HSCGD Human Single Cell Genome Database


Current publications of single-cell genomics

IDPublicationBrief InfoDOI (click to view)Project AccessionAmp Method
1Concurrent analysis of genome and transcriptome in one single cell,10.1186/s13104-024-06927-0,"Heid et al., BMC Res Notes(2024)",SRP439158,PCR,2024
2Pre-existing subclones determine radioresistance in rectal cancer organoids,10.1016/j.celrep.2024.113735,"Daan et al., Cell Reports(2024)",SRP459717,PCR,2024
3Tumour Evolution Inferred by Single Cell Sequencing"Navin et al., Nature (2011)"10.1038/nature09807SRP002535DOP-PCR
4Genome-Wide Detection of Single Nucleotide and Copy Number Variations of a Single Human Cell"Zong et al., Science (2012)"10.1126/science.1229164SRP017032MALBAC
5Genome-Wide Single-Cell Analysis of Recombination Activity and de novo Mutation Rates in Human Sperm"Wang et al., Cell (2012)"10.1016/j.cell.2012.06.030SRP013494MDA
6Single-Neuron Sequencing Analysis of L1 Retrotransposition and Somatic Mutation in the Human Brain"Evrony et al., Cell (2012)"10.1016/j.cell.2012.09.035SRP014781MDA
7Probing Meiotic Recombination and Aneuploidy of Single Sperm Cells by Whole-Genome Sequencing"Lu et al., Science (2012)"10.1126/science.1229112SRP017186MALBAC
8Sequencing of isolated sperm cells for direct haplotyping of a human genome"Kirkness et al., Genome Research (2013)"10.1101/gr.144600.112SRP017516MDA
9Reproducible copy number variation patterns among single circulating tumor cells of lung cancer patients"Ni et al., Proceedings of the National Academy of Sciences (2013)"10.1073/pnas.1320659110SRP029757MALBAC
10Genome analyses of single human oocytes"Hou et al., Cell (2013)"10.1016/j.cell.2013.11.040SRP026609MALBAC
11Mosaic copy number variation in human neurons"Mcconnell et al., Science (2013)"10.1126/science.1243472SRP030642"DOP-PCR,MDA"
12A Single Cell Level Based Method for Copy Number Variation Analysis by Low Coverage Massively Parallel Sequencing"Zhang et al., Plos One (2013)"10.1371/journal.pone.0054236SRP016866DOP-PCR
13"Single-Cell, Genome-wide Sequencing Identifies Clonal Somatic Copy-Number Variation in the Human Brain""Cai et al., Cell Reports (2014)"10.1016/j.celrep.2014.07.043SRP051114"DOP-PCR,MDA"
14Clonal Evolution in Breast Cancer Revealed by Single Nucleus Genome Sequencing"Wang et al., Nature (2014)"10.1038/nature13600SRP013572MDA
15Single cell sequencing reveals low levels of aneuploidy across mammalian tissues"Knouse et al., Proceedings of the National Academy of Sciences (2014)"10.1073/pnas.1415287111SRP041670DOP-PCR
16EGFR variant heterogeneity in glioblastoma resolved through single-nucleus sequencing"Francis et al., Cancer discovery(2014)"10.1158/2159-8290.CD-13-0879SRP052627MDA
17Calibrating genomic and allelic coverage bias in single-cell sequencing"Zhang et al., Nature (2015)"10.1038/ncomms7822SRP052954"MDA,MALBAC,DOP-PCR"
17Calibrating genomic and allelic coverage bias in single-cell sequencing"Zhang et al., Nature (2015)"10.1038/ncomms7822SRP052627"MDA,MALBAC,DOP-PCR"
18Uniform and accurate single-cell sequencing based on emulsion whole-genome amplification"Fu et al., Proceedings of the National Academy of Sciences (2015)"10.1073/pnas.1513988112SRP052908"eMDA,MDA,MALBAC,DOP-PCR"
19Cell lineage analysis in human brain using endogenous retroelements"Evrony et al., Neuron (2015)"10.1016/j.neuron.2014.12.028SRP041470MDA
20Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing"Hou et al., Gigascience (2015) "10.1186/s13742-015-0068-3SRP017032"MDA,MALBAC,DOP-PCR"
20Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing"Hou et al., Gigascience (2015) "10.1186/s13742-015-0068-3SRP050588"MDA,MALBAC,DOP-PCR"
21Somatic mutation in single human neurons tracks developmental and transcriptional history"Lodato et al., Science (2015)"10.1126/science.aab1785SRP041470MDA
21Somatic mutation in single human neurons tracks developmental and transcriptional history"Lodato et al., Science (2015)"10.1126/science.aab1785SRP061939MDA
22Optimizing sparse sequencing of single cells for highly multiplex copy number profiling"Baslan et al., Genome Research (2015)"10.1101/gr.188060.114SRP055057DOP-PCR
23Chromothripsis from DNA damage in micronuclei"Zhang et al., Nature (2015)"10.1038/nature14493SRP052954MDA
24Punctuated copy number evolution and clonal stasis in triple-negative breast cancer"Gao et al., Nature Genetics (2016)"10.1038/ng.3641SRP064210DOP-PCR
24Punctuated copy number evolution and clonal stasis in triple-negative breast cancer"Gao et al., Nature Genetics (2016)"10.1038/ng.3641SRP002535DOP-PCR
25Assessment of megabase-scale somatic copy number variation using single-cell sequencing"Knouse et al., Genome Research (2016)"10.1101/gr.198937.115SRP041670DOP-PCR
25Assessment of megabase-scale somatic copy number variation using single-cell sequencing"Knouse et al., Genome Research (2016)"10.1101/gr.198937.115SRP030642DOP-PCR
25Assessment of megabase-scale somatic copy number variation using single-cell sequencing"Knouse et al., Genome Research (2016)"10.1101/gr.198937.115SRP051114DOP-PCR
26Highly multiplexed targeted DNA sequencing from single nuclei"Leung et al., Nature Protocol (2016)"10.1038/nprot.2016.005SRP058890MDA
27Tracing the origin of disseminated tumor cells in breast cancer using single-cell sequencing"Demeulemeester et al., Genome Biology (2016)"10.1186/s13059-016-1109-7EGAS00001002102DOP-PCR
28Accurate identification of single nucleotide variants in whole genome amplified single cells"Dong et al., Nature Methods (2017)"10.1038/nmeth.4227SRP067062"SCMDA,MDA"
29Ultraaccurate genome sequencing and haplotyping of single human cells"Chu et al., Proceedings of the National Academy of Sciences (2017)"10.1073/pnas.1707609114SRP106579MDA
30Multi-region and single-cell sequencing reveal variable genomic heterogeneity in rectal cancer"Liu et al., BMC Cancer (2017)"10.1186/s12885-017-3777-4SRP093555 MALBAC
31Single-cell whole-genome analyses by Linear Amplification via Transposon Insertion (LIANTI)"Chen et al., Science (2017)"10.1126/science.aak9787SRP102259LIANTI
32Single-cell DNA sequencing reveals a late-dissemination model in metastatic colorectal cancer"Leung et al., Genome Research (2017)"10.1101/gr.209973.116SRP074289MDA
33Scalable whole-genome single-cell library preparation without preamplification"Zahn et al., Nature Methods (2017)"10.1038/nmeth.4140EGAS00001002170DLP
34Whole-genome single-cell copy number profiling from formalin-fixed paraffin-embedded samples"Martelotto et al., Nature Medicine (2017)"10.1038/nm.4279SRP008292DOP-PCR
35Sequencing thousands of single-cell genomes with combinatorial indexing"Vitak et al., Nature Methods (2017)"10.1038/nmeth.4154SRP081010DOP-PCR
36Single-cell sequencing deciphers a convergent evolution of copy number alterations from primary to circulating tumor cells"Gao et al., Genome Research (2017)"10.1101/gr.216788.116SRP068920MALBAC
37Spatial Intratumor Genomic Heterogeneity within Localized Prostate Cancer Revealed by Single-nucleus Sequencing"Su et al., European Urology (2018)"10.1016/j.eururo.2018.06.005SRP127755MALBAC
38Multiclonal Invasion in Breast Tumors Identified by Topographic Single Cell Sequencing"Casasent et al., Cell (2018)"10.1016/j.cell.2017.12.007SRP116771DOP-PCR
39Chemoresistance Evolution in Triple-Negative Breast Cancer Delineated by Single-Cell Sequencing"Kim et al., Cell (2018)"10.1016/j.cell.2018.03.041SRP114962DOP-PCR
40Single-cell whole-genome sequencing reveals the functional landscape of somatic mutations in B lymphocytes across the human lifespan"Zhang et al., Proceedings of the National Academy of Sciences (2019)"10.1073/pnas.1902510116SRP219003MDA
41Inferring the Evolution and Progression of Small-Cell Lung Cancer by Single-Cell Sequencing of Circulating Tumor Cells"Su et al., Clinical Cancer Research (2019)"10.1158/1078-0432.CCR-18-3571SRP186739MALBAC
42Clonal Decomposition and DNA Replication States Defined by Scaled Single-Cell Genome Sequencing"Laks et al., Cell (2019)"10.1016/j.cell.2019.10.026EGAS00001003190DLP+
43High-throughput single-cell whole-genome amplification through centrifugal emulsification and eMDA"Fuet al., Communications biology (2019)"10.1038/s42003-019-0401-ySRP188831MiCA-eMDA
44Novel insights into breast cancer copy number genetic heterogeneity revealed by single-cell genome sequencing"Baslan et al., Elife (2020)"10.7554/eLife.51480SRP215441DOP-PCR
45Copolymerization of single-cell nucleic acids into balls of acrylamide gel"Li et al., Genome Research (2020)"10.1101/gr.253047.119SRP222840DOP-PCR
46Mapping replication timing domains genome wide in single mammalian cells with single-cell DNA replication sequencing"Miura et al., Nature Protocols (2020)"10.1038/s41596-020-0378-5SRP224945DOP-PCR
47Single-cell analysis reveals different age-related somatic mutation profiles between stem and differentiated cells in human liver"Brazhnik et al., Science advances (2020)"10.1126/sciadv.aax2659SRP091915MDA
48Accurate genomic variant detection in single cells with primary template-directed amplification"Gonzalez-Pena et al., Proceedings of the National Academy of Sciences (2021)"10.1073/pnas.2024176118SRP178894PTA
49Breast tumours maintain a reservoir of subclonal diversity during expansion"Minussi et al., Nature (2021)"10.1038/s41586-021-03357-xSRP259526ACT
50Accurate SNV detection in single cells by transposon-based whole-genome amplification of complementary strands"Xing et al., Proceedings of the National Academy of Sciences (2021)"10.1073/pnas.2013106118SRP194057META-CS
51Maintenance of genome sequence integrity in long- and short-lived rodent species"Zhang et al., Science advances (2021)"10.1126/sciadv.abj3284SRP345275SCMDA
52Comparison of seven single cell whole genome amplification commercial kits using targeted sequencing"Biezuner et al., Scientific reports (2021)"10.1038/s41598-021-96045-9ERP024468"LA-PCR,MALBAC,DOP-PCR,MDA"
53Single-cell genomic variation induced by mutational processes in cancer"Funnell et al., Nature (2022)"10.1038/s41586-022-05249-0EGAS00001006343DLP+
53Single-cell genomic variation induced by mutational processes in cancer"Funnell et al., Nature (2022)"10.1038/s41586-022-05249-0EGAS00001004448DLP+
53Single-cell genomic variation induced by mutational processes in cancer"Funnell et al., Nature (2022)"10.1038/s41586-022-05249-0EGAS00001003190DLP+
54Single-cell analysis of somatic mutations in human bronchial epithelial cells in relation to aging and smoking"Huang et al., Nature genetics (2022)"10.1038/s41588-022-01035-wSRP366675MDA
55Single-cell analysis of somatic mutation burden in mammary epithelial cells of pathogenic BRCA1/2 mutation carriers"Sun et al., The Journal of clinical investigation (2022)"10.1172/JCI148113SRP320769SCMDA
56"Whole-Genome Amplification-Surveying Yield, Reproducibility, and Heterozygous Balance, Reported by STR-Targeting MIPs""Raz et al., International journal of molecular sciences (2022)"10.3390/ijms23116161ERP137498"MALBAC,DOP-PCR,MDA"
57High-throughput analysis of single human cells reveals the complex nature of DNA replication timing control"Massey et al., Nature communications (2022) "10.1038/s41467-022-30212-ySRP341378"MDA,DLP+"
58Single-cell genome sequencing of human neurons identifies somatic point mutation and indel enrichment in regulatory elements"Luquette et al., Nature genetics (2022)"10.1038/s41588-022-01180-2SRP126192PTA
59Clonal origin and development of high hyperdiploidy in childhood acute lymphoblastic leukaemia"Woodward et al., Nature communications (2023)"10.1038/s41467-023-37356-5EGAS00001006347
60Genetic analysis of heterogeneous subsets of circulating tumour cells from high grade serous ovarian carcinoma patients"Asante et al., Scientific reports (2023)"10.1038/s41598-023-29416-zSRP418207LAPCR
61Archival single-cell genomics reveals persistent subclones during DCIS progression"Wang et al., Cell (2023)"10.1016/j.cell.2023.07.024SRP356287Arc-well
62Digital microfluidics-based digital counting of single-cell copy number variation (dd-scCNV Seq)"Yu et al., Proceedings of the National Academy of Sciences of the United States of America (2023)"10.1073/pnas.2221934120SRP408873dd-scCNV Seq
63"Single-cell whole-genome sequencing, haplotype analysis in prenatal diagnosis of monogenic diseases""Chang et al., Life science alliance (2023)"10.26508/lsa.202201761SRP398595DOP-PCR
64Application of high-throughput single-nucleus DNA sequencing in pancreatic cancer"Zhang et al., Nature communications (2023)"10.1038/s41467-023-36344-zEGAS00001006024snDNA-seq
65Accessible high-throughput single-cell whole-genome sequencing with paired chromatin accessibility"Queitsch et al., Cell reports methods (2023)"10.1016/j.crmeth.2023.100625SRP461548scATAC-seq
66Comprehensive single-cell genome analysis at nucleotide resolution using the PTA Analysis Toolbox"Middelkam et al., Cell genomics (2023)"10.1016/j.xgen.2023.100389EGAS00001007288PTA

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