Human Genome Project

When did the Human Genome Project run

1990–2003

Why sequence genomes

To identify variants, compare samples, study AMR genes, identify species in mixed samples, build reference genomes, and support applications like RNA-seq, ChIP-seq, WGS, and WES

Purpose of the HGP mapping stage

To create a genome framework and determine how close genomic features are to each other

Techniques used in HGP mapping

Restriction mapping, FISH, genetic linkage maps, microsatellite markers, YACs, BACs

Why were BACs used in sequencing

To clone large chromosome fragments for stable propagation and maintenance

What did the 2001 draft genome achieve

83% coverage, <1/1000 error rate

What did the 2003 final genome achieve

99% of gene-containing regions, ~1/20,000 error rate

Main bioinformatics tasks in the HGP

Genome assembly, gene identification & annotation, data storage in databases like GenBank and Ensembl

Main stages of sequence analysis

QC → trimming → alignment → variant calling → annotation → interpretation

What types of variants may be found

SNPs, indels, structural variants, frameshift variants

What does variant annotation do

Predicts functional impact of variants

What is a table in a database

A structure storing data for one entity type

What is a field in a database

A column describing attributes of the entity

What is a record in a database

A row containing data for one instance

What is a key in a database

A unique identifier used for sorting, searching, and linking tables

Five attributes of a good database

Accurate, consistent, accessible, well-documented, regularly updated

Examples of NCBI resources

PubMed, GenBank, BLAST, dbSNP, RefSeq

Examples of EMBL-EBI resources

UniProt, Ensembl, ArrayExpress, ENA

What does AND do in Boolean searching

Narrows a search by requiring both terms

What does OR do in Boolean searching

Broadens a search by allowing either term

What does NOT do in Boolean searching

Excludes specified terms

Why use parentheses in Boolean searching

To control search logic and processing order

Example Boolean search string

inflammation AND (diet OR nutrition) NOT supplements
What is BLAST used for

What does Primer3 design

PCR primers, considering Tm, GC content, dimers, product size, and positional constraints

What does a genome browser do

Visualises genomic annotations and features

What is BioMart used for

Integrated querying and filtering of biological datasets

What is R used for in bioinformatics

Statistics, data visualisation, and genomics packages

What is Galaxy

A user-friendly web platform for analysing sequence data without coding