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Article ; Online: Genetic and Epigenetic Regulation in

Andrews, Jessica L / Zalesky, Andrew / Nair, Shalima / Sullivan, Ryan P / Green, Melissa J / Pantelis, Christos / Newell, Kelly A / Fernandez, Francesca

International journal of molecular sciences

2023 Volume 24, Issue 21

Abstract: Leucine-rich repeat and immunoglobulin domain-containing protein (Lingo-1) plays a vital role in a large number of neuronal processes underlying learning and memory, which are known to be disrupted in schizophrenia. However, Lingo-1 has never been ... ...

Abstract	Leucine-rich repeat and immunoglobulin domain-containing protein (Lingo-1) plays a vital role in a large number of neuronal processes underlying learning and memory, which are known to be disrupted in schizophrenia. However, Lingo-1 has never been examined in the context of schizophrenia. The genetic association of a single-nucleotide polymorphism (SNP, rs3144) and methylation (CpG sites) in the
MeSH term(s)	Humans ; Brain/metabolism ; Case-Control Studies ; Cognition ; Epigenesis, Genetic ; Magnetic Resonance Imaging ; Schizophrenia/diagnostic imaging ; Schizophrenia/genetics ; Schizophrenia/metabolism ; White Matter/pathology ; Nerve Tissue Proteins/genetics
Chemical Substances	LINGO1 protein, human ; Nerve Tissue Proteins
Language	English
Publishing date	2023-10-26
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms242115624
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Article ; Online: Characterisation and reproducibility of the HumanMethylationEPIC v2.0 BeadChip for DNA methylation profiling.

Peters, Timothy J / Meyer, Braydon / Ryan, Lauren / Achinger-Kawecka, Joanna / Song, Jenny / Campbell, Elyssa M / Qu, Wenjia / Nair, Shalima / Loi-Luu, Phuc / Stricker, Phillip / Lim, Elgene / Stirzaker, Clare / Clark, Susan J / Pidsley, Ruth

BMC genomics

2024 Volume 25, Issue 1, Page(s) 251

Abstract: Background: The Illumina family of Infinium Methylation BeadChip microarrays has been widely used over the last 15 years for genome-wide DNA methylation profiling, including large-scale and population-based studies, due to their ease of use and cost ... ...

Abstract	Background: The Illumina family of Infinium Methylation BeadChip microarrays has been widely used over the last 15 years for genome-wide DNA methylation profiling, including large-scale and population-based studies, due to their ease of use and cost effectiveness. Succeeding the popular HumanMethylationEPIC BeadChip (EPICv1), the recently released Infinium MethylationEPIC v2.0 BeadChip (EPICv2) claims to extend genomic coverage to more than 935,000 CpG sites. Here, we comprehensively characterise the reproducibility, reliability and annotation of the EPICv2 array, based on bioinformatic analysis of both manifest data and new EPICv2 data from diverse biological samples. Results: We find a high degree of reproducibility with EPICv1, evidenced by comparable sensitivity and precision from empirical cross-platform comparison incorporating whole genome bisulphite sequencing (WGBS), and high correlation between technical sample replicates, including between samples with DNA input levels below the manufacturer's recommendation. We provide a full assessment of probe content, evaluating genomic distribution and changes from previous array versions. We characterise EPICv2's new feature of replicated probes and provide recommendations as to the superior probes. In silico analysis of probe sequences demonstrates that probe cross-hybridisation remains a significant problem in EPICv2. By mapping the off-target sites at single nucleotide resolution and comparing with WGBS we show empirical evidence for preferential off-target binding. Conclusions: Overall, we find EPICv2 a worthy successor to the previous Infinium methylation microarrays, however some technical issues remain. To support optimal EPICv2 data analysis we provide an expanded version of the EPICv2 manifest to aid researchers in understanding probe design, data processing, choosing appropriate probes for analysis and for integration with methylation datasets from previous versions of the Infinium Methylation BeadChip.
MeSH term(s)	DNA Methylation ; Reproducibility of Results ; Computational Biology ; Data Analysis ; Sulfites
Chemical Substances	hydrogen sulfite (OJ9787WBLU) ; Sulfites
Language	English
Publishing date	2024-03-06
Publishing country	England
Document type	Journal Article
ZDB-ID	2041499-7
ISSN	1471-2164 ; 1471-2164
ISSN (online)	1471-2164
ISSN	1471-2164
DOI	10.1186/s12864-024-10027-5
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Article ; Online: The potential of epigenetic therapy to target the 3D epigenome in endocrine-resistant breast cancer.

Achinger-Kawecka, Joanna / Stirzaker, Clare / Portman, Neil / Campbell, Elyssa / Chia, Kee-Ming / Du, Qian / Laven-Law, Geraldine / Nair, Shalima S / Yong, Aliza / Wilkinson, Ashleigh / Clifton, Samuel / Milioli, Heloisa H / Alexandrou, Sarah / Caldon, C Elizabeth / Song, Jenny / Khoury, Amanda / Meyer, Braydon / Chen, Wenhan / Pidsley, Ruth /

Qu, Wenjia / Gee, Julia M W / Schmitt, Anthony / Wong, Emily S / Hickey, Theresa E / Lim, Elgene / Clark, Susan J

Nature structural & molecular biology

2024 Volume 31, Issue 3, Page(s) 498–512

Abstract: Three-dimensional (3D) epigenome remodeling is an important mechanism of gene deregulation in cancer. However, its potential as a target to counteract therapy resistance remains largely unaddressed. Here, we show that epigenetic therapy with decitabine ( ... ...

Abstract	Three-dimensional (3D) epigenome remodeling is an important mechanism of gene deregulation in cancer. However, its potential as a target to counteract therapy resistance remains largely unaddressed. Here, we show that epigenetic therapy with decitabine (5-Aza-mC) suppresses tumor growth in xenograft models of pre-clinical metastatic estrogen receptor positive (ER+) breast tumor. Decitabine-induced genome-wide DNA hypomethylation results in large-scale 3D epigenome deregulation, including de-compaction of higher-order chromatin structure and loss of boundary insulation of topologically associated domains. Significant DNA hypomethylation associates with ectopic activation of ER-enhancers, gain in ER binding, creation of new 3D enhancer-promoter interactions and concordant up-regulation of ER-mediated transcription pathways. Importantly, long-term withdrawal of epigenetic therapy partially restores methylation at ER-enhancer elements, resulting in a loss of ectopic 3D enhancer-promoter interactions and associated gene repression. Our study illustrates the potential of epigenetic therapy to target ER+ endocrine-resistant breast cancer by DNA methylation-dependent rewiring of 3D chromatin interactions, which are associated with the suppression of tumor growth.
MeSH term(s)	Humans ; Female ; Breast Neoplasms/drug therapy ; Breast Neoplasms/genetics ; Breast Neoplasms/pathology ; Decitabine/pharmacology ; Decitabine/therapeutic use ; Decitabine/metabolism ; Epigenome ; DNA Methylation/genetics ; Chromatin ; Epigenesis, Genetic ; DNA/metabolism ; Gene Expression Regulation, Neoplastic
Chemical Substances	Decitabine (776B62CQ27) ; Chromatin ; DNA (9007-49-2)
Language	English
Publishing date	2024-01-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	2126708-X
ISSN	1545-9985 ; 1545-9993
ISSN (online)	1545-9985
ISSN	1545-9993
DOI	10.1038/s41594-023-01181-7
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Article ; Online: Comprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA.

Skvortsova, Ksenia / Zotenko, Elena / Luu, Phuc-Loi / Gould, Cathryn M / Nair, Shalima S / Clark, Susan J / Stirzaker, Clare

Epigenetics & chromatin

2017 Volume 10, Page(s) 16

Abstract: Background: The discovery that 5-methylcytosine (5mC) can be oxidized to 5-hydroxymethylcytosine (5hmC) by the ten-eleven translocation (TET) proteins has prompted wide interest in the potential role of 5hmC in reshaping the mammalian DNA methylation ... ...

Abstract	Background: The discovery that 5-methylcytosine (5mC) can be oxidized to 5-hydroxymethylcytosine (5hmC) by the ten-eleven translocation (TET) proteins has prompted wide interest in the potential role of 5hmC in reshaping the mammalian DNA methylation landscape. The gold-standard bisulphite conversion technologies to study DNA methylation do not distinguish between 5mC and 5hmC. However, new approaches to mapping 5hmC genome-wide have advanced rapidly, although it is unclear how the different methods compare in accurately calling 5hmC. In this study, we provide a comparative analysis on brain DNA using three 5hmC genome-wide approaches, namely whole-genome bisulphite/oxidative bisulphite sequencing (WG Bis/OxBis-seq), Infinium HumanMethylation450 BeadChip arrays coupled with oxidative bisulphite (HM450K Bis/OxBis) and antibody-based immunoprecipitation and sequencing of hydroxymethylated DNA (hMeDIP-seq). We also perform loci-specific TET-assisted bisulphite sequencing (TAB-seq) for validation of candidate regions. Results: We show that whole-genome single-base resolution approaches are advantaged in providing precise 5hmC values but require high sequencing depth to accurately measure 5hmC, as this modification is commonly in low abundance in mammalian cells. HM450K arrays coupled with oxidative bisulphite provide a cost-effective representation of 5hmC distribution, at CpG sites with 5hmC levels >~10%. However, 5hmC analysis is restricted to the genomic location of the probes, which is an important consideration as 5hmC modification is commonly enriched at enhancer elements. Finally, we show that the widely used hMeDIP-seq method provides an efficient genome-wide profile of 5hmC and shows high correlation with WG Bis/OxBis-seq 5hmC distribution in brain DNA. However, in cell line DNA with low levels of 5hmC, hMeDIP-seq-enriched regions are not detected by WG Bis/OxBis or HM450K, either suggesting misinterpretation of 5hmC calls by hMeDIP or lack of sensitivity of the latter methods. Conclusions: We highlight both the advantages and caveats of three commonly used genome-wide 5hmC profiling technologies and show that interpretation of 5hmC data can be significantly influenced by the sensitivity of methods used, especially as the levels of 5hmC are low and vary in different cell types and different genomic locations.
Language	English
Publishing date	2017
Publishing country	England
Document type	Journal Article
ZDB-ID	2462129-8
ISSN	1756-8935 ; 1756-8935
ISSN (online)	1756-8935
ISSN	1756-8935
DOI	10.1186/s13072-017-0123-7
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Article ; Online: Evaluation of cross-platform and interlaboratory concordance via consensus modelling of genomic measurements

Peters, Timothy J. / French, Hugh J. / Bradford, Stephen T. / Pidsley, Ruth / Stirzaker, Clare / Varinli, Hilal / Nair, Shalima / Qu, Wenjia / Song, Jenny / Giles, Katherine A. / Statham, Aaron L. / Speirs, Helen / Speed, Terence P. / Clark, Susan J.

Bioinformatics. 2019 Feb. 15, v. 35, no. 4, p. 560-570

2019 , Page(s) 560–570

Abstract: A synoptic view of the human genome benefits chiefly from the application of nucleic acid sequencing and microarray technologies. These platforms allow interrogation of patterns such as gene expression and DNA methylation at the vast majority of ... ...

Abstract	A synoptic view of the human genome benefits chiefly from the application of nucleic acid sequencing and microarray technologies. These platforms allow interrogation of patterns such as gene expression and DNA methylation at the vast majority of canonical loci, allowing granular insights and opportunities for validation of original findings. However, problems arise when validating against a “gold standard” measurement, since this immediately biases all subsequent measurements towards that particular technology or protocol. Since all genomic measurements are estimates, in the absence of a ”gold standard” we instead empirically assess the measurement precision and sensitivity of a large suite of genomic technologies via a consensus modelling method called the row-linear model. This method is an application of the American Society for Testing and Materials Standard E691 for assessing interlaboratory precision and sources of variability across multiple testing sites. Both cross-platform and cross-locus comparisons can be made across all common loci, allowing identification of technology- and locus-specific tendencies. We assess technologies including the Infinium MethylationEPIC BeadChip, whole genome bisulfite sequencing (WGBS), two different RNA-Seq protocols (PolyA+ and Ribo-Zero) and five different gene expression array platforms. Each technology thus is characterised herein, relative to the consensus. We showcase a number of applications of the row-linear model, including correlation with known interfering traits. We demonstrate a clear effect of cross-hybridisation on the sensitivity of Infinium methylation arrays. Additionally, we perform a true interlaboratory test on a set of samples interrogated on the same platform across twenty-one separate testing laboratories. A full implementation of the row-linear model, plus extra functions for visualisation, are found in the R package consensus at https://github.com/timpeters82/consensus. Supplementary data are available at Bioinformatics online.
Keywords	DNA methylation ; bioinformatics ; bisulfites ; gene expression ; genome ; genomics ; humans ; microarray technology ; models ; nucleic acids ; sequence analysis
Language	English
Dates of publication	2019-0215
Size	p. 560-570
Publishing place	Oxford University Press
Document type	Article ; Online
Note	Use and reproduction
ZDB-ID	1468345-3
ISSN	1367-4811 ; 1460-2059
ISSN	1367-4811 ; 1460-2059
DOI	10.1093/bioinformatics/bty675
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Article ; Online: Replication timing and epigenome remodelling are associated with the nature of chromosomal rearrangements in cancer.

Du, Qian / Bert, Saul A / Armstrong, Nicola J / Caldon, C Elizabeth / Song, Jenny Z / Nair, Shalima S / Gould, Cathryn M / Luu, Phuc-Loi / Peters, Timothy / Khoury, Amanda / Qu, Wenjia / Zotenko, Elena / Stirzaker, Clare / Clark, Susan J

Nature communications

2019 Volume 10, Issue 1, Page(s) 416

Abstract: DNA replication timing is known to facilitate the establishment of the epigenome, however, the intimate connection between replication timing and changes to the genome and epigenome in cancer remain largely uncharacterised. Here, we perform Repli-Seq and ...

Abstract	DNA replication timing is known to facilitate the establishment of the epigenome, however, the intimate connection between replication timing and changes to the genome and epigenome in cancer remain largely uncharacterised. Here, we perform Repli-Seq and integrated epigenome analyses and demonstrate that genomic regions that undergo long-range epigenetic deregulation in prostate cancer also show concordant differences in replication timing. A subset of altered replication timing domains are conserved across cancers from different tissue origins. Notably, late-replicating regions in cancer cells display a loss of DNA methylation, and a switch in heterochromatin features from H3K9me3-marked constitutive to H3K27me3-marked facultative heterochromatin. Finally, analysis of 214 prostate and 35 breast cancer genomes reveal that late-replicating regions are prone to cis and early-replication to trans chromosomal rearrangements. Together, our data suggests that the nature of chromosomal rearrangement in cancer is related to the spatial and temporal positioning and altered epigenetic states of early-replicating compared to late-replicating loci.
MeSH term(s)	Breast Neoplasms ; Cell Line, Tumor ; Chromosome Aberrations ; DNA Methylation ; DNA Replication ; DNA Replication Timing/physiology ; Deoxyribonuclease I/analysis ; Epigenesis, Genetic/physiology ; Epigenomics ; Female ; Gene Expression Regulation, Neoplastic ; Genome ; Genomics ; Heterochromatin ; Humans ; Male ; Neoplasms/genetics ; Prostatic Neoplasms ; Whole Genome Sequencing
Chemical Substances	Heterochromatin ; DNASE1 protein, human (EC 3.1.21.1) ; Deoxyribonuclease I (EC 3.1.21.1)
Language	English
Publishing date	2019-01-24
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-019-08302-1
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Article: Widespread Aberrant Alternative Splicing despite Molecular Remission in Chronic Myeloid Leukaemia Patients.

Schmitz, Ulf / Shah, Jaynish S / Dhungel, Bijay P / Monteuuis, Geoffray / Luu, Phuc-Loi / Petrova, Veronika / Metierre, Cynthia / Nair, Shalima S / Bailey, Charles G / Saunders, Verity A / Turhan, Ali G / White, Deborah L / Branford, Susan / Clark, Susan J / Hughes, Timothy P / Wong, Justin J-L / Rasko, John E J

Cancers

2020 Volume 12, Issue 12

Abstract: Vast transcriptomics and epigenomics changes are characteristic of human cancers, including leukaemia. At remission, we assume that these changes normalise so that omics-profiles resemble those of healthy individuals. However, an in-depth transcriptomic ... ...

Abstract	Vast transcriptomics and epigenomics changes are characteristic of human cancers, including leukaemia. At remission, we assume that these changes normalise so that omics-profiles resemble those of healthy individuals. However, an in-depth transcriptomic and epigenomic analysis of cancer remission has not been undertaken. A striking exemplar of targeted remission induction occurs in chronic myeloid leukaemia (CML) following tyrosine kinase inhibitor (TKI) therapy. Using RNA sequencing and whole-genome bisulfite sequencing, we profiled samples from chronic-phase CML patients at diagnosis and remission and compared these to healthy donors. Remarkably, our analyses revealed that abnormal splicing distinguishes remission samples from normal controls. This phenomenon is independent of the TKI drug used and in striking contrast to the normalisation of gene expression and DNA methylation patterns. Most remarkable are the high intron retention (IR) levels that even exceed those observed in the diagnosis samples. Increased IR affects cell cycle regulators at diagnosis and splicing regulators at remission. We show that aberrant splicing in CML is associated with reduced expression of specific splicing factors, histone modifications and reduced DNA methylation. Our results provide novel insights into the changing transcriptomic and epigenomic landscapes of CML patients during remission. The conceptually unanticipated observation of widespread aberrant alternative splicing after remission induction warrants further exploration. These results have broad implications for studying CML relapse and treating minimal residual disease.
Language	English
Publishing date	2020-12-11
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2527080-1
ISSN	2072-6694
ISSN	2072-6694
DOI	10.3390/cancers12123738
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Article ; Online: Macrophage development and activation involve coordinated intron retention in key inflammatory regulators.

Green, Immanuel D / Pinello, Natalia / Song, Renhua / Lee, Quintin / Halstead, James M / Kwok, Chau-To / Wong, Alex C H / Nair, Shalima S / Clark, Susan J / Roediger, Ben / Schmitz, Ulf / Larance, Mark / Hayashi, Rippei / Rasko, John E J / Wong, Justin J-L

Nucleic acids research

2020 Volume 48, Issue 12, Page(s) 6513–6529

Abstract: Monocytes and macrophages are essential components of the innate immune system. Herein, we report that intron retention (IR) plays an important role in the development and function of these cells. Using Illumina mRNA sequencing, Nanopore direct cDNA ... ...

Abstract	Monocytes and macrophages are essential components of the innate immune system. Herein, we report that intron retention (IR) plays an important role in the development and function of these cells. Using Illumina mRNA sequencing, Nanopore direct cDNA sequencing and proteomics analysis, we identify IR events that affect the expression of key genes/proteins involved in macrophage development and function. We demonstrate that decreased IR in nuclear-detained mRNA is coupled with increased expression of genes encoding regulators of macrophage transcription, phagocytosis and inflammatory signalling, including ID2, IRF7, ENG and LAT. We further show that this dynamic IR program persists during the polarisation of resting macrophages into activated macrophages. In the presence of proinflammatory stimuli, intron-retaining CXCL2 and NFKBIZ transcripts are rapidly spliced, enabling timely expression of these key inflammatory regulators by macrophages. Our study provides novel insights into the molecular factors controlling vital regulators of the innate immune response.
MeSH term(s)	Adaptor Proteins, Signal Transducing/genetics ; Adaptor Proteins, Signal Transducing/metabolism ; Cells, Cultured ; Chemokine CXCL2/genetics ; Chemokine CXCL2/metabolism ; Endoglin/genetics ; Endoglin/metabolism ; Humans ; Inhibitor of Differentiation Protein 2/genetics ; Inhibitor of Differentiation Protein 2/metabolism ; Interferon Regulatory Factor-7/genetics ; Interferon Regulatory Factor-7/metabolism ; Introns ; Macrophage Activation ; Macrophages/immunology ; Membrane Proteins/genetics ; Membrane Proteins/metabolism ; RNA Splicing ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; THP-1 Cells
Chemical Substances	Adaptor Proteins, Signal Transducing ; CXCL2 protein, human ; Chemokine CXCL2 ; ENG protein, human ; Endoglin ; ID2 protein, human ; IRF7 protein, human ; Inhibitor of Differentiation Protein 2 ; Interferon Regulatory Factor-7 ; LAT protein, human ; Membrane Proteins ; NFKBIZ protein, human ; RNA, Messenger
Language	English
Publishing date	2020-05-25
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkaa435
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Article ; Online: DNA methylation is required to maintain both DNA replication timing precision and 3D genome organization integrity.

Du, Qian / Smith, Grady C / Luu, Phuc Loi / Ferguson, James M / Armstrong, Nicola J / Caldon, C Elizabeth / Campbell, Elyssa M / Nair, Shalima S / Zotenko, Elena / Gould, Cathryn M / Buckley, Michael / Chia, Kee-Ming / Portman, Neil / Lim, Elgene / Kaczorowski, Dominik / Chan, Chia-Ling / Barton, Kirston / Deveson, Ira W / Smith, Martin A /

Powell, Joseph E / Skvortsova, Ksenia / Stirzaker, Clare / Achinger-Kawecka, Joanna / Clark, Susan J

Cell reports

2021 Volume 36, Issue 12, Page(s) 109722

Abstract: DNA replication timing and three-dimensional (3D) genome organization are associated with distinct epigenome patterns across large domains. However, whether alterations in the epigenome, in particular cancer-related DNA hypomethylation, affects higher- ... ...

Abstract	DNA replication timing and three-dimensional (3D) genome organization are associated with distinct epigenome patterns across large domains. However, whether alterations in the epigenome, in particular cancer-related DNA hypomethylation, affects higher-order levels of genome architecture is still unclear. Here, using Repli-Seq, single-cell Repli-Seq, and Hi-C, we show that genome-wide methylation loss is associated with both concordant loss of replication timing precision and deregulation of 3D genome organization. Notably, we find distinct disruption in 3D genome compartmentalization, striking gains in cell-to-cell replication timing heterogeneity and loss of allelic replication timing in cancer hypomethylation models, potentially through the gene deregulation of DNA replication and genome organization pathways. Finally, we identify ectopic H3K4me3-H3K9me3 domains from across large hypomethylated domains, where late replication is maintained, which we purport serves to protect against catastrophic genome reorganization and aberrant gene transcription. Our results highlight a potential role for the methylome in the maintenance of 3D genome regulation.
Language	English
Publishing date	2021-10-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2021.109722
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Article ; Online: Evaluation of cross-platform and interlaboratory concordance via consensus modelling of genomic measurements.

Peters, Timothy J / French, Hugh J / Bradford, Stephen T / Pidsley, Ruth / Stirzaker, Clare / Varinli, Hilal / Nair, Shalima / Qu, Wenjia / Song, Jenny / Giles, Katherine A / Statham, Aaron L / Speirs, Helen / Speed, Terence P / Clark, Susan J

Bioinformatics (Oxford, England)

2018 Volume 35, Issue 4, Page(s) 560–570

Abstract: Motivation: A synoptic view of the human genome benefits chiefly from the application of nucleic acid sequencing and microarray technologies. These platforms allow interrogation of patterns such as gene expression and DNA methylation at the vast ... ...

Abstract	Motivation: A synoptic view of the human genome benefits chiefly from the application of nucleic acid sequencing and microarray technologies. These platforms allow interrogation of patterns such as gene expression and DNA methylation at the vast majority of canonical loci, allowing granular insights and opportunities for validation of original findings. However, problems arise when validating against a "gold standard" measurement, since this immediately biases all subsequent measurements towards that particular technology or protocol. Since all genomic measurements are estimates, in the absence of a "gold standard" we instead empirically assess the measurement precision and sensitivity of a large suite of genomic technologies via a consensus modelling method called the row-linear model. This method is an application of the American Society for Testing and Materials Standard E691 for assessing interlaboratory precision and sources of variability across multiple testing sites. Both cross-platform and cross-locus comparisons can be made across all common loci, allowing identification of technology- and locus-specific tendencies. Results: We assess technologies including the Infinium MethylationEPIC BeadChip, whole genome bisulfite sequencing (WGBS), two different RNA-Seq protocols (PolyA+ and Ribo-Zero) and five different gene expression array platforms. Each technology thus is characterised herein, relative to the consensus. We showcase a number of applications of the row-linear model, including correlation with known interfering traits. We demonstrate a clear effect of cross-hybridisation on the sensitivity of Infinium methylation arrays. Additionally, we perform a true interlaboratory test on a set of samples interrogated on the same platform across twenty-one separate testing laboratories. Availability and implementation: A full implementation of the row-linear model, plus extra functions for visualisation, are found in the R package consensus at https://github.com/timpeters82/consensus. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Computational Biology ; DNA Methylation ; Genome, Human ; Genomics ; Humans ; Oligonucleotide Array Sequence Analysis ; Software
Language	English
Publishing date	2018-07-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/bty675
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