Exome Sequencing

The Analytical and Translational Genomics Shared Resource is a Certified Exome Sequencing provider using the Ion Ampliseq Exome Sequencing system and the Ion Proton sequencing instrument. The Ion Ampliseq system is a targeted multiplex-PCR assay that amplifies >250,000 amplicons from all of the exomes covering protein-coding regions in the human genome. The highly multiplexed products are then converted into sequencing libraries for the Ion Proton. The assays are usually barcoded and run two at a time on a P1 chip, which typically produces about 80 million "reads" and >100x average coverage across the targeted regions (about 2% of the human genome), which is more than adequate to detect germline variants (SNPs). The Ion Ampliseq assay is very robust and is ideal for the analysis of family units (trios) or genetic markers linked to ethnicity.

The ATG staff provide several types of bioinformatics analysis for exome sequencing data, including some standardized pipelines provided by the Life Technologies Ion Reporter tool, as well as customized analysis pipelines utilizing R/Bioconductor tools.

The level of coverage offered by the Ion Ampliseq Exome assay may be sufficient for analyzing tumor samples, but because tumors are a mixture of tumor cells and normal cells, and may include subclones (e.g. tumor heterogeneity), this coverage may not be sufficient to detect all tumor variants, especially those present in only a subset of tumor cells (i.e. tumor subclones). For "deep" sequencing of rare subpopulations in a tumor or to characterize tumor heterogeneity, it is preferable to use a targeted assay such as the Comprehensive Cancer Panel

Certified Provider of Ion Ampliseq Exome SequencingExome provider

Technical Director:
Gavin Pickett, Ph.D.
CRF G-21
Tel: (505) 272-0680

Bioinformatics:
Jason Byars
CRF G-21
Tel: (505) 272-0675

Senior Technical Staff:
Jamie Padilla, M.S.
CRF 118
Tel: (505) 272-5564

Jennifer Woods
CRF 121
Tel: (505) 272-3464

Faculty Director:
Scott A. Ness, Ph.D.
Professor, Internal Medicine
Office: CRF 121; Tel: (505) 272-9883