PT  - JOURNAL ARTICLE
AU  - Asia Mendelevich
AU  - Svetlana Vinogradova
AU  - Saumya Gupta
AU  - Andrey A. Mironov
AU  - Shamil Sunyaev
AU  - Alexander A. Gimelbrant
TI  - Unexpected variability of allelic imbalance estimates from RNA sequencing
AID  - 10.1101/2020.02.18.948323
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.02.18.948323
4099  - http://biorxiv.org/content/early/2020/02/25/2020.02.18.948323.short
4100  - http://biorxiv.org/content/early/2020/02/25/2020.02.18.948323.full
AB  - RNA sequencing and other experimental methods that produce large amounts of data are increasingly dominant in molecular biology. However, the noise properties of these techniques have not been fully understood. We assessed the reproducibility of allele-specific expression measurements by conducting replicate sequencing experiments from the same RNA sample. Surprisingly, variation in the estimates of allelic imbalance (AI) between technical replicates was up to 7-fold higher than expected from commonly applied noise models. We show that AI overdispersion varies substantially between replicates and between experimental series, appears to arise during the construction of sequencing libraries, and can be measured by comparing technical replicates. We demonstrate that compensation for AI overdispersion greatly reduces technical variation and enables reliable differential analysis of allele-specific expression across samples and across experiments. Conversely, not taking AI overdispersion into account can lead to a substantial number of false positives in analysis of allele-specific gene expression