Genetic Variations: SNPs, DIPs, and Ancestry Insights

Unique SNPs per person

Around 3 million SNPs unique to each individual

DNA variations and phenotype

Because less than 2% of DNA codes for proteins, most coding mutations are silent, and natural selection eliminates harmful changes

SNPs

Single Nucleotide Polymorphisms - changes to a single base pair

DIPs/InDels

Deletion-Insertion Polymorphisms - small changes due to replication or repair mistakes

SSRs

Simple Sequence Repeats - short sequences that can multiply spontaneously

CNVs

Copy Number Variants - large segments of DNA that vary in number and may include genes

Causes of SNPs

DNA replication mistakes or mutagen exposure

Consequence of SNPs

Usually no effect; rarely results in a phenotype

Causes of DIPs

Errors in DNA replication or repair

Effect of DIPs in coding regions

Can result in the loss of a protein

Causes of SSRs to change

Spontaneous events; can expand rapidly

Disease caused by SSRs

Huntington's disease

Causes of CNVs

Unequal crossing over during meiosis I

Effects of CNVs

Phenotypes vary greatly depending on the affected region

Inheritance of mtDNA

Maternally (passed only from mothers)

Use of mtDNA in ancestry

To trace the most recent common maternal ancestor (~150,000 years ago)

Mutation rate of mtDNA

Approximately once every 3,400 years

Use of Y chromosome in ancestry

To trace the most recent common paternal ancestor

Pan-genome

The entire genetic content of a species

Importance of the pan-genome

It helps identify disease-associated genotypes and resilient individuals

Neanderthal gene variant linked to COVID-19

A variant of the DPP4 gene (dipeptidylpeptidase 4)

Effect of Neanderthal DPP4 variant on COVID-19

Increases the likelihood of severe symptoms

Effect of modern DPP4 variant on COVID-19

Decreases the likelihood of severe symptoms

Gene associated with lactose tolerance

The LCT gene, which encodes lactase

Lactose tolerance in European descent

About 80% have the mutation allowing lactose digestion

Selection of lactose tolerance trait

Around 10,000 years ago during cattle domestication

Protein linked to malaria resistance

The Duffy glycoprotein (FY) on red blood cells

Mutation effect on Duffy protein

One allele has a point mutation; the other is silenced in the promoter region

Commonality of Duffy-negative genotype

Most common in Sub-Saharan Africa

Advantage of Duffy-negative genotype

It provides resistance to P. vivax malaria