CoChat
Sign Up
Cited by 1,144

The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.

Detection and quantification of rare mutations with massively parallel sequencing

Kinde, Isaac, Wu, Jian, Papadopoulos, Nick, Kinzler, Kenneth W., Vogelstein, Bert·2011·Proceedings of the National Academy of Sciences
DOI 10.1073/pnas.1105422108
Open this paper in CoChat — free account

Abstract

The identification of mutations that are present in a small fraction of DNA templates is essential for progress in several areas of biomedical research. Although massively parallel sequencing instruments are in principle well suited to this task, the error rates in such instruments are generally too high to allow confident identification of rare variants. We here describe an approach that can substantially increase the sensitivity of massively parallel sequencing instruments for this purpose. The keys to this approach, called the Safe - Seq uencing S ystem (“Safe-SeqS”), are ( i ) assignment of a unique identifier (UID) to each template molecule, ( ii ) amplification of each uniquely tagged template molecule to create UID families, and ( iii ) redundant sequencing of the amplification products. PCR fragments with the same UID are considered mutant (“supermutants”) only if ≥95% of them contain the identical mutation. We illustrate the utility of this approach for determining the fidelity of a polymerase, the accuracy of oligonucleotides synthesized in vitro, and the prevalence of mutations in the nuclear and mitochondrial genomes of normal cells.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1073/pnas.1105422108

Cites

2 of 2 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Show all 2 references

Research works printed but not linked: 49

  1. 10.1093/genetics/28.6.491 · DOI · Paper page
  2. 10.1126/science.1186802 · DOI · Paper page
  3. 10.1093/carcin/bgq239 · DOI
  4. 10.1056/NEJMoa067710 · DOI
  5. 10.1086/514228 · DOI
  6. 10.1073/pnas.0810641105 · DOI
  7. 10.1073/pnas.0808319105 · DOI
  8. MO Hoque, et al., High-throughput molecular analysis of urine sediment for the detection of bladder cancer by high-density single-nucleotide polymorphism array. Cancer Res 63, 5723–5726 (2003).
  9. 10.1136/jcp.56.11.805 · DOI
  10. 10.1053/j.gastro.2008.05.039 · DOI
  11. 10.1016/0378-1119(92)90299-5 · DOI
  12. 10.1158/0008-5472.CAN-04-1198 · DOI
  13. 10.1002/(SICI)1096-9896(199809)186:1<31::AID-PATH146>3.0.CO;2-F · DOI
  14. 10.1021/bi00416a027 · DOI
  15. 10.1016/S0021-9258(18)89090-1 · DOI
  16. 10.1016/0009-8981(91)90247-A · DOI
  17. 10.1016/0027-5107(92)90186-6 · DOI
  18. 10.2144/04361DD03 · DOI
  19. 10.1073/pnas.82.9.2895 · DOI · Paper page
  20. 10.1038/nmeth713 · DOI
  21. 10.1073/pnas.86.23.9253 · DOI
  22. 10.1126/science.2024123 · DOI
  23. 10.1038/nmeth751 · DOI
  24. 10.1073/pnas.96.16.9236 · DOI · Paper page
  25. 10.1073/pnas.0936399100 · DOI
  26. 10.2144/02331md03 · DOI
  27. 10.1002/pd.2150 · DOI
  28. 10.1073/pnas.1133470100 · DOI
  29. 10.1126/science.1131370 · DOI
  30. 10.1038/nmeth.1270 · DOI
  31. 10.1038/nature09626 · DOI
  32. 10.1038/nature08802 · DOI
  33. 10.1093/nar/gkn425 · DOI · Paper page
  34. 10.1038/nmeth.1230 · DOI
  35. 10.1186/1471-2105-9-431 · DOI
  36. 10.1038/nmeth.1307 · DOI
  37. 10.1101/gr.109157.110 · DOI
  38. 10.1007/s10528-007-9114-x · DOI
  39. 10.1093/nar/gkm760 · DOI
  40. 10.1038/nmeth.1251 · DOI
  41. 10.1093/nar/gnh132 · DOI
  42. 10.1038/nmeth.1343 · DOI
  43. 10.1016/j.cell.2007.01.029 · DOI · Paper page
  44. 10.1093/genetics/118.2.181 · DOI
  45. 10.1093/nar/18.13.3739 · DOI
  46. 10.1038/nbt.1716 · DOI
  47. 10.1038/nbt.1710 · DOI
  48. 10.1038/nm1708 · DOI
  49. 10.1126/science.1162986 · DOI · Paper page

Cited by

Sorted by citations

Metadata

Authors
Kinde, I., Wu, J., Papadopoulos, N., Kinzler, K. W., & Vogelstein, B.
Affiliations
The Ludwig Center for Cancer Genetics and Therapeutics and The Howard Hughes Medical Institute, Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231
Venue
Proceedings of the National Academy of Sciences
Publisher
National Academy of Sciences
Published
2011-05-17
Volume
108
Issue
23
Pages
9530-9535
ISSN
  • 0027-8424
  • 1091-6490
DOI
10.1073/pnas.1105422108
Cited by
1,144
References
2
Language
en

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review