https://openworks.mdanderson.org/edwk22/1008/thumbnail.jp

Hoballah, Yasmine M, MS

Hu, Peter, PhD

Kalia, Awdhesh, PhD

Liu, Xiaojun, PhD, MEd

English

OpenWorks @ MD Anderson

Integration of  Long-Read Whole Genome Sequencing in Graduate Curriculum of  Diagnostic Genetics and GenomicsBackground of  Nanopore Sequencing • Concept and mechanism Video https://nanoporetech.com/applications/dna-nanopore-sequencing• Advantages over Illumina-based NGS platform [4]Evaluation of  Educational Outcome• Student lab notes and group presentation (Fig. 8) upon completion of instruction• CPRIT summer student’s abstract and poster (Fig. 9)• Current first-year students’ abstract (submitted to Association of Genetic Technologists annual joint meeting) and poster (to do in April-May 2022)Implementation• Timeline of project phases (Fig. 2): staff training, instructional design, single/group student trainings • Program coordination among DGG courses (Fig. 3): scheduling in alignment with Nanopore sequencing need• Lecture (Fig. 4) followed by wet lab (Fig. 5, Fig. 6, and video in PDF Attachments ) and dry lab (Fig. 7)Xiaojun Liu, Yasmine M. Hoballah *, Peter Hu, Awdhesh KaliaGraduate Program in Diagnostic Genetics and Genomics, School of Health Professions, UT MD Anderson Cancer Center2022 Education WeekEducational Goal and Performance Objectives• Goal: Students in the MGG teaching lab will demonstrate an understanding of the principle  of Nanopore sequencing to be applied in hands-on practice by generating and analyzing bacterial whole genome sequencing (WGS) data and presenting results. • Objectives: 1. Explain the concept of Nanopore sequencing and elaborate how it works (intellectual skill)2. Prepare libraries for WGS using MinION and perform sequencing (psychomotor skill)3. Analyze sequencing data using bioinfomatic tools (intellectual & psychomotor)4. Summarize data from both wet and dry labs and present results in groups (cognitive & social)Rationale for Integration into Curriculum• The existing MGG core curriculum deploys first-generation sequencing (Sanger method) and next-generation sequencing (NGS, Illumina platform) for the first-year students’ training. • Third-generation sequencing (TGS) offers high speed and long sequence reads and is increasingly being used in genomic studies [2] as well as pathogen surveillance [3]. • Benefits of including the emerging TGS technology in the core curriculum: (a) expand our sequencing platforms; (b) supplement and help fill the gaps in genome assemblies made from short reads generated by NGS • MinION (launched in 2015), along with the associated MinIT (2018), is a portable TGS device from Oxford Nanopore Technologies (ONT) that is readily meeting our teaching need.  Instructional Strategies and MaterialsThe design of instruction is based on the Constructivist learning theory using active learning approaches [5,6].Students are ensured to apply their new learning through concept application. The focus of instructional activities is on learner engagement, group work (collaboration), and critical thinking skills. Conclusions and Implications• We have successfully adopted Nanopore sequencing technology (MinION) and implemented instruction in the teaching lab for master’s students specialized in Molecular Diagnostics.    • This project has introduced novel, state-of-the-art sequencing technology into the DGG training program and increased the depth of the teaching curriculum.• This practice of teaching long-read sequencing of whole genomes benefit DGG students in that they get exposed to the most advanced technology and pre-pared for future positions as technologists in the molecular diagnostics field.  • The favorable learning outcomes of this practice warrant replication and  improvement in the near future. Besides implementation in the upcoming fall semester, we will seek opportunities to host workshops on Nanopore sequen-cing and help educate the educators. References[1] Wang, et al., Nanopore sequencing technology, bioinformatics and applications. Nature Biotech., 2021, 39, 1348–1365. https://www.nature.com/articles/s41587-021-01108-x.pdf[2] Bold Predictions for Human Genomics by 2030: Session 1. National Human Genome Research Institute, 2021.  https://www.youtube.com/watch?v=fOLlXSu5k14&t=11s[3] González-Recio, et al., Sequencing of SARS-CoV-2 genome using different nanopore chemistries. Applied Microbiol. & Biotech., 2021,105:3225–3234. https://doi.org/10.1007/s00253-021-11250-w[4] C-H Shen, Diagnostic Molecular Biology, Chap. 11 – Techniques in Sequencing, 2019: 277-302, Elsevier.[5] Richardson, Constructivist Pedagogy, Teachers College Record, 2003, 105(9):1623-1640.DOI:10.1046/j.1467-9620.2003.00303.x[6] Bonwell & Eison, Active Learning: Creating Excitement in the Classroom. 1991 ASHE-ERIC Higher Education Reports. https://files.eric.ed.gov/fulltext/ED336049.pdf* Current affiliation of YMH: Department of Genomic Medicine, MDACCFigure 5. Nanopore sequencing lab workflowFigure 9. 2021 CPRIT summer student’s poster, also seen in a screencast in PDF AttachmentsFigure 6. Students perform Nanopore sequencing on MinIONEnd of 2020 – Jan 2021Feb 2021Mar 2021 May 2021Apr 2021 Jul 2021Nov 2021Mar-Apr 2022May-Aug 2022Preparation phaseTraining of instructors with ONT scientistPractice by instructorsDevelopment of instructional materialsNanopore sequencing workshop for 2nd-year studentsTraining of CPRIT summer studentTraining of 1st-year studentsPreparation of AGT meeting abstract & poster by 1st-year students Revision of instructional materials for implementation in fall semesterFigure 8. Student presentations in 2021 fall semester1Prepare Genomic DNAgDNA Extraction from Bacterial Isolates2Prepare LibraryNative Barcoding Genomic DNA Protocol3Sequence SequenceMinION & MinITSystem4Analyze Data Anlyze taBioinformaticsTaxonomyEPI2ME WIMP NanoPlotQCFiltlongTrimmingNanoPlotQCCanuAssemblyMapperminimap2AlignmentFilter SAM or BAM, output SAM or BAM SortSamSAM toolsRaconPolishingComplete polished whole genomeAssemblyFigure 7. An example of the workflow for Nanopore sequencing data analysisFigure 2. Project timelineFigure 4. An outline of  Nanopore sequencing lecture• Pre-instruction assignment• Lecture before wet lab• Hands-on experiment• Individual & collabora-tive lab notes• Bioinformatic analysis• Student presentations1. The Third-Generation Sequencing2. Nanopore Sequencing Platform3. Devices: Focusing on MinION4. Control Software: MinKNOW5. MinION Flow Cell6. Library Preparation7. Monitoring of MinION sequencing8. Nanopore Sequencing Data Analysis9. Applications of Nanopore SequencingOutlinePurpose of  the Project• Two tracks in Diagnostic Genetics and Genomics (DGG) master’s program at SHP: Molecular Genetics and Genomics (MGG) and Cytogenetics and Cytogenomics (CGG) • Overarching goal of DGG-MGG: to train technologists/scientists with expertise in high capacity data generation (wet lab) and bioinformatic/computational analyses (dry lab)  • To serve one of the institution’s core values, Discovery, we strive to introduce cutting-edge technologies to maintain our program at the forefront of graduate education. • The current project aims to incorporate the innovative Nanopore sequencing technology [1]into our curriculum. Figure 1. Principle of Nanopore sequencing (only MinIONdevice shown) [1]Students Present & Publish Project OutcomesStudents AnalyzeDataStudents Generate DataMolecular ApplicationsDGG 6510: Advanced Molecular Diagnostic Techniques Intellectural & Interpretive FoundationsDGG 6280: Concepts in Molecular Diagnostics Core Technical FoundationsDGG 6181: Advanced Mol. Biol. & Techniques Intellectual & Interpretive FoundationsDGG 6320: BioinformaticsAnalytical Computer ApplicationsDGG 6110: Bioinformatics labs Figure 3. An overview of the Project-based Integrated Core Curriculum Development Initiative (PICCDIn). Five core courses are taught in the entering fall semester. The first eight weeks are devoted to laying down solid foundations in theories, techniques and interpretive skills. In the next eight weeks, students perform a supervised project geared toward real-time, real-world problem solving using cutting-edge genomic technology. a. Long read (> 5k bp), high speed (1 bp/ns), and real-time base callingb. Fluorescent tag-free detection of basesc. Less sensitive to temperature throughout sequencing; reliable outcome d. Shortened hands-on time 

Integration of Long-Read Whole Genome Sequencing in Graduate Curriculum of Diagnostic Genetics and Genomics

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Integration of Long-Read Whole Genome Sequencing in Graduate Curriculum of Diagnostic Genetics and Genomics

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