657
Views
5
CrossRef citations to date
0
Altmetric
Editorial

Molecular copy-number counting: potential of single-molecule diagnostics

Pages 309-312 | Published online: 09 Jan 2014

References

  • Iafrate AJ, Feuk L, Rivera MN et al. Detection of large-scale variation in the human genome. Nat. Genet.36(9), 949–951 (2004).
  • Redon R, Ishikawa S, Fitch KR et al. Global variation in copy number in the human genome. Nature444(7118), 444–454 (2006).
  • Sebat J, Lakshmi B, Troge J et al. Large-scale copy number polymorphism in the human genome. Science305(5683), 525–528 (2004).
  • Lupski JR, de Oca-Luna RM, Slaugenhaupt S et al. DNA duplication associated with Charcot–Marie–Tooth disease type 1A. Cell66(2), 219–232 (1991).
  • McCarroll SA, Altshuler, DM. Copy-number variation and association studies of human disease. Nat. Genet.39(7 Suppl.), S37–S42 (2007).
  • Schwab M, Alitalo K, Klempnauer KH et al. Amplified DNA with limited homology to myc cellular oncogene is shared by human neuroblastoma cell lines and a neuroblastoma tumour. Nature305(5931), 245–248 (1983).
  • King CR, Kraus MH, Aronson SA. Amplification of a novel v-erbB-related gene in a human mammary carcinoma. Science229(4717), 974–976 (1985).
  • Wolff AC, Hammond ME, Schwartz JN et al. American Society of Clinical Oncology/College of American Pathologists guideline recommendations for human epidermal growth factor receptor 2 testing in breast cancer. Arch. Pathol. Lab. Med.131(1), 18 (2007).
  • Tsao MS, Sakurada A, Cutz JC et al. Erlotinib in lung cancer – molecular and clinical predictors of outcome. N. Engl. J. Med.353(2), 133–144 (2005).
  • Greer CE, Lund JK, Manos MM. PCR amplification from paraffin-embedded tissues: recommendations on fixatives for long-term storage and prospective studies. PCR Methods Appl.1(1), 46–50 (1991).
  • Tang EP. Path to Effective Recovering of DNA from Formalin-Fixed Biological Samples in Natural History Collections: Workshop Summary. The National Academies Press, DC, USA (2006).
  • van Beers EH, Joosse SA, Ligtenberg MJ et al. A multiplex PCR predictor for aCGH success of FFPE samples. Br. J. Cancer94(2), 333–337 (2006).
  • Feuk L, Carson AR, Scherer SW. Structural variation in the human genome. Nat. Rev. Genet.7(2), 85–97 (2006).
  • McCarroll SA, Kuruvilla FG, Korn JM et al. Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat. Genet.40(10), 1166–1174 (2008).
  • Stoecklein NH, Erbersdobler A, Schmidt-Kittler O et al. SCOMP is superior to degenerated oligonucleotide primed-polymerase chain reaction for global amplification of minute amounts of DNA from microdissected archival tissue samples. Am. J. Pathol.161(1), 43–51 (2002).
  • Lage JM, Leamon JH, Pejovic T et al. Whole genome analysis of genetic alterations in small DNA samples using hyperbranched strand displacement amplification and array-CGH. Genome Res.13(2), 294–307 (2003).
  • Bredel M, Bredel C, Juric D et al. Amplification of whole tumor genomes and gene-by-gene mapping of genomic aberrations from limited sources of fresh-frozen and paraffin-embedded DNA. J. Mol. Diagn.7(2), 171–182 (2005).
  • Campbell PJ, Stephens PJ, Pleasance ED et al. Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat. Genet.40(6), 685–686 (2008).
  • Armour JA, Sismani C, Patsalis PC, Cross G. Measurement of locus copy number by hybridisation with amplifiable probes. Nucleic Acids Res.28(2), 605–609 (2000).
  • Charbonnier F, Raux G, Wang Q et al. Detection of exon deletions and duplications of the mismatch repair genes in hereditary nonpolyposis colorectal cancer families using multiplex polymerase chain reaction of short fluorescent fragments. Cancer Res.60(11), 2760–2763 (2000).
  • Armour JA, Palla R, Zeeuwen PL, den Heijer M, Schalkwijk J, Hollox EJ. Accurate, high-throughput typing of copy number variation using paralogue ratios from dispersed repeats. Nucleic Acids Res.35(3), e19 (2007).
  • Schouten JP, McElgunn CJ, Waaijer R, Zwijnenburg D, Diepvens F, Pals G. Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification. Nucleic Acids Res.30(12), e57 (2002).
  • Sellner LN, Taylor GR. MLPA and MAPH: new techniques for detection of gene deletions. Hum. Mutat.23(5), 413–419 (2004).
  • Dear PH, Cook PR. Happy mapping: linkage mapping using a physical analogue of meiosis. Nucleic Acids Res.21(1), 13–20 (1993).
  • Daser A, Thangavelu M, Pannell R et al. Interrogation of genomes by molecular copy-number counting (MCC). Nat. Methods3(6), 447–453 (2006).
  • McCaughan F, Darai-Ramqvist E, Bankier AT et al. Microdissection molecular copy-number counting (microMCC) – unlocking cancer archives with digital PCR. J. Pathol.216(3), 307–316 (2008).
  • Jalali GR, An Q, Konn ZJ et al. Disruption of ETV6 in intron 2 results in upregulatory and insertional events in childhood acute lymphoblastic leukaemia. Leukemia22(1), 114–123 (2008).
  • Lun FM, Tsui NB, Chan KC et al. Noninvasive prenatal diagnosis of monogenic diseases by digital size selection and relative mutation dosage on DNA in maternal plasma. Proc. Natl Acad. Sci. USA105(50), 19920–19925 (2008).
  • Qin J, Jones RC, Ramakrishnan R. Studying copy number variations using a nanofluidic platform. Nucleic Acids Res.36(18), e116 (2008).
  • Eberhard DA, Giaccone G, Johnson BE. Biomarkers of response to epidermal growth factor receptor inhibitors in Non-Small-Cell Lung Cancer Working Group: standardization for use in the clinical trial setting. J. Clin. Oncol.26(6), 983–994 (2008).
  • Engelman JA, Zejnullahu K, Mitsudomi T et al. MET amplification leads to gefitinib resistance in lung cancer by activating ERBB3 signaling. Science316(5827), 1039–1043 (2008).
  • Little SE, Vuononvirta R, Reis-Filho JS et al. Array CGH using whole genome amplification of fresh-frozen and formalin-fixed, paraffin-embedded tumor DNA. Genomics87(2), 298–306 (2006).
  • Holst F, Stahl PR, Ruiz C et al. Estrogen receptor a (ESR1) gene amplification is frequent in breast cancer. Nat. Genet.39(5), 655–660 (2007).
  • Brown LA, Hoog J, Chin SF et al.ESR1 gene amplification in breast cancer: a common phenomenon. Nat. Genet.40(7), 806–807; author reply: 810–812 (2008).

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.