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Detection of Cross-Sample Contamination in Multiple Myeloma Samples and Sequencing Data

  • Owen W. Stephens
  • Tobias Meißner
  • Niels WeinholdEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1792)

Abstract

The increasing applicability and sensitivity of next generation sequencing methods exacerbate one of the main issues in the molecular biology laboratory, namely cross-sample contamination. This type of contamination, which could massively increase the rate of false-positive calls in sequencing experiments, can originate at each step during the processing of multiple myeloma samples, such as CD138-selection of tumor cells, RNA and DNA isolation or the processing of sequencing libraries. Here we describe a Droplet Digital PCR (ddPCR) method and a simple bioinformatic solution for the detection of contamination in patient’s samples and derived sequencing data, which are based on the same principle: detection of alternative alleles for single-nucleotide polymorphisms (SNPs) that are homozygous according to the control (germ line) sample.

Key words

Multiple myeloma Cross-sample contamination SNP-based assay Droplet digital PCR Bioinformatics solution 

Notes

Acknowledgement

This work was supported by the National Institute Of General Medical Sciences of the National Institutes of Health under Award Number P20GM125503. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Owen W. Stephens
    • 1
  • Tobias Meißner
    • 2
  • Niels Weinhold
    • 1
    Email author
  1. 1.The Myeloma InstituteUniversity of Arkansas for Medical SciencesLittle RockUSA
  2. 2.Department of Molecular and Experimental MedicineAvera Cancer InstituteSioux FallsUSA

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