PCR amplification and high throughput sequencing of immunoglobulin heavy chain genes from formalin-fixed paraffin-embedded human biopsies

Hilla Tabibian-Keissar; Ginette Schibby; Miri Michaeli; Aviya Rakovsky-Shapira; Noemie Azogui-Rosenthal; Deborah K. Dunn-Walters; Kinneret Rosenblatt; Ramit Mehr; Iris Barshack

doi:10.1016/j.yexmp.2012.08.002

PCR amplification and high throughput sequencing of immunoglobulin heavy chain genes from formalin-fixed paraffin-embedded human biopsies

Hilla Tabibian-Keissar, Ginette Schibby, Miri Michaeli, Aviya Rakovsky-Shapira, Noemie Azogui-Rosenthal, Deborah K. Dunn-Walters, Kinneret Rosenblatt, Ramit Mehr, Iris Barshack

The Mina and Everard Goodman Faculty of Life Sciences

Research output: Contribution to journal › Article › peer-review

7 Scopus citations

Abstract

The use of high throughput sequencing (HTS) technologies in biomedicine is expanding in a variety of fields in recent years. The 454 system is an HTS platform that is ideally suited to characterize B cell receptor (BCR) repertoires by sequencing of immunoglobulin (Ig) genes, as it is able to sequence stretches of several hundred nucleotides. Most studies that used this platform for antibody repertoire analyses have started from fresh or frozen tissues or peripheral blood samples, and rely on starting with optimal quality DNA. In this paper we demonstrate that BCR repertoire analysis can be done using DNA from formalin-fixed paraffin-embedded (FFPE) human tissue samples. The heterogeneity of BCR repertoires we obtained confirms the plausibility of HTS of DNA from FFPE specimens. The establishment of experimental protocols and computational tools that enable sequence data analysis from the low quality DNA of FFPE tissues is important for enabling research, as it would enable the use of the rich source of preserved samples in clinical biobanks and biopsy archives.

Original language	English
Pages (from-to)	182-187
Number of pages	6
Journal	Experimental and Molecular Pathology
Volume	94
Issue number	1
DOIs	https://doi.org/10.1016/j.yexmp.2012.08.002
State	Published - Feb 2013

Bibliographical note

Funding Information:
This work was supported in parts by the Israel Science Foundation (grant number 270/09 ), a grant from the Israel Cancer Association (to RM and IB), a grant from the Israel Cancer Association USA (to IB) and a Human Frontiers Science Program Research Grant (to RM and DDW). The funding sources had no role in the study design, in the collection, analysis and interpretation of data, in the writing of the report, or in the decision to submit the article for publication. The work was included in MM's studies towards the MSc degree in Bar-Ilan University, and she was supported by a Combined Technologies Scholarship from the Israeli Council for Higher Education. The work was also included in ARS and NAR's studies towards the MSc degree in Bar-Ilan University.

Funding

This work was supported in parts by the Israel Science Foundation (grant number 270/09 ), a grant from the Israel Cancer Association (to RM and IB), a grant from the Israel Cancer Association USA (to IB) and a Human Frontiers Science Program Research Grant (to RM and DDW). The funding sources had no role in the study design, in the collection, analysis and interpretation of data, in the writing of the report, or in the decision to submit the article for publication. The work was included in MM's studies towards the MSc degree in Bar-Ilan University, and she was supported by a Combined Technologies Scholarship from the Israeli Council for Higher Education. The work was also included in ARS and NAR's studies towards the MSc degree in Bar-Ilan University.

Funders	Funder number
Israeli Council for Higher Education
Israel Cancer Association USA
Israel Science Foundation	270/09

Keywords

FFPE tissues
Formalin-fixed paraffin-embedded tissues
HTS
High throughput sequencing
Ig
Ig variable region genes
MID
PCR
SHM

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10.1016/j.yexmp.2012.08.002

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Tabibian-Keissar, H., Schibby, G., Michaeli, M., Rakovsky-Shapira, A., Azogui-Rosenthal, N., Dunn-Walters, D. K., Rosenblatt, K., Mehr, R., & Barshack, I. (2013). PCR amplification and high throughput sequencing of immunoglobulin heavy chain genes from formalin-fixed paraffin-embedded human biopsies. Experimental and Molecular Pathology, 94(1), 182-187. https://doi.org/10.1016/j.yexmp.2012.08.002

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title = "PCR amplification and high throughput sequencing of immunoglobulin heavy chain genes from formalin-fixed paraffin-embedded human biopsies",

abstract = "The use of high throughput sequencing (HTS) technologies in biomedicine is expanding in a variety of fields in recent years. The 454 system is an HTS platform that is ideally suited to characterize B cell receptor (BCR) repertoires by sequencing of immunoglobulin (Ig) genes, as it is able to sequence stretches of several hundred nucleotides. Most studies that used this platform for antibody repertoire analyses have started from fresh or frozen tissues or peripheral blood samples, and rely on starting with optimal quality DNA. In this paper we demonstrate that BCR repertoire analysis can be done using DNA from formalin-fixed paraffin-embedded (FFPE) human tissue samples. The heterogeneity of BCR repertoires we obtained confirms the plausibility of HTS of DNA from FFPE specimens. The establishment of experimental protocols and computational tools that enable sequence data analysis from the low quality DNA of FFPE tissues is important for enabling research, as it would enable the use of the rich source of preserved samples in clinical biobanks and biopsy archives.",

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author = "Hilla Tabibian-Keissar and Ginette Schibby and Miri Michaeli and Aviya Rakovsky-Shapira and Noemie Azogui-Rosenthal and Dunn-Walters, {Deborah K.} and Kinneret Rosenblatt and Ramit Mehr and Iris Barshack",

note = "Funding Information: This work was supported in parts by the Israel Science Foundation (grant number 270/09 ), a grant from the Israel Cancer Association (to RM and IB), a grant from the Israel Cancer Association USA (to IB) and a Human Frontiers Science Program Research Grant (to RM and DDW). The funding sources had no role in the study design, in the collection, analysis and interpretation of data, in the writing of the report, or in the decision to submit the article for publication. The work was included in MM's studies towards the MSc degree in Bar-Ilan University, and she was supported by a Combined Technologies Scholarship from the Israeli Council for Higher Education. The work was also included in ARS and NAR's studies towards the MSc degree in Bar-Ilan University.",

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Tabibian-Keissar, H, Schibby, G, Michaeli, M, Rakovsky-Shapira, A, Azogui-Rosenthal, N, Dunn-Walters, DK, Rosenblatt, K, Mehr, R & Barshack, I 2013, 'PCR amplification and high throughput sequencing of immunoglobulin heavy chain genes from formalin-fixed paraffin-embedded human biopsies', Experimental and Molecular Pathology, vol. 94, no. 1, pp. 182-187. https://doi.org/10.1016/j.yexmp.2012.08.002

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AU - Tabibian-Keissar, Hilla

AU - Schibby, Ginette

AU - Michaeli, Miri

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AU - Azogui-Rosenthal, Noemie

AU - Dunn-Walters, Deborah K.

AU - Rosenblatt, Kinneret

AU - Mehr, Ramit

AU - Barshack, Iris

N1 - Funding Information: This work was supported in parts by the Israel Science Foundation (grant number 270/09 ), a grant from the Israel Cancer Association (to RM and IB), a grant from the Israel Cancer Association USA (to IB) and a Human Frontiers Science Program Research Grant (to RM and DDW). The funding sources had no role in the study design, in the collection, analysis and interpretation of data, in the writing of the report, or in the decision to submit the article for publication. The work was included in MM's studies towards the MSc degree in Bar-Ilan University, and she was supported by a Combined Technologies Scholarship from the Israeli Council for Higher Education. The work was also included in ARS and NAR's studies towards the MSc degree in Bar-Ilan University.

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N2 - The use of high throughput sequencing (HTS) technologies in biomedicine is expanding in a variety of fields in recent years. The 454 system is an HTS platform that is ideally suited to characterize B cell receptor (BCR) repertoires by sequencing of immunoglobulin (Ig) genes, as it is able to sequence stretches of several hundred nucleotides. Most studies that used this platform for antibody repertoire analyses have started from fresh or frozen tissues or peripheral blood samples, and rely on starting with optimal quality DNA. In this paper we demonstrate that BCR repertoire analysis can be done using DNA from formalin-fixed paraffin-embedded (FFPE) human tissue samples. The heterogeneity of BCR repertoires we obtained confirms the plausibility of HTS of DNA from FFPE specimens. The establishment of experimental protocols and computational tools that enable sequence data analysis from the low quality DNA of FFPE tissues is important for enabling research, as it would enable the use of the rich source of preserved samples in clinical biobanks and biopsy archives.

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KW - Ig variable region genes

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PCR amplification and high throughput sequencing of immunoglobulin heavy chain genes from formalin-fixed paraffin-embedded human biopsies

Abstract

Bibliographical note

Funding

Keywords

Access to Document

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