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Somatic Mutation Allelic Ratio Test Using ddPCR (SMART-ddPCR): An Accurate Method for Assessment of Preferential Allelic Imbalance in Tumor DNA.

Publication ,  Journal Article
de Smith, AJ; Walsh, KM; Hansen, HM; Endicott, AA; Wiencke, JK; Metayer, C; Wiemels, JL
Published in: PLoS One
2015

The extent to which heritable genetic variants can affect tumor development has yet to be fully elucidated. Tumor selection of single nucleotide polymorphism (SNP) risk alleles, a phenomenon called preferential allelic imbalance (PAI), has been demonstrated in some cancer types. We developed a novel application of digital PCR termed Somatic Mutation Allelic Ratio Test using Droplet Digital PCR (SMART-ddPCR) for accurate assessment of tumor PAI, and have applied this method to test the hypothesis that heritable SNPs associated with childhood acute lymphoblastic leukemia (ALL) may demonstrate tumor PAI. These SNPs are located at CDKN2A (rs3731217) and IKZF1 (rs4132601), genes frequently lost in ALL, and at CEBPE (rs2239633), ARID5B (rs7089424), PIP4K2A (rs10764338), and GATA3 (rs3824662), genes located on chromosomes gained in high-hyperdiploid ALL. We established thresholds of AI using constitutional DNA from SNP heterozygotes, and subsequently measured allelic copy number in tumor DNA from 19-142 heterozygote samples per SNP locus. We did not find significant tumor PAI at these loci, though CDKN2A and IKZF1 SNPs showed a trend towards preferential selection of the risk allele (p = 0.17 and p = 0.23, respectively). Using a genomic copy number control ddPCR assay, we investigated somatic copy number alterations (SCNA) underlying AI at CDKN2A and IKZF1, revealing a complex range of alterations including homozygous and hemizygous deletions and copy-neutral loss of heterozygosity, with varying degrees of clonality. Copy number estimates from ddPCR showed high agreement with those from multiplex ligation-dependent probe amplification (MLPA) assays. We demonstrate that SMART-ddPCR is a highly accurate method for investigation of tumor PAI and for assessment of the somatic alterations underlying AI. Furthermore, analysis of publicly available data from The Cancer Genome Atlas identified 16 recurrent SCNA loci that contain heritable cancer risk SNPs associated with a matching tumor type, and which represent candidate PAI regions warranting further investigation.

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Published In

PLoS One

DOI

EISSN

1932-6203

Publication Date

2015

Volume

10

Issue

11

Start / End Page

e0143343

Location

United States

Related Subject Headings

  • Transcription Factors
  • Sequence Analysis, DNA
  • Precursor Cell Lymphoblastic Leukemia-Lymphoma
  • Polymorphism, Single Nucleotide
  • Multiplex Polymerase Chain Reaction
  • Humans
  • Heterozygote
  • Genotype
  • Genome-Wide Association Study
  • General Science & Technology
 

Citation

APA
Chicago
ICMJE
MLA
NLM
de Smith, A. J., Walsh, K. M., Hansen, H. M., Endicott, A. A., Wiencke, J. K., Metayer, C., & Wiemels, J. L. (2015). Somatic Mutation Allelic Ratio Test Using ddPCR (SMART-ddPCR): An Accurate Method for Assessment of Preferential Allelic Imbalance in Tumor DNA. PLoS One, 10(11), e0143343. https://doi.org/10.1371/journal.pone.0143343
Smith, Adam J. de, Kyle M. Walsh, Helen M. Hansen, Alyson A. Endicott, John K. Wiencke, Catherine Metayer, and Joseph L. Wiemels. “Somatic Mutation Allelic Ratio Test Using ddPCR (SMART-ddPCR): An Accurate Method for Assessment of Preferential Allelic Imbalance in Tumor DNA.PLoS One 10, no. 11 (2015): e0143343. https://doi.org/10.1371/journal.pone.0143343.
de Smith AJ, Walsh KM, Hansen HM, Endicott AA, Wiencke JK, Metayer C, et al. Somatic Mutation Allelic Ratio Test Using ddPCR (SMART-ddPCR): An Accurate Method for Assessment of Preferential Allelic Imbalance in Tumor DNA. PLoS One. 2015;10(11):e0143343.
de Smith, Adam J., et al. “Somatic Mutation Allelic Ratio Test Using ddPCR (SMART-ddPCR): An Accurate Method for Assessment of Preferential Allelic Imbalance in Tumor DNA.PLoS One, vol. 10, no. 11, 2015, p. e0143343. Pubmed, doi:10.1371/journal.pone.0143343.
de Smith AJ, Walsh KM, Hansen HM, Endicott AA, Wiencke JK, Metayer C, Wiemels JL. Somatic Mutation Allelic Ratio Test Using ddPCR (SMART-ddPCR): An Accurate Method for Assessment of Preferential Allelic Imbalance in Tumor DNA. PLoS One. 2015;10(11):e0143343.

Published In

PLoS One

DOI

EISSN

1932-6203

Publication Date

2015

Volume

10

Issue

11

Start / End Page

e0143343

Location

United States

Related Subject Headings

  • Transcription Factors
  • Sequence Analysis, DNA
  • Precursor Cell Lymphoblastic Leukemia-Lymphoma
  • Polymorphism, Single Nucleotide
  • Multiplex Polymerase Chain Reaction
  • Humans
  • Heterozygote
  • Genotype
  • Genome-Wide Association Study
  • General Science & Technology