Questions: Genomics and DNA Sequencing

Question 1

What is the key technological advantage of next-generation sequencing (NGS) over Sanger sequencing that allowed genome costs to drop from billions of dollars to hundreds?

• A. NGS reads longer fragments, reducing the number of overlaps needed for assembly
• B. NGS sequences millions of short fragments simultaneously in a massively parallel process
• C. NGS does not require PCR amplification, eliminating a major source of error
• D. NGS uses RNA instead of DNA, making it compatible with any tissue type

Answer: (B)

The defining feature of NGS is massively parallel sequencing — millions of DNA fragments are sequenced at the same time in a single run, rather than sequencing one fragment at a time as in Sanger sequencing. This throughput is what drove costs down by orders of magnitude. NGS reads are actually shorter than Sanger reads (a disadvantage), not longer, and PCR amplification is typically used in NGS library preparation.

Question 2

Once a genome is fully sequenced, researchers know the function of nearly every gene it contains.

• T. True
• F. False

Answer: False

Sequencing produces a string of nucleotides — a blueprint — but does not reveal what each segment does. Determining gene function requires annotation (identifying where genes are, using computational tools and comparison to known genomes) and functional experiments such as knockouts, overexpression, and expression profiling. As of now, the function of a substantial fraction of human genes remains unknown or poorly characterized, even though the genome was sequenced over 20 years ago.

Question 3

What role does bioinformatics play in a genomics project, and why can't sequencing data be interpreted without it?

Model answer: Bioinformatics provides the computational tools to assemble millions of short sequencing reads into a continuous genome sequence, align reads to a reference, identify variants (SNPs, insertions, deletions), annotate genes and regulatory regions, and perform statistical analysis. Without these tools, raw sequencing output is just millions of short, unordered nucleotide strings with no biological meaning.

Modern NGS produces reads of 100–300 bp each; a human genome is ~3 billion bp. Assembly means computationally finding overlaps among millions of reads and stitching them into chromosomes — a problem requiring substantial computing power and algorithms. Variant calling, expression analysis (RNA-seq), and functional annotation each require additional specialized tools. Genomics is as much a computational discipline as a wet-lab one.