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

Mykyta Artomov; Alexander J. Stratigos; Ivana Kim; Raj Kumar; Martin Lauss; Bobby Y. Reddy; Benchun Miao; Carla Daniela Robles-Espinoza; Aravind Sankar; Ching Ni Njauw; Kristen Shannon; Evangelos S. Gragoudas; Anne Marie Lane; Vivek Iyer; Julia A. Newton-Bishop; D. Timothy Bishop; Elizabeth A. Holland; Graham J. Mann; Tarjinder Singh; Mark J. Daly; Hensin Tsao

doi:10.1093/jnci/djx083

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

Mykyta Artomov, Alexander J. Stratigos, Ivana Kim, Raj Kumar, Martin Lauss, Bobby Y. Reddy, Benchun Miao, Carla Daniela Robles-Espinoza, Aravind Sankar, Ching Ni Njauw, Kristen Shannon, Evangelos S. Gragoudas, Anne Marie Lane, Vivek Iyer, Julia A. Newton-Bishop, D. Timothy Bishop, Elizabeth A. Holland, Graham J. Mann, Tarjinder Singh, Mark J. DalyHensin Tsao^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

23 Citations (Scopus)

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 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_min = 6.16×10^-8) in the CM cohort (n=273) and BAP1 (P_min = 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.

Original language	English
Article number	djx083
Journal	Journal of the National Cancer Institute
Volume	109
Issue number	12
DOIs	https://doi.org/10.1093/jnci/djx083
Publication status	Published - 1 Jul 2018
Externally published	Yes

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Artomov, M., Stratigos, A. J., Kim, I., Kumar, R., Lauss, M., Reddy, B. Y., Miao, B., Robles-Espinoza, C. D., Sankar, A., Njauw, C. N., Shannon, K., Gragoudas, E. S., Lane, A. M., Iyer, V., Newton-Bishop, J. A., Bishop, D. T., Holland, E. A., Mann, G. J., Singh, T., ... Tsao, H. (2018). Rare variant, gene-based association study of hereditary melanoma using whole-exome sequencing. Journal of the National Cancer Institute, 109(12), Article djx083. https://doi.org/10.1093/jnci/djx083

@article{a0d89405cf3d4594899a942c9be813c7,

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

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 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.",

author = "Mykyta Artomov and Stratigos, {Alexander J.} and Ivana Kim and Raj Kumar and Martin Lauss and Reddy, {Bobby Y.} and Benchun Miao and Robles-Espinoza, {Carla Daniela} and Aravind Sankar and Njauw, {Ching Ni} and Kristen Shannon and Gragoudas, {Evangelos S.} and Lane, {Anne Marie} and Vivek Iyer and Newton-Bishop, {Julia A.} and Bishop, {D. Timothy} and Holland, {Elizabeth A.} and Mann, {Graham J.} and Tarjinder Singh and Daly, {Mark J.} and Hensin Tsao",

year = "2018",

month = jul,

day = "1",

doi = "10.1093/jnci/djx083",

language = "English",

volume = "109",

journal = "Journal of the National Cancer Institute",

issn = "0027-8874",

publisher = "Oxford University Press ",

number = "12",

}

Artomov, M, Stratigos, AJ, Kim, I, Kumar, R, Lauss, M, Reddy, BY, Miao, B, Robles-Espinoza, CD, Sankar, A, Njauw, CN, Shannon, K, Gragoudas, ES, Lane, AM, Iyer, V, Newton-Bishop, JA, Bishop, DT, Holland, EA, Mann, GJ, Singh, T, Daly, MJ & Tsao, H 2018, 'Rare variant, gene-based association study of hereditary melanoma using whole-exome sequencing', Journal of the National Cancer Institute, vol. 109, no. 12, djx083. https://doi.org/10.1093/jnci/djx083

TY - JOUR

T1 - Rare variant, gene-based association study of hereditary melanoma using whole-exome sequencing

AU - Artomov, Mykyta

AU - Stratigos, Alexander J.

AU - Kim, Ivana

AU - Kumar, Raj

AU - Lauss, Martin

AU - Reddy, Bobby Y.

AU - Miao, Benchun

AU - Robles-Espinoza, Carla Daniela

AU - Sankar, Aravind

AU - Njauw, Ching Ni

AU - Shannon, Kristen

AU - Gragoudas, Evangelos S.

AU - Lane, Anne Marie

AU - Iyer, Vivek

AU - Newton-Bishop, Julia A.

AU - Bishop, D. Timothy

AU - Holland, Elizabeth A.

AU - Mann, Graham J.

AU - Singh, Tarjinder

AU - Daly, Mark J.

AU - Tsao, Hensin

PY - 2018/7/1

Y1 - 2018/7/1

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85055343042&partnerID=8YFLogxK

U2 - 10.1093/jnci/djx083

DO - 10.1093/jnci/djx083

M3 - Article

SN - 0027-8874

VL - 109

JO - Journal of the National Cancer Institute

JF - Journal of the National Cancer Institute

IS - 12

M1 - djx083

ER -

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

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