{"id":407602,"date":"2025-09-08T10:44:12","date_gmt":"2025-09-08T10:44:12","guid":{"rendered":"https:\/\/www.europesays.com\/uk\/407602\/"},"modified":"2025-09-08T10:44:12","modified_gmt":"2025-09-08T10:44:12","slug":"2025-innovator-of-the-year-sneha-goenka-for-developing-an-ultra-fast-sequencing-technology","status":"publish","type":"post","link":"https:\/\/www.europesays.com\/uk\/407602\/","title":{"rendered":"2025 Innovator of the Year: Sneha Goenka for developing an ultra-fast sequencing technology"},"content":{"rendered":"\n

Goenka saw a better way: Build a real-time system that could \u201cstream\u201d the sequencing data, analyzing it as it was being generated, like streaming a film on Netflix rather than downloading it to watch later.<\/p>\n

\"Sneha <\/p>\n

To do this, she designed a cloud computing architecture to pull in more processing power. Goenka\u2019s first challenge was to increase the speed at which her team could upload the raw data for processing, by streamlining the requests between the sequencer and the cloud to avoid unnecessary \u201cchatter.\u201d She worked out the exact number of communication channels needed\u2014and created algorithms that allowed those channels to be reused in the most efficient way.<\/p>\n

The next challenge was \u201cbase calling\u201d\u2014converting the raw signal from the sequencing machine into the nucleotide bases A, C, T, and G, the language that makes up our DNA. Rather than using a central node to orchestrate this process, which is an inefficient, error-prone approach, Goenka wrote software to automatically assign dozens of data streams directly from the sequencer to dedicated nodes in the cloud.<\/p>\n

\n

Meet the rest of this year’s\u00a0
Innovators Under 35<\/a>.<\/p>\n<\/blockquote>\n

Then, to identify mutations, the sequences were aligned for comparison with a reference genome. She coded a custom program that triggers alignment as soon as base calling finishes for one batch of sequences while simultaneously initiating base calling for the next batch, thus ensuring that the system\u2019s computational resources are used efficiently.<\/p>\n

Add all these im\u00ad\u00adprove\u00ad\u00adments together, and Goenka\u2019s approach reduced the total time required to analyze a genome for mutations from around 20 hours to 1.5 hours. Finally, the team worked with genetic counselors and physicians to create a filter that identified which mutations were most critical to a person\u2019s health, and that set was then given a final manual curation by a genetic specialist. These final stages take up to three hours. The technology was close to being fully operational when, suddenly, the first patient arrived.\u00a0<\/p>\n

A critical test <\/p>\n

When 13-year-old Matthew was flown to Stanford\u2019s children\u2019s hospital in 2021, he was struggling to breathe and his heart was failing. Doctors needed to know whether the inflammation in his heart was due to a virus or to a genetic mutation that would necessitate a transplant.\u00a0\u00a0<\/p>\n

His blood was drawn on a Thursday. The transplant committee made its decisions on Fridays. \u201cIt meant we had a small window of time,\u201d says Goenka.<\/p>\n

Goenka was in Mumbai when the sequencing began. She stayed up all night, monitoring the computations. That was when the project stopped being about getting faster for the sake of it, she says: \u201cIt became about \u2018How fast can we get this result to save this person\u2019s life?\u2019\u201d<\/p>\n","protected":false},"excerpt":{"rendered":"Goenka saw a better way: Build a real-time system that could \u201cstream\u201d the sequencing data, analyzing it as…\n","protected":false},"author":2,"featured_media":407603,"comment_status":"","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[3846],"tags":[267,70,16,15],"class_list":{"0":"post-407602","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-genetics","8":"tag-genetics","9":"tag-science","10":"tag-uk","11":"tag-united-kingdom"},"share_on_mastodon":{"url":"https:\/\/pubeurope.com\/@uk\/115168271948782145","error":""},"_links":{"self":[{"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/posts\/407602","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/comments?post=407602"}],"version-history":[{"count":0,"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/posts\/407602\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/media\/407603"}],"wp:attachment":[{"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/media?parent=407602"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/categories?post=407602"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/tags?post=407602"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}