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Germline whole exome sequencing and large-scale replication identifies .

Oncotarget

Dicks E, Song H, Ramus SJ, Oudenhove EV, Tyrer JP, Intermaggio MP, Kar S, Harrington P, Bowtell DD, Group AS, Cicek MS, Cunningham JM, Fridley BL, Alsop J, Jimenez-Linan M, Piskorz A, Goranova T, Kent E, Siddiqui N, Paul J, Crawford R, Poblete S, Lele S, Sucheston-Campbell L, Moysich KB, Sieh W, McGuire V, Lester J, Odunsi K, Whittemore AS, Bogdanova N, Dürst M, Hillemanns P, Karlan BY, Gentry-Maharaj A, Menon U, Tischkowitz M, Levine D, Brenton JD, Dörk T, Goode EL, Gayther SA, Pharoah DPP.
PMID: 28881617
Oncotarget. 2017 Mar 03;8(31):50930-50940. doi: 10.18632/oncotarget.15871. eCollection 2017 Aug 01.

We analyzed whole exome sequencing data in germline DNA from 412 high grade serous ovarian cancer (HGSOC) cases from The Cancer Genome Atlas Project and identified 5,517 genes harboring a predicted deleterious germline coding mutation in at least one...

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Dicks E, Song H, Ramus SJ, et al. Germline whole exome sequencing and large-scale replication identifies . Oncotarget. 2017;8(31):50930-50940doi: 10.18632/oncotarget.15871.
Dicks, E., Song, H., Ramus, S. J., Oudenhove, E. V., Tyrer, J. P., Intermaggio, M. P., Kar, S., Harrington, P., Bowtell, D. D., Group, A. S., Cicek, M. S., Cunningham, J. M., Fridley, B. L., Alsop, J., Jimenez-Linan, M., Piskorz, A., Goranova, T., Kent, E., Siddiqui, N., Paul, J., Crawford, R., Poblete, S., Lele, S., Sucheston-Campbell, L., Moysich, K. B., Sieh, W., McGuire, V., Lester, J., Odunsi, K., Whittemore, A. S., Bogdanova, N., Dürst, M., Hillemanns, P., Karlan, B. Y., Gentry-Maharaj, A., Menon, U., Tischkowitz, M., Levine, D., Brenton, J. D., Dörk, T., Goode, E. L., Gayther, S. A., & Pharoah, D. P. P. (2017). Germline whole exome sequencing and large-scale replication identifies . Oncotarget, 8(31), 50930-50940. https://doi.org/10.18632/oncotarget.15871
Dicks, Ed, et al. "Germline whole exome sequencing and large-scale replication identifies ." Oncotarget vol. 8,31 (2017): 50930-50940. doi: https://doi.org/10.18632/oncotarget.15871
Dicks E, Song H, Ramus SJ, Oudenhove EV, Tyrer JP, Intermaggio MP, Kar S, Harrington P, Bowtell DD, Group AS, Cicek MS, Cunningham JM, Fridley BL, Alsop J, Jimenez-Linan M, Piskorz A, Goranova T, Kent E, Siddiqui N, Paul J, Crawford R, Poblete S, Lele S, Sucheston-Campbell L, Moysich KB, Sieh W, McGuire V, Lester J, Odunsi K, Whittemore AS, Bogdanova N, Dürst M, Hillemanns P, Karlan BY, Gentry-Maharaj A, Menon U, Tischkowitz M, Levine D, Brenton JD, Dörk T, Goode EL, Gayther SA, Pharoah DPP. Germline whole exome sequencing and large-scale replication identifies . Oncotarget. 2017 Mar 03;8(31):50930-50940. doi: 10.18632/oncotarget.15871. eCollection 2017 Aug 01. PMID: 28881617; PMCID: PMC5584218.
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Assessment of genotype imputation methods.

BMC proceedings

Biernacka JM, Tang R, Li J, McDonnell SK, Rabe KG, Sinnwell JP, Rider DN, de Andrade M, Goode EL, Fridley BL.
PMID: 20018042
BMC Proc. 2009 Dec 15;3:S5. doi: 10.1186/1753-6561-3-s7-s5.

Several methods have been proposed to impute genotypes at untyped markers using observed genotypes and genetic data from a reference panel. We used the Genetic Analysis Workshop 16 rheumatoid arthritis case-control dataset to compare the performance of four of...

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Biernacka JM, Tang R, Li J, et al. Assessment of genotype imputation methods. BMC Proc. 2009;3:S5doi: 10.1186/1753-6561-3-s7-s5.
Biernacka, J. M., Tang, R., Li, J., McDonnell, S. K., Rabe, K. G., Sinnwell, J. P., Rider, D. N., de Andrade, M., Goode, E. L., & Fridley, B. L. (2009). Assessment of genotype imputation methods. BMC proceedings, 3S5. https://doi.org/10.1186/1753-6561-3-s7-s5
Biernacka, Joanna M, et al. "Assessment of genotype imputation methods." BMC proceedings vol. 3 (2009): S5. doi: https://doi.org/10.1186/1753-6561-3-s7-s5
Biernacka JM, Tang R, Li J, McDonnell SK, Rabe KG, Sinnwell JP, Rider DN, de Andrade M, Goode EL, Fridley BL. Assessment of genotype imputation methods. BMC Proc. 2009 Dec 15;3:S5. doi: 10.1186/1753-6561-3-s7-s5. PMID: 20018042; PMCID: PMC2795949.
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Common Genetic Variation in Circadian Rhythm Genes and Risk of Epithelial Ovarian Cancer (EOC).

Journal of genetics and genome research

Jim HS, Lin HY, Tyrer JP, Lawrenson K, Dennis J, Chornokur G, Chen Z, Chen AY, Permuth-Wey J, Aben KK, Anton-Culver H, Antonenkova N, Bruinsma F, Bandera EV, Bean YT, Beckmann MW, Bisogna M, Bjorge L, Bogdanova N, Brinton LA, Brooks-Wilson A, Bunker CH, Butzow R, Campbell IG, Carty K, Chang-Claude J, Cook LS, Cramer DW, Cunningham JM, Cybulski C, Dansonka-Mieszkowska A, du Bois A, Despierre E, Sieh W, Doherty JA, Dörk T, Dürst M, Easton DF, Eccles DM, Edwards RP, Ekici AB, Fasching PA, Fridley BL, Gao YT, Gentry-Maharaj A, Giles GG, Glasspool R, Goodman MT, Gronwald J, Harter P, Hasmad HN, Hein A, Heitz F, Hildebrandt MA, Hillemanns P, Hogdall CK, Hogdall E, Hosono S, Iversen ES, Jakubowska A, Jensen A, Ji BT, Karlan BY, Kellar M, Kiemeney LA, Krakstad C, Kjaer SK, Kupryjanczyk J, Vierkant RA, Lambrechts D, Lambrechts S, Le ND, Lee AW, Lele S, Leminen A, Lester J, Levine DA, Liang D, Lim BK, Lissowska J, Lu K, Lubinski J, Lundvall L, Massuger LF, Matsuo K, McGuire V, McLaughlin JR, McNeish I, Menon U, Milne RL, Modugno F, Thomsen L, Moysich KB, Ness RB, Nevanlinna H, Eilber U, Odunsi K, Olson SH, Orlow I, Orsulic S, Palmieri Weber R, Paul J, Pearce CL, Pejovic T, Pelttari LM, Pike MC, Poole EM, Schernhammer E, Risch HA, Rosen B, Rossing MA, Rothstein JH, Rudolph A, Runnebaum IB, Rzepecka IK, Salvesen HB, Schwaab I, Shu XO, Shvetsov YB, Siddiqui N, Song H, Southey MC, Spiewankiewicz B, Sucheston-Campbell L, Teo SH, Terry KL, Thompson PJ, Tangen IL, Tworoger SS, van Altena AM, Vergote I, Walsh CS, Wang-Gohrke S, Wentzensen N, Whittemore AS, Wicklund KG, Wilkens LR, Wu AH, Wu X, Woo YL, Yang H, Zheng W, Ziogas A, Amankwah E, Berchuck A, Schildkraut JM, Kelemen LE, Ramus SJ, Monteiro AN, Goode EL, Narod SA, Gayther SA, Pharoah PD, Sellers TA, Phelan CM.
PMID: 26807442
J Genet Genome Res. 2015;2(2). doi: 10.23937/2378-3648/1410017. Epub 2015 Sep 15.

Disruption in circadian gene expression, whether due to genetic variation or environmental factors (e.g., light at night, shiftwork), is associated with increased incidence of breast, prostate, gastrointestinal and hematologic cancers and gliomas. Circadian genes are highly expressed in the...

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Jim HS, Lin HY, Tyrer JP, et al. Common Genetic Variation in Circadian Rhythm Genes and Risk of Epithelial Ovarian Cancer (EOC). J Genet Genome Res. 2015;2(2)doi: 10.23937/2378-3648/1410017.
Jim, H. S., Lin, H. Y., Tyrer, J. P., Lawrenson, K., Dennis, J., Chornokur, G., Chen, Z., Chen, A. Y., Permuth-Wey, J., Aben, K. K., Anton-Culver, H., Antonenkova, N., Bruinsma, F., Bandera, E. V., Bean, Y. T., Beckmann, M. W., Bisogna, M., Bjorge, L., Bogdanova, N., Brinton, L. A., Brooks-Wilson, A., Bunker, C. H., Butzow, R., Campbell, I. G., Carty, K., Chang-Claude, J., Cook, L. S., Cramer, D. W., Cunningham, J. M., Cybulski, C., Dansonka-Mieszkowska, A., du Bois, A., Despierre, E., Sieh, W., Doherty, J. A., Dörk, T., Dürst, M., Easton, D. F., Eccles, D. M., Edwards, R. P., Ekici, A. B., Fasching, P. A., Fridley, B. L., Gao, Y. T., Gentry-Maharaj, A., Giles, G. G., Glasspool, R., Goodman, M. T., Gronwald, J., Harter, P., Hasmad, H. N., Hein, A., Heitz, F., Hildebrandt, M. A., Hillemanns, P., Hogdall, C. K., Hogdall, E., Hosono, S., Iversen, E. S., Jakubowska, A., Jensen, A., Ji, B. T., Karlan, B. Y., Kellar, M., Kiemeney, L. A., Krakstad, C., Kjaer, S. K., Kupryjanczyk, J., Vierkant, R. A., Lambrechts, D., Lambrechts, S., Le, N. D., Lee, A. W., Lele, S., Leminen, A., Lester, J., Levine, D. A., Liang, D., Lim, B. K., Lissowska, J., Lu, K., Lubinski, J., Lundvall, L., Massuger, L. F., Matsuo, K., McGuire, V., McLaughlin, J. R., McNeish, I., Menon, U., Milne, R. L., Modugno, F., Thomsen, L., Moysich, K. B., Ness, R. B., Nevanlinna, H., Eilber, U., Odunsi, K., Olson, S. H., Orlow, I., Orsulic, S., Palmieri Weber, R., Paul, J., Pearce, C. L., Pejovic, T., Pelttari, L. M., Pike, M. C., Poole, E. M., Schernhammer, E., Risch, H. A., Rosen, B., Rossing, M. A., Rothstein, J. H., Rudolph, A., Runnebaum, I. B., Rzepecka, I. K., Salvesen, H. B., Schwaab, I., Shu, X. O., Shvetsov, Y. B., Siddiqui, N., Song, H., Southey, M. C., Spiewankiewicz, B., Sucheston-Campbell, L., Teo, S. H., Terry, K. L., Thompson, P. J., Tangen, I. L., Tworoger, S. S., van Altena, A. M., Vergote, I., Walsh, C. S., Wang-Gohrke, S., Wentzensen, N., Whittemore, A. S., Wicklund, K. G., Wilkens, L. R., Wu, A. H., Wu, X., Woo, Y. L., Yang, H., Zheng, W., Ziogas, A., Amankwah, E., Berchuck, A., Schildkraut, J. M., Kelemen, L. E., Ramus, S. J., Monteiro, A. N., Goode, E. L., Narod, S. A., Gayther, S. A., Pharoah, P. D., Sellers, T. A., & Phelan, C. M. (2015). Common Genetic Variation in Circadian Rhythm Genes and Risk of Epithelial Ovarian Cancer (EOC). Journal of genetics and genome research, 2(2), . https://doi.org/10.23937/2378-3648/1410017
Jim, Heather S L, et al. "Common Genetic Variation in Circadian Rhythm Genes and Risk of Epithelial Ovarian Cancer (EOC)." Journal of genetics and genome research vol. 2,2 (2015). doi: https://doi.org/10.23937/2378-3648/1410017
Jim HS, Lin HY, Tyrer JP, Lawrenson K, Dennis J, Chornokur G, Chen Z, Chen AY, Permuth-Wey J, Aben KK, Anton-Culver H, Antonenkova N, Bruinsma F, Bandera EV, Bean YT, Beckmann MW, Bisogna M, Bjorge L, Bogdanova N, Brinton LA, Brooks-Wilson A, Bunker CH, Butzow R, Campbell IG, Carty K, Chang-Claude J, Cook LS, Cramer DW, Cunningham JM, Cybulski C, Dansonka-Mieszkowska A, du Bois A, Despierre E, Sieh W, Doherty JA, Dörk T, Dürst M, Easton DF, Eccles DM, Edwards RP, Ekici AB, Fasching PA, Fridley BL, Gao YT, Gentry-Maharaj A, Giles GG, Glasspool R, Goodman MT, Gronwald J, Harter P, Hasmad HN, Hein A, Heitz F, Hildebrandt MA, Hillemanns P, Hogdall CK, Hogdall E, Hosono S, Iversen ES, Jakubowska A, Jensen A, Ji BT, Karlan BY, Kellar M, Kiemeney LA, Krakstad C, Kjaer SK, Kupryjanczyk J, Vierkant RA, Lambrechts D, Lambrechts S, Le ND, Lee AW, Lele S, Leminen A, Lester J, Levine DA, Liang D, Lim BK, Lissowska J, Lu K, Lubinski J, Lundvall L, Massuger LF, Matsuo K, McGuire V, McLaughlin JR, McNeish I, Menon U, Milne RL, Modugno F, Thomsen L, Moysich KB, Ness RB, Nevanlinna H, Eilber U, Odunsi K, Olson SH, Orlow I, Orsulic S, Palmieri Weber R, Paul J, Pearce CL, Pejovic T, Pelttari LM, Pike MC, Poole EM, Schernhammer E, Risch HA, Rosen B, Rossing MA, Rothstein JH, Rudolph A, Runnebaum IB, Rzepecka IK, Salvesen HB, Schwaab I, Shu XO, Shvetsov YB, Siddiqui N, Song H, Southey MC, Spiewankiewicz B, Sucheston-Campbell L, Teo SH, Terry KL, Thompson PJ, Tangen IL, Tworoger SS, van Altena AM, Vergote I, Walsh CS, Wang-Gohrke S, Wentzensen N, Whittemore AS, Wicklund KG, Wilkens LR, Wu AH, Wu X, Woo YL, Yang H, Zheng W, Ziogas A, Amankwah E, Berchuck A, Schildkraut JM, Kelemen LE, Ramus SJ, Monteiro AN, Goode EL, Narod SA, Gayther SA, Pharoah PD, Sellers TA, Phelan CM. Common Genetic Variation in Circadian Rhythm Genes and Risk of Epithelial Ovarian Cancer (EOC). J Genet Genome Res. 2015;2(2). doi: 10.23937/2378-3648/1410017. Epub 2015 Sep 15. PMID: 26807442; PMCID: PMC4722961.
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Frequent POLE-driven hypermutation in ovarian endometrioid cancer revealed by mutational signatures in RNA sequencing.

BMC medical genomics

Davila JI, Chanana P, Sarangi V, Fogarty ZC, Weroha SJ, Guo R, Goode EL, Huang Y, Wang C.
PMID: 34158040
BMC Med Genomics. 2021 Jun 22;14(1):165. doi: 10.1186/s12920-021-01017-7.

BACKGROUND: DNA polymerase epsilon (POLE) is encoded by the POLE gene, and POLE-driven tumors are characterized by high mutational rates. POLE-driven tumors are relatively common in endometrial and colorectal cancer, and their presence is increasingly recognized in ovarian cancer...

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Davila JI, Chanana P, Sarangi V, et al. Frequent POLE-driven hypermutation in ovarian endometrioid cancer revealed by mutational signatures in RNA sequencing. BMC Med Genomics. 2021;14(1):165doi: 10.1186/s12920-021-01017-7.
Davila, J. I., Chanana, P., Sarangi, V., Fogarty, Z. C., Weroha, S. J., Guo, R., Goode, E. L., Huang, Y., & Wang, C. (2021). Frequent POLE-driven hypermutation in ovarian endometrioid cancer revealed by mutational signatures in RNA sequencing. BMC medical genomics, 14(1), 165. https://doi.org/10.1186/s12920-021-01017-7
Davila, Jaime I, et al. "Frequent POLE-driven hypermutation in ovarian endometrioid cancer revealed by mutational signatures in RNA sequencing." BMC medical genomics vol. 14,1 (2021): 165. doi: https://doi.org/10.1186/s12920-021-01017-7
Davila JI, Chanana P, Sarangi V, Fogarty ZC, Weroha SJ, Guo R, Goode EL, Huang Y, Wang C. Frequent POLE-driven hypermutation in ovarian endometrioid cancer revealed by mutational signatures in RNA sequencing. BMC Med Genomics. 2021 Jun 22;14(1):165. doi: 10.1186/s12920-021-01017-7. PMID: 34158040; PMCID: PMC8218518.
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Identification of a Locus Near .

Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology

Quinn MCJ, McCue K, Shi W, Johnatty SE, Beesley J, Civitarese A, O'Mara TA, Glubb DM, Tyrer JP, Armasu SM, Ong JS, Gharahkhani P, Lu Y, Gao B, Patch AM, Fasching PA, Beckmann MW, Lambrechts D, Vergote I, Velez Edwards DR, Beeghly-Fadiel A, Benitez J, Garcia MJ, Goodman MT, Dörk T, Dürst M, Modugno F, Moysich K, du Bois A, Pfisterer J, Bauman K, Karlan BY, Lester J, Cunningham JM, Larson MC, McCauley BM, Kjaer SK, Jensen A, Hogdall CK, Hogdall E, Schildkraut JM, Riggan MJ, Berchuck A, Cramer DW, Terry KL, Bjorge L, Webb PM, Friedlander M, Pejovic T, Moffitt M, Glasspool R, May T, Ene GEV, Huntsman DG, Woo M, Carney ME, Hinsley S, Heitz F, Fereday S, Kennedy CJ, Edwards SL, Winham SJ, deFazio A, Pharoah PDP, Goode EL, MacGregor S, Chenevix-Trench G.
PMID: 34162658
Cancer Epidemiol Biomarkers Prev. 2021 Sep;30(9):1669-1680. doi: 10.1158/1055-9965.EPI-20-1817. Epub 2021 Jun 23.

BACKGROUND: Many loci have been found to be associated with risk of epithelial ovarian cancer (EOC). However, although there is considerable variation in progression-free survival (PFS), no loci have been found to be associated with outcome at genome-wide levels...

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Quinn MCJ, McCue K, Shi W, et al. Identification of a Locus Near . Cancer Epidemiol Biomarkers Prev. 2021;30(9):1669-1680doi: 10.1158/1055-9965.EPI-20-1817.
Quinn, M. C. J., McCue, K., Shi, W., Johnatty, S. E., Beesley, J., Civitarese, A., O'Mara, T. A., Glubb, D. M., Tyrer, J. P., Armasu, S. M., Ong, J. S., Gharahkhani, P., Lu, Y., Gao, B., Patch, A. M., Fasching, P. A., Beckmann, M. W., Lambrechts, D., Vergote, I., Velez Edwards, D. R., Beeghly-Fadiel, A., Benitez, J., Garcia, M. J., Goodman, M. T., Dörk, T., Dürst, M., Modugno, F., Moysich, K., du Bois, A., Pfisterer, J., Bauman, K., Karlan, B. Y., Lester, J., Cunningham, J. M., Larson, M. C., McCauley, B. M., Kjaer, S. K., Jensen, A., Hogdall, C. K., Hogdall, E., Schildkraut, J. M., Riggan, M. J., Berchuck, A., Cramer, D. W., Terry, K. L., Bjorge, L., Webb, P. M., Friedlander, M., Pejovic, T., Moffitt, M., Glasspool, R., May, T., Ene, G. E. V., Huntsman, D. G., Woo, M., Carney, M. E., Hinsley, S., Heitz, F., Fereday, S., Kennedy, C. J., Edwards, S. L., Winham, S. J., deFazio, A., Pharoah, P. D. P., Goode, E. L., MacGregor, S., Chenevix-Trench, G. (2021). Identification of a Locus Near . Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology, 30(9), 1669-1680. https://doi.org/10.1158/1055-9965.EPI-20-1817
Quinn, Michael C J, et al. "Identification of a Locus Near ." Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology vol. 30,9 (2021): 1669-1680. doi: https://doi.org/10.1158/1055-9965.EPI-20-1817
Quinn MCJ, McCue K, Shi W, Johnatty SE, Beesley J, Civitarese A, O'Mara TA, Glubb DM, Tyrer JP, Armasu SM, Ong JS, Gharahkhani P, Lu Y, Gao B, Patch AM, Fasching PA, Beckmann MW, Lambrechts D, Vergote I, Velez Edwards DR, Beeghly-Fadiel A, Benitez J, Garcia MJ, Goodman MT, Dörk T, Dürst M, Modugno F, Moysich K, du Bois A, Pfisterer J, Bauman K, Karlan BY, Lester J, Cunningham JM, Larson MC, McCauley BM, Kjaer SK, Jensen A, Hogdall CK, Hogdall E, Schildkraut JM, Riggan MJ, Berchuck A, Cramer DW, Terry KL, Bjorge L, Webb PM, Friedlander M, Pejovic T, Moffitt M, Glasspool R, May T, Ene GEV, Huntsman DG, Woo M, Carney ME, Hinsley S, Heitz F, Fereday S, Kennedy CJ, Edwards SL, Winham SJ, deFazio A, Pharoah PDP, Goode EL, MacGregor S, Chenevix-Trench G. Identification of a Locus Near . Cancer Epidemiol Biomarkers Prev. 2021 Sep;30(9):1669-1680. doi: 10.1158/1055-9965.EPI-20-1817. Epub 2021 Jun 23. PMID: 34162658; PMCID: PMC8419101.
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Germline copy number variation and ovarian cancer survival.

Frontiers in genetics

Fridley BL, Chalise P, Tsai YY, Sun Z, Vierkant RA, Larson MC, Cunningham JM, Iversen ES, Fenstermacher D, Barnholtz-Sloan J, Asmann Y, Risch HA, Schildkraut JM, Phelan CM, Sutphen R, Sellers TA, Goode EL.
PMID: 22891074
Front Genet. 2012 Aug 08;3:142. doi: 10.3389/fgene.2012.00142. eCollection 2012.

Copy number variants (CNVs) have been implicated in many complex diseases. We examined whether inherited CNVs were associated with overall survival among women with invasive epithelial ovarian cancer. Germline DNA from 1,056 cases (494 deceased, average of 3.7 years...

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Fridley BL, Chalise P, Tsai YY, et al. Germline copy number variation and ovarian cancer survival. Front Genet. 2012;3:142doi: 10.3389/fgene.2012.00142.
Fridley, B. L., Chalise, P., Tsai, Y. Y., Sun, Z., Vierkant, R. A., Larson, M. C., Cunningham, J. M., Iversen, E. S., Fenstermacher, D., Barnholtz-Sloan, J., Asmann, Y., Risch, H. A., Schildkraut, J. M., Phelan, C. M., Sutphen, R., Sellers, T. A., & Goode, E. L. (2012). Germline copy number variation and ovarian cancer survival. Frontiers in genetics, 3142. https://doi.org/10.3389/fgene.2012.00142
Fridley, Brooke L, et al. "Germline copy number variation and ovarian cancer survival." Frontiers in genetics vol. 3 (2012): 142. doi: https://doi.org/10.3389/fgene.2012.00142
Fridley BL, Chalise P, Tsai YY, Sun Z, Vierkant RA, Larson MC, Cunningham JM, Iversen ES, Fenstermacher D, Barnholtz-Sloan J, Asmann Y, Risch HA, Schildkraut JM, Phelan CM, Sutphen R, Sellers TA, Goode EL. Germline copy number variation and ovarian cancer survival. Front Genet. 2012 Aug 08;3:142. doi: 10.3389/fgene.2012.00142. eCollection 2012. PMID: 22891074; PMCID: PMC3413872.
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Polymorphisms in ABCB1 and ERCC2 associated with ovarian cancer outcome.

International journal of molecular epidemiology and genetics

Peethambaram P, Fridley BL, Vierkant RA, Larson MC, Kalli KR, Elliott EA, Oberg AL, White KL, Rider DN, Keeney GL, Cunningham JM, Hartmann LC, Goode EL.
PMID: 21686133
Int J Mol Epidemiol Genet. 2011;2(2):185-95. Epub 2011 May 02.

Using the most comprehensive approach to selecting polymorphisms to date, we sought to examine whether time to recurrence in ovarian cancer was associated with common inherited variation in eight genes involved in drug metabolism, multi-drug resistance, or DNA repair,...

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Peethambaram P, Fridley BL, Vierkant RA, et al. Polymorphisms in ABCB1 and ERCC2 associated with ovarian cancer outcome. Int J Mol Epidemiol Genet. 2011;2(2):185-95
Peethambaram, P., Fridley, B. L., Vierkant, R. A., Larson, M. C., Kalli, K. R., Elliott, E. A., Oberg, A. L., White, K. L., Rider, D. N., Keeney, G. L., Cunningham, J. M., Hartmann, L. C., & Goode, E. L. (2011). Polymorphisms in ABCB1 and ERCC2 associated with ovarian cancer outcome. International journal of molecular epidemiology and genetics, 2(2), 185-95.
Peethambaram, Prema, et al. "Polymorphisms in ABCB1 and ERCC2 associated with ovarian cancer outcome." International journal of molecular epidemiology and genetics vol. 2,2 (2011): 185-95.
Peethambaram P, Fridley BL, Vierkant RA, Larson MC, Kalli KR, Elliott EA, Oberg AL, White KL, Rider DN, Keeney GL, Cunningham JM, Hartmann LC, Goode EL. Polymorphisms in ABCB1 and ERCC2 associated with ovarian cancer outcome. Int J Mol Epidemiol Genet. 2011;2(2):185-95. Epub 2011 May 02. PMID: 21686133; PMCID: PMC3110393.
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Population-based targeted sequencing of 54 candidate genes identifies .

Journal of medical genetics

Song H, Dicks EM, Tyrer J, Intermaggio M, Chenevix-Trench G, Bowtell DD, Traficante N, Group A, Brenton J, Goranova T, Hosking K, Piskorz A, van Oudenhove E, Doherty J, Harris HR, Rossing MA, Duerst M, Dork T, Bogdanova NV, Modugno F, Moysich K, Odunsi K, Ness R, Karlan BY, Lester J, Jensen A, Krüger Kjaer S, Høgdall E, Campbell IG, Lázaro C, Pujara MA, Cunningham J, Vierkant R, Winham SJ, Hildebrandt M, Huff C, Li D, Wu X, Yu Y, Permuth JB, Levine DA, Schildkraut JM, Riggan MJ, Berchuck A, Webb PM, Group OS, Cybulski C, Gronwald J, Jakubowska A, Lubinski J, Alsop J, Harrington P, Chan I, Menon U, Pearce CL, Wu AH, de Fazio A, Kennedy CJ, Goode E, Ramus S, Gayther S, Pharoah P.
PMID: 32546565
J Med Genet. 2021 May;58(5):305-313. doi: 10.1136/jmedgenet-2019-106739. Epub 2020 Jun 16.

PURPOSE: The known epithelial ovarian cancer (EOC) susceptibility genes account for less than 50% of the heritable risk of ovarian cancer suggesting that other susceptibility genes exist. The aim of this study was to evaluate the contribution to ovarian...

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Song H, Dicks EM, Tyrer J, et al. Population-based targeted sequencing of 54 candidate genes identifies . J Med Genet. 2020;58(5):305-313doi: 10.1136/jmedgenet-2019-106739.
Song, H., Dicks, E. M., Tyrer, J., Intermaggio, M., Chenevix-Trench, G., Bowtell, D. D., Traficante, N., Group, A., Brenton, J., Goranova, T., Hosking, K., Piskorz, A., van Oudenhove, E., Doherty, J., Harris, H. R., Rossing, M. A., Duerst, M., Dork, T., Bogdanova, N. V., Modugno, F., Moysich, K., Odunsi, K., Ness, R., Karlan, B. Y., Lester, J., Jensen, A., Krüger Kjaer, S., Høgdall, E., Campbell, I. G., Lázaro, C., Pujara, M. A., Cunningham, J., Vierkant, R., Winham, S. J., Hildebrandt, M., Huff, C., Li, D., Wu, X., Yu, Y., Permuth, J. B., Levine, D. A., Schildkraut, J. M., Riggan, M. J., Berchuck, A., Webb, P. M., Group, O. S., Cybulski, C., Gronwald, J., Jakubowska, A., Lubinski, J., Alsop, J., Harrington, P., Chan, I., Menon, U., Pearce, C. L., Wu, A. H., de Fazio, A., Kennedy, C. J., Goode, E., Ramus, S., Gayther, S., & Pharoah, P. (2021). Population-based targeted sequencing of 54 candidate genes identifies . Journal of medical genetics, 58(5), 305-313. https://doi.org/10.1136/jmedgenet-2019-106739
Song, Honglin, et al. "Population-based targeted sequencing of 54 candidate genes identifies ." Journal of medical genetics vol. 58,5 (2021): 305-313. doi: https://doi.org/10.1136/jmedgenet-2019-106739
Song H, Dicks EM, Tyrer J, Intermaggio M, Chenevix-Trench G, Bowtell DD, Traficante N, Group A, Brenton J, Goranova T, Hosking K, Piskorz A, van Oudenhove E, Doherty J, Harris HR, Rossing MA, Duerst M, Dork T, Bogdanova NV, Modugno F, Moysich K, Odunsi K, Ness R, Karlan BY, Lester J, Jensen A, Krüger Kjaer S, Høgdall E, Campbell IG, Lázaro C, Pujara MA, Cunningham J, Vierkant R, Winham SJ, Hildebrandt M, Huff C, Li D, Wu X, Yu Y, Permuth JB, Levine DA, Schildkraut JM, Riggan MJ, Berchuck A, Webb PM, Group OS, Cybulski C, Gronwald J, Jakubowska A, Lubinski J, Alsop J, Harrington P, Chan I, Menon U, Pearce CL, Wu AH, de Fazio A, Kennedy CJ, Goode E, Ramus S, Gayther S, Pharoah P. Population-based targeted sequencing of 54 candidate genes identifies . J Med Genet. 2021 May;58(5):305-313. doi: 10.1136/jmedgenet-2019-106739. Epub 2020 Jun 16. PMID: 32546565; PMCID: PMC8086250.
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Analyses of germline variants associated with ovarian cancer survival identify functional candidates at the 1q22 and 19p12 outcome loci.

Oncotarget

Glubb DM, Johnatty SE, Quinn MCJ, O'Mara TA, Tyrer JP, Gao B, Fasching PA, Beckmann MW, Lambrechts D, Vergote I, Velez Edwards DR, Beeghly-Fadiel A, Benitez J, Garcia MJ, Goodman MT, Thompson PJ, Dörk T, Dürst M, Modungo F, Moysich K, Heitz F, du Bois A, Pfisterer J, Hillemanns P, Karlan BY, Lester J, Goode EL, Cunningham JM, Winham SJ, Larson MC, McCauley BM, Kjær SK, Jensen A, Schildkraut JM, Berchuck A, Cramer DW, Terry KL, Salvesen HB, Bjorge L, Webb PM, Grant P, Pejovic T, Moffitt M, Hogdall CK, Hogdall E, Paul J, Glasspool R, Bernardini M, Tone A, Huntsman D, Woo M, Group A, deFazio A, Kennedy CJ, Pharoah PDP, MacGregor S, Chenevix-Trench G.
PMID: 29029385
Oncotarget. 2017 Jun 15;8(39):64670-64684. doi: 10.18632/oncotarget.18501. eCollection 2017 Sep 12.

We previously identified associations with ovarian cancer outcome at five genetic loci. To identify putatively causal genetic variants and target genes, we prioritized two ovarian outcome loci (1q22 and 19p12) for further study. Bioinformatic and functional genetic analyses indicated...

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Glubb DM, Johnatty SE, Quinn MCJ, et al. Analyses of germline variants associated with ovarian cancer survival identify functional candidates at the 1q22 and 19p12 outcome loci. Oncotarget. 2017;8(39):64670-64684doi: 10.18632/oncotarget.18501.
Glubb, D. M., Johnatty, S. E., Quinn, M. C. J., O'Mara, T. A., Tyrer, J. P., Gao, B., Fasching, P. A., Beckmann, M. W., Lambrechts, D., Vergote, I., Velez Edwards, D. R., Beeghly-Fadiel, A., Benitez, J., Garcia, M. J., Goodman, M. T., Thompson, P. J., Dörk, T., Dürst, M., Modungo, F., Moysich, K., Heitz, F., du Bois, A., Pfisterer, J., Hillemanns, P., Karlan, B. Y., Lester, J., Goode, E. L., Cunningham, J. M., Winham, S. J., Larson, M. C., McCauley, B. M., Kjær, S. K., Jensen, A., Schildkraut, J. M., Berchuck, A., Cramer, D. W., Terry, K. L., Salvesen, H. B., Bjorge, L., Webb, P. M., Grant, P., Pejovic, T., Moffitt, M., Hogdall, C. K., Hogdall, E., Paul, J., Glasspool, R., Bernardini, M., Tone, A., Huntsman, D., Woo, M., Group, A., deFazio, A., Kennedy, C. J., Pharoah, P. D. P., MacGregor, S., & Chenevix-Trench, G. (2017). Analyses of germline variants associated with ovarian cancer survival identify functional candidates at the 1q22 and 19p12 outcome loci. Oncotarget, 8(39), 64670-64684. https://doi.org/10.18632/oncotarget.18501
Glubb, Dylan M, et al. "Analyses of germline variants associated with ovarian cancer survival identify functional candidates at the 1q22 and 19p12 outcome loci." Oncotarget vol. 8,39 (2017): 64670-64684. doi: https://doi.org/10.18632/oncotarget.18501
Glubb DM, Johnatty SE, Quinn MCJ, O'Mara TA, Tyrer JP, Gao B, Fasching PA, Beckmann MW, Lambrechts D, Vergote I, Velez Edwards DR, Beeghly-Fadiel A, Benitez J, Garcia MJ, Goodman MT, Thompson PJ, Dörk T, Dürst M, Modungo F, Moysich K, Heitz F, du Bois A, Pfisterer J, Hillemanns P, Karlan BY, Lester J, Goode EL, Cunningham JM, Winham SJ, Larson MC, McCauley BM, Kjær SK, Jensen A, Schildkraut JM, Berchuck A, Cramer DW, Terry KL, Salvesen HB, Bjorge L, Webb PM, Grant P, Pejovic T, Moffitt M, Hogdall CK, Hogdall E, Paul J, Glasspool R, Bernardini M, Tone A, Huntsman D, Woo M, Group A, deFazio A, Kennedy CJ, Pharoah PDP, MacGregor S, Chenevix-Trench G. Analyses of germline variants associated with ovarian cancer survival identify functional candidates at the 1q22 and 19p12 outcome loci. Oncotarget. 2017 Jun 15;8(39):64670-64684. doi: 10.18632/oncotarget.18501. eCollection 2017 Sep 12. PMID: 29029385; PMCID: PMC5630285.
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EGFR as a prognostic biomarker and therapeutic target in ovarian cancer: evaluation of patient cohort and literature review.

Genes & cancer

Mehner C, Oberg AL, Goergen KM, Kalli KR, Maurer MJ, Nassar A, Goode EL, Keeney GL, Jatoi A, Radisky DC, Radisky ES.
PMID: 28740577
Genes Cancer. 2017 May;8(5):589-599. doi: 10.18632/genesandcancer.142.

BACKGROUND: Limited effectiveness of therapeutic agents targeting epidermal growth factor receptor (EGFR) in clinical trials using unselected ovarian cancer patients has prompted efforts to more effectively stratify patients who might best benefit from these therapies. A series of studies...

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Mehner C, Oberg AL, Goergen KM, et al. EGFR as a prognostic biomarker and therapeutic target in ovarian cancer: evaluation of patient cohort and literature review. Genes Cancer. 2017;8(5):589-599doi: 10.18632/genesandcancer.142.
Mehner, C., Oberg, A. L., Goergen, K. M., Kalli, K. R., Maurer, M. J., Nassar, A., Goode, E. L., Keeney, G. L., Jatoi, A., Radisky, D. C., & Radisky, E. S. (2017). EGFR as a prognostic biomarker and therapeutic target in ovarian cancer: evaluation of patient cohort and literature review. Genes & cancer, 8(5), 589-599. https://doi.org/10.18632/genesandcancer.142
Mehner, Christine, et al. "EGFR as a prognostic biomarker and therapeutic target in ovarian cancer: evaluation of patient cohort and literature review." Genes & cancer vol. 8,5 (2017): 589-599. doi: https://doi.org/10.18632/genesandcancer.142
Mehner C, Oberg AL, Goergen KM, Kalli KR, Maurer MJ, Nassar A, Goode EL, Keeney GL, Jatoi A, Radisky DC, Radisky ES. EGFR as a prognostic biomarker and therapeutic target in ovarian cancer: evaluation of patient cohort and literature review. Genes Cancer. 2017 May;8(5):589-599. doi: 10.18632/genesandcancer.142. PMID: 28740577; PMCID: PMC5511892.
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Single versus multiple imputation for genotypic data.

BMC proceedings

Fridley BL, McDonnell SK, Rabe KG, Tang R, Biernacka JM, Sinnwell JP, Rider DN, Goode EL.
PMID: 20018064
BMC Proc. 2009 Dec 15;3:S7. doi: 10.1186/1753-6561-3-s7-s7.

Due to the growing need to combine data across multiple studies and to impute untyped markers based on a reference sample, several analytical tools for imputation and analysis of missing genotypes have been developed. Current imputation methods rely on...

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Fridley BL, McDonnell SK, Rabe KG, et al. Single versus multiple imputation for genotypic data. BMC Proc. 2009;3:S7doi: 10.1186/1753-6561-3-s7-s7.
Fridley, B. L., McDonnell, S. K., Rabe, K. G., Tang, R., Biernacka, J. M., Sinnwell, J. P., Rider, D. N., & Goode, E. L. (2009). Single versus multiple imputation for genotypic data. BMC proceedings, 3S7. https://doi.org/10.1186/1753-6561-3-s7-s7
Fridley, Brooke L, et al. "Single versus multiple imputation for genotypic data." BMC proceedings vol. 3 (2009): S7. doi: https://doi.org/10.1186/1753-6561-3-s7-s7
Fridley BL, McDonnell SK, Rabe KG, Tang R, Biernacka JM, Sinnwell JP, Rider DN, Goode EL. Single versus multiple imputation for genotypic data. BMC Proc. 2009 Dec 15;3:S7. doi: 10.1186/1753-6561-3-s7-s7. PMID: 20018064; PMCID: PMC2795971.
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Regular Multivitamin Supplement Use, Single Nucleotide Polymorphisms in ATIC, SHMT2, and SLC46A1, and Risk of Ovarian Carcinoma.

Frontiers in genetics

Kelemen LE, Wang Q, Dinu I, Vierkant RA, Tsai YY, Cunningham JM, Phelan CM, Fridley BL, Amankwah EK, Iversen ES, Berchuck A, Schildkraut JM, Goode EL, Sellers TA.
PMID: 22461784
Front Genet. 2012 Mar 19;3:33. doi: 10.3389/fgene.2012.00033. eCollection 2012.

ATIC, SHMT2, and SLC46A1 have essential roles in one-carbon (1-C) transfer. The authors examined whether associations between ovarian carcinoma and 15 variants in these genes are modified by regular multivitamin use, a source of 1-C donors, among Caucasian participants...

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Kelemen LE, Wang Q, Dinu I, et al. Regular Multivitamin Supplement Use, Single Nucleotide Polymorphisms in ATIC, SHMT2, and SLC46A1, and Risk of Ovarian Carcinoma. Front Genet. 2012;3:33doi: 10.3389/fgene.2012.00033.
Kelemen, L. E., Wang, Q., Dinu, I., Vierkant, R. A., Tsai, Y. Y., Cunningham, J. M., Phelan, C. M., Fridley, B. L., Amankwah, E. K., Iversen, E. S., Berchuck, A., Schildkraut, J. M., Goode, E. L., & Sellers, T. A. (2012). Regular Multivitamin Supplement Use, Single Nucleotide Polymorphisms in ATIC, SHMT2, and SLC46A1, and Risk of Ovarian Carcinoma. Frontiers in genetics, 333. https://doi.org/10.3389/fgene.2012.00033
Kelemen, Linda E, et al. "Regular Multivitamin Supplement Use, Single Nucleotide Polymorphisms in ATIC, SHMT2, and SLC46A1, and Risk of Ovarian Carcinoma." Frontiers in genetics vol. 3 (2012): 33. doi: https://doi.org/10.3389/fgene.2012.00033
Kelemen LE, Wang Q, Dinu I, Vierkant RA, Tsai YY, Cunningham JM, Phelan CM, Fridley BL, Amankwah EK, Iversen ES, Berchuck A, Schildkraut JM, Goode EL, Sellers TA. Regular Multivitamin Supplement Use, Single Nucleotide Polymorphisms in ATIC, SHMT2, and SLC46A1, and Risk of Ovarian Carcinoma. Front Genet. 2012 Mar 19;3:33. doi: 10.3389/fgene.2012.00033. eCollection 2012. PMID: 22461784; PMCID: PMC3306919.
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