ANKRD17.md
... ...
@@ -1,5 +1,7 @@
1 1
# ANKRD17
2 2
3
+<<Warn("The variants reported in this gene in DLBCL failed QC")>>
4
+
3 5
## History
4 6
Mutations in this gene were first described in DLBCL in 2017 by Reddy et al.<sup>1</sup> Subsequent exome and genome-wide studies of DLBCL did not reproduce this observation.
5 7
papers/reddyGeneticFunctionalDrivers2017.md
... ...
@@ -49,7 +49,7 @@ All other DLBCL studies, DLBCL Tier 2, 145
49 49
|Novel gene|DLBCL tier|Average variant quality|QC outcome|
50 50
|:-|:-:|:-:|:-:|
51 51
|[ARID5B](../ARID5B)|2 |&starf; &starf; &starf; &starf; &star;|**Pass**|
52
-|[ANKRD17](../ANKRD17)|2 |&starf; &starf; &starf; &star; &star;|**Pass**|
52
+|[ANKRD17](../ANKRD17)|2 |&starf; &starf; &starf; &star; &star;|**Fail**|
53 53
|[BTBD3](../BTBD3)|2 |&starf; &starf; &starf; &starf; &star;|**Pass**|
54 54
|[SETD5](../SETD5)|2 |&starf; &starf; &starf; &star; &star;|**Pass**|
55 55
|[ATR](../ATR)|2 |&starf; &starf; &starf; &star; &star;|**Pass**|
papers/reddyGeneticFunctionalDrivers2017_tmp.html
... ...
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+ </script>
368
+<h1 id="reddygeneticfunctionaldrivers2017">@reddyGeneticFunctionalDrivers2017</h1>
369
+<h2 id="summary-of-novel-genes">Summary of novel genes</h2>
370
+<table>
371
+<thead>
372
+<tr>
373
+<th style="text-align:center">Entity</th>
374
+<th style="text-align:center">Tier 1 genes</th>
375
+<th style="text-align:center">Tier 2 genes</th>
376
+</tr>
377
+</thead>
378
+<tbody>
379
+<tr>
380
+<td style="text-align:center">DLBCL</td>
381
+<td style="text-align:center">7</td>
382
+<td style="text-align:center">53</td>
383
+</tr>
384
+</tbody>
385
+</table>
386
+<pre><code class="language-mermaid"><div class="mermaid">---
387
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388
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389
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390
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391
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392
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393
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394
+ prefix: '('
395
+ suffix: ' genes)'
396
+---
397
+sankey-beta
398
+This study, New Tier 1, 7
399
+New Tier 1, DLBCL Tier 1, 7
400
+This study, New Tier 2, 53
401
+New Tier 2, DLBCL Tier 2, 53
402
+All other DLBCL studies, DLBCL Tier 1, 121
403
+All other DLBCL studies, DLBCL Tier 2, 145
404
+</div></code></pre>
405
+<h2 id="novel-genes-reported-in-this-study">Novel genes reported in this study</h2>
406
+<h3 id="tier-1">Tier 1</h3>
407
+<table>
408
+<thead>
409
+<tr>
410
+<th style="text-align:left">Novel gene</th>
411
+<th style="text-align:center">DLBCL tier</th>
412
+<th style="text-align:center">Average variant quality</th>
413
+</tr>
414
+</thead>
415
+<tbody>
416
+<tr>
417
+<td style="text-align:left"><a href="../ATM">ATM</a></td>
418
+<td style="text-align:center">1</td>
419
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
420
+</tr>
421
+<tr>
422
+<td style="text-align:left"><a href="../BIRC6">BIRC6</a></td>
423
+<td style="text-align:center">1</td>
424
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
425
+</tr>
426
+<tr>
427
+<td style="text-align:left"><a href="../HIST1H2BC">HIST1H2BC</a></td>
428
+<td style="text-align:center">1</td>
429
+<td style="text-align:center">★ ★ ★ ★ ☆</td>
430
+</tr>
431
+<tr>
432
+<td style="text-align:left"><a href="../HNRNPU">HNRNPU</a></td>
433
+<td style="text-align:center">1</td>
434
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
435
+</tr>
436
+<tr>
437
+<td style="text-align:left"><a href="../SETD1B">SETD1B</a></td>
438
+<td style="text-align:center">1</td>
439
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
440
+</tr>
441
+<tr>
442
+<td style="text-align:left"><a href="../TOX">TOX</a></td>
443
+<td style="text-align:center">1</td>
444
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
445
+</tr>
446
+<tr>
447
+<td style="text-align:left"><a href="../UBE2A">UBE2A</a></td>
448
+<td style="text-align:center">1</td>
449
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
450
+</tr>
451
+</tbody>
452
+</table>
453
+<h3 id="tier-2">Tier 2</h3>
454
+<table>
455
+<thead>
456
+<tr>
457
+<th style="text-align:left">Novel gene</th>
458
+<th style="text-align:center">DLBCL tier</th>
459
+<th style="text-align:center">Average variant quality</th>
460
+<th style="text-align:center">QC outcome</th>
461
+</tr>
462
+</thead>
463
+<tbody>
464
+<tr>
465
+<td style="text-align:left"><a href="../ARID5B">ARID5B</a></td>
466
+<td style="text-align:center">2</td>
467
+<td style="text-align:center">★ ★ ★ ★ ☆</td>
468
+<td style="text-align:center"><strong>Pass</strong></td>
469
+</tr>
470
+<tr>
471
+<td style="text-align:left"><a href="../ANKRD17">ANKRD17</a></td>
472
+<td style="text-align:center">2</td>
473
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
474
+<td style="text-align:center"><strong>Fail</strong></td>
475
+</tr>
476
+<tr>
477
+<td style="text-align:left"><a href="../BTBD3">BTBD3</a></td>
478
+<td style="text-align:center">2</td>
479
+<td style="text-align:center">★ ★ ★ ★ ☆</td>
480
+<td style="text-align:center"><strong>Pass</strong></td>
481
+</tr>
482
+<tr>
483
+<td style="text-align:left"><a href="../SETD5">SETD5</a></td>
484
+<td style="text-align:center">2</td>
485
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
486
+<td style="text-align:center"><strong>Pass</strong></td>
487
+</tr>
488
+<tr>
489
+<td style="text-align:left"><a href="../ATR">ATR</a></td>
490
+<td style="text-align:center">2</td>
491
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
492
+<td style="text-align:center"><strong>Pass</strong></td>
493
+</tr>
494
+<tr>
495
+<td style="text-align:left"><a href="../BRINP3">BRINP3</a></td>
496
+<td style="text-align:center">2</td>
497
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
498
+<td style="text-align:center"><strong>Pass</strong></td>
499
+</tr>
500
+<tr>
501
+<td style="text-align:left"><a href="../CASP8">CASP8</a></td>
502
+<td style="text-align:center">2</td>
503
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
504
+<td style="text-align:center"><strong>Pass</strong></td>
505
+</tr>
506
+<tr>
507
+<td style="text-align:left"><a href="../TGFBR2">TGFBR2</a></td>
508
+<td style="text-align:center">2</td>
509
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
510
+<td style="text-align:center"><strong>Pass</strong></td>
511
+</tr>
512
+<tr>
513
+<td style="text-align:left"><a href="../TIPARP">TIPARP</a></td>
514
+<td style="text-align:center">2</td>
515
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
516
+<td style="text-align:center"><strong>Pass</strong></td>
517
+</tr>
518
+<tr>
519
+<td style="text-align:left"><a href="../CD22">CD22</a></td>
520
+<td style="text-align:center">2</td>
521
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
522
+<td style="text-align:center"><strong>Pass</strong></td>
523
+</tr>
524
+<tr>
525
+<td style="text-align:left"><a href="../NF1">NF1</a></td>
526
+<td style="text-align:center">2</td>
527
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
528
+<td style="text-align:center"><strong>Pass</strong></td>
529
+</tr>
530
+<tr>
531
+<td style="text-align:left"><a href="../IKBKB">IKBKB</a></td>
532
+<td style="text-align:center">2</td>
533
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
534
+<td style="text-align:center"><strong>Pass</strong></td>
535
+</tr>
536
+<tr>
537
+<td style="text-align:left"><a href="../JUNB">JUNB</a></td>
538
+<td style="text-align:center">2</td>
539
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
540
+<td style="text-align:center"><strong>Pass</strong></td>
541
+</tr>
542
+<tr>
543
+<td style="text-align:left"><a href="../KCMF1">KCMF1</a></td>
544
+<td style="text-align:center">2</td>
545
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
546
+<td style="text-align:center"><strong>Pass</strong></td>
547
+</tr>
548
+<tr>
549
+<td style="text-align:left"><a href="../MAGT1">MAGT1</a></td>
550
+<td style="text-align:center">2</td>
551
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
552
+<td style="text-align:center"><strong>Pass</strong></td>
553
+</tr>
554
+<tr>
555
+<td style="text-align:left"><a href="../MECOM">MECOM</a></td>
556
+<td style="text-align:center">2</td>
557
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
558
+<td style="text-align:center"><strong>Pass</strong></td>
559
+</tr>
560
+<tr>
561
+<td style="text-align:left"><a href="../PTPN6">PTPN6</a></td>
562
+<td style="text-align:center">2</td>
563
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
564
+<td style="text-align:center"><strong>Pass</strong></td>
565
+</tr>
566
+<tr>
567
+<td style="text-align:left"><a href="../MET">MET</a></td>
568
+<td style="text-align:center">2</td>
569
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
570
+<td style="text-align:center"><strong>Pass</strong></td>
571
+</tr>
572
+<tr>
573
+<td style="text-align:left"><a href="../ZFX">ZFX</a></td>
574
+<td style="text-align:center">2</td>
575
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
576
+<td style="text-align:center"><strong>Pass</strong></td>
577
+</tr>
578
+<tr>
579
+<td style="text-align:left"><a href="../YY1">YY1</a></td>
580
+<td style="text-align:center">2</td>
581
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
582
+<td style="text-align:center"><strong>Pass</strong></td>
583
+</tr>
584
+<tr>
585
+<td style="text-align:left"><a href="../FOXP1">FOXP1</a></td>
586
+<td style="text-align:center">2</td>
587
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
588
+<td style="text-align:center"><strong>Pass</strong></td>
589
+</tr>
590
+<tr>
591
+<td style="text-align:left"><a href="../FUBP1">FUBP1</a></td>
592
+<td style="text-align:center">2</td>
593
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
594
+<td style="text-align:center"><strong>Pass</strong></td>
595
+</tr>
596
+<tr>
597
+<td style="text-align:left"><a href="../GOLGA5">GOLGA5</a></td>
598
+<td style="text-align:center">2</td>
599
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
600
+<td style="text-align:center"><strong>Pass</strong></td>
601
+</tr>
602
+<tr>
603
+<td style="text-align:left"><a href="../MSH6">MSH6</a></td>
604
+<td style="text-align:center">2</td>
605
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
606
+<td style="text-align:center"><strong>Pass</strong></td>
607
+</tr>
608
+<tr>
609
+<td style="text-align:left"><a href="../CDC73">CDC73</a></td>
610
+<td style="text-align:center">2</td>
611
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
612
+<td style="text-align:center"><strong>Fail</strong></td>
613
+</tr>
614
+<tr>
615
+<td style="text-align:left"><a href="../CHD1">CHD1</a></td>
616
+<td style="text-align:center">2</td>
617
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
618
+<td style="text-align:center"><strong>Fail</strong></td>
619
+</tr>
620
+<tr>
621
+<td style="text-align:left"><a href="../CHD8">CHD8</a></td>
622
+<td style="text-align:center">2</td>
623
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
624
+<td style="text-align:center"><strong>Fail</strong></td>
625
+</tr>
626
+<tr>
627
+<td style="text-align:left"><a href="../CHST2">CHST2</a></td>
628
+<td style="text-align:center">2</td>
629
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
630
+<td style="text-align:center"><strong>Fail</strong></td>
631
+</tr>
632
+<tr>
633
+<td style="text-align:left"><a href="../DCAF6">DCAF6</a></td>
634
+<td style="text-align:center">2</td>
635
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
636
+<td style="text-align:center"><strong>Fail</strong></td>
637
+</tr>
638
+<tr>
639
+<td style="text-align:left"><a href="../DDX10">DDX10</a></td>
640
+<td style="text-align:center">2</td>
641
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
642
+<td style="text-align:center"><strong>Fail</strong></td>
643
+</tr>
644
+<tr>
645
+<td style="text-align:left"><a href="../DICER1">DICER1</a></td>
646
+<td style="text-align:center">2</td>
647
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
648
+<td style="text-align:center"><strong>Fail</strong></td>
649
+</tr>
650
+<tr>
651
+<td style="text-align:left"><a href="../HRAS">HRAS</a></td>
652
+<td style="text-align:center">2</td>
653
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
654
+<td style="text-align:center"><strong>Fail</strong></td>
655
+</tr>
656
+<tr>
657
+<td style="text-align:left"><a href="../LIN54">LIN54</a></td>
658
+<td style="text-align:center">2</td>
659
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
660
+<td style="text-align:center"><strong>Fail</strong></td>
661
+</tr>
662
+<tr>
663
+<td style="text-align:left"><a href="../MAP4K4">MAP4K4</a></td>
664
+<td style="text-align:center">2</td>
665
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
666
+<td style="text-align:center"><strong>Fail</strong></td>
667
+</tr>
668
+<tr>
669
+<td style="text-align:left"><a href="../MCL1">MCL1</a></td>
670
+<td style="text-align:center">2</td>
671
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
672
+<td style="text-align:center"><strong>Fail</strong></td>
673
+</tr>
674
+<tr>
675
+<td style="text-align:left"><a href="../MSH2">MSH2</a></td>
676
+<td style="text-align:center">2</td>
677
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
678
+<td style="text-align:center"><strong>Fail</strong></td>
679
+</tr>
680
+<tr>
681
+<td style="text-align:left"><a href="../GNAS">GNAS</a></td>
682
+<td style="text-align:center">2</td>
683
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
684
+<td style="text-align:center"><strong>Fail</strong></td>
685
+</tr>
686
+<tr>
687
+<td style="text-align:left"><a href="../MYB">MYB</a></td>
688
+<td style="text-align:center">2</td>
689
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
690
+<td style="text-align:center"><strong>Fail</strong></td>
691
+</tr>
692
+<tr>
693
+<td style="text-align:left"><a href="../NCOR1">NCOR1</a></td>
694
+<td style="text-align:center">2</td>
695
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
696
+<td style="text-align:center"><strong>Fail</strong></td>
697
+</tr>
698
+<tr>
699
+<td style="text-align:left"><a href="../NFKB2">NFKB2</a></td>
700
+<td style="text-align:center">2</td>
701
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
702
+<td style="text-align:center"><strong>Fail</strong></td>
703
+</tr>
704
+<tr>
705
+<td style="text-align:left"><a href="../PHF6">PHF6</a></td>
706
+<td style="text-align:center">2</td>
707
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
708
+<td style="text-align:center"><strong>Fail</strong></td>
709
+</tr>
710
+<tr>
711
+<td style="text-align:left"><a href="../PIK3CD">PIK3CD</a></td>
712
+<td style="text-align:center">2</td>
713
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
714
+<td style="text-align:center"><strong>Fail</strong></td>
715
+</tr>
716
+<tr>
717
+<td style="text-align:left"><a href="../PTPRK">PTPRK</a></td>
718
+<td style="text-align:center">2</td>
719
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
720
+<td style="text-align:center"><strong>Fail</strong></td>
721
+</tr>
722
+<tr>
723
+<td style="text-align:left"><a href="../ZFAT">ZFAT</a></td>
724
+<td style="text-align:center">2</td>
725
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
726
+<td style="text-align:center"><strong>Fail</strong></td>
727
+</tr>
728
+<tr>
729
+<td style="text-align:left"><a href="../ARID1B">ARID1B</a></td>
730
+<td style="text-align:center">2</td>
731
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
732
+<td style="text-align:center"><strong>Fail</strong></td>
733
+</tr>
734
+<tr>
735
+<td style="text-align:left"><a href="../RUNX1">RUNX1</a></td>
736
+<td style="text-align:center">2</td>
737
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
738
+<td style="text-align:center"><strong>Fail</strong></td>
739
+</tr>
740
+<tr>
741
+<td style="text-align:left"><a href="../CBLB">CBLB</a></td>
742
+<td style="text-align:center">2</td>
743
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
744
+<td style="text-align:center"><strong>Fail</strong></td>
745
+</tr>
746
+<tr>
747
+<td style="text-align:left"><a href="../SYK">SYK</a></td>
748
+<td style="text-align:center">2</td>
749
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
750
+<td style="text-align:center"><strong>Fail</strong></td>
751
+</tr>
752
+<tr>
753
+<td style="text-align:left"><a href="../WAC">WAC</a></td>
754
+<td style="text-align:center">2</td>
755
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
756
+<td style="text-align:center"><strong>Fail</strong></td>
757
+</tr>
758
+<tr>
759
+<td style="text-align:left"><a href="../ZBTB7A">ZBTB7A</a></td>
760
+<td style="text-align:center">2</td>
761
+<td style="text-align:center">★ ☆ ☆ ☆ ☆</td>
762
+<td style="text-align:center"><strong>Fail</strong></td>
763
+</tr>
764
+<tr>
765
+<td style="text-align:left"><a href="../RARA">RARA</a></td>
766
+<td style="text-align:center">2</td>
767
+<td style="text-align:center">★ ☆ ☆ ☆ ☆</td>
768
+<td style="text-align:center"><strong>Fail</strong></td>
769
+</tr>
770
+<tr>
771
+<td style="text-align:left"><a href="../DNMT3A">DNMT3A</a></td>
772
+<td style="text-align:center">2</td>
773
+<td style="text-align:center">★ ☆ ☆ ☆ ☆</td>
774
+<td style="text-align:center"><strong>Fail</strong></td>
775
+</tr>
776
+<tr>
777
+<td style="text-align:left"><a href="../MARK1">MARK1</a></td>
778
+<td style="text-align:center">2</td>
779
+<td style="text-align:center">★ ☆ ☆ ☆ ☆</td>
780
+<td style="text-align:center"><strong>Fail</strong></td>
781
+</tr>
782
+</tbody>
783
+</table>
784
+<h2 id="see-also">See Also</h2>
785
+<p>The primary data supporting each of the mutations reported in this study can be viewed in <a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/">IGV reports</a> along with mutations unique to the GAMBL re-analysis.[@drevalRevisitingReddyDLBCL2023]</p>
786
+<h1 id="references">References</h1>
787
+
788
+</body>
789
+</html>