2020 Short Course - Essential Fundamentals - Next Generation Sequencing From The Beginning-Basic Principles in Bioinformatics for Identification and Interpretation of Genomic Alterations

Video Transcription

Video Summary

In this video, Susan Hsiao, an assistant professor and director of bioinformatics at Columbia University Medical Center, discusses the basic principles of bioinformatics for the identification and interpretation of genomic alterations. She starts by explaining the infrastructure requirements for clinical next-generation sequencing, highlighting the data flow and interaction between different systems throughout the process. She then focuses on the primary, secondary, and tertiary analyses of bioinformatics.<br /><br />During primary analysis, sequencing data is generated and converted into nucleotide sequences stored in FASTQ format. Hsiao explains the format of FASTQ files, including the sequence identifier, nucleotide sequence, and quality value. She discusses quality scores, which are expressed in ASCII format and represent the accuracy of base calls.<br /><br />Moving on to secondary analysis, Hsiao explains the processes of mapping and alignment. She discusses the SAM file format, which is commonly used for storing read alignments against reference sequences, and provides an example of a SAM file. Hsiao also highlights factors that can affect mapping quality, such as repetitive regions and low-quality bases.<br /><br />Hsiao then discusses variant calling, in which algorithms are used to predict the likelihood of variants based on quality scores and allele counts. She explains the variant call format (VCF) and shares examples of quality metrics for variant calling, such as transition-transversion ratio and heterozygous-homozygous ratio.<br /><br />In the final part of the video, Hsiao briefly touches on additional bioinformatics analyses, including copy number variant detection and RNA sequencing. She explains the approaches for copy number variant detection, such as read depth, paired end mapping, and split reads. For RNA sequencing, she discusses preprocessing steps, mapping to the genome or transcriptome, variant analysis, and transcript annotation.<br /><br />Hsiao concludes by mentioning the importance of annotation in variant interpretation and referring to guidelines for interpretation and reporting of germline and somatic variants. She also suggests additional resources for those interested in learning more about bioinformatics analysis.<br /><br />Note: No credits were granted in the video transcript.

Asset Subtitle

Susan J. Hsiao

Keywords

bioinformatics

genomic alterations

clinical next-generation sequencing

FASTQ format

SAM file format

variant calling

copy number variant detection

RNA sequencing