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Sakthikumar S, Warrier M, Whitley D, Facista S, Adkins J, Aman S, Tsinajinnie D, Duran N, Siravegna G, Ahmed Z, Day K, Jenkins B, Patel N, Ryden K, Nadai J, Banovich K, Powers B, Edwards J, Steinberg J, Fielder S, Wong S, Byron SA, Izatt T, Zismann V, Boateng M, Zhu Z, Chuang HY, Trent JM, Haworth D, Chon E, Hendricks W, Wang G. Genomic analysis across 53 canine cancer types reveals novel mutations and high clinical actionability potential. Vet Comp Oncol 2024; 22:30-41. [PMID: 38053317 DOI: 10.1111/vco.12944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/27/2023] [Accepted: 11/12/2023] [Indexed: 12/07/2023]
Abstract
A genomic understanding of the oncogenic processes and individual variability of human cancer has steadily fueled improvement in patient outcomes over the past 20 years. Mutations within tumour tissues are routinely assessed through clinical genomic diagnostic assays by academic and commercial laboratories to facilitate diagnosis, prognosis and effective treatment stratification. The application of genomics has unveiled a wealth of mutation-based biomarkers in canine cancers, suggesting that the transformative principles that have revolutionized human cancer medicine can be brought to bear in veterinary oncology. To advance clinical genomics and genomics-guided medicine in canine oncology, we have developed and validated a canine cancer next-generation sequencing gene panel for the identification of multiple mutation types in clinical specimens. With this panel, we examined the genomic landscapes of 828 tumours from 813 dogs, spanning 53 cancer types. We identified 7856 alterations, encompassing copy number variants, single nucleotide variants, indels and internal tandem duplications. Additionally, we evaluated the clinical utility of these alterations by incorporating a biomarker framework from comprehensive curation of primary canine literature and inferences from human cancer genomic biomarker literature and clinical diagnostics. Remarkably, nearly 90% of the cases exhibited mutations with diagnostic, prognostic or therapeutic implications. Our work represents a thorough assessment of genomic landscapes in a large cohort of canine cancers, the first of its kind for its comprehensive inclusion of multiple mutation types and structured annotation of biomarkers, demonstrating the clinical potential of leveraging mutation-based biomarkers in veterinary oncology.
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Affiliation(s)
| | | | | | | | | | - Sara Aman
- Vidium Animal Health, Phoenix, Arizona, USA
| | | | | | | | | | | | | | | | - Kirk Ryden
- Vidium Animal Health, Phoenix, Arizona, USA
| | - Joe Nadai
- Vidium Animal Health, Phoenix, Arizona, USA
| | | | | | | | - Jennifer Steinberg
- Center for Cancer Research at the National Cancer Institute, National Cancer Institute, Bethesda, Maryland, USA
| | | | - Shukmei Wong
- Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Sara A Byron
- Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Tyler Izatt
- Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Victoria Zismann
- Translational Genomics Research Institute, Phoenix, Arizona, USA
| | | | | | | | - Jeffrey M Trent
- Translational Genomics Research Institute, Phoenix, Arizona, USA
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Diñeiro M, Capín R, Cifuentes GÁ, Fernández‐Vega B, Villota E, Otero A, Santiago A, Pruneda PC, Castillo D, Viejo‐Díaz M, Hernando I, Durán NS, Álvarez R, Lago CG, Ordóñez GR, Fernández‐Vega Á, Cabanillas R, Cadiñanos J. Comprehensive genomic diagnosis of inherited retinal and optical nerve disorders reveals hidden syndromes and personalized therapeutic options. Acta Ophthalmol 2020; 98:e1034-e1048. [PMID: 32483926 PMCID: PMC7754416 DOI: 10.1111/aos.14479] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/29/2020] [Indexed: 01/14/2023]
Abstract
PURPOSE In the era of precision medicine, genomic characterization of blind patients is critical. Here, we evaluate the effects of comprehensive genetic analysis on the etiologic diagnosis of potentially hereditary vision loss and its impact on clinical management. METHODS We studied 100 non-syndromic and syndromic Spanish patients with a clinical diagnosis of blindness caused by alterations on the retina, choroid, vitreous and/or optic nerve. We used a next-generation sequencing (NGS) panel (OFTALMOgenics™), developed and validated within this study, including up to 362 genes previously associated with these conditions. RESULTS We identified the genetic cause of blindness in 45% of patients (45/100). A total of 28.9% of genetically diagnosed cases (13/45) were syndromic and, of those, in 30.8% (4/13) extraophthalmic features had been overlooked and/or not related to visual impairment before genetic testing, including cases with Mainzer-Saldino, Bardet-Biedl, mucolipidosis and MLCRD syndromes. In two additional cases-syndromic blindness had been proposed before, but not specifically diagnosed, and one patient with Heimler syndrome had been misdiagnosed as an Usher case before testing. 33.3% of the genetically diagnosed patients (15/45) had causative variants in genes targeted by clinical trials exploring the curative potential of gene therapy approaches. CONCLUSION Comprehensive genomic testing provided clinically relevant insights in a large proportion of blind patients, identifying potential therapeutic opportunities or previously undiagnosed syndromes in 42.2% of the genetically diagnosed cases (19/45).
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Affiliation(s)
- Marta Diñeiro
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
| | - Raquel Capín
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
| | | | | | - Eva Villota
- Instituto Oftalmológico Fernández‐Vega (IOFV)OviedoSpain
| | - Andrea Otero
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
| | - Adrián Santiago
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
| | | | - David Castillo
- Disease Research And Medicine (DREAMgenics) S. L.OviedoSpain
| | | | - Inés Hernando
- Hospital Universitario Central de AsturiasOviedoSpain
| | - Noelia S. Durán
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
| | - Rebeca Álvarez
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
| | - Claudia G. Lago
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
| | | | | | - Rubén Cabanillas
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
| | - Juan Cadiñanos
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A.OviedoSpain
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Lalonde E, Rentas S, Lin F, Dulik MC, Skraban CM, Spinner NB. Genomic Diagnosis for Pediatric Disorders: Revolution and Evolution. Front Pediatr 2020; 8:373. [PMID: 32733828 PMCID: PMC7360789 DOI: 10.3389/fped.2020.00373] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 06/02/2020] [Indexed: 12/14/2022] Open
Abstract
Powerful, recent advances in technologies to analyze the genome have had a profound impact on the practice of medical genetics, both in the laboratory and in the clinic. Increasing utilization of genome-wide testing such as chromosomal microarray analysis and exome sequencing have lead a shift toward a "genotype-first" approach. Numerous techniques are now available to diagnose a particular syndrome or phenotype, and while traditional techniques remain efficient tools in certain situations, higher-throughput technologies have become the de facto laboratory tool for diagnosis of most conditions. However, selecting the right assay or technology is challenging, and the wrong choice may lead to prolonged time to diagnosis, or even a missed diagnosis. In this review, we will discuss current core technologies for the diagnosis of classic genetic disorders to shed light on the benefits and disadvantages of these strategies, including diagnostic efficiency, variant interpretation, and secondary findings. Finally, we review upcoming technologies posed to impart further changes in the field of genetic diagnostics as we move toward "genome-first" practice.
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Affiliation(s)
- Emilie Lalonde
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Stefan Rentas
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Fumin Lin
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Matthew C. Dulik
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Cara M. Skraban
- Division of Human Genetics, Department of Pediatrics, School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Nancy B. Spinner
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
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Issa AM, Hutchinson JF, Tufail W, Fletcher E, Ajike R, Tenorio J. Provision of personalized genomic diagnostic technologies for breast and colorectal cancer: an analysis of patient needs, expectations and priorities. Per Med 2011; 8:401-411. [PMID: 29783336 DOI: 10.2217/pme.11.39] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
AIM Several novel pharmacogenomic diagnostic tests are commercially available for breast and colorectal cancer, and are increasingly being used in clinical practice for improving treatment decisions. However, there is little evidence evaluating the value of these new genomic technologies from the perspective of patients. As part of an ongoing effort to understand the continuum of the process of adoption of genomic diagnostics, our aim in this study was to examine the value of genomic diagnostics to breast and colorectal cancer patients, and their willingness to adopt and use genomic diagnostics. PATIENTS & METHODS We conducted six focus groups of breast and colorectal cancer patients from the oncology clinics at The Methodist Hospital, Houston, TX, USA. An adapted Q-sort instrument was also administered to focus group participants. RESULTS The majority of breast and colorectal cancer patients are interested in using novel genomic diagnostics for deciding about treatment options. Most participants in our study expressed a willingness to pay out-of-pocket for genomic testing (z = 0.736). Reliability and validity of genomic testing were of significant concern (z = 1.32) for the majority of breast and colorectal cancer patients. Participants identified several facilitators and barriers within health systems that might either facilitate or impede the widespread adoption and use of genomic diagnostics in healthcare delivery. CONCLUSION This study demonstrates breast and colorectal cancer patients' willingness to adopt and pay for novel genomic diagnostics, as well as identifies several salient factors associated with patient preferences for genomic diagnostics.
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Affiliation(s)
- Amalia M Issa
- Pharmacy Administration & Public Health, Department of Clinical Sciences & Administration, College of Pharmacy, University of Houston, 1441 Moursund Street, Houston, TX 77030, USA.
| | - Janis F Hutchinson
- Program in Personalized Medicine & Targeted Therapeutics, University of Houston, Houston, TX 77030, USA.,Department of Anthropology, University of Houston, Houston, TX 77204, USA
| | - Waqas Tufail
- Program in Personalized Medicine & Targeted Therapeutics, University of Houston, Houston, TX 77030, USA
| | - Erica Fletcher
- Program in Personalized Medicine & Targeted Therapeutics, University of Houston, Houston, TX 77030, USA
| | - Roseline Ajike
- Program in Personalized Medicine & Targeted Therapeutics, University of Houston, Houston, TX 77030, USA.,The Methodist Hospital Research Institute, Houston, TX 77030, USA
| | - Jose Tenorio
- Program in Personalized Medicine & Targeted Therapeutics, University of Houston, Houston, TX 77030, USA.,The Methodist Hospital Research Institute, Houston, TX 77030, USA
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