Peng Zhang, Ji-Han Xia, Jing Zhu, Ping Gao, Yi-Jun Tian et al.
Functional characterization of disease-causing variants at risk loci has been a significant challenge. Here we report a high-throughput single-nucleotide polymorphisms sequencing (SNPs-seq) technology to simultaneously screen hundreds to thousands of SNPs for their allele-dependent protein-binding differences. This technology takes advantage of higher retention rate of protein-bound DNA oligos in protein purification column to quantitatively sequence these SNP-containing oligos. We apply this technology to test prostate cancer-risk loci and observe differential allelic protein binding in a significant number of selected SNPs. We also test a unique application of self-transcribing active regulatory region sequencing (STARR-seq) in characterizing allele-dependent transcriptional regulation and provide detailed functional analysis at two risk loci (RGS17 and ASCL2). Together, we introduce a powerful high-throughput pipeline for large-scale screening of functional SNPs at disease risk loci.
Peng Zhang, Ji-Han Xia, Jing Zhu, Ping Gao, Yi-Jun Tian, Meijun Du, Yong-Chen Guo, Sufyan Suleman, Qin Zhang, Manish Kohli, Lori S. Tillmans, Stephen N. Thibodeau, Amy J. French, James R. Cerhan, Li-Dong Wang, Gong-Hong Wei, Liang Wang. High-throughput screening of prostate cancer risk loci by single nucleotide polymorphisms sequencing. 2018-05-22. https://doi.org/10.1038/s41467-018-04451-x
A pooled allele-specific STARR-seq library containing 96 amplicons covering 101 prostate-cancer risk SNPs (202 allele sequences) was assayed in human LNCaP cells under the ethanol vehicle condition. This experiment represents the 0.1% ethanol control with two technical replicates and matched plasmid input controls; the processed table retains 100 SNP rows after condition-specific coverage/BAE QC.
A pooled allele-specific STARR-seq library containing 96 amplicons covering 101 prostate-cancer risk SNPs (202 allele sequences) was assayed in human LNCaP cells under androgen stimulation. This experiment represents the 10 nM dihydrotestosterone condition with two technical replicates and matched plasmid input controls; the processed table retains 96 SNP rows after condition-specific coverage/BAE QC.
Original supplemental and deposited inputs retained for this study. Download files individually or together as a ZIP; nested folders are preserved. Source reuse terms apply, and sequencing reads may be omitted.
Download all 4 files (ZIP)source_notes.txtsupplementary_data_1_candidate_snp_annotations.xlsxsupplementary_data_3_starr_library_primers_and_bab_scores.xlsxsupplementary_data_4_starr_seq_read_counts_and_bae_scores.xlsx