21.1 A Fully Integrated Genetic Variant Discovery SoC for Next-Generation Sequencing

Yi Chung Wu, Yen Lung Chen, Chung Hsuan Yang, Chao Hsi Lee, Chao Yang Yu, Nian Shyang Chang, Ling Chien Chen, Jia Rong Chang, Chun Pin Lin, Hung Lieh Chen, Chi Shi Chen, Jui Hung Hung, Chia Hsiang Yang

研究成果: Conference contribution同行評審

摘要

Next-generation sequencing (NGS) is now indispensable for genetics research and biomedical applications, such as disease analysis and evolution tracking [1]. However, it still takes up to a couple of days to analyze all genetic mutations (variants) of a human genome, which consists of 3 billion nucleotides, through GPU acceleration. Fig. 21.1.1 shows an overview of NGS and the data analysis workflow. The NGS technology enables sequencing hundreds of millions of DNA segments, anchored and amplified on a microarray, in parallel. In each sequencing cycle, the nucleotides (A, T, C, G) are individually detected by their unique fluorescence labels and DNA segments can then be constructed as short reads. The NGS data analysis workflow consists of Preprocessing, Short-Read Mapping (including Exact Matching and Inexact Matching), Haplotype Calling, and Variant Calling [2]. Short reads are first mapped to a reference DNA and further used to assemble the genome of the DNA sample. Preprocessing is essential for constructing the data structure for indexing the reference DNA. In Short-Read Mapping, a seeding-and-extension scheme is applied to perform both Exact and Inexact Matching. The equal-length sub-sequences (seeds) of the short reads are used to find the exact locations on the reference DNA. Then, the seeds are extended to identify the most-likely locations through global alignment, allowing mismatches and insertions/deletions [2]. Next, in Haplotype Calling, the reads mapped to a specific region are assembled to reconstruct the paternal and maternal genomes (i.e. haplotypes) of the DNA sample. Finally, in Variant Calling, the assembled haplotypes are used to determine the variants between the reference DNA and the sample DNA. The outputs of Variant Calling indicate the location and likelihood of each variant. Dedicated VLSI solutions have been developed for acceleration, but only Suffix-Array (SA) Sorting for Preprocessing and Exact Matching for Short-Read Mapping were realized on silicon [3]. This work presents a fully integrated SoC for the entire NGS data analysis process.
原文English
主出版物標題2020 IEEE INTERNATIONAL SOLID- STATE CIRCUITS CONFERENCE (ISSCC)
發行者Institute of Electrical and Electronics Engineers Inc.
頁面322-324
頁數3
ISBN(電子)9781728132044
ISBN(列印)978-1-7281-3206-8
DOIs
出版狀態Published - 二月 2020
事件2020 IEEE International Solid-State Circuits Conference, ISSCC 2020 - San Francisco, United States
持續時間: 16 二月 202020 二月 2020

出版系列

名字IEEE International Solid State Circuits Conference
發行者IEEE
ISSN(列印)0193-6530

Conference

Conference2020 IEEE International Solid-State Circuits Conference, ISSCC 2020
國家United States
城市San Francisco
期間16/02/2020/02/20

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