Aug 26, 2016

Haplotype analysis using linked-reads

Shauna Clark

Human genetic variation is complex and the role it plays in disease processes is not commonly straightforward. Humans are diploid organisms, inheriting genetic material from both parents; thus, understanding the order, structure and origin of variants across the genome is important for advancing our knowledge of disease pathogenicity.  An important part of this understanding is haplotype analysis.

Haplotypes are the contiguous phased blocks of genomic variants specific to a given homolog.  Phasing of germline variants can be used to identify causative mutations for inherited disease research, including structural rearrangements and tricky cis- versus trans-relationships of variants.  Additionally, phasing of somatic mutations for cancer research helps to create a clearer picture of genomic rearrangements and chromosomal aneuploidy that may play roles in oncogenesis.

The journal article "Haplotyping Germline and Cancer Genomes with High-Throughput Linked-Read Sequencing" (Ji, et al.) published in Nature Biotechnology, demonstrates the utility of 10x Genomics® GemCode™ Technology for haplotype analysis.  Using microfluidic technology, high molecular weight (HMW) DNA molecules are distributed across > 100,000 droplet partitions and molecularly barcoded.  After whole genome or exome library preparation and standard Illumina short-read next generation sequencing (NGS), Longer Ranger software uses the barcodes to link sequencing reads to the originating HMW DNA molecule, enabling the construction of contiguous segments of phased variants.

The resulting linked-read data was used to phase a set of structural variants of a nuclear trio, identify the structure of an EML4 - ALK gene fusion in a cancer cell line and, finally, assign variants to megabase-scale haplotypes generated from whole-genome sequencing of a primary colorectal adenocarcinoma.

To learn more about using 10x Genomics GemCode Technology and software for haplotype analysis:

  • Read the full Nature Biotechology article "Haplotyping Germline and Cancer Genomes with High-Throughput Linked-Read Sequencing".   Download article ->
  • Watch the webinar "Gain insights into human genetics and cancer genomics with Linked-Reads and phased genome analysis" featuring Dr. Hanlee Ji of the Stanford University School of Medicine.   Watch webinar ->