10X Genomics is on a roll: Chromium System for 3′ single-cell RNA-seq on 48K cells, haplotyping and assembly

10X-Genomics Launches Chromium System

10X-Genomics Launches Chromium System

The new year has begun with a bang for 10X Genomics, one of the hottest genomics technology company. It all started last year, when 10X Genomics, a stealthy California-based company, made waves with raising $55.5 M with the lofty goal of changing the definition of sequencing. At last year’s AGBT (AGBT 2015) , 10x Genomics launched its platform “GemCode” with software, a microfluidics based library prep system that can offer long range sequence with existing Short Read Sequencers, kind of similar to Moleculo. 10xGenomics technology linking short reads to offer long linked reads can be of great use in phasing, structural variant analysis, de novo genome assembly, and remapping of difficult regions of the genome

This year,  in a span of few weeks, 10x Genomics

  • unveiled a product of single-cell genomic analysis at JAM 2016
  • ressearchers using GemCode platform published a paper  on haplotyping germline and cancer genomes with input DNA as low as nanograms in Nature Biotechnology
  • nabbed the leading reference genome expert Deanna Church as 10x Genomics’ Senior Director of Applications
  • announced partnership with Illumina (which already owns Moleculo technology as truSeq) and Qiagen for offering Sequencing and Single Cell Analysis Workflows and solutions
  • partnership with Agilent on developing exome by enabling phasing, CNV, and access to difficult regions
10x Genomics Chromium System for single-cell RNA-seq, long-range read information for phasing

10x Genomics Chromium System for single-cell RNA-seq, long-range read information for phasing

In addition to all these, at this year’s AGBT, 10x Genomics unveiled Chromium system, a single system for profiling single-cell gene expression, providing long range information for variant calling, phasing, CNV, SV and Supernova™ Assembler for low-cost, everyday diploid de novo assemblies.

Chromium system using Single Cell 3′ reagent kit offers academic Drop-seq like scalability for  3′ end single-cell RNA-seq. With complete end-to-end workflow and no limit on cell size, Chromium offers efficient solution for single-cell RNA-seq. Chromium can encapulate up to 48K single cells in 10 minutes.

Chromium Exome and Genome kit offers long range read information with just 1ng starting DNA. The Exome kit can  call variants and phase variants across the entire exome. The Genome kit can provide “greater than 10 Mb haplotype blocks with phased SNVs, indels, and structural variants”. At AGBT 2016, David Jaffe gave talk on 10x Genomics can help with producing “everyday high quality de novo genomes”. Here are tweets from David Jaffe’s talk at AGBT.

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