EGAD00001006459
Bottleneck sequencing of human tissue including neurons, cord blood, sperm.
This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ .
This dataset contains all the data available for this study on 2020-10-20.
HiSeq X Ten
Illumina HiSeq 2500
Illumina HiSeq 4000
Illumina NovaSeq 6000
194
EGAD00001007958
Cellular DNA damage caused by reactive oxygen species is repaired by the base excision repair (BER) pathway which includes the DNA glycosylase MUTYH. Inherited biallelic MUTYH mutations cause predisposition to colorectal adenomas and carcinoma. However, the mechanistic progression from germline MUTYH mutations to MUTYH-Associated Polyposis (MAP) is incompletely understood. Here, we sequenced normal cell DNAs from 10 individuals with MAP and study the somatic mutation burden and mutational signatures.
Illumina NovaSeq 6000
210
EGAD00001007997
Cellular DNA damage caused by reactive oxygen species is repaired by the base excision repair (BER) pathway which includes the DNA glycosylase MUTYH. Inherited biallelic MUTYH mutations cause predisposition to colorectal adenomas and carcinoma. However, the mechanistic progression from germline MUTYH mutations to MUTYH-Associated Polyposis (MAP) is incompletely understood. Here, we sequenced normal cell DNAs from 10 individuals with MAP and study the somatic mutation burden and mutational signatures.
Illumina NovaSeq 6000
31
EGAD00001015455
Primary human cells cultured in organoid format have great promise as potential regenerative cellular therapies. However, their immunogenicity and mutagenic profile remain unresolved, impeding effective long-term translation to the clinic. In this study we report, for the first time, the generation of human leukocyte antigen (HLA)-I and HLA-II knock-out human expandable primary cholangiocyte organoids (PCOs) using CRISPR-Cas9 as a potential ‘universal’ low-immunogenic therapy for bile duct disorders. HLA-edited PCOs (ePCOs) displayed the same phenotypic and functional characteristics as parental unedited PCOs. Despite minimal off-target edits, duplex sequencing approaches demonstrated that ePCOs and PCOs acquire mutations in culture at similar rates, but without evident selection for cancer-driver mutations. ePCOs induced reduced T cell-mediated immunity and donor-dependent NK cell cytotoxicity in vitro and evaded cytotoxic responses with increased graft survival in humanized mice in vivo. Our findings have important implications for assessment of safety and immunogenicity of primary cell-derived organoid cellular therapies.
Illumina NovaSeq 6000
6
EGAD00001015624
Bottleneck sequencing of human tissue including neurons, cord blood, sperm
This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/. As we age, many tissues become colonised by microscopic clones carrying somatic driver mutations. Some of these clones represent a first step towards cancer whereas others may contribute to ageing and other diseases. However, our understanding of the clonal landscapes of human tissues, and their impact on cancer risk, ageing and disease, remains limited due to the challenge of detecting somatic mutations present in small numbers of cells. Here, we introduce a new version of nanorate sequencing (NanoSeq), a duplex sequencing method with error rates of less than 5 per billion base pairs, which is compatible with whole-exome and targeted gene sequencing. Deep sequencing of polyclonal samples with single-molecule sensitivity enables the simultaneous detection of mutations in large numbers of clones, yielding accurate somatic mutation rates, mutational signatures and driver mutation frequencies in any tissue. Applying targeted NanoSeq to 1,042 non-invasive samples of oral epithelium and 371 samples of blood from a twin cohort, we found an unprecedentedly rich landscape of selection, with 46 genes under positive selection driving clonal expansions in the oral epithelium, over 62,000 driver mutations, and evidence of negative selection in some genes. The high number of positively selected mutations in multiple genes provides high-resolution maps of selection across coding and non-coding sites, a form of in vivo saturation mutagenesis. Multivariate regression models enable mutational epidemiology studies on how carcinogenic exposures and cancer risk factors, such as age, tobacco or alcohol, alter the acquisition and selection of somatic mutations. Accurate single-molecule sequencing has the potential to unveil the polyclonal landscape of any tissue, providing a powerful tool to study early carcinogenesis, cancer prevention and the role of somatic mutations in ageing and disease.
Illumina NovaSeq 6000
32
EGAD00001016070
Mutations accumulate in normal human cells over the course of an individual’s lifetime. Early studies have shown differences in mutation rates and mutational signatures between cell types, but the range of tissues investigated has been constrained by limitations of DNA sequencing technologies. Here, we employ genome-wide NanoSeq single molecule duplex sequencing to survey the mutation landscapes of 53 normal cell types and tissue structures purified by laser-capture microdissection and flow sorting. Single base substitution mutation rates ranged from ~3/year in spermatogonia and sperm contributing to the male germline, to ~20/year in postmitotic neurons, ~50/year in mitotically active colorectal epithelial cells, ~60/year in kidney proximal tubule cells and hepatocytes, 100s/year in ultraviolet light exposed skin epidermis and from 10-50/year across the other cell types. At least 18 single base substitution and 9 small insertion and deletion mutational signatures contribute to mutation burdens, some to all cell types, some to subsets of cell types and others to a single cell type. Known exogenous mutagen exposures and endogenous mutational processes account for some mutational signatures but the origins and mechanisms underlying many are uncertain. This comprehensive survey of mutagenesis provides a foundation for understanding somatic evolution in human cell populations in health and disease.
Illumina NovaSeq 6000
790
EGAD00001016803
Mutations accumulate in normal human cells over the course of an individual’s lifetime. Early studies have shown differences in mutation rates and mutational signatures between cell types, but the range of tissues investigated has been constrained by limitations of DNA sequencing technologies. Here, we employ genome-wide NanoSeq single molecule duplex sequencing to survey the mutation landscapes of 53 normal cell types and tissue structures purified by laser-capture microdissection and flow sorting. Single base substitution mutation rates ranged from ~3/year in spermatogonia and sperm contributing to the male germline, to ~20/year in postmitotic neurons, ~50/year in mitotically active colorectal epithelial cells, ~60/year in kidney proximal tubule cells and hepatocytes, 100s/year in ultraviolet light exposed skin epidermis and from 10-50/year across the other cell types. At least 18 single base substitution and 9 small insertion and deletion mutational signatures contribute to mutation burdens, some to all cell types, some to subsets of cell types and others to a single cell type. Known exogenous mutagen exposures and endogenous mutational processes account for some mutational signatures but the origins and mechanisms underlying many are uncertain. This comprehensive survey of mutagenesis provides a foundation for understanding somatic evolution in human cell populations in health and disease.
Illumina NovaSeq 6000
1
EGAD00001016809
Mutations accumulate in normal human cells over the course of an individual’s lifetime. Early studies have shown differences in mutation rates and mutational signatures between cell types, but the range of tissues investigated has been constrained by limitations of DNA sequencing technologies. Here, we employ genome-wide NanoSeq single molecule duplex sequencing to survey the mutation landscapes of 53 normal cell types and tissue structures purified by laser-capture microdissection and flow sorting. Single base substitution mutation rates ranged from ~3/year in spermatogonia and sperm contributing to the male germline, to ~20/year in postmitotic neurons, ~50/year in mitotically active colorectal epithelial cells, ~60/year in kidney proximal tubule cells and hepatocytes, 100s/year in ultraviolet light exposed skin epidermis and from 10-50/year across the other cell types. At least 18 single base substitution and 9 small insertion and deletion mutational signatures contribute to mutation burdens, some to all cell types, some to subsets of cell types and others to a single cell type. Known exogenous mutagen exposures and endogenous mutational processes account for some mutational signatures but the origins and mechanisms underlying many are uncertain. This comprehensive survey of mutagenesis provides a foundation for understanding somatic evolution in human cell populations in health and disease.
HiSeq X Ten
Illumina NovaSeq 6000
6
