11 results on '"Fowler, Anna"'
Search Results
2. Benchmarking UMI-aware and standard variant callers for low frequency ctDNA variant detection.
- Author
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Maruzani, Rugare, Brierley, Liam, Jorgensen, Andrea, and Fowler, Anna
- Subjects
CELL-free DNA ,NUCLEOTIDE sequencing ,EARLY detection of cancer ,SENSITIVITY & specificity (Statistics) ,TUMOR classification - Abstract
Background: Circulating tumour DNA (ctDNA) is a subset of cell free DNA (cfDNA) released by tumour cells into the bloodstream. Circulating tumour DNA has shown great potential as a biomarker to inform treatment in cancer patients. Collecting ctDNA is minimally invasive and reflects the entire genetic makeup of a patient's cancer. ctDNA variants in NGS data can be difficult to distinguish from sequencing and PCR artefacts due to low abundance, particularly in the early stages of cancer. Unique Molecular Identifiers (UMIs) are short sequences ligated to the sequencing library before amplification. These sequences are useful for filtering out low frequency artefacts. The utility of ctDNA as a cancer biomarker depends on accurate detection of cancer variants. Results: In this study, we benchmarked six variant calling tools, including two UMI-aware callers for their ability to call ctDNA variants. The standard variant callers tested included Mutect2, bcftools, LoFreq and FreeBayes. The UMI-aware variant callers benchmarked were UMI-VarCal and UMIErrorCorrect. We used both datasets with known variants spiked in at low frequencies, and datasets containing ctDNA, and generated synthetic UMI sequences for these datasets. Variant callers displayed different preferences for sensitivity and specificity. Mutect2 showed high sensitivity, while returning more privately called variants than any other caller in data without synthetic UMIs – an indicator of false positive variant discovery. In data encoded with synthetic UMIs, UMI-VarCal detected fewer putative false positive variants than all other callers in synthetic datasets. Mutect2 showed a balance between high sensitivity and specificity in data encoded with synthetic UMIs. Conclusions: Our results indicate UMI-aware variant callers have potential to improve sensitivity and specificity in calling low frequency ctDNA variants over standard variant calling tools. There is a growing need for further development of UMI-aware variant calling tools if effective early detection methods for cancer using ctDNA samples are to be realised. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
3. DECoN: A Detection and Visualization Tool for Exonic Copy Number Variants
- Author
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Fowler, Anna, primary
- Published
- 2022
- Full Text
- View/download PDF
4. An Interpretable Classification Model Using Gluten-Specific TCR Sequences Shows Diagnostic Potential in Coeliac Disease
- Author
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Fowler, Anna, primary, FitzPatrick, Michael, additional, Shanmugarasa, Aberami, additional, Ibrahim, Amro Sayed Fadel, additional, Kockelbergh, Hannah, additional, Yang, Han-Chieh, additional, Williams-Walker, Amelia, additional, Luu Hoang, Kim Ngan, additional, Evans, Shelley, additional, Provine, Nicholas, additional, Klenerman, Paul, additional, and Soilleux, Elizabeth J., additional
- Published
- 2023
- Full Text
- View/download PDF
5. An Exploration of Identification Practices for Twice-Exceptional Students in the Early Years of Schooling
- Author
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Pendergast, Donna L, Ronksley-Pavia, Michelle, Neumann, Michelle M, Fowler, Anna C, Pendergast, Donna L, Ronksley-Pavia, Michelle, Neumann, Michelle M, and Fowler, Anna C
- Abstract
Twice-exceptional learners are difficult to identify in educational settings. In turn, it is challenging for educators to support the unique learning needs of these students in their classrooms. With a co-occurrence of high potential and disability, twice-exceptional learners require specific supports to address their unique needs, such as differentiated instruction, intervention support for their disabilities, and/or acceleration for advanced abilities. Without accurate identification, twice-exceptional students may not receive appropriate educational programming and provisions, further exacerbating educational difficulties where students are unable to reach their full potential. Approaches to identification, the timing and purpose of chosen tools, along with educator knowledge, all impact on the identification (or lack of identification) of twice-exceptional learners. Previous research has suggested that key influences on accurate and timely identification of these learners are early identification, a comprehensive identification approach, and increased teacher education. This qualitative exploratory case study into early identification practices involved one Queensland state school and considered the suitability of practices for identifying both exceptions (giftedness and disabilities) for these students. The theoretical lens of the bioecological systems theory (Bronfenbrenner & Morris, 2006), synthesised with Gagné’s differentiating model of giftedness and talent, created a unique lens to frame the exploration through the developing twice-exceptional child’s bioecological system. Data were gathered through a four-stage process with document reviews and two interviews with one specialist educator participant. A hybrid inductive-deductive, reflexive thematic analysis approach was used to construct meaning from the data. Findings, presented through the synthesised theoretical lens, provide insight into a comprehensive assessment approach and collaborative processes, Thesis (Masters), Master of Education and Professional Studies Research (MEdProfStRes), School Educ & Professional St, Arts, Education and Law, Full Text
- Published
- 2023
6. Genetic Insights from Consanguineous Cardiomyopathy Families
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Maurer, Constance, primary, Boleti, Olga, additional, Najarzadeh Torbati, Paria, additional, Norouzi, Farzaneh, additional, Fowler, Anna Nicole Rebekah, additional, Minaee, Shima, additional, Salih, Khalid Hama, additional, Taherpour, Mehdi, additional, Birjandi, Hassan, additional, Alizadeh, Behzad, additional, Salih, Aso Faeq, additional, Bijari, Moniba, additional, Houlden, Henry, additional, Pittman, Alan Michael, additional, Maroofian, Reza, additional, Almashham, Yahya H., additional, Karimiani, Ehsan Ghayoor, additional, Kaski, Juan Pablo, additional, Faqeih, Eissa Ali, additional, Vakilian, Farveh, additional, and Jamshidi, Yalda, additional
- Published
- 2023
- Full Text
- View/download PDF
7. College faculty experiences with online teaching during the COVID-19 pandemic
- Author
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Rogers, Jennifer, primary, Reid, Kristin, additional, Byers, Dina, additional, Cross, Summer, additional, Fowler, Anna, additional, Thurmond, Janice, additional, and Todd, Dana, additional
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- 2022
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8. Utility of Bulk T-Cell Receptor Repertoire Sequencing Analysis in Understanding Immune Responses to COVID-19
- Author
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Kockelbergh, Hannah, Evans, Shelley, Deng, Tong, Clyne, Ella, Kyriakidou, Anna, Economou, Andreas, Luu Hoang, Kim Ngan, Woodmansey, Stephen, Foers, Andrew, Fowler, Anna, Soilleux, Elizabeth J, Evans, Shelley [0000-0003-3242-6017], Clyne, Ella [0000-0001-8945-4508], Kyriakidou, Anna [0000-0001-8964-8345], Economou, Andreas [0000-0002-3305-5804], Luu Hoang, Kim Ngan [0000-0001-5670-1832], Foers, Andrew [0000-0002-5036-7906], Soilleux, Elizabeth J [0000-0002-4032-7249], Apollo - University of Cambridge Repository, and Soilleux, Elizabeth [0000-0002-4032-7249]
- Subjects
T-cell receptor repertoire ,immunological memory ,machine learning ,SARS-CoV-2 ,immunoreceptor ,antibody ,Clinical Biochemistry ,coronavirus ,COVID-19 ,immune response ,diversity - Abstract
Measuring immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 19 (COVID-19), can rely on antibodies, reactive T cells and other factors, with T-cell-mediated responses appearing to have greater sensitivity and longevity. Because each T cell carries an essentially unique nucleic acid sequence for its T-cell receptor (TCR), we can interrogate sequence data derived from DNA or RNA to assess aspects of the immune response. This review deals with the utility of bulk, rather than single-cell, sequencing of TCR repertoires, considering the importance of study design, in terms of cohort selection, laboratory methods and analysis. The advances in understanding SARS-CoV-2 immunity that have resulted from bulk TCR repertoire sequencing are also be discussed. The complexity of sequencing data obtained by bulk repertoire sequencing makes analysis challenging, but simple descriptive analyses, clonal analysis, searches for specific sequences associated with immune responses to SARS-CoV-2, motif-based analyses, and machine learning approaches have all been applied. TCR repertoire sequencing has demonstrated early expansion followed by contraction of SARS-CoV-2-specific clonotypes, during active infection. Maintenance of TCR repertoire diversity, including the maintenance of diversity of anti-SARS-CoV-2 response, predicts a favourable outcome. TCR repertoire narrowing in severe COVID-19 is most likely a consequence of COVID-19-associated lymphopenia. It has been possible to follow clonotypic sequences longitudinally, which has been particularly valuable for clonotypes known to be associated with SARS-CoV-2 peptide/MHC tetramer binding or with SARS-CoV-2 peptide-induced cytokine responses. Closely related clonotypes to these previously identified sequences have been shown to respond with similar kinetics during infection. A possible superantigen-like effect of the SARS-CoV-2 spike protein has been identified, by means of observing V-segment skewing in patients with severe COVID-19, together with structural modelling. Such a superantigen-like activity, which is apparently absent from other coronaviruses, may be the basis of multisystem inflammatory syndrome and cytokine storms in COVID-19. Bulk TCR repertoire sequencing has proven to be a useful and cost-effective approach to understanding interactions between SARS-CoV-2 and the human host, with the potential to inform the design of therapeutics and vaccines, as well as to provide invaluable pathogenetic and epidemiological insights.
- Published
- 2022
- Full Text
- View/download PDF
9. Utility of Bulk T-Cell Receptor Repertoire Sequencing Analysis in Understanding Immune Responses to COVID-19
- Author
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Kockelbergh, Hannah, primary, Evans, Shelley, additional, Deng, Tong, additional, Clyne, Ella, additional, Kyriakidou, Anna, additional, Economou, Andreas, additional, Luu Hoang, Kim Ngan, additional, Woodmansey, Stephen, additional, Foers, Andrew, additional, Fowler, Anna, additional, and Soilleux, Elizabeth J., additional
- Published
- 2022
- Full Text
- View/download PDF
10. All Bottled Up: Hazard Assessment of an Historic Pharmaceutical Collection
- Author
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Fowler, Anna, Koss Schrager, Kerith, and Ravenel, Nancie
- Abstract
Shelburne Museum’s extensive pharmaceutical collection, located in northwestern Vermont, USA, has been the subject of a multi-year inventory project partially funded by the Institute of Museum and Library Services (IMLS) grant. Amounting to over 9,000 objects, 5,000 to 6,000 of which are unique products, the collection has been largely untouched since its acquisition circa 1947 to 1970. Housed in a historic general store and custom annex, the collection encompasses roughly 200 years of American pharmaceutical, veterinary, and cosmetic history. This article explores the discovery, research, triage, and disposal of the hazards found within the collection during the inventory.
- Published
- 2024
- Full Text
- View/download PDF
11. An Exploration of Identification Practices for Twice-Exceptional Students in the Early Years of Schooling
- Author
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Fowler, Anna C
- Subjects
- twice-exceptional students, identification, comprehensive assessment
- Abstract
Twice-exceptional learners are difficult to identify in educational settings. In turn, it is challenging for educators to support the unique learning needs of these students in their classrooms. With a co-occurrence of high potential and disability, twice-exceptional learners require specific supports to address their unique needs, such as differentiated instruction, intervention support for their disabilities, and/or acceleration for advanced abilities. Without accurate identification, twice-exceptional students may not receive appropriate educational programming and provisions, further exacerbating educational difficulties where students are unable to reach their full potential. Approaches to identification, the timing and purpose of chosen tools, along with educator knowledge, all impact on the identification (or lack of identification) of twice-exceptional learners. Previous research has suggested that key influences on accurate and timely identification of these learners are early identification, a comprehensive identification approach, and increased teacher education. This qualitative exploratory case study into early identification practices involved one Queensland state school and considered the suitability of practices for identifying both exceptions (giftedness and disabilities) for these students. The theoretical lens of the bioecological systems theory (Bronfenbrenner & Morris, 2006), synthesised with Gagné’s differentiating model of giftedness and talent, created a unique lens to frame the exploration through the developing twice-exceptional child’s bioecological system. Data were gathered through a four-stage process with document reviews and two interviews with one specialist educator participant. A hybrid inductive-deductive, reflexive thematic analysis approach was used to construct meaning from the data. Findings, presented through the synthesised theoretical lens, provide insight into a comprehensive assessment approach and collaborative processes, which in turn provide the ability for both exceptions to be identified, with further investigation into possible twice-exceptional learners taking place. The case study school’s local policy initiative to identify gifted learners was found to be responsible for much of the success of practices within that site. This success also came from support given by the principal and the unique role of the specialist educator of gifted learners in driving local practice. Key recommendations include the instalment of state policy for identifying gifted learners across all schools in Queensland, with this case presenting a possible framework for identification practices. Further recommendations include increased education for principals, and professional development and preservice education for teachers for identifying and providing for twice-exceptional learners. Future research is suggested into identification practices taking place at other local schools across the state, along with the development of an appropriate Australian-based tool to identify gifted and twice-exceptional learners.
- Published
- 2023
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