Discovery of common sequences absent in the human reference genome using pooled samples from next generation...

Area of Science:

• Genomics
• Population Genetics
• Evolutionary Biology

Background:

• Large DNA sequences present in individuals are sometimes missing from the human reference genome.
• This absence can bias genomic studies and variant analysis, especially in microarray and next-generation sequencing (NGS).
• Previous methods using paired-end sequencing reads identified novel sequences, but their population distribution, evolution, and function remained unstudied.

Purpose of the Study:

• To systematically identify and characterize missing common sequences (micSeqs) in the human genome.
• To investigate the evolutionary history and functional significance of these micSeqs in human populations.

Main Methods:

• Developed a pipeline to pool and filter One End Anchor (OEA) reads from the 1000 Genomes Project to identify micSeqs.
• Applied comparative genomics with primate and individual genomes, gene expression data, and PCR validation.
• Analyzed functional elements using RNA-seq and ChIP-seq data.

Main Results:

• Identified 309 micSeqs present in at least 1% of the population but absent in the reference genome.
• Confirmed 76% of identified micSeqs through comparative genomics and PCR validation.
• Found eleven micSeqs highly expressed in the human brain and three containing transcription factor binding regions, indicating functional roles. Identified primate-specific sequences with dynamic evolution.

Conclusions:

• A significant portion of missing common sequences (micSeqs) were validated, suggesting they are real genomic features.
• Several micSeqs exhibit functional relevance, particularly in brain tissue and gene regulation.
• These micSeqs are important for understanding human diversity and primate evolution, with some being primate-specific.