IMMUNOLOGY &

IMMUNOINFORMATICS

MODULE 2 TARGET 3

Investigating the Genetic and Phenotypic Implications of

Lactase Persistence in European Population

SUBMITTED TO SUBMITTED BY

Dr V Chari 211FA01103

Assisstant Professor 211FA01074

Department of Biotechnology
Investigating the Genetic and Phenotypic Implications of Lactase Persistence
in European Population

Abstract

This study examines the genetic basis of lactase persistence (LP) in European populations, where
the trait—enabled by the rs4988235 SNP near the LCT gene—allows for lifelong lactose
digestion. This SNP, beneficial in dairy-consuming societies, underwent positive selection,
leading researchers to investigate whether this region might carry harmful mutations affecting
health risks like prostate cancer, coronary artery disease (CAD), and bone mineral density
(BMD). Using genome-wide association studies (GWAS), the study found limited connections
between LP-related genetic markers and these diseases. There was a slight association with lower
BMD, but overall, the impact was minimal. This research highlights how positively selected
traits, like LP, can influence population genetics without significant health drawbacks, offering
insights for personalized dietary advice and health assessments.

Background on Lactase Persistence and Genetic Variation

Lactase persistence allows individuals to continue digesting lactose post-weaning. In European

populations, this trait is primarily linked to an SNP located 13.9 kb upstream of the lactase
(LCT) gene, within the regulatory region of the MCM6 gene. This SNP arose around 7,500 years
ago and was rapidly selected for due to the nutritional benefits of dairy consumption. Although
this positive selection has been studied extensively, recent research has shown that regions under
strong positive selection can accumulate slightly deleterious mutations that “hitchhike” with the
beneficial mutation. This phenomenon raises questions about potential health implications
associated with the LP haplotype block, such as disease susceptibility.

Objective and Relevance of Research on SNPs and Larger Mutations

 Studying SNPs like rs4988235 and their associated genomic regions can reveal important
links between individual genetic variations and complex traits, including disease
susceptibility and growth.
  The LP SNP is particularly valuable because it serves as a model for understanding how a
single genetic variation can alter gene expression across an individual’s lifetime and
influence diet adaptability.
 Beyond LP, there are thousands of SNPs associated with complex traits, and research on
these variations helps us understand genetic predispositions to various diseases.
Exploring the functional implications of these SNPs is critical for precision medicine,
which aims to personalize treatments based on an individual’s genetic profile.

Protocol for Examining Genetic Associations with Traits

To investigate associations between LP and disease phenotypes, the study utilized the following
methods:

1. Genotype Collection:

Data from the 1000 Genomes Project identified individuals of European descent with the
LP SNP. This cohort included five major subgroups: Northern and Western Europeans
(CEU), Finns (FIN), British (GBR), Iberians (IBS), and Tuscans (TSI).

2. Genome-Wide Association Studies (GWAS):

The research team utilized publicly available GWAS datasets from large cohorts to
analyze associations between LP-related SNPs and disease risk. Specifically:

o BMD data from the GEFOS Consortium (32,965 individuals) for femoral neck,
lumbar spine, and forearm BMD.

o Prostate Cancer data from the PRACTICAL Consortium (79,194 cases and
61,112 controls).

o Coronary Artery Disease (CAD) data from CARDIoGRAMplusC4D (60,801

cases and 123,504 controls).
 Wilcoxon rank sum tests showing beta signed p-values for

(A) femoral neck BMD associated SNPs in high LD with the lactase persistence SNP;

(B) lumbar spine BMD associated SNPs in high LD with the lactase persistence SNP

(C) forearm BMD associated SNPs in high LD with the lactase persistence SNP.
 3. Linkage Disequilibrium (LD) and Class-Based Association Testing:

The LD pattern with rs4988235 was examined to delineate the LP haplotype block (1.9
Mb encompassing nine genes and one microRNA). Class-level association tests with
GenCAT software assessed whether the collective effect of SNPs in the LP haplotype was
significant across different disease phenotypes. Additionally, enrichment tests determined
if LP-associated SNPs were more likely to contribute to phenotype significance than
SNPs outside the LP locus.

4. Enrichment Analysis: To further clarify associations, the researchers conducted

enrichment analyses using Wilcoxon and Fisher’s exact tests to compare SNP
significance across the locus with broader datasets, assessing how LP-associated
mutations impact disease risks.

Findings on Lactase Persistence and Health Risks

The study found limited evidence to support a direct association between LP-associated SNPs
and significant health risks for the three primary diseases examined. Here are the specific
findings for each health phenotype:

 Bone Mineral Density (BMD):

While SNPs within the LP haplotype block showed some enrichment for lower BMD
values, the effect sizes were minimal. For instance, femoral neck, lumbar spine, and
forearm BMDs had mean beta values close to 1, indicating near-neutral impacts on BMD.
This suggests that although dairy consumption generally supports bone health, the genetic
basis of lactase persistence itself does not strongly impact bone density.

 Prostate Cancer:

No significant link was found between LP-associated SNPs and prostate cancer risk.
Although individual SNPs within the LP haplotype had slightly lower p-values for
association with prostate cancer than those outside, these results did not reach statistical
significance, indicating that the LP allele may not elevate prostate cancer risk.
  Coronary Artery Disease (CAD):

For CAD, similar patterns emerged, with some SNPs within the LP haplotype showing
slightly smaller p-values than non-LP SNPs. However, the effect sizes for CAD risk were
too small to suggest a clinically significant association. This finding is in line with
existing research suggesting that dairy intake may have a minimal impact on CAD risk.

Discussion: The Significance of LP-Associated Mutations and Hitchhiking Effects

The study contributes to understanding how positive selection can shape genetic traits while
mitigating potential health risks. Although the LP allele underwent strong selection in European
populations, it appears that the hitchhiking of deleterious mutations within this haplotype block
has not significantly impacted the prevalence of diseases such as prostate cancer, CAD, or
reduced BMD. This outcome is noteworthy because it highlights how the selective advantage of
LP—allowing adult dairy consumption—has outweighed any minor risks associated with
deleterious mutations.

Moreover, the study’s findings emphasize the utility of class-based genetic association testing in
assessing how grouped SNPs, rather than isolated mutations, influence complex phenotypes. As
this study shows, high LD around an adaptive SNP like rs4988235 can provide insights into how
genetic variations accumulate in response to dietary or environmental pressures.

Relevance of SNP Research and Novel Mutation Discovery

Understanding the effects of SNPs, particularly in high-LD regions like the LP haplotype block,
helps explain the genetic underpinnings of traits and diseases. The research underscores that
studying SNPs can reveal insights into how positive selection operates at a molecular level. With
the rise of precision medicine, identifying SNPs associated with health risks can guide
personalized therapies tailored to an individual’s genetic profile.

If a novel mutation is discovered, its functional impact can be determined through a series of
investigative steps:

 In Silico Predictions: Tools like PolyPhen-2, SIFT, and MutationTaster predict mutation
effects on protein function or stability. For example, these tools could predict if a novel
mutation alters the activity of the LCT gene or nearby regulatory elements.
  CRISPR and Functional Studies: CRISPR/Cas9 technology enables researchers to
introduce specific mutations into cell lines or model organisms, allowing for direct
observation of phenotypic changes. In this case, introducing an LP-associated SNP in a
model system could reveal how it affects lactase production or enzyme stability.

 Expression and Enzymatic Activity Assays: Assessing protein expression, enzyme

activity, or stability can clarify a mutation’s biochemical impact, potentially linking it to a
metabolic or health-related phenotype.

Conclusion

The study on the lactase persistence haplotype in European populations illustrates how genetic
adaptations can shape human health and disease susceptibility. While LP SNPs were initially
thought to potentially carry increased disease risk due to genetic hitchhiking, this research
suggests that such risks are minimal, underscoring the resilience of human genetic adaptation.
The findings support further exploration of SNPs and genomic regions under positive selection
to understand the complex relationship between genetics and health traits, ultimately advancing
the field of precision medicine.