Unassociated genomic region in reference genome

Introduction

The human reference genome is a critical tool for genomics research, yet it remains incomplete and contains unassociated genomic regions. These gaps and missing sequences can have significant implications for understanding genetic variation, structural polymorphisms, and functional genomics.

Key Insights

Missing and Misassigned Sequences:
- A substantial fraction of new insertion sequences are either missing, fragmented, or misassigned in the reference genome, with 18-37% being copy-number polymorphic.
- Many non-reference sequences (NRS) and alternate alleles, which are not present in the reference genome, have been identified, including those associated with tandem repeats.
Heterochromatic Gaps:
- Large heterochromatic regions, composed mainly of Human Satellites 2 and 3, remain unexplored due to their repetitive nature, challenging standard mapping and assembly algorithms.
- An alignment-free method has been developed to classify these sequences into subfamilies, aiding in the study of these complex regions.
Unalignable Regions with Functional Elements:
- Thousands of regions in the human and mouse genomes are unalignable in primary sequence but contain common RNA structures, suggesting functional significance.
- Many of these regions are expressed as non-coding RNA sequences, indicating their potential regulatory roles.
Transcribed Non-Reference Sequences:
- RNA-Seq data has revealed that many novel sequences absent from the reference genome are transcribed, including sequences conserved across different human populations and other primates.
- These findings highlight the presence of functional genes and novel transcript contigs that are missing from the current reference genome.

Conclusion

The human reference genome is incomplete, with significant portions of genomic sequences either missing, misassigned, or unalignable. These gaps include both structural variations and functional elements such as non-coding RNAs and conserved genes. Advances in sequencing and alignment methods are crucial for identifying and characterizing these unassociated genomic regions, thereby refining the reference genome and enhancing our understanding of human genetic diversity and function.

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Unassociated genomic region in reference genome

Summary

Introduction

Key Insights

Conclusion

Sources and full results

Characterization of Missing Human Genome Sequences and Copy-number Polymorphic Insertions

This study identified 2,363 new insertion sequences in the human genome, revealing new exons and conserved noncoding sequences not yet represented in the reference genome, and developed a method to accurately genotype these new insertions using next-generation sequencing datasets.

Genomic Characterization of Large Heterochromatic Gaps in the Human Genome Assembly

This study presents a novel method for generating reference databases for unassembled genomic regions enriched with complex satellite DNA, enabling genomic studies of heterochromatic regions and studying patterns of sequence variation within human populations.

Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure.

Thousands of unalignable human and mouse genomic regions contain common RNA structures, suggesting shared non-coding RNA sequences in these regions.

Recovery of non-reference sequences missing from the human reference genome

This study identified 6113 non-reference sequences and 3041 alternate alleles in the human genome, enriching the spectrum of genetic variations and suggesting their origin is associated with tandem repeats.

Revealing the missing expressed genes beyond the human reference genome by RNA-Seq

A significant number of functional human genes are still absent from the incomplete human reference genome, highlighting the need for further refining and curating these genes.

The new bovine reference genome assembly provides new insight into genomic organization of the bovine major histocompatibility complex

The new bovine reference genome assembly ARS-UCD 1.2 reveals significant differences in the genomic organization of the bovine major histocompatibility complex compared to previous assemblies.

Integrative analysis of 111 reference human epigenomes

The 111 reference human epigenomes provide a valuable resource for understanding gene regulation, cellular differentiation, and human disease.

The mosaic structure of human pericentromeric DNA: a strategy for characterizing complex regions of the human genome.

Large portions of human pericentromeric DNA consist of a mosaic of different genomic segments with different duplication propensities, making it a valuable tool for rapid characterization of complex human genome regions.

Utilizing mapping targets of sequences underrepresented in the reference assembly to reduce false positive alignments

Mapping targets representing 8% of the human genome, which are underrepresented in the reference assembly, can reduce false positive alignments and improve mapping sensitivity in whole-genome short-read datasets.

Analysis of Flanking Sequences from Dissociation Insertion Lines: A Database for Reverse Genetics in Arabidopsis

Dissociation element insertions in Arabidopsis are evenly dispersed throughout the genome, with a preference for regions near nucleolus organizer regions on chromosomes 2 and 4.

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