Human Genetics

, Volume 132, Issue 10, pp 1153–1163

The new sequencer on the block: comparison of Life Technology’s Proton sequencer to an Illumina HiSeq for whole-exome sequencing

  • Joseph F. Boland
  • Charles C. Chung
  • David Roberson
  • Jason Mitchell
  • Xijun Zhang
  • Kate M. Im
  • Ji He
  • Stephen J. Chanock
  • Meredith Yeager
  • Michael Dean
Original Investigation

DOI: 10.1007/s00439-013-1321-4

Cite this article as:
Boland, J.F., Chung, C.C., Roberson, D. et al. Hum Genet (2013) 132: 1153. doi:10.1007/s00439-013-1321-4

Abstract

We assessed the performance of the new Life Technologies Proton sequencer by comparing whole-exome sequence data in a Centre d’Etude du Polymorphisme Humain trio (family 1463) to the Illumina HiSeq instrument. To simulate a typical user’s results, we utilized the standard capture, alignment and variant calling methods specific to each platform. We restricted data analysis to include the capture region common to both methods. The Proton produced high quality data at a comparable average depth and read length, and the Ion Reporter variant caller identified 96 % of single nucleotide polymorphisms (SNPs) detected by the HiSeq and GATK pipeline. However, only 40 % of small insertion and deletion variants (indels) were identified by both methods. Usage of the trio structure and segregation of platform-specific alleles supported this result. Further comparison of the trio data with Complete Genomics sequence data and Illumina SNP microarray genotypes documented high concordance and accurate SNP genotyping of both Proton and Illumina platforms. However, our study underscored the problem of accurate detection of indels for both the Proton and HiSeq platforms.

Supplementary material

439_2013_1321_MOESM1_ESM.pdf (1.1 mb)
Supplementary material 1 (PDF 1075 kb)

Copyright information

© Springer-Verlag Berlin Heidelberg (outside the USA) 2013

Authors and Affiliations

  • Joseph F. Boland
    • 1
    • 2
  • Charles C. Chung
    • 1
    • 2
  • David Roberson
    • 1
    • 2
  • Jason Mitchell
    • 1
    • 2
  • Xijun Zhang
    • 1
    • 2
  • Kate M. Im
    • 3
  • Ji He
    • 1
    • 2
  • Stephen J. Chanock
    • 1
  • Meredith Yeager
    • 1
    • 2
  • Michael Dean
    • 3
  1. 1.Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and GeneticsNational Cancer Institute, NIH, DHHSGaithersburgUSA
  2. 2.Frederick National Laboratory for Cancer Research, SAIC-Frederick IncGaithersburgUSA
  3. 3.Laboratory of Experimental Immunology, Center for Cancer ResearchNational Cancer Institute, NIH, DHHSFrederickUSA