{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":[null],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15079"],"description":["Capture-HiC was conducted to map chromatin interactions at all melanoma GWAS identified risk-associated regions across five individual primary human melanocyte cultures. Capture-HiC baits were designed by Arima Genomics (San Diego, CA, 2x tiling, least stringent masking, XTHSBoosting) to obtain an Agilent Sure Select library (Santa Clara, CA) targeting all restriction fragments (recognition sequences: ^GATC, ^GANTC) covering entire regions of association for the 68 independent genome-wide significant signals. Fifteen Capture-HiC libraries were generated from five human primary melanocyte cultures (C56, C140, C205, C24, and C27), with three technical replicates for each culture, except C56 third technical replicate, where the same library was also sequenced in a different batch labeled as rep4. The barcoded Capture-HiC libraries were pooled and sequenced using an Illumina Novaseq. This included one run on an SP flow cell and a second run on an S1 flow cell, resulting in approximately 5.7 billion paired-end reads with a read length of 150 bp. This sequencing yielded a median coverage of about 350 million read pairs per technical replicate and approximately 1.1 billion read pairs per culture."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Early passages of primary human melanocytes were isolated from foreskin healthy newborn males, following an established protocol (Halaban et al, J Exp Med (2000) 191(6):1005-1016) from the Specialized Programs of Research Excellence (SPORE) in Skin Cancer Specimen Resource Core at Yale University. Cells were grown in Dermal Cell Basal Medium (American Type Culture Collection/ATCC PCS-200-030) supplemented with Melanocyte Growth Kit (ATCC PCS-200-041) and 1% amphotericin B/penicillin/streptomycin (120-096-711, Quality Biological). C56, C140 and C205 are of European ancestry(CEU) and C24 and C27 are of African descent(YRI). For each library, 50,000 live cells were harvested.","Nucleic Acid Extraction - The initial Hi-C libraries were generated using the Arima HiC kit (Arima Genomics) following the manufacturer's protocol. Briefly, 2-4 million cells were crosslinked, enzyme digested, and ligated. The ligated DNA were purified by Ampure beads.","Library Construction - The ligated DNA was reverse-crosslinked, fragmented by sonication, and size-selected (200-600bp) for adaptor ligation and library amplification using KAPA HyperPrep kit (KAPA Biosystems) following the manufacturer's protocol.The HiC library was then hybridized with the custom capture baits and captured by the SureSelect XT HS and XT low input library preparation kit for ILM (Agilent).","Sequencing - Each library was sequenced by Novaseq to generate averagely 350milliaon pair-end reads with 150bp read length."],"figure_sub":["MINSEQE Score","Assays and Data","Processed Data","organisation","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Paired-end sequencing reads were pre-processed using the HiCUP pipeline and aligned to the human genome version 19 using Bowtie2. For each melanocyte culture, the aligned reads were pooled across the technical replicates.","Data Transformation - Chromatin interaction loops were detected at one and four restriction fragment resolutions, separately, using CHiCAGO pipeline version 1.16.063, treating each of the five melanocyte cultures as biological replicates. We used the default parameters for one-fragment analysis except for minFragLen, maxFragLen, binsize, maxLBrownEst which were set to 75, 1200, 2000, and 150000 respectively (Table S6). Four-fragment analysis was conducted using default parameters except for minFragLen, maxFragLen, binsize, maxLBrownEst which were set to 150, 5000, 8000, and 600000 respectively. For four fragment analysis the removeAdjacent parameter was set to FALSE. Following CHiCAGO tool recommendations, chromatin interaction capture-HiC loops with CHiCAGO scores ≥ 5 were considered high-confidence interactions and were further analyzed. The output file was generated using the long range interaction format."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"pubmed_abstract":["Genome-wide association studies (GWAS) of melanoma risk have identified 68 independent signals at 54 loci. For most loci, specific functional variants and their respective target genes remain to be established. Capture-HiC is an assay that links fine-mapped risk variants to candidate target genes by comprehensively mapping cell-type specific chromatin interactions. We performed a melanoma GWAS region-focused capture-HiC assay in human primary melanocytes to identify physical interactions between fine-mapped risk variants and potential causal melanoma susceptibility genes. Overall, chromatin interaction data alone nominated potential causal genes for 61 of the 68 melanoma risk signals, identifying many candidates beyond those reported by previous studies. We further integrated these data with cell-type specific epigenomic (chromatin state, accessibility), gene expression (eQTL/TWAS), DNA methylation (meQTL/MWAS), and massively parallel reporter assay (MPRA) data to prioritize potentially <i>cis</i>-regulatory variants and their respective candidate gene targets. From the set of fine-mapped variants across these loci, we identified 140 prioritized candidate causal variants linked to 195 candidate genes at 42 risk signals. In addition, we developed an integrative scoring system to facilitate candidate gene prioritization, integrating melanocyte and melanoma datasets. Notably, at several GWAS risk signals we observed long-range chromatin connections (500 kb to >1 Mb) with distant candidate target genes. We validated several such <i>cis</i>-regulatory interactions using CRISPR inhibition, providing evidence for known cancer driver genes <i>MDM4</i> and <i>CBL</i>, as well as the SRY-box transcription factor <i>SOX4</i>, as likely melanoma risk genes."],"study_type":["Hi-C"],"species":["Homo sapiens"],"pubmed_title":["Mapping chromatin interactions at melanoma susceptibility loci and cell-type specific dataset integration uncovers distant gene targets of cis-regulation"],"additional_accession":["ERP171941"],"pubmed_authors":["Rohit Thakur","Kevin Brown","Rohit Thakur, Mai Xu, Hayley Sowards, Joshuah Yon, Lea Jessop, Timothy Myers, Tongwu Zhang, Raj Chari, Erping Long, Thomas Rehling, Rebecca Hennessey, Karen Funderburk, Jinhu Yin, Mitchell J. Machiela, Matthew E. Johnson, Andrew D. Wells, Alessandra Chesi, Struan F.A. Grant, Mark M. Iles, Maria Teresa Landi, Matthew H. Law, Melanoma Meta-Analysis Consortium, Jiyeon Choi, Kevin M. Brown"]},"is_claimable":false,"name":"GWAS region focused capture-HiC of primary melanocytes from five human donors","description":"Capture-HiC was conducted to map chromatin interactions at all melanoma GWAS identified risk-associated regions across five individual primary human melanocyte cultures. Capture-HiC baits were designed by Arima Genomics (San Diego, CA, 2x tiling, least stringent masking, XTHSBoosting) to obtain an Agilent Sure Select library (Santa Clara, CA) targeting all restriction fragments (recognition sequences: ^GATC, ^GANTC) covering entire regions of association for the 68 independent genome-wide significant signals. Fifteen Capture-HiC libraries were generated from five human primary melanocyte cultures (C56, C140, C205, C24, and C27), with three technical replicates for each culture, except C56 third technical replicate, where the same library was also sequenced in a different batch labeled as rep4. The barcoded Capture-HiC libraries were pooled and sequenced using an Illumina Novaseq. This included one run on an SP flow cell and a second run on an S1 flow cell, resulting in approximately 5.7 billion paired-end reads with a read length of 150 bp. This sequencing yielded a median coverage of about 350 million read pairs per technical replicate and approximately 1.1 billion read pairs per culture.","dates":{"release":"2025-04-24T00:00:00Z","modification":"2026-05-27T16:02:22.936Z","creation":"2025-04-24T13:39:56.236Z"},"accession":"E-MTAB-15079","cross_references":{"ENA":["ERP171941"],"EFO":["EFO_0007693","EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"],"doi":["10.1101/2024.11.14.24317204"]}}