Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing

2007 ◽  
Vol 4 (8) ◽  
pp. 651-657 ◽  
Author(s):  
Gordon Robertson ◽  
Martin Hirst ◽  
Matthew Bainbridge ◽  
Misha Bilenky ◽  
Yongjun Zhao ◽  
...  
Keyword(s):  
Chromatin Immunoprecipitation ◽  
Massively Parallel Sequencing ◽  
Massively Parallel ◽  
Parallel Sequencing ◽  
Genome Wide

scholarly journals Genome-Wide Analyses of ChIP-Seq Derived FOXA2 DNA Occupancy in Liver Points to Genetic Networks Underpinning Multiple Complex Traits

2014 ◽  
Vol 99 (8) ◽  
pp. E1580-E1585 ◽  
Author(s):  
Matthew E. Johnson ◽  
Jonathan Schug ◽  
Andrew D. Wells ◽  
Klaus H. Kaestner ◽  
Struan F. A. Grant
Keyword(s):  
Chromatin Immunoprecipitation ◽  
Complex Traits ◽  
Genome Wide Association Study ◽  
Massively Parallel Sequencing ◽  
Gene List ◽  
Gene Set Enrichment Analysis ◽  
Massively Parallel ◽  
Sequencing Data ◽  
Parallel Sequencing ◽  
Genome Wide

Background: Forkhead Box A2 (FOXA2) exerts an influence on glucose homeostasis via activity in the liver. In addition, a key genome-wide association study (GWAS) recently demonstrated that genetic variation, namely rs6048205, at the FOXA2 locus is robustly associated with fasting glucose levels. Our hypothesis was that this DNA-binding protein regulates the expression of a set of molecular pathways critical to endocrine traits. Methods: Drawing on our laboratory and bioinformatic experience with chromatin immunoprecipitation followed by massively parallel sequencing, we analyzed our existing FOXA2 chromatin immunoprecipitation followed by massively parallel sequencing data generated in human liver, using the algorithm hypergeometric optimization of motif enrichment, to gain insight into its global genomic binding pattern from a disease perspective. Results: We performed a pathway analysis of the gene list using the gene set enrichment analysis algorithm, which yielded a number of significant annotations. Motivated by the fact that the FOXA2 locus has been implicated by GWAS, we cross-referenced the occupancy sites with the National Institutes of Health GWAS catalog and found strong evidence for the enrichment of loci implicated in endocrine, neuropsychiatric, cardiovascular, and cancer trait categories, but interestingly there was no evidence for enrichment for inflammation related traits. Intriguingly, a FOXA2 occupancy site coincided with rs6048205, suggesting that this variant confers its effect, at least partially, via a perturbation of a FOXA2 feedback mechanism. Conclusion: Our data strongly suggest that FOXA2 is acting as a master regulator of key pathways that are enriched for loci implicated by GWAS for most trait categories, with the clear exception of inflammation, suggesting that this factor exerts its effect in this context via noninflammatory processes.

Comprehensive preimplantation genetic testing by massively parallel sequencing

2020 ◽  
Author(s):  
Songchang Chen ◽  
Xuyang Yin ◽  
Sijia Zhang ◽  
Jun Xia ◽  
Ping Liu ◽  
...  
Keyword(s):  
Genetic Testing ◽  
Genome Sequencing ◽  
Massively Parallel Sequencing ◽  
Science And Technology ◽  
Family Members ◽  
Snp Array ◽  
Massively Parallel ◽  
Preimplantation Genetic Testing ◽  
Parallel Sequencing ◽  
Genome Wide

Abstract STUDY QUESTION Can whole genome sequencing (WGS) offer a relatively cost-effective approach for embryonic genome-wide haplotyping and preimplantation genetic testing (PGT) for monogenic disorders (PGT-M), aneuploidy (PGT-A) and structural rearrangements (PGT-SR)? SUMMARY ANSWER Reliable genome-wide haplotyping, PGT-M, PGT-A and PGT-SR could be performed by WGS with 10× depth of parental and 4× depth of embryonic sequencing data. WHAT IS KNOWN ALREADY Reduced representation genome sequencing with a genome-wide next-generation sequencing haplarithmisis-based solution has been verified as a generic approach for automated haplotyping and comprehensive PGT. Several low-depth massively parallel sequencing (MPS)-based methods for haplotyping and comprehensive PGT have been developed. However, an additional family member, such as a sibling, or a proband, is required for PGT-M haplotyping using low-depth MPS methods. STUDY DESIGN, SIZE, DURATION In this study, 10 families that had undergone traditional IVF-PGT and 53 embryos, including 13 embryos from two PGT-SR families and 40 embryos from eight PGT-M families, were included to evaluate a WGS-based method. There were 24 blastomeres and 29 blastocysts in total. All embryos were used for PGT-A. Karyomapping validated the WGS results. Clinical outcomes of the 10 families were evaluated. PARTICIPANTS/MATERIALS, SETTING, METHODS A blastomere or a few trophectoderm cells from the blastocyst were biopsied, and multiple displacement amplification (MDA) was performed. MDA DNA and bulk DNA of family members were used for library construction. Libraries were sequenced, and data analysis, including haplotype inheritance deduction for PGT-M and PGT-SR and read-count analysis for PGT-A, was performed using an in-house pipeline. Haplotyping with a proband and parent-only haplotyping without additional family members were performed to assess the WGS methodology. Concordance analysis between the WGS results and traditional PGT methods was performed. MAIN RESULTS AND THE ROLE OF CHANCE For the 40 PGT-M and 53 PGT-A embryos, 100% concordance between the WGS and single-nucleotide polymorphism (SNP)-array results was observed, regardless of whether additional family members or a proband was included for PGT-M haplotyping. For the 13 embryos from the two PGT-SR families, the embryonic balanced translocation was detected and 100% concordance between WGS and MicroSeq with PCR-seq was demonstrated. LIMITATIONS, REASONS FOR CAUTION The number of samples in this study was limited. In some cases, the reference embryo for PGT-M or PGT-SR parent-only haplotyping was not available owing to failed direct genotyping. WIDER IMPLICATIONS OF THE FINDINGS WGS-based PGT-A, PGT-M and PGT-SR offered a comprehensive PGT approach for haplotyping without the requirement for additional family members. It provided an improved complementary method to PGT methodologies, such as low-depth MPS- and SNP array-based methods. STUDY FUNDING/COMPETING INTEREST(S) This research was supported by the research grant from the National Key R&D Program of China (2018YFC0910201 and 2018YFC1004900), the Guangdong province science and technology project of China (2019B020226001), the Shenzhen Birth Defect Screening Project Lab (JZF No. [2016] 750) and the Shenzhen Municipal Government of China (JCYJ20170412152854656). This work was also supported by the National Natural Science Foundation of China (81771638, 81901495 and 81971344), the National Key R&D Program of China (2018YFC1004901 and 2016YFC0905103), the Shanghai Sailing Program (18YF1424800), the Shanghai Municipal Commission of Science and Technology Program (15411964000) and the Shanghai ‘Rising Stars of Medical Talent’ Youth Development Program Clinical Laboratory Practitioners Program (201972). The authors declare no competing interests. TRIAL REGISTRATION NUMBER N/A.

scholarly journals Genome-wide identification and annotation of HIF-1α binding sites in two cell lines using massively parallel sequencing

2010 ◽  
Vol 4 (1-4) ◽  
pp. 35-48 ◽  
Author(s):  
Kousuke Tanimoto ◽  
Katsuya Tsuchihara ◽  
Akinori Kanai ◽  
Takako Arauchi ◽  
Hiroyasu Esumi ◽  
...  
Keyword(s):  
Cell Lines ◽  
Binding Sites ◽  
Massively Parallel Sequencing ◽  
Massively Parallel ◽  
Parallel Sequencing ◽  
Genome Wide

scholarly journals Genome-Wide Massively Parallel Sequencing of Formaldehyde Fixed-Paraffin Embedded (FFPE) Tumor Tissues for Copy-Number- and Mutation-Analysis

PLoS ONE ◽  
2009 ◽  
Vol 4 (5) ◽  
pp. e5548 ◽  
Author(s):  
Michal R. Schweiger ◽  
Martin Kerick ◽  
Bernd Timmermann ◽  
Marcus W. Albrecht ◽  
Tatjana Borodina ◽  
...  
Keyword(s):  
Mutation Analysis ◽  
Copy Number ◽  
Massively Parallel Sequencing ◽  
Massively Parallel ◽  
Parallel Sequencing ◽  
Genome Wide ◽  
Tumor Tissues ◽  
Ffpe Tumor

scholarly journals Massively parallel sequencing of Chikso (Korean brindle cattle) to discover genome-wide SNPs and InDels

2013 ◽  
Vol 36 (3) ◽  
pp. 203-211 ◽  
Author(s):  
Jung-Woo Choi ◽  
Xiaoping Liao ◽  
Sairom Park ◽  
Heoyn-Jeong Jeon ◽  
Won-Hyong Chung ◽  
...  
Keyword(s):  
Massively Parallel Sequencing ◽  
Massively Parallel ◽  
Parallel Sequencing ◽  
Genome Wide
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