Open Access

Erratum To: Discovery and validation of breast cancer subtypes

  • Amy V Kapp1Email author,
  • Stefanie S Jeffrey2,
  • Anita Langerød3,
  • Anne-Lise Børresen-Dale3, 4,
  • Wonshik Han5,
  • Dong-Young Noh5,
  • Ida RK Bukholm6, 7,
  • Monica Nicolau2,
  • Patrick O Brown8 and
  • Robert Tibshirani1, 9
BMC Genomics20078:101

DOI: 10.1186/1471-2164-8-101

Received: 08 March 2007

Accepted: 13 April 2007

Published: 13 April 2007

The original article was published in BMC Genomics 2006 7:231

Abstract

Following the publication of our recent article (Kapp et al., BMC Genomics 2006, 7:231), we (the authors) regrettably found several errors in the published Table 5. This correction article not only describes what makes the published Table 5 incorrect, it also presents the correct Table 5.

I regret to say that several errors exist in Table 5 of our recently published paper [1]. Here we present the correct version of Table 5 and explain what is incorrect about the published Table 5. (See Table 1 of this manuscript.)
Table 1

The (original) incorrect Table 5 as published in Kapp et al. (2006).

  

BCMP11/ABCC11

  

Group 1

Group 2

Group 3

SLC39A6/GATA3

Group 1

42

0

6

 

Group 2

8

21

3

 

Group 3

0

0

16

Sørlie subtype

Normal-like

6

0

0

 

ERBB2+

4

7

0

 

Luminal A

28

0

0

 

Luminal B

9

2

0

 

Basal

5

8

6

A typographical error exists in Table 5 (upper panel). The 6 that is presented in the upper right-hand corner of the published Table 5 (upper panel) should be a zero. The correct version of Table 5 (upper panel) is shown in Table 2 of the present manuscript.
Table 2

The correct Table 5 (upper panel).

  

BCMP11/ABCC11

  

Group 1

Group 2

Group 3

SLC39A6/GATA3

Group 1

42

0

0

 

Group 2

8

21

3

 

Group 3

0

0

16

The paragraphs in the paper associated with Table 5 (upper panel) are correct as published.

Table 5 (lower panel) has a more significant error. The correct version of Table 5 (lower panel) is shown in Table 3 of the present manuscript.
Table 3

The correct Table 5 (lower panel).

  

BCMP11/ABCC11

  

Group 1

Group 2

Group 3

Sørlie subtype

ERBB2+

1

6

0

 

Luminal A

15

0

0

 

Luminal B

3

0

0

 

Basal

0

1

8

 

None

11

0

0

What was presented in the paper was a comparison of the Sørlie et al. (2003) classifications of the Sørlie dataset (without a cutoff), not a subset of the Norway/Stanford arrays.

Moreover, the Comparison of ESR1/ERBB2 subtypes and Sørlie et al. (2003) subtypes section is incorrect. The text in this section is associated with Table 5 (lower panel) and describes the results for the Sørlie dataset, not the results for a subset of the Norway/Stanford dataset as intended (and as stated in the table's legend). Based upon the correct Table 5 (lower panel) which presents the results for the Norway/Stanford arrays of samples from Ullevål University Hospital, the subtypes described by [2] are fairly similar to the ESR1/ERBB2 subtypes we defined. All of the luminal A and luminal B samples were classified to Group 1 (the ESR1+/ERBB2- subtype). All but one of the Ullevål samples in the Norway/Stanford dataset that were classified to the ERBB2-overexpressing Sørlie et al. (2003) subtype were classified by us to Group 2 (the ERBB2+ subtype). Finally, except for one sample, all of the basal samples were classified to Group 3 (the ESR1-/ERBB2- subtype). All of the samples that were not classified to any of the Sørlie et al. (2003) subtypes were classified to our ESR1+/ERBB2- subtype rather than being uniformly distributed among all three of our subtypes.

It may be surprising to see one of the basal samples in our ERBB2+subtype and not with the rest of the basal samples in our ESR1-/ERBB2- subtype. In all other papers, the basal subtype has been the most cohesive. Our ESR1/ERBB2 centroids consist of approximately four times as many genes as the Sørlie et al. (2003) centroids do (1908 genes and 496 genes, respectively). Not all of the genes in the ESR1/ERBB2 centroids belong to the ESR1 gene cluster or to the ERBB2 gene cluster. It is the influence of the genes which do not belong to these clusters that causes one of the basal samples to not be classified with the others.

Table 4 of the present document contains the 45 arrays used to make the correct Table 5 (lower panel). Anita Langerød classified each array to one of the Sørlie et al. (2003) subtypes if the array's correlation with one of the subtypes centroids was at least 0.2. These classifications will appear in an upcoming publication.
Table 4

The arrays used to make the correct Table 5 (lower panel)

Array

Sørlie et al.(2003) subtype

ESR1/ERBB2 subtype

ULL-D-002

Luminal A

ESR1+/ERBB2-

ULL-D-016

Luminal A

ESR1+/ERBB2-

ULL-D-020

Luminal A

ESR1+/ERBB2-

ULL-D-022

Luminal A

ESR1+/ERBB2-

ULL-D-023

Luminal B

ESR1+/ERBB2-

ULL-D-037

Luminal A

ESR1+/ERBB2-

ULL-D-044

Luminal A

ESR1+/ERBB2-

ULL-D-048

Luminal A

ESR1+/ERBB2-

ULL-D-056

Luminal B

ESR1+/ERBB2-

ULL-D-057

Basal-like

ESR1-/ERBB2-

ULL-D-066

None

ESR1+/ERBB2-

ULL-D-071

ERBB2

ERBB2+

ULL-D-075

Basal-like

ERBB2+

ULL-D-080

Basal-like

ESR1-/ERBB2-

ULL-D-083

ERBB2

ERBB2+

ULL-D-085

None

ESR1+/ERBB2-

ULL-D-113

Luminal B

ESR1+/ERBB2-

ULL-D-134

Luminal A

ESR1+/ERBB2-

ULL-D-150

Luminal A

ESR1+/ERBB2-

ULL-D-165

None

ESR1+/ERBB2-

ULL-D-167

Basal-like

ESR1-/ERBB2-

ULL-D-169

ERBB2

ERBB2+

ULL-D-177

Basal-like

ESR1-/ERBB2-

ULL-D-184

None

ESR1+/ERBB2-

ULL-D-007

None

ESR1+/ERBB2-

ULL-D-011

Luminal A

ESR1+/ERBB2-

ULL-D-013

Luminal A

ESR1+/ERBB2-

ULL-D-026

Basal-like

ESR1-/ERBB2-

ULL-D-027

ERBB2

ERBB2+

ULL-D-038

None

ESR1+/ERBB2-

ULL-D-053

None

ESR1+/ERBB2-

ULL-D-065

Basal-like

ESR1-/ERBB2-

ULL-D-067

None

ESR1+/ERBB2-

ULL-D-074

Luminal A

ESR1+/ERBB2-

ULL-D-087

ERBB2

ESR1+/ERBB2-

ULL-D-096

ERBB2

ERBB2+

ULL-D-099

Basal-like

ESR1-/ERBB2-

ULL-D-101

ERBB2

ERBB2+

ULL-D-122

Luminal A

ESR1+/ERBB2-

ULL-D-132

None

ESR1+/ERBB2-

ULL-D-135

None

ESR1+/ERBB2-

ULL-D-139

Basal-like

ESR1-/ERBB2-

ULL-D-143

Luminal A

ESR1+/ERBB2-

ULL-D-144

Luminal A

ESR1+/ERBB2-

ULL-D-183

None

ESR1+/ERBB2-

Notes

Authors’ Affiliations

(1)
Department of Statistics, Stanford University
(2)
Department of Surgery, Stanford University School of Medicine
(3)
Department of Genetics, Institute for Cancer Research, Rikshospitalet-Radiumhospitalet Medical Center
(4)
Medical Faculty, University of Oslo
(5)
Department of Surgery, Seoul National University College of Medicine
(6)
Department of Surgery, Akershus University Hospital
(7)
University of Oslo
(8)
Department of Biochemistry, Stanford University School of Medicine
(9)
Department of Health Research and Policy, Stanford University School of Medicine

References

  1. Kapp AV, Jeffrey SS, Langerød A, Børresen-Dale AL, Han W, Noh DY, Bukholm IR, Nicolau M, Brown PO, Tibshirani R: Discovery and validation of breast cancer subtypes. BMC Genomics. 2006, 7: 231-10.1186/1471-2164-7-231.PubMed CentralPubMedView ArticleGoogle Scholar
  2. Sørlie T, Tibshirani R, Parker J, Hastie T, Marron JS, Nobel A, Deng S, Johnsen H, Pesich R, Geisler S, Demeter J, Perou CM, Lønning PE, Brown PO, Børresen-Dale AL, Botstein D: Repeated observation of breast tumor subtypes in independent gene expression data sets. Proceedings of the National Academy of Sciences of the United States of America. 2003, 100 (14): 8418-8423. 10.1073/pnas.0932692100.PubMed CentralPubMedView ArticleGoogle Scholar

Copyright

© Kapp et al; licensee BioMed Central Ltd. 2007

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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