CNV Analysis Using TaqMan Copy Number Assays

Ping Mayo1, Toinette Hartshorne2, Kelly Li2, Chara McMunn‐Gibson1, Kylee Spencer1, Nathalie Schnetz‐Boutaud1

1 Center for Human Genetic Research, Vanderbilt University, Nashville, Tennessee, 2 Applied Biosystems, Foster City, California
Publication Name:  Current Protocols in Human Genetics
Unit Number:  Unit 2.13
DOI:  10.1002/0471142905.hg0213s67
Online Posting Date:  October, 2010
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Abstract

Copy number variations are important polymorphisms that can influence the expression of genes within and close to the rearranged region. This allows transcription levels to be higher or lower than those that can be achieved by control of transcription of a single copy. Recently, copy number variations have been associated with genetic diseases such as cancer, immune diseases, and neurological disorders. TaqMan copy number assays are designed to detect and measure copy number variation in the human genome using real‐time polymerase chain reaction and unquenching of fluorescent probes for the target sequence. Curr. Protoc. Hum. Genet. 67:2.13.1‐2.13.10 © 2010 by John Wiley & Sons, Inc.

Keywords: CNV; TaqMan; copy number assays

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Quantifying Copy Numbers in Genomic DNA Using the TaqMan Copy Number Assay
  • Basic Protocol 2: Statistical Analysis of COPYCALLER Data
  • Support Protocol 1: Preparation and Normalization of the Genomic DNA Samples
  • Support Protocol 2: Installing the CopyCaller Software
  • Commentary
  • Literature Cited
  • Figures
  • Tables
     
 
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Materials

Basic Protocol 1: Quantifying Copy Numbers in Genomic DNA Using the TaqMan Copy Number Assay

  Materials
  • TaqMan genotyping master mix containing AmpliTaq Gold DNA polymerase, ultra‐pure, containing dNTPs (recommended for optimal performance of TaqMan copy number assays)
  • TaqMan copy number assay mix (pre‐designed or custom assays; Applied Biosystems): store at –15° to –25°C, protected from light, minimize freeze‐thaw cycles by diluting 60× stocks to 20× working stock and dispensing into smaller volumes (recommended)
    • Two unlabeled primers for amplifying the target sequence of interest
    • One TaqMan MGB probe for detecting the target sequence of interest, including FAM reporter dye attached to the 5′ end, a nonfluorescent quencher (NFQ), and a minor groove binder (MGB) attached to the 3′ end (MGBs increase the melting temperature (T m) without increasing probe length and allow the design of shorter probes)
  • TaqMan copy number reference assay mix (Applied Biosystems): store at –15° to –25°C, protected from light, minimize freeze‐thaw cycles by diluting 60× stocks to 20× working stock and dispensing into smaller volumes (recommended)
    • RNase P (recommended standard reference assay for copy number quantitation experiments; this assay detects the ribonuclease P RNA component H1 (H1RNA) gene (RPPH1) on chromosome 14, cytoband 14q11.2)
    • Each tube of TaqMan copy number reference assay contains:
    • Two unlabeled primers for amplifying the reference sequence.
    • One TaqMan TAMRA probe for detecting the reference sequence, including VIC reporter dye attached to the 5′ end and TAMRA quencher attached to the 3′ end
  • Millipore water
  • Genomic DNA samples in a 384‐well MicroAmp optical reaction plate (see protocol 3)
  • 7900HT real‐time PCR system with automation accessory (384‐well block; Applied Biosystems)
  • 1.5‐ml microcentrifuge tubes
  • Motorized microliter pipettor (e.g., Rainin), optional
  • Microcentrifuge
  • Vortexer
  • MicroAmp optical adhesive film (Applied Biosystems)
  • Centrifuge with plate adapter (e.g., Sorvall)
  • CopyCaller software (for installation, see protocol 4)

Basic Protocol 2: Statistical Analysis of COPYCALLER Data

  Materials
  • Blood samples
  • Commercial DNA extraction kit (Puregene; Gentra Systems)
  • 1× TBE ( appendix 2D)
  • BioRobot8000 workstation (Qiagen)
  • 384‐well MicroAmp optical reaction plate (optical compatible plates required for real‐time PCR; Applied Biosystems)
  • Additional reagents and equipment for quantifying DNA with absorption spectroscopy ( appendix 3D)
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Figures

Videos

Literature Cited

Literature Cited
   Hastings, P.J., Lupski, J.R., Rosenberg, S.M., and Ira, G. 2009. Mechanisms of change in gene copy number. Nat. Rev. Genet. 10:551‐564.
   Henrichsen, C.N., Chaignat, E., and Reymond, A. 2009. Copy number variants, diseases and gene expression. Hum. Mol. Genet. 18:R1‐R8.
   Stankiewicz, P. and Lupski, J.R. 2010. Structural variation in the human genome and its role in disease. Annu. Rev. Med. 61:437‐455.
   TaqMan Copy Number Assays Protocol. 2009. Applied Biosystems, Foster City, California.
   Wang, K., Li, M., Hadley, D., Liu, R., Glessner, J., Grant, S.F., Hakonarson, H., and Bucan, M. 2007. PennCNV: An integrated hidden Markov model designed for high‐resolution copy number variation detection in whole‐genome SNP genotyping data. Genome Res. 17:1665‐1674.
   Xie, C. and Tammi, M.T. 2009. CNV‐seq, a new method to detect copy number variation using high‐throughput sequencing. BMC Bioinformatics 10:80.
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