Next-Gen Sequencing

Applications of Next-Gen Sequencing

Next-generation (massively parallel) sequencing is useful for a variety of experimental approaches. It is not a replacement for normal (Sanger) sequencing of plasmids or PCR products. Instead, next-gen sequencing relies on capturing millions or billions of individual DNA molecules (e.g. genomic DNA fragments, cDNAs), which are then amplified separately and sequenced in parallel, generating millions or billions of sequencing "reads", each of which originated from a different template molecule. It is similar to individually cloning and sequencing millions or billions of independent DNA fragments, but it all happens at once and in just a few days.Proton Sequencer

The following types of scientific applications are easily adaptable to next-gen sequencing approaches:

  • Genotyping (identification of SNPs)
  • Exome sequencing to identify inherited (germline) variants
  • Targeted gene panel sequencing of cancer- or disease-relevant genes
  • Gene expression studies using RNA-seq
  • Chromatin Immunoprecipitation - sequencing (ChIP-seq) for transcription factor or epigenetic studies
  • DNA methylation studies (e.g. RRBS)
  • Transcriptome sequencing (e.g. identification of alternatively-spiced RNAs)
  • Analysis of non-coding RNAs (ncRNAs, lincRNAs, miRs)

Technologies and Instruments

The ATG facility currently has or has access to several types of next-gen sequencing instruments:PGM

  • Ion Torrent PGM: The semiconductor sequencing instrument, ideal for small-medium next-gen assays.
  • Ion Proton: A whole exome and whole genome sequencing instrument using Ion Torrent technology.

These instruments provide cost-efficient and rapid next-generation sequencing for applications such as targeted sequencing, exome sequencing, RNA-seq, ChIP-seq, MeDIP-seq and even whole-genome sequencing.

Please contact the ATG Facility staff for more information about assays and pricing.

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