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Dhatterwal P, Mehrotra S, Mehrotra R. Primer Designing for Amplifying an AT-Rich Promoter from Arabidopsis thaliana. Methods Mol Biol 2022; 2392:115-123. [PMID: 34773619 DOI: 10.1007/978-1-0716-1799-1_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The aim of the present study is to optimize the PCR conditions required to amplify the promoter sequence of an amino acid transporter having an AT-rich base composition with a high number of tandem repeats. The present study also covers the key parameters that need to be kept in mind while designing primers. Results show that successful can be achieved by performing a 2-step PCR reaction at a lower extension temperature of 65 ̊C for an increased extension period of 1.5 min/kb, with MgCl2 concentration ranging from 2.5 to 3.0mM. The results also suggest that the DNA concentration of around 25-30 ng/µl was essential to achieve this amplification.
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Affiliation(s)
- Pinky Dhatterwal
- Department of Biological Sciences, Birla Institute of Technology & Science Pilani, Sancoale, Goa, India
| | - Sandhya Mehrotra
- Department of Biological Sciences, Birla Institute of Technology & Science Pilani, Sancoale, Goa, India
| | - Rajesh Mehrotra
- Department of Biological Sciences, Birla Institute of Technology & Science Pilani, Sancoale, Goa, India.
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2
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Ichimaru Y, Kato K, Okuno Y, Yamaguchi Y, Jin W, Fujita M, Otsuka M, Imai M, Kurosaki H. Design and synthesis of an anthranyl bridged optically active dinuclear iron(II)-ligand and evaluation of DNA-cleaving activity. Bioorg Med Chem Lett 2021; 35:127782. [PMID: 33422608 DOI: 10.1016/j.bmcl.2021.127782] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/23/2020] [Accepted: 01/02/2021] [Indexed: 11/26/2022]
Abstract
It is necessary to design a ligand that is compatible with the target molecule to optimally use the DNA-cleaving ability of metal complexes. In this study, we synthesized an optically active dinuclear ligand, (1R,1'R,2R,2'R)-N1,N1'-(anthracene-1,8-diylbis(methylene))bis(N2,N2-bis(pyridin-2-ylmethyl)cyclohexane-1,2-diamine) (R-ABDC, 4a) and its enantiomer (S-ABDC, 4b). We then prepared their Fe(II) complexes by mixing the ligand with FeSO4·7H2O in situ and investigated DNA-cleaving activities using plasmid DNA in the presence of excess sodium ascorbate at atmospheric conditions. The Fe(II) complexes efficiently cleaved DNA and selectively recognized two consecutive A and/or T sequences.
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Affiliation(s)
- Yoshimi Ichimaru
- College of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyamaku, Nagoya, Aichi 463-8521, Japan
| | - Koichi Kato
- College of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyamaku, Nagoya, Aichi 463-8521, Japan
| | - Yoshinori Okuno
- Department of Medicinal Chemistry, Yokohama University of Pharmacy, 601 Matano-cho Totsuka-ku, Yokohama 245-0066 Japan.
| | - Yoshihiro Yamaguchi
- Environmental Safety Center, Kumamoto University, 39-1 Kurokami 2-Chome, Chuo-ku, Kumamoto 860-8555, Japan
| | - Wanchun Jin
- College of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyamaku, Nagoya, Aichi 463-8521, Japan
| | - Mikako Fujita
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Masami Otsuka
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto 862-0973, Japan; Department of Drug Discovery, Science Farm Ltd., 1-7-30 Kuhonji, Chuo-ku, Kumamoto 862-0976, Japan
| | - Masanori Imai
- College of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyamaku, Nagoya, Aichi 463-8521, Japan
| | - Hiromasa Kurosaki
- College of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyamaku, Nagoya, Aichi 463-8521, Japan.
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Lemskaya NA, Kulemzina AI, Beklemisheva VR, Biltueva LS, Proskuryakova AA, Hallenbeck JM, Perelman PL, Graphodatsky AS. A combined banding method that allows the reliable identification of chromosomes as well as differentiation of AT- and GC-rich heterochromatin. Chromosome Res 2018; 26:307-315. [PMID: 30443803 DOI: 10.1007/s10577-018-9589-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 10/10/2018] [Accepted: 10/11/2018] [Indexed: 02/06/2023]
Abstract
Сonstitutive heterochromatin areas are revealed by differential staining as C-positive chromosomal regions. These C-positive bands may greatly vary by location, size, and nucleotide composition. CBG-banding is the most commonly used method to detect structural heterochromatin in animals. The difficulty in identification of individual chromosomes represents an unresolved problem of this method as the body of the chromosome is stained uniformly and does not have banding pattern beyond C-bands. Here, we present the method that we called CDAG for sequential heterochromatin staining after differential GTG-banding. The method uses G-banding followed by heat denaturation in the presence of formamide with consecutive fluorochrome staining. The new technique is valid for the concurrent revealing of heterochromatin position due to differential banding of chromosomes and heterochromatin composition (AT-/GC-rich) in animal karyotyping.
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Affiliation(s)
- Natalya A Lemskaya
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia.
| | | | | | - Larisa S Biltueva
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Anastasia A Proskuryakova
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - John M Hallenbeck
- Stroke Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NINDS/NIH), Bethesda, MD, USA
| | - Polina L Perelman
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Alexander S Graphodatsky
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
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4
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Shastri N, Tsai YC, Hile S, Jordan D, Powell B, Chen J, Maloney D, Dose M, Lo Y, Anastassiadis T, Rivera O, Kim T, Shah S, Borole P, Asija K, Wang X, Smith KD, Finn D, Schug J, Casellas R, Yatsunyk LA, Eckert KA, Brown EJ. Genome-wide Identification of Structure-Forming Repeats as Principal Sites of Fork Collapse upon ATR Inhibition. Mol Cell 2018; 72:222-238.e11. [PMID: 30293786 DOI: 10.1016/j.molcel.2018.08.047] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 07/11/2018] [Accepted: 08/30/2018] [Indexed: 01/22/2023]
Abstract
DNA polymerase stalling activates the ATR checkpoint kinase, which in turn suppresses fork collapse and breakage. Herein, we describe use of ATR inhibition (ATRi) as a means to identify genomic sites of problematic DNA replication in murine and human cells. Over 500 high-resolution ATR-dependent sites were ascertained using two distinct methods: replication protein A (RPA)-chromatin immunoprecipitation (ChIP) and breaks identified by TdT labeling (BrITL). The genomic feature most strongly associated with ATR dependence was repetitive DNA that exhibited high structure-forming potential. Repeats most reliant on ATR for stability included structure-forming microsatellites, inverted retroelement repeats, and quasi-palindromic AT-rich repeats. Notably, these distinct categories of repeats differed in the structures they formed and their ability to stimulate RPA accumulation and breakage, implying that the causes and character of replication fork collapse under ATR inhibition can vary in a DNA-structure-specific manner. Collectively, these studies identify key sources of endogenous replication stress that rely on ATR for stability.
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Patel A, Yang P, Tinkham M, Pradhan M, Sun MA, Wang Y, Hoang D, Wolf G, Horton JR, Zhang X, Macfarlan T, Cheng X. DNA Conformation Induces Adaptable Binding by Tandem Zinc Finger Proteins. Cell 2018; 173:221-233.e12. [PMID: 29551271 DOI: 10.1016/j.cell.2018.02.058] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 10/24/2017] [Accepted: 02/22/2018] [Indexed: 11/24/2022]
Abstract
Tandem zinc finger (ZF) proteins are the largest and most rapidly diverging family of DNA-binding transcription regulators in mammals. ZFP568 represses a transcript of placental-specific insulin like growth factor 2 (Igf2-P0) in mice. ZFP568 binds a 24-base pair sequence-specific element upstream of Igf2-P0 via the eleven-ZF array. Both DNA and protein conformations deviate from the conventional one finger-three bases recognition, with individual ZFs contacting 2, 3, or 4 bases and recognizing thymine on the opposite strand. These interactions arise from a shortened minor groove caused by an AT-rich stretch, suggesting adaptability of ZF arrays to sequence variations. Despite conservation in mammals, mutations at Igf2 and ZFP568 reduce their binding affinity in chimpanzee and humans. Our studies provide important insights into the evolutionary and structural dynamics of ZF-DNA interactions that play a key role in mammalian development and evolution.
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Affiliation(s)
- Anamika Patel
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA
| | - Peng Yang
- The Eunice Kennedy Shriver National Institutes of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Matthew Tinkham
- The Eunice Kennedy Shriver National Institutes of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Mihika Pradhan
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA
| | - Ming-An Sun
- The Eunice Kennedy Shriver National Institutes of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Yixuan Wang
- The Eunice Kennedy Shriver National Institutes of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Don Hoang
- The Eunice Kennedy Shriver National Institutes of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Gernot Wolf
- The Eunice Kennedy Shriver National Institutes of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - John R Horton
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xing Zhang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Todd Macfarlan
- The Eunice Kennedy Shriver National Institutes of Child Health and Human Development, NIH, Bethesda, MD 20892, USA.
| | - Xiaodong Cheng
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA 30322, USA; Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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Dhatterwal P, Mehrotra S, Mehrotra R. Optimization of PCR conditions for amplifying an AT-rich amino acid transporter promoter sequence with high number of tandem repeats from Arabidopsis thaliana. BMC Res Notes 2017; 10:638. [PMID: 29183338 PMCID: PMC5706289 DOI: 10.1186/s13104-017-2982-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 11/22/2017] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE The aim of the present study is to optimize the PCR conditions required to amplify the promoter sequence of an amino acid transporter having an AT-rich base composition with a high number of tandem repeats. RESULT Results show that successful amplification can be achieved by performing a 2-step PCR at a lower extension temperature of 65 °C for an increased extension period of 1.5 min/kb, with MgCl2 concentration ranging from 2.5 to 3.0 mM. The results also suggest that the DNA concentration of about 25-30 ng/µl was essential to achieve this amplification.
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Affiliation(s)
- Pinky Dhatterwal
- Department of Biological Sciences, Birla Institute of Technology & Sciences, Pilani, Rajasthan, 333031, India
| | - Sandhya Mehrotra
- Department of Biological Sciences, Birla Institute of Technology & Sciences, Pilani, Rajasthan, 333031, India.
| | - Rajesh Mehrotra
- Department of Biological Sciences, Birla Institute of Technology & Sciences, Pilani, Rajasthan, 333031, India.
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7
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Kirti A, Kumar A, Rajaram H. Differential regulation of ssb genes in the nitrogen-fixing cyanobacterium, Anabaena sp. strain PCC7120 1. J Phycol 2017; 53:322-332. [PMID: 28000228 DOI: 10.1111/jpy.12500] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 09/23/2016] [Indexed: 06/06/2023]
Abstract
Anabaena sp. PCC7120 possesses three genes coding for single-stranded DNA-binding (SSB) protein, of which ssb1 was a single gene, and ssb2 and ssb3 are the first genes of their corresponding operons. Regulation of the truncated ssb genes, ssb1 (alr0088) and ssb2 (alr7559), was unaffected by N-status of growth. They were negatively regulated by the SOS-response regulatory protein LexA, as indicated by the (i) binding of Anabaena LexA to the LexA box of regulatory regions of ssb1 and ssb2, and (ii) decreased expression of the downstream gfp reporter gene in Escherichia coli upon co-expression of LexA. However, the full-length ssb gene, ssb3 (all4779), was regulated by the availability of Fe2+ and combined nitrogen, as indicated by (i) increase in the levels of SSB3 protein on Fe2+ -depletion and decrease under Fe2+ -excess conditions, and (ii) 1.5- to 1.6-fold decrease in activity under nitrogen-fixing conditions compared to nitrogen-supplemented conditions. The requirement of Fe2+ as a co-factor for repression by FurA and the increase in levels of FurA under nitrogen-deficient conditions in Anabaena (Lopez-Gomollon et al. 2007) indicated a possible regulation of ssb3 by FurA. This was substantiated by (i) the binding of FurA to the regulatory region of ssb3, (ii) repression of the expression of the downstream gfp reporter gene in E. coli upon co-expression of FurA, and (iii) negative regulation of ssb3 promoter activity by the upstream AT-rich region in Anabaena. This is the first report on possible role of FurA, an important protein for iron homeostasis, in DNA repair of cyanobacteria.
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Affiliation(s)
- Anurag Kirti
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
| | - Arvind Kumar
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
| | - Hema Rajaram
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
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Ricci DP, Melfi MD, Lasker K, Dill DL, McAdams HH, Shapiro L. Cell cycle progression in Caulobacter requires a nucleoid-associated protein with high AT sequence recognition. Proc Natl Acad Sci U S A 2016; 113:E5952-E5961. [PMID: 27647925 PMCID: PMC5056096 DOI: 10.1073/pnas.1612579113] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Faithful cell cycle progression in the dimorphic bacterium Caulobacter crescentus requires spatiotemporal regulation of gene expression and cell pole differentiation. We discovered an essential DNA-associated protein, GapR, that is required for Caulobacter growth and asymmetric division. GapR interacts with adenine and thymine (AT)-rich chromosomal loci, associates with the promoter regions of cell cycle-regulated genes, and shares hundreds of recognition sites in common with known master regulators of cell cycle-dependent gene expression. GapR target loci are especially enriched in binding sites for the transcription factors GcrA and CtrA and overlap with nearly all of the binding sites for MucR1, a regulator that controls the establishment of swarmer cell fate. Despite constitutive synthesis, GapR accumulates preferentially in the swarmer compartment of the predivisional cell. Homologs of GapR, which are ubiquitous among the α-proteobacteria and are encoded on multiple bacteriophage genomes, also accumulate in the predivisional cell swarmer compartment when expressed in Caulobacter The Escherichia coli nucleoid-associated protein H-NS, like GapR, selectively associates with AT-rich DNA, yet it does not localize preferentially to the swarmer compartment when expressed exogenously in Caulobacter, suggesting that recognition of AT-rich DNA is not sufficient for the asymmetric accumulation of GapR. Further, GapR does not silence the expression of H-NS target genes when expressed in E. coli, suggesting that GapR and H-NS have distinct functions. We propose that Caulobacter has co-opted a nucleoid-associated protein with high AT recognition to serve as a mediator of cell cycle progression.
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Affiliation(s)
- Dante P Ricci
- Department of Developmental Biology, Stanford University, Stanford, CA 94305
| | - Michael D Melfi
- Department of Developmental Biology, Stanford University, Stanford, CA 94305; Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Keren Lasker
- Department of Developmental Biology, Stanford University, Stanford, CA 94305
| | - David L Dill
- Department of Computer Science, Stanford University, Stanford, CA 94305
| | - Harley H McAdams
- Department of Developmental Biology, Stanford University, Stanford, CA 94305
| | - Lucy Shapiro
- Department of Developmental Biology, Stanford University, Stanford, CA 94305;
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Abstract
AT-rich repetitive DNA sequences become late replicating during cell differentiation. Replication timing is not correlated with LINE density in human cells (Ryba et al. 2010). However, short and properly spaced runs of oligo dA or dT present in nuclear matrix attachment regions (MARs) of the genome are good candidates for elements of AT-rich repetitive late replicating DNA. MAR attachment to the nuclear matrix is negatively regulated by chromatin binding of H1 histone, but this is counteracted by H1 phosphorylation, high mobility group proteins or, indirectly, core histone acetylation. Fewer MAR attachments correlates positively with longer average DNA loop size, longer replicons and an increase of late replicating DNA.
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Affiliation(s)
- Reed A Flickinger
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, 14260, New York, USA
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Oyola SO, Manske M, Campino S, Claessens A, Hamilton WL, Kekre M, Drury E, Mead D, Gu Y, Miles A, MacInnis B, Newbold C, Berriman M, Kwiatkowski DP. Optimized whole-genome amplification strategy for extremely AT-biased template. DNA Res 2014; 21:661-71. [PMID: 25240466 PMCID: PMC4263299 DOI: 10.1093/dnares/dsu028] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Pathogen genome sequencing directly from clinical samples is quickly gaining importance in genetic and medical research studies. However, low DNA yield from blood-borne pathogens is often a limiting factor. The problem worsens in extremely base-biased genomes such as the AT-rich Plasmodium falciparum. We present a strategy for whole-genome amplification (WGA) of low-yield samples from P. falciparum prior to short-read sequencing. We have developed WGA conditions that incorporate tetramethylammonium chloride for improved amplification and coverage of AT-rich regions of the genome. We show that this method reduces amplification bias and chimera formation. Our data show that this method is suitable for as low as 10 pg input DNA, and offers the possibility of sequencing the parasite genome from small blood samples.
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Affiliation(s)
| | | | | | | | | | - Mihir Kekre
- Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Daniel Mead
- Wellcome Trust Sanger Institute, Hinxton, UK
| | - Yong Gu
- Wellcome Trust Sanger Institute, Hinxton, UK
| | - Alistair Miles
- MRC Centre for Genomics and Global Health, University of Oxford, Oxford OX3 7BN, UK Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Bronwyn MacInnis
- Wellcome Trust Sanger Institute, Hinxton, UK MRC Centre for Genomics and Global Health, University of Oxford, Oxford OX3 7BN, UK
| | - Chris Newbold
- Wellcome Trust Sanger Institute, Hinxton, UK Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | | | - Dominic P Kwiatkowski
- Wellcome Trust Sanger Institute, Hinxton, UK MRC Centre for Genomics and Global Health, University of Oxford, Oxford OX3 7BN, UK Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
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