Comprehensive Somatic Copy Number Analysis Using Aqueous Humor Liquid Biopsy for Retinoblastoma

Aqueous humor (AH) liquid biopsy has been established as a surrogate tumor biopsy for retinoblastoma (RB). Previous AH studies have focused on highly recurrent RB somatic copy number alterations (SCNAs) including gain of 1q, 2p, 6p, and loss of 13q and 16q. In this retrospective study, we provide a...
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Autor*in:	Mary E. Kim [verfasserIn] Ashley Polski [verfasserIn] Liya Xu [verfasserIn] Rishvanth K. Prabakar [verfasserIn] Chen-Ching Peng [verfasserIn] Mark W. Reid [verfasserIn] Rachana Shah [verfasserIn] Peter Kuhn [verfasserIn] David Cobrinik [verfasserIn] James Hicks [verfasserIn] Jesse L. Berry [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2021

Schlagwörter:	retinoblastoma aqueous humor liquid biopsy cell-free DNA circulating tumor DNA SCNA

Übergeordnetes Werk:	In: Cancers - MDPI AG, 2010, 13(2021), 13, p 3340
Übergeordnetes Werk:	volume:13 ; year:2021 ; number:13, p 3340

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.3390/cancers13133340

Katalog-ID:	DOAJ058290605

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spelling	10.3390/cancers13133340 doi (DE-627)DOAJ058290605 (DE-599)DOAJ83b62ecbef954b0d8bd7776986597aa0 DE-627 ger DE-627 rakwb eng RC254-282 Mary E. Kim verfasserin aut Comprehensive Somatic Copy Number Analysis Using Aqueous Humor Liquid Biopsy for Retinoblastoma 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Aqueous humor (AH) liquid biopsy has been established as a surrogate tumor biopsy for retinoblastoma (RB). Previous AH studies have focused on highly recurrent RB somatic copy number alterations (SCNAs) including gain of 1q, 2p, 6p, and loss of 13q and 16q. In this retrospective study, we provide a comprehensive, whole-genome analysis of RB SCNAs and evaluate associated clinical features for 68 eyes of 64 RB patients from whom AH was obtained between December 2014 and October 2020. Shallow whole-genome sequencing of AH cell-free DNA was performed to assess for SCNAs. The prevalence of specific non-highly recurrent SCNAs, such as 20q gain and 8p loss, differed between primarily and secondarily enucleated eyes. Increases in chromosomal instability predict more advanced seeding morphology (<i<p</i< = 0.015); later age of diagnosis (<i<p</i< < 0.0001); greater odds of an endophytic tumor growth pattern (without retinal detachment; <i<p</i< = 0.047); tumor heights <10 mm (<i<p</i< = 0.09); and containing 6p gain, a biomarker of poor ocular prognosis (<i<p</i< = 0.004). The AH liquid biopsy platform is a high-yield method of whole-genome RB SCNA analysis, and SCNAs are associated with numerous clinical findings in RB eyes. Prospective analyses are encouraged to further elucidate the clinical relevance of specific SCNAs in RB. retinoblastoma aqueous humor liquid biopsy cell-free DNA circulating tumor DNA SCNA Neoplasms. Tumors. Oncology. Including cancer and carcinogens Ashley Polski verfasserin aut Liya Xu verfasserin aut Rishvanth K. Prabakar verfasserin aut Chen-Ching Peng verfasserin aut Mark W. Reid verfasserin aut Rachana Shah verfasserin aut Peter Kuhn verfasserin aut David Cobrinik verfasserin aut James Hicks verfasserin aut Jesse L. Berry verfasserin aut In Cancers MDPI AG, 2010 13(2021), 13, p 3340 (DE-627)614095670 (DE-600)2527080-1 20726694 nnns volume:13 year:2021 number:13, p 3340 https://doi.org/10.3390/cancers13133340 kostenfrei https://doaj.org/article/83b62ecbef954b0d8bd7776986597aa0 kostenfrei https://www.mdpi.com/2072-6694/13/13/3340 kostenfrei https://doaj.org/toc/2072-6694 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2021 13, p 3340
allfields_unstemmed	10.3390/cancers13133340 doi (DE-627)DOAJ058290605 (DE-599)DOAJ83b62ecbef954b0d8bd7776986597aa0 DE-627 ger DE-627 rakwb eng RC254-282 Mary E. Kim verfasserin aut Comprehensive Somatic Copy Number Analysis Using Aqueous Humor Liquid Biopsy for Retinoblastoma 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Aqueous humor (AH) liquid biopsy has been established as a surrogate tumor biopsy for retinoblastoma (RB). Previous AH studies have focused on highly recurrent RB somatic copy number alterations (SCNAs) including gain of 1q, 2p, 6p, and loss of 13q and 16q. In this retrospective study, we provide a comprehensive, whole-genome analysis of RB SCNAs and evaluate associated clinical features for 68 eyes of 64 RB patients from whom AH was obtained between December 2014 and October 2020. Shallow whole-genome sequencing of AH cell-free DNA was performed to assess for SCNAs. The prevalence of specific non-highly recurrent SCNAs, such as 20q gain and 8p loss, differed between primarily and secondarily enucleated eyes. Increases in chromosomal instability predict more advanced seeding morphology (<i<p</i< = 0.015); later age of diagnosis (<i<p</i< < 0.0001); greater odds of an endophytic tumor growth pattern (without retinal detachment; <i<p</i< = 0.047); tumor heights <10 mm (<i<p</i< = 0.09); and containing 6p gain, a biomarker of poor ocular prognosis (<i<p</i< = 0.004). The AH liquid biopsy platform is a high-yield method of whole-genome RB SCNA analysis, and SCNAs are associated with numerous clinical findings in RB eyes. Prospective analyses are encouraged to further elucidate the clinical relevance of specific SCNAs in RB. retinoblastoma aqueous humor liquid biopsy cell-free DNA circulating tumor DNA SCNA Neoplasms. Tumors. Oncology. Including cancer and carcinogens Ashley Polski verfasserin aut Liya Xu verfasserin aut Rishvanth K. Prabakar verfasserin aut Chen-Ching Peng verfasserin aut Mark W. Reid verfasserin aut Rachana Shah verfasserin aut Peter Kuhn verfasserin aut David Cobrinik verfasserin aut James Hicks verfasserin aut Jesse L. Berry verfasserin aut In Cancers MDPI AG, 2010 13(2021), 13, p 3340 (DE-627)614095670 (DE-600)2527080-1 20726694 nnns volume:13 year:2021 number:13, p 3340 https://doi.org/10.3390/cancers13133340 kostenfrei https://doaj.org/article/83b62ecbef954b0d8bd7776986597aa0 kostenfrei https://www.mdpi.com/2072-6694/13/13/3340 kostenfrei https://doaj.org/toc/2072-6694 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2021 13, p 3340
allfieldsGer	10.3390/cancers13133340 doi (DE-627)DOAJ058290605 (DE-599)DOAJ83b62ecbef954b0d8bd7776986597aa0 DE-627 ger DE-627 rakwb eng RC254-282 Mary E. Kim verfasserin aut Comprehensive Somatic Copy Number Analysis Using Aqueous Humor Liquid Biopsy for Retinoblastoma 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Aqueous humor (AH) liquid biopsy has been established as a surrogate tumor biopsy for retinoblastoma (RB). Previous AH studies have focused on highly recurrent RB somatic copy number alterations (SCNAs) including gain of 1q, 2p, 6p, and loss of 13q and 16q. In this retrospective study, we provide a comprehensive, whole-genome analysis of RB SCNAs and evaluate associated clinical features for 68 eyes of 64 RB patients from whom AH was obtained between December 2014 and October 2020. Shallow whole-genome sequencing of AH cell-free DNA was performed to assess for SCNAs. The prevalence of specific non-highly recurrent SCNAs, such as 20q gain and 8p loss, differed between primarily and secondarily enucleated eyes. Increases in chromosomal instability predict more advanced seeding morphology (<i<p</i< = 0.015); later age of diagnosis (<i<p</i< < 0.0001); greater odds of an endophytic tumor growth pattern (without retinal detachment; <i<p</i< = 0.047); tumor heights <10 mm (<i<p</i< = 0.09); and containing 6p gain, a biomarker of poor ocular prognosis (<i<p</i< = 0.004). The AH liquid biopsy platform is a high-yield method of whole-genome RB SCNA analysis, and SCNAs are associated with numerous clinical findings in RB eyes. Prospective analyses are encouraged to further elucidate the clinical relevance of specific SCNAs in RB. retinoblastoma aqueous humor liquid biopsy cell-free DNA circulating tumor DNA SCNA Neoplasms. Tumors. Oncology. Including cancer and carcinogens Ashley Polski verfasserin aut Liya Xu verfasserin aut Rishvanth K. Prabakar verfasserin aut Chen-Ching Peng verfasserin aut Mark W. Reid verfasserin aut Rachana Shah verfasserin aut Peter Kuhn verfasserin aut David Cobrinik verfasserin aut James Hicks verfasserin aut Jesse L. Berry verfasserin aut In Cancers MDPI AG, 2010 13(2021), 13, p 3340 (DE-627)614095670 (DE-600)2527080-1 20726694 nnns volume:13 year:2021 number:13, p 3340 https://doi.org/10.3390/cancers13133340 kostenfrei https://doaj.org/article/83b62ecbef954b0d8bd7776986597aa0 kostenfrei https://www.mdpi.com/2072-6694/13/13/3340 kostenfrei https://doaj.org/toc/2072-6694 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2021 13, p 3340
allfieldsSound	10.3390/cancers13133340 doi (DE-627)DOAJ058290605 (DE-599)DOAJ83b62ecbef954b0d8bd7776986597aa0 DE-627 ger DE-627 rakwb eng RC254-282 Mary E. Kim verfasserin aut Comprehensive Somatic Copy Number Analysis Using Aqueous Humor Liquid Biopsy for Retinoblastoma 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Aqueous humor (AH) liquid biopsy has been established as a surrogate tumor biopsy for retinoblastoma (RB). Previous AH studies have focused on highly recurrent RB somatic copy number alterations (SCNAs) including gain of 1q, 2p, 6p, and loss of 13q and 16q. In this retrospective study, we provide a comprehensive, whole-genome analysis of RB SCNAs and evaluate associated clinical features for 68 eyes of 64 RB patients from whom AH was obtained between December 2014 and October 2020. Shallow whole-genome sequencing of AH cell-free DNA was performed to assess for SCNAs. The prevalence of specific non-highly recurrent SCNAs, such as 20q gain and 8p loss, differed between primarily and secondarily enucleated eyes. Increases in chromosomal instability predict more advanced seeding morphology (<i<p</i< = 0.015); later age of diagnosis (<i<p</i< < 0.0001); greater odds of an endophytic tumor growth pattern (without retinal detachment; <i<p</i< = 0.047); tumor heights <10 mm (<i<p</i< = 0.09); and containing 6p gain, a biomarker of poor ocular prognosis (<i<p</i< = 0.004). The AH liquid biopsy platform is a high-yield method of whole-genome RB SCNA analysis, and SCNAs are associated with numerous clinical findings in RB eyes. Prospective analyses are encouraged to further elucidate the clinical relevance of specific SCNAs in RB. retinoblastoma aqueous humor liquid biopsy cell-free DNA circulating tumor DNA SCNA Neoplasms. Tumors. Oncology. Including cancer and carcinogens Ashley Polski verfasserin aut Liya Xu verfasserin aut Rishvanth K. Prabakar verfasserin aut Chen-Ching Peng verfasserin aut Mark W. Reid verfasserin aut Rachana Shah verfasserin aut Peter Kuhn verfasserin aut David Cobrinik verfasserin aut James Hicks verfasserin aut Jesse L. Berry verfasserin aut In Cancers MDPI AG, 2010 13(2021), 13, p 3340 (DE-627)614095670 (DE-600)2527080-1 20726694 nnns volume:13 year:2021 number:13, p 3340 https://doi.org/10.3390/cancers13133340 kostenfrei https://doaj.org/article/83b62ecbef954b0d8bd7776986597aa0 kostenfrei https://www.mdpi.com/2072-6694/13/13/3340 kostenfrei https://doaj.org/toc/2072-6694 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 13 2021 13, p 3340
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callnumber-first	R - Medicine
author	Mary E. Kim
spellingShingle	Mary E. Kim misc RC254-282 misc retinoblastoma misc aqueous humor misc liquid biopsy misc cell-free DNA misc circulating tumor DNA misc SCNA misc Neoplasms. Tumors. Oncology. Including cancer and carcinogens Comprehensive Somatic Copy Number Analysis Using Aqueous Humor Liquid Biopsy for Retinoblastoma
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topic_title	RC254-282 Comprehensive Somatic Copy Number Analysis Using Aqueous Humor Liquid Biopsy for Retinoblastoma retinoblastoma aqueous humor liquid biopsy cell-free DNA circulating tumor DNA SCNA
topic	misc RC254-282 misc retinoblastoma misc aqueous humor misc liquid biopsy misc cell-free DNA misc circulating tumor DNA misc SCNA misc Neoplasms. Tumors. Oncology. Including cancer and carcinogens
topic_unstemmed	misc RC254-282 misc retinoblastoma misc aqueous humor misc liquid biopsy misc cell-free DNA misc circulating tumor DNA misc SCNA misc Neoplasms. Tumors. Oncology. Including cancer and carcinogens
topic_browse	misc RC254-282 misc retinoblastoma misc aqueous humor misc liquid biopsy misc cell-free DNA misc circulating tumor DNA misc SCNA misc Neoplasms. Tumors. Oncology. Including cancer and carcinogens
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title	Comprehensive Somatic Copy Number Analysis Using Aqueous Humor Liquid Biopsy for Retinoblastoma
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title_sort	comprehensive somatic copy number analysis using aqueous humor liquid biopsy for retinoblastoma
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title_auth	Comprehensive Somatic Copy Number Analysis Using Aqueous Humor Liquid Biopsy for Retinoblastoma
abstract	Aqueous humor (AH) liquid biopsy has been established as a surrogate tumor biopsy for retinoblastoma (RB). Previous AH studies have focused on highly recurrent RB somatic copy number alterations (SCNAs) including gain of 1q, 2p, 6p, and loss of 13q and 16q. In this retrospective study, we provide a comprehensive, whole-genome analysis of RB SCNAs and evaluate associated clinical features for 68 eyes of 64 RB patients from whom AH was obtained between December 2014 and October 2020. Shallow whole-genome sequencing of AH cell-free DNA was performed to assess for SCNAs. The prevalence of specific non-highly recurrent SCNAs, such as 20q gain and 8p loss, differed between primarily and secondarily enucleated eyes. Increases in chromosomal instability predict more advanced seeding morphology (<i<p</i< = 0.015); later age of diagnosis (<i<p</i< < 0.0001); greater odds of an endophytic tumor growth pattern (without retinal detachment; <i<p</i< = 0.047); tumor heights <10 mm (<i<p</i< = 0.09); and containing 6p gain, a biomarker of poor ocular prognosis (<i<p</i< = 0.004). The AH liquid biopsy platform is a high-yield method of whole-genome RB SCNA analysis, and SCNAs are associated with numerous clinical findings in RB eyes. Prospective analyses are encouraged to further elucidate the clinical relevance of specific SCNAs in RB.
abstractGer	Aqueous humor (AH) liquid biopsy has been established as a surrogate tumor biopsy for retinoblastoma (RB). Previous AH studies have focused on highly recurrent RB somatic copy number alterations (SCNAs) including gain of 1q, 2p, 6p, and loss of 13q and 16q. In this retrospective study, we provide a comprehensive, whole-genome analysis of RB SCNAs and evaluate associated clinical features for 68 eyes of 64 RB patients from whom AH was obtained between December 2014 and October 2020. Shallow whole-genome sequencing of AH cell-free DNA was performed to assess for SCNAs. The prevalence of specific non-highly recurrent SCNAs, such as 20q gain and 8p loss, differed between primarily and secondarily enucleated eyes. Increases in chromosomal instability predict more advanced seeding morphology (<i<p</i< = 0.015); later age of diagnosis (<i<p</i< < 0.0001); greater odds of an endophytic tumor growth pattern (without retinal detachment; <i<p</i< = 0.047); tumor heights <10 mm (<i<p</i< = 0.09); and containing 6p gain, a biomarker of poor ocular prognosis (<i<p</i< = 0.004). The AH liquid biopsy platform is a high-yield method of whole-genome RB SCNA analysis, and SCNAs are associated with numerous clinical findings in RB eyes. Prospective analyses are encouraged to further elucidate the clinical relevance of specific SCNAs in RB.
abstract_unstemmed	Aqueous humor (AH) liquid biopsy has been established as a surrogate tumor biopsy for retinoblastoma (RB). Previous AH studies have focused on highly recurrent RB somatic copy number alterations (SCNAs) including gain of 1q, 2p, 6p, and loss of 13q and 16q. In this retrospective study, we provide a comprehensive, whole-genome analysis of RB SCNAs and evaluate associated clinical features for 68 eyes of 64 RB patients from whom AH was obtained between December 2014 and October 2020. Shallow whole-genome sequencing of AH cell-free DNA was performed to assess for SCNAs. The prevalence of specific non-highly recurrent SCNAs, such as 20q gain and 8p loss, differed between primarily and secondarily enucleated eyes. Increases in chromosomal instability predict more advanced seeding morphology (<i<p</i< = 0.015); later age of diagnosis (<i<p</i< < 0.0001); greater odds of an endophytic tumor growth pattern (without retinal detachment; <i<p</i< = 0.047); tumor heights <10 mm (<i<p</i< = 0.09); and containing 6p gain, a biomarker of poor ocular prognosis (<i<p</i< = 0.004). The AH liquid biopsy platform is a high-yield method of whole-genome RB SCNA analysis, and SCNAs are associated with numerous clinical findings in RB eyes. Prospective analyses are encouraged to further elucidate the clinical relevance of specific SCNAs in RB.
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title_short	Comprehensive Somatic Copy Number Analysis Using Aqueous Humor Liquid Biopsy for Retinoblastoma
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Comprehensive Somatic Copy Number Analysis Using Aqueous Humor Liquid Biopsy for Retinoblastoma

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