Phasing analysis of lung cancer genomes using a long read sequencer

Yoshitaka Sakamoto, Shuhei Miyake, Miho Oka, Akinori Kanai, Yosuke Kawai, Satoi Nagasawa, Yuichi Shiraishi, Katsushi Tokunaga, Takashi Kohno, Masahide Seki, Yutaka Suzuki () and Ayako Suzuki ()
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Yoshitaka Sakamoto: The University of Tokyo
Shuhei Miyake: The University of Tokyo
Miho Oka: The University of Tokyo
Akinori Kanai: The University of Tokyo
Yosuke Kawai: National Center for Global Health and Medicine
Satoi Nagasawa: The University of Tokyo
Yuichi Shiraishi: National Cancer Center Research Institute
Katsushi Tokunaga: National Center for Global Health and Medicine
Takashi Kohno: National Cancer Center Research Institute
Masahide Seki: The University of Tokyo
Yutaka Suzuki: The University of Tokyo
Ayako Suzuki: The University of Tokyo

Nature Communications, 2022, vol. 13, issue 1, 1-17

Abstract: Abstract Chromosomal backgrounds of cancerous mutations still remain elusive. Here, we conduct the phasing analysis of non-small cell lung cancer specimens of 20 Japanese patients. By the combinatory use of short and long read sequencing data, we obtain long phased blocks of 834 kb in N50 length with >99% concordance rate. By analyzing the obtained phasing information, we reveal that several cancer genomes harbor regions in which mutations are unevenly distributed to either of two haplotypes. Large-scale chromosomal rearrangement events, which resemble chromothripsis events but have smaller scales, occur on only one chromosome, and these events account for the observed biased distributions. Interestingly, the events are characteristic of EGFR mutation-positive lung adenocarcinomas. Further integration of long read epigenomic and transcriptomic data reveal that haploid chromosomes are not always at equivalent transcriptomic/epigenomic conditions. Distinct chromosomal backgrounds are responsible for later cancerous aberrations in a haplotype-specific manner.

Date: 2022
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DOI: 10.1038/s41467-022-31133-6

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