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Contiguity-Preserving Transposition Sequencing (CPT-Seq) for Genome-Wide Haplotyping, Assembly, and Single-Cell
Lena Christiansen1, Sasan Amini2, Fan Zhang1
1Advanced Research Group, Illumina, Inc., 5200 Illumina Way, San Diego, CA, 92122, USA.
Methods in Molecular Biology (Clifton, N.J.)
|February 1, 2017
Summary
Contiguity Preserving Transposition sequencing (CPT-seq) is a rapid, cost-effective method for genome-wide haplotyping. This technique accurately phases over 95% of the human genome, aiding genetic variation interpretation and population studies.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Most genome sequencing ignores diploidy, limiting understanding of gene regulation and medical genetics.
- Understanding variant distribution on individual chromosomes is crucial for accurate genetic interpretation.
Purpose of the Study:
- To introduce Contiguity Preserving Transposition sequencing (CPT-seq), a novel haplotyping method.
- To provide a comprehensive protocol for ultra-fast, cost-effective, and scalable genome-wide haplotyping.
Main Methods:
- Developed Contiguity Preserving Transposition sequencing (CPT-seq) for rapid library preparation (<3 hours).
- Applied CPT-seq to phase large blocks (>Mb) of the human genome.
Main Results:
- CPT-seq accurately phases over 95% of the human genome.
- The CPT-seq workflow supports de novo assembly, structural variant detection, and single-cell ATAC-seq analysis.
Conclusions:
- CPT-seq offers a significant advancement in genome-wide haplotyping.
- This method enhances the interpretation of genetic variation and has broad applications in genomics research.
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