149:
different cancer types. Accurate identification of copy neutral chromosomal abnormalities is particularly important as translocation can lead to fusion proteins, chimeric proteins, or misregulated proteins that can be seen in tumors. This technique can also be used in evolution studies by identifying large structural variation between different populations. Similar methods are being developed for various applications. For example, a barcoded
Illumina paired-end sequencing (BIPES) approach was used to assess microbial diversity by sequencing the 16S V6 tag.
115:
93:
106:
mapping will show a fragment of size (l) in the reference genome. If the paired-ends are closer than distance (l), an insertion is suspected in the sampled DNA. A distance of (l< μ-3σ) can be used as a cut-off to detect an insertion, where μ is the mean length of the insert and σ is the standard deviation. In case of a deletion, the paired-ends are mapped further away in the reference genome compared to the expected distance (l> μ-3σ).
71:(BAC). Basically, the target chromosome is randomly digested and inserted into plasmids which are transformed and cloned in bacteria. The size of fragments inserted is 150–350 kb. Another commonly used artificial chromosome is fosmid. The difference between BAC and fosmids is the size of the DNA inserted. Fosmids can only hold 40 kb DNA fragments, which allows a more accurate breakpoint determination.
59:
38:
136:
karyotyping at that time. In 2007, Dr. Snyder and his group improved the ESP to 3kb resolution by sequencing both pairs of 3-kb DNA fragments without BAC construction. Their approach is able to identify deletions, inversions, insertions with an average breakpoint resolution of 644bp, which close to the resolution of
605:
Korbel, J. O.; Urban, A. E.; Affourtit, J. P.; Godwin, B.; Grubert, F.; Simons, J. F.; Kim, P. M.; Palejev, D.; Carriero, N. J.; Du, L.; Taillon, B. E.; Chen, Z.; Tanzer, A.; Saunders, A. C. E.; Chi, J.; Yang, F.; Carter, N. P.; Hurles, M. E.; Weissman, S. M.; Harkins, T. T.; Gerstein, M. B.; Egholm,
105:
In the case of an insertion or a deletion, mapping of the paired-end is consistent with the reference genome. But the read are disconcordant in apparent size. The apparent size is the distance of the BAC sequenced-ends mapped in the reference genome. If a BAC has an insert of length (l), a concordant
88:
Inversions and translocations are relatively easy to detect by an invalid pair of sequenced-end. For instance, a translocation can be detected if the paired-ends are mapped onto different chromosomes on the reference genome. Inversion can be detected by divergent orientation of the reads, where the
148:
Various bioinformatics tools can be used to analyze end-sequence profiling. Common ones include BreakDancer, PEMer, Variation Hunter, common LAW, GASV, and
Spanner. ESP can be used to map structural variation at high-resolution in disease tissue. This technique is mainly used on tumor samples from
166:
to analyze the function of these arrangements. However, BAC construction is still expensive and labor-intensive. Researchers should be really careful to choose which strategy they need for particular project. Because ESP only looks at short paired-end sequences, it has the advantage of providing
135:
ESP was first developed and published in 2003 by Dr. Collins and his colleagues in
University of California, San Francisco. Their study revealed the chromosome rearrangements and CNV of MCF7 human cancer cells at a 150kb resolution, which is much more accurate compared to both CGH and spectral
157:
Resolution of structural variation detection by ESP has been increased to the similar level as PCR, and can be further improved by selection of more evenly sized DNA fragments. ESP can be applied for either with or without constructed artificial chromosome. With BAC, precious samples can be
79:
End sequence profiling (ESP) can be used to detect structural variations such as insertions, deletions, and chromosomal rearrangement. Compare to other methods that look at chromosomal abnormalities, ESP is particularly useful to identify copy neutral abnormalities such as inversions and
496:
Korbel, JO; Urban, AE; Affourtit, JP; Godwin, B; Grubert, F; Simons, JF; Kim, PM; Palejev, D; Carriero, NJ; Du, L; Taillon, BE; Chen, Z; Tanzer, A; Saunders, AC; Chi, J; Yang, F; Carter, NP; Hurles, ME; Weissman, SM; Harkins, TT; Gerstein, MB; Egholm, M; Snyder, M (19 October 2007).
80:
translocations that would not be apparent when looking at copy number variation. From the BAC library, both ends of the inserted fragments are sequenced using a sequencing platform. Detection of variations is then achieved by mapping the sequenced reads onto a reference genome.
272:
Tuzun, Eray; Sharp, Andrew J; Bailey, Jeffrey A; Kaul, Rajinder; Morrison, V Anne; Pertz, Lisa M; Haugen, Eric; Hayden, Hillary; Albertson, Donna; Pinkel, Daniel; Olson, Maynard V; Eichler, Evan E (15 May 2005). "Fine-scale structural variation of the human genome".
66:
Before analyzing target genome structural aberration and copy number variation (CNV) with ESP, the target genome is usually amplified and conserved with artificial chromosome construction. The classic strategy to construct an artificial chromosome is
50:(BAC) which are then sequenced and compared to the reference genome. The differences, including orientation and length variations between constructed chromosomes and the reference genome, will suggest copy number and structural aberration.
126:
for example in sequences repeats. For larger CNV, the density of the reads will vary accordingly to the copy number. An increase of copy numbers will be reflected by increasing mapping of the same region on the reference genome.
45:
Briefly, the target genomic DNA is isolated and partially digested with restriction enzymes into large fragments. Following size-fractionation, the fragments are cloned into plasmids to construct artificial chromosomes such as
158:
immortalized and conserved, which is particularly important for small quantity of smalls which are planned for extensive analyses. Furthermore, BACs carrying rearranged DNA fragments can be directly transfected
167:
useful information genome-wide without the need for large-scale sequencing. Approximately 100-200 tumors can be sequenced at a resolution greater than 150kb when compared to sequencing an entire genome.
385:
Volik, S.; Zhao, S.; Chin, K.; Brebner, J. H.; Herndon, D. R.; Tao, Q.; Kowbel, D.; Huang, G.; Lapuk, A.; Kuo, W.-L.; Magrane, G.; de Jong, P.; Gray, J. W.; Collins, C. (4 June 2003).
233:"Construction of a 750-kb bacterial clone contig and restriction map in the region of human chromosome 21 containing the progressive myoclonus epilepsy gene"
447:
Yang, R; Chen, L; Newman, S; Gandhi, K; Doho, G; Moreno, CS; Vertino, PM; Bernal-Mizarchi, L; Lonial, S; Boise, LH; Rossi, M; Kowalski, J; Qin, ZS (2014).
663:
Zhou, Hong-Wei; Li, Dong-Fang; Tam, Nora Fung-Yee; Jiang, Xiao-Tao; Zhang, Hai; Sheng, Hua-Fang; Qin, Jin; Liu, Xiao; Zou, Fei (21 October 2010).
449:"Integrated analysis of whole-genome paired-end and mate-pair sequencing data for identifying genomic structural variations in multiple myeloma"
782:
231:
Stone, NE; Fan, JB; Willour, V; Pennacchio, LA; Warrington, JA; Hu, A; de la
Chapelle, A; Lehesjoki, AE; Cox, DR; Myers, RM (March 1996).
47:
556:"Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives"
68:
777:
319:
Bashir, Ali; Volik, Stanislav; Collins, Colin; Bafna, Vineet; Raphael, Benjamin J.; Ouzounis, Christos A. (25 April 2008).
772:
745:
137:
30:
725:
19:(sometimes "Paired-end mapping (PEM)") is a method based on sequence-tagged connectors developed to facilitate
787:
750:
755:
730:
123:
114:
92:
26:
735:
619:
510:
398:
332:
197:
740:
321:"Evaluation of Paired-End Sequencing Strategies for Detection of Genome Rearrangements in Cancer"
298:
694:
645:
587:
536:
478:
426:
360:
290:
254:
213:
25:
genome sequencing to identify high-resolution copy number and structural aberrations such as
684:
676:
635:
627:
577:
567:
526:
518:
468:
460:
416:
406:
350:
340:
282:
244:
205:
623:
514:
402:
336:
201:
689:
664:
640:
607:
582:
555:
531:
498:
473:
448:
355:
320:
421:
386:
188:; Bender, W (16 June 1989). "Construction of large DNA segments in Escherichia coli".
766:
302:
665:"BIPES, a cost-effective high-throughput method for assessing microbial diversity"
345:
572:
185:
58:
37:
608:"Paired-End Mapping Reveals Extensive Structural Variation in the Human Genome"
499:"Paired-end mapping reveals extensive structural variation in the human genome"
631:
522:
411:
209:
698:
680:
649:
591:
554:
Zhao, Min; Wang, Qingguo; Wang, Quan; Jia, Peilin; Zhao, Zhongming (2013).
540:
482:
430:
364:
294:
258:
217:
20:
464:
249:
232:
387:"End-sequence profiling: Sequence-based analysis of aberrant genomes"
286:
113:
91:
57:
36:
62:
Work flow of bacteria artificial chromosome construction
122:
In some cases, discordant reads can also indicate a
89:insert will have two plus-end or two minus-end.
391:Proceedings of the National Academy of Sciences
380:
378:
376:
374:
8:
314:
312:
688:
639:
581:
571:
530:
472:
420:
410:
354:
344:
248:
96:Chromosome rearrangements detected by ESP
176:
118:Copy number alterations detected by ESP
442:
440:
7:
41:Work flow of End-sequence profiling
606:M.; Snyder, M. (19 October 2007).
54:Artificial chromosome construction
14:
48:bacterial artificial chromosomes
75:Structural aberration detection
69:bacterial artificial chromosome
1:
783:Molecular biology techniques
346:10.1371/journal.pcbi.1000051
17:End-sequence profiling (ESP)
573:10.1186/1471-2105-14-S11-S1
84:Inversion and translocation
804:
325:PLOS Computational Biology
153:Advantages and limitations
746:Chromosomal translocation
138:polymerase chain reaction
726:Chromosome abnormalities
632:10.1126/science.1149504
523:10.1126/science.1149504
412:10.1073/pnas.1232418100
210:10.1126/science.2660262
751:Chromosome abnormality
681:10.1038/ismej.2010.160
119:
101:Insertion and deletion
97:
63:
42:
778:Laboratory techniques
756:Copy-number variation
731:Chromosomal inversion
117:
110:Copy number variation
95:
61:
40:
736:Insertion (genetics)
741:Deletion (genetics)
624:2007Sci...318..420K
515:2007Sci...318..420K
403:2003PNAS..100.7696V
337:2008PLSCB...4E0051B
202:1989Sci...244.1307O
560:BMC Bioinformatics
465:10.4137/CIN.S13783
459:(Suppl 2): 49–53.
453:Cancer Informatics
250:10.1101/gr.6.3.218
120:
98:
64:
43:
773:Molecular biology
618:(5849): 420–426.
397:(13): 7696–7701.
196:(4910): 1307–12.
795:
703:
702:
692:
669:The ISME Journal
660:
654:
653:
643:
602:
596:
595:
585:
575:
566:(Suppl 11): S1.
551:
545:
544:
534:
493:
487:
486:
476:
444:
435:
434:
424:
414:
382:
369:
368:
358:
348:
316:
307:
306:
269:
263:
262:
252:
228:
222:
221:
181:
144:ESP applications
803:
802:
798:
797:
796:
794:
793:
792:
763:
762:
722:
707:
706:
662:
661:
657:
604:
603:
599:
553:
552:
548:
509:(5849): 420–6.
495:
494:
490:
446:
445:
438:
384:
383:
372:
331:(4): e1000051.
318:
317:
310:
275:Nature Genetics
271:
270:
266:
237:Genome Research
230:
229:
225:
183:
182:
178:
173:
155:
146:
133:
112:
103:
86:
77:
56:
34:
12:
11:
5:
801:
799:
791:
790:
788:DNA sequencing
785:
780:
775:
765:
764:
759:
758:
753:
748:
743:
738:
733:
728:
721:
718:
717:
716:
714:
712:
710:
705:
704:
675:(4): 741–749.
655:
597:
546:
488:
436:
370:
308:
287:10.1038/ng1562
281:(7): 727–732.
264:
223:
175:
174:
172:
169:
154:
151:
145:
142:
132:
129:
111:
108:
102:
99:
85:
82:
76:
73:
55:
52:
31:translocations
13:
10:
9:
6:
4:
3:
2:
800:
789:
786:
784:
781:
779:
776:
774:
771:
770:
768:
761:
757:
754:
752:
749:
747:
744:
742:
739:
737:
734:
732:
729:
727:
724:
723:
719:
715:
713:
711:
709:
708:
700:
696:
691:
686:
682:
678:
674:
670:
666:
659:
656:
651:
647:
642:
637:
633:
629:
625:
621:
617:
613:
609:
601:
598:
593:
589:
584:
579:
574:
569:
565:
561:
557:
550:
547:
542:
538:
533:
528:
524:
520:
516:
512:
508:
504:
500:
492:
489:
484:
480:
475:
470:
466:
462:
458:
454:
450:
443:
441:
437:
432:
428:
423:
418:
413:
408:
404:
400:
396:
392:
388:
381:
379:
377:
375:
371:
366:
362:
357:
352:
347:
342:
338:
334:
330:
326:
322:
315:
313:
309:
304:
300:
296:
292:
288:
284:
280:
276:
268:
265:
260:
256:
251:
246:
243:(3): 218–25.
242:
238:
234:
227:
224:
219:
215:
211:
207:
203:
199:
195:
191:
187:
184:O'Connor, M;
180:
177:
170:
168:
165:
161:
152:
150:
143:
141:
139:
130:
128:
125:
116:
109:
107:
100:
94:
90:
83:
81:
74:
72:
70:
60:
53:
51:
49:
39:
35:
32:
28:
24:
23:
18:
760:
672:
668:
658:
615:
611:
600:
563:
559:
549:
506:
502:
491:
456:
452:
394:
390:
328:
324:
278:
274:
267:
240:
236:
226:
193:
189:
179:
163:
159:
156:
147:
134:
121:
104:
87:
78:
65:
44:
21:
16:
15:
131:ESP history
767:Categories
171:References
27:inversions
186:Peifer, M
720:See also
699:20962877
650:17901297
592:24564169
541:17901297
483:25288879
431:12788976
365:18404202
303:14162962
295:15895083
160:in vitro
690:3105743
641:2674581
620:Bibcode
612:Science
583:3846878
532:2674581
511:Bibcode
503:Science
474:4179644
399:Bibcode
356:2278375
333:Bibcode
259:8963899
218:2660262
198:Bibcode
190:Science
164:in vivo
140:(PCR).
22:de novo
697:
687:
648:
638:
590:
580:
539:
529:
481:
471:
429:
422:164650
419:
363:
353:
301:
293:
257:
216:
299:S2CID
695:PMID
646:PMID
588:PMID
537:PMID
479:PMID
427:PMID
361:PMID
291:PMID
255:PMID
214:PMID
29:and
685:PMC
677:doi
636:PMC
628:doi
616:318
578:PMC
568:doi
527:PMC
519:doi
507:318
469:PMC
461:doi
417:PMC
407:doi
395:100
351:PMC
341:doi
283:doi
245:doi
206:doi
194:244
162:or
124:CNV
769::
693:.
683:.
671:.
667:.
644:.
634:.
626:.
614:.
610:.
586:.
576:.
564:14
562:.
558:.
535:.
525:.
517:.
505:.
501:.
477:.
467:.
457:13
455:.
451:.
439:^
425:.
415:.
405:.
393:.
389:.
373:^
359:.
349:.
339:.
327:.
323:.
311:^
297:.
289:.
279:37
277:.
253:.
239:.
235:.
212:.
204:.
192:.
33:.
701:.
679::
673:5
652:.
630::
622::
594:.
570::
543:.
521::
513::
485:.
463::
433:.
409::
401::
367:.
343::
335::
329:4
305:.
285::
261:.
247::
241:6
220:.
208::
200::
Text is available under the Creative Commons Attribution-ShareAlike License. Additional terms may apply.
