Stanford

Genomics Services Overview

Genomics Services Overview


Have Questions?

Please see the individual resource websites for contact information. If you cannot find what you are looking for, please
contact Bruce D. Koch, PhD  email


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Sequencing

There are three steps in a sequencing-based experiment:


1. Nucleic acid extraction and library preparation

This list assumes that you are starting with cells, tissues, or paraffin sections. The centers listed may not be able to perform the entire workflow in-house, but they are able to perform the initial steps and will guide you through the rest of the workflow.

Library Prep Services:
  • Whole Genome Sequencing — Aka “resequencing” because one is sequencing the genomes of individuals or tumors for which there is already a reference genome. This method explores genetic variation between individuals or between healthy and cancerous tissue. (SFGF)
  • Exome Sequencing — A form of resequencing (i.e. sequencing a genome that has a reference sequence) that explores genetic variation in the subset of the genome (~1% in humans) that encodes proteins. Exome sequencing is typically substantially less expensive than whole genome sequencing. (PAN, SFGF)
  • Gene Subset Sequencing — A form of resequencing (i.e. sequencing a genome that has a reference sequence) that explores genetic variation in a defined subset of the genome (e.g. recombined T-cell receptor sequences). Subset sequencing is typically substantially less expensive than either whole genome or exome sequencing. (PAN, SFGF)
  • De Novo Genome Sequencing (i.e. an organism that has not been previously sequenced) — Sequencing of a new genome is considerably more complicated than resequencing because there is no reference genome that can be used to align the short next-gen sequencing reads. Typically additional methods are required to provide that longer range information. (SFGF)
  • DNA Methylation Analysis: Whole Genome (BSseq) — Bisulphite sequencing provides information about the cytosine methylation of DNA sequences, which is thought to regulate gene expression. Treatment with bisulphite has no effect on methyl-cytosine, but converts unmethylated cytosine to uracil. Comparing DNA sequences with and without bisulphite treatment reveals which cytosines are methylated. (SFGF)
  • DNA Methylation Analysis: Focused (Pyrosequencing) — A method for measuring DNA methylation on cytosines, which is thought to regulate gene expression. Parallel sequencing of single clones (96 channels). In combination, that data gives % methylation at each base. (PAN)
  • Genome-Wide DNA-Protein Interaction Analysis (ChIP-seq) — Chromatin immunoprecipitation followed by sequencing (CHIP-seq) provides information on the sites in the genome which interact with the particular protein that is being immunoprecipitated. (PAN, SFGF)
  • Gene Expression Analysis: RNAseq — Measures gene expression via deep sequencing to report the sequence and relative abundance of the various mRNA transcripts. Typically RNA is extracted from the biological sample and that RNA is converted to cDNA using reverse transcriptase and a poly-T primer, which selects for polyadenylated mRNA. That library is then subjected to deep sequencing (typically 100s of millions of reads). (PAN, SFGF)
  • Gene Expression Libraries using automated size selection — e.g. from Sage Science. Used to increase library quality. (SFGF)
  • Single Cell Gene Expression Analysis: RNAseq — Measures gene expression via deep sequencing of reverse transcribed transcripts from single cells. PAN offers the Fluidigm C1 system. SFGF offers library prep from single FACS-sorted cells. (PAN, SFGF)
  • Targeted Single Cell Gene Expression Panels — e.g. from Cellular Research. A preselected or custom set of transcripts are uniquely tagged during the RT reaction and then the number of transcripts in the cell can be accurately counted. (PAN)
  • Single Cell Sequencing: Exome or Directed —Sequences a particular portion of the genome of single cells from organisms with a reference genome sequence. PAN offers the Fluidigm C1 system. SFGF offers library prep from single FACS-sorted cells. (PAN, SFGF)
  • Microbiome Analysis (16S rRNA) — 16S ribosomal RNA is a component prokaryotic, chloroplast, and mitochondrial ribosomes. 16S rRNA sequences are used to identify the species of bacteria in a sample. (SFGF)



2. Sequencing

Instrumentation Reads
(Millions)
PAN SSC SFGF
Illumina Miseq 25
Illumina GAIIx 50
Illumina Hiseq 2000 200
Illumina Hiseq 4000 600
Illumina Nextseq 400
Qiagen PyroMark Q24 96 parallel
single
clones
Sanger sequencing Single
clone



3. Data Analysis

(See also Illumina Basespace).

Tools:
  • SCG Cluster — A large computer cluster for running genomics analysis pipelines. Primarily for more advanced users. (GBSC)
  • Bina — Bina Box is a small computer cluster with GUI driven software for data analysis of whole genome, exome, targeted, tumor vs normal, and RNAseq experiments. Available to SCG cluster users only. Recommended for novice users. (GBSC)
  • CLCbio — CLC Genomics Workbench for analyzing all kinds of next-gen sequencing experiments using your desktop computer. (CSBF)
  • DNA Nexus — Cloud-based analysis pipelines for next-gen sequencing. Many of the commonly used data analysis pipelines are available. Suitable for novice to intermediate level users. No affiliation with GBSC required. (GBSC)
  • DNAstar — A desktop program for analyzing next-gen sequencing experiments. (CSBF)
  • Galaxy — Open source web-based system with a GUI interface for analyzing sequencing experiments. Suitable for novice to intermediate users. It is free courtesy of funding from the University Dean of Research. (GBSC)
  • Geneious — A desktop program for analyzing lower throughput sequencing experiments. (CSBF)
  • Geneious Server — For analyzing next-gen sequencing experiments. (CSBF)
  • Golden Helix SNP and Variant Suite — A GUI –driven desktop analysis program. (CSBF)
  • HugeSeq — A pipeline for alignment and variant calling of next-gen sequencing data developed by Prof. Michael Snyder’s lab. On the SCG Cluster. (GBSC)
  • Ingenuity Pathway Analysis — Downstream analysis of RNAseq experiments by placing the results in biological pathways to add context. (CSBF)
  • Ingenuity Variant Analysis — GUI-driven analysis platform. No affiliation with GBSC required. (GBSC)
  • Real Time Genomics rtg variant — An analysis pipeline that uses familial relationships to identify rare variants that may be causal for a Mendelianly inherited disease. On the SCG Cluster. (GBSC)
  • Stanovar — A pipeline that can further analyze the output of HugeSeq by providing annotations as to single nucleotide variants (SNV), indels, and structural variants (SV). On the SCG Cluster. (GBSC)
  • Sequencer — Desktop software for the analysis of next-gen and Sanger sequencing experiments. (CSBF)
  • Partek — Desktop software for the QC and visualization of data from sequencing experiments. (CSBF)
  • Google Cloud Platform — GBSC has a special legal agreement with Google Cloud Platform that allows integration with Google Services. This is only available to GBSC members. For advanced users. (GBSC)




Other Genomics Technologies
Service PAN SFGF
Human Whole Genome Gene Copy Number (Microarray)
Gene Expression Analysis: Microarray
Focused Gene Expression Analysis: qPCR
Highly Mulitiplexed Gene Expression Analysis: NanoString
Quantitation of SNPs (Qiagen PyroMark Q24)
Quantitation of SNPs (OpenArray RT-PCR)
Oligonucleotide synthesis