Bioinformatics lecture 6 (kinda important)

What is the exome? 🧬

The exome is all the exons in the genome, meaning the protein-coding parts of genes.

Why is the exome important? ⭐

Although it is only about 1–2% of the genome, around 85% of known disease-causing mutations occur in exons.

Why sequence the exome instead of the whole genome? 💰

Exome sequencing is cheaper, faster, easier to analyse, and focuses on the most biologically informative regions.

How many genes and exons are in the human exome? 🔢

About 20,000 genes and roughly 150,000 exons.

What types of problems is exome sequencing especially good for? 🧠

Rare Mendelian disease discovery, cancer mutation detection, and clinical diagnostics.

What is a FASTQ file? 📄

A sequencing file format that stores DNA sequences together with their quality scores.

What are the four lines in a FASTQ entry? 4️⃣

Identifier, DNA sequence, separator (+), and quality scores.

What do quality scores (Phred scores) represent? 🎯

They show how confident we are that each base is correct.

What does a Phred score of 20 mean? ✅

It means 99% accuracy, or about 1 error in 100 bases.

What is paired-end sequencing? 🔁

A method where both ends of a DNA fragment are sequenced.

Why is paired-end sequencing useful? 🧩

It improves read mapping, alignment accuracy, and variant detection.

What is the first step in the exome sequencing analysis pipeline? 🧭

Alignment – mapping sequencing reads to the reference genome.

What is the goal of variant calling? 🔍

To identify positions where the sample DNA differs from the reference genome.

What is variant annotation? 🏷️

Adding biological meaning to variants, such as which gene they affect and how.

About how many variants are found in a typical exome? 😮

Around 23,000 variants per individual.

Why is exome analysis mainly a filtering problem? 🧹

Because only one or a few variants cause disease, but thousands are detected.

What information does variant annotation add? 📚

Gene name, exon location, mutation type, known databases, and predicted functional effects.

What is a SNP? 🔤

A single-nucleotide polymorphism, meaning a one-base change in DNA.

Do most SNPs cause disease? ❌

No, most SNPs are harmless and have no effect on health.

Why does exome sequencing focus on coding variants? 🎯

Because changes in coding regions are easier to interpret and more likely to affect proteins.

What is the main challenge in finding a disease-causing variant? 🧠

Finding the one harmful variant among thousands of harmless ones.

What is the key idea behind variant filtering? 🔎

Systematically removing unlikely variants to narrow down candidates.

What is the first filtering step for rare disease analysis? 🚫

Remove common variants found in public databases.

Why are common variants usually removed? 📉

Rare diseases are unlikely to be caused by variants common in the population.

What types of variants are prioritised during filtering? ⭐

Protein-altering variants in conserved regions.

Why are conserved regions important? 🧬

They are preserved by evolution, so changes there are more likely harmful.

Why compare variants across affected individuals? 👨‍👩‍👧‍👦

True disease-causing variants should be shared among affected people.

What does the “RARE” filtering mnemonic stand for? 🧠

Remove common variants, Affect protein, Retained in affected, Evolutionarily conserved.

What is OMIM? 📘

Online Mendelian Inheritance in Man, a curated database of Mendelian diseases and their genes.

Why is OMIM useful in exome analysis? 🔗

It links genes to known disease phenotypes, helping prioritise candidates.

What was the key lesson from the Miller syndrome exome study? 🧪

Exome sequencing can identify new disease genes by filtering a small number of patients.

What are major limitations of exome sequencing? ⚠️

It misses intronic and regulatory variants and may not explain complex diseases.

Why can exome sequencing fail for some diseases? 🧩

Some diseases are multifactorial or caused by non-coding variants.

What are incidental findings in genomic medicine? ⚠️

Unexpected variants that may indicate unrelated health risks.

Why do ethical issues arise in exome sequencing? 🛡️

Because of privacy concerns, uncertain results, and informed consent.

What is the future direction of genomic medicine? 🚀

A move toward whole-genome sequencing and personalised medicine.

What does personalised medicine aim to do? 🎯

Use genetic information to predict risk, guide treatment, and choose the best drugs.

Why is bioinformatics essential in genomic medicine? 💻

It turns raw sequencing data into meaningful diagnoses and clinical decisions.