Perspectives and opportunities in forensic human, animal, and plant integrative genomics in the Pangenome era

The Human Pangenome Reference Consortium, the Chinese Pangenome Consortium, and other plant and animal pangenome projects have announced the completion of pilot work aimed at constructing high-quality, haplotype-resolved reference graph genomes representative of global ethno-linguistically different...

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Bibliographic Details
Published in:Forensic science international Vol. 367; p. 112370
Main Authors: He, Guanglin, Liu, Chao, Wang, Mengge
Format: Journal Article
Language:English
Published: Ireland Elsevier B.V 01.02.2025
Elsevier Limited
Subjects:
Algorithms
Animal human relations
Animal species
Animals
Bias
Biomarkers
Consortia
DNA Fingerprinting
DNA sequencing
Drug resistance
Epigenetics
Forensic Genetics
Forensic integrative genomics
Forensic science
Gene sequencing
Genetic diversity
Genetic Markers
Genetic research
Genome
Genomes
Genomic diversity
Genomics
Genotyping
Haplotypes
High-Throughput Nucleotide Sequencing
Humans
Long-read third-generation sequencing
Microbiomes
Microbiota
Multiculturalism & pluralism
Pangenome reference
Paradigm shift
Population
Sequence Analysis, DNA
Technological change
Transcriptomics
Southeast Asia
China
Africa
Oceania
Pangenome reference
Long-read third-generation sequencing
Forensic integrative genomics
Genomic diversity
Paradigm shift
ISSN:0379-0738, 1872-6283, 1872-6283
Online Access:Get full text
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Summary:The Human Pangenome Reference Consortium, the Chinese Pangenome Consortium, and other plant and animal pangenome projects have announced the completion of pilot work aimed at constructing high-quality, haplotype-resolved reference graph genomes representative of global ethno-linguistically different populations or different plant and animal species. These graph-based, gapless pangenome references, which are enriched in terms of genomic diversity, completeness, and contiguity, have the potential for enhancing long-read sequencing (LRS)-based genomic research, as well as improving mappability and variant genotyping on traditional short-read sequencing platforms. We comprehensively discuss the advancements in pangenome-based genomic integrative genomic discoveries across forensic-related species (humans, animals, and plants) and summarize their applications in variant identification and forensic genomics, epigenetics, transcriptomics, and microbiome research. Recent developments in multiplexed array sequencing have introduced a highly efficient and programmable technique to overcome the limitations of short forensic marker lengths in LRS platforms. This technique enables the concatenation of short RNA transcripts and DNA fragments into LRS-optimal molecules for sequencing, assembly, and genotyping. The integration of new pangenome reference coordinates and corresponding computational algorithms will benefit forensic integrative genomics by facilitating new marker identification, accurate genotyping, high-resolution panel development, and the updating of statistical algorithms. This review highlights the necessity of integrating LRS-based platforms, pangenome-based study designs, and graph-based pangenome references in short-read mapping and LRS-based innovations to achieve precision forensic science. •Global pangenome projects have built high-quality, haplotype-resolved reference genomes representing diverse populations.•Graph-based pangenome references enhance genomic diversity, benefiting long-read and short-read sequencing research.•Pangenome advances improve variant identification, forensic genomics, epigenetics, transcriptomics, and microbiome research.•MAS-seq addresses short forensic marker limitations by enabling optimal RNA and DNA fragment sequencing.•New pangenome coordinates and algorithms improve accurate genotyping, marker discovery, and forensic genomics innovations.
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ISSN:0379-0738
1872-6283
1872-6283
DOI:10.1016/j.forsciint.2025.112370