报告链（SSRTs）整合到Xpandomer结构中。

Furthermore, Kokoris said the team deployed rational design as well as high-throughput screening to engineer and select appropriate polymerases that can

此外，Kokoris 表示团队运用了理性设计和高通量筛选来设计和选择合适的聚合酶，这些聚合酶能够

incorporate X-NTPs with high affinity.

结合具有高亲和力的X-NTP。

He also offered an overview of the instrumentation for SBX sequencing, an Xpandomer

他还概述了SBX测序和Xpandomer的仪器。

synthesis instrument as well as an SBX sequencer.

合成器以及SBX音序器。

The Xpandomer

Xpandomer

synthesis platform is essentially a liquid handling system that directs reagents onto a so-called XP chip, where Xpandomers are produced through solid-phase synthesis, Kokoris said.

Kokoris说，合成平台本质上是一个液体处理系统，它将试剂引导到所谓的XP芯片上，在那里通过固相合成产生Xpandomers。

Meanwhile, the SBX sequencer can achieve single-molecule sequencing using a

同时，SBX测序仪可以使用以下方法实现单分子测序

Complementary Metal Oxide Semiconductor (CMOS)-based sensor module, an array that combines microwells, electrodes, and detection circuits and that handles the analog to digital conversion.

基于互补金属氧化物半导体（CMOS）的传感器模块，该阵列结合了微孔、电极和检测电路，并负责模拟到数字的转换。

According to Kokoris, a lipid bilayer with embedded protein nanopores is created for every sequencing run. Of the 8 million parallel sensors, the company typically uses about 7 million to 7.5 million functioning pores per run. After each run, the sequencing sensor module can be reused.

根据Kokoris的说法，每次测序运行都会创建一个嵌有蛋白质纳米孔的脂质双层。在800万个平行传感器中，公司通常每次运行使用大约700万到750万个功能正常的孔。每次运行后，测序传感器模块可以重复使用。

Kokoris declined to go into the details of Roche's nanopore design other than noting that the company has its 'own pore' for SBX sequencing. He also declined to comment on whether there is any overlap between Roche's protein nanopore and those owned by Oxford Nanopore Technologies, which claims a strong grip on the IP in the field..

科科里斯拒绝透露罗氏纳米孔设计的细节，仅指出公司拥有用于SBX测序的“自己的孔”。他还拒绝评论罗氏的蛋白质纳米孔与牛津纳米孔技术公司所拥有的纳米孔之间是否存在重叠，后者声称在该领域拥有强大的知识产权。

Kokoris said his team believes having dedicated instruments for Xpandomer

科科里斯表示，他的团队认为拥有专门用于Xpandomer的仪器非常重要。

synthesis and sequencing 'actually maximizes the flexibility of the technology,' though it might also be possible to integrate the platforms down the road.

合成和测序“实际上最大化了技术的灵活性”，尽管未来也有可能整合这些平台。

During his presentation, he highlighted two modes of sequencing for SBX: simplex, which Roche promises to be 'ultra-high throughput,' and duplex, which has increased accuracy.

在他的演讲中，他强调了SBX的两种测序模式：罗氏承诺“超高通量”的单工模式，以及准确性更高的双工模式。

For SBX duplex sequencing, a hairpin Y adapter is added to the template DNA molecule during library prep, which in turn produces an Xpandomer that contains both parental strands of the original molecule, resulting in increased sequencing accuracy, Kokoris noted.

Kokoris 指出，对于 SBX 双工测序，在文库制备过程中会向模板 DNA 分子添加一个发夹型 Y 接头，这将产生包含原始分子两条亲本链的 Xpandomer，从而提高测序准确性。

The duplex library requires 20 ng to 50 ng of unfragmented genomic DNA or 2.5 ng to 10 ng of cell-free DNA, though Kokoris said there is 'room to whittle that down and use even less' DNA input. Additionally, the duplex library is produced using linear amplification rather than PCR amplification to boost accuracy for homopolymer indels, he noted.

双链文库需要20至50纳克的未片段化基因组DNA或2.5至10纳克的无细胞DNA，不过Kokoris表示有“进一步减少甚至使用更少DNA输入”的空间。此外，他指出，双链文库是通过线性扩增而非PCR扩增生成的，以提高对均聚物插入缺失的准确性。

.

。

Using the HG001 cell line as a benchmarking sample, Roche claimed SBX duplex whole-genome sequencing can achieve a quality score of

使用HG001细胞系作为基准样本，罗氏声称SBX双工全基因组测序可以达到的质量评分为

Q39, with F-1 scores of 99.80 percent for single nucleotide variants and 99.56 percent for indels.

Q39，单核苷酸变异的F-1评分为99.80％，插入缺失的F-1评分为99.56％。

In another sequencing experiment using seven Genome in a Bottle (GIAB) samples, the sequencer generated 5.3 billion duplex reads in an hour with each sample having 34X to 38X coverage.

在另一个使用七个“瓶中基因组”（GIAB）样本的测序实验中，测序仪在一小时内生成了53亿条双工读取，每个样本的覆盖率为34倍到38倍。

In terms of read length, Roche quoted a 150 bp to 350 bp insert length for duplex sequencing and 200 bp to more than 1,000 bp for simplex sequencing.

在读长方面，罗氏引用的双工测序插入长度为150 bp至350 bp，而单工测序为200 bp至超过1,000 bp。

Besides speed and throughput, Roche emphasized the flexible scalability of SBX.

除了速度和吞吐量，罗氏还强调了SBX的灵活扩展性。

'The one thing on our mind from the very beginning of SBX was flexible operation,' Kokoris said. 'We want to be able to sequence up and down the throughput spectrum with impunity.'

“从 SBX 开始之初，我们心中唯一的想法就是灵活操作，”科科里斯说。“我们希望能够自如地在吞吐量范围内上下调整。”

Raw sequence data from the sensor are base called instantly, according to John Mannion, head of computational sciences at Roche's molecular labs systems. 'Real-time analysis is important,' he said during the webinar. 'We want to make sure that we are able to compress that data as it's streaming off and then allow users to move that to their location of secondary analysis.' .

传感器的原始序列数据会根据罗氏分子实验室系统计算科学主管约翰·曼尼昂的说法即时进行碱基识别。他在网络研讨会上表示：“实时分析非常重要。我们要确保在数据流式传输时能够对其进行压缩，然后让用户将数据转移到他们进行二级分析的位置。”

In addition, Mannion said duplex sequencing, mapping, alignment, and germline variant calling are 'all accelerated through various means.'

此外，曼尼翁表示，双工测序、作图、比对和生殖系变异检测“都通过各种手段得到了加速。”

Regarding the detection of epigenetic signatures, Kokoris said the technology is 'compatible with all the conversion chemistries,' and the team is still working to decide whether to optimize duplex or simplex sequencing for such assays.

关于表观遗传特征的检测，Kokoris表示该技术“兼容所有的转化化学方法”，团队仍在努力决定是否优化双链或单链测序以用于此类检测。

In addition, Kokoris said the SBX workflow is compatible with automation, and users can convert their existing Illumina libraries for the technology.

此外，Kokoris 表示 SBX 工作流程兼容自动化，用户可以将其现有的 Illumina 文库转换为该技术。

So far, Roche has deployed the SBX platforms to two early-access collaborators: the Hartwig Medical Foundation in the Netherlands and the Broad Institute.

到目前为止，罗氏已将SBX平台部署给两个早期访问的合作者：荷兰的哈特维格医学基金会和布罗德研究所。

According to Gustav Karlberg, Roche's life cycle leader of sequencing systems, the company will continue to work with these early-access collaborators throughout 2025 to demonstrate the performance of the SBX technology. In addition, Roche is looking to expand the early-access program 'in a selective way' by including additional collaborators with other applications and workflows of interest..

根据罗氏测序系统生命周期负责人古斯塔夫·卡尔伯格的说法，该公司将在 2025 年全年继续与这些早期访问的合作者合作，以展示 SBX 技术的性能。此外，罗氏希望通过纳入其他具有不同应用和工作流程的合作者，以“选择性的方式”扩展早期访问计划。

After that, Roche aims to first release the SBX platform as research product in 2026, Karlberg said.

卡尔伯格表示，之后罗氏的目标是首先在 2026 年将 SBX 平台作为研究产品发布。

Palani Kumaresan, global head of Roche diagnostics solutions, said that at launch, the company will introduce SBX 'as an open, standalone sequencing solution that both academic researchers and translational researchers can use to advance their work.'

罗氏诊断解决方案全球主管帕拉尼·库马雷桑表示，公司将在推出时将SBX“作为一款开放的、独立的测序解决方案，学术研究人员和转化研究人员都可以使用它来推进他们的工作。”

At the same time, 'we will have it as part of an end-to-end sequencing ecosystem that we can bring into a clinical setting, along with our assay kits,' he added.

他补充道：“同时，‘我们将把它作为端到端测序生态系统的一部分，可以与我们的检测套件一起引入临床环境。’”

Whenever Roche is ready to launch its SBX sequencer, it will find an NGS landscape vastly different from what it was a decade ago, when it acquired Genia and Stratos.

每当罗氏准备推出其 SBX 测序仪时，它将发现 NGS 领域与十年前收购 Genia 和 Stratos 时的情况大不相同。

Besides Oxford Nanopore and Pacific Biosciences, which continue to improve their accuracy,

除了牛津纳米孔公司和太平洋生物科学公司，这两家公司仍在不断提高其准确性，

throughput

吞吐量

, and cost, legacy players such as Illumina are also racing to enhance their read length.

，以及成本，Illumina等老牌企业也在努力提升其读取长度。

Additionally, China's

此外，中国的

BGI Group

华大集团

and Santa Clara, California-based

加利福尼亚州圣克拉拉县的

AxBio

AxBio

, which maintains operations in the US and China, are also entering the nanopore sequencing space.

，该公司在美国和中国都有业务，也正在进入纳米孔测序领域。

Roche declined to disclose the cost of SBX during the webinar. Kokoris said

罗氏在网路研讨会上拒绝透露SBX的成本。科科里斯表示

the firm strives to make the technology efficient and cost-competitive

公司致力于使这项技术高效且具有成本竞争力。

.

。

'If you're developing a sequencing technology, you have to be relentlessly thinking about the efficiencies of your process,' he said. 'That is top of mind for us always.'

“如果你正在开发一种测序技术，你必须始终不懈地思考你的流程效率，”他说。“这始终是我们最关心的问题。”