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Updated: May 13, 2026
05:53
Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry
Published on: June 21, 2018
Whole-genome haplotyping by dilution, amplification, and sequencing
Fiona Kaper1, Sajani Swamy, Brandy Klotzle
1Illumina, Inc., San Diego, CA 92122, USA.
Summary
This study introduces a rapid, cost-effective method for long-range haplotyping using DNA dilution and amplification. The technique successfully phases large genomic regions, enabling accurate whole-genome haplotyping.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Standard whole-genome genotyping methods cannot determine DNA haplotypes.
- Haplotyping is crucial for understanding genetic variation and disease association.
Purpose of the Study:
- To develop a rapid and cost-effective method for long-range haplotyping.
- To enable accurate phasing of heterozygous single nucleotide polymorphisms (SNPs) across targeted regions and the entire genome.
Main Methods:
- Genomic DNA dilution and distribution into multiple aliquots.
- Multiple displacement amplification (MDA) of DNA in each aliquot.
- Nextera library preparation, multiplex sequencing, and targeted pull-down for specific regions.
Main Results:
- Successfully phased the Duchenne muscular dystrophy gene region into two haplotype blocks (mean length 494 kb) with 99% agreement.
- Phased over 95% of heterozygous SNPs from diploid sequence data in human genomes.
- Achieved N50 lengths of 702 kb for Yoruba male DNA and 358 kb for European female DNA.
Conclusions:
- The described dilution-amplification-based sequencing strategy is effective for long-range haplotyping.
- This method is suitable for haplotyping targeted genomic regions and entire genomes.
- Offers a cost-effective and rapid solution for haplotype determination.
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