READINGS
Recommended Text: Exploring Personal Genomics by Joel Dudley and Konrad Karczewski
These papers are to supplement the content provided in lecture.
Lecture 01/02/03
Examples of genetic diversity
CarcinogenesisConstitutional CHEK2 mutations are associated with a decreased risk of lung and laryngeal cancers
Nature2008 Nov 6;456(7218):98-101. Epub 2008 Aug 31. Genes mirror geography within Europe.
Next Generation Sequencing
Technology: The $1,000 genome.
Nat Biotechnol2008; 26, 1125 - 1133. What would you do if you could sequence everything?
Nat Biotechnol2009 Sep;27(9):847-50. doi: 10.1038/nbt.1561. Epub 2009 Aug 10. Single-molecule sequencing of an individual human genome.
Characterizing multi-omic data in systems biology.
Zero-gravity genomics passes first test.
Nat Biotechnol2016 Mar;34(3):303-11. doi: 10.1038/nbt.3432. Epub 2016 Feb 1. Haplotyping germline and cancer genomes with high-throughput linked-read sequencing.
Brief Bioinform2010 Sep; 11(5): 473–483. A survey of sequence alignment algorithms for next-generation sequencing
Nat Biotechnol 27, 455 - 457 (2009) doi:10.1038/nbt0509-455. How to map billions of short reads onto genomes.
ILMN/LIFE sequencing workflow.
Nature 2005 Sep 15;437(7057):376-80. Epub 2005 Jul 31. Genome sequencing in microfabricated high-density picolitre reactors.
Nature 2008 Nov 6;456(7218):53-9. Accurate whole human genome sequencing using reversible terminator chemistry.
Nucleic Acids Res2000 Oct 15;28(20):E87. Solid phase DNA amplification.
Genome Res2009 Sep;19(9):1527-41. Epub 2009 Jun 22. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding.
Nature2011 Jul 20;475(7356):348-52. An integrated semiconductor device enabling non-optical genome sequencing.
Science2003 Jan 31;299(5607):682-6. Zero-mode waveguides for single-molecule analysis at high concentrations.
Nat Biotechnol2009 Nov;27(11):1013-23. Epub 2009 Nov 6. The challenges of sequencing by synthesis.
Annu Rev Genomics Hum Genet2008;9:387-402. Next-generation DNA sequencing methods.
Trends Genet. 2008 Mar;24(3):133-41. Epub 2008 Feb 11. The impact of next-generation sequencing technology on genetics.
Nat Rev Genet. 2010 Jan;11(1):31-46. Epub 2009 Dec 8. Sequencing technologies - the next generation.
Nat Biotechnol. 2008 Oct;26(10):1135-45. Next-generation DNA sequencing.
Illumina Sequencing Technology Poster
Large-scale sequencing projects
Genomics England100,000 Genomes Project
TCGAThe Cancer Genome Atlas
The Genome 10K ProjectAssembling a “Noah’s Ark” of genomic data to save dying species
Cancer
Nature481, 506–510 (26 January 2012). Clonal evolution in relapsed acute myeloid leukemia revealed by whole-genome sequencing
NGS and Epigenetics
Trends Biochem Sci2010 Nov;35(11):618-26. Fast signals and slow marks: the dynamics of histone modifications.
Nat Methods2010 Jun;7(6):461-5. doi: 10.1038/nmeth.1459. Epub 2010 May 9. Direct detection of DNA methylation during single-molecule, real-time sequencing.
Genome Biol2014 Feb 3;15(2):R24. doi: 10.1186/gb-2014-15-2-r24. Aging of blood can be tracked by DNA methylation changes at just three CpG sites.
Genome Biol2013, 14:R115. doi:10.1186/gb-2013-14-10-r115. DNA methylation age of human tissues and cell types.
Lecture 07/08/09
Histone Modifications
Mol Syst Biol. 2008;4:188. Genomic analysis of estrogen cascade reveals histone variant H2A.Z associated with breast cancer progression.
Dev Cell. 2011 Dec 13;21(6):993-1004. Prepatterning of developmental gene expression by modified histones before zygotic genome activation.
Proc Natl Acad Sci USA. 2013 Mar 11. [Epub ahead of print]. Social environment is associated with gene regulatory variation in the rhesus macaque immune system.
Proc Natl Acad Sci USA.. 2008 Oct;26(10):1135-45. Reversible epigenetic down-regulation of MHC molecules by devil facial tumour disease illustrates immune escape by a contagious cancer.
Nature. 2012 Jan 29;482(7384):226-31. Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma.
Cell. 2011 Sep 16;146(6):1016-28. Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification.