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Rare variant, gene-based association study of hereditary melanoma using whole-exome sequencing

Artomov, Mykyta ; Stratigos, Alexander J. ; Kim, Ivana ; Kumar, Raj ; Lauss, Martin LU ; Reddy, Bobby Y. ; Miao, Benchun ; Robles-Espinoza, Carla Daniela ; Sankar, Aravind and Njauw, Ching Ni , et al. (2017) In Journal of the National Cancer Institute 109(12).
Abstract

Background: Extraordinary progress has been made in our understanding of common variants in many diseases, including melanoma. Because the contribution of rare coding variants is not as well characterized, we performed an exome-wide, gene-based association study of familial cutaneous melanoma (CM) and ocular melanoma (OM). Methods: Using 11 990 jointly processed individual DNA samples, whole-exome sequencing was performed, followed by largescale joint variant calling using GATK (Genome Analysis ToolKit). PLINK/SEQ was used for statistical analysis of genetic variation. Fourmodels were used to estimate the association among different types of variants. In vitro functional validation was performed using three humanmelanoma cell lines in... (More)

Background: Extraordinary progress has been made in our understanding of common variants in many diseases, including melanoma. Because the contribution of rare coding variants is not as well characterized, we performed an exome-wide, gene-based association study of familial cutaneous melanoma (CM) and ocular melanoma (OM). Methods: Using 11 990 jointly processed individual DNA samples, whole-exome sequencing was performed, followed by largescale joint variant calling using GATK (Genome Analysis ToolKit). PLINK/SEQ was used for statistical analysis of genetic variation. Fourmodels were used to estimate the association among different types of variants. In vitro functional validation was performed using three humanmelanoma cell lines in 2D and 3D proliferation assays. In vivo tumor growth was assessed using xenografts of humanmelanoma A375melanoma cells in nudemice (eightmice per group). All statistical tests were two-sided. Results: Strong signals were detected for CDKN2A (Pmin = 6.16×10-8) in the CM cohort (n=273) and BAP1 (Pmin = 3.83×10-6) in the OM (n=99) cohort. Eleven genes that exhibited borderline association (P < 10-4) were independently validated using The Cancer Genome Atlas melanoma cohort (379 CM, 47 OM) and a matched set of 3563 European controls with CDKN2A (P = .009), BAP1 (P = .03), and EBF3 (P = 4.75×10-4), a candidate risk locus, all showing evidence of replication. EBF3 was then evaluated using germline data from a set of 132 familial melanoma cases and 4769 controls of UK origin (joint P = 1.37×10-5). Somatically, loss of EBF3 expression correlated with progression, poorer outcome, and high MITF tumors. Functionally, induction of EBF3 in melanoma cells reduced cell growth in vitro, retarded tumor formation in vivo, and reduced MITF levels. Conclusions: The results of this large rare variant germline association study further define the mutational landscape of hereditary melanoma and implicate EBF3 as a possible CM predisposition gene.

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Contribution to journal
publication status
published
subject
in
Journal of the National Cancer Institute
volume
109
issue
12
article number
djx083
publisher
Oxford University Press
external identifiers
  • scopus:85055343042
ISSN
0027-8874
DOI
10.1093/jnci/djx083
language
English
LU publication?
yes
id
fe57645c-531e-43e9-8f90-debe0c832ede
date added to LUP
2019-01-09 13:49:48
date last changed
2022-03-02 19:02:22
@article{fe57645c-531e-43e9-8f90-debe0c832ede,
  abstract     = {{<p>Background: Extraordinary progress has been made in our understanding of common variants in many diseases, including melanoma. Because the contribution of rare coding variants is not as well characterized, we performed an exome-wide, gene-based association study of familial cutaneous melanoma (CM) and ocular melanoma (OM). Methods: Using 11 990 jointly processed individual DNA samples, whole-exome sequencing was performed, followed by largescale joint variant calling using GATK (Genome Analysis ToolKit). PLINK/SEQ was used for statistical analysis of genetic variation. Fourmodels were used to estimate the association among different types of variants. In vitro functional validation was performed using three humanmelanoma cell lines in 2D and 3D proliferation assays. In vivo tumor growth was assessed using xenografts of humanmelanoma A375melanoma cells in nudemice (eightmice per group). All statistical tests were two-sided. Results: Strong signals were detected for CDKN2A (P<sub>min</sub> = 6.16×10<sup>-8</sup>) in the CM cohort (n=273) and BAP1 (P<sub>min</sub> = 3.83×10<sup>-6</sup>) in the OM (n=99) cohort. Eleven genes that exhibited borderline association (P &lt; 10<sup>-4</sup>) were independently validated using The Cancer Genome Atlas melanoma cohort (379 CM, 47 OM) and a matched set of 3563 European controls with CDKN2A (P = .009), BAP1 (P = .03), and EBF3 (P = 4.75×10<sup>-4</sup>), a candidate risk locus, all showing evidence of replication. EBF3 was then evaluated using germline data from a set of 132 familial melanoma cases and 4769 controls of UK origin (joint P = 1.37×10<sup>-5</sup>). Somatically, loss of EBF3 expression correlated with progression, poorer outcome, and high MITF tumors. Functionally, induction of EBF3 in melanoma cells reduced cell growth in vitro, retarded tumor formation in vivo, and reduced MITF levels. Conclusions: The results of this large rare variant germline association study further define the mutational landscape of hereditary melanoma and implicate EBF3 as a possible CM predisposition gene.</p>}},
  author       = {{Artomov, Mykyta and Stratigos, Alexander J. and Kim, Ivana and Kumar, Raj and Lauss, Martin and Reddy, Bobby Y. and Miao, Benchun and Robles-Espinoza, Carla Daniela and Sankar, Aravind and Njauw, Ching Ni and Shannon, Kristen and Gragoudas, Evangelos S. and Lane, Anne Marie and Iyer, Vivek and Newton-Bishop, Julia A. and Bishop, D. Timothy and Holland, Elizabeth A. and Mann, Graham J. and Singh, Tarjinder and Barrett, Jeffrey C and Adams, David J and Jönsson, Göran and Daly, Mark J. and Tsao, Hensin}},
  issn         = {{0027-8874}},
  language     = {{eng}},
  number       = {{12}},
  publisher    = {{Oxford University Press}},
  series       = {{Journal of the National Cancer Institute}},
  title        = {{Rare variant, gene-based association study of hereditary melanoma using whole-exome sequencing}},
  url          = {{http://dx.doi.org/10.1093/jnci/djx083}},
  doi          = {{10.1093/jnci/djx083}},
  volume       = {{109}},
  year         = {{2017}},
}