Blog @ Illumina
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The promise of the first human phasing product, delivered.

by
Jeannine Stuzka
| Feb 26, 2014

We are pleased to be offering whole human phasing analysis, originated by Moleculo, in the Illumina FastTrack Services Laboratory through the Illumina Genome Network (IGN). This service complements whole-genome sequencing by distinguishing between variants originating from separate chromosomes, thereby inferring haplotype from genotype data. Phasing expands insight into human genomes by capturing the unique content of homologous chromosomes; making it possible to accelerate discovery, gain mechanistic insights, and generate actionable information.

Discovery is accelerated in population or ancestry studies by efficiently resolving haplotypes, providing insight to human migrations and evolutionary selection. In the investigation of genetic diseases the number of candidate genes can be reduced (e.g. identification of compound heterozygous mutations for recessive disorders). Phasing can provide mechanistic insights by relating genetic variation to genome function, phenotype, and disease. Phasing untangles the potential causal variants in regions of complex heterozygosity, and resolves the cis or trans links between regulatory and coding variants to understand the mechanism of allele-specific expression and gene regulation. These mechanistic discoveries can generate actionable information by determining if variants mean a higher disease risk, poorer therapeutic effect, or if an individual is a carrier or affected by genetic disease. 

The Illumina FastTrack Services Laboratory, through the Illumina Genome Network (IGN), offers phasing analysis as an add-on to our Whole-genome Sequencing (WGS) service. One Phasing library is prepared per WGS sample, regardless of coverage; with an input requirement of 1 ug (unamplified DNA samples from saliva, blood, and cell lines are also accepted). Phasing can be ordered as stand-alone service by customers who have previously sequenced whole human genomes through the FastTrack Services Laboratory in 2013. The analysis typically results in ~94-98% phased SNPs.



We have made available a Phasing Analysis Demo Dataset in BaseSpace, for free viewing or download (quick log-in required). This dataset is representative of the quality one expects from the Illumina FastTrack Services laboratory. For each of the individuals of the CEPH family trio, we combined data sequenced from Illumina’s Phasing library preparation with variants previously discovered through deep Whole-Genome Sequencing (WGS)  as input to Illumina’s proprietary Phasing Analysis Pipeline. The project dataset includes WGS & Phasing VCF files, phasing FASTQ files, and a PDF summary report. 

We invite you to view this example IGN project using the IGV app on BaseSpace, or by downloading files and exploring the data using your favorite tools. See for yourself the unmatched performance, data quality and expertise of the Illumina Genome Network.

Post updated 3/10/14 by author, to include reference to Kuleshov et al. (2014) Nature Biotechnology (32) 261.


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