Estimation of intrafamilial DNA contamination in family trio genome sequencing using deviation from Mendelian inheritance

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<jats:p>With the increasing number of sequencing projects involving families, quality control tools optimized for family genome sequencing are needed. However, accurately quantifying contamination in a DNA mixture is particularly difficult when genetically related family members are the sources. We developed TrioMix, a maximum likelihood estimation (MLE) framework based on Mendel's law of inheritance, to quantify DNA mixture between family members in genome sequencing data of parent–offspring trios. TrioMix can accurately deconvolute any intrafamilial DNA contamination, including parent–offspring, sibling–sibling, parent–parent, and even multiple familial sources. In addition, TrioMix can be applied to detect genomic abnormalities that deviate from Mendelian inheritance patterns, such as uniparental disomy (UPD) and chimerism. A genome-wide depth and variant allele frequency plot generated by TrioMix facilitates tracing the origin of Mendelian inheritance deviations. We showed that TrioMix could accurately deconvolute genomes in both simulated and real data sets.</jats:p>
Publisher
COLD SPRING HARBOR LAB PRESS
Issue Date
2022-11
Language
English
Article Type
Article
Citation

GENOME RESEARCH, v.32, no.11-12, pp.2134 - 2144

ISSN
1088-9051
DOI
10.1101/gr.276794.122
URI
http://hdl.handle.net/10203/305334
Appears in Collection
MSE-Journal Papers(저널논문)BS-Journal Papers(저널논문)
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