Related Experiment Video
Updated: Jul 13, 2026
04:58
Introductory Analysis and Validation of CUT&RUN Sequencing Data
Published on: December 13, 2024
Comparison of ENCODE region SNPs between Cebu Filipino and Asian HapMap samples
Amanda F Marvelle1, Leslie A Lange1, Li Qin1
1Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, 4109-F Neuroscience Research Building, 103 Mason Farm Road, Chapel Hill, NC, 27599-7264, USA.
Journal of Human Genetics
|July 20, 2007
Summary
HapMap data effectively represents genetic variation in Cebu Filipino populations. Tag single nucleotide polymorphisms (SNPs) from Asian panels, especially Han Chinese from Beijing, are transferable for genetic association studies in this group.
Area of Science:
- Genetics
- Population Genetics
- Genomic Variation
Background:
- Linkage Disequilibrium (LD) patterns are crucial for designing genetic association studies.
- The International HapMap Project catalogs these patterns globally.
- Assessing the applicability of HapMap data to diverse populations is essential for broad research utility.
Purpose of the Study:
- To evaluate the transferability of tag single nucleotide polymorphisms (SNPs) from HapMap panels to a Cebu Filipino cohort.
- To determine the similarity of genetic variants in Cebu Filipinos compared to HapMap reference panels.
- To assess the utility of HapMap data for future genetic studies in the Philippines.
Main Methods:
- Analyzed 627 single nucleotide polymorphisms (SNPs) within 10 HapMap ENCODE regions.
- Examined allele frequency, pairwise linkage disequilibrium (LD), and haplotype frequency estimates.
- Compared genetic variants in 80 Cebu Filipino samples (Cebu Longitudinal Health and Nutrition Survey) with HapMap panels.
Main Results:
- Strong correlations were found between Cebu Filipino samples and HapMap Asian panels.
- The Han Chinese from Beijing (CHB) panel showed the highest correlation with Cebu Filipino genetic variants.
- Tag SNPs selected from the HapMap CHB panel effectively captured genetic variation in the Cebu Filipino cohort.
Conclusions:
- HapMap data, particularly from Asian panels like CHB, is a valuable resource for genetic studies in Cebu Filipino populations.
- Tag SNPs identified using HapMap data are transferable and can represent local genetic variation.
- The findings support the use of HapMap resources for future association studies in this demographic.
Related Concept Videos
02:26Comparing Copy Number Variations and SNPs
Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
01:05Single Nucleotide Polymorphisms-SNPs
A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
02:54Evolutionary Relationships through Genome Comparisons
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
02:51Multi-species Conserved Sequences
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
02:02Cis-regulatory Sequences
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
02:30Histone Variants at the Centromere
Histone variants are the histone proteins with structural and sequence variations. These variants may be regarded as “mutant” forms that replace their canonical histone counterparts in the nucleosomes. Specific post-translational modifications on the histone variants enable further chromatin complexity and regulate tissue-specific gene expression. The most common histone variants are from histone H2A, H2B, and linker histone H1 families. However, several variants of histone H3 variants are also...