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Q42 - Variant Call Format Genomics

Theoretical 2 Real exam question - full text reproduced under IBO's CC BY-NC-SA 4.0 license
Recombinant DNA & Biotechnology Techniques

As more and more human genomes are being sequenced, storing this information has become an issue.

One way to reduce the size of the files containing sequence data is to store only the information about the differences between the sequenced genomes and a “reference genome”. (The reference genome is haploid).

Such file format is called Variant Call Format (vcf), and is in essence a table like the one below. In this example there is information about the genomes of 2 individuals, but any number of genomes (from 1 to many thousands) can be stored in one file.

Chromosome Position Reference allele Alternative alleles Individual 1 Individual 2
1 5897 G A 0/1 0/0
1 6908 C T 0/0 1/1
1 7100 A C,T 0/2 1/2
… … … … … …

In the columns “Genotypes” 0 stands for the nucleotide being the same as the reference allele, while other numbers stand for the nucleotide being the same as alternative alleles in the order they appear in the “Alternative alleles” column.

Note: In this question ONLY consider single nucleotide variants (SNVs, SNPs, switches of a single base) and consider the genomes of all people to be exactly equal length.

True or false?

Q42.1. Individual 1 from the example above is homozygous at position 7100 on chromosome 1.
Q42.2. At any given chromosomal position 25% of individuals in the population are expected to have 1/1 genotype.
Q42.3. The size of a vcf file storing the genome of a single individual increases with increasing genetic difference between this individual and the reference genome.
Q42.4. The size of a vcf file storing the genomes of two individuals and their daughter is expected to be smaller than a vcf file storing the genomes of the same two individuals and a genome of an unrelated female.
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Question reproduced from IBO 2023, Theoretical Paper 2, licensed under CC BY-NC-SA 4.0 - attributed to the International Biology Olympiad. Open the full exam PDF