Pan-human consensus genome significantly improves the accuracy of RNA-seq analyses.
Genome Res
; 32(4): 738-749, 2022 04.
Article
en En
| MEDLINE
| ID: mdl-35256454
ABSTRACT
The Human Reference Genome serves as the foundation for modern genomic analyses. However, in its present form, it does not adequately represent the vast genetic diversity of the human population. In this study, we explored the consensus genome as a potential successor of the current reference genome and assessed its effect on the accuracy of RNA-seq read alignment. To find the best haploid genome representation, we constructed consensus genomes at the pan-human, superpopulation, and population levels, using variant information from The 1000 Genomes Project Consortium. Using personal haploid genomes as the ground truth, we compared mapping errors for real RNA-seq reads aligned to the consensus genomes versus the reference genome. For reads overlapping homozygous variants, we found that the mapping error decreased by a factor of approximately two to three when the reference was replaced with the pan-human consensus genome. We also found that using more population-specific consensuses resulted in little to no increase over using the pan-human consensus, suggesting a limit in the utility of incorporating a more specific genomic variation. Replacing the reference with consensus genomes impacts functional analyses, such as differential expressions of isoforms, genes, and splice junctions.
Texto completo:
1
Banco de datos:
MEDLINE
Asunto principal:
Genoma Humano
/
Genómica
Tipo de estudio:
Guideline
Límite:
Humans
Idioma:
En
Revista:
Genome Res
Asunto de la revista:
BIOLOGIA MOLECULAR
/
GENETICA
Año:
2022
Tipo del documento:
Article
País de afiliación:
Estados Unidos