Determination of complete chromosomal haplotypes by bulk DNA sequencing

Haplotype phase represents the collective genetic variation between homologous chromosomes and is an essential feature of non-haploid genomes. Here we describe a computational strategy to reliably determine complete whole-chromosome haplotypes using a combination of bulk long-range sequencing and Hi...

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Bibliographic Details
Published in:Genome Biology 2021-05, Vol.22 (1), p.139-139, Article 139
Main Authors: Tourdot, Richard W, Brunette, Gregory J, Pinto, Ricardo A, Zhang, Cheng-Zhong
Format: Article
Language:English
Subjects:
Accuracy
Aneuploidy
Cancer genomics
Chromatin
Chromosome rearrangement
Chromosomes
Chromosomes, Human - genetics
Computer applications
Deoxyribonucleic acid
Diploids
Diploidy
DNA
DNA sequencing
Gene Dosage
Gene expression
Genetic diversity
Genetic Linkage
Genome, Human
Genomes
Haplotype
Haplotypes
Haplotypes - genetics
Humans
Method
Mutation
Sequence Analysis, DNA
Sparsity
Statistics as Topic
Synteny
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Summary:Haplotype phase represents the collective genetic variation between homologous chromosomes and is an essential feature of non-haploid genomes. Here we describe a computational strategy to reliably determine complete whole-chromosome haplotypes using a combination of bulk long-range sequencing and Hi-C sequencing. We demonstrate that this strategy can resolve the haplotypes of parental chromosomes in diploid human genomes with high precision (>99%) and completeness (>98%) and assemble the syntenic structure of rearranged chromosomes in aneuploid cancer genomes at base pair level resolution. Our work enables direct interrogation of chromosome-specific alterations and chromatin reorganization using bulk DNA sequencing.
ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-021-02330-1