Study

Clonal Decomposition and DNA Replication States Defined by Scaled Single-Cell Genome Sequencing

Study ID Alternative Stable ID Type
EGAS00001003190 Other

Study Description

Accurate measurement of clonal genotypes, mutational processes, and replication states from individual tumor-cell genomes will facilitate improved understanding of tumor evolution. We have developed DLP+, a scalable single-cell whole-genome sequencing platform implemented using commodity instruments, image-based object recognition, and open source computational methods. Using DLP+, we have generated a resource of 51,926 single-cell genomes and matched cell images from diverse cell types including cell lines, xenografts, and diagnostic samples with limited material. From this resource we have defined variation in mitotic mis-segregation rates across tissue types and genotypes. Analysis of matched genomic and image measurements revealed correlations between cellular morphology and genome ploidy states. Aggregation of cells sharing copy number profiles allowed for calculation of single-nucleotide resolution clonal genotypes and inference of clonal phylogenies and avoided the limitations of bulk deconvolution. Finally, joint analysis over the above features defined clone-specific ... (Show More)

Study Datasets 62 datasets.

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID Description Technology Samples
EGAD00001004553
Direct library preparation+ single-cell DNA-sequencing of (i) patient derived triple negative breast cancer xenograft (ii) primary tumour and ascites ovarian cancer cell lines at tumour recurrence.
Illumina HiSeq 2500 980
EGAD00001004719
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 1340 samples; filetype=bam
Illumina HiSeq 2500 1340
EGAD00001004720
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 2057 samples; filetype=bam
Illumina HiSeq 2500 2057
EGAD00001004721
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 1970 samples; filetype=bam
Illumina HiSeq 2500 1970
EGAD00001004722
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 2091 samples; filetype=bam
Illumina HiSeq 2500 2091
EGAD00001004723
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 1267 samples; filetype=bam
Illumina HiSeq 2500 1267
EGAD00001004724
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 230 samples; filetype=bam
Illumina HiSeq 2500 230
EGAD00001004725
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 232 samples; filetype=bam
Illumina HiSeq 2500 232
EGAD00001004726
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 239 samples; filetype=bam
Illumina HiSeq 2500 239
EGAD00001004727
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 692 samples; filetype=bam
Illumina HiSeq 2500 692
EGAD00001004728
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 612 samples; filetype=bam
Illumina HiSeq 2500 612
EGAD00001004729
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 1700 samples; filetype=bam
Illumina HiSeq 2500 1700
EGAD00001004730
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 628 samples; filetype=bam
Illumina HiSeq 2500 628
EGAD00001004731
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 596 samples; filetype=bam
Illumina HiSeq 2500 596
EGAD00001004732
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 1735 samples; filetype=bam
Illumina HiSeq 2500 1735
EGAD00001004733
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 585 samples; filetype=bam
NextSeq 550 585
EGAD00001004734
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 766 samples; filetype=bam
NextSeq 550 766
EGAD00001004735
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 2055 samples; filetype=bam
Illumina HiSeq 2500 2055
EGAD00001004736
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 620 samples; filetype=bam
Illumina HiSeq 2500 620
EGAD00001004737
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 624 samples; filetype=bam
NextSeq 550 624
EGAD00001004738
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 481 samples; filetype=bam
NextSeq 550 481
EGAD00001004739
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 378 samples; filetype=bam
Illumina HiSeq 2500 378
EGAD00001004740
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 735 samples; filetype=bam
Illumina HiSeq 2500 735
EGAD00001004741
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 718 samples; filetype=bam
Illumina HiSeq 2500 718
EGAD00001004742
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 493 samples; filetype=bam
NextSeq 550 493
EGAD00001004743
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 1222 samples; filetype=bam
Illumina HiSeq 2500 1222
EGAD00001004744
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 522 samples; filetype=bam
Illumina HiSeq 2500 522
EGAD00001004745
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 488 samples; filetype=bam
Illumina HiSeq 2500 488
EGAD00001004746
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 509 samples; filetype=bam
NextSeq 550 509
EGAD00001004747
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 604 samples; filetype=bam
NextSeq 550 604
EGAD00001004748
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 626 samples; filetype=bam
NextSeq 550 626
EGAD00001004749
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 635 samples; filetype=bam
Illumina HiSeq 2500 635
EGAD00001004750
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 1522 samples; filetype=bam
HiSeq X Five 1522
EGAD00001004751
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 465 samples; filetype=bam
NextSeq 550 465
EGAD00001004752
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 606 samples; filetype=bam
Illumina HiSeq 2500 606
EGAD00001004753
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 615 samples; filetype=bam
NextSeq 550 615
EGAD00001004754
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 636 samples; filetype=bam
NextSeq 550 636
EGAD00001004755
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 968 samples; filetype=bam
HiSeq X Five 968
EGAD00001004756
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 480 samples; filetype=bam
NextSeq 550 480
EGAD00001004757
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 561 samples; filetype=bam
NextSeq 550 561
EGAD00001004758
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 844 samples; filetype=bam
HiSeq X Five 844
EGAD00001004759
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 928 samples; filetype=bam
HiSeq X Five 928
EGAD00001004760
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 635 samples
HiSeq X Five 635
EGAD00001004761
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 1072 samples
HiSeq X Five 1072
EGAD00001004762
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 1436 samples; filetype=bam
HiSeq X Five 1436
EGAD00001004763
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 589 samples; filetype=bam
HiSeq X Five 589
EGAD00001004764
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 656 samples; filetype=bam
HiSeq X Five 656
EGAD00001004765
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 648 samples; filetype=bam
HiSeq X Five 648
EGAD00001004766
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 375 samples; filetype=bam
HiSeq X Five 375
EGAD00001004767
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 755 samples; filetype=bam
HiSeq X Five 755
EGAD00001004768
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 492 samples; filetype=bam
HiSeq X Five 492
EGAD00001004769
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 531 samples; filetype=bam
HiSeq X Five 531
EGAD00001004770
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 1222 samples; filetype=bam
HiSeq X Five 1063
EGAD00001004771
Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 522 samples; filetype=bam
HiSeq X Five,Illumina HiSeq 2500 742
EGAD00001005338
Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A96146A 1195 samples; filetype=bam
HiSeq X Five 3
EGAD00001005340
Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A96172B 1694 samples; filetype=bam
HiSeq X Five 3
EGAD00001005345
Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A96226B 1274 samples; filetype=bam
HiSeq X Five 4
EGAD00001005347
Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A96193B 2410 samples; filetype=bam
HiSeq X Five 3
EGAD00001005348
Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A96199A 843 samples; filetype=bam
HiSeq X Five 3
EGAD00001005353
Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A96199B 1170 samples; filetype=bam
HiSeq X Five 3
EGAD00001005354
Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A96211C 1397 samples; filetype=bam
HiSeq X Five 3
EGAD00001005355
Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A96225C 1034 samples; filetype=bam
HiSeq X Five 2

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