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Low depth whole genome sequencing across multiple isolated populations

ABSTRACT: Isolated populations have unique population genetics characteristics that can help boost power in genetic association studies for complex traits. Leveraging these advantageous characteristics requires an in-depth understanding of parameters that have shaped sequence variation in isolates. This study performs a comprehensive investigation of these parameters using low-depth whole genome sequencing (WGS) across multiple isolates.

PROVIDER: EGAS00001001597 | EGA |

REPOSITORIES: EGA

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Project description:Dynamic tyrosine phosphorylation is fundamental to a myriad of cellular processes. However, the inherently low abundance of tyrosine phosphorylation in the proteome and the inefficient enrichment of phosphotyrosine(pTyr)-containing peptides has led to poor pTyr peptide identification and quantitation, critically hindering researchers’ ability to elucidate signaling pathways regulated by tyrosine phosphorylation in systems where cellular material is limited. The most popular approaches to wide-scale characterization of the tyrosine phosphoproteome use pTyr enrichment with pan-specific, anti-pTyr antibodies from a large amount of starting material. Methods that decrease the amount of starting material and increase the characterization depth of the tyrosine phosphoproteome while maintaining quantitative accuracy and precision would enable the discovery of tyrosine phosphorylation networks in rarer cell populations. To achieve these goals, a novel method leveraging the multiplexing capability of tandem mass tags (TMT) and the use of trigger channels – cells treated with the promiscuous tyrosine phosphatase inhibitor pervanadate (PV) – selectively increased the relative abundance of pTyr-containing peptides. After PV facilitated selective fragmentation of pTyr-containing peptides, TMT reporter ions delivered sensitive quantitation of each peptide for the experimental samples while the quantitation from PV trigger channels was ignored. This method yielded up to 6.3-fold boost in quantification depth of statistically significant data derived from contrived ratios, compared to TMT without trigger channels or intensity-based label-free (LF) quantitation while maintaining quantitative accuracy and precision, allowing quantitation of over 2300 unique pTyr peptides from only 1 mg of T cell receptor-stimulated Jurkat T cells. The trigger channel strategy can potentially be applied in analyses of other post-translational modifications where treatments that broadly boost the levels of those modifications across the proteome are available.

Dataset Information

Low depth whole genome sequencing across multiple isolated populations

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