Detecting, quantifying, and discriminating the mechanism of mosaic chromosomal aneuploidies using MAD-seq

Yu Kong, Esther R. Berko, Anthony Marcketta, Shahina B. Maqbool, Claudia A. Simões-Pires, David F. Kronn, Qian K. Ye, Masako Suzuki, Adam Auton, John M. Greally

Research output: Contribution to journalArticle

Abstract

Current approaches to detect and characterize mosaic chromosomal aneuploidy are limited by sensitivity, efficiency, cost, or the need to culture cells. We describe the mosaic aneuploidy detection by massively parallel sequencing (MAD-seq) capture assay and the MADSEQ analytical approach that allow low (<10%) levels of mosaicism for chromosomal aneuploidy or regional loss of heterozygosity to be detected, assigned to a meiotic or mitotic origin, and quantified as a proportion of the cells in the sample. We show results from a multi-ethnic MAD-seq (meMAD-seq) capture design that works equally well in populations of diverse racial and ethnic origins and how the MADSEQ analytical approach can be applied to exome or whole-genome sequencing data, revealing previously unrecognized aneuploidy or copy number neutral loss of heterozygosity in samples studied by the 1000 Genomes Project, cell lines from public repositories, and one of the Illumina Platinum Genomes samples. We have made the meMAD-seq capture design and MADSEQ analytical software open for unrestricted use, with the goal that they can be applied in clinical samples to allow new insights into the unrecognized prevalence of mosaic chromosomal aneuploidy in humans and its phenotypic associations.

Original languageEnglish (US)
Pages (from-to)1039-1052
Number of pages14
JournalGenome Research
Volume28
Issue number7
DOIs
StatePublished - Jul 1 2018

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Aneuploidy
Loss of Heterozygosity
Genome
Exome
High-Throughput Nucleotide Sequencing
Mosaicism
Platinum
Software
Cell Culture Techniques
mycophenolic adenine dinucleotide
Costs and Cost Analysis
Cell Line
Population

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Detecting, quantifying, and discriminating the mechanism of mosaic chromosomal aneuploidies using MAD-seq. / Kong, Yu; Berko, Esther R.; Marcketta, Anthony; Maqbool, Shahina B.; Simões-Pires, Claudia A.; Kronn, David F.; Ye, Qian K.; Suzuki, Masako; Auton, Adam; Greally, John M.

In: Genome Research, Vol. 28, No. 7, 01.07.2018, p. 1039-1052.

Research output: Contribution to journalArticle

Kong, Yu ; Berko, Esther R. ; Marcketta, Anthony ; Maqbool, Shahina B. ; Simões-Pires, Claudia A. ; Kronn, David F. ; Ye, Qian K. ; Suzuki, Masako ; Auton, Adam ; Greally, John M. / Detecting, quantifying, and discriminating the mechanism of mosaic chromosomal aneuploidies using MAD-seq. In: Genome Research. 2018 ; Vol. 28, No. 7. pp. 1039-1052.
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