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Diagnostic utility of whole genome sequencing in adults with B-other acute lymphoblastic leukemia - RNA

Genomic profiling at diagnosis of B-cell precursor Acute Lymphoblastic Leukemia (BCP-ALL) in adults is used to guide disease classification, risk stratification and treatment decisions. Patients for which diagnostic screening fails to identify disease defining or risk stratifying lesions are classified as B-other ALL. We screened a cohort of 652 BCP-ALL cases enrolled in UKALL14 to identify and perform whole genome sequencing (WGS) on paired tumor-normal samples. For 52 B-other patients we compared WGS findings to data from clinical and research cytogenetics. WGS identifies a cancer associated event in 51/52 cases, this includes an established subtype defining genetic alteration in 5/52 that were previously missed by standard-of-care genetics. Of the 47 true B-other ALL we identified a recurrent driver in 87% (41).  Complex karyotype by cytogenetics emerges as a heterogeneous group, underlied by distinct genetic alterations associated with either favorable (DUX4-r) or poor outcomes (MEF2D-r, IGK::BCL2). For a subset of 31 cases, we integrate findings from RNA-sequencing (RNA-seq) analysis to include fusion gene detection, and classification by gene expression. Compared to RNA-seq, WGS was sufficient to detect and resolve recurrent genetic subtypes, however RNA-seq can provide orthogonal validation of findings. In conclusion, we demonstrate that WGS can identify clinically relevant genetic abnormalities missed by standard-of-care testing and identify leukemia driver events in virtually all cases of B-other ALL.

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Wellcome Trust Sanger Institute Data Sharing Policy

Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID Study Title Study Type
EGAS00001003428 Other

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID File Type Size Located in
EGAF00006901510 cram 474.2 MB
EGAF00006901511 cram 551.2 MB
EGAF00006901512 cram 528.3 MB
EGAF00006901513 cram 583.4 MB
EGAF00006901514 cram 608.3 MB
EGAF00006901515 cram 683.7 MB
EGAF00006901516 cram 651.1 MB
EGAF00006901517 cram 567.2 MB
EGAF00006901518 cram 544.6 MB
EGAF00006901519 cram 604.8 MB
EGAF00006901520 cram 637.4 MB
EGAF00006901521 cram 693.6 MB
EGAF00006901522 cram 719.6 MB
EGAF00006901523 cram 667.2 MB
EGAF00006901524 cram 599.3 MB
EGAF00006901525 cram 724.4 MB
EGAF00006901526 cram 635.8 MB
EGAF00006901527 cram 589.6 MB
EGAF00006901528 cram 539.6 MB
EGAF00006901529 cram 699.6 MB
EGAF00006901530 cram 641.2 MB
EGAF00006901531 cram 584.2 MB
EGAF00006901532 cram 605.7 MB
EGAF00006901533 cram 654.9 MB
EGAF00006901534 cram 622.0 MB
EGAF00006901535 cram 722.7 MB
EGAF00006901536 cram 527.7 MB
EGAF00006901537 cram 640.3 MB
EGAF00006901538 cram 586.5 MB
EGAF00006901539 cram 570.1 MB
EGAF00006901540 cram 550.9 MB
EGAF00006901541 cram 744.2 MB
EGAF00006901542 cram 640.0 MB
EGAF00006901543 cram 466.8 MB
EGAF00006901544 cram 543.7 MB
EGAF00006901545 cram 521.4 MB
EGAF00006901546 cram 575.8 MB
EGAF00006901547 cram 596.0 MB
EGAF00006901548 cram 671.5 MB
EGAF00006901549 cram 638.3 MB
EGAF00006901550 cram 557.7 MB
EGAF00006901551 cram 536.3 MB
EGAF00006901552 cram 594.8 MB
EGAF00006901553 cram 623.9 MB
EGAF00006901554 cram 681.9 MB
EGAF00006901555 cram 706.0 MB
EGAF00006901556 cram 653.8 MB
EGAF00006901557 cram 588.8 MB
EGAF00006901558 cram 708.6 MB
EGAF00006901559 cram 627.1 MB
EGAF00006901560 cram 579.0 MB
EGAF00006901561 cram 531.5 MB
EGAF00006901562 cram 686.9 MB
EGAF00006901563 cram 631.3 MB
EGAF00006901564 cram 572.4 MB
EGAF00006901565 cram 592.8 MB
EGAF00006901566 cram 642.8 MB
EGAF00006901567 cram 611.1 MB
EGAF00006901568 cram 711.3 MB
EGAF00006901569 cram 518.4 MB
EGAF00006901570 cram 629.3 MB
EGAF00006901571 cram 577.2 MB
EGAF00006901572 cram 562.3 MB
EGAF00006901573 cram 541.2 MB
EGAF00006901574 cram 729.2 MB
EGAF00006901575 cram 630.5 MB
EGAF00006901576 cram 463.1 MB
EGAF00006901577 cram 538.0 MB
EGAF00006901578 cram 515.5 MB
EGAF00006901579 cram 568.5 MB
EGAF00006901580 cram 589.7 MB
EGAF00006901581 cram 665.7 MB
EGAF00006901582 cram 632.1 MB
EGAF00006901583 cram 551.3 MB
EGAF00006901584 cram 529.9 MB
EGAF00006901585 cram 588.5 MB
EGAF00006901586 cram 619.6 MB
EGAF00006901587 cram 676.0 MB
EGAF00006901588 cram 698.2 MB
EGAF00006901589 cram 650.8 MB
EGAF00006901590 cram 583.6 MB
EGAF00006901591 cram 707.5 MB
EGAF00006901592 cram 619.4 MB
EGAF00006901593 cram 574.7 MB
EGAF00006901594 cram 528.0 MB
EGAF00006901595 cram 679.4 MB
EGAF00006901596 cram 624.6 MB
EGAF00006901597 cram 568.5 MB
EGAF00006901598 cram 595.7 MB
EGAF00006901599 cram 637.1 MB
EGAF00006901600 cram 605.6 MB
EGAF00006901601 cram 703.8 MB
EGAF00006901602 cram 516.4 MB
EGAF00006901603 cram 622.8 MB
EGAF00006901604 cram 569.8 MB
EGAF00006901605 cram 558.7 MB
EGAF00006901606 cram 538.2 MB
EGAF00006901607 cram 723.5 MB
EGAF00006901608 cram 621.0 MB
EGAF00006901609 cram 453.2 MB
EGAF00006901610 cram 527.4 MB
EGAF00006901611 cram 502.9 MB
EGAF00006901612 cram 554.8 MB
EGAF00006901613 cram 575.7 MB
EGAF00006901614 cram 656.3 MB
EGAF00006901615 cram 619.2 MB
EGAF00006901616 cram 539.0 MB
EGAF00006901617 cram 521.5 MB
EGAF00006901618 cram 576.7 MB
EGAF00006901619 cram 608.8 MB
EGAF00006901620 cram 663.4 MB
EGAF00006901621 cram 688.3 MB
EGAF00006901622 cram 637.7 MB
EGAF00006901623 cram 573.3 MB
EGAF00006901624 cram 707.9 MB
EGAF00006901625 cram 607.8 MB
EGAF00006901626 cram 564.9 MB
EGAF00006901627 cram 515.5 MB
EGAF00006901628 cram 666.6 MB
EGAF00006901629 cram 612.3 MB
EGAF00006901630 cram 554.9 MB
EGAF00006901631 cram 583.0 MB
EGAF00006901632 cram 625.4 MB
EGAF00006901633 cram 592.3 MB
EGAF00006901634 cram 688.6 MB
EGAF00006901635 cram 506.8 MB
EGAF00006901636 cram 609.9 MB
EGAF00006901637 cram 556.7 MB
EGAF00006901638 cram 546.8 MB
EGAF00006901639 cram 527.4 MB
EGAF00006901640 cram 712.9 MB
EGAF00006901641 cram 609.4 MB
EGAF00006901642 cram 455.1 MB
EGAF00006901643 cram 529.5 MB
EGAF00006901644 cram 505.8 MB
EGAF00006901645 cram 556.0 MB
EGAF00006901646 cram 578.4 MB
EGAF00006901647 cram 658.8 MB
EGAF00006901648 cram 620.4 MB
EGAF00006901649 cram 542.2 MB
EGAF00006901650 cram 521.5 MB
EGAF00006901651 cram 578.7 MB
EGAF00006901652 cram 610.5 MB
EGAF00006901653 cram 666.7 MB
EGAF00006901654 cram 691.7 MB
EGAF00006901655 cram 640.3 MB
EGAF00006901656 cram 575.1 MB
EGAF00006901657 cram 691.4 MB
EGAF00006901658 cram 613.5 MB
EGAF00006901659 cram 564.2 MB
EGAF00006901660 cram 518.9 MB
EGAF00006901661 cram 671.5 MB
EGAF00006901662 cram 615.0 MB
EGAF00006901663 cram 557.3 MB
EGAF00006901664 cram 586.5 MB
EGAF00006901665 cram 627.7 MB
EGAF00006901666 cram 594.3 MB
EGAF00006901667 cram 692.2 MB
EGAF00006901668 cram 506.6 MB
EGAF00006901669 cram 612.5 MB
EGAF00006901670 cram 560.0 MB
EGAF00006901671 cram 549.2 MB
EGAF00006901672 cram 529.1 MB
EGAF00006901673 cram 717.0 MB
EGAF00006901674 cram 613.5 MB
EGAF00006901675 cram 469.9 MB
EGAF00006901676 cram 547.5 MB
EGAF00006901677 cram 523.4 MB
EGAF00006901678 cram 577.0 MB
EGAF00006901679 cram 600.6 MB
EGAF00006901680 cram 680.2 MB
EGAF00006901681 cram 642.3 MB
EGAF00006901682 cram 561.3 MB
EGAF00006901683 cram 538.7 MB
EGAF00006901684 cram 598.0 MB
EGAF00006901685 cram 630.4 MB
EGAF00006901686 cram 687.5 MB
EGAF00006901687 cram 715.4 MB
EGAF00006901688 cram 660.8 MB
EGAF00006901689 cram 593.9 MB
EGAF00006901690 cram 721.7 MB
EGAF00006901691 cram 631.7 MB
EGAF00006901692 cram 584.1 MB
EGAF00006901693 cram 537.2 MB
EGAF00006901694 cram 693.2 MB
EGAF00006901695 cram 636.7 MB
EGAF00006901696 cram 575.0 MB
EGAF00006901697 cram 608.7 MB
EGAF00006901698 cram 649.3 MB
EGAF00006901699 cram 614.9 MB
EGAF00006901700 cram 716.1 MB
EGAF00006901701 cram 523.3 MB
EGAF00006901702 cram 633.5 MB
EGAF00006901703 cram 580.1 MB
EGAF00006901704 cram 567.9 MB
EGAF00006901705 cram 547.2 MB
EGAF00006901706 cram 739.6 MB
EGAF00006901707 cram 634.5 MB
198 Files (119.6 GB)