Semiconductor-based DNA sequencing of histone modification states

Nature Communications

Volumn 4, Issue , 2013, Pages

  Cheng, Christine S ^a   Rai, Kunal ^b   Garber, Manuel ^a,c   Hollinger, Andrew ^a   Robbins, Dana ^a   Anderson, Scott ^a   Macbeth, Alyssa ^a   Tzou, Austin ^a   Carneiro, Mauricio O ^a   Raychowdhury, Raktima ^a   Russ, Carsten ^a   Hacohen, Nir ^a,d,e   Gershenwald, Jeffrey E ^b   Lennon, Niall ^a   Nusbaum, Chad ^a   Chin, Lynda ^b   Regev, Aviv ^a,f   Amit, Ido ^a,g  

^a BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^b UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

^c UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

^d MASSACHUSETTS GENERAL HOSPITAL   (United States)

^e HARVARD MEDICAL SCHOOL   (United States)

^f MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^g WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; HISTONE; IMMUNOGLOBULIN G;

ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL MODEL; ARTICLE; CANCER GENETICS; CANCER GROWTH; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; DATA BASE; DNA SEQUENCE; EMBRYONIC STEM CELL; EPIGENETICS; FEMALE; GENE EXPRESSION PROFILING; HISTONE MODIFICATION; HUMAN; HUMAN CELL; HUMAN TISSUE; MELANOMA; METASTASIS; MOLECULAR LIBRARY; MOUSE; NONHUMAN; SEMICONDUCTOR BASED DNA SEQUENCING; ANIMAL; C57BL MOUSE; CHEMISTRY; CHROMATIN; CYTOLOGY; DENDRITIC CELL; EQUIPMENT; GENETIC EPIGENESIS; GENETICS; HUMAN GENOME; METABOLISM; METHODOLOGY; PROTEIN PROCESSING; SEMICONDUCTOR; SKIN TUMOR;

ANIMALS; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; DENDRITIC CELLS; EPIGENESIS, GENETIC; FEMALE; GENOME, HUMAN; HISTONES; HUMANS; MELANOMA; MICE; MICE, INBRED C57BL; PROTEIN PROCESSING, POST-TRANSLATIONAL; SEMICONDUCTORS; SEQUENCE ANALYSIS, DNA; SKIN NEOPLASMS;

EID: 84901836907     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms3672     Document Type: Article

References (30)

1. Rothberg, J. M. et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature 475, 348-352 (2011).
2. Ferain, I., Colinge, C. A. & Colinge, J. P. Multigate transistors as the future of classical metal-oxide-semiconductor field-effect transistors. Nature 479, 310-316 (2011).
3. Glenn, T. C. Field guide to next-generation DNA sequencers. Mol. Ecol. Resour. 11, 759-769 (2011).
4. Merriman, B. & Rothberg, J. M. Progress in ion torrent semiconductor chip based sequencing. Electrophoresis 33, 3397-3417 (2012).
5. Vogel, U. et al. Ion torrent personal genome machine sequencing for genomic typing of Neisseria meningitidis for rapid determination of multiple layers of typing information. J. Clin. Microbiol. 50, 1889-1894 (2012).
6. Elliott, A. M., Radecki, J., Moghis, B., Li, X. & Kammesheidt, A. Rapid detection of the ACMG/ACOG-recommended 23 CFTR disease-causing mutations using ion torrent semiconductor sequencing. J. Biomol. Tech. 23, 24-30 (2012).
7. Ernst, J. et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473, 43-49 (2011).
8. Gerstein, M. B. et al. Architecture of the human regulatory network derived from ENCODE data. Nature 489, 91-100 (2012).
9. Ram, O. et al. Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells. Cell 147, 1628-1639 (2011).
10. Adli, M. & Bernstein, B. E. Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq. Nat. Protoc. 6, 1656-1668 (2011).
11. Adli, M., Zhu, J. & Bernstein, B. E. Genome-wide chromatin maps derived from limited numbers of hematopoietic progenitors. Nat. Methods 7, 615-618 (2010).
12. Lennon, N. J. et al. A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454. Genome Biol. 11, R15 (2010).
13. Quail, M. A. et al. Optimal enzymes for amplifying sequencing libraries. Nat. Methods 9, 10-11 (2012).
14. Landt, S. G. et al. ChIP-seq guidelines and practices of the ENCODE and mod ENCODE consortia. Genome Res. 22, 1813-1831 (2012).
15. ENCODE Project Consortium. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 9, e1001046 (2011).
16. Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102, 15545-15550 (2005).
17. Lee, T. I. et al. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 125, 301-313 (2006).
18. Bernstein, B. E. et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125, 315-326 (2006).
19. Ben-Porath, I. et al. An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumors. Nat. Genet. 40, 499-507 (2008).
20. Kim, J. et al. A Myc network accounts for similarities between embryonic stem and cancer cell transcription programs. Cell 143, 313-324 (2010).
21. Chi, P., Allis, C. D. & Wang, G. G. Covalent histone modifications-miswritten, misinterpreted and mis-erased in human cancers. Nat. Rev. Cancer 10, 457-469 (2010).
22. Min, J. et al. An oncogene-tumor suppressor cascade drives metastatic prostate cancer by coordinately activating Ras and nuclear factor-kappaB. Nat. Med. 16, 286-294 (2010).
23. Tsang, D. P. & Cheng, A. S. Epigenetic regulation of signaling pathways in cancer: role of the histone methyltransferase EZH2. J. Gastroenterol. Hepatol. 26, 19-27 (2011).
24. Yu, J. et al. A polycomb repression signature in metastatic prostate cancer predicts cancer outcome. Cancer Res. 67, 10657-10663 (2007).
25. Ben-Neriah, Y. & Karin, M. Inflammation meets cancer, with NF-kappaB as the matchmaker. Nat. Immunol. 12, 715-723 (2011).
26. Coussens, L. M. & Werb, Z. Inflammation and cancer. Nature 420, 860-867 (2002).
27. Mantovani, A., Allavena, P., Sica, A. & Balkwill, F. Cancer-related inflammation. Nature 454, 436-444 (2008).
28. Garber, M. et al. A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Mol. Cell 47, 810-822 (2012).
29. De Pristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491-498 (2011).
30. Bernstein, B. E. et al. The NIH Roadmap Epigenomics Mapping Consortium. Nat. Biotechnol. 28, 1045-1048 (2010).