Initial sequencing and analysis of the human genome

Lander, Eric S.; Linton, Lauren; Birren, Bruce; Nusbaum, Chad; Zody, Michael C.; Baldwin, Jennifer; Devon, Keri; Dewar, Ken; Doyle, Michael J.; Fitzhugh, William W.; Funke, Roel; Gage, Diane; Harris, Katrina; Heaford, Andrew; Howland, John G.; Kann, Lisa; Lehoczky, Jessica A.; Levine, Rosie; McEwan, Paul; McKernan, Kevin; Meldrim, James C.; Mesirov, Jill P.; Miranda, Cher; Morris, William; Naylor, Jerome; Raymond, Christina; Rosetti, Mark; Santos, Ralph; Sheridan, Andrew; Sougnez, Carrie; Stange-Thomann, Nicole; Stojanović, Nikola; Subramanian, Aravind; Wyman, Dudley; Rogers, Jane; Sulston, John; Ainscough, R.; Beck, Stephan; Bentley, David; Burton, John H.; Clee, Christopher M.; Carter, Nigel; Coulson, Alan; Deadman, Rebecca; Deloukas, Panos; Dunham, Andrew; Dunham, Ian; Durbin, Richard; French, Lisa; Grafham, Darren; Gregory, Simon G.; Hubbard, Tim; Humphray, Sean; Hunt, Adrienne; Jones, Matthew C.; Lloyd, Christine; McMurray, Amanda; Matthews, Lucy; Mercer, Simon; Milne, Sarah; Mullikin, James C.; Mungall, Andrew J.; Plumb, Robert; Ross, Mark T.; Shownkeen, Ratna; Sims, Sarah; Waterston, Robert H.; Wilson, Richard K.; Hillier, LaDeana W.; Mcpherson, John Douglas; Marra, Marco A.; Mardis, Elaine R.; Fulton, Lucinda A.; Chinwalla, Asif T.; Pepin, Kymberlie H.; Gish, Warren; Chissoe, Stephanie L.; Wendl, Michael C.; Delehaunty, Kim D.; Miner, Tracie L.; Delehaunty, Andrew; Kramer, Jason; Cook, Lisa L.; Fulton, Robert S.; Johnson, D.; Minx, Patrick; Clifton, Sandra W.; Hawkins, Trevor; Branscomb, Elbert; Predki, Paul; Richardson, Paul M.; Wenning, Sarah; Slezak, Tom; Doggett, Norman A.; Cheng, Jan‐Fang; Olsen, Anne S.; Lucas, Susan; Elkin, Christopher J.; Uberbacher, Edward C.; Frazier, M.E.; Gibbs, Richard A.; Muzny, Donna M.; Scherer, Steven E.; Bouck, John; Sodergren, Erica; Worley, Kim C.; Rives, Catherine M.; Gorrell, James H.; Metzker, Michael L.; Naylor, Susan L.; Kucherlapati, Raju; Nelson, David L.; Weinstock, George M.; Sakaki, Yoshiyuki; Fujiyama, Asao; Hattori, Masahira; Yada, Tetsushi; Toyoda, Atsushi; Itoh, Takehiko; Kawagoe, Chiharu; Watanabe, Hidemi; Totoki, Yasushi; Taylor, Todd D.; Weissenbach, Jean; Heilig, Roland; Saurin, William; Artiguenave, François; Brottier, Philippe; Brüls, Thomas; Pelletier, Éric; Robert, Caroline; Wincker, Patrick; Rosenthal, André; Platzer, Matthias; Nyakatura, Gerald; Taudien, Stefan; Rump, Andreas; Smith, Douglas R.; Doucette‐Stamm, Lynn; Rubenfield, Marc; Weinstock, Keith G.; Hong, Mei; Dubois, J.; Yang, Huanming; Yu, Jun; Wang, Jian; Huang, Guyang Matthew; Gu, Jun; Hood, Leroy; Rowen, Lee; Madan, Anup; Qin, Shizen; Davis, Ronald W.; Federspiel, Nancy A.; Abola, A. Pia; Proctor, Michael; Roe, Bruce A.; Chen, Feng; Pan, Huaqin; Ramser, Juliane; Lehrach, Hans; Reinhardt, Richard; McCombie, W. Richard; Bastide, M. de la; Dedhia, Neilay; Blöcker, Helmut; Hornischer, Klaus; Nordsiek, Gabriele; Agarwala, Richa; Aravind, L.; Bailey, Jeffrey A.; Bateman, Alex; Batzoglou, Serafim; Birney, Ewan; Bork, Peer; Brown, Daniel G.; Burge, Christopher B.; Cerutti, Lorenzo; Chen, Hsiu Chuan; Church, Deanna M.; Clamp, Michele; Copley, Richard R.; Doerks, Tobias; Eddy, Sean R.; Eichler, Evan E.; Furey, Terrence S.; Galagan, James E.; Gilbert, James; Harmon, Cyrus; Hayashizaki, Yoshihide; Haussler, David; Hermjakob, Henning; Hokamp, Karsten; Jang, Wonhee; Johnson, L. Steven; Jones, Thomas A.; Kasif, Simon; Kaspryzk, Arek; Kennedy, Scot; Kent, W. James; Kitts, Paul; Koonin, Eugene V.; Korf, Ian F; Kulp, David; Lancet, Doron; Lowe, Todd M.; McLysaght, Aoife; Mikkelsen, Tarjei S.; Moran, John V.; Mulder, Nicola; Pollara, Victor J.; Ponting, Chris P.; Schuler, Greg; Schultz, Jörg; Slater, Guy; Smit, Arian F. A.; Stupka, Elia; Szustakowki, Joseph; Thierry-Mieg, Danielle; Thierry‐Mieg, Jean; Wagner, Lukas; Wallis, John W.; Wheeler, Raymond M.; Williams, Alan J.; Wolf, Yuri I.; Wolfe, Kenneth H.; Yang, Shiaw Pyng; Yeh, Ru Fang; Collins, Francis S.; Guyer, Mark S.; Peterson, Jane; Felsenfeld, Adam; Wetterstrand, Kris A.; Myers, R; Schmutz, Jeremy; Dickson, Mark; Grimwood, Jane; Cox, David; Olson, Maynard V.; Kaul, Rajinder; Raymond, Christopher K.; Shimizu, Nobuyoshi; Kawasaki, Kazuhiko; Minoshima, Shinsei; Evans, Glen A.; Αθανασίου, Μαρία; Schultz, Roger A.; Patrinos, A.A.N.; Morgan, Michael J.

doi:10.1038/35057062

Cited by 20,305 publications

(5,496 citation statements)

References 426 publications

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“…Additionally, reads mapping to more than one location were also discarded. Pre-capture paired-end reads were analyzed as described above except that alignment was performed to the full human genome (Hg18, NCBI Build 36.1, March 2006) (Lander et al 2001). The substitution error rate (incorrect/correct high quality aligned nucleotides) for each of the DNA polymerases used in this study was calculated by comparing the reads generated using each enzyme library to the consensus mtDNA genome for that enzyme library using the above BWA settings and Picard Tools v 1.137.…”

Section: Methodsmentioning

confidence: 99%

Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus

Ozga

Nieves-Colón

Honap

et al. 2016

American J Phys Anthropol

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Objectives Archaeological dental calculus is a rich source of host-associated biomolecules. Importantly, however, dental calculus is more accurately described as a calcified microbial biofilm than a host tissue. As such, concerns regarding destructive analysis of human remains may not apply as strongly to dental calculus, opening the possibility of obtaining human health and ancestry information from dental calculus in cases where destructive analysis of conventional skeletal remains is not permitted. Here we investigate the preservation of human mitochondrial DNA (mtDNA) in archaeological dental calculus and its potential for full mitochondrial genome (mitogenome) reconstruction in maternal lineage ancestry analysis. Materials and Methods Extracted DNA from six individuals at the 700-year-old Norris Farms #36 cemetery in Illinois was enriched for mtDNA using in-solution capture techniques, followed by Illumina high-throughput sequencing. Results Full mitogenomes (7-34x) were successfully reconstructed from dental calculus for all six individuals, including three individuals who had previously tested negative for DNA preservation in bone using conventional PCR techniques. Mitochondrial haplogroup assignments were consistent with previously published findings, and additional comparative analysis of paired dental calculus and dentine from two individuals yielded equivalent haplotype results. All dental calculus samples exhibited damage patterns consistent with ancient DNA, and mitochondrial sequences were estimated to be 92–100% endogenous. DNA polymerase choice was found to impact error rates in downstream sequence analysis, but these effects can be mitigated by greater sequencing depth. Discussion Dental calculus is a viable alternative source of human DNA that can be used to reconstruct full mitogenomes from archaeological remains.

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Section: Methodsmentioning

confidence: 99%

Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus

Ozga

Nieves-Colón

Honap

et al. 2016

American J Phys Anthropol

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“…The PH domain consists of approximately ~130 residues and is found in a variety of organisms from yeast to humans. PH domains are found in about 252 human proteins and it is the 11th most abundant domain in the human genome 22. PH domains are best known for their ability to bind phosphoinositides and to target their host proteins to cellular membranes 23.…”

Section: Resultsmentioning

confidence: 99%

The possible roles of B‐cell novel protein‐1 (BCNP1) in cellular signalling pathways and in cancer

Patel

Trivedi

Darie

et al. 2016

J Cellular Molecular Medi

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B‐cell novel protein‐1 (BCNP1) or Family member of 129C (FAM129C) was identified as a B‐cell‐specific plasma‐membrane protein. Bioinformatics analysis predicted that BCNP1 might be heavily phosphorylated. The BCNP1 protein contains a pleckstrin homology (PH) domain, two proline‐rich (PR) regions and a Leucine Zipper (LZ) domain suggesting that it may be involved in protein‐protein interactions. Using The Cancer Genome Atlas (TCGA) data sets, we investigated the correlation of alteration of the BCNP1 copy‐number changes and mutations in several cancer types. We also investigated the function of BCNP1 in cellular signalling pathways. We found that BCNP1 is highly altered in some types of cancers and that BCNP1 copy‐number changes and mutations co‐occur with other molecular alteration events for TP53 (tumour protein P53), PIK3CA (Phosphatidylinositol‐4,5‐Bisphosphate 3‐Kinase, Catalytic Subunit Alpha), MAPK1 (mitogen‐activated protein kinase‐1; ERK: extracellular signal regulated kinase), KRAS (Kirsten rat sarcoma viral oncogene homolog) and AKT2 (V‐Akt Murine Thymoma Viral Oncogene Homolog 2). We also found that PI3K (Phoshoinositide 3‐kinase) inhibition and p38 MAPK (p38 mitogen‐activated protein kinase) activation leads to reduction in phosphorylation of BCNP1 at serine residues, suggesting that BCNP1 phosphorylation is PI3K and p38MAPK dependent and that it might be involved in cancer. Its degradation depends on a proteasome‐mediated pathway.

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“…The completion of the draft sequence of the human genome in 2001 1 heralded intense interest in the management and implementation of gene expression programmes, understanding the basis of cell differentiation and cell type specification. These studies have begun to reveal how an individual cell type establishes and maintains its ability to express a distinct repertoire of genes and how this output capacity can be modulated under the influence of intrinsic and extrinsic stimuli.…”

Section: Epigeneticsmentioning

confidence: 99%

CRISPR-based reagents to study the influence of the epigenome on gene expression

Lavender

Kelly

Hendy

et al. 2018

Clinical and Experimental Immunology

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SummaryThe use of epigenome editing is set to expand our knowledge of how epigenetic landscapes facilitate gene expression capacity within a given cell. As epigenetic landscape profiling in health and disease becomes more commonplace, so does the requirement to assess the functional impact that particular regulatory domains and DNA methylation profiles have upon gene expression capacity. That functional assessment is particularly pertinent when analysing epigenomes in disease states where the reversible nature of histone and DNA modification might yield plausible therapeutic targets. In this review we discuss first the nature of the epigenetic landscape, secondly the types of factors that deposit and erase the various modifications, consider how modifications transduce their signals, and lastly address current tools for experimental epigenome editing with particular emphasis on the immune system.

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Initial sequencing and analysis of the human genome

Cited by 20,305 publications

References 426 publications

Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus

Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus

The possible roles of B‐cell novel protein‐1 (BCNP1) in cellular signalling pathways and in cancer

CRISPR-based reagents to study the influence of the epigenome on gene expression

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