Bioinformatic Analysis for Cancer Genomics (2024-2025)

Lectures

Lecture 00: Course overview "Bioinformatic Analysis for Cancer Genomics" (15/12/2024) [Loi]

• PDF
• YOUTUBE

Lecture 01: Introduction to Next-Generation Sequencing and its clinical applications (15/12/2024) [Loi]

• PDF
• YOUTUBE
• Q&A

Lecture 02.1: Introduction to Next-Generation Sequencing and its clinical applications (22/12/2024) [Loi]

• PDF
• YOUTUBE
• Q&A

Lecture 02.2: Introduction to Ubuntu, Linux command-lines, Google Colab and Github - Part I (22/12/2024) [Quy, Hung]

• INTRODUCTION GOOGLE COLAB   Youtube
• PDF   Youtube
• Basic Linux - PART I   Youtube
• • Practice:

Lecture 03.1: Human Genome, Gene Annotation and UCSC Genome Browser (29/12/2024) [Loi]

• YOUTUBE
• PDF
• Q&A

Lecture 03.2: Introduction to Ubuntu, Linux command-lines, Google Colab and Github - Part II (29/12/2024) [Quy, Hung]

• YOUTUBE - INTRODUCTION TO UBUNTU PART II
• YOUTUBE - INTRODUCTION TO GITHUB
• • Practice:
• Q&A

Lecture 04.1: Introduction to GENETIC DISORDER, HPO, OMIM, gnomAD and ClinVar - Part I (05/01/2025) [Loi]

• YOUTUBE
• PDF
• Q&A

Lecture 04.2: Introduction to basic Shell/Bash script - Part I (05/01/2024) [Khai, Tuan Thanh]

• YOUTUBE
• PDF
• Practice:

Lecture 05.1: Introduction to GENETIC DISORDER, HPO, OMIM, gnomAD and ClinVar - Part II (12/01/2025) [Loi]

• PDF
• YOUTUBE
• Q&A

Lecture 05.2: Introduction to basic Shell/Bash script - Part II (12/01/2025) [Khai, Tuan Thanh]

• YOUTUBE

Lecture 06.1: Somatic mutations in Cancer and COSMIC database - Part I (19/01/2025) [Loi]

• YOUTUBE
• Q&A

Lecture 06.2: Introduction to basic AWK - Part I (19/01/2025) [Kim, Tu]

• YOUTUBE
• Q&A
• LINK
• Practice:

Lecture 07.1: Review: Next-Generation Sequencing, Germline vs. Somatic mutation (16/02/2025) [Loi]

• PDF
• YOUTUBE
• Q&A

Lecture 07.2: Introduction to basic AWK - Part II (16/02/2025) [Kim, Tu]

• PPTX
• Practice:
• Homework:   Answer:
• YOUTUBE
• EXAMPLE

Lecture 08.1: COSMIC database (23/02/2025) [Loi]

• YOUTUBE

Lecture 08.2: Introduction to basic R programming - Part I (23/02/2025) [Huy, Dr. Son]

• PDF
• PPTX
• Practice:

Lecture 09.1: Introduction to Cancer Biology - Part I (02/03/2025) [ThS.BS. Nguyễn Huy Thịnh]

• PDF
• YOUTUBE
• Q&A

Lecture 09.2: Introduction to basic plots with R - Part II (02/03/2025) [Huy, Dr. Son]

• YOUTUBE
• PPTX
• Code

Lecture 10.1: Introduction to Cancer Biology - Part II (09/03/2025) [ThS.BS. Nguyễn Huy Thịnh]

• PDF
• YOUTUBE
• Q&A

Lecture 10.2: Introduction to ggplots with R - Part III (09/03/2025) [Huy, Dr. Son]

• PPTX
• Practice:
• YOUTUBE

Lecture 11.1: Introduction to Cancer Biology - Part III (16/03/2025) [ThS.BS. Nguyễn Huy Thịnh]

• PDF
• YOUTUBE
• Q&A

Lecture 11.2: Introduction to basic statistics with R - Part IV (16/03/2025) [Huy, Dr. Son]

• YOUTUBE
• PPTX
• Practice:

Lecture 12.1: Introduction to Cancer Biology - Part IV (23/03/2025) [ThS.BS. Nguyễn Huy Thịnh]

• PDF
• YOUTUBE
• Q&A

Lecture 12.2: Review R - Part V (23/03/2025) [Huy, Dr. Son]

• YOUTUBE
• Practice:

Lecture 13: Wetlab for NGS DNA-seq (30/03/2025)

Lecture 13.1: Introduction to DNA extraction [Phu]

• YOUTUBE
• Q&A

Lecture 13.2: Introduction to Library Prep [Phu]

• YOUTUBE
• Q&A

Lecture 14: Upstream analysis for DNA-seq (06/04/2025)

Lecture 14.1: Raw Data Processing [Duy]

• YOUTUBE
• Q&A

Lecture 14.2: Alignment/Mapping, BAM format and QC BAM [Duy]

• YOUTUBE
• Q&A
• 

Lecture 15: Downstream analysis for DNA-seq - Part I (13/04/2025) [Dr. Minh]

Lecture 15.1: Variant Calling and Variant Filtering for DNA-seq

• LECTURE
• YOUTUBE
• Q&A

Lecture 15.2: Variant Annotation and Variant Annotation databases for DNA-seq - Part I

• LECTURE
• YOUTUBE

Lecture 16: Downstream analysis for DNA-seq - Part II (20/04/2025) [Dr. Minh]

Lecture 16.1: Variant Annotation and its databases for DNA-seq - Part II

• LECTURE
• YOUTUBE

Lecture 16.2: Cancer Gene Panel DNA testing

• LECTURE
• YOUTUBE
• Q&A

Practice on DNA-seq Downstream Analysis (Dr. Minh)

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Lecture 17: Metastatic Cancer Genomics (27/04/2025) [Dr. Ngu]

• PDF
• YOUTUBE
• Q&A

Lecture 18.1: Structual Variant (SV) and Copy Number Variant Calling with short-read DNA-seq (04/05/2025) [Loi]

• PDF
• YOUTUBE
• Q&A

Lecture 18.2: Hands-on: Structual Variant (SV) Calling with short-read DNA-seq (04/05/2025) [Nhu]

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• PDF
• YOUTUBE
• Q&A

Lecture 19.1: Structual Variant (SV) and Copy Number Variant Calling with long-read DNA-seq (11/05/2025) [Loi]

• PDF
• YOUTUBE
• Q&A

Lecture 19.2: Hands-on: Structual Variant (SV) and Copy Number Variant Calling with long-read DNA-seq (11/05/2025) [Nhu]

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• PDF
• YOUTUBE
• Q&A

Lecture 20.1: Liquid Biopsy (cfDNA and ctDNA) for Cancer Genomics (18/05/2025) [Loi]

• [PDF]
• YOUTUBE
• Q&A

Lecture 20.2: Cancer Somatic Variant Annotation (18/05/2025) [Dr. Minh]

• LECTURE
• YOUTUBE

Lecture 21.1: Genetic counseling for Mendelian inheritance diseases (25/05/2025) [Dr. Trang]

• YOUTUBE

Lecture 21.2: Genetic counseling for Cancer (25/05/2025) [Dr. Bac]

• YOUTUBE
• Q&A

Lecture 22: MGI solutions for Cancer Genomics (01/06/2025)

• Application of DNBSEQ Technology ONcology Screening & Targeted Treatment - 1
• Application of DNBSEQ Technology ONcology Screening & Targeted Treatment - 2
• Ứng dụng công nghệ giải trình tự gen thế hệ mới (NGS) trong xét nghiệm đột biến gen - MAIA CENTER

  • Q&A

    • Q&A for Lecture 22.1

    • Q&A for Lecture 22.2

    • Q&A for Lecture 22.3

Lecture 23: QIAGEN solutions for Cancer Genomics (08/06/2025)

• High-Quality Nucleid Acid Extraction from Challenging Oncology Samples
• Comprehesive Solution for Oncology NGS: QIAseq Targeted DNA, RNA and Multimodal DNA/RNA
• Simplify oncology NGS testing and clinical reporting for high-throughput data using QIAGEN CLC Genomics Workbench and QCI Interpret tools
  • Q&A

    • Q&A for Lecture 23.1

    • Q&A for Lecture 23.2

    • Q&A for Lecture 23.3

Lecture 24: PacBio solutions for Cancer Genomics (15/06/2025)

• A new age in cancer genomics - Comprehensive somatic variant detection with accurate long- and short-read sequencing

  • Q&A

    -Questions and Aswrers for Lecture 24

Lecture 25: GeneMind solutions for Cancer Genomics (22/06/2025)

• Bioinformatic pipeline for Oncology from Genemind
• Genemind Oncology Solutions

  • Q&A

    - Questions and Answers for Lecture 25.1

    - Questions and Answers for Lecture 25.2

Lecture 26: Mtialab and SISC group solutions for Cancer Genomics (06/07/2025)

• PDF - SISC Group
• Streamlining data analysis of genomes and exomes in oncology clinical research - Mitalab
• Giới thiệu kỹ thuật - Microarray trong phát hiện sớm ung thư - SISC Group

  • Q&A

    • Questions and Answers for Lecture 26.1

    • Questions and Answers for Lecture 26.2

Lecture 27: Việt Huy solutions for Cancer Genomics (13/07/2025)

• PDF
• Giải pháp xét nghiệm gen trong điều trị ung thư - Việt Huy
• Giải pháp xét nghiệm gen trong điều trị ung thư - Việt Huy

  • Q&A

    • Questions and Answers for Lecture 27.1

    • Questions and Answers for Lecture 27.2

Lecture 28: SOPHiA solutions for Cancer Genomics (17/07/2025)

• SOPHiA solutions for Cancer Genomics

  • Q&A

    -Questions and Answers for Lecture 28

Lecture 29: An Thịnh solutions for Cancer Genomics (20/07/2025)

• PDF

• Lecture 29.1: An Thịnh solutions for Cancer Genomics

• Lecture 29.2: An Thịnh solutions for Cancer Genomics

  • Q&A

    - Questions and Answers for Lecture 29.1

    - Questions and Answers for Lecture 29.2

Lecture 30: Biomedic solutions for Cancer Genomics (03/08/2025)

• Lecture 30: Biomedic solutions for Cancer Genomics

  • Q&A

    • Questions and Answers for Lecture 30

Materials

• R book
• Bioinformatics Linux
• Online resources