Статті в журналах: "Clinical exome sequencing"

1

Gomez, Christopher M., and Soma Das. "Clinical Exome Sequencing." JAMA Neurology 71, no. 10 (October 1, 2014): 1215. http://dx.doi.org/10.1001/jamaneurol.2014.2015.

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2

Friedman, Jan M., Kenneth Lyons Jones, and John C. Carey. "Exome Sequencing and Clinical Diagnosis." JAMA 324, no. 7 (August 18, 2020): 627. http://dx.doi.org/10.1001/jama.2020.11126.

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3

Vilarinho, Sílvia, and Pramod K. Mistry. "Exome Sequencing in Clinical Hepatology." Hepatology 70, no. 6 (November 29, 2019): 2185–92. http://dx.doi.org/10.1002/hep.30826.

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4

Liu, Pengfei, Linyan Meng, Elizabeth A. Normand, Fan Xia, Xiaofei Song, Andrew Ghazi, Jill Rosenfeld, et al. "Reanalysis of Clinical Exome Sequencing Data." New England Journal of Medicine 380, no. 25 (June 20, 2019): 2478–80. http://dx.doi.org/10.1056/nejmc1812033.

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5

Miyatake, Satoko, and Naomichi Matsumoto. "Clinical exome sequencing in neurology practice." Nature Reviews Neurology 10, no. 12 (November 4, 2014): 676–78. http://dx.doi.org/10.1038/nrneurol.2014.213.

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6

Fogel, Brent L., Saty Satya-Murti, and Bruce H. Cohen. "Clinical exome sequencing in neurologic disease." Neurology: Clinical Practice 6, no. 2 (March 21, 2016): 164–76. http://dx.doi.org/10.1212/cpj.0000000000000239.

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7

Sutton, Amelia L. M., and Nathaniel H. Robin. "Clinical application of whole exome sequencing." Current Opinion in Pediatrics 24, no. 6 (December 2012): 663–64. http://dx.doi.org/10.1097/mop.0b013e32835a1996.

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8

Liew, Wendy K. M., Tawfeg Ben-Omran, Basil T. Darras, Sanjay P. Prabhu, Darryl C. De Vivo, Matteo Vatta, Yaping Yang, Christine M. Eng, and Wendy K. Chung. "Clinical Application of Whole-Exome Sequencing." JAMA Neurology 70, no. 6 (June 1, 2013): 788. http://dx.doi.org/10.1001/jamaneurol.2013.247.

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9

Koch, Linda. "Whole-exome sequencing for clinical diagnostics." Nature Reviews Genetics 17, no. 5 (March 21, 2016): 252. http://dx.doi.org/10.1038/nrg.2016.38.

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10

Biesecker, Leslie G., and Robert C. Green. "Diagnostic Clinical Genome and Exome Sequencing." New England Journal of Medicine 370, no. 25 (June 19, 2014): 2418–25. http://dx.doi.org/10.1056/nejmra1312543.

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11

Lee, Hane, and Stanley F. Nelson. "Rethinking clinical practice: clinical implementation of exome sequencing." Personalized Medicine 9, no. 8 (November 2012): 785–87. http://dx.doi.org/10.2217/pme.12.101.

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12

Vance, J., and M. Tekin. "Exome sequencing for neurological disorders." Journal of the Neurological Sciences 381 (October 2017): 21. http://dx.doi.org/10.1016/j.jns.2017.08.096.

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13

Bras, JM, and AB Singleton. "Exome sequencing in Parkinson's disease." Clinical Genetics 80, no. 2 (June 16, 2011): 104–9. http://dx.doi.org/10.1111/j.1399-0004.2011.01722.x.

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14

Timmermans, Stefan, and Tanya Stivers. "The social utility of clinical exome sequencing." Patient Education and Counseling 101, no. 2 (February 2018): 221–26. http://dx.doi.org/10.1016/j.pec.2017.08.010.

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15

O’Donnell-Luria, Anne H., and David T. Miller. "A Clinician’s perspective on clinical exome sequencing." Human Genetics 135, no. 6 (April 28, 2016): 643–54. http://dx.doi.org/10.1007/s00439-016-1662-x.

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16

Tada, Hayato, Akihiro Nomura, Hirofumi Okada, Takuya Nakahashi, Tsuyoshi Nozue, Kenshi Hayashi, Atsushi Nohara, et al. "Clinical whole exome sequencing in severe hypertriglyceridemia." Clinica Chimica Acta 488 (January 2019): 31–39. http://dx.doi.org/10.1016/j.cca.2018.10.041.

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17

Retterer, Kyle, Jane Juusola, Megan T. Cho, Patrik Vitazka, Francisca Millan, Federica Gibellini, Annette Vertino-Bell, et al. "Clinical application of whole-exome sequencing across clinical indications." Genetics in Medicine 18, no. 7 (December 3, 2015): 696–704. http://dx.doi.org/10.1038/gim.2015.148.

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18

Park, Jason Y., Peter Clark, Eric Londin, Marialuisa Sponziello, Larry J. Kricka, and Paolo Fortina. "Clinical Exome Performance for Reporting Secondary Genetic Findings." Clinical Chemistry 61, no. 1 (January 1, 2015): 213–20. http://dx.doi.org/10.1373/clinchem.2014.231456.

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Abstract BACKGROUND Reporting clinically actionable incidental genetic findings in the course of clinical exome testing is recommended by the American College of Medical Genetics and Genomics (ACMG). However, the performance of clinical exome methods for reporting small subsets of genes has not been previously reported. METHODS In this study, 57 exome data sets performed as clinical (n = 12) or research (n = 45) tests were retrospectively analyzed. Exome sequencing data was examined for adequacy in the detection of potentially pathogenic variant locations in the 56 genes described in the ACMG incidental findings recommendation. All exons of the 56 genes were examined for adequacy of sequencing coverage. In addition, nucleotide positions annotated in HGMD (Human Gene Mutation Database) were examined. RESULTS The 56 ACMG genes have 18 336 nucleotide variants annotated in HGMD. None of the 57 exome data sets possessed a HGMD variant. The clinical exome test had inadequate coverage for >50% of HGMD variant locations in 7 genes. Six exons from 6 different genes had consistent failure across all 3 test methods; these exons had high GC content (76%–84%). CONCLUSIONS The use of clinical exome sequencing for the interpretation and reporting of subsets of genes requires recognition of the substantial possibility of inadequate depth and breadth of sequencing coverage at clinically relevant locations. Inadequate depth of coverage may contribute to false-negative clinical exome results.

19

Braathen, G. J., Ø. L. Holla, Ø. L. Busk, and C. F. Skjelbred. "Diagnostic exome sequencing in neurological disorders." Journal of the Neurological Sciences 333 (October 2013): e78. http://dx.doi.org/10.1016/j.jns.2013.07.546.

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20

Huang, K. "Exome sequencing expedites disease gene discovery." Clinical Genetics 80, no. 2 (February 24, 2011): 133–34. http://dx.doi.org/10.1111/j.1399-0004.2011.01645.x.

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21

Lelieveld, Stefan H., Joris A. Veltman, and Christian Gilissen. "Novel bioinformatic developments for exome sequencing." Human Genetics 135, no. 6 (April 13, 2016): 603–14. http://dx.doi.org/10.1007/s00439-016-1658-6.

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22

Balabanski, Lubomir, Dimitar Serbezov, Dragomira Nikolova, Olga Antonova, Desislava Nesheva, Zora Hammoudeh, Radoslava Vazharova, et al. "Centenarian Exomes as a Tool for Evaluating the Clinical Relevance of Germline Tumor Suppressor Mutations." Technology in Cancer Research & Treatment 19 (January 1, 2020): 153303382091108. http://dx.doi.org/10.1177/1533033820911082.

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Objectives: The aim of the present study was to evaluate the clinical relevance of mutations in tumor suppressor genes using whole-exome sequencing data from centenarians and young healthy individuals. Methods: Two pools, one of centenarians and one of young individuals, were constructed and whole-exome sequencing was performed. We examined the whole-exome sequencing data of Bulgarian individuals for carriership of tumor suppressor gene variants. Results: Of all variants annotated in both pools, 5080 (0.06%) are variants in tumor suppressor genes but only 46 show significant difference in allele frequencies between the two studied groups. Four variants (0.004%) are pathogenic/risk factors according to single nucleotide polymorphism database: rs1566734 in PTPRJ, rs861539 in XRCC3, rs203462 in AKAP10, and rs486907 in RNASEL. Discussion: Based on their high minor allele frequencies and presence in the centenarian group, we could reclassify them from pathogenic/risk factors to benign. Our study shows that centenarian exomes can be used for re-evaluating the clinically uncertain variants.

23

Zalar, Bojan, Ales Maver, Ana Kovanda, Ana Peterlin, and Borut Peterlin. "CLINICAL EXOME SEQUENCING IN DEMENTIAS: A PRELIMINARY STUDY." Psychiatria Danubina 30, no. 2 (June 19, 2018): 216–19. http://dx.doi.org/10.24869/psyd.2018.216.

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24

Zalar, Bojan, Ales Maver, Ana Kovanda, Ana Peterlin, and Borut Peterlin. "CLINICAL EXOME SEQUENCING IN DEMENTIAS: A PRELIMINARY STUDY." Psychiatria Danubina 30, no. 2 (June 19, 2018): 216–19. http://dx.doi.org/10.24869/spsih.2018.216.

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25

Levenson, Deborah. "Whole-exome sequencing emerges as clinical diagnostic tool." American Journal of Medical Genetics Part A 164, no. 1 (December 18, 2013): ix—x. http://dx.doi.org/10.1002/ajmg.a.36385.

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26

Kim, Se Hee, Borahm Kim, Joon Soo Lee, Heung Dong Kim, Jong Rak Choi, Seung-Tae Lee, and Hoon-Chul Kang. "Proband-Only Clinical Exome Sequencing for Neurodevelopmental Disabilities." Pediatric Neurology 99 (October 2019): 47–54. http://dx.doi.org/10.1016/j.pediatrneurol.2019.02.017.

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27

Fogel, Brent L., Hane Lee, Samuel P. Strom, Joshua L. Deignan, and Stanley F. Nelson. "Clinical exome sequencing in neurogenetic and neuropsychiatric disorders." Annals of the New York Academy of Sciences 1366, no. 1 (August 6, 2015): 49–60. http://dx.doi.org/10.1111/nyas.12850.

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28

Niguidula, Nancy, Christina Alamillo, Layla Shahmirzadi Mowlavi, Zöe Powis, Julie S. Cohen, and Kelly D. Farwell Hagman. "Clinical whole-exome sequencing results impact medical management." Molecular Genetics & Genomic Medicine 6, no. 6 (October 14, 2018): 1068–78. http://dx.doi.org/10.1002/mgg3.484.

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29

Srivastava, Siddharth, Julie S. Cohen, Hilary Vernon, Kristin Barañano, Rebecca McClellan, Leila Jamal, SakkuBai Naidu, and Ali Fatemi. "Clinical whole exome sequencing in child neurology practice." Annals of Neurology 76, no. 4 (August 30, 2014): 473–83. http://dx.doi.org/10.1002/ana.24251.

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30

Atwal, Paldeep Singh, Marie-Louise Brennan, Rachel Cox, Michael Niaki, Julia Platt, Margaret Homeyer, Andrea Kwan, et al. "Clinical whole-exome sequencing: are we there yet?" Genetics in Medicine 16, no. 9 (February 13, 2014): 717–19. http://dx.doi.org/10.1038/gim.2014.10.

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31

Gazzaz, Nour, Stephanie Hyunh, Ashley Moller-Hansen, Brandon Chalazan, Neal Boerkoel, and Hui-Lin Chin. "Single center experience in clinical whole-exome sequencing." Molecular Genetics and Metabolism 132 (April 2021): S142. http://dx.doi.org/10.1016/s1096-7192(21)00306-1.

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32

Stojanovic, Jelena Ruml, Aleksandra Miletic, Borut Peterlin, Ales Maver, Marija Mijovic, Nikola Borlja, Brankica Dimitrijevic, Ivan Soldatovic, and Goran Cuturilo. "Diagnostic and Clinical Utility of Clinical Exome Sequencing in Children With Moderate and Severe Global Developmental Delay / Intellectual Disability." Journal of Child Neurology 35, no. 2 (October 17, 2019): 116–31. http://dx.doi.org/10.1177/0883073819879835.

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Анотація:

Clinical exome sequencing is currently being used in diagnostics of various genetic disorders, but studies supporting its application in clinical setting are scarce. The aim of this study was to establish diagnostic and clinical utility of clinical exome sequencing in patients with moderate and severe global developmental delay/intellectual disability. Clinical diagnosis was made in 49 of 88 investigated patients, with overall diagnostic yield of 55.7%. Molecular findings are characterized in detail, including the impact of newly made diagnosis on clinical management. Several previously unreported genotype-phenotype correlations and 33 novel variants are described. Genetic and clinical data were shared through publicly available database. In conclusion, clinical exome sequencing allows identification of causative variants in a significant proportion of patients in investigated clinical subgroup. Compared to whole exome sequencing, it shows similar diagnostic and clinical utility with reduced costs, which could be of particular importance for institutions with limited resources.

33

Keogh, M. J., D. Daud, and P. F. Chinnery. "Exome sequencing: how to understand it." Practical Neurology 13, no. 6 (June 1, 2013): 399–407. http://dx.doi.org/10.1136/practneurol-2012-000498.

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34

Veltman, Joris A. "Diagnostic exome sequencing in intellectual disability." Clinical Biochemistry 46, no. 12 (August 2013): 1151. http://dx.doi.org/10.1016/j.clinbiochem.2013.05.023.

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35

Hegde, Madhuri, Avni Santani, Rong Mao, Andrea Ferreira-Gonzalez, Karen E. Weck, and Karl V. Voelkerding. "Development and Validation of Clinical Whole-Exome and Whole-Genome Sequencing for Detection of Germline Variants in Inherited Disease." Archives of Pathology & Laboratory Medicine 141, no. 6 (March 31, 2017): 798–805. http://dx.doi.org/10.5858/arpa.2016-0622-ra.

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Context.— With the decrease in the cost of sequencing, the clinical testing paradigm has shifted from single gene to gene panel and now whole-exome and whole-genome sequencing. Clinical laboratories are rapidly implementing next-generation sequencing–based whole-exome and whole-genome sequencing. Because a large number of targets are covered by whole-exome and whole-genome sequencing, it is critical that a laboratory perform appropriate validation studies, develop a quality assurance and quality control program, and participate in proficiency testing. Objective.— To provide recommendations for whole-exome and whole-genome sequencing assay design, validation, and implementation for the detection of germline variants associated in inherited disorders. Data Sources.— An example of trio sequencing, filtration and annotation of variants, and phenotypic consideration to arrive at clinical diagnosis is discussed. Conclusions.— It is critical that clinical laboratories planning to implement whole-exome and whole-genome sequencing design and validate the assay to specifications and ensure adequate performance prior to implementation. Test design specifications, including variant filtering and annotation, phenotypic consideration, guidance on consenting options, and reporting of incidental findings, are provided. These are important steps a laboratory must take to validate and implement whole-exome and whole-genome sequencing in a clinical setting for germline variants in inherited disorders.

36

Warr, Amanda, Christelle Robert, David Hume, Alan Archibald, Nader Deeb, and Mick Watson. "Exome Sequencing: Current and Future Perspectives." G3: Genes|Genomes|Genetics 5, no. 8 (July 2, 2015): 1543–50. http://dx.doi.org/10.1534/g3.115.018564.

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37

Kalynchuk, Eve J., Andrew Althouse, Lisa S. Parker, Devereux N. Saller, and Aleksandar Rajkovic. "Prenatal whole-exome sequencing: parental attitudes." Prenatal Diagnosis 35, no. 10 (July 6, 2015): 1030–36. http://dx.doi.org/10.1002/pd.4635.

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38

Lieber, D. S., S. E. Calvo, K. Shanahan, N. G. Slate, S. Liu, S. G. Hershman, N. B. Gold, et al. "Targeted exome sequencing of suspected mitochondrial disorders." Neurology 80, no. 19 (April 17, 2013): 1762–70. http://dx.doi.org/10.1212/wnl.0b013e3182918c40.

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39

Fekete, Robert, Matthew Bainbridge, Jose Fidel Baizabal-Carvallo, Andreana Rivera, Bradley Miller, Peicheng Du, Vladyslav Kholodovych, Suzanne Powell, and William Ondo. "Exome sequencing in familial corticobasal degeneration." Parkinsonism & Related Disorders 19, no. 11 (November 2013): 1049–52. http://dx.doi.org/10.1016/j.parkreldis.2013.06.016.

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40

Parsons, Donald W., Murali M. Chintagumpala, Stacey L. Berg, Dolores H. López-Terrada, Angshumoy Roy, Robin A. Kerstein, Sarah Scollon, et al. "Implementation and evaluation of clinical exome sequencing in childhood cancer care: The BASIC3 study." Journal of Clinical Oncology 31, no. 15_suppl (May 20, 2013): 10023. http://dx.doi.org/10.1200/jco.2013.31.15_suppl.10023.

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10023 Background: Advances in sequencing technologies allow for provision of genome-scale data to oncologists and geneticists caring for pediatric cancer patients. The goal of the BASIC3 (Baylor Advancing Sequencing into Childhood Cancer Care) study is to determine the clinical impact of incorporating CLIA-certified tumor and constitutional exome sequencing into the care of children with newly diagnosed solid tumors. Methods: Blood and frozen tumor samples obtained at initial surgery are submitted for clinical exome sequencing (target enrollment 280 patients). Results are deposited into the electronic medical record and disclosed to families by their oncologist and a genetic counselor. Identification of germline cancer susceptibility mutations is compared with standard testing practices. Oncologists are surveyed on prioritization of treatment options in the hypothetical event of tumor recurrence before and after receiving tumor exome results. Patients will be followed for two years to assess the clinical utility of exome data. Preferences for reporting this complex information are obtained by interviews and audiorecording of disclosure visits. Results: Initial results reveal that41 of 49 (84%) ethnically diverse families have consented to enroll on study. Adequate tumor samples were available from 35 of 41 patients (85%), including 11 of 15 (73%) patients with CNS tumors and 24 of 26 (92%) with non-CNS tumors. Pathogenic germline cancer susceptibility mutations (TP53, MSH2) were reported in 2 of the first 11 patients, with a medically-actionable mutation in a gene (SCN5A) unrelated to cancer in 1 patient and 0-4 (median of 2) recessive carrier mutations per patient. Between 9 and 33 protein altering mutations (median of 11) have been identified in tumors, including known cancer genes such as TP53 and others with no known link to pediatric cancer. Conclusions: A robust clinical pipeline for exome sequencing of blood and tumor samples has been successfully developed with significant parental interest. Data assessing the clinical utility of both the tumor and constitutional exomes and the preferences of oncologists and parents for reporting of these results are under study. Supported by NHGRI 1U01HG006485.

41

Kobelka, CE. "Exome sequencing: expanding the genetic testing toolbox." Clinical Genetics 78, no. 2 (January 20, 2010): 132–34. http://dx.doi.org/10.1111/j.1399-0004.2010.01452_1.x.

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42

Ostrer, H. "Changing the game with whole exome sequencing." Clinical Genetics 80, no. 2 (July 12, 2011): 101–3. http://dx.doi.org/10.1111/j.1399-0004.2011.01712.x.

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43

Majewski, J., J. Schwartzentruber, E. Lalonde, A. Montpetit, and N. Jabado. "What can exome sequencing do for you?" Journal of Medical Genetics 48, no. 9 (July 5, 2011): 580–89. http://dx.doi.org/10.1136/jmedgenet-2011-100223.

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44

Ritter, Alyssa, Emma Bedoukian, Justin H. Berger, Deborah Copenheaver, Christopher Gray, Ian Krantz, Kosuke Izumi, et al. "Clinical utility of exome sequencing in infantile heart failure." Genetics in Medicine 22, no. 2 (September 17, 2019): 423–26. http://dx.doi.org/10.1038/s41436-019-0654-3.

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45

Need, Anna C., Vandana Shashi, Yuki Hitomi, Kelly Schoch, Kevin V. Shianna, Marie T. McDonald, Miriam H. Meisler, and David B. Goldstein. "Clinical application of exome sequencing in undiagnosed genetic conditions." Journal of Medical Genetics 49, no. 6 (May 11, 2012): 353–61. http://dx.doi.org/10.1136/jmedgenet-2012-100819.

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46

Fowler, Sara A., Carol J. Saunders, and Mark A. Hoffman. "Variation among Consent Forms for Clinical Whole Exome Sequencing." Journal of Genetic Counseling 27, no. 1 (July 8, 2017): 104–14. http://dx.doi.org/10.1007/s10897-017-0127-2.

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47

Clift, Kristin E., Colin M. E. Halverson, Alexander S. Fiksdal, Ashok Kumbamu, Richard R. Sharp, and Jennifer B. McCormick. "Patients' views on incidental findings from clinical exome sequencing." Applied & Translational Genomics 4 (March 2015): 38–43. http://dx.doi.org/10.1016/j.atg.2015.02.005.

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48

Kwak, Soo Heon, Chan-hyeon Jung, Chang Ho Ahn, Jungsun Park, Jeesoo Chae, Hye Seung Jung, Young Min Cho, Dae Ho Lee, Jong-Il Kim, and Kyong Soo Park. "Clinical whole exome sequencing in early onset diabetes patients." Diabetes Research and Clinical Practice 122 (December 2016): 71–77. http://dx.doi.org/10.1016/j.diabres.2016.10.005.

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49

Suspitsin, Evgeny N., Vladislav I. Tyurin, Evgeny N. Imyanitov, and Anna P. Sokolenko. "Whole exome sequencing: principles and diagnostic capabilities." Pediatrician (St. Petersburg) 7, no. 4 (December 15, 2016): 142–46. http://dx.doi.org/10.17816/ped74142-146.

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Анотація:

Diagnostics of genetic diseases in clinical routine often presents a challenge. In particular, most of hereditary diseases are exceptionally rare and therefore unfamiliar to practicing physicians. Furthermore, even if the diagnosis of a particular genetic condition appears convincing on the level of clinical evidence, the causative mutation often remains unknown due to limitations in DNA testing procedures. Recently developed high-throughput sequencing technologies (Next Generation Sequencing, NGS; synonym: massive parallel sequencing) provide a breakthrough in medical genetics. While in the past genetic testing was limited to a single gene or, at best, to a small number of genes, NGS is compatible with a large-scale DNA analysis. One of the most popular applications of NGS is whole exome sequencing (WES), which allows simultaneous reading of coding sequences (exons) of all known genes. Although this technology exists only for a few years, its use has already led to discovery of the causes of more than 150 genetic syndromes. Furthermore, WES may be recommended for the use in clinical routine for selected patients with orphan disease, especially for the families with multiple affected relative. It is likely that WES will become a powerful screening tool in the near future. This review discusses general principles of WES as well as the applications of this technology in medicine.

50

Chang, Ya-Sian, Hsien-Da Huang, Kun-Tu Yeh, and Jan-Gowth Chang. "Evaluation of whole exome sequencing by targeted gene sequencing and Sanger sequencing." Clinica Chimica Acta 471 (August 2017): 222–32. http://dx.doi.org/10.1016/j.cca.2017.06.015.

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