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Comparison of somatic mutation landscapes in Chinese versus European breast cancer patients

Recent genomic studies suggest that Asian breast cancer (BC) may have distinct somatic features; however, most comparisons of BC genomic features across populations did not account for differences in age, subtype, and sequencing methods. In this study, we analyzed whole-exome sequencing (WES) data t...

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Autores principales: Zhu, Bin, Joo, Lijin, Zhang, Tongwu, Koka, Hela, Lee, DongHyuk, Shi, Jianxin, Lee, Priscilla, Wang, Difei, Wang, Feng, Chan, Wing-cheong, Law, Sze Hong, Tsoi, Yee-kei, Tse, Gary M., Lai, Shui Wun, Wu, Cherry, Yang, Shuyuan, Yang Chan, Emily Ying, Shan Wong, Samuel Yeung, Wang, Mingyi, Song, Lei, Jones, Kristine, Hutchinson, Amy, Hicks, Belynda, Prokunina-Olsson, Ludmila, Garcia-Closas, Montserrat, Chanock, Stephen, Tse, Lap Ah, Yang, Xiaohong R.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8756551/
https://www.ncbi.nlm.nih.gov/pubmed/35047861
http://dx.doi.org/10.1016/j.xhgg.2021.100076
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author Zhu, Bin
Joo, Lijin
Zhang, Tongwu
Koka, Hela
Lee, DongHyuk
Shi, Jianxin
Lee, Priscilla
Wang, Difei
Wang, Feng
Chan, Wing-cheong
Law, Sze Hong
Tsoi, Yee-kei
Tse, Gary M.
Lai, Shui Wun
Wu, Cherry
Yang, Shuyuan
Yang Chan, Emily Ying
Shan Wong, Samuel Yeung
Wang, Mingyi
Song, Lei
Jones, Kristine
Zhu, Bin
Hutchinson, Amy
Hicks, Belynda
Prokunina-Olsson, Ludmila
Garcia-Closas, Montserrat
Chanock, Stephen
Tse, Lap Ah
Yang, Xiaohong R.
author_facet Zhu, Bin
Joo, Lijin
Zhang, Tongwu
Koka, Hela
Lee, DongHyuk
Shi, Jianxin
Lee, Priscilla
Wang, Difei
Wang, Feng
Chan, Wing-cheong
Law, Sze Hong
Tsoi, Yee-kei
Tse, Gary M.
Lai, Shui Wun
Wu, Cherry
Yang, Shuyuan
Yang Chan, Emily Ying
Shan Wong, Samuel Yeung
Wang, Mingyi
Song, Lei
Jones, Kristine
Zhu, Bin
Hutchinson, Amy
Hicks, Belynda
Prokunina-Olsson, Ludmila
Garcia-Closas, Montserrat
Chanock, Stephen
Tse, Lap Ah
Yang, Xiaohong R.
author_sort Zhu, Bin
collection PubMed
description Recent genomic studies suggest that Asian breast cancer (BC) may have distinct somatic features; however, most comparisons of BC genomic features across populations did not account for differences in age, subtype, and sequencing methods. In this study, we analyzed whole-exome sequencing (WES) data to characterize somatic copy number alterations (SCNAs) and mutation profiles in 98 Hong Kong BC (HKBC) patients and compared with those from The Cancer Genome Atlas of European ancestry (TCGA-EA, N = 686), which had similar distributions of age at diagnosis and PAM50 subtypes as in HKBC. We developed a two-sample Poisson model to compare driver gene selection pressure, which reflects the effect sizes of cancer driver genes, while accounting for differences in sample size, sequencing platforms, depths, and mutation calling methods. We found that somatic mutation and SCNA profiles were overall very similar between HKBC and TCGA-EA. The selection pressure for small insertions and deletions (indels) in GATA3 (false discovery rate (FDR) corrected p < 0.01) and single-nucleotide variants (SNVs) in TP53 (nominal p = 0.02, FDR corrected p = 0.28) was lower in HKBC than in TCGA-EA. Among the 13 signatures of single-base substitutions (SBS) that are common in BC, we found a suggestively higher contribution of SBS18 and a lower contribution of SBS1 in HKBC than in TCGA-EA, while the two APOBEC-induced signatures showed similar prevalence. Our results suggest that the genomic landscape of BC was largely very similar between HKBC and TCGA-EA, despite suggestive differences in some driver genes and mutational signatures that warrant future investigations in large and diverse Asian populations.
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spelling pubmed-87565512022-01-18 Comparison of somatic mutation landscapes in Chinese versus European breast cancer patients Zhu, Bin Joo, Lijin Zhang, Tongwu Koka, Hela Lee, DongHyuk Shi, Jianxin Lee, Priscilla Wang, Difei Wang, Feng Chan, Wing-cheong Law, Sze Hong Tsoi, Yee-kei Tse, Gary M. Lai, Shui Wun Wu, Cherry Yang, Shuyuan Yang Chan, Emily Ying Shan Wong, Samuel Yeung Wang, Mingyi Song, Lei Jones, Kristine Zhu, Bin Hutchinson, Amy Hicks, Belynda Prokunina-Olsson, Ludmila Garcia-Closas, Montserrat Chanock, Stephen Tse, Lap Ah Yang, Xiaohong R. HGG Adv Article Recent genomic studies suggest that Asian breast cancer (BC) may have distinct somatic features; however, most comparisons of BC genomic features across populations did not account for differences in age, subtype, and sequencing methods. In this study, we analyzed whole-exome sequencing (WES) data to characterize somatic copy number alterations (SCNAs) and mutation profiles in 98 Hong Kong BC (HKBC) patients and compared with those from The Cancer Genome Atlas of European ancestry (TCGA-EA, N = 686), which had similar distributions of age at diagnosis and PAM50 subtypes as in HKBC. We developed a two-sample Poisson model to compare driver gene selection pressure, which reflects the effect sizes of cancer driver genes, while accounting for differences in sample size, sequencing platforms, depths, and mutation calling methods. We found that somatic mutation and SCNA profiles were overall very similar between HKBC and TCGA-EA. The selection pressure for small insertions and deletions (indels) in GATA3 (false discovery rate (FDR) corrected p < 0.01) and single-nucleotide variants (SNVs) in TP53 (nominal p = 0.02, FDR corrected p = 0.28) was lower in HKBC than in TCGA-EA. Among the 13 signatures of single-base substitutions (SBS) that are common in BC, we found a suggestively higher contribution of SBS18 and a lower contribution of SBS1 in HKBC than in TCGA-EA, while the two APOBEC-induced signatures showed similar prevalence. Our results suggest that the genomic landscape of BC was largely very similar between HKBC and TCGA-EA, despite suggestive differences in some driver genes and mutational signatures that warrant future investigations in large and diverse Asian populations. Elsevier 2021-12-03 /pmc/articles/PMC8756551/ /pubmed/35047861 http://dx.doi.org/10.1016/j.xhgg.2021.100076 Text en © 2021 The Authors https://creativecommons.org/licenses/by-nc-nd/3.0/igo/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/igo/).
spellingShingle Article
Zhu, Bin
Joo, Lijin
Zhang, Tongwu
Koka, Hela
Lee, DongHyuk
Shi, Jianxin
Lee, Priscilla
Wang, Difei
Wang, Feng
Chan, Wing-cheong
Law, Sze Hong
Tsoi, Yee-kei
Tse, Gary M.
Lai, Shui Wun
Wu, Cherry
Yang, Shuyuan
Yang Chan, Emily Ying
Shan Wong, Samuel Yeung
Wang, Mingyi
Song, Lei
Jones, Kristine
Zhu, Bin
Hutchinson, Amy
Hicks, Belynda
Prokunina-Olsson, Ludmila
Garcia-Closas, Montserrat
Chanock, Stephen
Tse, Lap Ah
Yang, Xiaohong R.
Comparison of somatic mutation landscapes in Chinese versus European breast cancer patients
title Comparison of somatic mutation landscapes in Chinese versus European breast cancer patients
title_full Comparison of somatic mutation landscapes in Chinese versus European breast cancer patients
title_fullStr Comparison of somatic mutation landscapes in Chinese versus European breast cancer patients
title_full_unstemmed Comparison of somatic mutation landscapes in Chinese versus European breast cancer patients
title_short Comparison of somatic mutation landscapes in Chinese versus European breast cancer patients
title_sort comparison of somatic mutation landscapes in chinese versus european breast cancer patients
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8756551/
https://www.ncbi.nlm.nih.gov/pubmed/35047861
http://dx.doi.org/10.1016/j.xhgg.2021.100076
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